MCB 250 EXAM II STUDY GUIDE
MCB 250 EXAM II STUDY GUIDE MCB 250
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This 23 page Study Guide was uploaded by Jessica Logner on Sunday May 15, 2016. The Study Guide belongs to MCB 250 at University of Illinois at Urbana-Champaign taught by Kirchner, N in Spring 2016. Since its upload, it has received 5 views.
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Date Created: 05/15/16
MCB 250 Exam II RecA protein A protein that helps with homologous paring & Strand invasion the filaments help with stable base pairing * required for ALL pathways RecBCD a helicase/nuclease protein that helps process DNA breaks to generate single strands for strand invasion Also helps load Rec A onto ssDNA ends Uses ATP hydrolysis generates a 3' overhang to allow strand invasion. Chi sites Specific DNA sequences that control RecBCD, stimulate the frequency of homologous recombination, 10fold When RecBCD encounters ______ (5'GCTGGTGG3') it's activity changes. It stops degrading the strand with 3' end and becomes more active degrading the strand with the 5' end. This generates the 3' tail needed to initiate recombination. Rec B Helicase & nuclease Rec C recognizes Chi sites Rec D contains 3>5 helicase & nuclease What are the functions of the subunits; Rec B? Rec C? Rec D? Ruv AB complex RuvA recognizes/binds to holliday junction RuvB ATP dependent helicase recognizes Holliday junctions and promotes branch migration Ruv C protein in charge of resoluting holliday junctions Cuts the Holliday Junction Randomly Choosing Orientation the Choice Determines if there is a "Crossover Oxidative damage Radiation damage Cellular nucleases Replication Through a Single Strand Break Collapses the Replication Fork Double strand breaks" (DSBs) can also be caused by; Homologous recombination is important for DNA repair (ds breaks (as we've seen) and other things). is required for meiosis in eukaryotes: crossovers between homologous chromosomes required for proper chromosome segregation and for generating diversity in the gametes. allows genes to be transmitted from one bacterial strain to a closely related strain. Pol I After strand invasion, recombination requires DNA synthesis mediated by _________ Ung and base excision repair Increased U incorporation leads to increased attempted repair, too many breaks in strands In the absence of recombination this double stranded break is lethal This is caused by ____________ & ________________ Sitespecific recombination type of recombination Specific short sequences in both donor and recipient and special enzymes can direct recombination between sequences with little or no homology. Can occur at high frequency. Transposition type of recombination Requires the ends of the transposable element and special enzymes. Allows the transposable element to be inserted at many different sites without requiring homology. Illegitimate recombination Very low frequency recombination between nonhomologous sequences. (HR) uses the information in an intact double stranded DNA molecule to repair the broken DNA molecule. HR can repair a DSB perfectly. (NHEJ) can repair DSBs without needing an intact copy of the damaged DNA molecule. NHEJ is the most important pathway for DSB repair in nonproliferating cells of higher eukaryotes. NHEJ cannot repair a DSB perfectly. Whats the difference b/w homologous recombinations and nonhomologous end joining? Double Strand Break Repair by Nonhomologous End Joining (NHEJ) joins linear, double stranded DNA molecules end to end. No significant homology between the two ends is required. Ends are trimmed before joining This process is called ________________ Ku recognizes the DSB DNAPKcs is a protein kinase that recruits Artemis. Artemis is a multifuntional nuclease that processes the ends. A ligase complexed to some other proteins joins the ends Various DNA polymerases may be required to fill in gaps. What are the steps of Nonhomologous End Joining (NHEJ) Telomeres coated with proteins, therefore not recognized by NHEJ apparatus. How is DNA protected from NHEJ? which leads to leukemia DSBs can lead to translocation.. gene that unit of DNA which encodes and is capable of expressing a particular RNA/protein. He elected to study characters that occurred in two clearly distinguishable forms, e.g. round peas vs. wrinkled peas. He established purebreeding lines for each of his traits. He controlled which individuals mated by using a fine brush to transfer pollen from one flower to another. Mendel wanted to study the inheritance of physical traits, and to do so he made three practical decisions 1) First, the DNA of interest must be in a form that will be stably maintained inside of cells. This is usually accomplished by recombining that DNA into some form of vector. 2)Second, the recombinant DNA vector is transformed into a compatible host cell that is propagated indefinitely. 2 steps of cloning? E. coli can be raised in large volumes at minimal expense. Cells double every 20 minutes with adequate nutrients. Bacteria can serve as hosts for certain naturally occurring DNA vectors: plasmids bacteriophage viruses Why is E. coli widely used for the propagation of cloned DNAs? Bacterial plasmid Plasmid DNA is easy to purify. Because the plasmid is much smaller than the bacterial chromosome, the two can be readily separated after lysing the cell. are selfreplicating extrachromosomal DNAs Once established in the bacterial cytoplasm, _____is replicated and its genes expressed in parallel with the bacterial chromosome. An origin of replication that will be recognized by the host cell. One or more selectable marker gene(s). This intact plasmid has two genes that convey antibiotic resistance. Cloning sites. pBR322 has 40 different unique restriction sites that can be used for DNA insertion. (Inserts are generally < 10 kb in length). A cloning vector must have which 3 key features? Restriction enzymes recognize specific dsDNA sequences, and digest these sequences by making a single cut in each of the two DNA strands. are endonucleases, i.e. they hydrolyze a phosphodiester bond to leave a 3'OH and a 5'phosphate This phosphodiester bond can be reformed by adding DNA ligase plus ATP. DNA library is a collection of host cells which carry the same DNA vector but with different DNA inserts, e.g. different short fragments of the human genome. Genomic DNA digested into millions of fragments by a particular restriction enzyme. Millions of copies of plasmid, digested with a restriction enzyme that produces sticky ends compatible with the insert fragments. Individual colonies grow from single bacteria, each carrying a different DNA insert. How do you construct a genomic DNA library? DNA hybridization Clones of interest are found by screening the DNA library. A common screening method ________ (similar to 'Southern blotting') with a labeled probe DNA that will only anneal to inserts with complementary base pair sequence. Reverse genetics Genes are first identified by analysis of their DNA sequence. This DNA sequence information is then used as a basis for studying the gene's function Step 1 The starting DNA sample is denatured with near boiling temperature in the presence of two short (1530 bp) DNA primers that are complementary to opposite strands. Step 2 The solution is cooled, allowing the primers to anneal to their complementary sequences. Step 3 A thermostable DNA polymerase like Taq is used to elongate each primer from its 3' end, copying the DNA sequence of the template strand. Steps of PCR reaction. basal transcription. the RNA polymerase holoenzyme can act by itself to recognize promoters and initiate transcription. This is called ________ _______________ promoter the site bound by RNA polymerase can be distinguished as the core promoter. the entire regulatory region of the gene, i.e. that portion of the DNA which binds proteins that influence the gene's transcription. transcription factors DNAbinding proteins that regulate the rate at which RNA polymerase initiates transcription are referred to in general as .... Specificity Transcription factors (TFs) display sequencespecific binding: i.e. they only bind to DNA that has a specific nucleotide sequence. Noncovalent bonds When it binds to DNA, the TF does so by forming multiple noncovalent bonds. Chemical affinity The cumulative strength of these noncovalent bonds determines the 'chemical affinity' between the TF protein and its DNA binding site. electrophoretic mobilityshift assay (EMSA). The binding of protein to DNA can be studied experimentally by means of the ... mutually exclusive states In the lac operon of E. coli, the binding sites for RNA polymerase and lac repressor protein are so close that the 2 proteins cannot bind at the same time. Hence, for this promoter transcription and repression are........ When a sequencespecific DNAbinding protein encounters the appropriate sequence of base pairs, it will adhere to the DNA by forming multiple chemical bonds. How does a sequencespecific dna binding protein attach to DNA? A + B A:B A = protein B = DNA binding site A:B = protein bound to DNA Increasing the concentration of Protein A will drive this reaction to the right. Hence: The likelihood that a given binding site on the DNA is occupied by the protein is a function of the protein's concentration. As protein concentration increases, so does the percentage of time that the DNA binding site is occupied by a molecule of that protein Expression is increased when lactose is available. Expression is decreased when glucose is also available. The enzymes responsible for lactose metabolism show this pattern of regulation: Lactose permease (Lac Y) membrane transport protein that allows lactose to enter the cell bgalactosidase (Lac Z) enzyme that cleaves disaccharide lactose into glucose and galactose for further metabolism. Thiogalactoside transacetylase (lac A) enzyme that inactivates certain toxic sugars that can enter the cell through lactose permease Transcription Expression of the lac operon is primarily regulated at the level of ______________ lacI aka Lac repressor The ability of lactose to induce lac operon transcription involves a transcription factor, Is not part of the lac operon. Has its own constitutively active promoter. binds to a DNA sequence, the lacO 'operator', adjacent to the lac promoter represses the lac operon Each of two identical protein subunits binds to the DNA. Each subunit has two ahelices joined by a short "turn". It is the socalled recognition helix that fits into the major groove of the DNA molecule. When the dimer binds to DNA, the two recognition helices insert into two sequential turns of the groove in opposite orientations. As a result, the sequence of the DNA binding site is an inverted repeat consisting of two symmetric "halfsites". LacI protein binds DNA by means of a 3dimensional structure called the helixturnhelix motif: Allolactase When lactose is present in the medium, it passes through the bacterial membrane into the cytoplasm. Some of this lactose is there converted by Bgal into the isomer allolactose. When lactose is present, an inducer molecule___________ (I) binds to the Lac Repressor protein (R) and prevents it from binding DNA. the affinity of RNA polymerase for its DNA sequence is low, and as a consequence the rate of basal transcription (RNAP alone) is low. The lac operon has a weak promoter catabolite activator protein or CAP/CRP The ability of glucose to repress lac operon transcription involves a second helixturnhelix transcription factor, the _____________ it uses a second domain to bind the Cterminal domains (CTDs) of the two RNA polymerase a subunits. This additional bond increases the affinity of RNA polymerase for the promoter, and thus increases the probability that transcription will occur. Allostery A chemical property of certain proteins: Protein function is turned on or off by the binding of a particular ligand molecule. The ligandbinding site is distant from the protein's active site, i.e. the change in function results from a global alteration in protein structure. In the case of LacI, ligandbinding reduces the chemical affinity of the protein's DNA binding domain. Cooperativity When two proteins that bind to DNA can also bind to one another, the cumulative nature of these bonds (i) favors the bound state and (ii) increases the probability that the binding sites will be occupied. CAP is expressed constitutively, i.e. it is always present in the bacterial cytoplasm. Rather, it is the affinity of CAP protein for its DNA binding site that is controlled by glucose concentration. In E. coli, the concentration of cAMP in the cytoplasm is inversely proportional to the amount of glucose being taken up by the cell. If glucose is removed from the medium, the concentration of cAMP will rise inside the cell: CAP will bind to cAMP and change conformation; CAPcAMP will bind to DNA; CAP will interact with RNAP, activating the maximal rate of lac operon transcription. How does the concentration of glucose influence CAP? cAMP is a chemical derivative of ATP. Both prokaryotes and eukaryotes use this chemical as an intracellular signaling molecule. Allolactose will be turned over, so its concentration will drop; LacI protein freed of allolactose will change conformation and bind DNA; LacI bound to LacO will block RNAP from the promoter, and repress lac transcription. If lactose is removed from the medium: Once the recognition helices (R) are parallel to one another, the CAP/cAMP complex can fit into two consecutive turns of the major groove in a DNA double helix. How does Cap/Camp bind? 1) RNA polymerase 2) Lac I (TF) 3) CAP (TF) Transcriptional regulation of the lac operon is accomplished by three proteins.... Trans! In contrast, two elements are said to function "in trans" if they can interact when located on the same or different DNA molecules. A lacI gene on one piece of DNA can repress the lac operon on the same DNA or a different chromosome as long as they occupy the same cell. Helixturnhelix protein structures. Bind to specific DNA target sequences (although their specific target sequences differ). Allosteric regulation of DNA binding affinity by a small intracellular ligand. Presence or absence of each ligand reflects the state of sugar metabolism. The transcription factor physically interacts with RNA polymerase to influence the rate of gene transcription. The LacI repressor and CAP activator proteins have several common features: Alternative sigma (w) factors It is the w factor subunit of the bacterial RNA polymerase holoenzyme which is responsible for binding to the promoter. In bacteria, a second method for transcriptional regulation is to modify RNA polymerase itself. This is achieved by employing different w factors in the RNA polymerase holoenzyme when the cell is in different physiological states Elevated temperatures disrupt noncovalent bonds, causing protein to lose their 3dimensional structure and cease to be functional. This process is called denaturation. WHAT IS HEAT SHOCK? Under normal growth conditions, E. coli primarily expresses w70, which directs RNA polymerase to a set of genes that have the appropriate 10 and 35 promoter sequences. But at elevated temperatures, the cell begins to express a high concentration of w32, which redirects RNA polymerase to a different set of genes that encode heat shock proteins. In E. coli, increasing the temperature from 37 C. to 42 C. causes a 15fold increase in the concentration of "heat shock proteins" w32 mRNA is translated more efficiently. w32 protein is degraded less rapidly. RESULT: increased levels of protein. Although it controls the transcription of downstream genes, the abundance of w32 protein itself is regulated at a posttranscriptional level. During heat shock ... Heat shock temperatures melt this secondary structure, exposing the RBS and allowing the mRNA to associate with a ribosome. This increases the rate of translation at 37 adopts a secondary structure that blocks the ribosome binding site (RBS). The core promoter of the E. coli ribosomal RNA operon contains functional binding sequences for both w70 and w32. As a result, rRNA expression continues normally during heat shock. During heat shock, what happens to those genes whose expression is essential at all times? Viruses are molecular parasites of cellular life Like cells, a virus has a nucleic acid genome that encodes its proteins. Viral genomes can be RNA or DNA, and single or doublestranded. Unlike cells, a virus cannot reproduce in isolation. To propagate it must infect a living cell and commandeer the host's internal biochemistry. Cells of different species have distinct viral parasites. Viruses that infect bacteria are known as 'bacteriophages'. infection For a bacteriophage, the initial steps of infection are binding of the viral particle to the host cell surface, and injection of the viral genome across the membrane into the cytoplasm cro is the key gene for lysis. cI is the key gene for lysogeny. Note that cro and cI are transcribed in opposite directions, i.e. they use different template strands of the DNA. There are two genes in the control region, cI and cro, whose protein products compete with one another to decide whether the phage becomes lytic or lysogenic. Lysis vs. lysogeny: promoters PL and PR are strong constitutive promoters, i.e. RNA polymerase alone is sufficient for active transcription. They control 2 polycistronic operons that extend in opposite directions around the chromosome. Active transcription from PRE leads to expression of the cI gene. However, transcription from the PR promoter also leads to synthesis of the cII protein, a transcription factor which serves as an activator at the weak PRE promoter When bound to OR3, Cro blocks the PRM promoter and represses cI transcription from this promoter. The PR promoter isn't blocked, and remains active. Cro protein has its highest affinity for the OR3 operator. When bound to OR1, cI blocks the PR promoter and represses cro transcription. The w repressor (cI) protein binds as a dimer to the DNA of the OR1 operator even at low concentrations. On the contrary, cI protein (also known as the w repressor) has its highest affinity for the OR1 operator ... On its own, the OR2 operator has a 10fold lower affinity for the w repressor (cI). However, when a cI dimer is bound at OR1, cooperative binding allows a second dimer to bind OR2 and form a tetramer. Linking number Total number of times BDNA crosses over itself Twist Number of helical turns Writhe Number of times the helix crosses itself Topoisomerase (Supercoiling) Enzymes that change the linking number of cccDNA molecule by altering the twist Topo II Cleaves both DNA strands, changing the linking number by 2. Requires ATP DNA gyrase A type of Topo II that introduces negative supercoils. Found only in bacteria Topo I Cleaves one DNA strand at a time without ATP, changing the linking number in increments of 1 M phase Chromatids condense G1 phase Chromosomes decondense S phase Diffuse chromosomes undergo DNA replication Heterochromatin Condensend chromatin Euchromatin Highly dispersed chromatin H2A, H2B, H3, and H4 Two copies of each of these histone proteins form a disk that the DNA wraps around in a lefthanded helix H1 Linker protein between the core histones oriC DNA Replication, Bacteria/Eukaryotes. The single initiation site in E. Coli. Many in eukaryotes DnaA DNA Replication, Bacteria/Eukaryotes. Initiator Protein. Complexed with ATP, binds oriC and recruits replisome proteins DnaB DNA Replication, Bacteria/Eukaryotes. Helicase. Melts parental DNA and interacts with DNA Pol III and Primase DnaG DNA Replication, Bacteria/Eukaryotes. Primase. An RNA polymerase that synthesizes RNA primers DNA Pol III DNA Replication, Bacteria/Eukaryotes. Synthesizes DNA but requires a primer. Possesses 35 exonuclease activity SSB DNA Replication, Bacteria/Eukaryotes. Single Strand Binding Protein. Binds ssDNA template cooperatively and prevents reannealing and hairpin formation RNase H DNA Replication, Bacteria/Eukaryotes. Removes RNA primers. Can only cleave bonds between ribonucleotides and thus leaves one ribonucleotide at the 5 end DNA Pol I DNA Replication, Bacteria/Eukaryotes. Removes RNA primers and replaces RNA with DNA while filling gaps between Okazaki fragments. Possesses 53 polymerase, 53 exonuclease, and 35 exonuclease activity DNA Ligase DNA Replication, Bacteria/Eukaryotes. Seals nicks between Okazaki fragments Topoisomerase (DNA Replication) Relaxes positively supercoiled dsDNA in front of the replication fork DnaC DNA Replication, Bacteria/Eukaryotes. Loads DnaB (Helicase) onto ssDNA Sliding Clamp DNA Replication, Bacteria/Eukaryotes. Aids in the binding of Pol III to the nucleic acid substrate Clamp loader DNA Replication, Bacteria/Eukaryotes. Recognizes the 3 end of the primerDNA hybrid. ATP hydrolysis opens the clamp and loads it Ter sites DNA Replication, Bacteria. Oneway sites in the terminator region Tus protein DNA Replication, Bacteria. The antihelicase protein. Bind DNA sites in the terminator region Dam DNA Replication, Bacteria/Eukaryotes. DNA adenine methyltransferase. Recognizes 5GATC3 and adds a methyl group to the A Methylation (DNA Replication) Enables the cell to determine which strand is the newly synthesized one (not methylated) versus the old one (is methylated) SeqA DNA Replication, Bacteria/Eukaryotes. Controls access to oriC by binding hemimethylated oriC. This prevents DnaA binding and slows down Dam methylation Telomeres DNA Replication, Eukaryotes. The ends of eukaryotic chromosomes. Contain tandem repeats of TGrich sequences Telomerase DNA Replication, Eukaryotes. Reverse transcriptase. A ribonucleoprotein that makes a DNA strand by copying an RNA strand Alkaline hydrolysis The 2OH on ribose can attack the phosphodiester bond NonWatsonCrick Base Pairs GU, AA, AUA Coding strand RNA Transcription, Bacteria. The nontemplate strand has the same sequence as the RNA transcript (except RNA has U instead of T) Template strand RNA Transcription, Bacteria. The noncoding strand complements the RNA sequence Sigma Subunit RNA Transcription, Bacteria. Confers recognition of the promoter Promoter RNA Transcription, Bacteria. The site in the DNA sequence where RNA Pol first binds to initiate transcription 10 and 35 sequence RNA Transcription, Bacteria. Parts of the promoter, bound by the sigma subunit CTD (Bacteria) RNA Transcription, Bacteria. Cterminal domain of the alpha subunit binds the UP element UP element RNA Transcription, Bacteria. Upstream of the 35 and 10 sequences. Bound by the CTD. Increases promoter strength Transition to Open Complex (Bacteria) RNA Transcription, Bacteria. Sigma factor flips out bases and binds the bases in the 10 site to facilitate the melting of the promoter region Abortive transcripts RNA Transcription, Bacteria. Associated with an apparent compression of the DNA. Eventually, the builtup energy allows for promoter clearance RNA Pol RNA Transcription, Bacteria. Relies on DNA template to elongate RNA strand. Does not require a sliding clamp, nor does it proofread the accuracy of the transcript. It can, however, reverse translocate, cleave the phosphate bond, and try again upon incorporation of a mismatched nucleotide Rhoindependent Termination RNA Transcription, Bacteria. Intrinsic. Hairpin structures in RNA are recognized by RNA polymerase and cause it to stall. GCrich inverted repeat followed by a run of U's Rhodependent Termination RNA Transcription, Bacteria. Rho is a helicase that acts on RNADNA hybrids. Rho binds to an exposed ssRNA site (rut site), moves along the ssRNA, and separates the RNADNA duplex RNA Pol I RNA Transcription, Eukaryotes. Transcribes rRNA genes RNA Pol II RNA Transcription, Eukaryotes. Transcribes mRNA genes RNA Pol III RNA Transcription, Eukaryotes. Transcribes tRNA genes mRNA modifications (Eukaryotes) RNA Transcription, Eukaryotes. 5capped and 3polyadenylated. Introns from premRNA are removed by RNA splicing CTD (Eukaryotes) RNA Transcription, Eukaryotes. Found in RNA Pol II. Not found in Pol I or III. Made up of a large number of 7 amino acid repeats. Can be regulated by phosphorylation TF RNA Transcription, Eukaryotes. Transcription factors. Bind to the core promoter for RNA Pol II and recruit RNA Pol II. Together they form the preinitiation complex TBP RNA Transcription, Eukaryotes. TATAbinding protein binds the TATABox, producing a sharp bend in the promoter DNA TATABox RNA Transcription, Eukaryotes. DNA sequence bound by TBP in one of the critical early steps of RNA Pol II transcription TFIIH RNA Transcription, Eukaryotes. ATPdependent helicase that helps melt the DNA to form a bubble during initiation. Part of the preinitiation complex Mediator complex RNA Transcription, Eukaryotes. Functions as a transcriptional coactivator that binds to the CTD of RNA Pol II and facilitates binding of TFs. Elicits promoter clearance by facilitating phosphorylation of the CTD 5'm7G cap RNA Transcription, Eukaryotes. Increases mRNA stability by protecting against RNases, regulates splicing, enhances efficiency of translation 3'PolyAdenylation RNA Transcription, Eukaryotes. Adds about 200 adenines 500 base pairs from the 3' end of the mRNA transcript. Protects from RNases and enhances translation Consensus Sequences for Splice Sites RNA Processing, Eukaryotes. 5' GU, 3' AG, and the branch site A are the only invariant bases The Spliceosome RNA Processing, Eukaryotes. Catalyzes splicing of premRNA. Composed of 5 snRNAs snRNA RNA Processing, Eukaryotes. Small nuclear RNAs. When complexed with proteins in the spliceosome they are called snRNPs U1, U2, U4, U5, and U6 RNA Processing, Eukaryotes. Components of the spliceosome tRNA Translation, Bacteria/Eukaryotes. Adapters between the mRNA codons and the amino acids Wobble Base Pairs Translation, Bacteria/Eukaryotes. AU, GU, IC, IU, IA Inosine Translation, Bacteria/Eukaryotes. Deaminated A included in the wobble position RBS Translation, Bacteria. Ribosome Binding Site aka ShineDalgarno site 16s rRNA Translation, Bacteria. 3' end basepairs with the RBS on the mRNA IF1, IF2(GTP), IF3 Translation, Bacteria. Initiation factors. Bind the RBS along with the 30S subunit 30S Initiation Complex Translation, Bacteria. The initiator aminoacyl tRNA, the 30S subunit, and IFs IF3 Translation, Bacteria. Release of IF3 allows the 50S subunit to bind 70S Initiation Complex Translation, Bacteria. Formed after the release of IF3. Consists of the 30S subunit, IF1, IF2(GTP), and the 50S subunit EFTs Translation, Bacteria. Elongation. GTP exchange factor EFTu Translation, Bacteria. Elongation. Brings the charged tRNA to the ribosome EFG Translation, Bacteria. Elongation. Translocation requires EFG and GTP hydrolysis. It mimics EFTutRNA RFs Translation, Bacteria. Termination. Releasing factors are proteins that look and act like tRNAs.Translation ends when RFs bind to STOP codons RRF Translation, Bacteria. Termination. Ribosome recycling factor looks like a tRNA. Dissociates the 30S and 50S subunits Preinitiation complex (Translation) Translation, Eukaryotes. Initiation. Forms without mRNA. Binds eIFmRNA complex. Then scans for the first AUG eIF4E Translation, Eukaryotes. Initiation. Cap Binding Protein eIF4A Translation, Eukaryotes. Initiation. ATPdependent RNA helicase AminoacyltRNA synthetase Translation, Bacteria/Eukaryotes. Charge tRNA with the correct amino acid through an aminoacyl AMP intermediate RT Reverse transcriptase is an RNAdependent DNA polymerase that can synthesize a cDNA (complementary DNA) strand using ssRNA as a template. RT requires a primer and works 53 Transition Mutation. Purine to purine or pyrimidine to pyrimidine. More common than transversion Transversion Mutation. Purine to pyrimidine or pyrimidine to purine Silent mutation The same amino acid is coded for Missense mutation A different amino acid is coded for Nonsense mutation A STOP codon is coded for Slipped strand mispairing Often occurs at long stretches of short tandem repeats during replication Spontaneous deamination of Cytosine Leads to formation of uracil. This is why thymine and not uracil is used in DNA Spontaneous hydrolysis of purines Results in an abasic site Oxidative DNA damage Oxygen radicals can create both ds and ssDNA breaks. 8oxoG is a base formed by oxidation of bases, and can pair with either C or A Thymine dimers Ultraviolet light can cause 2 adjacent T bases to bind, physically blocking DNA replication Dideoxy nucleotides Lack OH groups. Incorporation leads to strand termination MMR Mismatch Repair fixes mismatches resulting from replication errors BER Base Excision Repair. Udg in bacteria and Ung in humans, removes U from DNA. Other DNA glycosylases remove other types of damaged or modified bases. Fixes small lesions that do not distort the backbone NER Nucleotide Excision Repair. Removes the wrong base along with adjacent nucleotides. Associated with bulky distortions in DNA SOS Translesion DNA synthesis. Allows for DNA polymerases to complete replication, but with many errors MutS MMR. Associated with the clamp and forms a dimer at the mismatch basepair site MutH MMR. Binds to hemimethylated site. Nicks the DNA near the hemimethylation site and recruits helicase II MutL MMR. Dimer binds to the complex UvrAUvrB NER. Scan DNA for mismatches that distort the backbone using ATP hydrolysis. UvrB melts the region around the mismatch and UvrA is released UvrC NER. Recruited to the mismatch site and makes nicks on both sides of the damage. Leaves UvrD NER. Helicase II. Displaces the damaged DNA fragment Photolyase Repairs thymine dimers. Not present in human
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