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164 Cards in this Set
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Genetics |
the study of the inheritance, or heredity, of living things. It is a wide-ranging science that |
explores the transmission of biological properties (traits) from parent to offspring, the expression and variation of those traits, the structure and function of the genetic material, and how this material changes. |
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organismal genetics |
observes the heredity of the whole organism or cell |
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chromosomal genetics |
examines the characteristics and actions of chromosomes; |
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molecular genetics |
deals with the biochemistry of the genes |
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genome |
the sum total of genetic material of an organism. |
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plasmids |
tiny extra pieces of DNA found in bacteria and some fungi |
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Genomics |
the study of an organism’s entire genome |
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chromosome |
a discrete cellular structure composed of a neatly packaged DNA molecule. |
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Eukaryotic Chromosome |
The structure of eukaryotic chromosomes consists of a DNA molecule tightly wound around histone proteins, |
Eukaryotic chromosomes are located in the nucleus; they vary in number from a few to hundreds; they can occur in pairs (diploid) or singles (haploid); and they have a linear appearance. |
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Bacterial Chromosome |
bacterial chromosome is condensed and secured into a packet by means of histonelike proteins. |
bacteria have a single, circular (double-stranded) chromosome, although many bacteria have multiple circular chromosomes and some have linear chromosomes. |
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gene |
In classical genetics, the term gene refers to the fundamental unit of heredity responsible for a given trait in an organism. In the molecular and biochemical sense, it is a site on the chromosome that provides information for a certain cell function. |
we now prefer to speak of a gene as a segment of DNA that contains the necessary code to make a protein or an RNA. |
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Gene Category 1 |
Structural genes code for proteins, |
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Gene category 2 |
genes that code for the RNA machin- ery used in protein production, |
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Gene Category 3 |
regulatory genes that control gene expression. |
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phenotype |
The expression of the genotype creates traits (certain structures or functions) |
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nucleotide |
The basic unit of DNA structure |
a chromosome in a typical bacterium consists of several million nucleotides linked end to end. |
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nucleotide |
composed of phosphate, deoxyribose sugar, and a nitrogenous base. |
The nucleotides covalently bond to each other in a sugar-phosphate linkage that becomes the backbone of each strand. Each sugar attaches in a repetitive pattern to two phosphates. One of the bonds is to the number 5′ (read “five prime”) carbon on deoxyribose, and the other is to the 3′ carbon |
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Nucleotide Nitrogenous Base |
purines and pyrimidines, attach by covalent bonds at the 1′ position of the sugar |
in DNA, the purine adenine (A) always pairs with the pyrimidine thymine (T), and the purine guanine (G) always pairs with the pyrimidine cytosine (C). |
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Double Helix |
One side of the helix runs in the opposite direction of the other, in what is called an antiparallel arrangement |
Thus, one helix runs from the 5′ to 3′ direction, and the other runs from the 3′ to 5′ direction. This characteristic is a significant factor in DNA synthesis and protein production. |
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DNA Overall Replication Process |
DNA replication requires a careful orchestration of the actions of 30 different enzymes |
HelicaseUnzipping the DNA helix PrimaseSynthesizing an RNA primer DNA polymerase IIIAdding bases to the new DNA chain; proofreading the chain for mistakes DNA polymerase IRemoving primer, closing gaps, repairing mismatches LigaseFinal binding of nicks in DNA during synthesis and repair Topoisomerase IMaking single-stranded DNA breaks to relieve supercoiling at origin Topoisomerase II (DNA gyrase) and IVMaking double-stranded DNA breaks to remove supercoiling ahead of origin and separate replicated daughter DNA molecules |
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Origin of Replication uncoiling the parent DNA molecule |
The origin of replication is a short sequence rich in adenine and thymine bases that are held together by only two hydrogen bonds rather than three. Because the origin of replication is AT-rich, less energy is required to separate the two strands than would be required if the origin were rich in guanine and cytosine. |
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2: |
unzipping the hydrogen bonds between the base pairs, thus separating the two strands and exposing the nucleo- tide sequence of each strand (which is normally buried in the center of the helix) to serve as templates |
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3: 3: |
synthesizing two new strands by attachment of the correct complementary nucleotides to each single-stranded template. |
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semiconservative replication |
The preservation of the parent molecule each daughter molecule will be identical to the parent in composition, butneither one is completely new; |
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Details of Replication |
The process of synthesizing a new daughter strand of DNA using the parental strand as a template is carried out by the enzyme DNA polymerase III. |
1. The nucleotides that need to be copied by DNA polymer- ase III are buried deep within the double helix. Accessing these nucleotides requires both that the DNA molecule be unwound and that the two strands of the helix be separated from one another.2. DNA polymerase III is unable to begin synthesizing a chain of nucleotides but can only continue to add nucleo- tides to an already existing chain.3. DNA polymerase III can only add nucleotides in one direction, so a new strand is always synthesized in a 5′ to 3' direction |
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replication fork |
The place in the helix where the strands are unwound and replication is taking place. Each circular DNA molecule will have two replication forks |
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primer |
A length of RNA that is inserted initially during rep- lication before it is replaced by DNA. |
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leading strand |
The strand of new DNA that is synthesized in a continuous manner in the 5′ to 3′ direction. |
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lagging strand |
The strand of new DNA that must be synthe- sized in short segments and later sealed together to form a strand in the 3′ to 5′ direction. |
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Okazaki fragments |
The short segments of DNA synthe- sized in a 5′ to 3′ direction, which are then sealed together to form a 3′ to 5′ strand. |
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mutations |
DNA is occasionally “misspelled” |
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Replication of Linear DNA |
The replication of eukaryotic DNA is similar to that of bacteria and archaea, even though it exists in a linear form. This process also uses a variety of DNA polymerases, and replication proceeds in both directions but from multiple origins along the linear DNA molecule. |
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telomeres |
3′ end of DNA molecules that cannot be completely copied. |
Once they shorten to a certain length, they will trigger cell death (apoptosis). In this way, the problem of end replication also provides a beneficial mechanism for older cells to be removed in higher eukaryotes. |
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each protein is different, |
Because each protein is different, each gene must also differ somehow in its composition. |
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triplets |
DNA exists in the order of groups of three Thus, one gene differs from another in its composition of triplets. |
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genetics |
the study of the inhertitance or heredity of living things. It is a wide ranging science that explores
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The transmission of biological properties (traits) from parent to offspring, The expression and variation of those traits The structure and function of the genetic material and How this material changes. |
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The Nature of The Genetic Material |
For species to survive, it must have the capacity of self-replication. In single-celled microorganisms reproduction usually involves the division of the cell by means of binary fission or budding and the accurate duplication and separation of genetic material into each daughter cell. |
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genes |
The chromosomes of all cells are subdivided into basic informational packets called genes |
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The size and packaging of Genomes |
a human cell has about 23,000 genes on 46 chromosomes |
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James Watson |
put the pieces of the puzzle together in 1953 to discovered that DNA is a gigantic molecule, a type of nucleic acid, with two strands combined into a double helix. |
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Francis Crick |
put the pieces of the puzzle together in 1953 to discovered that DNA is a gigantic molecule, a type of nucleic acid, with two strands combined into a double helix. |
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Basic DNA Structure |
basic unit of DNA structure is a nucleotide, and a chromosome in a typical bacterium consists of several million nucleotides linked end to end. Each nucleotide is composed of phosphate, deoxyribose sugar, and a nitrogenous base |
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phosphate linkages |
Each sugar in DNA is attached in a repetitive pattern to two phosphates. One of the bond to the number 5' (read "five prime") carbon on deoxyribose, and the other is to the 3' carbon which confers a certain order and direction on each strand. The nitrogenous bases, purines and pyrimidine's attach by covalent bond at the 1' position of the sugar. They span the center of the molecule and pair with appropriate complementary bases form the other strand. |
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base pairing |
in DNA, the purine Adenine (A) always pairs with the pyrimidine Thymine (T), and the purine guanine (G) always pairs with the pyrimidine Cytosine ( c). The bases are attached to each other in this pattern because each has a complementary three-dimensional shape that matches its pairs. Although the base-paring partners generally do not vary, the sequence of base pairs along the DNA molecule can assume any order, resulting in an infinite number of possible nucleotide sequences. |
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The arrangement of nitrogenous bases in DNA |
has two essential effects: Maintenance of The code during reproduction Providing Variety |
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replication in bacteria |
Early in binary fission, the metabolic machinery of a bacterium initiates the duplication of the chromosome. This DNA replication must be completed during a single generation time. Uncoiling the parent DNA molecule Unzipping the hydrogen bonds between the base pairs thus separating the two strands and exposing the nucleotide sequence of each strand ( which is normally buried in the center of the helix) to serve as templates, and Synthesizing two new strands by attachment of the correct complementary nucleotides to each single-stranded template. |
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semiconservative replication |
A critical feature of DNA replication is that each daughter molecule will be identical to the parent in composition, but neither one is completely new; the strand that serves as a template is an original parental DNA strand. |
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DNA polymerase III |
he process of synthesizing a new daughter strand of DNA using the parental strand as template is carried out by the enzyme DNA polymerase III. |
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limitations of DNA polymerase III |
The nucleotides that need to be copied by DNA polymerase III are buried deep within the double helix. Accessing these nucleotides requires both that the DNA molecule be unwound and that the two strands of the helix be separated from one another. DNA polymerase III is unable to being synthesizing a chain of nucleotides but con only continue to add nucleotides to an already existing chain. DNA polymerase III can only add nucleotides in one direction so a new strand is always synthesized in a 5' to 3' direction. |
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Replication Fork: |
The place in the helix where the strands are unwound and replication is taking place. Each circular DNA molecule will have two replication forks. |
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Primer |
A length of RNA that is inserted initially during replication before it is replaced by DNA |
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Leading Strand |
The strand of new DNA that is synthesized in a continuous manner in the 5' to 3' direction. |
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Lagging Strand |
The strand of new DNA that must be synthesized in short segments and later sealed together to form a strand in the 3' to 5' direction |
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Okazaki Fragments |
The short segments of DNA synthesized in a 5' to 3' direction, which are then sealed together to form a 3' to 5' strand. |
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Elongation and Termination of the Daughter Molecules |
The addition of nucleotides proceeds at an astonishing pace estimated in some bacteria to be 750 bases per second at each fork. As replication proceeds the newly produced double strand loops away. DNA polymerase I removes the RNA primers used to initiate DNA synthesis and replaces them with DNA. When the forks come full circle and meet ligases move along the lagging strand to being the initial linking of the fragments. Topoisomerase IV then causes a double-stranded DNA break that allows for the completion of synthesis and the separation of the intertwined circles into two fully replicated daughter molecules. |
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Replication of Linear DNA: |
The replication of eukaryotic DNA is similar to that of bacteria and archaea, even though it exists in a linear form. This process also uses a variety of DNA polymerases, and replication proceeds in both directions but from multiple origins along the linear DNA molecule. Topoisomerases are utilized in replication to relieve the tension as it is copied but also to re-compact the DNA when the molecule is completely replicated. |
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Replication of Linear DNA: |
Due to the structure of eukaryotic DNA and the unidirectional action of DNA polymerase, the 3' end of DNA molecules cannot be completely copied. These areas, called telomeres, being to erode with each cell division. Once they shorten to a certain length they will trigger cell death (apoptosis). In this way the problem of end replication also provides a beneficial mechanism for older cells to be removed in higher eukaryotes. |
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Applications of the DNA Code |
Although the genome is full of critical information, the molecule itself does not perform cell processes directly. Its stored information is conveyed to RNA molecules, which carry out instructions. |
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Transcription |
The concept that genetic information flows from DNA to RNA More precisely it states that the master code of DNA is first used to synthesize an RNA molecule |
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Translation |
the information contained in the RNA is then used to produce proteins in a process known as |
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the language of DNA exists in the order of groups of three. |
Consecutive vases called triplets on one DNA strand. Thus on gene differ from another in its composition of triplets. AN equally important part of this concept is that each triplet represents a code for a particular amino acid |
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triplet code |
When the triplet code is transcribed and translated, it dictates the type and order of amino acids in a polypeptide (protein) chain. |
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A proteins Primary Structure |
the order and type of amino acids in the chain determines its characteristic shape and function. |
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phenotype |
Proteins ultimately determine phenotype, the expression of all aspects of cell function and structure. Put more simply, living things are what their proteins make them. Regulatory RNAs help determine which proteins are made. |
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Proteomics |
is the study of an organisms complete set of expressed proteins. |
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DNA |
DNA is mainly a blueprint that tells the cell which kinds of proteins and RNA's to make and how to make them. |
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Major Participants in Transcription |
Transcription, the formation of RNA using DNA as a template A number of components participate: most prominently, messenger RNA, transfer RNA, regulatory RNA's , ribosomes, several types of enzymes, and a storehouse of raw materials. |
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tRNA and rRNA |
specialized forms of RNA |
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RNA |
contains Uracil (u) instead of thymine, as the complementary base pairing mate for adenine. This does not change inherent DNA code in any way because the uracil still follows the pairing rules. |
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RNA |
Although RNA, like DNA, contains a backbone that consists of alternating sugar and phosphate molecules the sugar in RNA is ribose rather than deoxyribose. |
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Form and Function of the Eukaryotic Cell |
In general eukaryotic microbial cells have a cytoplasmic membrane, nucleus, mitochondria and endoplasmic reticulum, Golgi Apparatus, vacuoles, cytoskeleton, glycocalyx, cell wall, locomotor appendages, and chloroplasts ( in some groups). |
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mRNA |
is further translated into another type of molecule (protein). |
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Messenger RNA (mRNA) |
is a transcript (copy) of a structural gene or genes in the DNA. It is synthesized by a process similar to synthesis of the leading strand during DNA replication, |
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mRNA transcript |
The message of this transcribed strand is later read as a series of triplets called codons and the length of the mRNA molecule varies from about 100 nucleotides to several thousand. |
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Transfer RNA (tRNA) |
also a copy of a specific region of DNA; however it differs from mRNA. It is uniform in length 75 to 95 nucleotides long, and it contains sequences of bases that form hydrogen bonds with complementary section of the same tRNA strand bends back upon itself into several hairpin loops giving the molecule a secondary clover leaf structure that folds even further into a complex three dimensional helix. |
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anticodon |
AT the bottom loop of the cloverleaf designates the specificity of the tRNA and complements mRNA's codons. |
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binding site |
opposite to the anticodon site for the amino acid that is specific for that tRNA's anticodon. |
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charging |
Binding of an amino acid to its specific tRNA takes place in two enzyme driven steps: First an ATP activates the amino acid; then this group binds to the acceptor end of the tRNA. Because tRNA is the molecule that will convert the master code on mRNA into a protein, the accuracy of this step is crucial. |
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The Ribosome: |
A Mobile Molecular Factory for Translation The bacterial (70S) ribosome is a particle composed of tightly packaged ribosomal RNA (rRNA) and protein. The rRNA component of the ribosome is also a long polynucleotide molecule. It forms complex three-dimensional figures that contribute to the structure and function of ribosomes. The interactions of protein and rRNA create the two of the ribosome that engage in final translation of the genetic code. A metabolically active bacterial cell can contain up to 20,000 of these minuscule factories all actively engaged in reading the genetic program taking in raw materials, and producing proteins at an impressing rate. |
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The First Stage of Gene Expression |
Transcription |
During transcription the DNA code is converted to RNA through several stages directed by a huge and very complex enzyme system, RNA polymerase. Only one stand of the DNA the template strand contains meaningful instructions for synthesis of a functioning poly-peptide. The strand of DNA that serves as a template varies from one gene to another. |
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elongation |
proceeds the 5' to 3' direction (with regard to growing RNA molecule), the mRNA is assembled by the addition of nucleotides that are complementary to the DNA template. Remember that uracil (U) is placed adenines complement. As elongation continues, the part of DNA already transcribed is rewound into its original helical form |
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termination |
polymerases recognize another code that signals the separation and release of the mRNA stand, also called the transcript. mRNA may consist of 100 bases an average size mRNA may consist of 1,200 bases and a large one may consist of several thousand. |
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Translation |
relies on a central principle: The mRNA nucleotides are read in groups of three. Three nucleotides are called a codon, and it is the codon that dictates which amino acid is added to the growing peptide chain. in a very few cases this codes Is universal, whether for bacteria archaea, eukaryotes, or viruses. |
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redundancy |
Because there are 64 different triplet codes and only 20 different amino acids, it is not surprising that some amino acids are represented by several codons. this property of an amino acid being represented by several codons allows for the insertion of correct amino acid (sometimes) even when mistakes occur in the DNA sequence as they do with regularity. |
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wobble |
in codons such as leucine only the first two nucleotides are required to encode the correct amino acid, and the third nucleotide does not change its sense. |
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Eukaryotes |
the first eukaryotic cell appeared on the earth approximately 2 billion to 3 billion years ago. |
Eukaryotic cells evolved directly from ancient prokaryotic cell, bacteria archaea, and eukaryotes evolved from a different kind of cell. A pre curser to both prokaryotes and eukaryotes that biologists call the last common ancestor. This cell was neither prokaryotic or eukaryotic but gave rise to bacteria archaea and eukarya separately. Eukaryotic cells originated from more primitive cells that became trapped in them. |
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Organelles found in all Eukaryotes |
Lysosome Golgi Apparatus Mitochondrion Intermediate Filament Microtubule Actin Filaments Cell membrane Nuclear membrane with pores Nucleus Nucleolus Rough ER (endoplasmic Reticulum) Smooth ER |
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Organelles found in some Eukaryotes |
Flagellum Chloroplasts Centrioles Cell Wall Glycocalyx |
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eukaryotic Locomotor Appendages |
Cilia and Flagella Motility allows a microorganism to locate nutrients and to migrate towards positive stimuli such as sun light, and avoid harmful substances and negative stimuli. |
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Eukaryotic Flagella |
Eukaryotic Flagella are much different then bacterial & Archaea Flagella. The eukaryotic flagellum is thicker (by factor 10), structurally more complex, and covered by an extension of the cell membrane. A single flagellum is a long, sheathed cylinder containing regularly spaced hollow tubules (Microtubules) that extend along its entire length. A cross section reveal nine pairs of closely attached microtubules surrounding a single central pair. This scheme called the 9+2 arrangement is the pattern of eukaryotic flagella and cilia. During locomotion the adjacent microtubules slide past each other, whipping the flagellum back and forth. Although details of this process are too complex to discuss here, it involves expenditure of energy and a coordinating mechanism in the cell membrane. The placement and number of flagella can be useful in identifying flagellated protozoa. |
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Eukaryotic Cilia |
Cilia are very similar in overall architecture to flagella but they are shorter and more numerous (some cells have several thousand). They are found only on a single group of protozoa and certain animal cells. In the ciliated protozoa, the cilia occur in rows over the cell surface, where they beat back and forth in regular oar-like strokes. Such protozoa are among the fastest of all motile cells. On some cells cilia also function as feeding and filtering structures. |
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The Glycocalyx |
Most eukaryotic cells have a glycocalyx an outermost boundary that comes into direct contact with the environment. This structure, which is sometimes called an extracellular matrix is usually composed of polysaccharides and appears as a network of fibers, a slime layer, or a capsule much like the glycocalyx of bacteria. The glycocalyx contributes to protection, adherence of cells to surfaces, and reception of signals from other cells and from the environment. The nature of the layer beneath the glycocalyx varies among the several eukaryotic groups. Fungi and most algae have a thick, rigid cell wall surrounding a cell membrane, whereas protozoa a few algae and all animal cells lack a cell wall and have only a cell membrane. |
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The Cell Wall |
Fungi and algae have cell walls. They are rigid and provide structural support and shape, but they are different in chemical composition from bacterial cell walls. Fungal cell walls have a thick inner layer of polysaccharide fibers composed of chitin or cellulose and a thin outer layer of mixed glycans. The cell walls of algae are quite varied in chemical composition. |
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The Cytoplasmic Membrane |
The cytoplasmic (cell) membrane of eukaryotic cells is a typical bilayer of phospholipids in which protein molecules are embedded. In addition to phospholipids, eukaryotic membranes also contain sterols of various kinds. Sterols are different from phospholipids in both structure and behavior. Their relative rigidity makes eukaryotic membranes more stable. This strengthening feature is extremely important in those cells that lack a cell wall. Cytoplasmic membranes of eukaryotes have the same function as those of bacteria, serving as selectively permeable barriers. Membranes have extremely sophisticated mechanisms for transporting nutrients in and waste and other products out, which are very similar in both eukaryotes and bacteria. |
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The Nucleus: The Control Center |
he nucleus is a compact sphere that is the most prominent organelle of eukaryotic cells. It is separated from the cell cytoplasm by an external boundary called a Nuclear Envelope. The envelope has a unique architecture. It is composed of two parallel membranes separated by a narrow space and it is perforated with small regular spaced opening or pores formed at sites where the two membranes unite. The nuclear pores are passageways through which macromolecule migrate from the nucleus to the cytoplasm, and vice versa. The nucleus contains an inner substance called the nucleoplasm and a granular mass, the nucleolus that stains more intensely than the immediate surrounding because of its RNA content. The nucleolus is the site for ribosomal RNA synthesis and a collection area for ribosomal subunits. The subunits are transported through the nuclear pores into the cytoplasm for final assembly into ribosomes. |
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Nuclear Envelope |
boundary structutre that seperates the nucleus from the cytoplasm |
The envelope has a unique architecture. It is composed of two parallel membranes separated by a narrow space and it is perforated with small regular spaced opening or pores formed at sites where the two membranes unite. The nuclear pores are passageways through which macromolecule migrate from the nucleus to the cytoplasm, and vice versa |
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nucleolus |
granular mass located within the nucleus. the ucleolus stains more intensely than the immediate surrounding because of its RNA content. The nucleolus is the site for ribosomal RNA synthesis and a collection area for ribosomal subunits. The subunits are transported through the nuclear pores into the cytoplasm for final assembly into ribosomes. |
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neucleoplasm |
inner substance located within the nucleus |
A prominent feature of the nucleoplasm in stained preparations is a network of dark fibers known as chromatin |
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chromatin |
prominent feature of the nucleoplasm hromatin makes up the eukaryotic chromosomes |
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chromosomes |
large units of genetic information in the cell. The chromosomes in the nucleus of most cells are not readily visible because they are long, linear DNA molecules bound in varying degrees to histone proteins, and they are far too fine to be resolved as distinct structures without extremely high magnification. During mitosis, however when the duplicated chromosomes are separated equally into daughter cells, the chromosomes themselves become readily visible as discrete bodies. This happens when the DNA becomes highly condenses by forming coil and supercoils around the histones to prevent the chromosomes from tangling as they are separated into new cells. |
contain instructions in the form of DNA. Elaborate processes have evolved for transcription and duplication of this genetic material. |
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meiosis |
the process by which sex cells are created. Much of the protein synthesis and other work of the cell takes place outside the nucleus in the cell's other organelles. |
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Endoplasmic Reticulum: A Passageway in the Cell |
The endoplasmic reticulum (ER) is a microscopic series of tunnels used in transport and storage. Two kinds of endoplasmic reticulum are the Rough Endoplasmic Reticulum (RER) and the Smooth Endoplasmic Reticulum (SER). |
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Rough Endoplasmic Reticulum (RER) |
The RER originates from the outer membrane of the nuclear envelope and extends in a continuous network through the cytoplasm, even all the way out to the cell membrane. This architecture permits the spaces in the RER, called cisternae (cistern Singular) to transport material from the nucleus to the cytoplasm and ultimately to the cell's exterior. appears rough because of large number of ribosomes partly attached to its membrane surface. Proteins synthesized on the ribosomes are shunted into the inside space (the lumen) of the RER and held there for later packaging and transport |
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Smooth Endoplasmic Reticulum (SER). |
In contrast to the RER the SER is a closed tubular network without ribosomes that functions in nutrient processing and in synthesis and storage of nonprotein macromolecules such as lipids. |
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Golgi Apparatus: A Packaging Machine |
The Golgi Apparatus also called the Golgi Complex or Golgi Body is the site in the cell which proteins are modified and then sent to their final destinations. It is a discrete organelle consisting of a stack of several flattened disc shaped sacs, or cisternae. These sacs have outer limiting membranes and cavities like those of the endoplasmic reticulum, but they do not form a continues network. This organelle is always closely associated with the endoplasmic reticulum both in its location and function. At a site where it meets the Golgi Apparatus, the Endoplasmic Reticulum buds off tiny membrane-bound packets of protein called transitional vesicles that are picked up by the forming face of the Golgi Apparatus. Once in the complex itself, the proteins are often modified by the addition of polysaccharides and lipid. The final action of this apparatus is to pinch off finished condensing vesicles that will be conveyed to organelles such lysosomes or are transported outside the cell as secretory vesicles. |
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transitional vesicles |
tiny membrane-bound packets of protein that are picked up by the forming face of the Golgi Apparatus. Once in the complex itself, the proteins are often modified by the addition of polysaccharides and lipid |
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condensing vesicles |
membrane bound packets of protein that will be conveyed that will be conveyed to organelles such lysosomes or are transported outside the cell as secretory vesicles. |
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cisternae (cistern Singular) |
spaces in the RER transport material from the nucleus to the cytoplasm and ultimately to the cell's exterior |
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condensing vesicles |
membrane-bound packets of protein that will be conveyed to organelles such lysosomes or are transported outside the cell as secretory vesicles. |
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lysosome |
type of vesicle originating from the Golgi apparatus that contains a variety of enzymes. Lysosomes are involved in intracellular digestion of food particles and in protection against invading organisms. They also participate in digestion and removal of cell debris in damaged tissue. The formation of lysosomes involves the GERL ( Golgi-Endoplasmic Reticulum Lysosomal Complex) |
Lysosomal enzymes are synthesized by the rough endoplasmic reticulum and are then translocated through the smooth endoplasmic reticulum. Transistional vesicles then transport the enzymes to the Golgi where unique chemical tags on these proteins localize them to the condensing vesicles that will become the primary lysosomes. |
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Vacuoles |
membrane-bound sacs containing fluids or solid particles to be digested, excreted or stored. They are formed in phagocytic cells (certain white blood cells and protozoa) in response to food and other substances that have been engulfed. |
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phagosome |
the merger of the vacuole with a lysosome |
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contractile vacuoles |
Protozoa living in freshwater habitats regulate osmotic pressure by means of contractile vacuoles, which regularly expel excess water that has diffused into the cell (described later). |
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Mitochondria: Energy Generators of the Cell |
energy, the bulk of which is generated in most eukaryotes by mitochondria. mitochondria appear as round or elongated particles scattered throughout the cytoplasm. A single mitochondrion consists of a smooth continuous outer membrane that forms the external contour, and an inner membrane nestled neatly within the outer membrane. The folds on the inner membrane, called Cristae may be tubular like fingers or folded into shelf like bands. |
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Cristae |
folds on the inner membrane of a mitochondrion may be tubular like finfers or folded into shelf like bands |
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cristae membranes |
hold the enzymes and electron carriers of aerobic respiration. This is an oxygen-using process that extracts chemical energy contained in nutrient molecules and stores it in the form of high-energy molecules, or ATP. |
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matrix |
fluid that fills the spaces around the cristae. holds ribosomes, DNA, and the pool of enzymes and other componds involved in the metabolic cycle. |
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Chloroplasts: Photosynthesis Machine |
Chloroplasts are remarkable organelles found in algae and plant cells that are capable of converting the energy of sunlight into chemical energy through photosynthesis. The photosynthetic role of chloroplasts makes them the primary producers of organic nutrients upon which all other organisms (expert certain bacteria) ultimately depend. Another important photosynthetic product of chloroplasts is oxygen gas. Although chloroplasts resemble mitochondria, chloroplasts are larger, contain special pigments and are much more varied in shape. |
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thylakoids |
membrane folded into small disc like sacs inside the chloroplasts. stacked to one another on top of grana. These strucutures carry green pigment chlorophulland sometimes additonal pigmetns as well. |
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Stroma |
substance surrounding thylakoids |
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Ribosomes: Protein Synthesizers |
in an electron micrograph of a eukaryotic cell, ribosomes are numerous, tiny particles that give a dotted appearance to the cytoplasm. Ribosomes are distributed throughout the cell: Some are scattered feely in the cytoplasm and cytoskeleton; other are attached to the rough endoplasmic reticulum as previously described. Still other appear inside the mitochondria and in chloroplasts. Multiple ribosomes are often found arranged in short chains called Polyribosomes or polysomes. |
The basic structure of eukaryotic ribosomes is similar to that of bacterial ribosomes, described in chapter 4. Both are composed of large and small subunits of ribonucleoprotein. By contrast however the eukaryotic ribosome (except in the mitochondrion) is the larger 80S variety that is a combination of 60S and 40S subunits. As in the bacteria, eukaryotic ribosomes are the staging areas for protein synthesis. |
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The Cytoskeleton: A support Network |
flexible framework of molecules, appears to have several functions such as anchoring organelles moving RNA and vesicles and permitting shape changes and movement in some cells. Consist of: Actin FIllaments Intermediate Fillaments Microtubules |
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actin fillaments |
long thin protein strands about 7 nanometers in diameter. found through out the cell but are most highly concentrated just inside the cell membrane. |
Actin fillaments are responsible for cell movement such as contraction crawling pinching during cell division and formation of cellular extension |
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Microtubules |
long hollow tubes that maintain the shape of eukaryotic cells when they do have walls and transport substances from one part of the cell to another. |
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Spindle FIbers |
play an essential role in mitosis are actually microtubules that attach to chromosomes and seperate them into daughter cells. also responsible for the movement of cilia and flagella |
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intermediate filaments |
ropelike strucutures that are about 10 nanometers in diameter. provide structural reinforcement of the cell and organelles. |
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Fungi |
ingdom Fungi or Myceteae, is large and filled with forms of great variety and complexity. For practical purposes, the approximately 100,000 species of fungi can divided into two groups: the macroscopic fungi and the microscopic fungi unicellular or colonial, a few complex forms such as mushrooms and puffballs are considered multicellular. |
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microscopic fungi |
yeasts and hyphae |
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yest cell |
round to oval shape and uses asexual reproduction. grow swellings on its surface called buds whihc them become seperate cells. |
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Hyphae |
long threadlike cells found in the bodies of filamentous fugi or molds. some species form a pseudo-hypha, a chain of yeasts fromed when buds remain attached in a row. A few called dimorphic can take either form, depending on growth conditions such as changing temperature. This variability in growth form is particularly characteristic of some pathogenic molds. |
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Fungal Nutrition |
All fungi are Heterotrophic. This means that they acquire nutrients from a wide variety of organic material called Substrates. Most fungi are Saprobes, meaning they obtain these substrates from the remnants of dead plants and animals in soil or aquatic habitats. Fungi can also be parasites, meaning they live on the bodies of living animals or plants, although very few fungi absolutely require a living host. In general, the fungus penetrates the substrate and secretes enzymes that reduce it to small molecules that can be absorbed by the cells. Fungi have enzymes for digesting an incredible array of substances, including feathers, hair, cellulose, petroleum products, wood, and rubber. It has been said that every naturally occurring organic material on the earth can be attacked by some type of fungus. Fungi are often found in nutritionally poor or adverse environments. Various fungi thrive in substrates with high salt or sugar content, at relatively high temperature, and even in snow and glaciers. Their medical and agricultural impact is extensive. A number of species cause mycoses in animals and thousands of species are important plant pathogens. Fungal toxins may cause disease in humans, and airborne fungi are frequent cause of allergies and other medical conditions. Organization of Microscopic Fungi The cells of most microscopic fungi grow in loose associations or colonies. The colonies of yeasts are much like those of bacteria in that they have a soft, uniform texture and appearance. The colonies of filamentous fungi are noted for the strikingly cottony, hairy, or velvety textures that arise from their microscopic organization and morphology. The woven, intertwining mass of hyphae that makes up the body or colony of a mold is call a Mycelium. Although hyphae contain the usual eukaryotic organelles, they also have some unique organizational features. In most fungi the hyphae are divided into segments by cross walls, or septa, a condition called septate. The structure of the septa caries from solid partitions with no communication between the compartments to partial walls with small pores that allow the flow of organelles and nutrients between adjacent compartments. Nonseptate hyphae consist of one long, continuous cell not divided into individual compartments by cross walls. With this construction the cytoplasm and organelles move freely from one region to another, and each hyphal element can have several nuclei. Hyphae can also be classified according to their particular function. Vegetative hyphae (mycelia) are responsible for the visible mass of growth that appears on the surface of a substrate and penetrates it to digest and absorb nutrients. During the development of a fungal colony, the vegetative hyphae give rise to structures called reproductive or fertile hyphae, which branch off a vegetative mycelium. These hyphae are responsible for the production of fungal reproductive bodies called Spores. |
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Reproductive Strategies and Spore Formation |
rimary reproductive mode of fungi involves the production of various types of spores. |
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Asexual Spore Formation |
two types: sporangiospores & conidiospores |
Sporangiospore are formed by successive cleavages within a saclike head called a sporangium, which is attached to a stalk, the sporangiosphore. These spores are initially enclosed but are released when the sporangium ruptures. Conidiospores or conidia are free spores not enclosed by a spore-bearing sac. They develop either by the pinching off of the top of a special fertile hypha or by the segmentation of a preexisting vegetative hypha. There are many different forms of conidia. |
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Sexual Spore Formation |
fungi can also exhibit sexual spore formation. |
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The Roles of Fungi |
Nearly all fungi are free-living and do not require a host to complete their life cycles. Even among those fungi that are pathogenic, most human infection occurs through accidental contact with an environmental source such as soul, water, or dust. |
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Mycoses |
fungal infections |
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Protist |
algae and protozoa have been traditionally combined into the kingdom Protista. The two major taxonomic categories of this kingdom are subkingdom algae Algae and Subkingdom Protozoa. Although these general types of microbes are now known to occupy several kingdoms, it is still useful to retain the concept of a protist as any unicellular or colonial organism that lacks true tissues. We will only briefly mention algae as they do not cause human infections for the most part. |
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The Algae: Photosynthetic Protis |
The algae are a group of photosynthetic organism usually recognized by their larger members, such as seaweeds and kelps. In addition to being beautifully colored and diverse in appearance, they vary in length from a few micrometers to 100 meters. Algae occur in unicellular, colonial, and filamentous forms; the larger forms can possess tissues and simple organs. Algal cells as a group exhibit all of the eukaryotic organelles. The most noticeable of these are the chloroplasts, which contain, in addition to the green pigment chlorophyll, a number of other pigments that create the yellow, red, and brown coloration of some groups. |
Examples: plankton prottheca (non photosynthetic) Pfiesteria Piscicida, a toxic algal form, |
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Biology of the Protozoa |
if a poll were taken to choose the most engrossing g and vivid group of microorganisms, many biologists would choose protozoa. Although their name comes from the Greek for "first animals" they are far from being simple primitive organisms. The protozoa constitute a very large group (65,000 species) of creatures that, although single-celled, have startling properties when it comes to movement feeding and behavior. Although most members of this group are harmless, free-living inhabitants of water and soil, a few species are parasites collectively responsible for hundreds of millions of infections of humans each year. |
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Protozoan Form and Function |
Most protozoan cells are single cells containing all the major eukaryotic organelles except chloroplasts. Their organelles can be highly specialized and are essentially analogous to mouths, digestive systems, reproductive tracts, and "legs" or means of locomotion. The cytoplasm is usually divided into a clear outer layer called the ectoplasm and a granular inner region called the endoplasm. Many protozoa can convert to a resistant, dormant stage called a cyst. |
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Styles of Locomotion |
protozoa can move through fluids by means of pseudopods, flagella, or cilia |
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Pseudopodsd |
blunt branched or long and pointed depending on the particular species |
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calssification of protozoa |
Those using flagella to move: Motility is primarily by flagella alone or by both flagellar and amoeboid motion (single nucleus). Sexual reproduction, when present, by syngamy; division by longitudinal fission. Several parasitic forms lack mitochondria and Golgi apparatus. Most species form cysts and are free-living; the group also include several parasites. Some species are found in loose aggregates or colonies, but most are solitary. Members include Trypanosoma and Leishmania, important blood pathogend spred by insect vectors; Giardia, an intestinal parasite spread in water contaminated with feces; and Trichomonas, a parasite of the reproductive tract of humans spread by sexual contact. Those using amoeboid motion to move: Cell form is primarily an amoeba. Major locomotor organelles are pseudopods, although some species have flagellated reproductive states. Asexual reproduction by fission. Two groups have an external shell; mostly uninucleate; usually encyst. Most amoebas are free living and not infectious; Entamoeba is a pathogen or parasite of humans; shelled amoebas called foraminifera and radiolarians are responsible for chalk deposits in the ocean. Those using cilia to move: Trophozoites are motile by cilia; some have cilia in tufts for fedding and attachment; most develop cysts; have both macronuclei and micronuclei; division by transverse fission; most have definite mouth and feeding organelle; shoe relatively advanced behavior. The majority of ciliates are free-living and harmless. Those with no motility (sporozoa): Although motility is absent in most representatives, it's exhibited by the male gametes of many members of this group. Life cycles of the apicomplexa are, as the name implies, quite complex, with well-developed asexual and sexual stages. Sporozoa produce special spore like cells called sporozoites following sexual reproduction which are important in transmission of infections and have recently been discovered to exhibit a unique form of gliding motility. Most sporozoa form thick walled zygotes called oocysts, and this entire group of organisms is parasitic. Plasmodium the most prevalent protozoan parasite, causes 10 million to 300 million cases of malaria each year worldwide. It is an intracellular parasite with a complex cycle alternating between humans and mosquitoes. Toxoplasma gondii causes infection (toxoplasmosis) in humans, which is acquired from cats and other animals. Just as with bacteria and other eukaryotes, protozoans that cause disease produce symptoms in different organ systems. Protozoan Identification and Cultivation The unique appearance of most protozoa makes it possible for a knowledgeable person to identify them to the level of genus and often species by microscopic morphology alone. Characteristics to consider in identification include the shape and size of the cell; the type, number, and distribution of locomotor structures; the presence of special organelles or cysts; and the number of nuclei. Medical specimens taken from blood, sputum, cerebrospinal fluid, feces, or the vagina are smeared directly onto a slide and observed with or without special stains. Occasionally, protozoa are cultivated on artificial media or in laboratory animals for further identification or study. |
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helminths |
tape worms flukes and round worms |
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flat worms |
cestodes or tapeworms named for their long ribbon like arrangement, and the trematodes, or flukes |
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All helminths are multicellular animals equipped to some degree with organs and organ systems. |
All helminths are multicellular animals equipped to some degree with organs and organ systems. |
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helminths (nematodes) |
can be hermaphroditic meaning that male and femal sex organs are in the same worm |
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larval development |
larval development ocurs in the intermediate or secondary host |
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adulthood and mating |
adulthood and mating occur in the defenitive or secondary host. |
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transport host |
is intermediate host that experiences no parasitic development but is essential in the competion of the cycle |
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classifcation according to shape |
helminths are classified according to shape size and degree of development |
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about 50 species of helminths parasiize humans they are distributed in all areas that support human life with higher incidence in tropical regions |
about 50 species of helminths parasiize humans they are distributed in all areas that support human life with higher incidence in tropical regions |
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types of RNA |
types of RNA |
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initiation of translation |
about 50 species of helminths parasiize humans they are distributed in all areas that support human life with higher incidence in tropical regions |
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initiation, elongation, termination |
initiation, elongation, termination |
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Elongation |
. During elongation, which proceeds in the 5′ to 3′ direction (with regard to the growing RNA molecule), the mRNA is assembled by the addition of nucleotides that are complementary to the DNA template. Remember that uracil (U) is placed as adenine’s complement. As elongation continues, the part of DNA already transcribed is rewound into its original helical form. |
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termination |
. At termination, the polymerases recognize another code that signals the separation and release of the mRNA strand, or transcript. The smallest mRNA might consist of 100 bases; an average-size mRNA might consist of 1,200 bases; and a large one might consist of several thousand |
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DNA STRUCTURE |
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start codon The first three RNA nucleotides that signal the beginning of the message. The start codon is always AUG. |
start codon The first three RNA nucleotides that signal the beginning of the message. The start codon is always AUG. |
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stop codon One of three codons—UAA, UAG, or UGA— that has no corresponding tRNA and therefore causes translation to be terminated; also called nonsense codon. |
stop codon One of three codons—UAA, UAG, or UGA— that has no corresponding tRNA and therefore causes translation to be terminated; also called nonsense codon. |
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translocation The process of shifting the ribosome down themRNA strand to read new codons. |
translocation The process of shifting the ribosome down themRNA strand to read new codons. |
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protein synthesis |
1 mRNA molecule leaves the DNA transcription site and is transported to ribosomes in the cytoplasm. 2 Rules of pairing dictate that the anticodon of this tRNA must be complementary to the mRNA codon AUG; thus, the tRNA with anticodon UAC will first occupy site P. It happens that the amino acid carried by the initiator tRNA in bacteria is formyl methionine. T 3 The entry of tRNA 2 into the A site brings the two adjacent tRNAs in favorable proximity for a peptide bond to form between the amino acids (aa) they carry. The fMet is transferred from the first tRNA to aa 2, resulting in two coupled amino acids called a dipeptide. |
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conjugation transformation transduction |
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