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biochem 501 > unit 2 exam > Flashcards

unit 2 exam Flashcards

(52 cards)

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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?

22
Q

what happens in deamination?

Study These Flashcards
A

H-bond donor switched to H-bond acceptor

23
Q

what happens in depurination?

Study These Flashcards
A

the entire base is removed

24
Q

what happens in dimerization (UV-induced)?

Study These Flashcards
A

glues stacked pyrimidines

25
how to repair alkylation
alkyl group moved to alkyl transferase enzyme - transferase cannot be used again!
26
how to repair deamination
depurinate problem nucleotide, recognize abasic and repair
27
how to repair dimerization
cut both sides, pol 1 and ligase patch up hole
28
characteristics of homologous recombination
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
characteristics of sequence specific recombination
only occurs at defined sites more predictable and controllable viruses use it to bind to hosts has tyrosine and serine mechanisms
30
how does tyrosine recombinase work?
-OH attacks phosphate backbone, forms a junction, and then reseals
31
how does serine recombinase work?
double strand break, swap strands, reseal
32
characteristics of transposons
mobile genetic element can insert themselves into a gene to inactivate it
33
what is a class I transposon?
retrotransposons copy/paste from one region to another
34
what is a class II transposon?
DNA transposons cut/paste from one region to another
35
characteristics of DNA polymerase
DNA template RNA/DNA primer needed 3'-->5' exonuclease proof reader produces DNA replicates entire genome
36
characteristics of RNA polymerase
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
how do gene promoters work?
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
how does rho dependent termination work?
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
how does rho independent termination work?
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
characteristics of the spliceosome
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
which way does polymerase synthesize?
5'--->3'
42
what happens when primase is halted?
lagging strand stops synthesizing
43
base excision repair
damaged bases removed by glycosylase nucleotide excised by AP endonuclease
44
characteristics of DNA binding proteins
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
requirement for pre-mRNA to undergo splicing by spliceosome
"branch point A" RNA nucleotide
46
eukaryotic translation
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
CRISPR cas-9
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
telomerase
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
RNA characteristics
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
group 2 introns
splicing reaction initiated by internal adenosine produce RNA lariat structure that is excised during splicing
51
group 1 introns
splicing reaction initiated by guanosine cofactor
52
Shine-Delgarno sequence
ribosomal binding site in bacterial mRNA

biochem 501 (4 decks)

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