Study Boy Bio 2

Front 1

What are the three important roles of cell division?

Back 1

Three key roles of cell division include reproduction, growth, and repair. Thanks for using ChaCha and have a great night!

Front 2

Compare and contrast sexual and asexual reproduction.

Back 2

Asexual reproduction is the biological process by which an organism creates a genetically-similar or identical copy of itself without a contribution of genetic material from another individual. Bacteria divide asexually via binary fission; viruses take control of host cells to produce more viruses; Hydras (invertebrates of the order Hydroidea) and yeasts are able to reproduce by budding. These organisms do not have different sexes, and they are capable of "splitting" themselves into two or more individuals. Some 'asexual' species, like hydra and jellyfish, may also reproduce sexually. For instance, most plants are capable of vegetative reproduction-reproduction without seeds or spores-but can also reproduce sexually. Likewise, bacteria may exchange genetic information by conjugation. Other ways of asexual reproduction include fragmentation and spore formation that involves only mitosis.

Sexual reproduction is a biological process by which organisms create descendants that have a combination of genetic material contributed from two (usually) different members of the species. Each of two parent organisms contributes half of the offspring's genetic makeup by creating haploid gametes. Most organisms form two different types of gametes. In these anisogamous species, the two sexes are referred to as male (producing sperm or microspores) and female (producing ova or megaspores). In isogamous species the gametes are similar or identical in form, but may have separable properties and then may be given other different names. For example, in the green alga, Chlamydomonas reinhardtii, there are so-called "plus" and "minus" gametes. A few types of organisms, such as ciliates, have more than two kinds of gametes.

Most animals (including humans) and plants reproduce sexually. Sexually reproducing organisms have two sets of genes for every trait (called alleles). Offspring inherit one allele for each trait from each parent, thereby ensuring that offspring have a combination of the parents' genes. Having two copies of every gene, only one of which is expressed, allows deleterious alleles to be masked, an advantage believed to have led to the evolutionary development of diploidy (Otto and Goldstein).

Front 3

Distinguish between the terms: DNA, gene, chromosome, replicated chromosome, sister chromatid and centromere.

Back 3

DNA, the blueprint of life, is organized into structures called chromosomes. In prokaryotic cells, chromosomes are circular, whereas in eukaryotic cells, they are linear strands. Different organisms have different numbers of chromosomes: human cells usually have 46 chromosomes, dogs have 78 chromosomes, while kangaroos have only 12 chromosomes!

This karyotype of a human male cell shows the 46 chromosomes.

When you add all these chromosomes up, each cell actually contains about 2m of DNA! And all this DNA has to fit into a tiny nucleus of 5-10um in diameter. This is like trying to stuff a piece of string 2km long (it will take you about 20 minutes to walk from one end to the other) into a tiny bead smaller than 1cm!!! To do this seemingly impossible feat, cells devised an ingenious packaging system: it wraps DNA around proteins called histones. The resulting DNA-protein complex is called chromatin.

At the beginning of cell division (S-phase), the DNA is replicated, producing two identical copies of DNA, which are connected to each other at the centromere. This replicated X-like structure is now called a sister chromatid pair. A chromatid is therefore just one of the strands.

During mitosis, the sister chromatid pair condenses further, giving rise to the fat X chromosomes that you can see in the karyotype above. Therefore, chromosomes can be found in 3 forms: thread-like chromatin (during interphase), thread-like sister chromatids (during S-phase) and the condensed, visible form (during mitosis).

When a cell divides, the sister chromatids separate, and each daughter cell receives one of the strands. The chromatid then decondenses back into a long single chromatin strand when the new cell goes into interphase.

The centromere is the part of a chromosome that links sister chromatids. During mitosis, spindle fibers attach to the centromere via the kinetochore.[1] Centromeres were first defined as genetic loci that direct the behaviour of chromosomes. Their physical role is to act as the site of assembly of the kinetochore - a highly complex multiprotein structure that is responsible for the actual events of chromosome segregation - e.g. binding microtubules and signalling to the cell cycle machinery when all chromosomes have adopted correct attachments to the spindle, so that it is safe for cell division to proceed to completion (i.e. for cells to enter anaphase).[2] There are broadly speaking two types of centromeres. "Point centromeres" bind to specific proteins that recognise particular DNA sequences with high efficiency.[3] Any piece of DNA with the point centromere DNA sequence on it will typically form a centomere if present in the appropriate species. The best characterised point centromeres are those of the budding yeast, Saccharomyces cerevisiae. "Regional centromeres" is the term coined to describe most centromeres, which typically form on regions of preferred DNA sequence, but what can form on other DNA sequences as well.[3] The signal for formation of a regional centromere appears to be "epigenetic" - a widely used term that in this instance most likely refers to a particular set of post-translational modifications of the histone proteins, or different histone variants being present. Most organisms, ranging from the fission yeast Schizosaccharomyces pombe to humans, have regional centromeres.

Deoxyribonucleic acid (Listeni/diˌɒksiˌraɪbɵ.njuːˌkleɪ.ɨk ˈæsɪd/; DNA) is a nucleic acid containing the genetic instructions used in the development and functioning of all known living organisms (with the exception of RNA viruses). The DNA segments carrying this genetic information are called genes. Likewise, other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. Along with RNA and proteins, DNA is one of the three major macromolecules that are essential for all known forms of life.

A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a polypeptide or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains. Genes hold the information to build and maintain an organism's cells and pass genetic traits to offspring, although some organelles (e.g. mitochondria) are self-replicating and are not coded for by the organism's DNA. All organisms have many genes corresponding to various biological traits, some of which are immediately visible, such as eye color or number of limbs, and some of which are not, such as blood type or increased risk for specific diseases, or the thousands of basic biochemical processes that comprise life.

Front 4

What are the two phases of the cell cycle? What are the three stages of interphase?

Back 4

The cell cycle encompasses the changes a cell goes through to produce new, offspring cells. There are two major parts of the cell cycle: mitosis and interphase. Within these two parts are several other identifiable stages.



During interphase, three stages occur -- a first growth stage, a DNA synthesis stage and then another growth stage. The differences in these stages are subtle and not easily seen by the untrained eye. Traditionally, descriptions of interphase do not give specific attention to each stage.



When a cell undergoes mitosis, more pronounced alterations occur through a series of changes identified as prophase, metaphase, anaphase and telophase. The cells are split into two cells in a process known as cytokinesis.

Front 5

Mitosis is the division of the ______, while cytokinesis is the division of the ______.

Back 5

Two basic types of cells occur in the bodies of eukaryotes. Somatic cells are general body cells. These have the same number of chromosomes as each other within the body of an organism. The number of chromosomes in somatic cells is consistent among organisms of the same species, but varies from species to species. These chromosomes come in pairs, where one chromosome in each pair is from the mother and one is from the father. Actually, since most organisms have more than one pair of chromosomes, it would also be correct to say that the organism received one set of chromosomes from its mother and one matching set from its father, and that these sets match in pairs. The other type of cells found in eukaryotes is gametes or sex cells, consisting of eggs in females and sperm in males. These special reproductive cells have only one set (half as many) of chromosomes consisting of one chromosome from each pair. In humans ONLY, the somatic cells have 46 chromosomes arranged in 23 pairs (= two sets of 23 each), while gametes have 23 individual chromosomes (= one set). In fruit flies, somatic cells have 8 chromosomes (= 4 pairs or 2 sets) and gametes have 4 chromosomes (= 1 set). Geneticists use the term “-ploid” to refer to one set of chromosomes in an organism, and that term is typically combined with another wordstem that describes the number of sets of chromosomes present. For example, a cell with one set of chromosomes is called haploid, a cell with two sets of chromosomes is diploid, and a cell with four sets of chromosomes (not usually a “normal” condition, but sometimes possible) is tetraploid.

Technically, mitosis is specifically the process of division of the chromosomes, while cytokinesis is officially the process of division of the cytoplasm to form two cells. In most cells, cytokinesis follows or occurs along with the last part of mitosis.

Front 6

Describe the appearance and the location of the chromosomes during the four stages of mitotic cell division, as pictured in Figure 8.7.

Back 6

They do some shit. It looks pretty werid. Look it up.

Front 7

How is cytokinesis different between animals and plants?

Back 7

Cytokinesis is the division in two of the cytoplasm. It occurs near or after the end of nuclear division.

In animals, the cell membrane folds in all around the cell. From the outside, the cell looks like a half-deflated balloon that has an invisible thread looped around it; as cytokinesis proceeds the thread is increasingly tightened. Really, the tightening is by protein fibers of the cytoskeleton, orientated in various directions just below the cell membrane.

Plant cells cannot go through the same process, as the cell wall prevents changes to the cell's shape. Instead, the Golgi body manufactures a plate (middle lamella) of vesicles in a plane between the two daughter-nuclei. This plate spreads out from the center of the cell, eventually abutting against the cell membrane all round the cell in that plane. The cell then lays down a cell wall, replacing callose with cellulose and pectin.

Front 8

What is cancer? Distinguish between the terms: tumor, malignancy and metastasis.

Back 8

Cancer Listeni/ˈkænsər/, known medically as a malignant neoplasm, is a broad group of various diseases, all involving unregulated cell growth. In cancer, cells divide and grow uncontrollably, forming malignant tumors, and invade nearby parts of the body. The cancer may also spread to more distant parts of the body through the lymphatic system or bloodstream. Not all tumors are cancerous. Benign tumors do not grow uncontrollably, do not invade neighboring tissues, and do not spread throughout the body. There are over 200 different known cancers that afflict humans.

Malignancy (from Malign from Latin roots male "badly" + -gnus "born") is the tendency of a medical condition, especially tumors, to become progressively worse and to potentially result in death. Malignancy in cancers is characterized by anaplasia, invasiveness, and metastasis.[1] Malignant is a corresponding adjectival medical term used to describe a severe and progressively worsening disease. The term is most familiar as a description of cancer. A malignant tumor may be contrasted with a non-cancerous benign tumor in that a malignancy is not self-limited in its growth, is capable of invading into adjacent tissues, and may be capable of spreading to distant tissues (metastasizing), while a benign tumor has none of those properties. Malignant tumor is synonymous with cancer. Uses of "malignant" in oncology:

Metastasis, or metastatic disease (sometimes abbreviated mets), is the spread of a disease from one organ or part to another non-adjacent organ or part.[1][2] It was previously thought that only malignant tumor cells and infections have the capacity to metastasize; however, this is being reconsidered due to new research.[3] In origin metastasis is a Greek word meaning "displacement", from μετά, meta, "next", and στάσις, stasis, "placement". The plural is metastases.

Front 9

What are the three main types of cancer treatment?

Back 9

he three most common types of cancer treatment are chemotherapy, radiation therapy, and surgery.

Front 10

Explain what homologous chromosomes are and how we inherit them. What are sex chromosomes? Which ones are found in males and females? What are autosomes?

Back 10

Homologous chromosomes (also called homologs or homologues) are chromosome pairs of approximately the same length, centromere position, and staining pattern, with genes for the same characteristics at corresponding loci. One homologous chromosome is inherited from the organism's mother; the other from the organism's father.[1] They are usually not identical.

Homologous chromosomes pair (synapse) during meiosis—the cell division that occurs as part of the creation of gametes. Sections of the DNA can sometimes cross over between homologous pairs.

Each chromosome in the pair contains genes for the same biological features, such as eye color, at the same locations (loci) on the chromosome. However, each can contain either the same allele (e.g., both alleles for blue eyes) or different alleles (e.g., one allele for blue eyes and one allele for brown eyes) for each feature.

Homologous chromosomes are usually similar in length, except for the sex chromosomes in several taxa, where the X chromosome is considerably larger than the Y chromosome. These sex chromosomes share only small regions of homology.

Humans have 22 pairs of homologous non-sex chromosomes (called autosomes), and one pair of sex chromosomes, making a total of 46 chromosomes in a genetically normal human. Each member of a pair is inherited from one of the two parents. In addition to the 22 pairs of homologous autosomes, female humans have a homologous pair of sex chromosomes (two Xs), while males have an X and a Y chromosome.

Front 11

List in order (or better yet, draw out) the stages and events of the animal sexual life cycle. Include the role of meiosis and mitosis, and identify each stage as either haploid or diploid.

Back 11

In gametic meiosis, instead of immediately dividing meiotically to produce haploid cells, the zygote divides mitotically to produce a multicellular diploid individual or a group of more unicellular diploid cells. Cells from the diploid individuals then undergo meiosis to produce haploid cells or gametes. Haploid cells may divide again (by mitosis) to form more haploid cells, as in many yeasts, but the haploid phase is not the predominant life cycle phase. In most diplonts, mitosis occurs only in the diploid phase, i.e. gametes usually form quickly and fuse to produce diploid zygotes.

In the whole cycle, gametes are usually the only haploid cells, and mitosis usually occurs only in the diploid phase.

The diploid multicellular individual is a diplont, hence a gametic meiosis is also called a diplontic life cycle. Diplonts are:

Animals
Some brown algae
Some fungi, e.g. brewer's yeast

Front 12

Describe the appearance and location of the chromosomes during the stages of meiotic cell division, as pictured in 8.14.

Back 12

eat a dick.

Front 13

Compare and contrast mitosis and meiosis with regard to: 1) the number of cell divisions, 2) the number of daughter cells produced, 3) the number of chromosomes in each cell before and after each process, and 4) their function(s) in animals. In other words, make sure you know Figure 8.15 well.

Back 13

Mitosis is the process by which a cell duplicates its genetic information (DNA), in order to generate two, identical cells. It is generally followed immediately by cytokinesis which divides the cytoplasm and cell membrane. This results in two identical cells with a roughly equal distribution of organelles and other cellular components. Mitosis and cytokinesis together define the mitotic (M) phase of the cell cycle, the division of the mother cell into two daughter cells, each with the genetic equivalent of the parent cell. Mitosis occurs exclusively in eukaryotic cells. In multicellular organisms, the somatic cells undergo mitosis, while germ cells — cells destined to become sperm in males or ova in females — divide by a related process called meiosis. Prokaryotic cells, which lack a nucleus, divide by a process called binary fission.

The process of mitosis is complex and highly regulated. The sequence of events is divided into phases, corresponding to the completion of one set of activities and the start of the next. These stages are prophase, prometaphase, metaphase, anaphase and telophase. During the process of mitosis the pairs of chromosomes condense and attach to fibers that pull the sister chromatids to opposite sides of the cell. The cell then divides in cytokinesis, to produce two identical daughter cells.

Because cytokinesis usually occurs in conjunction with mitosis, "mitosis" is often used interchangeably with "mitotic phase". However, there are many cells where mitosis and cytokinesis occur separately, forming single cells with multiple nuclei. This occurs most notably among the fungi and slime moulds, but is found in various different groups. Even in animals, cytokinesis and mitosis may occur independently, for instance during certain stages of fruit fly embryonic development.[1] Errors in mitosis can either kill a cell through apoptosis or cause mutations that may lead to cancer.

[edit] Overview

[edit] Phases

[edit] Interphase

The cell cycle
The mitotic phase is a relatively short period of the cell cycle. It alternates with the much longer interphase, where the cell prepares itself for cell division. Interphase is divided into three phases, G1 (first gap), S (synthesis), and G2 (second gap). During all three phases, the cell grows by producing proteins and cytoplasmic organelles. However, chromosomes are replicated only during the S phase. Thus, a cell grows (G1), continues to grow as it duplicates its chromosomes (S), grows more and prepares for mitosis (G2), and divides (M).[2]


[edit] Preprophase
Main article: Preprophase
In plant cells only, prophase is preceded by a pre-prophase stage. In highly vacuolated plant cells, the nucleus has to migrate into the center of the cell before mitosis can begin. This is achieved through the formation of a phragmosome, a transverse sheet of cytoplasm that bisects the cell along the future plane of cell division. In addition to phragmosome formation, preprophase is characterized by the formation of a ring of microtubules and actin filaments (called preprophase band) underneath the plasmamembrane around the equatorial plane of the future mitotic spindle and predicting the position of cell plate fusion during telophase. The cells of higher plants (such as the flowering plants) lack centrioles. Instead, spindle microtubules aggregate on the surface of the nuclear envelope during prophase. The preprophase band disappears during nuclear envelope disassembly and spindle formation in prometaphase.[3]


[edit] Prophase

Prophase: The two round objects above the nucleus are the centrosomes. Note the condensed chromatin.Main article: Prophase
Normally, the genetic material in the nucleus is in a loosely bundled coil called chromatin. At the onset of prophase, chromatin condenses together into a highly ordered structure called a chromosome. Since the genetic material has already been duplicated earlier in S phase, the replicated chromosomes have two sister chromatids, bound together at the centromere by the cohesion complex. Chromosomes are visible at high magnification through a light microscope.

Close to the nucleus are two centrosomes. Each centrosome, which was replicated earlier independent of mitosis, acts as a coordinating center for the cell's microtubules. The two centrosomes nucleate microtubules (which may be thought of as cellular ropes or poles) by polymerizing soluble tubulin present in the cytoplasm. Molecular motor proteins create repulsive forces that will push the centrosomes to opposite side of the nucleus.

Some centrosomes contain a pair of centrioles that may help organize microtubule assembly, but they are not essential to formation of the mitotic spindle.[4]


[edit] Prometaphase

Prometaphase: The nuclear membrane has degraded, and microtubules have invaded the nuclear space. These microtubules can attach to kinetochores or they can interact with opposing microtubules.Main article: Prometaphase
The nuclear envelope disassembles and microtubules invade the nuclear space. This is called open mitosis, and it occurs in most multicellular organisms. Fungi and some protists, such as algae or trichomonads, undergo a variation called closed mitosis where the spindle forms inside the nucleus or its microtubules are able to penetrate an intact nuclear envelope.[5][6]

Each chromosome forms two kinetochores at the centromere, one attached at each chromatid. A kinetochore is a complex protein structure that is analogous to a ring for the microtubule hook; it is the point where microtubules attach themselves to the chromosome.[7] Although the kinetochore structure and function are not fully understood, it is known that it contains some form of molecular motor.[8] When a microtubule connects with the kinetochore, the motor activates, using energy from ATP to "crawl" up the tube toward the originating centrosome. This motor activity, coupled with polymerisation and depolymerisation of microtubules, provides the pulling force necessary to later separate the chromosome's two chromatids.[8]

When the spindle grows to sufficient length, kinetochore microtubules begin searching for kinetochores to attach to. A number of nonkinetochore microtubules find and interact with corresponding nonkinetochore microtubules from the opposite centrosome to form the mitotic spindle.[9] Prometaphase is sometimes considered part of prophase.


[edit] Metaphase

Metaphase: The chromosomes have aligned at the metaphase plate.Main article: Metaphase
As microtubules find and attach to kinetochores in prometaphase, the centromeres of the chromosomes convene along the metaphase plate or equatorial plane, an imaginary line that is equidistant from the two centrosome poles.[9] This even alignment is due to the counterbalance of the pulling powers generated by the opposing kinetochores, analogous to a tug-of-war between equally strong people. In certain types of cells, chromosomes do not line up at the metaphase plate and instead move back and forth between the poles randomly, only roughly lining up along the midline. Metaphase comes from the Greek μετα meaning "after."

Because proper chromosome separation requires that every kinetochore be attached to a bundle of microtubules (spindle fibers) , it is thought that unattached kinetochores generate a signal to prevent premature progression to anaphase[1] without all chromosomes being aligned. The signal creates the mitotic spindle checkpoint.[10]


[edit] Anaphase

Early anaphase: Kinetochore microtubules shortenMain article: Anaphase
When every kinetochore is attached to a cluster of microtubules and the chromosomes have lined up along the metaphase plate, the cell proceeds to anaphase (from the Greek ανα meaning “up,” “against,” “back,” or “re-”).

Two events then occur; First, the proteins that bind sister chromatids together are cleaved, allowing them to separate. These sister chromatids turned sister chromosomes are pulled apart by shortening kinetochore microtubules and toward the respective centrosomes to which they are attached. Next, the nonkinetochore microtubules elongate, pushing the centrosomes (and the set of chromosomes to which they are attached) apart to opposite ends of the cell.

These two stages are sometimes called early and late anaphase. Early anaphase is usually defined as the separation of the sister chromatids, while late anaphase is the elongation of the microtubules and the microtubules being pulled farther apart. At the end of anaphase, the cell has succeeded in separating identical copies of the genetic material into two distinct populations.


[edit] Telophase

Telophase: The decondensing chromosomes are surrounded by nuclear membranes. Note cytokinesis has already begun, the pinching is known as the cleavage furrow.Main article: Telophase
Telophase (from the Greek τελος meaning "end") is a reversal of prophase and prometaphase events. It "cleans up" the after effects of mitosis. At telophase, the nonkinetochore microtubules continue to lengthen, elongating the cell even more. Corresponding sister chromosomes attach at opposite ends of the cell. A new nuclear envelope, using fragments of the parent cell's nuclear membrane, forms around each set of separated sister chromosomes. Both sets of chromosomes, now surrounded by new nuclei, unfold back into chromatin. Mitosis is complete, but cell division is not yet complete.


[edit] Cytokinesis
Main article: Cytokinesis
Cytokinesis is often mistakenly thought to be the final part of telophase, however cytokinesis is a separate process that begins at the same time as telophase. Cytokinesis is technically not even a phase of mitosis, but rather a separate process, necessary for completing cell division. In animal cells, a cleavage furrow (pinch) containing a contractile ring develops where the metaphase plate used to be, pinching off the separated nuclei.[11] In both animal and plant cells, cell division is also driven by vesicles derived from the Golgi apparatus, which move along microtubules to the middle of the cell. [12] In plants this structure coalesces into a cell plate at the center of the phragmoplast and develops into a cell wall, separating the two nuclei. The phragmoplast is a microtubule structure typical for higher plants, whereas some green algae use a phycoplast microtubule array during cytokinesis.[13] Each daughter cell has a complete copy of the genome of its parent cell. The end of cytokinesis marks the end of the M-phase.


[edit] Significance
The importance of mitosis is the maintenance of the chromosomal set; each cell formed receives chromosomes that are alike in composition and equal in number to the chromosomes of the parent cell. Transcription is generally believed to cease during mitosis, but epigenetic mechanisms such as bookmarking function during this stage of the cell cycle to ensure that the "memory" of which genes were active prior to entry into mitosis are transmitted to the daughter cells.[14]


[edit] Consequences of errors
Although errors in mitosis are rare, the process may go wrong, especially during early cellular divisions in the zygote. Mitotic errors can be especially dangerous to the organism because future offspring from this parent cell will carry the same disorder.

In non-disjunction, a chromosome may fail to separate during anaphase. One daughter cell will receive both sister chromosomes and the other will receive none. This results in the former cell having three chromosomes coding for the same thing (two sisters and a homologue), a condition known as trisomy, and the latter cell having only one chromosome (the homologous chromosome), a condition known as monosomy. These cells are considered aneuploidic cells and these abnormal cells can cause cancer.[15]

Mitosis is a traumatic process. The cell goes through dramatic changes in ultrastructure, its organelles disintegrate and reform in a matter of hours, and chromosomes are jostled constantly by probing microtubules. Occasionally, chromosomes may become damaged. An arm of the chromosome may be broken and the fragment lost, causing deletion. The fragment may incorrectly reattach to another, non-homologous chromosome, causing translocation. It may reattach to the original chromosome, but in reverse orientation, causing inversion. Or, it may be treated erroneously as a separate chromosome, causing chromosomal duplication. The effect of these genetic abnormalities depend on the specific nature of the error. It may range from no noticeable effect, cancer induction, or organism death.


[edit] Endomitosis
Endomitosis is a variant of mitosis without nuclear or cellular division, resulting in cells with many copies of the same chromosome occupying a single nucleus. This process may also be referred to as endoreduplication and the cells as endoploid.[1]


[edit] Timeline in pictures
Real mitotic cells can be visualized through the microscope by staining them with fluorescent antibodies and dyes.
In biology, meiosis (IPA: /maɪˈəʊsɪs/) is the process by which one diploid eukaryotic cell divides to generate four haploid cells often called gametes. The word "meiosis" comes from the Greek meioun, meaning "to make smaller," since it results in a reduction in chromosome number in the gamete cell. Among fungi, spores in which the haploid nuclei are at first disseminated are called meiospores, or more specifically, ascospores in asci (Ascomycota) and basidospores on basidia (Basidiomycota).

Meiosis is essential for sexual reproduction and therefore occurs in all eukaryotes, including single-celled organisms that reproduce sexually. A few eukaryotes, notably the Bdelloid rotifers, have lost the ability to carry out meiosis and have acquired the ability to reproduce by parthenogenesis. Meiosis does not occur in archaea or prokaryotes, which reproduce by asexual mitotic cell division.

During meiosis, the genome of a diploid germ cell, which is composed of long segments of DNA packaged into chromosomes, undergoes DNA replication followed by two rounds of division, resulting in haploid cells called gametes. Each gamete contains one complete set of chromosomes, or half of the genetic content of the original cell. These resultant haploid cells can fuse with other haploid cells of the opposite sex or mating type during fertilization to create a new diploid cell, or zygote. Thus, the division mechanism of meiosis is a reciprocal process to the joining of two genomes that occurs at fertilization. Because the chromosomes of each parent undergo genetic recombination during meiosis, each gamete, and thus each zygote, will have a unique genetic blueprint encoded in its DNA. In other words, meiosis and sexual reproduction produce genetic variation.

Meiosis uses many of the same biochemical mechanisms employed during mitosis to accomplish the redistribution of chromosomes. There are several features unique to meiosis, most importantly the pairing and genetic recombination between homologous chromosomes.

History
Meiosis was discovered and described for the first time in sea urchin eggs in 1876, by noted German biologist Oscar Hertwig (1849-1922). It was described again in 1883, at the level of chromosomes, by Belgian zoologist Edouard Van Beneden (1846-1910), in Ascaris worms' eggs. The significance of meiosis for reproduction and inheritance, however, was described only in 1890 by German biologist August Weismann (1834-1914), who noted that two cell divisions were necessary to transform one diploid cell into four haploid cells if the number of chromosomes had to be maintained. In 1911 the American geneticist Thomas Hunt Morgan (1866-1945) observed crossover in Drosophila melanogaster meiosis and provided the first true genetic interpretation of meiosis.


[edit] Occurrence of meiosis in eukaryotic life cycles

Gametic life cycle.
Zygotic life cycle.
Sporic life cycle.Main article: Biological life cycle
Meiosis occurs in all eukaryotic life cycles involving sexual reproduction, comprising of the constant cyclical process of meiosis and fertilization. This takes place alongside normal mitotic cell division. In multicellular organisms, there is an intermediary step between the diploid and haploid transition where the organism grows. The organism will then produce the germ cells that continue in the life cycle. The rest of the cells, called somatic cells, function within the organism and will die with it.

The organism phase of the life cycle can occur between the haploid to diploid transition or the diploid to haploid transition. Some species are diploid, grown from a diploid cell called the zygote. Others are haploid instead, spawned by the proliferation and differentiation of a single haploid cell called the gamete. Humans, for example, are diploid creatures. Human stem cells undergo meiosis to create haploid gametes, which are spermatozoa for males or ova for females. These gametes then fertilize in the Fallopian tubes of the female, producing a diploid zygote. The zygote undergoes progressive stages of mitosis and differentiation, turns into a blastocyst and then gets implanted in the uterus endometrium to create an embryo.

There are three types of life cycles that utilize sexual reproduction, differentiated by the location of the organisms stage.

In the gametic life cycle, of which humans are a part, the living organism is diploid in nature. Here, we will generalize the example of human reproduction stated previously. The organism's diploid germ-line stem cells undergo meiosis to create haploid gametes, which fertilize to form the zygote. The diploid zygote undergoes repeated cellular division by mitosis to grow into the organism. Mitosis is a related process to meiosis that creates two cells that are genetically identical to the parent cell. The general principle is that mitosis creates somatic cells and meiosis creates germ cells.

In the zygotic life cycle, the living organism is haploid. Two organisms of opposing gender contribute their haploid germ cells to form a diploid zygote. The zygote undergoes meiosis immediately, creating four haploid cells. These cells undergo mitosis to create the organism. Many fungi and many protozoa are members of the zygotic life cycle.

Finally, in the sporic life cycle, the living organism alternates between haploid and diploid states. Consequently, this cycle is also known as the alternation of generations. The diploid organism's germ-line cells undergo meiosis to produce gametes. The gametes proliferate by mitosis, growing into a haploid organism. The haploid organism's germ cells then combine with another haploid organism's cells, creating the zygote. The zygote undergoes repeated mitosis and differentiation to become the diploid organism again. The sporic life cycle can be considered a fusion of the gametic and zygotic life cycles, and indeed its diagram supports this conclusion.


[edit] Process
Because meiosis is a "one-way" process, it cannot be said to engage in a cell cycle as mitosis does. However, the preparatory steps that lead up to meiosis are identical in pattern and name to the interphase of the mitotic cell cycle.

Interphase is divided into three phases:

Growth 1 (G1) phase: Characterized by increase in cell size due to accelerated manufacture of organelles, proteins, and other cellular matter.
Synthesis (S) phase: The genetic material is replicated: each of its chromosomes duplicates. The cell is still diploid, however, because it still contains the same number of centromeres.
Growth 2 (G2) phase: The cell continues to grow.
Interphase is immediately followed by meiosis I and meiosis II. Meiosis I consists of segregating the homologous chromosomes from each other, then dividing the tetraploid cell into two diploid cells each containing one of the segregates. Meiosis II consists of decoupling each chromosome's sister strands (chromatids), segregating the DNA into two sets of strands (each set containing one of each homolog), and dividing both diploid cells to produce four haploid cells. Meiosis I and II are both divided into prophase, metaphase, anaphase, and telophase subphases, similar in purpose to their analogous subphases in the mitotic cell cycle. Therefore, meiosis encompasses the interphase (G1, S, G2), meiosis I (prophase I, metaphase I, anaphase I, telophase I), and meiosis II (prophase II, metaphase II, anaphase II, telophase II).


[edit] Meiosis I

[edit] Prophase I
The first stage of Prophase I is the leptotene stage, also known as leptonema, from Greek words meaning "thin threads."[1] During this stage, individual chromosomes begin to condense into long strands within the nucleus. However the two sister chromatids are still so tightly bound that they are indistinguishable from one another.

The zygotene stage, also known as zygonema, from Greek words meaning "paired threads,"[1] occurs as the chromosomes approximately line up with each other into homologous chromosomes. The combined homologous chromosomes are said to be bivalent. They may also be referred to as a tetrad, a reference to the four sister chromatids. The two chromatids become "zipped" together, forming the synaptonemal complex, in a process known as synapsis.

The pachytene stage, also known as pachynema, from Greek words meaning "thick threads,"[1] heralds crossing over. Nonsister chromatids of homologous chromosomes randomly exchange segments of genetic information over regions of homology. (Sex chromosomes, however, are not identical, and only exchange information over a small region of homology.) Exchange takes place at sites where recombination nodules have formed. The exchange of information between the non-sister chromatids results in a recombination of information; each chromosome has the complete set of information it had before, and there are no gaps formed as a result of the process. Because the chromosomes cannot be distinguished in the synaptonemal complex, the actual act of crossing over is not perceivable through the microscope.

During the diplotene stage, also known as diplonema, from Greek words meaning "two threads,"[1] the synaptonemal complex degrades and homologous chromosomes separate from one another a little. The chromosomes themselves uncoil a bit, allowing some transcription of DNA. However, the homologous chromosomes of each bivalent remain tightly bound at chiasmata, the regions where crossing over occurred.

Chromosomes condense further during the diakinesis stage, from Greek words meaning "moving through."[1] This is the first point in meiosis where the four parts of the tetrads are actually visible. Sites of crossing over entangle together, effectively overlapping, making chiasmata clearly visible. Other than this observation, the rest of the stage closely resembles prometaphase of mitosis; the nucleoli disappears, the nuclear membrane disintegrates into vesicles, and the mitotic spindle begins to form.

During these stages, centrioles are migrating to the two poles of the cell. These centrioles, which were duplicated during interphase, function as microtubule coordinating centers. Centrioles sprout microtubules, essentially cellular ropes and poles, during crossing over. They invade the nuclear membrane after it disintegrates, attaching to the chromosomes at the kinetochore. The kinetochore functions as a motor, pulling the chromosome along the attached microtubule toward the originating centriole, like a train on a track. There are two kinetochores on each tetrad, one for each centrosome. Prophase I is the longest phase in meiosis.

Microtubules that attach to the kinetochores are known as kinetochore microtubules. Other microtubules will interact with microtubules from the opposite centriole. These are called nonkinetochore microtubules.


[edit] Metaphase I
Homologous pairs move together along the phase plate: as kinetochore microtubules from both centrioles attach to their respective kinetochores, the homologous chromosomes align along an equatorial plane that bisects the spindle, due to continuous counterbalancing forces exerted on the bivalents by the microtubules emanating from the two kinetochores. The physical basis of the independent assortment of chromosomes is the random orientation of each bivalent along the metaphase plate.


[edit] Anaphase I
Kinetochore microtubules shorten, severing the recombination nodules and pulling homologous chromosomes apart. Since each chromosome only has one kinetochore, whole chromosomes are pulled toward opposing poles, forming two diploid sets. Each chromosome still contains a pair of sister chromatids. Nonkinetochore microtubules lengthen, pushing the centrioles further apart. The cell elongates in preparation for division down the middle. In prophase 1 the DNA coils tightly and individual chromosomes become visible under the light microscope. Homologous chromosomes closely associated in synapsis and they exchange segments by crossing over.


[edit] Telophase I
The first meiotic division effectively ends when the centromeres arrive at the poles. Each daughter cell now has half the number of chromosomes but each chromosome consists of a pair of chromatids. This effect produces a variety of responses from the neuro-synrchromatic enzyme, also known as NSE. The microtubules that make up the spindle network disappear, and a new nuclear membrane surrounds each haploid set. The chromosomes uncoil back into chromatin. Cytokinesis, the pinching of the cell membrane in animal cells or the formation of the cell wall in plant cells, occurs, completing the creation of two daughter cells.

Cells enter a period of rest known as interkinesis or interphase II. No DNA replication occurs during this stage. Note that many plants skip telophase I and interphase II, going immediately into prophase II.


[edit] Meiosis II
Prophase II takes an inversely proportional time compared to telophase I. In this prophase we see the disappearance of the nucleoli and the nuclear envelope again as well as the shortening and thickening of the chromatids. Centrioles move to the polar regions and are arranged by spindle fibres. The new equatorial plane is rotated by 90 degrees when compared to meiosis I, perpendicular to the previous plane.

In metaphase II, the centromeres contain three kinetochores, organizing fibers from the centrosomes on each side.

This is followed by anaphase II, where the centromeres are cleaved, allowing the kinetochores to pull the sister chromatids apart. The sister chromatids by convention are now called sister chromosomes, and they are pulled toward opposing poles.

The process ends with telophase II, which is similar to telophase I, marked by uncoiling, lengthening, and disappearance of the chromosomes occur as the disappearance of the microtubules. Nuclear envelopes reform; cleavage or cell wall formation eventually produces a total of four daughter cells, each with a haploid set of chromosomes. Meiosis is now complete.


[edit] Significance of meiosis
Meiosis facilitates stable sexual reproduction. Without the halving of ploidy, or chromosome count, fertilization would result in zygotes that have twice the number of chromosomes than the zygotes from the previous generation. Successive generations would have an exponential increase in chromosome count, resulting in an unwieldy genome that would cripple the reproductive fitness of the species. Polyploidy, the state of having three or more sets of chromosomes, also results in developmental abnormalities or lethality.[citation needed]

Most importantly, however, meiosis produces genetic variety in gametes that propagate to offspring. Recombination and independent assortment allow for a greater diversity of genotypes in the population. As a system of creating diversity, meiosis allows a species to maintain stability under environmental changes.


[edit] Nondisjunction
The normal separation of chromosomes in Meiosis I or sister chromatids in meiosis II is termed disjunction. When the separation is not normal, it is called nondisjunction. This results in the production of gametes which have either more or less of the usual amount of genetic material, and is a common mechanism for trisomy or monosomy. Nondisjunction can occur in the meiosis I or meiosis II, phases of cellular reproduction, or during mitosis.

This is a cause of several medical conditions in humans, including:

Down's Syndrome - trisomy of chromosome 21
Patau Syndrome - trisomy of chromosome 13
Edward Syndrome - trisomy of chromosome 18
Klinefelter Syndrome - extra X chromosomes in males - ie XXY, XXXY, XXXXY
Turner Syndrome - atypical X chromosome dosage in in females - ie XO, XXX, XXXX
XYY Syndrome - an extra Y chromosome in males

[edit] Meiosis in humans
In females, meiosis occurs in precursor cells known as oogonia that divide twice into oocytes. These stem cells stop at the diplotene stage of meiosis I and lay dormant within a protective shell of somatic cells called the follicle. Follicles begin growth at a steady pace in a process known as folliculogenesis, and a small number enter the menstrual cycle. Menstruated oocytes continue meiosis I and arrest at meiosis II until fertilization. The process of meiosis in females is called oogenesis, and differs from the typical meiosis in that it features a long period of meiotic arrest known as the Dictyate stage and lacks the assistance of centrosomes.

In males, meiosis occurs in precursor cells known as spermatogonia that divide twice to become sperm. These cells continuously divide without arrest in the seminiferous tubules of the testicles. Sperm is produced at a steady pace. The process of meiosis in males is called spermatogenesis

Front 14

When do independent assortment of chromosomes, crossing over between homologous chromosomes, and random fertilization occur during sexual reproduction? Explain how each increases genetic variation.

Back 14

The previous page investigates the process of meiosis, where 4 haploid gametes are created from the parent cell. Half the genetic information from a parent is present in these haploids, which fuse with gametes of the opposite sex to create a zygote, with a complete chromosome compliment that will create offspring after prolonged growth.

The process of meiosis increases genetic diversity in a species. The sex organs which produce the haploid gametes are the site of many occurrences where genetic information is exchanged or manipulated.
Independent Assortment of Chromosomes

Alleles for a particular phenotype determine what characteristic an organism will express, as with the following example where

Chromosome 1 contains an allele for blonde hair
Chromosome 2 contains an allele for brown hair
Chromosome 3 contains an allele for blue eyes
Chromosome 4 contains an allele for brown eyes

Independent Assortment 1

The top assortment to the left produces 2 blonde hair/blue eyes gametes while the below produces 2 brown hair/brown eyes gametes

Independent Assortment 2

The top assortment on the right produces 2 blonde hair/brown eyes gametes while the below produces 2 brown hair/blue eyes gametes

The above indicates that even though the two homologous chromosomes contain the same genetic information, the assortment of the chromosomes (the order they lie in) can determine what genetic information is present in each of the 4 gametes produced. With 23 chromosomes in a human gamete, their are 223 combinations (8388608 combinations)
Crossing Over

During meiosis, when homologous chromosomes are paired together, there are points along the chromosomes that make contact with the other pair. This point of contact is deemed the chiasmata, and can allow the exchange of genetic information between chromosomes. This further increases genetic variation.

There are also many other ways in which genetic variation is increased in a species gene pool, all of which are described in the following pages.

The next page investigates the work of Gregor Mendel, an Austrian monk famous for his work involving monohybrid and dihybrid crossing, alongside the continuation into looking at genetic diversity through meiosis and genetics in general.

Front 15

What is non-disjunction?

Back 15

Non-disjunction ("not coming apart") is the failure of chromosome pairs to separate properly during meiosis stage 1 or stage 2, specifically in the anaphase. This could arise from a failure of homologous chromosomes to separate in meiosis I, or the failure of sister chromatids to separate during meiosis II or mitosis. The result of this error is a cell with an imbalance of chromosomes. Such a cell is said to be aneuploid. Loss of a single chromosome (2n-1), in which the daughter cell(s) with the defect will have one chromosome missing from one of its pairs, is referred to as a monosomy. Gaining a single chromosome, in which the daughter cell(s) with the defect will have one chromosome in addition to its pairs is referred to as a trisomy.

In the event that an aneuploidic gamete is fertilized, a number of syndromes might result. The only known survivable monosomy is Turner syndrome, where the individual is monosomic for the X chromosome. Examples of trisomies include Down syndrome (trisomy of chromosome 21), Edwards syndrome (trisomy 18), and Patau syndrome (trisomy 13).

The following diagram shows the two possible types of nondisjunction in meiosis:

Front 16

Individuals with Down syndrome have an extra chromosome _____, which gives them a total of _____ chromosomes in each cell. The incidence of this disease increases with the age of the ______.

Back 16

21, 24, mother

Front 17

Define the following terms: heredity, trait and character.

Back 17

Heredity is the passing of traits to offspring (from its parent or ancestors). This is the process by which an offspring cell or organism acquires or becomes predisposed to the characteristics of its parent cell or organism. Through heredity, variations exhibited by individuals can accumulate and cause some species to evolve. The study of heredity in biology is called genetics, which includes the field of epigenetics.

A trait is a distinct variant of a phenotypic character of an organism that may be inherited, be environmentally determined or be a combination of the two.[1] For example, eye color is a character or abstraction of an attribute, while blue, brown and hazel are traits.

Front 18

What is meant by a true-breeding variety of an organism?

Back 18

A true breeding organism, sometimes also called a pure-bred, is an organism having certain biological traits which are passed on to all subsequent generations when bred with another true breeding organism for the same traits. In other words, to "breed true" means that two organisms with a particular, inheritable phenotype produce only offspring with that (same) phenotype.

In the case of a gene with multiple different alleles in the population, the genotype of a true breeding organism is homozygous. For example, a pure-bred variety of cat, such as Siamese, only produce kittens with Siamese characteristics because their ancestors were inbred until they were homozygous for all of the genes that produce the physical characteristics and temperament associated with the Siamese breed.

True breeding is also used to refer to plants that produce only offspring of the same variety when they self-pollinate. For example, when a true-breeding plant with pink flowers is self-pollinated, all its seeds will only produce plants that also have pink flowers. Gregor Mendel cross-pollinated true-breeding peas in his experiments on patterns of inheritance of traits.

The definition of true breeding is : Pertaining to an individual all of whose offspring produced through self fertilization are identical to the parental type. True breeding individuals are homozygous for a given trait.

Front 19

Define the following terms: allele, homozygous, heterozygous, dominant, recessive, phenotype, genotype.

Back 19

The terms dominant and recessive refer to the interaction of alleles in producing the phenotype of the heterozygote. If there are two alternative phenotypes, by definition the phenotype exhibited by the heterozygote is called "dominant" and the "hidden" phenotype is called "recessive". The key concept of dominance is that the heterozygote is phenotypically identical to one of the two homozygotes. That trait corresponding to the dominant allele may then be called the "dominant" trait.

Dominance is a genotypic relationship between alleles, as manifested in the phenotype. It is unrelated to the nature of the phenotype itself, e.g., whether it is regarded as normal or abnormal, standard or nonstandard, healthy or diseased, stronger or weaker, or more or less extreme. It is also important to distinguish between the "round" gene locus, the "round" allele at that locus, and the "round" phenotype it produces. It is inaccurate to say that "the round gene dominates the wrinkled gene" or that "round peas dominate wrinkled peas."

If two alleles of a given gene are identical, the organism is called a homozygote and is homozygous with respect to that gene; if instead the two alleles are different, the organism is a heterozygote and is heterozygous. The genetic makeup of an organism, either at a single locus or over all its genes collectively, is called the genotype. The genotype of an organism directly or indirectly affects its molecular, physical,and other traits, which individually or collectively are called the phenotype. At heterozygous gene loci, the two alleles interact to produce the phenotype. The simplest form of allele interaction is the one described by Mendel, now called Mendelian, in which the appearance/phenotype caused by one allele is apparent, called dominant, and the appearance/phenotype caused by the other allele is not apparent, called recessive.

In the simplest case, the phenotypic effect of one allele completely masks the other in heterozygous combination; that is, the phenotype produced by the two alleles in heterozygous combination is identical to that produced by one of the two homozygous genotypes. The allele that masks the other is said to be dominant to the latter, and the alternative allele is said to be recessive to the former.[3]

A phenotype (from Greek phainein, 'to show' + typos, 'type') is the composite of an organism's observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, phenology, behavior, and products of behavior (such as a bird's nest). Phenotypes result from the expression of an organism's genes as well as the influence of environmental factors and the interactions between the two.

The genotype of an organism is the inherited instructions it carries within its genetic code. Not all organisms with the same genotype look or act the same way because appearance and behavior are modified by environmental and developmental conditions. Likewise, not all organisms that look alike necessarily have the same genotype.

Front 20

Mendel demonstrated two basic laws of heredity by following the inheritance of a single trait over three generations (a monohybrid cross, as in Figure 9.5) and by following two traits (a dihybrid cross as in Figure 9.8). List these two laws, explain their meanings, and state which type of cross (mono- or di-) demonstrated each.

Back 20

Mendelian inheritance (or Mendelian genetics or Mendelism or Monogenetic inheritance) is a scientific theory of how hereditary characteristics are passed from parent organisms to their offspring; it underlies much of genetics. This theoretical framework was initially derived from the work of Gregor Johann Mendel published in 1865 and 1866 which was re-discovered in 1900; it was initially very controversial. When Mendel's theories were integrated with the chromosome theory of inheritance by Thomas Hunt Morgan in 1915, they became the core of classical genetics.

The Law of Segregation states that every individual possesses a pair of alleles (assuming diploidy) for any particular trait and that each parent passes a randomly selected copy (allele) of only one of these to its offspring. The offspring then receives its own pair of alleles for that trait. Whichever of the two alleles in the offspring is dominant determines how the offspring expresses that trait (e.g. the color of a plant, the color of an animal's fur, the color of a person's eyes).

More precisely, the law states that when any individual produces gametes, the copies of a gene separate so that each gamete receives only one copy (allele). A gamete will receive one allele or the other. The direct proof of this was later found following the observation of meiosis by two independent scientists, the German botanist Oscar Hertwig in 1876, and the Belgian zoologist Edouard Van Beneden in 1883. In meiosis, the paternal and maternal chromosomes get separated and the alleles with the traits of a character are segregated into two different gametes.

OR

The two coexisting alleles of an individual for each trait segregate (separate) during gamete formation so that each gamete gets only one of the two alleles. Alleles again unite at random fertilization of gametes.

The Law of Independent Assortment, also known as "Inheritance Law", states that separate genes for separate traits are passed independently of one another from parents to offspring. That is, the biological selection of a particular gene in the gene pair for one trait to be passed to the offspring has nothing to do with the selection of the gene for any other trait. More precisely, the law states that alleles of different genes assort independently of one another during gamete formation. While Mendel's experiments with mixing one trait always resulted in a 3:1 ratio (Fig. 1) between dominant and recessive phenotypes, his experiments with mixing two traits (dihybrid cross) showed 9:3:3:1 ratios (Fig. 2). But the 9:3:3:1 table shows that each of the two genes is independently inherited with a 3:1 phenotypic ratio. Mendel concluded that different traits are inherited independently of each other, so that there is no relation, for example, between a cat's color and tail length. This is actually only true for genes that are not linked to each other.

Independent assortment occurs in eukaryotic organisms during meiotic metaphase I, and produces a gamete with a mixture of the organism's chromosomes. The physical basis of the independent assortment of chromosomes is the random orientation of each bivalent chromosome along the metaphase plate with respect to the other bivalent chromosomes. Along with crossing over, independent assortment increases genetic diversity by producing novel genetic combinations.

Of the 46 chromosomes in a normal diploid human cell, half are maternally derived (from the mother's egg) and half are paternally derived (from the father's sperm). This occurs as sexual reproduction involves the fusion of two haploid gametes (the egg and sperm) to produce a new organism having the full complement of chromosomes. During gametogenesis—the production of new gametes by an adult—the normal complement of 46 chromosomes needs to be halved to 23 to ensure that the resulting haploid gamete can join with another gamete to produce a diploid organism. An error in the number of chromosomes, such as those caused by a diploid gamete joining with a haploid gamete, is termed aneuploidy.

In independent assortment, the chromosomes that result are randomly sorted from all possible combinations of maternal and paternal chromosomes. Because gametes end up with a random mix instead of a pre-defined "set" from either parent, gametes are therefore considered assorted independently. As such, the gamete can end up with any combination of paternal or maternal chromosomes. Any of the possible combinations of gametes formed from maternal and paternal chromosomes will occur with equal frequency. For human gametes, with 23 pairs of chromosomes, the number of possibilities is 223 or 8,388,608 possible combinations.[3] The gametes will normally end up with 23 chromosomes, but the origin of any particular one will be randomly selected from paternal or maternal chromosomes. This contributes to the genetic variability of progeny.

Front 21

Be able to use a Punnett Square to determine the genotypic and phenotypic ratios of the offspring of a genetic cross. For examples: Refer to Figure 9.6, and questions 5-7 in the Post Test of Chapter 9 on Blackboard.

Back 21

The Punnett square is a diagram that is used to predict an outcome of a particular cross or breeding experiment. It is named after Reginald C. Punnett, who devised the approach, and is used by biologists to determine the probability of an offspring's having a particular genotype. The Punnett square is a tabular summary of every possible combination of one maternal allele with one paternal allele for each gene being studied in the cross.[1] These tables give the correct probabilities for the genotype outcomes of independent crosses where the probability of inheriting copies of each parental allele is independent. The Punnett Square is visual representation of Mendelian inheritance.

learn it nig.

Front 22

What is a testcross? Refer to questions 16 & 17 in the Post Test of Chapter 9 on Blackboard.

Back 22

n genetics, a test cross, first introduced by Gregor Mendel, is used to determine if an individual exhibiting a dominant trait is homozygous or heterozygous for that trait. Simplier, test crosses determine the genotype of an individual with a dominant phenotype.

Test crosses involve breeding the individual in question with another individual that expresses a recessive version of the same trait. If all offspring display the dominant phenotype, the individual in question is homozygous dominant; if the offspring display both dominant and recessive phenotypes, then the individual is heterozygous.

In some sources, the "test cross" is defined as being a type of backcross between the recessive homozygote and F1 generation or F2 generation crossed with recessive parent is said to be a test cross.

If the individual being tested produces any recessive offspring (except in cases of incomplete penetrance) its genotype is heterozygous. If all the offspring are phenotypically dominant, its genotype is homozygous.

for other crosses look for Di-hybrid and mono-hybrid crosses, these can provide more accurate and more detailed information on genotypes behind phenotypes in organisms.

Definition: Mendel devised a cross which is used to test the genotype of an individual showing a dominant phenotype. It is a mating in which an individual showing an dominant phenotype is cross with an individual showing its recessive phenotype.

Front 23

According to the multiplication rule, the probability of a compound event is the ______ of the separate probabilities of the independent events.

Back 23

less than. just trying to using sense on this one.

Front 24

What is a family pedigree?

Back 24

A pedigree chart is a diagram that shows the occurrence and appearance or phenotypes of a particular gene or organism and its ancestors from one generation to the next,[1][2][3] most commonly humans, show dogs, and race horses. The word pedigree is a corruption of the French "pied de grue" or crane's foot, because the typical lines and split lines (each split leading to different offspring of the one parent line) resemble the thin leg and foot of a crane.

Front 25

What is incomplete dominance? Be able to work out problems such as the cross shown in Figure 9.18. In other words, anticipate the phenotypic and genotypic ratios of crosses involving white/red/pink snapdragons. An example is question 35 in the Post Test of Chapter 9.

Back 25

Incomplete dominance occurs when the phenotype of the heterozygous genotype is an intermediate of the phenotypes of the homozygous genotypes. For example, the snapdragon flower color is either homozygous for red or white. When the red homozygous flower is paired with the white homozygous flower, the result yields a pink snapdragon flower. The pink snapdragon is the result of incomplete dominance. A similar type of incomplete dominance is found in the four o'clock plant wherein pink color is produced when true-bred parents of white and red flowers are crossed.

When plants of the F1 generation are self-pollinated, the phenotypic and genotypic ratio of the F2 generation will be 1:2:1 (Red:Pink:White) for both generations.[6]

Front 26

What is meant by the term multiple alleles? What is the definition of codominance?

Back 26

Codominance refers to a relationship between two alleles of a gene. It occurs when the contributions of both alleles (genes) are clearly visible and do not overpower each other in the phenotype. This also means that the genotype is heterozygous.

For instance, in the ABO system, the IA and IB alleles are co-dominant in producing the AB blood group phenotype, in which both A- and B-type antigens are made. Another example occurs at the locus for the Beta-globin component of hemoglobin, where the three molecular phenotypes of HbA/HbA, HbA/HbS, and HbS/HbS are all equally detectable by protein electrophoresis. For most gene loci at the molecular level, both alleles are expressed co-dominantly, because both are transcribed into RNA. Co-dominance and incomplete or semi-dominance are not the same thing. For example, in some plant species, white and red spotted flowers may be the product of codominance between the red allele for the gene and the white allele for the gene (co-dominance on the pigment level, no dominance on the color level), or the result of one allele that produces the usual amount of red pigment and another non-functional allele that produces no pigment, so as to produce a dilute, intermediate pink color (no dominance at either level).

An example of a co-dominant pathology is sickle cell anaemia.

Front 27

How are the ABO blood groups determined? What are the various genotypes and phenotypes? Be able to work out inheritance problems involving these various groups. For example, questions 36-39 in the Post Test of Chapter 9 on Blackboard.

Back 27

The ABO blood group system is the most important blood type system (or blood group system) in human blood transfusion. The associated anti-A antibodies and anti-B antibodies are usually IgM antibodies, which are usually produced in the first years of life by sensitization to environmental substances such as food, bacteria, and viruses. ABO blood types are also present in some other animals, for example apes such as chimpanzees, bonobos, and gorillas.[1]

Front 28

In blood donations, blood type ___ is considered the universal donor, while type ___ is considered the universal recipient.

Back 28

0-, AB+

Front 29

Distinguish between pleiotropy and polygenic inheritance. (Just know the definition. You will not be required to solve problems in this case.)

Back 29

Pleiotropy occurs when one gene influences multiple phenotypic traits. Consequently, a mutation in a pleiotropic gene may have an effect on some or all traits simultaneously. This can become a problem when selection on one trait favours one specific version of the gene (allele), while the selection on the other trait favours another allele.

Quantitative traits refer to phenotypes (characteristics) that vary in degree and can be attributed to polygenic effects, i.e., product of two or more genes, and their environment. Quantitative trait loci (QTLs) are stretches of DNA containing or linked to the genes that underlie a quantitative trait. Mapping regions of the genome that contain genes involved in specifying a quantitative trait is done using molecular tags such as AFLP or, more commonly SNPs. This is an early step in identifying and sequencing the actual genes underlying trait variation.

Front 30

The chromosome theory of inheritance states that ….

Back 30

t is a basic principle in biology stating that genes are located on chromosomes and that the behavior of chromosomes during meiosis accounts for inheritance patterns. it is also the only good theory

Front 31

What are sex-linked genes? Be able to work out problems like numbers 34-40 in the Activities Quiz of Chapter 9 on Blackboard.

Back 31

Sex linkage is the phenotypic expression of an allele related to the chromosomal sex of the individual. This mode of inheritance is in contrast to the inheritance of traits on autosomal chromosomes, where both sexes have the same probability of inheritance. Since humans have many more genes on the X than the Y, there are many more X-linked traits than Y-linked traits.

In mammals, the female is the homozygous sex, with two X chromosomes (XX), while the male is heterozygous, with one X and one Y chromosome (XY). Genes on the X or Y chromosome are called sex linked genes.

In birds, the opposite is true: the male is the homozygous sex, having two Z chromosomes (ZZ), and the female (hen) is heterozygous, having one Z and one W chromosome (ZW).

X-linked recessive traits are expressed in all heterogametics, but are only expressed in those homogametics that are homozygous for the recessive allele. For example, an X-linked recessive allele in humans causes hemophilia. Hemophilia is much more common in males than females because males are hemizygous - they only have one copy of the gene in question - and therefore express the trait when they inherit one mutant allele. In contrast, a female must inherit two mutant alleles, a less frequent event since the mutant allele is rare in the population. Tsarevich Alexei of Russia was the most famous sufferer of X-linked hemophilia, and his disease may have played an important role in the overthrow of the imperial regime, which changed the course of history for millions of people.

The incidence of recessive X-linked phenotypes in females is the square of that in males (squaring a proportion less than one gives an outcome closer to 0 than the original). If 1 in 20 males in a human population are green colour blind, then 1 in 400 females in the population are expected to be colour blind (1/20)*(1/20).

X-linked traits are maternally inherited from carrier mothers or from an affected father. Each son born to a carrier mother has a 50% probability of inheriting the X-chromosome carrying the mutant allele. There are a few Y-linked traits; these are inherited from the father.

In classical genetics, a reciprocal cross is performed to test if a trait is sex-linked.

Front 32

What three parts does every nucleotide have? What are the four bases in DNA?

Back 32

DNA is a long polymer or chain of smaller subunits called nucleotides. Each nucleotide has three components. Two of these components are the same in all the nucleotides of the DNA chain; the third component, however, can be one of four different structures. The sequence of these structures in the DNA serves as a way to chemically encode information.

The central component of a DNA nucleotide is a five-carbon sugar called 2-deoxyribose (hence the name deoxyribonucleic acid or DNA). One oxygen and four carbon atoms in this sugar form a five-membered pentagonal ring. The carbons are numbered 1' through 5', where the 1' carbon is immediately adjacent to the oxygen atom in the ring and the 5' carbon is attached to the 4' carbon in the ring. At carbon 3', 2-deoxyribose has a hydroxyl group.

Nucleotides also contain a phosphate (PO4) group. This group is tetrahedral in shape; the phosphorous atom forms the center of a tetrahedron, with oxygen atoms at each corner. One of these oxygen atoms is bonded to the 5' carbon in the 2-deoxyribose sugar. When the nucleotides have been assembled together to form a chain, the phosphate group on one nucleotide will be connected to the 3' carbon on the neighboring nucleotide.

The base is the structural component that differs between the four nucleotides. Two of the DNA bases are pyrimindines, which have only one ring; these are cytosine and thymine, commonly abbreviated C and T. The other two DNA bases are purines, which have two fused rings; these are adenine and guanine, which are commonly abbreviated A and G. All of these bases are heterocyclic, meaning the rings are composed of atoms of two different elements: nitrogen and carbon.

The base in any DNA nucleotide is always attached to the 1' carbon. Bases in the two strands form weak interactions called hydrogen bonds with each other; these hydrogen bonds hold the two strains together. Adenine and thymine can form two hydrogen bonds, so they are complementary to each other and are always found opposite each other in the two strands, while cytosine and guanine can form three hydrogen bonds and are complementary to each other.

Front 33

List the three main differences between DNA and RNA.

Back 33

Number of strands
The sugar
One of the bases

1 Number of strands

In nature, RNA usually has one strand, DNA two. There are exceptions in viruses. Also, single-stranded DNA can be synthesized in laboratories for use e.g. as primers and probes.

2 The sugar

Both nucleic acids have a pentose. In RNA it is ribose, in DNA deoxyribose.

3 One of the bases

RNA has uracil where DNA has thymine.

Another difference is speculative: many scientists believe RNA preceded DNA in the history of living organisms. Among other pieces of evidence is the fact that the distinctive components of DNA (thymine and deoxyribose) are synthesized in cells via the RNA equivalent: thymine by methylation of uracil, and deoxyribose by reduction of ribose.

Front 34

Describe the structure of the DNA double helix, making use of the following terms or phrases: sugar-phosphate backbone, nitrogenous bases, helix, and complementary base-pairing. What type of chemical interaction holds the strands of a DNA molecule together?

Back 34

In 1869, the Swiss doctor Friedrich Miescher discovered the presence of DNA, which he called "nuclein." Later, researchers determined that DNA consisted of linked nucleotide units that were arranged in a regular structure.
In 1953, Francis Crick and James Watson accurately determined the structure of DNA---a double helix with paired nitrogenous bases in the middle of the helix.

DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These two strands run in opposite directions to each other and are therefore anti-parallel. Attached to each sugar is one of four types of molecules called nucleobases (informally, bases). It is the sequence of these four nucleobases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA in a process called transcription.

n a DNA double helix, each type of nucleobase on one strand normally interacts with just one type of nucleobase on the other strand. This is called complementary base pairing. Here, purines form hydrogen bonds to pyrimidines, with A bonding only to T, and C bonding only to G. This arrangement of two nucleotides binding together across the double helix is called a base pair. As hydrogen bonds are not covalent, they can be broken and rejoined relatively easily. The two strands of DNA in a double helix can therefore be pulled apart like a zipper, either by a mechanical force or high temperature.[16] As a result of this complementarity, all the information in the double-stranded sequence of a DNA helix is duplicated on each strand, which is vital in DNA replication. Indeed, this reversible and specific interaction between complementary base pairs is critical for all the functions of DNA in living organisms.[3]

Front 35

Which two scientists discovered that DNA was a double helix? They relied on X-ray crystallography data generated by which other scientist?

Back 35

Watson and Crick, Rosalind Franklin

Front 36

Explain the basics of DNA replication (shown in Figures 10.6 and 10.7); include in your answer the terms DNA polymerase, template strand, and complementary base pairing.
If the sequence of a parental (or template strand) is AAGCTCG, then the sequence of the new daughter strand would be ….

Back 36

DNA replication is a biological process that occurs in all living organisms and copies their DNA; it is the basis for biological inheritance. The process starts when one double-stranded DNA molecule produces two identical copies of the molecule. The cell cycle (mitosis) also pertains to the DNA replication/reproduction process. The cell cycle includes interphase, prophase, metaphase, anaphase, and telophase. Each strand of the original double-stranded DNA molecule serves as template for the production of the complementary strand, a process referred to as semiconservative replication. Cellular proofreading and error toe-checking mechanisms ensure near perfect fidelity for DNA replication.[1][2]

In a cell, DNA replication begins at specific locations in the genome, called "origins".[3] Unwinding of DNA at the origin, and synthesis of new strands, forms a replication fork. In addition to DNA polymerase, the enzyme that synthesizes the new DNA by adding nucleotides matched to the template strand, a number of other proteins are associated with the fork and assist in the initiation and continuation of DNA synthesis.

DNA replication can also be performed in vitro (artificially, outside a cell). DNA polymerases, isolated from cells, and artificial DNA primers are used to initiate DNA synthesis at known sequences in a template molecule. The polymerase chain reaction (PCR), a common laboratory technique, employs such artificial synthesis in a cyclic manner to amplify a specific target DNA fragment from a pool of DNA.

DNA usually exists as a double-stranded structure, with both strands coiled together to form the characteristic double-helix. Each single strand of DNA is a chain of four types of nucleotides having the bases: adenine, cytosine, guanine, and thymine (commonly noted as A,C, G & T). A nucleotide is a mono-, di-, or triphosphate deoxyribonucleoside; that is, a deoxyribose sugar is attached to one, two, or three phosphates, and a base. Chemical interaction of these nucleotides forms phosphodiester linkages, creating the phosphate-deoxyribose backbone of the DNA double helix with the bases pointing inward. Nucleotides (bases) are matched between strands through hydrogen bonds to form base pairs. Adenine pairs with thymine (two hydrogen bonds), and cytosine pairs with guanine (three hydrogen bonds) because a purine must pair with a pyrimidine: a purine cannot pair with another purine because the strands would be very close to each other; in a pyrimidine pair, the strands would be too far apart and the structure would be unstable. If A-C paired, there would be one hydrogen not bound to anything, making the DNA unstable.

DNA strands have a directionality, and the different ends of a single strand are called the "3' (three-prime) end" and the "5' (five-prime) end" with the direction of the naming going 5 prime to the 3 prime region. The strands of the helix are anti-parallel with one being 5 prime to 3 then the opposite strand 3 prime to 5. These terms refer to the carbon atom in deoxyribose to which the next phosphate in the chain attaches. Directionality has consequences in DNA synthesis, because DNA polymerase can synthesize DNA in only one direction by adding nucleotides to the 3' end of a DNA strand.

The pairing of bases in DNA through hydrogen bonding means that the information contained within each strand is redundant. The nucleotides on a single strand can be used to reconstruct nucleotides on a newly synthesized partner strand.[4]

DNA polymerases are a family of enzymes that carry out all forms of DNA replication.[6] However, a DNA polymerase can only extend an existing DNA strand paired with a template strand; it cannot begin the synthesis of a new strand. To begin synthesis, a short fragment of DNA or RNA, called a primer, must be created and paired with the template DNA strand.

Front 37

Define the terms transcription and translation.

Back 37

Transcription is the process of creating a complementary RNA copy of a sequence of DNA.[1] Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes. During transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, antiparallel RNA strand. As opposed to DNA replication, transcription results in an RNA complement that includes uracil (U) in all instances where thymine (T) would have occurred in a DNA complement. Also unlike DNA replication where DNA is synthesised, transcription does not involve an RNA primer to initiate RNA synthesis.

In molecular biology and genetics, translation is the third stage of protein biosynthesis (part of the overall process of gene expression). In translation, messenger RNA (mRNA) produced by transcription is decoded by the ribosome to produce a specific amino acid chain, or polypeptide, that will later fold into an active protein. In Bacteria, translation occurs in the cell's cytoplasm, where the large and small subunits of the ribosome are located, and bind to the mRNA. In Eukaryotes, translation occurs across the membrane of the endoplasmic reticulum in a process called vectorial synthesis. The ribosome facilitates decoding by inducing the binding of tRNAs with complementary anticodon sequences to that of the mRNA. The tRNAs carry specific amino acids that are chained together into a polypeptide as the mRNA passes through and is "read" by the ribosome in a fashion reminiscent to that of a stock ticker and ticker tape.

Front 38

What are codons? How many are there? How many specify or code for amino acids? How many stop codons are there? What is special about the AUG codon?

Back 38

The code defines how sequences of three nucleotides, called codons, specify which amino acid will be added next during protein synthesis. With some exceptions,[1] a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. Because the vast majority of genes are encoded with exactly the same code (see the RNA codon table), this particular code is often referred to as the canonical or standard genetic code, or simply the genetic code, though in fact some variant codes have evolved. For example, protein synthesis in human mitochondria relies on a genetic code that differs from the standard genetic code.

Translation starts with a chain initiation codon (start codon). Unlike stop codons, the codon alone is not sufficient to begin the process. Nearby sequences (such as the Shine-Dalgarno sequence in E. coli) and initiation factors are also required to start translation. The most common start codon is AUG, which is read as methionine or, in bacteria, as formylmethionine. Alternative start codons (depending on the organism), include "GUG" or "UUG"; these codons normally represent valine and leucine, respectively, but, as a start codon, they are translated as methionine or formylmethionine.[9]

The three stop codons have been given names: UAG is amber, UGA is opal (sometimes also called umber), and UAA is ochre. "Amber" was named by discoverers Richard Epstein and Charles Steinberg after their friend Harris Bernstein, whose last name means "amber" in German. The other two stop codons were named "ochre" and "opal" in order to keep the "color names" theme. Stop codons are also called "termination" or "nonsense" codons. They signal release of the nascent polypeptide from the ribosome because there is no cognate tRNA that has anticodons complementary to these stop signals, and so a release factor binds to the ribosome instead.[10]

Front 39

Explain the basics of transcription (shown in Figures 10.13 and 10.14); include in your answer the terms promoter, RNA polymerase, terminator, template strand, and complementary base pairing.

Back 39

Transcription is explained easily in 4 or 5 steps, each moving like a wave along the DNA.

RNA polymerase moves the transcription bubble, a stretch of unpaired nucleotides, by breaking the hydrogen bonds between complementary nucleotides.
RNA polymerase adds matching RNA nucleotides that are paired with complementary DNA bases.
RNA sugar-phosphate backbone forms with assistance from RNA polymerase.
Hydrogen bonds of the untwisted RNA + DNA helix break, freeing the newly synthesized RNA strand.
If the cell has a nucleus, the RNA is further processed (addition of a 3' poly-A tail and a 5' cap) and exits through to the cytoplasm through the nuclear pore complex.

Transcription is the first step leading to gene expression. The stretch of DNA transcribed into an RNA molecule is called a transcription unit and encodes at least one gene. If the gene transcribed encodes a protein, the result of transcription is messenger RNA (mRNA), which will then be used to create that protein via the process of translation. Alternatively, the transcribed gene may encode for either non-coding RNA genes (such as microRNA, lincRNA, etc.) or ribosomal RNA (rRNA) or transfer RNA (tRNA), other components of the protein-assembly process, or other ribozymes.[2]

A DNA transcription unit encoding for a protein contains not only the sequence that will eventually be directly translated into the protein (the coding sequence) but also regulatory sequences that direct and regulate the synthesis of that protein. The regulatory sequence before (upstream from) the coding sequence is called the five prime untranslated region (5'UTR), and the sequence following (downstream from) the coding sequence is called the three prime untranslated region (3'UTR).[2]

Transcription has some proofreading mechanisms, but they are fewer and less effective than the controls for copying DNA; therefore, transcription has a lower copying fidelity than DNA replication.[3]

As in DNA replication, DNA is read from 3' → 5' during transcription. Meanwhile, the complementary RNA is created from the 5' → 3' direction. This means its 5' end is created first in base pairing. Although DNA is arranged as two antiparallel strands in a double helix, only one of the two DNA strands, called the template strand, is used for transcription. This is because RNA is only single-stranded, as opposed to double-stranded DNA. The other DNA strand is called the coding (lagging) strand, because its sequence is the same as the newly created RNA transcript (except for the substitution of uracil for thymine). The use of only the 3' → 5' strand eliminates the need for the Okazaki fragments seen in DNA replication.[2]

Transcription is divided into 5 stages: pre-initiation, initiation, promoter clearance, elongation and termination.[2]

Front 40

RNA processing includes the addition of a ______ and a ______ to protect the RNA and enhance its translation by ______. It also involves RNA splicing, which involves the removal of ______ (regions that do not code for proteins) and the joining of ______ (protein-coding regions). The end result is a mature ______ RNA

Back 40

RNA processing includes the addition of a cap and a tail to protect the RNA and enhance its translation by the ribosomes. It also involves RNA splicing, which involves the removal of introns (regions that do not code for proteins) and the joining of exons (protein-coding regions). The end result is a mature messenger (mRNA).

Front 41

The machinery used to translate mRNA requires four ingredients. List them.

Back 41

The basic process of protein production is addition of one amino acid at a time to the end of a protein. This operation is performed by a ribosome. The choice of amino acid type to add is determined by an mRNA molecule. Each amino acid added is matched to a three nucleotide subsequence of the mRNA. For each such triplet possible, only one particular amino acid type is accepted. The successive amino acids added to the chain are matched to successive nucleotide triplets in the mRNA. In this way the sequence of nucleotides in the template mRNA chain determines the sequence of amino acids in the generated amino acid chain.[1] Addition of an amino acid occurs at the C-terminus of the peptide and thus translation is said to be amino-to-carboxyl directed.[2]

The mRNA carries genetic information encoded as a ribonucleotide sequence from the chromosomes to the ribosomes. The ribonucleotides are "read" by translational machinery in a sequence of nucleotide triplets called codons. Each of those triplets codes for a specific amino acid.

The ribosome molecules translate this code to a specific sequence of amino acids. The ribosome is a multisubunit structure containing rRNA and proteins. It is the "factory" where amino acids are assembled into proteins. tRNAs are small noncoding RNA chains (74-93 nucleotides) that transport amino acids to the ribosome. tRNAs have a site for amino acid attachment, and a site called an anticodon. The anticodon is an RNA triplet complementary to the mRNA triplet that codes for their cargo amino acid.

Aminoacyl tRNA synthetase (an enzyme) catalyzes the bonding between specific tRNAs and the amino acids that their anticodon sequences call for. The product of this reaction is an aminoacyl-tRNA molecule. This aminoacyl-tRNA travels inside the ribosome, where mRNA codons are matched through complementary base pairing to specific tRNA anticodons. The ribosome has three sites for tRNA to bind. They are the aminoacyl site (abbreviated A), the peptidyl site (abbreviated P) and the exit site (abbreviated E). With respect to the mRNA, the three sites are oriented 5’to 3’ E-P-A, because ribosomes moves toward the 3' end of mRNA. The A site binds the incoming tRNA with the complementary codon on the mRNA. The P site holds the tRNA with the growing polypeptide chain. The E site holds the tRNA without its amino acid. When an aminoacyl-tRNA initially binds to its corresponding codon on the mRNA, it is in the A site. Then, a peptide bond forms between the amino acid of the tRNA in the A site and the amino acid of the charged tRNA in the P site. The growing polypeptide chain is transferred to the tRNA in the A site. Translocation occurs, moving the tRNA in the P site, now without an amino acid, to the E site; the tRNA that was in the A site, now charged with the polypeptide chain, is moved to the P site. The tRNA in the E site leaves and another aminoacyl-tRNA enters the A site to repeat the process.[3]

After the new amino acid is added to the chain, the energy provided by the hydrolysis of a GTP bound to the translocase EF-G (in prokaryotes) and eEF-2 (in eukaryotes) moves the ribosome down one codon towards the 3' end. The energy required for translation of proteins is significant. For a protein containing n amino acids, the number of high-energy Phosphate bonds required to translate it is 4n-1[citation needed]. The rate of translation varies; it is significantly higher in prokaryotic cells (up to 17-21 amino acid residues per second) than in eukaryotic cells (up to 6-9 amino acid residues per second).[4]

Front 42

What is the function of tRNA? What are the two business ends?

Back 42

Transfer RNA (tRNA) is an adaptor molecule composed of RNA, typically 73 to 93 nucleotides in length, that is used in biology to bridge the four-letter genetic code (ACGU) in messenger RNA (mRNA) with the twenty-letter code of amino acids in proteins.[1] The role of tRNA as an adaptor is best understood by considering its three-dimensional structure. One end of the tRNA carries the genetic code in a three-nucleotide sequence called the anticodon. The anticodon forms three base pairs with a codon in mRNA during protein biosynthesis. The mRNA encodes a protein as a series of contiguous codons, each of which is recognized by a particular tRNA. On the other end of its three-dimensional structure, each tRNA is covalently attached to the amino acid that corresponds to the anticodon sequence. This covalent attachment to the tRNA 3’ end is catalyzed by enzymes called aminoacyl-tRNA synthetases. Each type of tRNA molecule can be attached to only one type of amino acid, but, because the genetic code contains multiple codons that specify the same amino acid, tRNA molecules bearing different anticodons may also carry the same amino acid.

During protein synthesis, tRNAs are delivered to the ribosome by proteins called elongation factors (EF-Tu in bacteria, eEF-1 in eukaryotes), which aid in decoding the mRNA codon sequence. Once delivered, a tRNA already bound to the ribosome transfers the growing polypeptide chain from its 3’ end to the amino acid attached to the 3’ end of the newly-delivered tRNA, a reaction catalyzed by the ribosome.

Front 43

How many subunits does a ribosome contain? List the type of RNA they contain, as well as the three tRNA binding sites.

Back 43

Ribosomes are the workhorses of protein biosynthesis, the process of translating mRNA into protein. The mRNA comprises a series of codons that dictate to the ribosome the sequence of the amino acids needed to make the protein. Using the mRNA as a template, the ribosome traverses each codon (3 nucleotides) of the mRNA, pairing it with the appropriate amino acid provided by an aminoacyl-tRNA. aminoacyl-tRNA contains a complementary anticodon on one end and the appropriate amino acid on the other. The small ribosomal subunit, typically bound to a aminoacyl-tRNA containing the amino acid methionine, binds to an AUG codon on the mRNA and recruits the large ribosomal subunit. The ribosome then contains three RNA binding sites, designated A, P and E. The A site binds an aminoacyl-tRNA; the P site binds a peptidyl-tRNA (a tRNA bound to the peptide being synthesized); and the E site binds a free tRNA before it exits the ribosome. Protein synthesis begins at a start codon AUG near the 5' end of the mRNA. mRNA binds to the P site of the ribosome first. The ribosome is able to identify the start codon by use of the Shine-Dalgarno sequence of the mRNA in prokaryotes and Kozak box in eukaryotes.

In Figure 3, both ribosomal subunits (small and large) assemble at the start codon (towards the 5' end of the mRNA). The ribosome uses tRNA that matches the current codon (triplet) on the mRNA to append an amino acid to the polypeptide chain. This is done for each triplet on the mRNA, while the ribosome moves towards the 3' end of the mRNA. Usually in bacterial cells, several ribosomes are working parallel on a single mRNA, forming what is called a polyribosome or polysome.

Front 44

Explain the basics of translation (shown in Figures 10.18 and 10.19); include in your answer the terms mRNA, ribosome, tRNA, complementary base pairing, start codon, stop codon, A site, P site, E site, amino acid, peptide bond, and translocation.

Back 44

The basic process of protein production is addition of one amino acid at a time to the end of a protein. This operation is performed by a ribosome. The choice of amino acid type to add is determined by an mRNA molecule. Each amino acid added is matched to a three nucleotide subsequence of the mRNA. For each such triplet possible, only one particular amino acid type is accepted. The successive amino acids added to the chain are matched to successive nucleotide triplets in the mRNA. In this way the sequence of nucleotides in the template mRNA chain determines the sequence of amino acids in the generated amino acid chain.[1] Addition of an amino acid occurs at the C-terminus of the peptide and thus translation is said to be amino-to-carboxyl directed.[2]

The mRNA carries genetic information encoded as a ribonucleotide sequence from the chromosomes to the ribosomes. The ribonucleotides are "read" by translational machinery in a sequence of nucleotide triplets called codons. Each of those triplets codes for a specific amino acid.

The ribosome molecules translate this code to a specific sequence of amino acids. The ribosome is a multisubunit structure containing rRNA and proteins. It is the "factory" where amino acids are assembled into proteins. tRNAs are small noncoding RNA chains (74-93 nucleotides) that transport amino acids to the ribosome. tRNAs have a site for amino acid attachment, and a site called an anticodon. The anticodon is an RNA triplet complementary to the mRNA triplet that codes for their cargo amino acid.

Aminoacyl tRNA synthetase (an enzyme) catalyzes the bonding between specific tRNAs and the amino acids that their anticodon sequences call for. The product of this reaction is an aminoacyl-tRNA molecule. This aminoacyl-tRNA travels inside the ribosome, where mRNA codons are matched through complementary base pairing to specific tRNA anticodons. The ribosome has three sites for tRNA to bind. They are the aminoacyl site (abbreviated A), the peptidyl site (abbreviated P) and the exit site (abbreviated E). With respect to the mRNA, the three sites are oriented 5’to 3’ E-P-A, because ribosomes moves toward the 3' end of mRNA. The A site binds the incoming tRNA with the complementary codon on the mRNA. The P site holds the tRNA with the growing polypeptide chain. The E site holds the tRNA without its amino acid. When an aminoacyl-tRNA initially binds to its corresponding codon on the mRNA, it is in the A site. Then, a peptide bond forms between the amino acid of the tRNA in the A site and the amino acid of the charged tRNA in the P site. The growing polypeptide chain is transferred to the tRNA in the A site. Translocation occurs, moving the tRNA in the P site, now without an amino acid, to the E site; the tRNA that was in the A site, now charged with the polypeptide chain, is moved to the P site. The tRNA in the E site leaves and another aminoacyl-tRNA enters the A site to repeat the process.[3]

After the new amino acid is added to the chain, the energy provided by the hydrolysis of a GTP bound to the translocase EF-G (in prokaryotes) and eEF-2 (in eukaryotes) moves the ribosome down one codon towards the 3' end. The energy required for translation of proteins is significant. For a protein containing n amino acids, the number of high-energy Phosphate bonds required to translate it is 4n-1[citation needed]. The rate of translation varies; it is significantly higher in prokaryotic cells (up to 17-21 amino acid residues per second) than in eukaryotic cells (up to 6-9 amino acid residues per second).[4]

Front 45

What is a mutation? What is the difference between base substitution, insertion and deletion?

Back 45

In molecular biology and genetics, mutations are changes in a genomic sequence: the DNA sequence of a cell's genome or the DNA or RNA sequence of a virus. These random sequences can be defined as sudden and spontaneous changes in the cell. Mutations are caused by radiation, viruses, transposons and mutagenic chemicals, as well as errors that occur during meiosis or DNA replication.[1][2][3] They can also be induced by the organism itself, by cellular processes such as hypermutation.

In genetics, the mutation rate is a measure of the rate at which various types of mutations occur during some unit of time. Mutation rates are typically given for a specific class of mutation, for instance point mutations, small or large scale insertions or deletions. The rate of substitutions can be further subdivided into a mutation spectrum which describes the influence of genetic context on the mutation rate.

There are several natural units of time for each of these rates, with rates being characterized either as mutations per base pair per cell division, per gene per generation, or per genome per generation. The mutation rate of an organisms is an evolved characteristic and is strongly influenced by the genetics of each organisms, in addition to strong influence from the environment. The upper and lower limits to which mutation rates can evolve is the subject of ongoing investigation.

Many sites in an organism's genome may not admit mutations with large fitness effects. These sites are typically called neutral sites. Theoretically mutations under no selection become fixed between organisms at precisely the mutation rate. Fixed synonymous mutations, i.e. synonymous substitutions, are changes to the sequence of a gene that do not change the protein produced by that gene. They are often used as estimates of that mutation rate, despite the fact that some synonymous mutations have fitness effects.

n genetics, an insertion (also called an insertion mutation) is the addition of one or more nucleotide base pairs into a DNA sequence. This can often happen in microsatellite regions due to the DNA polymerase slipping. Insertions can be anywhere in size from one base pair incorrectly inserted into a DNA sequence to a section of one chromosome inserted into another.

In genetics, a deletion (also called gene deletion, deficiency, or deletion mutation) (sign: Δ) is a mutation (a genetic aberration) in which a part of a chromosome or a sequence of DNA is missing. Deletion is the loss of genetic material. Any number of nucleotides can be deleted, from a single base to an entire piece of chromosome.[1] Deletions can be caused by errors in chromosomal crossover during meiosis. This causes several serious genetic diseases. Deletion also causes frameshift.

Front 46

Distinguish between silent, missense and nonsense mutations.

Back 46

A nonsense mutation is a point mutation in a sequence of DNA that results in a premature stop codon, or a nonsense codon in the transcribed mRNA, and possibly a truncated, and often nonfunctional protein product.
Missense mutations or nonsynonymous mutations are types of point mutations where a single nucleotide is changed to cause substitution of a different amino acid. This in turn can render the resulting protein nonfunctional. Such mutations are responsible for diseases such as Epidermolysis bullosa, sickle-cell disease, and SOD1 mediated ALS (Boillée 2006, p. 39).
A neutral mutation is a mutation that occurs in an amino acid codon which results in the use of a different, but chemically similar, amino acid. The similarity between the two is enough that little or no change is often rendered in the protein. For example, a change from AAA to AGA will encode arginine, a chemically similar molecule to the intended lysine.
Silent mutations are mutations that do not result in a change to the amino acid sequence of a protein. They may occur in a region that does not code for a protein, or they may occur within a codon in a manner that does not alter the final amino acid sequence. The phrase silent mutation is often used interchangeably with the phrase synonymous mutation; however, synonymous mutations are a subcategory of the former, occurring only within exons. The name silent could be a misnomer. For example, a silent mutation in the exon/intron border may lead to alternative splicing by changing the splice site (see Splice site mutation), thereby leading to a changed protein. Silent mutations occur because of the degenerate nature of the genetic code.

Front 47

What is a mutagen? Give examples.

Back 47

In genetics, a mutagen (Latin, literally origin of change) is a physical or chemical agent that changes the genetic material, usually DNA, of an organism and thus increases the frequency of mutations above the natural background level. As many mutations cause cancer, mutagens are therefore also likely to be carcinogens. Not all mutations are caused by mutagens: so-called "spontaneous mutations" occur due to spontaneous hydrolysis, errors in DNA replication, repair and recombination.

utagens may be of physical, chemical or biological origin. They may act directly on the DNA, causing direct damage to the DNA, and most often result in replication error. Some however may act on the replication mechanism and chromosomal partition. Many mutagens are not mutagenic by themselves, but can form mutagenic metabolites through cellular processes. Such mutagens are called promutagens.
Physical mutagens

Ionizing radiations such as X-rays, gamma rays and alpha particles may cause DNA breakage and other damages.
Ultraviolet radiations with wavelength above 260 nm are absorbed strongly by bases, producing pyrimidine dimers, which can cause error in replication if left uncorrected.
Radioactive decay, such as 14C in DNA which decays into nitrogen.

Front 48

What is a virus? What is a bacteriophage? Compare and contrast the lytic and lysogenic cycles.

Back 48

A virus is a small infectious agent that can replicate only inside the living cells of an organism. Viruses can infect all types of organism, from animals and plants to bacteria and archaea.[1]

Since Dmitri Ivanovsky's 1892 article describing a non-bacterial pathogen infecting tobacco plants, and the discovery of the tobacco mosaic virus by Martinus Beijerinck in 1898,[2] about 5,000 viruses have been described in detail,[3] although there are millions of different types.[4] Viruses are found in almost every ecosystem on Earth and are the most abundant type of biological entity.[5][6] The study of viruses is known as virology, a sub-speciality of microbiology.

Virus particles (known as virions) consist of two or three parts: the genetic material made from either DNA or RNA, long molecules that carry genetic information; a protein coat that protects these genes; and in some cases an envelope of lipids that surrounds the protein coat when they are outside a cell. The shapes of viruses range from simple helical and icosahedral forms to more complex structures. The average virus is about one one-hundredth the size of the average bacterium. Most viruses are too small to be seen directly with an optical microscope.

The origins of viruses in the evolutionary history of life are unclear: some may have evolved from plasmids – pieces of DNA that can move between cells – while others may have evolved from bacteria. In evolution, viruses are an important means of horizontal gene transfer, which increases genetic diversity.[7]

A bacteriophage (from 'bacteria' and Greek φαγεῖν phagein "to devour") is any one of a number of viruses that infect bacteria. They do this by injecting genetic material, which they carry enclosed in an outer protein capsid. The genetic material can be ssRNA, dsRNA, ssDNA, or dsDNA ('ss-' or 'ds-' prefix denotes single-strand or double-strand) along with either circular or linear arrangement.

Bacteriophages are among the most common and diverse entities in the biosphere.[1] The term is commonly used in its shortened form, phage.

Phages are widely distributed in locations populated by bacterial hosts, such as soil or the intestines of animals. One of the densest natural sources for phages and other viruses is sea water, where up to 9×108 virions per milliliter have been found in microbial mats at the surface,[2] and up to 70% of marine bacteria may be infected by phages.[3] They have been used for over 90 years as an alternative to antibiotics in the former Soviet Union and Eastern Europe, as well as in France.[4] They are seen as a possible therapy against multi-drug-resistant strains of many bacteria.[5]
Contents

The lytic cycle is one of the two cycles of viral reproduction, the other being the lysogenic cycle. The lytic cycle is typically considered the main method of viral replication, since it results in the destruction of the infected cell.[citation needed] A key difference between the lytic and lysogenic phage cycles is that in the lytic phage, the viral DNA exists as a separate molecule within the bacterial cell, and replicates separately from the host bacterial DNA. The location of viral DNA in the lysogenic phage cycle is within the host DNA, therefore in both cases the virus/phage replicates using the host DNA machinery, but in the lytic phage cycle, the phage is a free floating separate molecule to the host DNA.

Lysogeny, or the lysogenic cycle, is one of two methods of viral reproduction (the lytic cycle is the other). Lysogeny is characterized by integration of the bacteriophage nucleic acid into the host bacterium's genome. The newly integrated genetic material, called a prophage can be transmitted to daughter cells at each subsequent cell division, and a later event (such as UV radiation) can release it, causing proliferation of new phages via the lytic cycle. Lysogenic cycles can also occur in eukaryotes, although the method of incorporation of DNA is not fully understood. The distinction between lysogenic and lytic cycles is that the spread of the viral DNA occurs through the usual prokaryotic reproduction, while the lytic phage is spread through the production of thousands of individual phages capable of surviving and infecting other bacterium.

Front 49

HIV is a retrovirus. What does that mean? What is the role of reverse transcriptase?

Back 49

A retrovirus is an RNA virus that is duplicated in a host cell using the reverse transcriptase enzyme to produce DNA from its RNA genome. The DNA is then incorporated into the host's genome by an integrase enzyme. The virus thereafter replicates as part of the host cell's DNA. Retroviruses are enveloped viruses that belong to the viral family Retroviridae.

A special variant of retroviruses are endogenous retroviruses which are integrated into the genome of the host and inherited across generations.

The virus itself stores its nucleic acid in the form of a +mRNA (including the 5'cap and 3'PolyA inside the virion) genome and serves as a means of delivery of that genome into cells it targets as an obligate parasite, and constitutes the infection. Once in the host's cell, the RNA strands undergo reverse transcription in the cytoplasm and are integrated into the host's genome, at which point the retroviral DNA is referred to as a provirus. It is difficult to detect the virus until it has infected the host.

In most viruses, DNA is transcribed into RNA, and then RNA is translated into protein. However, retroviruses function differently - their RNA is reverse-transcribed into DNA, which is integrated into the host cell's genome (when it becomes a provirus), and then undergoes the usual transcription and translational processes to express the genes carried by the virus. So, the information contained in a retroviral gene is used to generate the corresponding protein via the sequence: RNA → DNA → RNA → protein. This extends the fundamental process identified by Francis Crick, in which the sequence is: DNA → RNA → protein.

Retroviruses are proving to be valuable research tools in molecular biology and have been used successfully in gene delivery systems.[1]

In the fields of molecular biology and biochemistry, a reverse transcriptase, also known as RNA-dependent DNA polymerase, is a DNA polymerase enzyme that transcribes single-stranded RNA into single-stranded DNA. It also is a DNA-dependent DNA polymerase which synthesizes a second strand of DNA complementary to the reverse-transcribed single-stranded cDNA after degrading the original mRNA with its RNaseH activity. Normal transcription involves the synthesis of RNA from DNA; hence, reverse transcription is the reverse of this.

Well studied reverse transcriptases include:

HIV-1 reverse transcriptase from human immunodeficiency virus type 1 (PDB 1HMV)
M-MLV reverse transcriptase from the Moloney murine leukemia virus
AMV reverse transcriptase from the avian myeloblastosis virus
Telomerase reverse transcriptase that maintains the telomeres of eukaryotic chromosomes

Front 50

What are prions? List diseases they cause.

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A prion Listeni/ˈpriːɒn/[1] is an infectious agent composed of protein in a misfolded form.[2] This is in contrast to all other known infectious agents (virus/bacteria/fungus/parasite) which must contain nucleic acids (either DNA, RNA, or both). The word prion, coined in 1982 by Stanley B. Prusiner, is derived from the words protein and infection.[3] Prions are responsible for the transmissible spongiform encephalopathies in a variety of mammals, including bovine spongiform encephalopathy (BSE, also known as "mad cow disease") in cattle and Creutzfeldt–Jakob disease (CJD) in humans. All known prion diseases affect the structure of the brain or other neural tissue and all are currently untreatable and universally fatal.[4]

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What is cellular differentiation? What is gene expression?

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n developmental biology, cellular differentiation is the process by which a less specialized cell becomes a more specialized cell type. Differentiation occurs numerous times during the development of a multicellular organism as the organism changes from a simple zygote to a complex system of tissues and cell types. Differentiation is a common process in adults as well: adult stem cells divide and create fully differentiated daughter cells during tissue repair and during normal cell turnover. Differentiation dramatically changes a cell's size, shape, membrane potential, metabolic activity, and responsiveness to signals. These changes are largely due to highly controlled modifications in gene expression. With a few exceptions, cellular differentiation almost never involves a change in the DNA sequence itself. Thus, different cells can have very different physical characteristics despite having the same genome.

Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA (rRNA), transfer RNA (tRNA) or small nuclear RNA (snRNA) genes, the product is a functional RNA. The process of gene expression is used by all known life - eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea), possibly induced by viruses - to generate the macromolecular machinery for life. Several steps in the gene expression process may be modulated, including the transcription, RNA splicing, translation, and post-translational modification of a protein. Gene regulation gives the cell control over structure and function, and is the basis for cellular differentiation, morphogenesis and the versatility and adaptability of any organism. Gene regulation may also serve as a substrate for evolutionary change, since control of the timing, location, and amount of gene expression can have a profound effect on the functions (actions) of the gene in a cell or in a multicellular organism.

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What are the many ways in which gene expression can be regulated? Refer to Figure 11.3.

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Regulation of gene expression (or gene regulation) includes the processes that cells and viruses use to regulate the way that the information in genes is turned into gene products. Although a functional gene product can be an RNA, the majority of known mechanisms regulate protein coding genes. Any step of the gene's expression may be modulated, from DNA-RNA transcription to the post-translational modification of a protein.

Gene regulation is essential for viruses, prokaryotes and eukaryotes as it increases the versatility and adaptability of an organism by allowing the cell to express protein when needed. Although as early as 1951 Barbara McClintock showed interaction between two genetic loci, Activator (Ac) and Dissociator (Ds), in the color formation of maize seeds, the first discovery of a gene regulation system is widely considered to be the identification in 1961 of the lac operon, discovered by Jacques Monod, in which some enzymes involved in lactose metabolism are expressed by the genome of E. coli only in the presence of lactose and absence of glucose.

Furthermore, in multicellular organisms, gene regulation drives the processes of cellular differentiation and morphogenesis, leading to the creation of different cell types that possess different gene expression profiles, and hence produce different proteins/have different ultrastructures that suit them to their functions (though they all possess the genotype, which follows the same genome sequence).

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What is X chromosome inactivation?

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X-inactivation (also called lyonization) is a process by which one of the two copies of the X chromosome present in female mammals is inactivated. The inactive X chromosome is silenced by packaging into transcriptionally inactive heterochromatin. As female mammals have two X chromosomes, X-inactivation causes them not to have twice as many X chromosome gene products as males, which only possess a single copy of the X chromosome (see dosage compensation). The choice of which X chromosome will be inactivated is random in placental mammals such as mice and humans, but once an X chromosome is inactivated it will remain inactive throughout the lifetime of the cell and its descendants in the organism. Unlike the random X-inactivation in placental mammals, inactivation in marsupials applies exclusively to the paternally derived X chromosome.

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Define the following terms transcription factors, enhancers, activators, silencers.

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In molecular biology and genetics, a transcription factor (sometimes called a sequence-specific DNA-binding factor) is a protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to mRNA.[1][2] Transcription factors perform this function alone or with other proteins in a complex, by promoting (as an activator), or blocking (as a repressor) the recruitment of RNA polymerase (the enzyme that performs the transcription of genetic information from DNA to RNA) to specific genes.[3][4][5]

A defining feature of transcription factors is that they contain one or more DNA-binding domains (DBDs), which attach to specific sequences of DNA adjacent to the genes that they regulate.[6][7] Additional proteins such as coactivators, chromatin remodelers, histone acetylases, deacetylases, kinases, and methylases, while also playing crucial roles in gene regulation, lack DNA-binding domains, and, therefore, are not classified as transcription factors.[8]

In genetics, an enhancer is a short region of DNA that can be bound with proteins (namely, the trans-acting factors, much like a set of transcription factors) to enhance transcription levels of genes (hence the name) in a gene cluster. While enhancers are usually cis-acting, an enhancer does not need to be particularly close to the genes it acts on, and sometimes need not be located on the same chromosome.[1]

A transcriptional activator is a protein that increases gene transcription of a gene or set of genes.

Most activators are DNA-binding proteins.

Most activators function by binding sequence-specifically to a DNA site located in or near a promoter and making protein-protein interactions with the general transcription machinery (RNA polymerase and general transcription factors), thereby facilitating the binding of the general transcription machinery to the promoter. The DNA site bound by the activator is referred to as an "activator site." The part of the activator that makes protein-protein interactions with the general transcription machinery is referred to as an "activating region." The part of the general transcription machinery that makes protein-protein interactions with the activator is referred to as an "activation target."

In genetics a silencer is a DNA sequence capable of binding transcription regulation factors termed repressors. Upon binding, RNA polymerase is prevented from initiating transcription thus decreasing or fully suppressing RNA synthesis.

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What are microRNAs?

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A microRNA (abbreviated miRNA) is a short ribonucleic acid (RNA) molecule found in eukaryotic cells. A microRNA molecule has very few nucleotides (an average of 22) compared with other RNAs.

miRNAs are post-transcriptional regulators that bind to complementary sequences on target messenger RNA transcripts (mRNAs), usually resulting in translational repression or target degradation and gene silencing.[1][2] The human genome may encode over 1000 miRNAs,[3][4] which may target about 60% of mammalian genes[5][6] and are abundant in many human cell types.[7]

miRNAs show very different characteristics between plants and metazoans. In plants, repressions on transcriptional level usually require perfect or near perfect target match, while mismatched target can lead to gene silence on translational level.[8] In metazoans, on the other hand, miRNA complementarity typically encompasses the 5' bases 2-7 of the microRNA, the microRNA seed region,[5][9] and one miRNA can target many different sites on the same mRNA or on many different mRNAs. Another difference is the location of target sites on mRNAs. In metazoans, the miRNA target sites are in the three prime untranslated regions (3'UTR) of the mRNA. This is how microRNA may target several mRNAs.[10] In plants, targets can be located in the 3' UTR but are more often in the coding region itself.[11] miRNAs are well conserved in eukaryotic organisms and are thought to be a vital and evolutionarily ancient component of genetic regulation.[12][13][14][15]

The first miRNAs were characterized in the early 1990s.[16] However, miRNAs were not recognized as a distinct class of biological regulators with conserved functions until the early 2000s. Since then, miRNA research has revealed multiple roles in negative regulation (transcript degradation and sequestering, translational suppression) and possible involvement in positive regulation (transcriptional and translational activation). By affecting gene regulation, miRNAs are likely to be involved in most biological processes.[17][18][19][20][21][22][23] Different sets of expressed miRNAs are found in different cell types and tissues.[24]

Aberrant expression of miRNAs has been implicated in numerous disease states, and miRNA-based therapies are under investigation.[25][26][27]

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What role do homeotic genes play in multicellular organisms?

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Homeotic genes are genes that determine which parts of the body form what body parts. One example are the Hox and ParaHox genes which are important for segmentation,[1] another example is the MADS-box-containing genes in the ABC model of flower development.[2]

Homeotic genes are genes involved in developmental patterns and sequences. For example, homeotic genes are involved in determining where, when, and how body segments develop in flies. Alterations in these genes cause changes in patterns of body parts, sometimes causing dramatic effects such as legs growing in place of antennae or an extra set of wings or, in the case of plants, flowers with abnormal numbers of parts. An individual carrying an altered (mutant) version of a homeotic gene is known as a homeotic mutant.

Rather surprisingly it has been found that the sequence of homeotic genes in fruit flies known as the Hox genes are lined up in exactly the same order as the part of the fly they affect. That is to say, the first gene affects the mouth, the second the face, the third the top of the head and so on up until the eighth and final gene that affects the abdomen.[3]

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Describe the technique of nuclear transplantation.

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In genetics and developmental biology, somatic-cell nuclear transfer (SCNT) is a laboratory technique for creating a clone embryo with a donor nucleus (see process below). It can be used in embryonic stem cell research, or, potentially, in regenerative medicine where it is sometimes referred to as "therapeutic cloning". It can also be used as the first step in the process of reproductive cloning.

The nucleus of a somatic cell is removed and kept, and the host's egg cell is kept and nucleus removed and discarded. Now we have a lone nucleus and an empty (or deprogrammed) egg cell. The lone nucleus is then fused with the 'deprogrammed' egg cell. After being inserted into the egg, the lone (somatic-cell) nucleus is reprogrammed by the host egg cell. The egg, now containing the somatic cell's nucleus, is stimulated with a shock and will begin to divide. After many mitotic divisions, this single cell forms a blastocyst (an early stage embryo with about 100 cells) with almost identical DNA to the original organism. The technique of transferring a nucleus from a somatic cell into an egg that produced Dolly was an extension of experiments that had been ongoing for over 40 years. In the simplest terms, the technique used to produce Dolly the sheep – somatic-cell nuclear transplantation cloning – involves removing the nucleus of an egg and replacing it with the diploid nucleus of a somatic cell.

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Compare and contrast reproductive cloning and therapeutic cloning.

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Cloning in biology is the process of producing similar populations of genetically identical individuals that occurs in nature when organisms such as bacteria, insects or plants reproduce asexually. Cloning in biotechnology refers to processes used to create copies of DNA fragments (molecular cloning), cells (cell cloning), or organisms. The term also refers to the production of multiple copies of a product such as digital media or software.

In genetics and developmental biology, somatic-cell nuclear transfer (SCNT) is a laboratory technique for creating a clone embryo with a donor nucleus (see process below). It can be used in embryonic stem cell research, or, potentially, in regenerative medicine where it is sometimes referred to as "therapeutic cloning". It can also be used as the first step in the process of reproductive cloning.

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Distinguish between embryonic and adult stem cells.

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Embryonic stem (ES) cell lines are cultures of cells derived from the epiblast tissue of the inner cell mass (ICM) of a blastocyst or earlier morula stage embryos.[9] A blastocyst is an early stage embryo—approximately four to five days old in humans and consisting of 50–150 cells. ES cells are pluripotent and give rise during development to all derivatives of the three primary germ layers: ectoderm, endoderm and mesoderm. In other words, they can develop into each of the more than 200 cell types of the adult body when given sufficient and necessary stimulation for a specific cell type. They do not contribute to the extra-embryonic membranes or the placenta. The endoderm is composed of the entire gut tube and the lungs, the ectoderm gives rise to the nervous system and skin, and the mesoderm gives rise to muscle, bone, blood—in essence, everything else that connects the endoderm to the ectoderm.

Nearly all research to date has made use of mouse embryonic stem cells (mES) or human embryonic stem cells (hES). Both have the essential stem cell characteristics, yet they require very different environments in order to maintain an undifferentiated state. Mouse ES cells are grown on a layer of gelatin as an extracellular matrix (for support) and require the presence of leukemia inhibitory factor (LIF).[10] Human ES cells are grown on a feeder layer of mouse embryonic fibroblasts (MEFs) and require the presence of basic fibroblast growth factor (bFGF or FGF-2).[11] Without optimal culture conditions or genetic manipulation,[12] embryonic stem cells will rapidly differentiate.

A human embryonic stem cell is also defined by the expression of several transcription factors and cell surface proteins. The transcription factors Oct-4, Nanog, and Sox2 form the core regulatory network that ensures the suppression of genes that lead to differentiation and the maintenance of pluripotency.[13] The cell surface antigens most commonly used to identify hES cells are the glycolipids stage specific embryonic antigen 3 and 4 and the keratan sulfate antigens Tra-1-60 and Tra-1-81. The molecular definition of a stem cell includes many more proteins and continues to be a topic of research.[14]

There are currently no approved treatments using embryonic stem cells. The first human trial was approved by the US Food and Drug Administration in January 2009.[15] However, the human trial was not initiated until October 13, 2010 in Atlanta for spinal injury victims. On November 14, 2011 the company conducting the trial announced that it will discontinue further development of its stem cell programs.[16] ES cells, being pluripotent cells, require specific signals for correct differentiation—if injected directly into another body, ES cells will differentiate into many different types of cells, causing a teratoma. Differentiating ES cells into usable cells while avoiding transplant rejection are just a few of the hurdles that embryonic stem cell researchers still face.[17] Many nations currently have moratoria on either ES cell research or the production of new ES cell lines. Because of their combined abilities of unlimited expansion and pluripotency, embryonic stem cells remain a theoretically potential source for regenerative medicine and tissue replacement after injury or disease.

adult stem cells

Also known as somatic (from Greek Σωματικóς, "of the body") stem cells and germline (giving rise to gametes) stem cells, they can be found in children, as well as adults.[19]

Pluripotent adult stem cells are rare and generally small in number but can be found in a number of tissues including umbilical cord blood.[20] A great deal of adult stem cell research to date has had the aim of characterizing the capacity of the cells to divide or self-renew indefinitely and their differentiation potential.[21] In mice, pluripotent stem cells are directly generated from adult fibroblast cultures. Unfortunately, many mice do not live long with stem cell organs.[22]

Most adult stem cells are lineage-restricted (multipotent) and are generally referred to by their tissue origin (mesenchymal stem cell, adipose-derived stem cell, endothelial stem cell, dental pulp stem cell, etc.).[23][24]

Adult stem cell treatments have been successfully used for many years to treat leukemia and related bone/blood cancers through bone marrow transplants.[25] Adult stem cells are also used in veterinary medicine to treat tendon and ligament injuries in horses.[26]

The use of adult stem cells in research and therapy is not as controversial as the use of embryonic stem cells, because the production of adult stem cells does not require the destruction of an embryo. Additionally, in instances where adult stem cells are obtained from the intended recipient (an autograft), the risk of rejection is essentially non-existent. Consequently, more US government funding is being provided for adult stem cell research.[27]

An extremely rich source for adult mesenchymal stem cells is the developing tooth bud of the mandibular third molar.[28] The stem cells eventually form enamel (ectoderm), dentin, periodontal ligament, blood vessels, dental pulp, nervous tissues, and a minimum of 29 different end organs. Because of extreme ease in collection at 8–10 years of age before calcification and minimal to no morbidity, these will probably constitute a major source of cells for personal banking, research and current or future therapies. These stem cells have been shown capable of producing hepatocytes.[citation nee

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Explain the normal function of proto-oncogenes and tumor suppressor genes in cells. How does this function change when cancer-causing mutations occur in each type of gene?

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A proto-oncogene is a normal gene that can become an oncogene due to mutations or increased expression. The resultant protein may be termed an oncoprotein.[7] Proto-oncogenes code for proteins that help to regulate cell growth and differentiation. Proto-oncogenes are often involved in signal transduction and execution of mitogenic signals, usually through their protein products. Upon activation, a proto-oncogene (or its product) becomes a tumor-inducing agent, an oncogene.[8] Examples of proto-oncogenes include RAS, WNT, MYC, ERK, and TRK. The MYC gene is implicated in Burkitt's Lymphoma, which starts when a chromosomal translocation moves an enhancer sequence within the vicinity of the MYC gene. The MYC gene codes for widely used transcription factors. When the enhancer sequence is wrongly placed, these transcription factors are produced at much higher rates. Another example of an oncogene is the Bcr-Abl gene found on the Philadelphia Chromosome, a piece of genetic material seen in Chronic Myelogenous Leukemia caused by the translocation of pieces from chromosomes 9 and 22. Bcr-Abl codes for a receptor tyrosine kinase, which is constitutively active, leading to uncontrolled cell proliferation.
Activation

The proto-oncogene can become an oncogene by a relatively small modification of its original function. There are three basic activation types:

A mutation within a proto-oncogene can cause a change in the protein structure, causing
an increase in protein (enzyme) activity
a loss of regulation
An increase in protein concentration, caused by
an increase of protein expression (through misregulation)
an increase of protein (mRNA) stability, prolonging its existence and thus its activity in the cell
a gene duplication (one type of chromosome abnormality), resulting in an increased amount of protein in the cell
A chromosomal translocation (another type of chromosome abnormality), causing
an increased gene expression in the wrong cell type or at wrong times
the expression of a constitutively active hybrid protein. This type of aberration in a dividing stem cell in the bone marrow leads to adult leukemia

The expression of oncogenes can be regulated by microRNAs (miRNAs), small RNAs 21-25 nucleotides in length that control gene expression by downregulating them.[9] Mutations in such microRNAs (known as oncomirs) can lead to activation of oncogenes.[10] Antisense messenger RNAs could theoretically be used to block the effects of oncogenes.

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What are carcinogens? Give examples.

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A carcinogen is any substance, radionuclide, or radiation that is an agent directly involved in causing cancer. This may be due to the ability to damage the genome or to the disruption of cellular metabolic processes. Several radioactive substances are considered carcinogens, but their carcinogenic activity is attributed to the radiation, for example gamma rays and alpha particles, which they emit. Common examples of carcinogens are inhaled asbestos, certain dioxins, and tobacco smoke. Although the public generally associates carcinogenicity with synthetic chemicals, it is equally likely to arise in both natural and synthetic substances.[1]

Cancer is a disease in which damaged cells do not undergo programmed cell death. Carcinogens may increase the risk of cancer by altering cellular metabolism or damaging DNA directly in cells, which interferes with biological processes, and induces the uncontrolled, malignant division, ultimately leading to the formation of tumors. Usually DNA damage, if too severe to repair, leads to programmed cell death, but if the programmed cell death pathway is damaged, then the cell cannot prevent itself from becoming a cancer cell.

There are many natural carcinogens. Aflatoxin B1, which is produced by the fungus Aspergillus flavus growing on stored grains, nuts and peanut butter, is an example of a potent, naturally occurring microbial carcinogen. Certain viruses such as Hepatitis B and human papilloma viruses have been found to cause cancer in humans. The first one shown to cause cancer in animals is Rous sarcoma virus, discovered in 1910 by Peyton Rous.

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What is a restriction enzyme? Does it cut DNA at random or only at specific sites?

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A restriction enzyme (or restriction endonuclease) is an enzyme that cuts DNA at specific recognition nucleotide sequences (with Type II restriction enzymes cutting double-stranded DNA) known as restriction sites.[1][2][3] Such enzymes, found in bacteria and archaea, are thought to have evolved to provide a defense mechanism against invading viruses.[4][5] Inside a bacterial host, the restriction enzymes selectively cut up foreign DNA in a process called restriction; host DNA is methylated by a modification enzyme (a methylase) to protect it from the restriction enzyme’s activity. Collectively, these two processes form the restriction modification system.[6] To cut the DNA, a restriction enzyme makes two incisions, once through each sugar-phosphate backbone (i.e. each strand) of the DNA double helix.

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What is the role of DNA ligase in the creation of recombinant DNA molecules?

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In molecular biology, DNA ligase is a specific type of enzyme, a ligase, (EC 6.5.1.1) that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond. It plays a role in repairing single-strand breaks in duplex DNA in living organisms, but some forms (such as DNA ligase IV) may specifically repair double-strand breaks (i.e. a break in both complementary strands of DNA). Single-strand breaks are repaired by DNA ligase using the complementary strand of the double helix as a template,[1], with DNA ligase creating the final phosphodiester bond to fully repair the DNA.

DNA ligase has applications in both DNA repair and DNA replication (see Mammalian ligases). In addition, DNA ligase has extensive use in molecular biology laboratories for genetic recombination experiments (see Applications in molecular biology research). Purified DNA ligase is used in gene cloning to join DNA molecules together to form recombinant DNA.

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Gel electrophoresis is a method used to separate DNA fragments based on what two characteristics?

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Gel electrophoresis is a method used in clinical chemistry to separate proteins by charge and or size (IEF agarose, essentially size independent) and in biochemistry and molecular biology to separate a mixed population of DNA and RNA fragments by length, to estimate the size of DNA and RNA fragments or to separate proteins by charge.[1] Nucleic acid molecules are separated by applying an electric field to move the negatively charged molecules through an agarose matrix. Shorter molecules move faster and migrate farther than longer ones because shorter molecules migrate more easily through the pores of the gel. This phenomenon is called sieving.[2] Proteins are separated by charge in agarose because the pores of the gel are too large to sieve proteins. Gel electrophoresis can also be used for separation of nanoparticles.

Gel electrophoresis uses a gel as an anticonvective medium and or sieving medium during electrophoresis, the movement of a charged particle in an electrical field. Gels suppress the thermal convection caused by application of the electric field, and can also act as a sieving medium, retarding the passage of molecules; gels can also simply serve to maintain the finished separation, so that a post electrophoresis stain can be applied.[3] DNA Gel electrophoresis is usually performed for analytical purposes, often after amplification of DNA via PCR, but may be used as a preparative technique prior to use of other methods such as mass spectrometry, RFLP, PCR, cloning, DNA sequencing, or Southern blotting for further characterization.

In simple terms: Electrophoresis is a procedure which enables the sorting of molecules based on size and charge. Using an electric field, molecules (such as DNA) can be made to move through a gel made of agar or polyacrylamide. The molecules being sorted are dispensed into a well in the gel material. The gel is placed in an electrophoresis chamber, which is then connected to a power source. When the electric current is applied, the larger molecules move more slowly through the gel while the smaller molecules move faster. The different sized molecules form distinct bands on the gel.[citation needed]

The term "gel" in this instance refers to the matrix used to contain, then separate the target molecules. In most cases, the gel is a crosslinked polymer whose composition and porosity is chosen based on the specific weight and composition of the target to be analyzed. When separating proteins or small nucleic acids (DNA, RNA, or oligonucleotides) the gel is usually composed of different concentrations of acrylamide and a cross-linker, producing different sized mesh networks of polyacrylamide. When separating larger nucleic acids (greater than a few hundred bases), the preferred matrix is purified agarose. In both cases, the gel forms a solid, yet porous matrix. Acrylamide, in contrast to polyacrylamide, is a neurotoxin and must be handled using appropriate safety precautions to avoid poisoning. Agarose is composed of long unbranched chains of uncharged carbohydrate without cross links resulting in a gel with large pores allowing for the separation of macromolecules and macromolecular complexes.[citation needed]

"Electrophoresis" refers to the electromotive force (EMF) that is used to move the molecules through the gel matrix. By placing the molecules in wells in the gel and applying an electric field, the molecules will move through the matrix at different rates, determined largely by their mass when the charge to mass ratio (Z) of all species is uniform, toward the (negatively charged) cathode if positively charged or toward the (positively charged) anode if negatively charged.[4]

If several samples have been loaded into adjacent wells in the gel, they will run parallel in individual lanes. Depending on the number of different molecules, each lane shows separation of the components from the original mixture as one or more distinct bands, one band per component. Incomplete separation of the components can lead to overlapping bands, or to indistinguishable smears representing multiple unresolved components.[citation needed] Bands in different lanes that end up at the same distance from the top contain molecules that passed through the gel with the same speed, which usually means they are approximately the same size. There are molecular weight size markers available that contain a mixture of molecules of known sizes. If such a marker was run on one lane in the gel parallel to the unknown samples, the bands observed can be compared to those of the unknown in order to determine their size. The distance a band travels is approximately inversely proportional to the logarithm of the size of the molecule.[citation needed]

There are limits to electrophoretic techniques. Since passing current through a gel causes heating, gels may melt during electrophoresis. Electrophoresis is performed in buffer solutions to reduce pH changes due to the electric field, which is important because the charge of DNA and RNA depends on pH, but running for too long can exhaust the buffering capacity of the solution. Further, different preparations of genetic material may not migrate consistently with each other, for morphological or other reasons.

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A population is ….

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A population is all the organisms that both belong to the same group or species and live in the same geographical area. In ecology the population of a certain species in a certain area is estimated using the Lincoln Index. The area that is used to define a sexual population is such that inter-breeding is possible between any pair within the area and more probable than cross-breeding with individuals from other areas. Normally breeding is substantially more common within the area than across the border.[1]

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Describe the theory proposed by Lamarck to explain how species evolved.

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Lamarck stressed two main themes in his biological work. The first was that the environment gives rise to changes in animals. He cited examples of blindness in moles, the presence of teeth in mammals and the absence of teeth in birds as evidence of this principle. The second principle was that life was structured in an orderly manner and that many different parts of all bodies make it possible for the organic movements of animals.[14]

Although he was not the first thinker to advocate organic evolution, he was the first to develop a truly coherent evolutionary theory.[6] He outlined his theories regarding evolution first in his Floreal lecture of 1800, and then in three later published works:

Recherches sur l'organisation des corps vivants, 1802.
Philosophie Zoologique, 1809.
Histoire naturelle des animaux sans vertèbres, (in seven volumes, 1815–1822).

Lamarck employed several mechanisms as drivers of evolution, drawn from the common knowledge of his day and from his own belief in chemistry pre-Lavoisier. He used these mechanisms to explain the two forces he saw as comprising evolution; a force driving animals from simple to complex forms, and a force adapting animals to their local environments and differentiating them from each other. He believed that these forces must be explained as a necessary consequence of basic physical principles, favoring a materialistic attitude toward biology.
Le pouvoir de la vie: The complexifying force

Lamarck referred to a tendency for organisms to become more complex, moving 'up' a ladder of progress. He referred to this phenomenon as Le pouvoir de la vie or la force qui tend sans cesse à composer l'organisation (The force that perpetually tends to make order). Like many natural historians, Lamarck believed that organisms arose in their simplest forms via spontaneous generation.

Lamarck ran against the modern chemistry promoted by Lavoisier (whose ideas he regarded with disdain), preferring to embrace a more traditional alchemical view of the elements as influenced primarily by earth, air, fire and water. He asserted that the natural movements of fluids in living organisms drove them toward ever greater levels of complexity:

The rapid motion of fluids will etch canals between delicate tissues. Soon their flow will begin to vary, leading to the emergence of distinct organs. The fluids themselves, now more elaborate, will become more complex, engendering a greater variety of secretions and substances composing the organs.

- Histoire naturelle des animaux sans vertebres, 1815.

He argued that organisms thus moved from simple to complex in a steady, predictable way based on the fundamental physical principles of alchemy. In this view, simple organisms never disappeared because they were constantly being created by spontaneous generation in what has been described as a 'steady-state biology'. Lamarck saw spontaneous generation as being ongoing, with the simple organisms thus created being transmuted over time becoming more complex. He is sometimes regarded as believing in a teleological (goal-oriented) process where organisms became more perfect as they evolved, though as a materialist, he emphasized that these forces must originate necessarily from underlying physical principles.
L'influence des circonstances: The adaptive force

The second component of Lamarck's theory of evolution was the adaptation of organisms to their environment. This could move organisms upward from the ladder of progress into new and distinct forms with local adaptations. It could also drive organisms into evolutionary blind alleys, where the organism became so finely adapted that no further change could occur. Lamarck argued that this adaptive force was powered by the interaction of organisms with their environment, by the use and disuse of certain characteristics.

First Law: In every animal which has not passed the limit of its development, a more frequent and continuous use of any organ gradually strengthens, develops and enlarges that organ, and gives it a power proportional to the length of time it has been so used; while the permanent disuse of any organ imperceptibly weakens and deteriorates it, and progressively diminishes its functional capacity, until it finally disappears".[20]

This first law says little except "an exaggerated generalization of the belief that exercise develops an organ".[21]

Second Law: All the acquisitions or losses wrought by nature on individuals, through the influence of the environment in which their race has long been placed, and hence through the influence of the predominant use or permanent disuse of any organ; all these are preserved by reproduction to the new individuals which arise, provided that the acquired modifications are common to both sexes, or at least to the individuals which produce the young.[20]

The last clause of this law introduces what is now called soft inheritance. "The second law was widely accepted at the time..[but] has been decisively rejected by modern genetics."[21] However, in the field of epigenetics, there is growing evidence that soft inheritance plays a part in the changing of some organisms' phenotypes: it leaves the DNA unaltered but affects DNA by preventing the expression of genes.[22] Some epigenetic changes such as the methylation of genes alter the likelihood of DNA transcription and can be produced by changes in behaviour and environment. Many epigenetic changes are themselves heritable to a degree. Thus, while DNA itself is not directly altered by the environment and behavior except through selection, the relationship of the genotype to the phenotype can be altered, even across generations, by experience within the lifetime of an individual. This has led to calls for biology to reconsider Lamarckian processes in evolution in light of modern advances in molecular biology.[23] These calls might not be justified as there is no evidence that any acquisitions in the phenotype can be passed on to the next generation. In fact this is very improbable, the germ line exists of a distinct population of cells that do not seem to be influenced in their characteristics by environmental changes. There is no apparent reason to assume that the epigenetics of the DNA of germ cells are more directively altered than the DNA of germ cells. All changes in the epigenetics of germ cells appear to be equally arbitrary as the changes that may occur in the DNA of the latter.

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What two main points did Darwin propose in his Origin of Species?

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Darwin's theory of evolution is based on key facts and the inferences drawn from them, which biologist Ernst Mayr summarised as follows:[3]

Every species is fertile enough that if all offspring survived to reproduce the population would grow (fact).
Despite periodic fluctuations, populations remain roughly the same size (fact).
Resources such as food are limited and are relatively stable over time (fact).
A struggle for survival ensues (inference).
Individuals in a population vary significantly from one another (fact).
Much of this variation is inheritable (fact).
Individuals less suited to the environment are less likely to survive and less likely to reproduce; individuals more suited to the environment are more likely to survive and more likely to reproduce and leave their inheritable traits to future generations, which produces the process of natural selection (inference).
This slowly effected process results in populations changing to adapt to their environments, and ultimately, these variations accumulate over time to form new species (inference).

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The textbook presents five lines of evidence in support of evolution. List them.

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Evidence of common descent of living things has been discovered by scientists working in a variety of fields over many years. This evidence has demonstrated and verified the occurrence of evolution and provided a wealth of information on the natural processes by which the variety and diversity of life on Earth developed. This evidence supports the modern evolutionary synthesis, the current scientific theory that explains how and why life changes over time. Evolutionary biologists document the fact of common descent: making testable predictions, testing hypotheses, and developing theories that illustrate and describe its causes.

Comparison of the DNA genetic sequences of organisms has revealed that organisms that are phylogenetically close have a higher degree of DNA sequence similarity than organisms that are phylogenetically distant. Further evidence for common descent comes from genetic detritus such as pseudogenes, regions of DNA that are orthologous to a gene in a related organism, but are no longer active and appear to be undergoing a steady process of degeneration from cumulative mutations.

Fossils are important for estimating when various lineages developed in geologic time. As fossilization is an uncommon occurrence, usually requiring hard body parts and death near a site where sediments are being deposited, the fossil record only provides sparse and intermittent information about the evolution of life. Evidence of organisms prior to the development of hard body parts such as shells, bones and teeth is especially scarce, but exists in the form of ancient microfossils, as well as impressions of various soft-bodied organisms. The comparative study of the anatomy of groups of animals shows structural features that are fundamentally similar or homologous, demonstrating phylogenetic and ancestral relationships with other organism, most especially when compared with fossils of ancient extinct organisms. Vestigial structures and comparisons in embryonic development are largely a contributing factor in anatomical resemblance in concordance with common descent. Since metabolic processes do not leave fossils, research into the evolution of the basic cellular processes is done largely by comparison of existing organisms’ physiology and biochemistry. Many lineages diverged at different stages of development, so it is possible to determine when certain metabolic processes appeared by comparing the traits of the descendants of a common ancestor. Universal biochemical organization and molecular variance patterns in all organisms also show a direct correlation with common descent.

Further evidence comes from the field of biogeography because evolution with common descent provides the best and most thorough explanation for a variety of facts concerning the geographical distribution of plants and animals across the world. This is especially obvious in the field of island biogeography. Combined with the theory of plate tectonics common descent provides a way to combine facts about the current distribution of species with evidence from the fossil record to provide a logically consistent explanation of how the distribution of living organisms has changed over time.

The development and spread of antibiotic resistant bacteria, like the spread of pesticide resistant forms of plants and insects provides evidence that evolution due to natural selection is an ongoing process in the natural world. Alongside this, are observed instances of the separation of populations of species into sets of new species (speciation). Speciation has been observed directly and indirectly in the lab and in nature. Multiple forms of such have been described and documented as examples for individual modes of speciation. Furthermore, evidence of common descent extends from direct laboratory experimentation with the artificial selection of organisms—historically and currently—and other controlled experiments involving many of the topics in the article. This article explains the different types of evidence for evolution with common descent along with many specialized examples of each.

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Define fossils. What is the fossil record?

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Fossils (from Latin fossus, literally "having been dug up") are the preserved remains or traces of animals (also known as zoolites), plants, and other organisms from the remote past. The totality of fossils, both discovered and undiscovered, and their placement in fossiliferous (fossil-containing) rock formations and sedimentary layers (strata) is known as the fossil record.

The study of fossils across geological time, how they were formed, and the evolutionary relationships between taxa (phylogeny) are some of the most important functions of the science of paleontology. Such a preserved specimen is called a "fossil" if it is older than some minimum age, most often the arbitrary date of 10,000 years ago.[1] Hence, fossils range in age from the youngest at the start of the Holocene Epoch to the oldest from the Archaean Eon, up to 3.4 billion years old.[2][3] The observations that certain fossils were associated with certain rock strata led early geologists to recognize a geological timescale in the 19th century. The development of radiometric dating techniques in the early 20th century allowed geologists to determine the numerical or "absolute" age of the various strata and thereby the included fossils.

Like extant organisms, fossils vary in size from microscopic, such as single bacterial cells[4] only one micrometer in diameter, to gigantic, such as dinosaurs and trees many meters long and weighing many tons. A fossil normally preserves only a portion of the deceased organism, usually that portion that was partially mineralized during life, such as the bones and teeth of vertebrates, or the chitinous or calcareous exoskeletons of invertebrates. Preservation of soft tissues is rare in the fossil record. Fossils may also consist of the marks left behind by the organism while it was alive, such as the footprint or feces (coprolites) of a reptile. These types of fossil are called trace fossils (or ichnofossils), as opposed to body fossils. Finally, past life leaves some markers that cannot be seen but can be detected in the form of biochemical signals; these are known as chemofossils or biomarkers.

Ever since recorded history began, and probably before, people have noticed and gathered fossils, including pieces of rock and minerals that have replaced the remains of biologic organisms, or preserved their external form. Fossils themselves, and the totality of their occurrence within the sequence of Earth's rock strata, is referred to as the fossil record.

The fossil record was one of the early sources of data relevant to the study of evolution and continues to be relevant to the history of life on Earth. Paleontologists examine the fossil record in order to understand the process of evolution and the way particular species have evolved.
Explanations
Fossil shrimp (Cretaceous)
A fossil gastropod from the Pliocene of Cyprus. A serpulid worm is attached.

Various explanations have been put forth throughout history to explain what fossils are and how they came to be where they were found. Many of these explanations relied on folktales or mythologies. In China the fossil bones of ancient mammals including Homo erectus were often mistaken for “dragon bones” and used as medicine and aphrodisiacs. In the West the presence of fossilized sea creatures high up on mountainsides was seen as proof of the biblical deluge.

In 1027, the Persian Avicenna explained how the stoniness of fossils was caused in The Book of Healing. Avicenna gave the following explanation for the origin of fossils from the petrifaction of plants and animals:

If what is said concerning the petrifaction of animals and plants is true, the cause of this (phenomenon) is a powerful mineralizing and petrifying virtue which arises in certain stony spots, or emanates suddenly from the earth during earthquake and subsidences, and petrifies whatever comes into contact with it. As a matter of fact, the petrifaction of the bodies of plants and animals is not more extraordinary than the transformation of waters.[5]

Greek scholar Aristotle realized that fossil seashells from rocks were similar to those found on the beach, indicating the fossils were once living animals. Leonardo da Vinci concurred with Aristotle's view that fossils were the remains of ancient life.[6] Aristotle previously explained it in terms of vaporous exhalations, which Avicenna modified into the theory of petrifying fluids (succus lapidificatus), which was elaborated on by Albert of Saxony in the 14th century and accepted in some form by most naturalists by the 16th century.[7]

More scientific views of fossils emerged during the Renaissance. For example, Leonardo Da Vinci noticed discrepancies with the use of the biblical flood narrative as an explanation for fossil origins:

"If the Deluge had carried the shells for distances of three and four hundred miles from the sea it would have carried them mixed with various other natural objects all heaped up together; but even at such distances from the sea we see the oysters all together and also the shellfish and the cuttlefish and all the other shells which congregate together, found all together dead; and the solitary shells are found apart from one another as we see them every day on the sea-shores.

And we find oysters together in very large families, among which some may be seen with their shells still joined together, indicating that they were left there by the sea and that they were still living when the strait of Gibraltar was cut through. In the mountains of Parma and Piacenza multitudes of shells and corals with holes may be seen still sticking to the rocks...."[8]

Ichthyosaurus and Plesiosaurus from the 1834 Czech edition of Cuvier's Discours sur les revolutions de la surface du globe.

William Smith (1769–1839), an English canal engineer, observed that rocks of different ages (based on the law of superposition) preserved different assemblages of fossils, and that these assemblages succeeded one another in a regular and determinable order. He observed that rocks from distant locations could be correlated based on the fossils they contained. He termed this the principle of faunal succession.

Smith, who preceded Charles Darwin, was unaware of biological evolution and did not know why faunal succession occurred. Biological evolution explains why faunal succession exists: as different organisms evolve, change and go extinct, they leave behind fossils. Faunal succession was one of the chief pieces of evidence cited by Darwin that biological evolution had occurred.

Georges Cuvier came to believe that most if not all the animal fossils he examined were remains of species that were now extinct. This led Cuvier to become an active proponent of the geological school of thought called catastrophism. Near the end of his 1796 paper on living and fossil elephants he said:

All of these facts, consistent among themselves, and not opposed by any report, seem to me to prove the existence of a world previous to ours, destroyed by some kind of catastrophe.[9]

Biological explanations

Early naturalists well understood the similarities and differences of living species leading Linnaeus to develop a hierarchical classification system still in use today. It was Darwin and his contemporaries who first linked the hierarchical structure of the great tree of life in living organisms with the then very sparse fossil record. Darwin eloquently described a process of descent with modification, or evolution, whereby organisms either adapt to natural and changing environmental pressures, or they perish.
Petrified cone of Araucaria mirabilis from Patagonia, Argentina dating from the Jurassic Period (approx. 210 Ma)

When Charles Darwin wrote On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life, the oldest animal fossils were those from the Cambrian Period, now known to be about 540 million years old. The absence of older fossils worried Darwin about the implications for the validity of his theories, but he expressed hope that such fossils would be found, noting that: "only a small portion of the world is known with accuracy." Darwin also pondered the sudden appearance of many groups (i.e. phyla) in the oldest known Cambrian fossiliferous strata.[10]
Further discoveries

Since Darwin's time, the fossil record has been pushed back to between 2.3 and 3.5 billion years before the present.[11] Most of these Precambrian fossils are microscopic bacteria or microfossils. However, macroscopic fossils are now known from the late Proterozoic. The Ediacara biota (also called Vendian biota) dating from 575 million years ago collectively constitutes a richly diverse assembly of early multicellular eukaryotes.

The fossil record and faunal succession form the basis of the science of biostratigraphy or determining the age of rocks based on the fossils they contain. For the first 150 years of geology, biostratigraphy and superposition were the only means for determining the relative age of rocks. The geologic time scale was developed based on the relative ages of rock strata as determined by the early paleontologists and stratigraphers.

Since the early years of the twentieth century, absolute dating methods, such as radiometric dating (including potassium/argon, argon/argon, uranium series, and, for very recent fossils, radiocarbon dating) have been used to verify the relative ages obtained by fossils and to provide absolute ages for many fossils. Radiometric dating has shown that the earliest known stromatolites are over 3.4 billion years old. Various dating methods have been used and are used today depending on local geology and context, and while there is some variance in the results from these dating methods, nearly all of them provide evidence for a very old Earth, approximately 4.6 billion years.
Modern view

"The fossil record is life’s evolutionary epic that unfolded over four billion years as environmental conditions and genetic potential interacted in accordance with natural selection."[12] The earth’s climate, tectonics, atmosphere, oceans, and periodic disasters invoked the primary selective pressures on all organisms, which they either adapted to, or they perished with or without leaving descendants. Modern paleontology has joined with evolutionary biology to share the interdisciplinary task of unfolding the tree of life, which inevitably leads backwards in time to the microscopic life of the Precambrian when cell structure and functions evolved. Earth’s deep time in the Proterozoic and deeper still in the Archean is only "recounted by microscopic fossils and subtle chemical signals."[13] Molecular biologists, using phylogenetics, can compare protein amino acid or nucleotide sequence homology (i.e., similarity) to infer taxonomy and evolutionary distances among organisms, but with limited statistical confidence. The study of fossils, on the other hand, can more specifically pinpoint when and in what organism branching occurred in the tree of life. Modern phylogenetics and paleontology work together in the clarification of science’s still dim view of the appearance of life and its evolution during deep time on earth.[14]
Phacopid trilobite Eldredgeops rana crassituberculata, the genus is named after Niles Eldredge
Crinoid columnals (Isocrinus nicoleti) from the Middle Jurassic Carmel Formation at Mount Carmel Junction, Utah; scale in mm

Niles Eldredge’s study of the Phacops trilobite genus supported the hypothesis that modifications to the arrangement of the trilobite’s eye lenses proceeded by fits and starts over millions of years during the Devonian.[15] Eldredge's interpretation of the Phacops fossil record was that the aftermaths of the lens changes, but not the rapidly occurring evolutionary process, were fossilized. This and other data led Stephen Jay Gould and Niles Eldredge to publish the seminal paper on punctuated equilibrium in 1971.
Example of modern development

An example of modern paleontological progress is the application of synchrotron X-ray tomographic techniques to early Cambrian bilaterian embryonic microfossils that has recently yielded new insights of metazoan evolution at its earliest stages. The tomography technique provides previously unattainable three-dimensional resolution at the limits of fossilization. Fossils of two enigmatic bilaterians, the worm-like Markuelia and a putative, primitive protostome, Pseudooides, provide a peek at germ layer embryonic development. These 543-million-year-old embryos support the emergence of some aspects of arthropod development earlier than previously thought in the late Proterozoic. The preserved embryos from China and Siberia underwent rapid diagenetic phosphatization resulting in exquisite preservation, including cell structures. This research is a notable example of how knowledge encoded by the fossil record continues to contribute otherwise unattainable information on the emergence and development of life on Earth. For example, the research suggests Markuelia has closest affinity to priapulid worms, and is adjacent to the evolutionary branching of Priapulida, Nematoda and Arthropoda.[16]

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What is biogeography? What is the difference between marsupial and placental mammals, and where are they found?

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Biogeography is the study of the distribution of species (biology), organisms, and ecosystems in geographic space and through geological time. Organisms and biological communities vary in a highly regular fashion along geographic gradients of latitude, elevation, isolation and habitat area.

Knowledge of spatial variation in the numbers and types of organisms is as vital to us today as it was to our early human ancestors, as we adapt to heterogeneous but geographically predictable environments. Biogeography is an integrative field of inquiry that unites concepts and information from ecology, evolutionary biology, geology, and physical geography.

Modern biogeographic research combines information and ideas from many fields, from the physiological and ecological constraints on organismal dispersal to geological and climatological phenomena operating at global spatial scales and evolutionary time frames.

Marsupials' reproductive systems differ markedly from those of placental mammals (Placentalia). Females have two lateral vaginas, which lead to separate uteri but both open externally through the same orifice. A third canal, the median vagina, is used for birth. This canal can be transitory or permanent.[19] The males generally have a two-pronged penis, which corresponds to the females' two vaginas.[20] The penis is used only for discharging semen into females, while a urogenital sac stores waste before expulsion.[further explanation needed]

Pregnant females develop something similar to a yolk sac in their wombs, which delivers nutrients to the embryo. Marsupials give birth at a very early stage of development (about 4–5 weeks); after birth, newborn marsupials crawl up the bodies of their mothers and attach themselves to a nipple, which is located on the underside of the mother either inside a pouch called the marsupium or open to the environment. To crawl to the nipple and attach to it, the marsupial must have well developed forelimbs and facial structures.[21][22] This is accomplished by accelerating forelimb and facial development in marsupials compared to placental mammals. As a result, there is decelerated development of such structures as the hindlimb and brain. There they remain for a number of weeks, attached to the nipple. The offspring are eventually able to leave the marsupium for short periods, returning to it for warmth, protection and nourishment.

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What are homologous structures? What are vestigial structures?

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The principle of homology: The biological derivation relationship (shown by colors) of the various bones in the forelimbs of four vertebrates is known as homology and was one of Darwin’s arguments in favor of evolution.

Homology forms the basis of organization for comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying structure of bones and muscles. Owen reasoned that there must be a common structural plan for all vertebrates, as well as for each class of vertebrates.
Forelimbs in mammals provide one example of homology.

Homologous[Etymology 1] traits of organisms are due to sharing a common ancestor, and such traits often have similar embryological origins and development. This is contrasted with analogous traits: similarities between organisms that were not present in the last common ancestor of the taxa being considered but rather evolved separately. An example of analogous traits would be the wings of bats and birds, which evolved separately but both of which evolved from the vertebrate forelimb and therefore have similar early embryology.

The concept of vestigiality applies to genetically determined structures or attributes that have apparently lost most or all function in a given species. Assessment of the vestigial status must generally rely on comparison with homologous features in related species. The emergence of vestigiality occurs by normal evolutionary processes, typically by loss of function of a feature that is no longer subject to positive selection pressures when it loses its value in a changing environment. More urgently the feature may be selected against when its function becomes definitely harmful. Typical examples of both types occur in the loss of flying capability in island-dwelling species.

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Using molecular biology techniques, the evolutionary relationships among species can be determined by comparing ______ and ______ of different organisms.

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genetics. whatever.

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Darwin based his theory of natural selection on which two key observations? What was his inescapable conclusion regarding these observations?

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Every species is fertile enough that if all offspring survived to reproduce the population would grow (fact).
Despite periodic fluctuations, populations remain roughly the same size (fact).
Resources such as food are limited and are relatively stable over time (fact).
A struggle for survival ensues (inference).
Individuals in a population vary significantly from one another (fact).
Much of this variation is inheritable (fact).
Individuals less suited to the environment are less likely to survive and less likely to reproduce; individuals more suited to the environment are more likely to survive and more likely to reproduce and leave their inheritable traits to future generations, which produces the process of natural selection (inference).
This slowly effected process results in populations changing to adapt to their environments, and ultimately, these variations accumulate over time to form new species (inference).

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The textbook emphasizes three key but subtle points about evolution by natural selection:
1) It is ________, and not individuals, that evolve
2) Natural selection can amplify or diminish only ________ traits
3) Evolution is not __________: it does not lead to perfectly adapted organisms
This is because ________ factors vary from time to time and place to place

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who cares

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Describe evolutionary trees.

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A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics. The taxa joined together in the tree are implied to have descended from a common ancestor.

In a rooted phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of the descendants, and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units (HTUs) as they cannot be directly observed. Trees are useful in fields of biology such as bioinformatics, systematics and comparative phylogenetics.

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What are the three main causes of evolutionary change?

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Mutations are changes in the DNA sequence of a cell's genome. When mutations occur, they can either have no effect, alter the product of a gene, or prevent the gene from functioning. Based on studies in the fly Drosophila melanogaster, it has been suggested that if a mutation changes a protein produced by a gene, this will probably be harmful, with about 70% of these mutations having damaging effects, and the remainder being either neutral or weakly beneficial.[66]

Mutations can involve large sections of a chromosome becoming duplicated (usually by genetic recombination), which can introduce extra copies of a gene into a genome.[67] Extra copies of genes are a major source of the raw material needed for new genes to evolve.[68] This is important because most new genes evolve within gene families from pre-existing genes that share common ancestors.[69] For example, the human eye uses four genes to make structures that sense light: three for colour vision and one for night vision; all four are descended from a single ancestral gene.[70]

New genes can be generated from an ancestral gene when a duplicate copy mutates and acquires a new function. This process is easier once a gene has been duplicated because it increases the redundancy of the system; one gene in the pair can acquire a new function while the other copy continues to perform its original function.[71][72] Other types of mutations can even generate entirely new genes from previously noncoding DNA.[73][74]

The generation of new genes can also involve small parts of several genes being duplicated, with these fragments then recombining to form new combinations with new functions.[75][76] When new genes are assembled from shuffling pre-existing parts, domains act as modules with simple independent functions, which can be mixed together to produce new combinations with new and complex functions.[77] For example, polyketide synthases are large enzymes that make antibiotics; they contain up to one hundred independent domains that each catalyze one step in the overall process, like a step in an assembly line.[78]
Sex and recombination
Further information: Sexual reproduction, Genetic recombination, and Evolution of sexual reproduction

In asexual organisms, genes are inherited together, or linked, as they cannot mix with genes of other organisms during reproduction. In contrast, the offspring of sexual organisms contain random mixtures of their parents' chromosomes that are produced through independent assortment. In a related process called homologous recombination, sexual organisms exchange DNA between two matching chromosomes.[79] Recombination and reassortment do not alter allele frequencies, but instead change which alleles are associated with each other, producing offspring with new combinations of alleles.[80] Sex usually increases genetic variation and may increase the rate of evolution.[81][82]
Gene flow
Further information: Gene flow

Gene flow is the exchange of genes between populations and between species.[83] It can therefore be a source of variation that is new to a population or to a species. Gene flow can be caused by the movement of individuals between separate populations of organisms, as might be caused by the movement of mice between inland and coastal populations, or the movement of pollen between heavy metal tolerant and heavy metal sensitive populations of grasses.

Gene transfer between species includes the formation of hybrid organisms and horizontal gene transfer. Horizontal gene transfer is the transfer of genetic material from one organism to another organism that is not its offspring; this is most common among bacteria.[84] In medicine, this contributes to the spread of antibiotic resistance, as when one bacteria acquires resistance genes it can rapidly transfer them to other species.[85] Horizontal transfer of genes from bacteria to eukaryotes such as the yeast Saccharomyces cerevisiae and the adzuki bean beetle Callosobruchus chinensis has occurred.[86][87] An example of larger-scale transfers are the eukaryotic bdelloid rotifers, which have received a range of genes from bacteria, fungi and plants.[88] Viruses can also carry DNA between organisms, allowing transfer of genes even across biological domains.[89]

Large-scale gene transfer has also occurred between the ancestors of eukaryotic cells and bacteria, during the acquisition of chloroplasts and mitochondria. It is possible that eukaryotes themselves originated from horizontal gene transfers between bacteria and archaea.[90]

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Define genetic drift. Compare and contrast the founder effect and the bottleneck effect.

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Genetic drift or allelic drift is the change in the frequency of a gene variant (allele) in a population due to random sampling.[1] The alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces. A population's allele frequency is the fraction of the copies of one gene that share a particular form.[2] Genetic drift may cause gene variants to disappear completely and thereby reduce genetic variation.

When there are few copies of an allele, the effect of genetic drift is larger, and when there are many copies the effect is smaller. Vigorous debates occurred over the relative importance of natural selection versus neutral processes, including genetic drift. Ronald Fisher held the view that genetic drift plays at the most a minor role in evolution, and this remained the dominant view for several decades. In 1968 Motoo Kimura rekindled the debate with his neutral theory of molecular evolution, which claims that most instances where a genetic change spreads across a population (although not necessarily changes in phenotypes) are caused by genetic drift.[3]

In population genetics, the founder effect is the loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population. It was first fully outlined by Ernst Mayr in 1942,[1] using existing theoretical work by those such as Sewall Wright.[2] As a result of the loss of genetic variation, the new population may be distinctively different, both genetically and phenotypically, from the parent population from which it is derived. In extreme cases, the founder effect is thought to lead to the speciation and subsequent evolution of new species.

In the figure shown, the original population has nearly equal numbers of blue and red individuals. The three smaller founder populations show that one or the other color may predominate (founder effect), due to random sampling of the original population. A population bottleneck may also cause a founder effect even though it is not strictly a new population.

The founder effect is a special case of genetic drift.[3][4] In addition to founder effects, the new population is often a very small population and so shows increased sensitivity to genetic drift, an increase in inbreeding, and relatively low genetic variation. This can be observed in the limited gene pool of Iceland, Faroe Islands, Isles of Scilly Scilly Isles Easter Islanders and those native to Pitcairn Island. Another example is the legendarily high deaf population of Martha's Vineyard, which resulted in the development of Martha's Vineyard Sign Language.

A population bottleneck (or genetic bottleneck) is an evolutionary event in which a significant percentage of a population or species is killed or otherwise prevented from reproducing.[1]

A slightly different sort of genetic bottleneck can occur if a small group becomes reproductively separated from the main population. This is called a founder effect.

Population bottlenecks reduce the genetic variation and, therefore, the population's ability to adapt to new selective pressures, such as climatic change or shift in available resources. Genetic drift can eliminate alleles that could have been positively selected on by the environment if they had not already drifted out of the population.[2]

Population bottlenecks increase genetic drift, as the rate of drift is inversely proportional to the population size. The reduction in a population's dispersal leads, over time, to increased genetic homogeneity. If severe, population bottlenecks can also markedly increase inbreeding due to the reduced pool of possible mates (see small population size).

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What is gene flow?

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In population genetics, gene flow (also known as gene migration) is the transfer of alleles or genes from one population to another.

Migration into or out of a population may be responsible for a marked change in allele frequencies (the proportion of members carrying a particular variant of a gene). Immigration may also result in the addition of new genetic variants to the established gene pool of a particular species or population.

There are a number of factors that affect the rate of gene flow between different populations. One of the most significant factors is mobility, as greater mobility of an individual tends to give it greater migratory potential. Animals tend to be more mobile than plants, although pollen and seeds may be carried great distances by animals or wind.

Maintained gene flow between two populations can also lead to a combination of the two gene pools, reducing the genetic variation between the two groups. It is for this reason that gene flow strongly acts against speciation, by recombining the gene pools of the groups, and thus, repairing the developing differences in genetic variation that would have led to full speciation and creation of daughter species.

For example, if a species of grass grows on both sides of a highway, pollen is likely to be transported from one side to the other and vice versa. If this pollen is able to fertilize the plant where it ends up and produce viable offspring, then the alleles in the pollen have effectively been able to move from the population on one side of the highway to the other.

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What is Darwinian fitness?

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Fitness (often denoted w in population genetics models) is a central idea in evolutionary theory. It can be defined either with respect to a genotype or to a phenotype in a given environment. In either case, it describes the ability to both survive and reproduce, and is equal to the average contribution to the gene pool of the next generation that is made by an average individual of the specified genotype or phenotype. If differences between alleles at a given gene affect fitness, then the frequencies of the alleles will change over generations; the alleles with higher fitness become more common. This process is called natural selection.

An individual's fitness is manifested through its phenotype. The phenotype is affected by the developmental environment as well as by genes, and the fitness of a given phenotype can be different in different environments. The fitnesses of different individuals with the same genotype are therefore not necessarily equal. However, since the fitness of the genotype is an averaged quantity, it will reflect the reproductive outcomes of all individuals with that genotype in a given environment or set of environments.

Inclusive fitness differs from individual fitness by including the ability of an allele in one individual to promote the survival and/or reproduction of other individuals that share that allele, in preference to individuals with a different allele. One mechanism of inclusive fitness is kin selection.

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Distinguish between the three general outcomes of natural selection: directional, disruptive, and stabilizing.

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In population genetics, directional selection is a mode of natural selection in which a single phenotype is favored, causing the allele frequency to continuously shift in one direction. Under directional selection, the advantageous allele increases in frequency independently of its dominance relative to other alleles; that is, even if the advantageous allele is recessive, it will eventually become fixed.

Directional selection occurs most often under environmental changes and when populations migrate to new areas with different environmental pressures. An example of directional selection is fossil records that show that the size of the black bears in Europe decreased during interglacial periods of the ice ages, but increased during each glacial period. Another example is the beak size in a population of finches. Throughout the wet years, small seeds were more common and there was such a large supply of the small seeds that the finches rarely ate large seeds. During the dry years, none of the seeds were in great abundance, but the birds usually ate more large seeds. The change in diet of the finches affected the depth of the birds’ beaks in the future generations.Their beaks range from large and tough to small and smooth.[1

Disruptive selection, also called diversifying selection, describes changes in population genetics in which extreme values for a trait are favored over intermediate values. In this case, the variance of the trait increases and the population is divided into two distinct groups.[1][2] This evolutionary process is believed to be the driving force behind sympatric speciation.[citation needed]

Stabilizing or ambidirectional selection, (not the same thing as negative or purifying selection[1][2]), is a type of natural selection in which genetic diversity decreases as the population stabilizes on a particular trait value. This is probably the most common mechanism of action for natural selection. Stabilizing selection commonly uses negative selection (a.k.a. purifying selection) to select against extreme values of the character.

Stabilizing Selection is the opposite of disruptive selection. Instead of favoring individuals with extreme phenotypes, it favors the intermediate variants. It reduces phenotypic variation and maintains the status quo. Natural selection tends to remove the more severe phenotypes, resulting in the reproductive success of the norm or average phenotypes.[3]

A classic example of this is human birth weight. Babies of low weight lose heat more quickly and get ill from infectious disease more easily, whereas babies of large body weight are more difficult to deliver through the pelvis. Infants of a more medium weight survive much more often. For the larger or smaller babies, the baby mortality rate is much higher.

Stabilizing selection operates most of the time in most populations. This type of selection acts to prevent divergence of form and function. In this way, the anatomy of some organisms, such as sharks and ferns, has remained largely unchanged for millions of years.

Stabilizing selection can sometimes be detected by measuring the fitness of the range of different phenotypes by various direct measures, but it can also be detected by a variety of tests of molecular sequence data, such as Ka/Ks ratios, changes in allele frequency distributions, and the McDonald-Kreitman test.[4][5]

In human populations, 5% of the genome DNA is under purified selection for common mammalian genes.[6] More loci may rapidly evolve including regulatory sequences and miRNAs.[7]

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What is sexual dimorphism?

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Sexual dimorphism is a phenotypic difference between males and females of the same species. Examples of such differences include differences in morphology, size, ornamentation, and behavior.

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What is sexual selection?

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Sexual selection, a concept introduced by Charles Darwin in his 1859 book On the Origin of Species, is a significant element of his theory of natural selection. The sexual form of selection
“ ... depends, not on a struggle for existence, but on a struggle between the males for possession of the females; the result is not death to the unsuccessful competitor, but few or no offspring.[1] ”
“ ... when the males and females of any animal have the same general habits ... but differ in structure, colour, or ornament, such differences have been mainly caused by sexual selection.[2] ”

A mate can be a single organism, mammal or animal. Does not have to be multiple.

His sexual selection examples include ornate peacock feathers, birds of Paradise, the antlers of stag (male deer), and the manes of lions.

Darwin greatly expands his initial three-page treatment of Sexual Selection in the 1871 book The Descent of Man and Selection in Relation to Sex. This 900-page, two-volume work includes 70 pages on sexual selection in human evolution, and 500 pages on sexual selection in other animals.[3] In summary, while natural selection results from the struggle to survive, sexual selection emerges from the struggle to reproduce.
“ The sexual struggle is of two kinds; in the one it is between individuals of the same sex, generally the males, in order to drive away or kill their rivals, the females remaining passive; whilst in the other, the struggle is likewise between the individuals of the same sex, in order to excite or charm those of the opposite sex, generally the females, which no longer remain passive, but select the more agreeable partners.[4]

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Define macroevolution. What does it include?

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Macroevolution is evolution on a scale of separated gene pools.[1] Macroevolutionary studies focus on change that occurs at or above the level of species, in contrast with microevolution,[2] which refers to smaller evolutionary changes (typically described as changes in allele frequencies) within a species or population.[3]

The process of speciation may fall within the purview of either, depending on the forces thought to drive it. Paleontology, evolutionary developmental biology, comparative genomics and genomic phylostratigraphy contribute most of the evidence for the patterns and processes that can be classified as macroevolution. An example of macroevolution is the appearance of feathers during the evolution of birds from theropod dinosaurs.

Abrupt transformations from one biologic system to another, for example the passing of life from water into land or the transition from invertebrates to vertebrates, are rare. Few major biological types have emerged during the evolutionary history of life and most of them survive till today. When lifeforms take such giant leaps, they meet little to no competition and are able to exploit a plethora of available niches, following a pattern of adaptive radiation. This can lead to convergent evolution, where unrelated populations display similar adaptations.[4]

The evolutionary course of Equidae (wide family including all horses and related animals) is often viewed as a typical example of macroevolution. The earliest known genus, Hyracotherium (now reclassified as a palaeothere), was a herbivore animal resembling a dog that lived in the early Cenozoic. As its habitat transformed into an open arid grassland, selective pressure required that the animal become a fast grazer. Thus elongation of legs and head as well as reduction of toes gradually occurred, producing the only extant genus of Equidae, Equus.[4]

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What is speciation? Distinguish between branching and nonbranching evolution.

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Speciation is the evolutionary process by which new biological species arise. The biologist Orator F. Cook seems to have been the first to coin the term 'speciation' for the splitting of lineages or "cladogenesis," as opposed to "anagenesis" or "phyletic evolution" occurring within lineages.[1][2] Whether genetic drift is a minor or major contributor to speciation is the subject matter of much ongoing discussion.

There are four geographic modes of speciation in nature, based on the extent to which speciating populations are isolated from one another: allopatric, peripatric, parapatric, and sympatric. Speciation may also be induced artificially, through animal husbandry, agriculture, or laboratory experiments. Observed examples of each kind of speciation are provided throughout.[3]

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Define clade.

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Cladistics (Ancient Greek: κλάδος, klados, "branch") is a method of classifying species of organisms into groups called clades, which consist of an ancestor organism and all its descendants (and nothing else). For example, birds, dinosaurs, crocodiles, and all descendants (living or extinct) of their most recent common ancestor form a clade.[1] In the terms of biological systematics, a clade is a single "branch" on the "tree of life", a monophyletic group.

Cladistics can be distinguished from other taxonomic systems, such as morphology-based phenetics, by its focus on shared derived characters (synapomorphies). Systems developed earlier usually employed overall morphological similarity to group species into genera, families and other higher level groups (taxa); cladistic classifications (usually in the form of trees called cladograms) are intended to reflect the relative recency of common ancestry or the sharing of homologous features. Cladistics is also distinguished by an emphasis on parsimony and hypothesis testing (particularly falsificationism), leading to a claim that cladistics is more objective than systems which rely on subjective judgements of relationship based on similarity.[2]

Cladistics originated in the work of the German entomologist Willi Hennig, who referred to it as "phylogenetic systematics" (also the name of his 1966 book); the use of the terms cladistics and clade was popularized by other researchers. The technique and sometimes the name have been successfully applied in other disciplines: for example, to determine the relationships between the surviving manuscripts of the Canterbury Tales[3] and 53 manuscripts of the Sanskrit Carakasaṃhitā.[4]

Cladists use cladograms – diagrams which show ancestral relations between species – to represent the monophyletic relationships of species, termed sister-group relationships. This is interpreted as representing phylogeny, or evolutionary relationships. Although traditionally such cladograms were generated largely on the basis of morphological characters, genetic sequencing data and computational phylogenetics are now very commonly used in the generation of cladograms.

Cladistics, either generally or in specific applications, has been criticized from its beginnings. A decision as to whether a particular character is a synapomorphy or not may be challenged as involving subjective judgements,[5] raising the issue of whether cladistics as actually practised is as objective as has been claimed. Formal classifications based on cladistic reasoning are said to emphasize ancestry at the expense of descriptive characteristics, and thus ignore biologically sensible, clearly defined groups which do not fall into clades (e.g. reptiles as traditionally defined or prokaryotes).[6]

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According to the biological species concept a species is …

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The biological species concept defines a species as members of populations that actually or potentially interbreed in nature, not according to similarity of appearance. Although appearance is helpful in identifying species, it does not define species.

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What is a reproductive barrier? What are the two main types?

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The mechanisms of reproductive isolation or hybridization barriers are a collection of mechanisms, behaviors and physiological processes that prevent the members of two different species that cross or mate from producing offspring, or which ensure that any offspring that may be produced is not fertile. These barriers maintain the integrity of a species over time, reducing or directly impeding gene flow between individuals of different species, allowing the conservation of each species’ characteristics.[1][2][3][4]

The mechanisms of reproductive isolation have been classified in a number of ways. Zoologist Ernst Mayr classified the mechanisms of reproductive isolation in two broad categories: those that act before fertilization (or before mating in the case of animals, which are called pre-copulatory) and those that act after.[5] These have also been termed pre-zygotic and post-zygotic mechanisms. The different mechanisms of reproductive isolation are genetically controlled and it has been demonstrated experimentally that they can evolve in species whose geographic distribution overlaps (sympatric speciation) or as the result of adaptive divergence that accompanies allopatric speciation.

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Define prezygotic barriers. List the five main examples.

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Pre-zygotic isolation mechanisms are the most economic in terms of the biological efficiency of a population, as resources are not wasted on the production of a descendent that is weak, non-viable or sterile.
Temporal or habitat isolation

Any of the factors that prevent potentially fertile individuals from meeting will reproductively isolate the members of distinct species. The types of barriers that can cause this isolation include: different habitats, physical barriers, and a difference in the time of sexual maturity or flowering.[6][7] When factors change, especially physical barriers, often, species will branch off.

An example of the ecological or habitat differences that impede the meeting of potential pairs occurs in two fish species of the family Gasterosteidae (sticklebacks). One species lives all year round in fresh water, mainly in small streams. The other species lives in the sea during winter, but in spring and summer individuals migrate to river estuaries to reproduce. The members of the two populations are reproductively isolated due to their adaptations to distinct salt concentrations.[6] An example of reproductive isolation due to differences in the mating season are found in the toad species Bufo americanus and Bufo fowleri . The members of these species can be successfully crossed in the laboratory producing healthy, fertile hybrids. However, mating does not occur in the wild even though the geographical distribution of the two species overlaps. The reason for the absence of inter-species mating is that B. americanus mates in early summer and B. fowleri in late summer.[6] Certain plant species, such as Tradescantia canaliculata and T. subaspera, are sympatric throughout their geographic distribution yet they are reproductively isolated as they flower at different times of the year. In addition, one species grows in sunny areas and the other in deeply shaded areas.[3][7]
Sexual isolation by behavior or conduct

The different mating rituals of animal species creates extremely powerful reproductive barriers, termed sexual or behavior isolation, that isolate apparently similar species in the majority of the groups of the animal kingdom. In dioecious species, males and females have to search for a partner, be in proximity to each other, carry out the complex mating rituals and finally copulate or release their gametes into the environment in order to breed. [8] [9] [10]
New Zealand cicada song.ogg
The songs of birds, insects and many other animals are part of a ritual to attract potential partners of their own species. The song presents specific patterns recognizable only by members of the same species, and therefore represents a mechanism of reproductive isolation. This recording is the song of a species of cicada, recorded in Lower Hutt, New Zealand on 15th February 2006.

Mating dances, the songs of males to attract females or the mutual grooming of pairs, are all examples of typical courtship behavior that allows both recognition and reproductive isolation. This is because each of the stages of courtship depend on the behavior of the partner. The male will only move onto the second stage of the exhibition if the female shows certain responses in her behavior. He will only pass onto the third stage when she displays a second key behavior. The behaviors of both interlink, are synchronized in time and lead finally to copulation or the liberation of gametes into the environment. No animal that is not physiologically suitable for fertilization can complete this demanding chain of behavior. In fact, the smallest difference in the courting patterns of two species is enough to prevent mating (for example, a specific song pattern acts as an isolation mechanism in distinct species of grasshopper of the genus Chorthippus.[11]). Even where there are minimal morphological differences between species, differences in behavior can be enough to prevent mating. For example, Drosophila melanogaster and D. simulans which are considered twin species due to their morphological similarity, do not mate even if they are kept together in a laboratory.[3][12] Drosophila ananassae and D. pallidosa are twin species from Melanesia. In the wild they rarely produce hybrids, although in the laboratory it is possible to produce fertile offspring. Studies of their sexual behavior show that the males court the females of both species but the females show a marked preference for mating with males of their own species. A different regulator region has been found on Chromosome II of both species that affects the selection behavior of the females.[12]

Pheromones play an important role in the sexual isolation of insect species.[13] These compounds serve to identify individuals of the same species and of the same or different sex. Evaporated molecules of volatile pheromones can serve as a wide-reaching chemical signal. In other cases, pheromones may be detected only at a short distance or by contact.

In species of the melanogaster group of Drosophila, the pheromones of the females are mixtures of different compounds, there is a clear dimorphism in the type and/or quantity of compounds present for each sex. In addition, there are differences in the quantity and quality of constituent compounds between related species, it is assumed that the pheromones serve to distinguish between individuals of each species. An example of the role of pheromones in sexual isolation is found in 'corn borers' in the genus Ostrinia. There are two twin species in Europe that occasionally cross. The females of both species produce pheromones that contain a volatile compound which has two isomers, E and Z; 99% of the compound produced by the females of one species is in the E isomer form, while the females of the other produce 99% isomer Z. The production of the compound is controlled by just one locus and the interspecific hybrid produces an equal mix of the two isomers. The males, for their part, almost exclusively detect the isomer emitted by the females of their species, such that the hybridization although possible is scarce. The perception of the males is controlled by one gene, distinct from the one for the production of isomers, the heterozygous males show a moderate response to the odour of either type. In this case, just 2 'loci' produce the effect of ethological isolation between species that are genetically very similar.[12]

Sexual isolation between two species can be asymmetrical. This can happen when the mating that produces descendants only allows one of the two species to function as the female progenitor and the other as the male, while the reciprocal cross does not occur. For instance, half of the wolves tested in the Great Lakes area of America show mitochondrial DNA sequences of coyotes. While mitochondrial DNA from wolves is never found in coyote populations. This probably reflects an asymmetry in inter-species mating due to the difference in size of the two species as male wolves take advantage of their greater size in order to mate with female coyotes, while female wolves and male coyotes do not mate[14] [a].
Mechanical isolation
The flowers of many species of Angiosperm have evolved to attract and reward a single or a few pollinator species (insects, birds, mammals). Their wide diversity of form, colour, fragrance and presence of nectar is, in many cases, the result of coevolution with the pollinator species. This dependency on its pollinator species also acts as a reproductive isolation barrier.

Mating pairs may not be able to couple successfully if their genitals are not compatible. The relationship between the reproductive isolation of species and the form of their genital organs was signaled for the first time in 1844 by the French entomologist Léon Dufour. Insects' rigid carapaces act in a manner analogous to a lock and key, as they will only allow mating between individuals with complementary structures, that is, males and females of the same species (termed co-specifics).

Evolution has led to the development of genital organs with increasingly complex and divergent characteristics, which will cause mechanical isolation between species. Certain characteristics of the genital organs will often have converted them into mechanisms of isolation. However, numerous studies show that organs that are anatomically very different can be functionally compatible, indicating that other factors also determine the form of these complicated structures.[15]

Mechanical isolation also occurs in plants and this is related to the adaptation and coevolution of each species in the attraction of a certain type of pollinator (where pollination is zoophilic) through a collection of morphophysiological characteristics of the flowers (called floral syndrome), in such a way that the transport of pollen to other species does not occur.[16]
Gametic Isolation

The synchronous spawning of many species of coral in marine reefs means that inter-species hybridization can take place as the gametes of hundreds of individuals of tens of species are liberated into the same water at the same time. Approximately a third of all the possible crosses between species are compatible, in the sense that the gametes will fuse and lead to individual hybrids. This hybridization apparently plays a fundamental role in the evolution of coral species.[17] However, the other two-thirds of possible crosses are incompatible. It has been observed that in sea urchins of the genus Strongylocentrotus the concentration of spermatocytes that allow 100% fertilization of the ovules of the same species is only able to fertilize 1.5% of the ovules of other species. This inability to produce hybrid offspring, despite the fact that the gametes are found at the same time and in the same place, is due to a phenomenon known as gamete incompatibility, which is often found between marine invertebrates, and whose physiological causes are not fully understood.[18][19]

In some Drosophila crosses, the swelling of the female's vagina has been noted following insemination. This has the effect of consequently, preventing the fertilization of the ovule by sperm of a different species.[20]

In plants the pollen grains of a species can germinate in the stigma and grow in the style of other species. However, the growth of the pollen tubes may be detained at some point between the stigma and the ovules, in such a way that fertilization does not take place. This mechanism of reproductive isolation is common in the Angiosperms and is called cross-incompatibility or incongruence.[21][22] A relationship exists between self-incompatibility and the phenomenon of cross-incompatibility. In general crosses between individuals of a self-compatible species (SC) with individuals of a self-incompatible (SI) species give hybrid offspring. On the other hand, a reciprocal cross (SI x SC) will not produce offspring, because the pollen tubes will not reach the ovules. This is known as unilateral incompatibility, which also occurs when two SC or two SI species are crossed.[23]

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Define postzygotic barriers. List the three main examples.

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A number of mechanisms which act after fertilisation preventing successful inter-population crossing are discussed below.
Zygote mortality and non-viability of hybrids

A type of incompatibility that is found as often in plants as in animals occurs when the ovule is fertilized but the zygote does not develop, or it develops and the resulting individual has a reduced viability.[3] This is the case for crosses between species of the frog genus, where widely differing results are observed depending of the species involved. In some crosses there is no segmentation of the zygote (or it may be that the hybrid is extremely non-viable and changes occur from the first mitosis). In others, normal segmentation occurs in the blastula but gastrulation fails. Finally, in other crosses, the initial stages are normal but errors occur in the final phases of embryo development. This indicates differentiation of the embryo development genes (or gene complexes) in these species and these differences determine the non-viability of the hybrids.[24]

Similar results are observed in mosquitos of the Culex genus, but the differences are seen between reciprocal crosses, from which it is concluded that the same effect occurs in the interaction between the genes of the cell nucleus (inherited from both parents) as occurs in the genes of the cytoplasmic organelles which are inherited solely from the female progenitor through the cytoplasm of the ovule.[3]

In Angiosperms, the successful development of the embryo depends on the normal functioning of its endosperm.[25]

The failure of endosperm development and its subsequent abortion has been observed in many interploidal crosses (that is, those between populations with a particular degree of intra or interspecific ploidy,[25] [26][27] [28] [29] and in certain crosses in species with the same level of ploidy.[29][30] [31] The collapse of the endosperm, and the subsequent abortion of the hybrid embryo is one of the most common post-fertilization reproductive isolation mechanism found in angiosperms.
Hybrid sterility
Mules are hybrids with interspecific sterility.
A hybrid between a polar bear and a brown bear, Rothschild Museum, Tring.

A hybrid has normal viability but is deficient in terms of reproduction or is sterile. This is demonstrated by the mule and in many other well known hybrids. In all of these cases sterility is due to the interaction between the genes of the two species involved; to chromosomal imbalances due to the different number of chromosomes in the parent species; or to nucleus-cytoplasmic interactions such as in the case of Culex described above.[3]

Hinnies and mules are hybrids resulting from a cross between a horse and an ass or between a mare and a donkey, respectively. These animals are nearly always sterile due to the difference in the number of chromosomes between the two parent species. Both horses and donkeys belong to the genus Equus, but Equus caballus has 64 chromosomes, while Equus asinus only has 62. A cross will produce offspring (mule or hinny) with 63 chromosomes, that will not form pairs, which means that they do not divide in a balanced manner during meiosis. It is curious that they can cross with each other but the mule and the hinny are actually animals created by humans, as in the wild the species ignore each other and do not cross. In order to obtain mules or hinnies it is necessary to train the progenitors to accept copulation between the species or create them through artificial insemination.

The sterility of many of the interspecific hybrids among the angiosperms is a widely recognised and studied phenomenon. [32] There are a variety of causes that can determine the interspecific sterility of hybrids in plants, these may be genetic, related to the genomes or the interaction between nuclear and cytoplasmic factors, as will be discussed in the corresponding section. Nevertheless, it should be pointed out that - on the contrary to the situation in animals - hybridization in plants is a stimulus for the creation of new species. [33] Indeed, although the hybrid may be sterile it can continue to multiply in the wild through the mechanisms of asexual reproduction, be they vegetative propagation or apomixis or the production of seeds. [34] [35] Indeed, interspecific hybridization can be associated with polyploidia and, in this way, the origin of new species that are called allopolyploids. Rosa canina, for example, is the result of multiple hybridizations.[36] or there is a type of wheat that is an allohexaploid that contains the genomes of three different species.[37]

Front 90

Compare and contrast allopatric speciation and sympatric speciation.

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Allopatric speciation (from the ancient Greek allos, "other" + Greek patra, "fatherland") or geographic speciation is speciation that occurs when biological populations of the same species become vicariant — isolated from each other to an extent that prevents or interferes with genetic interchange. This can be the result of population dispersal leading to emigration, or by geographical changes such as mountain formation, island formation, or large scale human activities (for example agricultural and civil engineering developments). The vicariant populations then undergo genotypic or phenotypic divergence as: (a) they become subjected to different selective pressures, (b) they independently undergo genetic drift, and (c) different mutations arise in the populations' gene pools.[1]

The separate populations over time may evolve distinctly different characteristics. If the geographical barriers are later removed, members of the two populations may be unable to successfully mate with each other, at which point, the genetically isolated groups have emerged as different species. Allopatric isolation is a key factor in speciation and a common process by which new species arise.[2] Adaptive radiation, as observed by Charles Darwin in Galapagos finches, is a consequence of allopatric speciation among island populations.

ympatric speciation is the process through which new species evolve from a single ancestral species while inhabiting the same geographic region. In evolutionary biology and biogeography, sympatric and sympatry are terms referring to organisms whose ranges overlap or are even identical, so that they occur together at least in some places. If these organisms are closely related (e.g. sister species), such a distribution may be the result of sympatric speciation. Etymologically, sympatry is derived from the Greek roots συν ("together", "with") and πατρίς ("homeland" or "fatherland").[1] The term was invented by Poulton in 1904, who explains the derivation.[2]

Sympatric speciation is one of three traditional geographic categories for the phenomenon of speciation.[3][4] Allopatric speciation is the evolution of geographically isolated populations into distinct species. In this case, divergence is facilitated by the absence of gene flow, which tends to keep populations genetically similar. Parapatric speciation is the evolution of geographically adjacent populations into distinct species. In this case, divergence occurs despite limited interbreeding where the two diverging groups come into contact. In sympatric speciation, there is no geographic constraint to interbreeding. It has been pointed out that these categories are special cases of a continuum from zero (sympatric) to complete (allopatric) spatial segregation of diverging groups.[4]

In multicellular eukaryotic organisms, sympatric speciation is thought to be an uncommon but plausible process by which genetic divergence (through reproductive isolation) of various populations from a single parent species and inhabiting the same geographic region leads to the creation of new species.[5] In bacteria, however, the analogous process (defined as "the origin of new bacterial species that occupy definable ecological niches") might be more common because bacteria are less constrained by the homogenizing effects of sexual reproduction and prone to comparatively dramatic and rapid genetic change through horizontal gene transfer.[6]

Front 91

Two models have been proposed to describe the pace of evolution: the graduated model and the punctuated equilibrium model. Distinguish between these two.

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Phyletic gradualism is a model of evolution which theorizes that most speciation is slow, uniform and gradual.[1] When evolution occurs in this mode, it is usually by the steady transformation of a whole species into a new one (through a process called anagenesis). In this view there is no clear line of demarcation between an ancestral species and a descendant species, unless splitting occurs.

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Punctuated equilibrium, bottom, consists of morphological stability and rare bursts of evolutionary change
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Punctuated equilibrium (also called punctuated equilibria) is a theory in evolutionary biology which proposes that most species will exhibit little net evolutionary change for most of their geological history, remaining in an extended state called stasis. When significant evolutionary change occurs, the theory proposes that it is generally restricted to rare and geologically rapid events of branching speciation called cladogenesis. Cladogenesis is the process by which a species splits into two distinct species, rather than one species gradually transforming into another.[1]

Punctuated equilibrium is commonly contrasted against the theory of phyletic gradualism, which states that evolution generally occurs uniformly and by the steady and gradual transformation of whole lineages (called anagenesis). In this view, evolution is seen as generally smooth and continuous.

In 1972, paleontologists Niles Eldredge and Stephen Jay Gould published a landmark paper developing this theory and called it punctuated equilibria.[2] Their paper built upon Ernst Mayr's theory of geographic speciation,[3] I. Michael Lerner's theories of developmental and genetic homeostasis,[4] as well as their own empirical research.[5][6] Eldredge and Gould proposed that the degree of gradualism commonly attributed to Charles Darwin is virtually nonexistent in the fossil record, and that stasis dominates the history of most fossil species.

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What is an exaptation? Give an example.

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Exaptation, cooption, and preadaptation are related terms referring to shifts in the function of a trait during evolution. For example, a trait can evolve because it served one particular function, but subsequently it may come to serve another. Exaptations are common in both anatomy and behaviour. Bird feathers are a classic example: initially these may have evolved for temperature regulation, but later were adapted for flight. Interest in exaptation relates to both the process and product of evolution: the process that creates complex traits and the product that may be imperfectly designed.[1]

Front 93

Define evo-devo. What is paedomorphosis?

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Evolutionary developmental biology (evolution of development or informally, evo-devo) is a field of biology that compares the developmental processes of different organisms to determine the ancestral relationship between them, and to discover how developmental processes evolved. It addresses the origin and evolution of embryonic development; how modifications of development and developmental processes lead to the production of novel features, such as the evolution of feathers;[1] the role of developmental plasticity in evolution; how ecology impacts in development and evolutionary change; and the developmental basis of homoplasy and homology.[2]

Although interest in the relationship between ontogeny and phylogeny extends back to the nineteenth century, the contemporary field of evo-devo has gained impetus from the discovery of genes regulating embryonic development in model organisms. General hypotheses remain hard to test because organisms differ so much in shape and form.[3]

Nevertheless, it now appears that just as evolution tends to create new genes from parts of old genes (molecular economy), evo-devo demonstrates that evolution alters developmental processes to create new and novel structures from the old gene networks (such as bone structures of the jaw deviating to the ossicles of the middle ear) or will conserve (molecular economy) a similar program in a host of organisms such as eye development genes in molluscs, insects, and vertebrates.[4] [5] Initially the major interest has been in the evidence of homology in the cellular and molecular mechanisms that regulate body plan and organ development. However more modern approaches include developmental changes associated with speciation.[6]

Neoteny (play /niːˈɒtɨniː/), also called juvenilization,[2] is one of the two ways by which pedomorphism can arise. Pedomorphism is the retention by adults of traits previously seen only in juveniles, and is a subject studied in the field of developmental biology. In neoteny, the physiological (or somatic) development of an animal or organism is slowed or delayed. In contrast, in progenesis, sexual development occurs faster. Both processes result in pedomorphism.[3] Ultimately this process results in the retention, in the adults of a species, of juvenile physical characteristics well into maturity and pedogenesis (paedogenesis), the reproduction in a neotenized state.[4

Front 94

Distinguish between systematics and taxonomy.

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Biological systematics is the study of the diversification of living forms, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees (synonyms: cladograms, phylogenetic trees, phylogenies). Phylogenies have two components, branching order (showing group relationships) and branch length (showing amount of evolution). Phylogenetic trees of species and higher taxa are used to study the evolution of traits (e.g., anatomical or molecular characteristics) and the distribution of organisms (biogeography). Systematics, in other words, is used to understand the evolutionary history of life on Earth.

Taxonomy (from Ancient Greek: τάξις taxis "arrangement" and Ancient Greek: νομία nomia "method"[1]) is the academic discipline of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. Each group is given a rank and groups of a given rank can be aggregated to form a super group of higher rank and thus create a hierarchical classification.[2][3] The groups created through this process are referred to as taxa (singular taxon). An example of a modern classification is the one published in 2009 by the Angiosperm Phylogeny Group for all living flowering plant families (the APG III system).[4]

Front 95

Recall how to name species scientifically. Organisms are given a two part name, italicized and latinized, and with the first letter of the genus capitalized. The names can also be underlined instead of italicized. Examples: Homo sapiens or Homo sapiens

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K bro