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biochem 501 > unit 2 exam > Flashcards

unit 2 exam Flashcards

1
Q

where are bases located in DNA?

A

on the inside of the helix

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2
Q

B-form DNA

A

asymmetric, major and minor grooves, major groove accessible to proteins

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3
Q

Z-form

A

left handed helix, Hoogstein base pairs, one base in syn formation and one in anti

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4
Q

A-form

A

RNA-RNA or RNA-DNA interactions

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5
Q

difference between RNA and DNA sugar

A

RNA has a 2’ OH and DNA does not

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6
Q

what affects melting points of DNA?

A

longer DNA fragment = higher Tm
more A-T pairs, less C-G pairs = lower Tm

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7
Q

what does topoisomerase do?

A

cuts DNA to decrease Lk

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8
Q

key points of topology

A

Lk = Tw + Wr
natural twist = #bp/10.4
Tw = -Wr is most favorable
highly supercoiled DNA moves faster in gel electrophoresis

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9
Q

key points of acetylation

A

added by enzymes called Histone Acetyl Transferases (HATs)
makes DNA more accessible
stimulates transcription
reversible!

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10
Q

process for compacting DNA

A

DNA –wound around histone–> nucleosome –compressed to 30nm fiber–> chromosome

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11
Q

heterochromatin

A

inaccessible
histone methylation

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12
Q

euchromatin

A

accessible
histone acetylation

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13
Q

purpose of S-methylcytosine

A

silences gene expression

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14
Q

how is the STOP codon different from other codons

A

it is recognized by a protein rather than W-C-F base pairing with tRNA

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15
Q

what catalyzes peptide bond formation in rRNA

A

the protein component

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16
Q

what is being copied in RNA translation?

A

The coding strand

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17
Q

what is necessary for group 1 introns to carry out splicing functions

A

a free guanosine nucleotide cofactor to perform first step of splicing

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18
Q

function of DNA pol III

A

workhorse polymerase

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19
Q

function of DNA pol I

A

handyperson polymerase

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20
Q

what is the opening enzyme?

A

helicase

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21
Q

what is the primer?

A

primase

22
Q

what happens in deamination?

A

H-bond donor switched to H-bond acceptor

23
Q

what happens in depurination?

A

the entire base is removed

24
Q

what happens in dimerization (UV-induced)?

A

glues stacked pyrimidines

25
Q

how to repair alkylation

A

alkyl group moved to alkyl transferase enzyme
- transferase cannot be used again!

26
Q

how to repair deamination

A

depurinate problem nucleotide, recognize abasic and repair

27
Q

how to repair dimerization

A

cut both sides, pol 1 and ligase patch up hole

28
Q

characteristics of homologous recombination

A

can be used to repair double strand breaks
uses 3’ overhangs on DNA to sample for base pairing interactions
can occur between ANY two homologous species
requires 5’ –> 3’ exonuclease

29
Q

characteristics of sequence specific recombination

A

only occurs at defined sites
more predictable and controllable
viruses use it to bind to hosts
has tyrosine and serine mechanisms

30
Q

how does tyrosine recombinase work?

A

-OH attacks phosphate backbone, forms a junction, and then reseals

31
Q

how does serine recombinase work?

A

double strand break, swap strands, reseal

32
Q

characteristics of transposons

A

mobile genetic element
can insert themselves into a gene to inactivate it

33
Q

what is a class I transposon?

A

retrotransposons
copy/paste from one region to another

34
Q

what is a class II transposon?

A

DNA transposons
cut/paste from one region to another

35
Q

characteristics of DNA polymerase

A

DNA template
RNA/DNA primer needed
3’–>5’ exonuclease proof reader
produces DNA
replicates entire genome

36
Q

characteristics of RNA polymerase

A

DNA template
no primer needed
no exonuclease to proof read
produces RNA
only replicates part of genome
transcription begins by melting the DNA
RNA holds on to coding and template strand during transcription

37
Q

how do gene promoters work?

A

10 or 35 nucleotides back from start site
tell the polymerase to start transcription
recognized in prokaryotes by sigma factor of RNA polymerase
specify which strand of DNA will be used as template

38
Q

how does rho dependent termination work?

A

the polymerase transcribes a binding site for rho factor
the rho factor is a helicase that translates from binding site to 3’ end
the helicase unwinds the DNA/RNA hybrid and RNA peels off

39
Q

how does rho independent termination work?

A

polymerase transcribes through a G/C rich region to produce a hairpin structure
the hairpin causes a stall
a U rich segment downstream has weaker base pairing with the template strand and the RNA falls off

40
Q

characteristics of the spliceosome

A

made up of protein AND RNA components
an RNA lariat structure is excised during splicing
splicing is a process thought to be evolutionarily related to splicing by group II introns

41
Q

which way does polymerase synthesize?

A

5’—>3’

42
Q

what happens when primase is halted?

A

lagging strand stops synthesizing

43
Q

base excision repair

A

damaged bases removed by glycosylase
nucleotide excised by AP endonuclease

44
Q

characteristics of DNA binding proteins

A

sequences read through H-bonding between protein side chains and nucleobases
part of protein that binds DNA can often be separated from part that activates transcription
typically involve interaction with major groove of B-form DNA

45
Q

requirement for pre-mRNA to undergo splicing by spliceosome

A

“branch point A” RNA nucleotide

46
Q

eukaryotic translation

A

occurs outside nucleus and separate from transcription
involves assembly of initiation complex mediated by 5’m7G cap and 3’ poly A tail of mRNA
can be regulated to control when and where mRNAs are translated into protein inside the cell

47
Q

CRISPR cas-9

A

locates specific locations in genome using guide RNA molecule
induces double strand breaks at sequences it is programmed to recognize
discovered as part of bacterial immune system to fight against phage

48
Q

telomerase

A

responsible for synthesis of telomeres on chromosomes
carries own RNA primer to template DNA synthesis at ends of telomeres
prevents shortening of lagging strand of DNA after replication

49
Q

RNA characteristics

A

can base pair with DNA to form A-form double stranded structures
can fold into 3D shapes to perform basic function in cell
not typically double-stranded in cells

50
Q

group 2 introns

A

splicing reaction initiated by internal adenosine
produce RNA lariat structure that is excised during splicing

51
Q

group 1 introns

A

splicing reaction initiated by guanosine cofactor

52
Q

Shine-Delgarno sequence

A

ribosomal binding site in bacterial mRNA

biochem 501 (4 decks)

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