Bio 34 Final

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Jean-Baptiste Lamark

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-French Botanist -1793
-Professor of Natural History
-Coined the term Invertebrate
-Started a new field in Biology

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Jean-Baptiste Lamark

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Believed every organism had a "Tendency to perfection"

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Jean-Baptiste Lamark

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Simple animals arose spontaneously and then became more complex, evolving in the direction of man

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Jean-Baptiste Lamark

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Animals stray from evolutionary paths to adapt to their surroundings and conditions of existence

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Jean-Baptiste Lamark

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As animals strove to satisfy their daily needs, the movement of their internal fluids caused parts of their bodies to swell and these changes were passed to the animals' offspring

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Jean-Baptiste Lamark

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Philosophie zoologique, published in 1809 states _____ theories of evolution?

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Jean-Baptiste Lamark

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The first to separate Crustacea, Arachnida, and Annelida from Insecta

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Jean-Baptiste Lamark

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Advanced classification of Mollusks and removed tunicates and barnacles from the Mollusk class

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Jean-Baptiste Lamark

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No body can have life if its constituent parts are not cellular tissue or are not formed by cellular tissue

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Jean-Baptiste Lamark

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– His ideas regarding use/disuse and the “need” to change do not fit well with Darwinian evolution

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Thomas Huxley

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-1825-1895
-had very little formal education
-known as "Darwin's Bulldog" for his advocacy Darwin’s theory of evolution

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Thomas Huxley

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-Studied under Thomas Wharton Jones, a Scotsman who had purchased cadavers from Burke and Hare
–They had murdered 17 people and sold the bodies for dissection

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Thomas Huxley

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-instrumental in developing scientific education in Britain

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Thomas Huxley

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-slow to accept gradualism and undecided about natural selection

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Thomas Huxley

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-Believed humans evolved from apes

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Thomas Huxley

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-theory that birds evolved from dinosaurs

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Thomas Huxley

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"until selection and breeding can be seen to give rise to varieties which are infertile with each other, natural selection cannot be proved."

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Thomas Huxley

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-position on selection was agnostic; yet he gave no credence to any other theory
-He strongly supported Darwin, but never really accepted “natural selection”

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Eugene Dubois

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-believed humans evolved from apes, but it wasn’t a simple direct line
-Shared a common ancestor

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Eugene Dubois

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-studied many skulls from multiple hominids
-modeled the path of human evolution.

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Gregor Mendel

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-found that the plants' respective offspring retained the essential traits of the parents, and therefore were not influenced by the environment. This simple test gave birth to the idea of heredity

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Gregor Mendel

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He grew their progeny side by side to see if there would be any approximation of the traits passed on to the next generation

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Gregor Mendel

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-Concluded that every trait must be controlled by two “elements”
-what we now call genes

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Gregor Mendel

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results were published in a local scientific journal in 1866, but other scientists did not understand the importance of his work for several decades

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Gregor Mendel

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-used mathematics to draw conclusions
-His work and theories, later became the basis for the study of modern genetics, and are still recognized and used today.

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Gregor Mendel

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a. His work led to the discovery of particulate inheritance,
b. dominant and recessive traits,
c. genotype and phenotype,
d. the concept of heterozygous and homozygous

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dihybrid cross

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Shows the results for two traits

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Human karyotype

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-Has 23 chromosomes
-Traits are sex-lined when the gene is on the X or Y chromosome

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“crossing over” or homologous recombination

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the swapping of chunks of chromosome

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closely linked genes

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When two different traits are near each other on the chromosome, they usually stay together

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during “crossing over”

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If genes are far apart from each other, they are more likely to become separated

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Thomas Hunt Morgan

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-1866-1945
-First American to make really big impact in terms of heredity and evolution
-Often considered “Father of Modern Genetics”
-Also a noted embryologist

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Thomas Hunt Morgan

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Studied mutations in the fruit fly, Drosophila melanogaster, in his famous Fly Room at Columbia University

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Thomas Hunt Morgan

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-Demonstrated that genes are carried on chromosomes
-This is the mechanical basis (mechanism) of heredity

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Wilhelm Roux’s mosaic theory of development

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hereditary material was divided among embryonic cells, which were then predestined to form particular parts of a mature organism.

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Driesch

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thought that development was due to epigenetic factors where interactions between the protoplasam and the nucleus of the egg and the environment could affect development (so not just genes).

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Thomas Hunt Morgan

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his work with Driesch demonstrated that blastomeres isolated from sea urchin and ctenophore eggs could develop into complete larvae, contrary to the predictions (and experimental evidence) of Roux's supporters.

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Thomas Hunt Morgan

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A debate about the role of epigenetic and environmental factors in development; showed that sea urchin eggs could be induced to divide without fertilization by adding magnesium chloride

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Thomas Hunt Morgan

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began cross-breeding experiments to find heritable mutations

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Thomas Hunt Morgan

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Mutation does not equal speciation

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Thomas Hunt Morgan

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idea of genetic linkage

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Thomas Hunt Morgan

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-Some traits were sex-linked
-the trait was probably carried on one of the sex chromosomes
-other genes were probably carried on specific chromosomes as well

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Thomas Hunt Morgan

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hypothesized the phenomenon of crossing over

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crossover frequency

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indicates the distance separating genes on the chromosome; later the unit of measurement for linkage was called the morgan

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Thomas Hunt Morgan

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studied X and Y chromosomes and how they are inherited. The male parent’s chromosome contribution determines the sex of the offspring

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Polytene Chromosomes

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original discovery was in the late 1800’s. Their rediscovery in 1933 allowed Morgan’s lab to confirm their results on a physical basis

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Polytene Chromosomes

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through repeated rounds of DNA replication without any cell division (called endoreplication), they become large, banded chromosomes

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Polytene Chromosomes

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• Those from the salivary glands are often studied
• have characteristic light and dark banding patterns
• used to identify chromosomal rearragements and deletions.

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Polytene Chromosomes

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• Dark banding frequently corresponds to inactive chromatin
• light banding is usually found at areas with higher transcriptional activity.
• banding patterns of the polytene chromosomes of Drosophila melanogaster were sketched in 1935 by Calvin B. Bridges in such detail that his maps are still widely used today.

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Polytene Chromosomes

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• banding patterns provide an excellent visualization of transcriptionally active chromatin and general chromatin structure.

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Chromosome puffs

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diffuse uncoiled regions of the polytene chromosome that are sites of RNA transcription.

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Balbiani ring

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A large chromosome puff

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Linus Pauling

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-1901 – 1994
• Chemist
• Caltech graduate
• Professor at Caltech, recruited by Morgan
• Received 2 Nobel prizes
– 1954 in Chemistry
– 1962 Peace Prize

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Linus Pauling

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• Made huge contributions in understanding how molecules are put together

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Linus Pauling

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• Demonstrated how Mendelian genetics worked at the molecular level

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Linus Pauling

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• Was concerned about air pollution and was working on an electric car (~1950)

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Linus Pauling

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worked on protein structures using X-ray diffraction.

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Linus Pauling

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• Was concerned about air pollution and was working on an electric car (~1950)

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Linus Pauling

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*****Came up with the idea of hydrogen bonding******

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Hydrogen bonding

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• Important because these interactions help give a molecule – such as DNA or a protein – secondary structure.
• Secondary structure is the basic 3-D form of molecules

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Hydrogen bonding

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• Key to deciphering how nucleic acids, the building blocks of DNA and RNA, are arranged in space

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Hydrogen bonding

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• Orbital hybridization
• Tetravalency of carbon
• Important because it tells you how many bonds carbon can make with other atoms (tetra = 4)
• Valencies for other atoms tell you how many bonds they can make

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Hydrogen bonding

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• Electronegativity and the scale to help predict the nature of chemical bonding
• Also tells us whether a chemical reaction is going to be likely to occur under a particular set of conditions and predict the mechanism by which the reaction will occur
• Gave us a set of rules that can be used to figure out what is likely to happen at the molecular level

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Linus Pauling

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***published in the journal Science the first proof of a human disease caused by an abnormal protein***

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Linus Pauling

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used electrophoresis which demonstrated that individuals with sickle cell disease had a modified form of hemoglobin in their red blood cells (homozygous for mutated gene)

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Linus Pauling

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• Individuals with sickle cell trait had both the normal and abnormal forms of hemoglobin (heterozygous for the mutated gene).

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Linus Pauling

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•First demonstration that Mendelian Inheritance determined the specific physical properties of proteins, not simply their presence or absence—the dawn of molecular genetics

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Francis Crick

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-1916-2004
-Physicist, neuroscientist, molecular biologist
-1962 co-recipient of Nobel Prize for Physiology or Medicine
-“Central dogma” : genetic info flow in cells is unidirectional from DNA to RNA to Protein
-Played important role in research related to revealing the Genetic Code

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James Watson

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1928 – present
-Zoologist by training
-Postdoctoral Fellow when his -DNA work started
-1962 co-recipient of Nobel Prize for Physiology or Medicine

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James Watson

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Wrote a few books – including The Double Helix
Has given a bunch of lectures and invited talks all over the world

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Maurice Wilkins

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Physicist
During WWII
– Developed improved cathode-ray tubes for radar
– Worked on Manhattan Project

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Maurice Wilkins

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Learned how to do X-Ray Crystallography
1962 co-recipient of Nobel Prize for Physiology or Medicine

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Rosalind Franklin

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1920 – 1958
• Chemist by training
• World-renowned X-ray crystallographer

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Rosalind Franklin

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• Made it possible to solve the structure of DNA
– DNA purified in a mixture of 2 forms, which prevented X-Ray analysis
– developed a method for separating them

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Rosalind Franklin

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-solving DNA structure were substantial, but subject to controversy
• Had already died of ovarian cancer several years before Nobel Prize awarded & Posthumous awarding of Nobel Prize is not done

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DNA Structure
(Deoxyribonucleic Acid)

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The spiral staircase-shaped double helix….two connected strands—winding together like parallel handrails—are complementary to each other, and this unlocked the secret of how genetic information is stored, transferred, and copied.

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DNA Structure
(Deoxyribonucleic Acid)

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Watson and Crick first made helical models with the phosphates at the center of the helices (and the nucleotides on the outside).

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DNA Structure
(Deoxyribonucleic Acid)

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Rosalind Franklin made the discovery that the sugar-phosphate faced the outside, not the inside, forming the backbone
Linus Pauling came - concept of hydrogen bonding, the force that stabilizes the “ladder rungs” of the double helix

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DNA Structure
(Deoxyribonucleic Acid)

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Key to solving the structure of DNA was the realization that the two strands had to run in opposite directions. They are anti-parallel.

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DNA Structure
(Deoxyribonucleic Acid)

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-The directions are called 5-prime to 3-prime for one direction; the other is called 3-prime to 5-prime.
-Nucleotides that make up DNA:
Adenine: A Guanine: G
Cytosine: C Thymine: T
How they pair up:
A with T
G with C

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DNA
(Deoxyribonucleic Acid)

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is a polymer of deoxynucleotides

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RNA (ribonucleic acid)

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is a polymer of ribonucleotides

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Deoxy- and ribonucleotides

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contain adenine, guanine and cytosine

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Deoxynucleotides

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also contain thymine

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Ribonucleotides

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also contain uracil

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DNA Replication

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each strand of the original molecule acts as a template for the synthesis of a new, complementary DNA strand.

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DNA Replication

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• DNA replication has to occur on both strands of the DNA double helix.
• DNA replication is always done in one direction – from the 5’ end toward the 3’ end

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DNA Replication

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• You have a “leading strand” and a “lagging strand”
• The “lagging strand” is made in pieces that are called “Okazaki fragments”
• These fragments are filled in to complete the strand

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Protein Production

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-RNA polymerase transcribes DNA to make messenger RNA
-The mRNA sequence is complementary to the DNA sequence.
-On ribosomes, transfer RNA helps convert mRNA into protein.
-Amino acids link up to make a protein.

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translation

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Reading the RNA information and fitting the building blocks of a protein together

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Protein Production

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Its principal actors are the ribosome and amino acids.

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Ribosomes

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are among the biggest and most intricate structures in the cell. The ribosomes of bacteria contain not only huge amounts of RNA, but also more than 50 different proteins

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Genes

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often interrupted by stretches of DNA (introns) that do not contain instructions for making a protein. The DNA segments that do contain protein-making instructions are known as exons.

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alternative splicing

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Arranging exons in different patterns,enables cells to make different proteins from a single gene

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codons

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are “3-letter words” that encode amino acids.
ATG (DNA; AUG - RNA) start codon – methionine
TAG (DNA; UAG – RNA) stop codon – no amino acid

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genes

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• have regulatory regions in addition to regions that explicitly code for a protein or RNA product.

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genes

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• Have a “consensus sequence” that is recognized by the transcription machinery

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Promoter

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provides a position that is recognized by the transcription machinery for expression.

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Eukaryotic genes

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• are transcribed one at a time; introns are transcribed but never translated into protein (they are spliced out before translation).

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Polyadenylation

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• The addition of multiple adenines to a pre-mRNA and is part of the end of the transcription process
• Three steps
– 1) the RNA strand is cleaved at a particular site
– 2) the addition of poly-A's to the 3' end
– 3) the degradation of the remainder of the RNA transcript

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Central Dogma

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-many genes that are spliced together including:
-DNA, pre-mRNA, mRNA, and protein

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pre-mRNA

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What DNA is transcribed into

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Barbara McClintock

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1902-1992
• American botanist and cytogeneticist
• 1983 – 1st woman to win Nobel Prize for Physiology or Medicine

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Barbara McClintock

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• Discovered and characterized transposable elements (transposons) AKA: “jumping genes”

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Barbara McClintock

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• Used microscopic analysis to demonstrate genetic recombination by crossing-over during meiosis

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Barbara McClintock

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• Made first genetic map of chromosomes – linking physical traits to certain places or loci on the chromosome (genetic locus)

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Barbara McClintock

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• Demonstrated the importance of centromeres and telomeres in the conservation of genetic material

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Barbara McClintock

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• Loss of telomere length is associated with aging and cell death
• Cancerous cells have regained ability to keep their telomeres longs (increased telomerase production)

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Anatomy of the chromosome

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• Centromere – in the middle, joins the two arms
• Telomeres – at each end, buffers the chromosome from damage
• Arms – two arms, often of unequal length
• “p” = the short arm
• “q” = long arm

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telomere

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a region of repetitive DNA at the end of chromosomes, protecting the chromosome from destruction

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“ring chromosome” formation

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is associated with certain diseases

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chromosome

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• Telomere length is important for the cellular lifespan
• X-rays and other forms of radiation are mutagens
• Mutagens can cause damage to the ends of the chromosome, resulting in “ring chromosomes”

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Ring chromosome 20

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syndrome associated with epilepsy

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Ring chromosome 14 and 13

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associated with mental retardation

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Ring chromosome 15

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associated with dwarfism and microcephaly

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Ring chromosome X

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associated with Turner Syndrome

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Transposons

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• are genetic controlling elements
• Can activate or suppress gene transcription

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Barbara McClintock

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• "jumping genes," or transposons, may be linked to some genetic disorders such as hemophilia, leukemia, and breast cancer, and may have played critical roles in human evolution

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Dolly

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1997 – 2003
• cloned from a cell taken from the mammary gland of an adult animal
• Reproduced – 6 lambs
• Died of contagious virus

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Cloning

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• to make an exact copy

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Arthritis

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another possible sign of premature aging – could not find cause

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Cloning\Gene Therapy

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• **Until this time, it was commonly believed that the cells in our bodies were fixed in their roles

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Nuclear transfer

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take the nucleus from a diploid cell (containing 30-40,000 genes and a full set of paired chromosomes) to an unfertilized egg cell from which the maternal nucleus has been removed

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Gene therapy

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-the insertion of genes into an individual's cells and tissues to treat a disease, and hereditary diseases in which a defective mutant allele is replaced with a functional one.
-two forms

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Gene therapy using an Adenovirus vector

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A new gene is inserted into an adenovirus vector, which is used to introduce the modified DNA into a human cell. If the treatment is successful, the new gene will make a functional protein.

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Germ line gene therapy

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• sperm or eggs are modified by the introduction of functional genes & these genes become incorporated into the genome and can be passed to offspring

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Somatic cell gene therapy

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• the gene is introduced only in somatic cells, especially of those tissues in which expression of the concerned gene is critical for health

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Methods of Gene Therapy

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• A normal gene may be inserted into a nonspecific location within the genome to replace a nonfunctional gene. This approach is most common.

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Methods of Gene Therapy

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• An abnormal gene could be swapped for a normal gene through homologous recombination.

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Methods of Gene Therapy

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• The abnormal gene could be repaired through selective reverse mutation, which returns the gene to its normal function.

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Methods of Gene Therapy

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• The regulation (the degree to which a gene is turned on or off) of a particular gene could be altered.

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Problems and ethics of gene therapy

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• Short-lived nature of gene therapy
• Immune response
• Problems with viral vectors

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Problems and ethics of gene therapy

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• toxicity, immune and inflammatory responses, and gene control and targeting issues
• the fear that the viral vector may recover its ability to cause disease

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Problems and ethics of gene therapy

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• Multigene disorders – may be due to more than one gene being mutated
• Chance of inducing a tumor (insertional mutagenesis)
• Religious concerns

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Genetic Testing

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analysis of RNA, chromosomes DNA, proteins, and certain metabolites in order to detect heritable disease-related genotypes, mutations, phenotypes, and karyotypes for clinical purposes

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Types of Genetic testing:
• Newborn screening

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is used just after birth to identify genetic disorders that can be treated early in life

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Types of Genetic testing:
• Diagnostic testing

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used to diagnose or rule out a specific genetic or chromosomal condition

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Types of Genetic testing:
• Carrier testing

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is used to identify people who carry one copy of a gene mutation that, when present in two copies, causes a genetic disorder

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Types of Genetic testing:
• Prenatal testing

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is used to detect changes in a fetus’s genes or chromosomes before birth – offered to couples with increased risk of genetic or chromosomal disorders

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Types of Genetic testing:
• Predictive and presymptomatic

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used to detect gene mutations associated with disorders that occur later in life (eg, cancer)

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Types of Genetic testing:
• Forensic testing

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uses DNA sequences to identify an individual for legal purposes.

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Seven Pairs of Contrasting Traits Mendel followed

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seed color (yellow or green);
seed shape (smooth or wrinkled);
pod color (yellow or green);
pod shape (inflated or pinched);
flower color (purple or white);
flower position (axial or terminal);
stem height (tall or short).

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Three basic laws which governed the passage of a trait from one member of a species to another member of the same species

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1. the sex cells of a plant may contain two different traits, but not both of those traits (one allele)
2. characteristics are inherited independently from another (the basis for recessive and dominant gene composition).
3. each inherited characteristic is determined by two hereditary factors (known more recently as genes)

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sexual reproduction

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elements separate and only one is passed down to the offspring

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traits appeared in predictable ratios

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elements governing traits were not linked, but passed separately to the offspring.

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pedigrees

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-method by which one can follow traits from generation to generation within a family
-typically traced to determine the probability of passing along an hereditary disease.

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Mitosis

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-division of non-germline cells
-2 daughter cells
- Diploid (two copies of gene)

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Meiosis

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-Division of germline cells
(gamates, sex cells)
-Traits are passed on to offspring in this manner.
-Haploid = 1 copy of each gene/allele
- 4 daughter cells

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Genes

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– piece of DNA that gives the instructions for making a kind of protein

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Chromosomes

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– genetic material made up of DNA
– contains instructions for making many different proteins

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Alleles

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– instructions for two or more variations of a kind of protein (like eye color, hair color, blood type)

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Segregation

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division of chromosomes

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Punnet squares

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invented by R.C. Punnett in the early 1900s, are used to determine the possible combinations of offspring traits given 1 or more genes that can cause different physical characteristics

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Genotype

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genetic constitution of the cell, the specific makeup of the individuals DNA

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Self-cross

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-Parents were homozygous Dominant(BB) and Recessive (bb)and their offspring is now Heterozygous(Bb)

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Phenotype

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The observable characteristics of an organism