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BIOL 1090
Marc Coppolino

Genetics Lecture 1 - Page 193 - 214 Chapter 9 Functions of the Genetic Material 1. The genotypic function, replication. The genetic material must store genetic information and accurately transmit that information from parents to offspring, generation after generation. 2. The phenotypic function, gene expression. The genetic material must control the development of the phenotype of the organism. That is, the genetic material must dictate the growth of the organism from the single-celled zygote to the mature adult. 3. The evolutionary function, mutation. The genetic material must undergo changes to produce variations that allow organisms to adapt to modifications in the environment so that evolution can occur. Chromosomes composed of proteins and nucleic acids - Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) Proof that genetic information is found in DNA - DNA is found only in chromosomes/RNA is also found in cytoplasm - Molecular composition of DNA is the same/RNA composition varies - DNA is more stable than RNA Deoxyribonuclease (DNase)  degrades DNA Ribonuclease (RNase)  degrades RNA Protease  degrades proteins The Structures of DNA and RNA - Genetic information of living organisms stored in DNA - DNA is doubled-stranded with Adenine paired with Thymine, and Guanine paired with Cytosine. - RNA is single-stranded with Uracil instead of Thymine Subunits in DNA and RNA called nucleotides - Nucleotides composed of: o 1 phosphate group o A five-carbon sugar (pentose) o Cyclic nitrogen-containing compound  base 1 o Sugar in DNA is 2-deoxyribose o Sugar in RNA is ribose o DNA: bases  Adenine, Guanine, Thymine, Cytosine o RNA: bases  Adenine, Guanine, Cytosine, Uracil o Adenine and Guanine are double-ring bases called purines o Cytosine, Thymine, Uracil are single-rings bases called pyrimidines. o RNA is single-stranded polymer o DNA  One additional double-stranded molecule - DNA  right- handed double helix  forming a spiral - Held together by hydrogen bonding - Adenine and Thymine form two hydrogen bonds - Guanine and Cytosine form three hydrogen bonds. - The two strands of a DNA said to be complementary - Go from a 3’ carbon of one nucleotide to a 5’ carbon of the adjacent nucleotide - Complementary strand  from a 5’ carbon to a 3’ carbon.  Plays important role in replication, transcription and recombination Alternate forms of the double helix B-DNA  Conformation that DNA takes under physiological conditions (in aqueous solutions containing low concentrations of salts) - DNA is not a static, invariant molecule. - Structures of DNA molecules change as a function of their environment.  In high concentrations of salts or in a partially dehydrated state, DNA exists as A-DNA, which is a right-handed helix like B-DNA, but with 11 nucleotide pairs per turn.  Certain DNA sequences have been shown to exist in a left-handed, double-helical form called Z-DNA  12 base pairs per turn Supercoils are introduced into a DNA molecule when one or both strands are cleaved and when the complementary strands at one end are rotated or twisted around each other with the other end held fixed in space—and thus not allowed to spin. Chromosomes contain chromatin - Chemical analysis of isolated chromatin shows that it consists primarily of DNA and
 proteins with lesser amounts of RNA - The proteins are of two major
 classes: o (1) Basic (positively charged at neutral pH) proteins called histones o (2) A
 heterogeneous, largely acidic (negatively charged at neutral pH) group of proteins collectively referred to as nonhistone chromosomal proteins. 2 - Histones play a major structural role in chromatin. - Four of the five types of histones are specifically complexed with DNA to produce the basic structural subunits of chromatin, small ellipsoidal beads called nucleosomes. One DNA per chromosome 3 steps to package DNA into a chromosome 1. The first level of condensation involves packaging DNA as a negative supercoil into nucleosomes, to produce the interphase chromatin fiber. This clearly involves an octamer of histone molecules, two each of histones H2a, H2b, H3, and H4. 2. The second level of condensation involves an additional folding or supercoiling of the nucleosome fiber, to produce the chromatin fiber. Histone H1 is involved in this supercoiling of the nucleosome fiber to produce the chromatin fiber. 3. Finally, nonhistone chromosomal proteins form a scaffold that is involved in condensing the chromatin fiber into the tightly packed metaphase chromosomes. This third level of condensation appears to involve the separation of segments of the giant DNA molecules present in eukaryotic chromosomes into independently supercoiled domains or loops. The mechanism by which this third level of condensation occurs is not known. Telomeres  end of eukaryotic chromosome - 1. Prevent deoxyribonucleases from degrading the ends of the linear DNA molecules, - 2. Prevent fusion of the ends with other DNA molecules - 3. Facilitate replication of the ends of the linear DNA molecules without loss of material. - Shorten with age (except for cancer ones) - Telomers of humans form structures called T-loops - DNA in T-loops protected by a protein complex called shelterin Chapter 12 Protein Synthesis: Translation - The process by which the genetic information stored in
 the sequence of nucleotides in an mRNA is translated, according to the specifications of the genetic code, into
 the sequence of amino acids in the polypeptide gene. - The first step in gene expression, transcription, involves the transfer of information stored in genes to messenger RNA (mRNA) intermediaries, which carry that information to the sites of polypeptide synthesis in the cytoplasm. - The second step, translation, involves the transfer of the information in mRNA molecules into the sequence of amino acids in polypeptide gene products. o Occurs on ribosomes 3 Translation 3 steps 1. Polypeptide Chain Initiation o The initiation of translation includes all events that precede the formation of a peptide bond between the first two amino acids of the new polypeptide chain. o AUG initiation codon 2. Polypeptide Chain Elongation 3. Polypeptide Chain Termination - Polypeptide chain elongation undergoes termination when any of three chain-termination codons (UAA, UAG, or UGA) enters the A site on the ribosome - Recognized by soluble proteins called release factors (RFs) - Termination is completed by the release of the mRNA molecule from the ribosome and the dissociation of the ribosome into its subunits. The ribosomal subunits are then ready to initiate another round of protein synthesis, as previously described. Genetic Code 4 - The codon AUG is used to initiate polypeptide chains - Three codons—UAG, UAA, and UGA—specify polypeptide chain termination - The occurrence of more than one codon per amino acid is called degeneracy o Differ by only one base, the 3’ base of the codon - Two types: o (1) Partial degeneracy occurs when the third base may be either of the two pyrimidines (U or C) or, alternatively, either of the two purines (A or G). o (2) In the case of complete degeneracy, any of the four bases may be present at the third position in the codon, and the codon will still specify the same amino acid. (Ex. GUU, GUC, GUA, and GUG) - Universal Chapter 11  256-267 Transfer of Genetic Information The transfer of genetic information from DNA to protein involves two steps: - Transcription, the transfer of the genetic information from DNA to RNA - Translation, the transfer of information from RNA to protein. o Takes place on ribosomes - During transcription, one strand of DNA of a gene is used as a template to synthesize a complementary strand of RNA, called the gene transcript. 5 - During translation, the sequence of nucleotides in the RNA transcript is converted into the sequence of amino acids in the polypeptide gene product. This conversion is governed by the genetic code, the specification of amino acids by nucleotide triplets called codons in the gene transcript. - The RNA molecules that are translated on ribosomes are called messenger RNAs (mRNAs). - In prokaryotes, the product of transcription, the primary transcript, usually is equivalent to the mRNA molecule. - In eukaryotes, primary transcripts often must be processed by the excision of specific sequences and the modification of both termini before they can be translated. Thus, in eukaryotes, primary transcripts usually are precursors to mRNAs and, as such, are called pre-mRNAs. - Noncoding sequences called introns that separate the expressed sequences or exons of these genes. 5 classes of RNA - Produced by transcription o Messenger RNA (mRNA)  Carry genetic information from DNA to the ribosomes where proteins are synthesized. o Transfer RNA (tRNA)  Small RNA molecules that function as adaptors between amino acids and the codons in mRNA during translation. o Ribosomal RNA (rRNA)  Structural and catalytic components of the ribosomes, the intricate machines that translate nucleotide sequences of mRNAs into amino acid sequences of polypeptides. o Small Nuclear RNA (snRNA)  Structural components of spliceosomes, the nuclear organelles that excise introns from gene transcripts o Micro RNA (miRNA)  Short, single-stranded RNAs that are cleaved from small hairpin- shaped precursors and block the expression of complementary or partially complementary mRNAs by either causing their degradation or repressing their translation. General Features of RNA Synthesis - RNA synthesis occurs by a mechanism that is similar to that of 
 DNA synthesis except that: o (1) The precursors are ribo
 nucleoside triphosphates rather than deoxyribonucleoside triphosphates
 o (2) Only one strand of DNA is used as a template for the synthesis of 
 a complementary RNA chain in any given region o (3) RNA chains
 can be initiated de novo, without any requirement for a preexisting
 primer strand. - The RNA molecule produced will be complementary 
 and antiparallel to the DNA template strand and identical, except that 
 uridine residues replace thymidines, to the DNA nontemplate strand 6 - Therefore, mRNA molecules are coding strands of RNA. They are also called sense strands of RNA because their nucleotide sequences “make sense” in that they specify sequences of amino acids in the protein gene products. An RNA molecule that is complementary to an mRNA is referred to as antisense RNA. - We will use template strand and nontemplate strand to refer to the transcribed and nontranscribed strands, respectively, of a gene. - 5’  3’ direction, with the addition of ribonucleotides to
 the 3’ hydroxyl group at the end of the chain - This reaction is catalyzed by enzymes called RNA polymerases. - RNA polymerases bind to specific nucleotide sequences called promoters, and with the help of proteins called transcription factors, initiate the synthesis of RNA molecules at transcription start sites near the promoters. - RNA synthesis takes place within a locally unwound segment of DNA, sometimes called a transcription bubble, which is produced by RNA polymerase. The nucleotide sequence of an RNA molecule is complementary to that of its DNA template strand, and RNA synthesis is governed by the same base-pairing rules as DNA synthesis, but uracil replaces thymine. Transcription in Prokaryotes - A segment of DNA that is transcribed to produce one RNA molecule is called a transcription unit. - The process of transcription can be divided into three stages: o (1) Initiation of a new RNA chain o (2) Elongation of the chain, and o (3) Termination of transcription and release of the nascent RNA molecule - - Upstream and downstream  5’ end towards 3’ end Initiation of RNA chains - (1) Binding of the RNA polymerase holoenzyme to a promoter region in DNA - (2) The localized unwinding of the two strands of DNA by RNA polymerase, providing a template strand free to base-pair with incoming ribonucleotides - (3) The formation of phosphodiester bonds between the first few ribonucleotides in the nascent RNA chain. - The holoenzyme remains bound at the promoter region during the synthesis of the first eight or nine bonds; then the sigma factor is released, and the core enzyme begins the elongation phase of RNA synthesis. - During initiation, short chains of two to nine ribonucleotides are synthesized and released. 7 - Nucleotide sequences preceding the initiation site are referred to as upstream sequences; those following the initiation site are called downstream sequences. Elongation of RNA chains - Elongation of RNA chains is catalyzed by the RNA polymerase core enzyme, after the release of the ơ subunit. - RNA polymerase continuously unwinds the DNA double helix ahead of the polymerization site and rewinds the complementary DNA strands behind the polymerization site as it moves along the double helix. Termination of RNA chains - Termination occurs when RNA polymerase encounters a termination signal. When it does, the transcription complex dissociates, releasing the nascent 
 RNA molecule. - 2 types o One
 type results in termination only in the presence of a protein called rho; therefore, 
 such termination sequences are called rho-dependent terminators. o The other type results 
 in the termination of transcription without
 the involvement of rho; such sequences are
 called rho-independent terminators. Transcription and RNA processing in Eukaryotes - In eukaryotes, RNA is synthesized in the nucleus, and most RNAs that encode proteins must be trans- ported to the cytoplasm for translation on ribosomes. - In eukaryotes, the population of primary transcripts in a nucleus is called heterogeneous nuclear RNA (hnRNA)  non coding intron sequences Five RNA polymerase RNA polymerase I, II, III  All eukaryotic RNA polymerases require the assistance of other proteins called transcription factors in order to initiate the synthesis of RNA chains. - RNA polymerase I  catalyzes the synthesis of rRNAs - RNA polymerase II  transcribes nuclear genes that encode proteins and perhaps other genes specifying hnRNAs - RNA polymerase III  catalyzes the synthesis of the tRNA molecules, to the rRNA molecules, and snRNAs. - RNA polymerase IV and RNA polymerase V Only found in plants  Important role in turning off the transcription genes by modifying the structure of chromosomes, a process called chromatin remodeling. - RNA polymerase IV  synthesizes transcripts that are processed into short RNAs called short interfering RNAs (siRNA) that are important regulators of gene expression. - RNA polymerase V  synthesizes a subset of siRNAs and noncoding (antisense) transcripts of genes that are regulated by siRNAs. 8 Initiation RNA polymerase II  transcription promoters  TATA box and CAAT box  Important in determining start point. - The initiation of transcription by RNA polymerase II requires the assistance of several basal transcription factors. o Denoted by TFIIX o TFIID  interacts with the promoter o TFIIA joins the complex, followed by TFIIB. o TFIIF first associates with RNA polymerase II, and then TFIIF and RNA polymerase II join the transcription initiation complex together. o TFIIF catalyzes the localized unwinding of the DNA double helix required to initiate transcription. o TFIIE then joins the initiation complex, binding to the DNA downstream from the transcription startpoint. o Two other factors, TFIIH and TFIIJ, join the complex after TFIIE, Elongation - Early in the elongation process, the 5’ ends of eukaryotic pre-mRNAs are modified by the addition of 7-methyl guanosine (7-MG) caps. o Helps protect the growing RNA chains from degradation by nucleases Termination - After cleavage, the enzyme poly (A) polymerase adds poly (A) tails, tracts of adenosine monophosphate to the 3’ end of the transcripts - The addition of poly (A) tails to eukaryotic mRNAs is called polyadenylation. - The poly (A) tails of eukaryotic mRNAs enhance their stability and play an important role in their transport from the nucleus to the cytoplasm. RNA editing - (1) By changing the structures of individual bases (rare) - (2) By inserting or deleting uridine monophosphate residues. o Mediated by guide RNAs Cell Division - A cell that is about to divide is called a mother cell, and the products of division are called daughter cells. - Cell Cycle o G1  S  G2  M o In this progression, S is the period in which the chromosomes are duplicated—an event that requires DNA synthesis, to which the label “S” refers. 9 o The M phase in the cell cycle is the time when the mother cell actually divides. This phase usually has two components:  Mitosis, which is the process that distributes the duplicated chromosomes equally and exactly to the daughter cells,  Cytokinesis, which is the process that physically separates the two daughter cells from each other. - The G1 and G2 phases are “gaps” between the S and M phases. Mitosis - The network of thin strands formed by all the chromosomes within the nucleus is referred to as chromatin. - Biologists often refer to the period when individual chromosomes cannot be seen as interphase. o When mitosis begins, each chromosome has already been duplicated  Sister chromatids - The distribution of duplicated chromosomes to the daughter cells is organized and executed by microtubules. - During mitosis the microtubules assemble into a complex array called the spindle. The formation of the spindle is associated with microtubule organizing centers (MTOCs) - In animal cells, the MTOCs are differentiated into small organelles called centrosomes. o Each centrosome contains two barrel-shaped centrioles. - As the cell enters mitosis, microtubules develop around each of the daughter centrosomes to form a sunburst pattern called an aster. - The final positions of the centrosomes define the poles of the dividing mother cell. - The initiation of spindle formation and the condensation of duplicated chromosomes from the diffuse network of chromatin are hallmarks of the first stage of mitosis, called prophase. o Endoplasmic reticulum, Golgi complex, nucleolus  also disappears o Mitochondria and chloroplasts remain intact. - Kinetochores, which are protein structures associated with the centromeres of the duplicated chromosomes. - Attachment of spindle microtubules to the kinetochores indicates that the cell is entering the metaphase of mitosis. o During metaphase the duplicated chromosomes move to positions midway between the spindle poles. - The sister chromatids of duplicated chromosomes are separated from each other during the anaphase of mitosis. o The separated sister chromatids are now referred to as chromosomes. 10 - The decondensation of the chromosomes and the restoration of the internal organelles are characteristi
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