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MCB Exam 2 - Part 1

DNA structure, Replication, Repair, and Recombination

Define "gene" ENTIRE nucleic acid sequence that is necessary to make a functional polpeptide or RNA
Where are the 5' and 3' UTR's located (in introns or exons)? exons
A group of related genes that have slight sequence variations and subtly different functions is a _____ gene family
A ___ is an evolutionary relic that is the result of a mutation that causes the gene to lose the ability to produce a functional gene. What is their importance? pseudogene increase genomic size
What 4 elements make up the repetitive sequences found in the genome? Approximately how much of the genome is repetitive? simple-sequence repeats; LINEs, SINEs, and Reterovirus-like elements (retrotransposons); DNA Transposons 50%
Which bases are bicyclic and which are composed of 6-membered rings? Bicyclic - Purines (A,G) 6-mem Ring - Pyrimadines (C,U,T)
What is the difference between a ribose sugar and a deoxyribose sugar? Ribose - OH on C2 Deoxyribose - H on C2 (more stable)
A _____ bond is between the 5' Phos. and 3' OH of 2 nucleotides. A _____ bond is between the N1 of a base and the C1 of a sugar. phosphodiester Beta-N-Glycosidic
A-type DNA is a dehydrated form with a ____shape, _____ rise/bp, ____-handed screw sense, and has _____ bp/turn broad 2.3 right 11
B-type DNA is the normal form with a ____shape, _____ rise/bp, ____-handed screw sense, and has _____ bp/turn intermediate 3.4 right 10.4
Z-type DNA is a GC-rich zig-zag form with a ____shape, _____ rise/bp, ____-handed screw sense, and has _____ bp/turn narrow 3.8 Left 12
The ____ # is the actual number of times DNA strands cross one another. The ___# is the theoretical # of times strands should cross one another. The ___# is the # of supercoils and becomes more negative as negative supercoils are added. Linking Twisting Writhing (L = T + W)
Enzyme that removes negative supercoils, does NOT require energy, and breaks one strand Topoisomerase I
Enzyme that adds negative supercoils, requires energy input, and breaks BOTH strands Topoisomerase II
What is the name of the topoisomerase II found in bacteria that is the target of Novobiocin and Ciproflaxin antibiotics Gyrase
What is a nucleosome composed of and how much does it compact DNA? core particle (2 copies of H2A, H2B, H3, H4), with DNA wrapped twice around and tied down by H1 compacts DNA 7-fold
H1 is critical to what level of DNA compaction? How much does this level compact DNA? Solenoid (30nm fiber) 70-fold
The _____ is the point on the chromosome where 2 chromatids are attached. What nucleotides are rich here and why? centromere A-T - only 2 H-bonds b/w, thus easier to break apart
What drives the equilibrium of DNA replication foward? pyrophosphatase cleaves PPi product
Which strand in DNA replication has bases added to it in the 5' to 3' direction and uses the parental strand that runs 3' to 5' as a template, and only needs a primer once? leading strand
How is DNA ligase able to fill in phosphodiester bonds? Adds 2 Hydrogen-phosphate bonds (one of which adds Pi to the 5' end so it can join up with 3' OH, the other is to hydrolyze ATP for energy)
What are the 3 prokarytoic DNA polymerases? DNA Pol I (distributive, repair, can add 20 bp's at once, rate of 10 bp/sec) DNA Pol II (repair?) DNA Pol III (processive, can add thousands of bases at once, rate of 1000 bp/sec)
What are the 5 eukaryotic DNA polymerases? Alpha (associated w/ primase, lagging strand) Gamma (Mt DNA) Epsilon (leading strand) Delta (adds to lagging after alpha/primase) Beta (main repair)
The ____ is the clamp loading protein/brace while the ____ is sliding clamp that holds strand down during replication. Gamma complex (RF) Beta protein (PCNA)
What is the current model of DNA replication that states that the lagging strand is looped out during replication? "Trombone" Model
Tautomers are mainly due to what? What is their occurrence and fidelity rate? resonance of nucleotides 10^4 10^9 - 10^10
What are the 3 active sites that can be found on DNA Pol I 3'-5' exonuclease (proofreading) 5'-3' exonuclease (removal of primases) 5'-3' addition of nucleotides
The ___ is 245 bp sequence that is A/T rich and found at prokaryotic origins to attract replication factors ori sequence
_______ are important to eukaryotic initiation of replication due to their binding site for Origin Replication Complexes (ORCs). Autonomosly Replicating Sequences(ARS)
How are telomere ends maintained? telomerase (carrying a RNA complimentary to a species-specific telomere sequence) binds telomeric DNA and extends the strand one repeat unit using its RNA as a template. The lagging strand can then use the leading strand as a template
What are the 2 types of spontaneous mutations? deamination (amine to carbonyl; causes C to U conversion) Depur/pyramidation (loose base, but backbone remains intact)
What are the 3 types of induced muatations? Thymine dimers, alkylation (add methyl to G), carcinogen reaction (add bulky bases)
How is alkylation repaired? direct reversal of chemical rxn: methyltransferase removes methyl groups from G
Huntington's disease is caused by ______. Normal individuals have ______ repeats while an individual with the disease has _____ repeats. triplet repeat expansion 6-31 repeats 36-82 repeats
During ___ an error in DNA is not recognized until DNA pol comes across it. The error caused the pol to fall off and be replaced by repair pol that "guesses" a base to pair with error so it can be repaired later after replication finishes. Translesion DNA synthesis
During _____ the DNA pol skips over errors when its replicating and a repair pol later fills in gap, using the parental homolog as a template. Recombination repair
______ is used to fix ionizing radiation damage. What are the 2 main types of this repair and which one results is a loss of bases? Double-Stranded Break Repair: Homologous recombination and end joining (results in loss of bases)
When is gene amplification most often used? to increase rRNA genes in oocytes
Why is p53 mutation associated with so many cancers? T-rich and thus susceptible to UV-induced thymine dimers. Because it regulates cell cycle (by activating p21 to inhibit CDK4/6 / cylin D and cause a G1 arrest) this can lead to uncontrolled cell growth
Where would you see site specific recombination (ie DNA rearrangement)? Immune system: variable regions of immunoglobins (B cells) and T cell receptors
Explain how immunoglobin light chain transcripts are formed. 1 of 250 V regions undergoes site specfic recombination to be placed next to 1 of 4 J regions. The 1° transcript includes this combo+remaining J's+constant region and is spliced to remove remaining J's - allows for 1,000 different combos
Explain how immunoglobin heavy chain transcripts are formed. same as light chain, but there are 2 site-specific recombinations: the 1st connects D and J regions, the 2nd combines DJ with a V region - allows for 24,000 different combos!
In T Cell receptors, 2 chains undergo site-specific recombination. The ___ chain undergoes VJ recombination, while the ____ chain undergoes VDJ recombination. Alpha Beta
What 2 proteins are responsible for V(D)J site-specific recombination? Where do they both bind and cleave? RAG 1 (binds V,D,J coding regions) RAG 2 (binds recombination sequence) cleave between coding and recombination sequences
In what process are V(D)J regions combined with a series of different heavy chain constant regions? What is this process responsible? class switch recombination classes of antibodies (IgG, IgE, etc.)
Bacterial Transposons consist of insertion sequences (IS) comprised of a gene encoding for ___ flanked by _____. It moves to a new part of the genome via a ___ intermediate and [DO/DO NOT] involve DNA replication. In introduces ___ cuts in target DNA. transposase; inverted repeats (IR); DNA; DOES NOT; staggered cuts
Retrotransposons insert into our genome via a ___ intermediate and comprise ___% of the genome. All of these transposons encode for ____ with the exception of ___ which uses cell machinery. ___ are flanked by LTRs, while ___ are followed by A-rich seq. RNA; 40%; reverse transcriptase; SINEs; LTR Retrotransposons (8%); LINEs (21%)
Created by: c.phill