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46 Cards in this Set
- Front
- Back
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WHat is an ORF?
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a set of continuous, non overlapping NT codons that in a DNA or RNA molecule that begin with a start codon, but do not contain any stop codons (even at the end of the sequence)
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What is a missense mutation?
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A change in a single Amino Acid.
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what is a nonsense mutation?
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Early stop codon
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What is a transition mutation?
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Exchange a purine with a purine, or a pyrimidine with a pyrimidine.
G -->A , C-->T |
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What is a transversion mutation?
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exchange a purine with a pyrimidine or vice versa
C-->G or A-->T |
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Which is more common, transition or transversion?
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transition
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Why does transition often happen?
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tautomeric shifts
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What molecule does the worst damage to DNA?
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Water.
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What guanine-like residue can get incorporated into DNA?
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8-oxo-dGTP
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what type of NT is most likely to get hydrolyzed by h2O?
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Purines (primarily G)
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What happens (structurally) during Deamination of NTs?
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An amino group falls off.
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What is depurination, and how does it occur?
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Most damaging effect on DNA. H2O attacks the glycosidic bond, and a purine (often Guanine) falls off.
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What type of reaction converts C-->U
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Deamination, and it would be a transition mutation
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What conformation os 8-oxoG in?
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It can be in both Anti and syn, but it is primarily in anti
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What base does Anti-8-oxoG bind to
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C
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What base does Anti-8-oxoG bind to? What type of mutation will this cause?
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It binds to A, this will cause a transversion mutation
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What is 5-Bromo-uracil?
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it is a nucleotide analogue.
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What are intercalating agents?
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They are molecules around the same shape as planar N -bases, and can slide in-between adjacent bases to disrupt the stacking interactions holding bases together.
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What is the most nucleophillic molecule on Guanine?
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the 7-Nitrogen. This molecule can attack molecules to add a m 7-N-methyl group
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what will happen in O^6 methylguanine?
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The lone pairs on the N's between bases will cause repulsion
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How doe thymine dimers form? (causative agent, and carbons where bonds occur)
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Occur from too much UV light exposure. Hthe double bonds between C5 and c6 are reactive, and cause bond formation between the C5 and C6 of the adjacent thymine.
A bond can also form between the 6 C of the 5' Thymine and the 4 Carbon of the 3' thymine. |
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How do prokaryotes know which strand is the template strand after replication?
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they methylate a GATC sequence, which occurs ever ~1000 bases, and immediately after replication, the new DNA strand will not be methylated, at this point the DNA is said to be
hemimethylated. after a short period of time, the DNA will become methylated, and the template strand to synthesis will be indistinguishable |
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What is the first step in mismatch DNA repair in proks? Is this DNA dependent?
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The Binding of MutS and MutL, this process requires 1ATP equivalent.
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How many ATP equivalents does it cost to add 500 nts?
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1000 ATP
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What is the second step in DNA mismatch repair in Proks?
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MutH binds to the MutL/S complex, and scans the DNA for the closest Methyl group, and cuts the strand with the non-methylated DNA.
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How many ATP equivalents does it cost for MutH to bind to the MutL/S complex.
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1 ATP equivalent.
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What is the activity of MutH?
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it is an ATP dependent translocator with endonuclease activity.
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Which enzymes work together to remove the bases between the mismatch mutation and the methylated site?
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helicase, and an exonuclease remove the bases up towards the mismatch or towards the methylated sequence (depending on the strand that the mutation is on)
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what is the result of the DNA after DNA glycosylase removes a base, and why is this bad?
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an AP site is formed, and this is bad, because if the ribose is exposed, it can linearize to expose a reactive aldehyde group
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WHat enzyme removes bases that have been damaged or modified?
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DNA glycosylase.
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How does DNA glycosylase work?
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They catalyze the glycosidic linkage between the nucleobase and the deoxyribose moiety.
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What enzyme removes the deamination product in DNA when Uracil is formed from Cytosine?
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Uracil glycosylase
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How many DNA? glycosylases are there
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should be 5, one per base
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If the mismatch repair is to the left of the closest methyl group, which way does the exonuclease activity go?
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towards the methyl group. (5'-->3')
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If the mismatch repair is to the right of the closest methyl group, which way does the exonuclease move?
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towards the mismatch repair (5'-->3)
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which polymerase adds NTs back to the DNA strand that has undergone base excision to fix a mismatch mutation?
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DNA Pol III
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which enzyme recognizes the AP site in DNA, and cleaves DNA near the point of the lesion?
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AP endonuclease
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Which enzyme synthesizes the new base in a nucleotide excision repair (nick translation)
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DNA pol I
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Which enzyme seals the nick in nick translation? HOw many ATP equivalents does this use?
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DNA ligase. 2 ATP equivs.
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What is the most common type of distortion in DNA?
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pyrimidine dimers
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What enzyme removes the bases around the DNA distortion in nucleotide excision repair? (In both proks and Euks)
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DNA Helicase
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Which enzyme adds NTs to the area of DNA where the NTs have been removed in DNA excision repair? (In Proks, and in Euks)
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in Proks - DNA pol I
In Euks - DNA pol |
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What is photolyase
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it is a system (not in animals or mammals) that is used for DNA repair of thymine dimers. Uses light energy to excite an electron in a molecule to Produce a flavin radical (FADH*), which is oxidizes the thymine dimer, turning it into two normal, adjacent thymine resides.
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How is an O^6 -methylguanine mutation in DNA repaired?
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An enzyme, O^6-methylguanine DNA Methyltransferase removes the methyl group and adds it to a Cys residue on the protein, inactivating it (the protein can only be used for one mutation)
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what type of DNA repair does O^6-methylguanine DNA Methyltransferase perform on DNA
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Direct Repair
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How is O^6-methylguanine DNA Methyltransferase regulated in the cell?
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The inactive form of the enzyme (with the methyl group bound to the cys resiude) binds to the DNA and activates transcription of the gene that produces O^6-methylguanine DNA Methyltransferase
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