B M B 251: EXAM 2
70 Cards in this Set
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7. What is the difference between positive and negative allosteric regulation?
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Positive: Occurs when the binding of one ligand enhances the attraction between substrate molecules and the binding sites of their respective enzymes. ex. The binding of oxygen molecules to hemoglobin where oxygen is both the substrate and the effector. In this case the allosteric site is…
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What is the definition of allostery
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The condition in which the binding of a substrate, product, or other effector to a subunit of a multi-subunit enzyme at a site other than the functional (active) site. Results in the modification of its conformation and therefore its functional properties.
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Do allosteric molecules bind to the active site
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No. Allosteric molecules, by definition, bind to the allosteric site of an enzyme which is a site other than the active site.
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What is the difference between a kinase and a phosphatase? What amino acids in a protein are chemically modified by these proteins?
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Kinase: Phosphorylates Phosphatase: De-phosphorylates These enzymes add or remove phosphate groups from protein/amino acid side chains thus activating or inhibiting them.
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No. Adding or removing a phosphate can either activate it or deactivate it.
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No. Adding or removing a phosphate can either activate it or deactivate it.
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Why would adding a methyl group to a lysine on a protein change the function/structure of a protein?
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Lysine, a positively-charged amino acid, is used as a DNA-binding protein. Adding a methyl group to it would dull the electrostatic interactions between the lysine side chain and the negatively-charged DNA molecules.
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How does a G-protein convert from the GDP bound state to the GTP bound state and back again?
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The GTP of the G-protein is hydrolyzed to the GDP-bound state. The GDP is slowly released to make way for a new GTP molecule which can then be reconverted to GDP. The G-protein is considered active when bound to GTP and inactive when bound to GDP
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How does a G-protein convert from the GDP bound state to the GTP bound state and back again?
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The numbers indicate a specific carbon on the Deoxyribose sugar ring.
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Why are the two strands in DNA considered anti-parallel
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One strand of the DNA runs in the 5'-3' direction while the other in the 3'-5'.
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Why are the two strands in DNA considered anti-parallel
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Adenine with Thymine; and Cytosine with Guanine. Adenine and Guanine are Purines, Thymine and Cytosine are Pyrimidines.
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What is bound covalently to the 5' and 3' carbons of nucleotides in DNA and RNA?
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Hydroxyl is bound to the 3' end and phosphate is bound to the 5' end.
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What is bound covalently to the 5' and 3' carbons of nucleotides in DNA and RNA?
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In DNA, a single H is bound to the 2' Carbon, in RNA, a hydroxyl group is bound to the 2' Carbon. Deoxyribose v. Ribose
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Distinguish between monomers of RNA or DNA Which carbons of the deoxyribose ring are connected by a phosphodiester bond?
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RNA: Uracil, Adenine, Cytosine, Guanine DNA: Thymine, Adenine, Cytosine, Guanine Phosphodiester bonds exist between the 5' Carbon of one ribose and the 3' carbon of an adjacent ribose sugar
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8. Where are the phosphodiester bonds located in the double helix of DNA? What is the name of the bond that links the base onto the ribose?
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They exist between the adjacent ribose sugars in the DNA double helix backbone. The base is linked to the ribose sugar by an N-glycosidic bond.
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What are the nuclear envelope, nucleolus, and nuclear pore? What do they do?
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Nuclear Envelope: The porous membrane that separates the nucleus from the cytoplasm of the cell Nucleolus: The central portion of the cellular nucleus. Composed of rRNA proteins and DNA and also contains ribosomes in various stages of synthesis. Function: Accomplishes the manufacturing of…
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What type of protein is most abundant in chromatin?
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Histones.
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Describe the structure of the nucleosome
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The basic unit of DNA packaging in eukaryotes consisting of a segment of DNA wound in sequence around 8 histone protein cores. The structure is analogous to thread wrapped around a spool. Histones associate with DNA to form nucleosomes which themselves bundle to form chromatin fibres whic…
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What makes up the histone octamer (core histones)? What is the function of histone H1?
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It's the 8-protein complex found at the center of the nucleosome-core particle. It consists of two copies of each of the 4 core histone proteins: H2A, H2B, H3, and H4. H1 does not make up the nucleosome bead, instead it binds to the linker DNA connecting the nucleosomes and helps to stabi…
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Which amino acids are abundant in histones and are involved in electrostatic attraction between the histones and DNA?
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The three positively charged amino acids: lysine, histidine, and arginine.
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What's the difference between heterochromatin and euchromatin? In which one are highly expressed genes found?
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The terms differentiate between the degree to which a particular portion of chromatin is coiled. The more coiled, the lower the expression is for the genes in that segment of DNA. Euchromatin is loosely coiled, and therefore has a higher rate of gene expression.
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What is the histone code hypothesis? What part of the histone is involved in this regulatory process?
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The hypothesis states that the transcription of genetic information encoded in DNA is in part regulated by chemical modifications to histone proteins, primarily on their unstructured ends. **The histone modifications serve to recruit other proteins by specific recognition of the modified …
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Why is DNA replication said to be semiconservative?
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Each single strand of the parent DNA is used as a template for the double stranded daughter DNAs
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Which carbon of the deoxyribose in the incoming nucleotide is linked to which carbon of the existing chain being elongated by DNA polymerase? In which direction does the chain grow?
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The 3' of the existing chain is bonded to the 5' carbon of the incoming nucleotide by a phosphodiester bond.
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What is the name of the bond formed by DNA polymerase when linking nucleotides together?
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Phosphodiester Bond.
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Which nucleotides does DNA polymerase use in DNA synthesis?
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Adenine, Guanine, Cytosine, Thymine.
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9. Which direction is DNA synthesized?
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DNA polymerase moves down the template strand from 3'-5' but synthesizes in the 5'-3' direction.
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The enzyme DNA helicase is responsible for separating the coding strand from the template strand. The replication fork refers to the portion of the DNA where helicase is separating the strands. There are two replication forks per bubble.
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The enzyme DNA helicase is responsible for separating the coding strand from the template strand. The replication fork refers to the portion of the DNA where helicase is separating the strands. There are two replication forks per bubble.
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What is the difference between the leading strand and the lagging strand?
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DNA polymerase always synthesizes in the 5'-3' direction. Because DNA replication is semiconservative, each strand is used to make the daughters. Since DNA is antiparallel, helicase is separating the 5'-3' strand from the 3'-5' strand and therefore DNA polymerase must synthesize in two di…
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What is the function of each of the following proteins in the replication complex? DNA polymerase, Primase, Helicase, Ligase The sliding clamp Single-strand Binding proteins (S-SBP) RNAse H Topoisomerases I and II.
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DNA Polyermase: Responsible for synthesizing new DNA strands DNA Primase: Responsible for adding a short RNA primer to the beginning of the strand to be synthesized so that Polymerase can recognize that as the site of replication DNA Helicase: Disrupts the hydrogen bonds between the stran…
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Which of these must function first in the replication process? Why? Which of these must function last in the replication process? Why? Which of these proteins requires ATP?
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DNA Polyermase: Responsible for synthesizing new DNA strands DNA Primase: Responsible for adding a short RNA primer to the beginning of the strand to be synthesized so that Polymerase can recognize that as the site of replication DNA Helicase: Disrupts the hydrogen bonds between the stran…
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What proteins are used to correct replication errors after DNA synthesis? How do they work?
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3'-5', exonuclease. MutS binds to the bubble in the DNA double helix that results from an improper base-pairing event and MutL will "scan" the following sequence until it comes across an un-ligated nick. MutS will then remove the daughter strand and polymerase will re-synthesize that port…
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10. How are sites of DNA synthesis selected? What DNA and protein factors are involved in this process?
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Specific sequences of DNA are recognized as origins of replication. A particular complex of proteins will recognize this sequence and will initiate replication. The SBP Cdc6 and Cdt1 recognize this sequence and bind to the double helix. Helicase then responds to these two proteins and wil…
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What is telomerase?
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Telomerase is a ribonuclear protein that is an enzyme that adds DNA sequence repeats to the 3' end of DNA template strands in the telomere regions which are found at the ends of eukaryotic chromosomes.
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Do bacteria have telomerase? What provides the template for telomerase?
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No, prokaryotes tend to have circular chromosomes and therefore do not run into trouble synthesizing at the ends like linear chromosomes do. DNA sequence repeats found at the ends of the chromosomes are recognized by the telomerase which has a complementary RNA sequence.
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What is the initiator protein and how does it relate to the origin recognition complex?
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The signal binding proteins Cdc6 and Cdt1 are the initiators and recognize the origin recognition complex as a site of replication.
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What is the difference in the number of replication origins in a prokaryotic chromosome compared to a eukaryotic chromosome?
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Eukaryotic chromosomes have a particular set number of origins of replication while prokaryotic organisms only have one site of replications.
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At what phase of the cell cycle is DNA replicated?
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S-phase.
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What else is synthesized during genome replication? What do histone chaperones do?
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Histone subunits are synthesized during genome synthesis. Histone chaperones act as mediators during histone synthesis and serve a variety of functions. They help to disrupt the histones ahead of the synthesizing DNA and then reassemble them after the DNA has been resynthesized.
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What is the end replication problem and how do eukaryotes deal with it?
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The end replication problem is the idea that at the ends of linear chromosomes, the sequence is too short for DNA Primase to add an RNA primer to the end; therefore telomerase can add repeats to the end of the template strand, making it longer, so that Primase can add the primer and polym…
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What is the relationship between telomere length and aging and immortality?
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Young cells have a longer average length and as time progresses, the average will shorten and level out.
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11. Hydrolysis causes what type of damage to bases?
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Hydrolysis can cause two different types of damage to bases. In purines, it can cause depurination, in which the N-glycosidic bond between the purine base and the sugar backbone is cleaved and the nucleotide is now missing a base. Another type of damage is called deamination. In which an …
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Distinguish depyrimidination from depurination from deamination
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Depyrimidination is similar to depurination in that an hydrolysis reaction cleaves the N-glycosidic bond holding the base to the deoxyribose sugar; however, depyr. removes a pyrimidine base rather than a purine base. Depurination and Depyrimidination are different from deamination in that…
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Suppose a cell has no functional genes encoding uracil DNA glycosylase. What aberrant nucleotide will accumulate in the DNA of this cell? What change in the DNA sequence will be found in this cell's progeny?
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A deaminated cytosine nucleotide will accumulate in the DNA of the cell. When the strand replicates, one of the daughter strands will have a uracil which will pair with an Adenine and the other strand will have the correct sequence. However, when the U-A strand is replicated again to part…
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How is damage to DNA bases recognized by the cellular machineries that repair them?
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Damage to DNA bases causes conformational changes in the shape of the double helix. DNA repair mechanisms can sense this change in shape and have the machineries to fix them.
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Nucleotide excision repair involves which four enzymes? What does each do during the repair process? What type of damage is repaired by this pathway
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Excision nuclease: Finds the mutation, and causes nicks upstream and downstream of the mutation DNA Helicase: removes the entire strand between the nucleated nicks DNA Polymerase: re-synthesizes the strand of DNA DNA Ligase: Seals the nicks This fixes Dimerized nucleotide damage
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Base excision repair involves which four enzymes? What does each do during the repair process? What type of damage is repaired by this pathway? Which of these enzymes produce phosphodiester bonds? Which of these enzymes break phosphodiester bonds?
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(N) DNA Glycosylase (N being a specific Nucleotide): Removes the aberrant nucleotide. AP Endonuclease and Phosphodiesterase remove the sugar phosphate. DNA Polymerase: Adds the new nucleotide DNA Ligase: Seals the nicks Fixes deaminated nucleotides
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How is the repair of double stranded breaks fundamentally different from the repair of UV-induced damage?
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UV-induced damage can be repaired much more easily because the damage typically only occurs on one strand; however, double stranded breaks cannot use the undamaged strand as a guide to fix it because both strands are damaged.
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As a means for repairing a double stranded break, why is homologous recombination advantageous for the cell compared to nonhomologous end jjoining? What is the major difference in the mechanism of the two?
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Homologous recombination uses the unbroken homologous chromosome that is formed during Meiosis as a guide to perfectly re-synthesis the damaged strands. Nonhomologous end joining requires the degradation of some of the genetic material because their is no guide to act as a template.
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12. Why is it necessary for a break to occur in the DNA before the process of homologous recombination can occur?
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Without a double-stranded break in the DNA, homologous recombination would not be necessary and thus would not occur.
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What role does DNA hybridization play in recombination?
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Pairing interactions are required for recombination to occur. For these interactions to occur, the DNA must line up perfectly with the complementary sequence of the homologous strand. During homologous recombination, the DNA strands must line up precisely with each other at complementary …
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When does homologous recombination occur in eukaryotes?
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Homologous recombination occurs when the homologous chromosomes pair during meiosis.
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How does RecA participate in recombination?
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RecA mediates strand invasion, an ATP dependent mechanism. RecA has a strong binding affinity for DNA and therefore is capable of holding a single strand of DNA and a double helix together as a heteroduplex.
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At what stage of homologous recombination is DNA polymerase required? DNA ligase?
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DNA polyermase synthesizes the new DNA strands after the formation of the heteroduplex during strand envasion. Ligase comes in after the the polymerase synthesizes the new strands.
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What are the differences between a DNA transposon and a retrotransposon?
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Transposons are small mobile DNA segments that can change positions in the genome and can replicate themeselves. Retrotransposons are a special type of transposons that are RNA segments which are transcribed into DNA segments.
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What is a transposase? Where is the gene encoding it found?
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A transposase is an enzyme required for the transcription of transposons. The gene encoding transposase is almost always found in the DNA segment of the transposon.
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What is an integrase? Where is the gene encoding it found?
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Integrase is an enzyme that is found in retroviruses that enables its genetic material to be integrated into the DNA of the host cell. Like the transposase, the DNA for the integrase is often found in the retrotransposon itself.
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What effects have transposons had on the mammalian genome?
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Transposons have the ability to transcribe independently of the rest of the genome, and therefore its transcription is not regulated by the same mechanisms as the rest of the genome. As a result, it has accumulated many copies of itself over the years and populated a large portion of the …
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What is the difference between a retrotransposon and a retrovirus?
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A retrovirus is a virus, contained in its DNA are retrotransposons which can insert themselves into a host cell's DNA and can lead to the replication of more virus particles.
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Which process requires more base pairing to occur: homologous recombination or site specific recombination?
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Homologous recombination requires more base pairing, while site specific recombination only requires short segments of base pairing.
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13. What are the chemical and structural differences between DNA and RNA?
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RNA has an oxygen at the 2' carbon site while DNA does not. DNA has Adenine, Guanine, Cytosine, and Thymine RNA has Adenine, Guanine, Cytosine, and Uracil RNA is almost always single stranded.
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What is the relationship between the template strand, the coding strand and the sequence of the RNA?
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The template strand is the complementary strand of both the coding strand and the RNA transcript. The coding strand has the same sequence as the RNA transcript but the RNA has thymine replaced with uracil.
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In what ways are DNA synthesis and RNA synthesis alike? In what ways are they different?
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Both process occur in the nucleus. Both involve specific complementary base pairing, both processes involving the unwinding of the double helix. Both involve the formation of hydrogen bonds between the original DNA and the product. Replication involves the forming of a new DNA molecule bu…
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Besides mRNA, what other types of RNA found in cells? What are their functions?
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rRNA: ribosomal RNAs which form the basic structure of the ribosome and catalyze protein synthesis tRNA: transfer RNAs which are central to protein synthesis as adapters between mRNA and amino acids snRNAs: small nuclear RNAs which function in a variety of nuclear processes including gene…
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How does the initiation of transcription by RNA polymerase differ from the initiation of replication by DNA polymerase?
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DNA replication is initiated by Cdc6 and Cdt1, they then are recognized by DNA helicase and the DNA is unwound. DNA Primase adds an RNA primer to the strand and DNA polymerase begins synthesis. RNA synthesis
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What is the structure and function of the promoter? The terminator? Where are they found?
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A promoter is a region of DNA that initiates transcription of a particular gene. They are located near the transcription start sites of genes on the 5' end of the gene on the coding strand. They have a conserved sequence, range from 100-1000 base pairs long, and include the TATA box. A te…
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To which carbon atom of the ribose at the end of a nascent RNA molecule does RNA polymerase catalyze the formation of a phosphodiester bond during elongation?
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2'
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What sequences are recognized by sigma factor?
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Promoter sequences are recognized by sigma factor.
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What are the steps in the transcription cycle? What changes occur during the transition into each phase of the cycle?
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Initiation: Sigma factor recognizes the promoter, it binds RNA polymerase, creates replication bubble
Elongation: RNA Polymerase synthesizes the pre-mRNA strand (with the help of sigma factor)
Termination: RNA Polymerase reaches the termination sequence and the pre-mRNA transcript is re…
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How does the transcription bubble form during transcription by prokaryotic RNA polymerase?
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Sigma factor recognizes the promoter sequence of a segment of DNA and binds to it. It brings RNA polymerase to the promoter and creates the replication bubble. Transcription bubble is a molecular structure that occurs during the transcription of DNA when a limited portion of the DNA doubl…
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If multiple RNA polymerases are transcribing a single gene simultaneously, which one would have the longest nascent RNA transcript attached?
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All of the nascent RNA transcripts would be the same lengths because they all were transcribed from the same gene.
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B M B 251: EXAM 3