Mmbio Exam 4

Front 1

transition mutation

Back 1

the positions of purines and pyrimidines have not changed

Front 2

transversion mutation

Back 2

if the positions of purines and pyrimidines have changed

Front 3

Ionizing radiation (X-rays, gamma-rays)

Back 3

Causes double-strand breaks, which are particularly sinister
Excites water molecules to form reactive oxygen species such as OH and O2-

Front 4

Agents of DNA damage

Back 4

Ultraviolet (UV) light
Oxidizing agents such as hydroxyl radicals (OH )
Ionizing radiation (X-rays, gamma-rays)
Alkylating agents
Water
DNA polymerase

Front 5

CPD photolyase

Back 5

uses light energy and the FADH- cofactor to split cyclobutane rings and restore the original chemical structure to adjacent pyrimidines. Not found in humans

Front 6

O6 - alkylguanine/O4 - alkylthymine

Back 6

alkylated guanine/thymine from which alkyl transferases can remove the alkyl groups

Front 7

suicide enzyme

Back 7

once it is used, it cannot be used again (alkyl transferases)

Front 8

DNA glycosylase

Back 8

are tuned to detect and remove particular types of damaged bases

Front 9

Ung

Back 9

DNA glycosylase in E coli, removes uracil that has ended up in DNA

Front 10

MutM

Back 10

DNA glycosylase in E coli, removes oxoG

Front 11

AP endonuclease

Back 11

In BER, it removes one or more nucleotides from the abasic strand, resulting in a gap.

Front 12

XP

Back 12

disorder that cannot repair DNA damage caused by UV light

Front 13

Dam

Back 13

a DNA methylase that gradually finds all the new GATC sites, and methylates the ‘A’ site so that mismatch repair can differentiate between the parent and daughter strands.

Front 14

Translesion Synthesis

Back 14

allowing replication to bypass a stalled fork

Front 15

pol IV and pol V

Back 15

can bypass thymine dimers or abasic sites, generally by incorporating random bases to allow Translesion Synthesis

Front 16

POLH

Back 16

human translesion polymerase that can actually polymerize two A's across from a thymine dimer.

Front 17

homologous recombination

Back 17

the swapping of DNA between homologous chromosomes

Front 18

homologous chromosomes

Back 18

chromosomes that are either identical or nearly identical

Front 19

DSB

Back 19

Double-strand break

Front 20

replication fork collapse

Back 20

occurs when a fork encounters a nick in the template DNA

Front 21

RecBCD complex

Back 21

consists of three polypeptides: RecB, RecC, and RecD. Together, they have both 5’-3’ and 3’-5’ exonuclease activities. So they chew up both DNA strands from one end. However, when the complex reaches the sequence GCTGGTGG (a chi site, which occurs far more often than you would expect by random chance in E. coli), the 5’-3’ exo activity is enhanced, resulting in the 3’ extension that is critical for strand invasion.

Front 22

chi site

Back 22

the sequence GCTGGTGG that triggers RecBCD to speed up 5’-3’ exo activity is enhanced, resulting in the 3’ extension that is critical for strand invasion.

Front 23

RecA

Back 23

binds to ssDNA, and scans it across dsDNA until it detects homology. RecA then catalyzes strand exchange

Front 24

strand exchange

Back 24

means it displaces one strand of a double helix and replaces it with the ssDNA

Front 25

RuvABC

Back 25

RuvA is a Holliday junction binding protein. RuvA/RuvB complex drives branch migration
RuvC is a Holliday junction resolvase

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Rad51 and Dmc1

Back 26

are RecA-like proteins active during eukaryotic meiosis

Front 27

MRX complex

Back 27

is functionally similar to the RecBCD complex active during eukaryotic meiosis

Front 28

Spo11

Back 28

during eukaryotic meiosis Spo11 binds to DNA and makes
a double-strand break

Front 29

Site-specific recombination

Back 29

process whereby a single enzyme (or a team of enzymes) catalyzes crossovers at very specific sites

Front 30

Cre

Back 30

Site-specific recombinase enzyme which catalyzes recombination between two sites known as loxP sites.

Front 31

RAG1 and RAG2

Back 31

catalyze the joining of V/D/J segments

Front 32

Non-homologous end-joining (NHEJ)

Back 32

factors that ligate the V and J segments

Front 33

activation-induced cytidine deaminase (AID

Back 33

a specialized protein that selectively mutates the V/D/J region

Front 34

Barbara McClintock

Back 34

she developed the technique for visualizing maize chromosomes and used microscopic analysis to demonstrate many fundamental genetic ideas, including genetic recombination by crossing-over during meiosis

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DDE Transposases

Back 35

Transposases that require aspartate (D) and glutamate (E) residues for their catalytic actvity

Front 36

nonautonomous

Back 36

mutated copy of transposon that relies on other for rep.

Front 37

composite transposition

Back 37

two transposons that usually flank genes

Front 38

replicative transposition

Back 38

create cointegrate, replicate selves, then recombination to resolve cointegrate

Front 39

retro transposition

Back 39

replicative transposons that copy themselves by transcription and reverse transcription, followed by integration in to target DNA

Front 40

non-LTR retrotransposons
and target-primed reverse transcription (TPRT)

Back 40

replicates by being transcribed, inserted, reverse transcribed, then replicated

Front 41

Forward Genetics

Back 41

cause random mutation, look for cool mutants, find gene responsible

Front 42

Reverse Genetics

Back 42

take gene of interest, knock it out, see what mutation results