exam 2

how do mutations arise?

by chance through errors in DNA synthesis or through chemical modifications/interactions with DNA

Natural selection acts on…

pre-existing genetic variation

What does replication fidelity rely on?

complementary base pairing, proofreading by 3’→5’ exonucleolytic activity, mismatch repair mechanism

Are the hydrogen bonding strengths strong?

no; only predicted to give 3 kcal/mol energy difference between correct and incorrect pairing

How does proofreading the nucleotides work?

DNA polymerases reread the nucleotides that they’ve just inserted, and if it detects a mismatch, it excises the wrong nucleotide and adds in the correct one

What mechanism helps improve fidelity after DNA synthesis?

Mismatch repair mechanism

How does the mismatch repair mechanism work?

improper base pairing leads to distortion in helix, enzymes look for the bulges that show that there’s improper base pairing, bad nucleotide gets excised and replaced with the correct one

How do we determine which of the nucleotides is the wrong one with the mismatch repair mechanism?

the parental strand has a methylation modification which allows us to distinguish it from the new strand; the strand without the methylation gets identified as the one with the incorrect base

Given our three methods to ensure DNA fidelity, what does the overall error rate turn out to be?

<1 in 10^9

What are the three potential consequences of mutations?

neutral, deleterious, advantageous

What can we classify the major groupings of mutations as being?

Single base substitution and single base insertion/deletion (indel)

What are the single base substitutions?

silent mutation, missense mutations, nonsense mutation

silent mutation

codes for the same amino acid so no changes in function

missense mutations

codes for a different amino acid; divided into conservative and non-conservative

What is a conservative missense mutation?

amino acid gets swapped with another amino acid with similar chemistry (aka pos charge to pos charge); generally less consequences on the functionality of the protein as a result

What is a non-conservative missense mutation?

amino acid switched to one with different chemistry (aka polar to nonpolar), which will likely have a consequence on protein functionality

nonsense mutation

amino acid switches to stop codon, which prematurely ends translation and creates bad truncated proteins (AKA very BAD)

What’s another way of referring to single-base indels?

frameshifts

How do indel mutations work?

a quantity of bases that is not a multiple of three is either inserted or deleted, which causes all the amino acids from that point of the DNA on to code for the wrong amino acids

What is the Luria and Delbruck fluctuation test?

When E. coli are infected with a bacteriaphage (virus), almost all die, but a few harbor a mutation that makes them resistant. Is the mutation preexisting (spontaneous) or was it induced by the bacteriaphage?