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biochem > exam 3 > Flashcards

exam 3 Flashcards

1
Q

nucleic acid

A

biopolymer made of monomer units called nucleotides

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2
Q

what are nucleotides?

A
  • nitrogenous base derived from purine or pyrimidine
  • contain: pentose sugar, ribose or deoxyribose, phosphoric acid
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3
Q

difference between dna and rna?

A

no U (uracil) in DNA, no T (thymine) in RNA

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4
Q

nucleotides are linked by what?

A

phosophodiester bond between phosphate group at C-5’ and the OH on the C-3’

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5
Q

T pairs to

A

A

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6
Q

G pairs to

A

C

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7
Q

how many h bonds between t and a?

A

2

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8
Q

how many h bonds between g and c?

A

3

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9
Q

double helix

A

two antiparallel strands are coiled in a right handed manner; structure is based on xray crystallography

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10
Q

histone

A

a protein particularly rich in basic AAs (lys and arg) found in eukaryotic dna

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11
Q

what is chromatin?

A

dna molecules wound around particles of histones in a beadlike structure

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12
Q

structure of chromatin

A

each bead is a nucleosome

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13
Q

each nucleosome consists of

A

DNA wrapped around histone core

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14
Q

RNA

A

pentose unit is ribose
- single stranded (can have double stranded regions)
- pyrimidine base uracil instead of thymine

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15
Q

prokaryotic replication (summarized)

A

separation of 2 original strands and synthesis of 2 new daughter strands using originals as templates

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16
Q

why is replication labelled as semiconservative?

A

b/c each daughter dna contains one template strand and one new one

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17
Q

dna replication steps

A
  • dna unwinds at origin of replication
  • new chains are synthesized in both directions from origin of replication (bidirectional)
  • there are TWO replication forks
  • 1 origin of replication and 2 replication forks in prokaryotes
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18
Q

in dna replication of euks, there are several…

A

origins of replication and two replication forks at each origin

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19
Q

dna polymerase functions have the following requirements:

A

dTTP, dATP, dGTP, dCTP (deoxyribonucleoside triphosphates)
- Mg2+ (cofactor)
- RNA primer

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20
Q

dna polymerase iii is responsible for

A

polymerization

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21
Q

dna polymerase i is responsible for

A

the removal of primer and replacing it with DNA

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22
Q

dna is synthesized in a

A

5’ to 3’ direction

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23
Q

leading strand is synthesized

A

continuously in a 5’ to 3’ direction

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24
Q

lagging strand is synthesized

A

discontinuously (okazaki fragments) in a 5’ to 3’ direction, AWAY from the replication fork

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25
Q

dna polymerase reaction

A
  • the 3’OH group at the end of the growing DNA chain acts as a nucleophile
  • phosphorus adjacent to the sugar is attacked and then added to the growing chain
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26
Q

helicase is

A

a helix-destabilizing protein, promotes unwinding by binding at the replication fork

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27
Q

SSB protein is responsible for

A

stabilizing single stranded regions by binding tightly to them

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28
Q

dna primase purpose

A
  • dna polymerase needs an existing 3’OH
  • RNA serves as a primer in dna replication
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29
Q

primase catalyzes

A

copying of a short stretch of dna template to produce rna primer (~10-20 nucleotides long)

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30
Q

which direction does DNA polymerase 3 synthesize in?

A

5’ to 3’ (thus the reason for the leading and lagging strands)

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31
Q

what are okazaki fragments?

A

produced from lagging strand that is replicated discontinuously

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32
Q

what are okazaki fragments sealed together by?

A

ligas

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33
Q

in prokaryotic dna replication, both dna strands are

A

synthesized concurrently by looping the lagging strand

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34
Q

topoisomerase function

A

relieves supercoiling

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35
Q

topoisomerase introduces

A

a nick in supercoiled dna
- a swivel point is created at the site of the nick
- opens and reseals the swivel point in advance of the replication fork

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36
Q

summary of dna replication in prokaryotes

A
  • dna synthesis is bidirectional
  • dna synthesis is in 5’ to 3’ direction
  • leading strand is formed continuously towards rep fork
  • lagging strand is formed as a series of okazaki fragments glued by ligase later
  • topoisomerase introduces a swivel point in advance of the rep fork
  • helicase binds and promotes unwinding at the rep fork
  • SSB protein protects exposed regions of SS dna and keeps DNA single stranded
  • primase catalyzes the synthesis of RNA
  • synthesis of new DNA strand (catalyzed pol III, RNA primer removed/replaced w/ DNA, DNA ligase seals nicks)
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37
Q

proofreading in dna is

A

the removal of incorrect nucleotides via exonuclease activity to prevent errors (mutations) that can occur every 10^6 to 10^9 base pairs

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38
Q

dna polymerase iii has (x) exonuclease activity

A

3’ to 5’

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39
Q

dna polymerase i has (x) exonuclease activity

A

5’ to 3’ (which is how RNA is removed and replaced with DNA, synthesized simultaneously in same direction)

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40
Q

what do telomeres do?

A
  • at the end of linear chromosomes
  • consist of long stretches of short repeating sequences
  • preserve integrity/stability of chromosomes
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41
Q

telomeres are in

A

eukaryotes

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42
Q

in dna rep in eukaryotes, synthesis at the end of the chromosome is a problem bc…

A

once RNA primer is gone, free 3’-OH group is not available to continue synthesis

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43
Q

telomerase is an

A

enzyme that synthesizes the telomere to fill the gap
- ribonucleoprotein with an RNA that serves as the template for the synthesis of its DNA complement
- reverse transcriptase

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44
Q

dna replication yields….

A

two dna molecules, identical to original one

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45
Q

transcription summary

A

sequences of bases in DNA is recorded as a sequence of complementary bases in a single stranded mRNA molecule

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46
Q

translation summary

A
  • three base codons on the mRNA corresponding to specific AAs direct the sequences of building a protein
  • these codons are recognized by tRNAs carrying AAs
  • ribosomes are the ‘machinery’ for protein synthesis
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47
Q

tRNA transports

A

AAs to site of protein synthesis (small in size)

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48
Q

ribosomal RNA combines

A

with proteins to form ribosomes (site of protein synthesis) - variable in size

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49
Q

mRNA directs

A

AA sequence of protein (variable in size)

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50
Q

small nuclear RNA processes

A

initial mRNA to its mature form in eukaryotes (small in size)

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51
Q

small interfering RNA affects

A

gene expression (small in size)

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52
Q

micro RNA affects

A

gene expression (important in growth and development) - small in size

53
Q

what does mRNA do?

A
  • delivers genetic info from DNA to ribosomes for the synthesis of proteins
  • present in cells in relatively small amounts and very short-lived
  • single stranded
54
Q

tRNA characteristics

A
  • single stranded
  • has double stranded regions
  • clover leaf structure
  • carries an AA at its 3’ end
55
Q

rRNA

A
  • ribonucleic acid found in ribosomes
  • ribosomes consist of 60-65% rRNA and 35-40% protein
  • both proks and euks, ribosomes have 2 subunits
56
Q

transcription overview

A
  • synthesized on DNA template by RNA polymerase
  • DNA template is unchanged
  • requires ATP, GTP, CTP, UTP, Mg2+
  • synthesized in 5’ to 3’ direction
  • DNA base sequence contains signals for initiation and termination of RNA synthesis
57
Q

DNA strand that serves as the template for RNA synthesis is the…

A

template strand

58
Q

transcription steps

A

intiation, elongation, termination

59
Q

what does the promoter sequence do in prokaryotes?

A

promoters are the instructions for the rna polymerase in the form of a dna sequence

60
Q

RNA polymerase in prokaryotes needs to know…

A
  • which strand is the template strand
  • what to transcribe
  • where first nucleotide of gene to be transcribed is
61
Q

first phase of transcription in prokaryotes

A

is initiation

62
Q

what happens during initiation in transcription?

A

rna polymerase binds to a promoter region in the dna
- dna unwinds at promoter to form an open complex (required for chain initiation)

63
Q

after initiation is…

A

chain elongation

64
Q

in chain elongation, after strands separate,

A
  • rna polymerase catalyzes formation of phosphodiester bonds b/w ribonucleotides
  • transcription bubble of 17 bp moves down DNA sequence to be transcribed
65
Q

what does topoisomerase do during chain elongation?

A

relaxes supercoils in front of and behind transcription bubble

66
Q

what is chain termination controlled by?

A

termination sites (characterized by two inverted repeats)

67
Q

what happens to the size of the rna post transcription?

A
  • initial size of rna transcript is greater than final size
  • ONLY occurs in eukaryotes
68
Q

RNA modification includes

A
  • leader sequences at the 5’ end
  • trailer sequences at the 3’ end
69
Q

mRNA modification includes…

A
  • 5’ cap (guanylate residue) that tells ribosomes which end of mRNA to start translating
  • polyadenylate “tail” added to 3’ end to protect mRNA from nucleases and phosphates
70
Q

eukaryotes genes frequently contain intervening base…

A

sequences that don’t appear in the final mRNA

71
Q

exons

A

expressed dna sequences

72
Q

introns

A

intervening dna sequences that aren’t expressed

73
Q

introns are (x) and exons get (y)

A

spliced out, ligated together

74
Q

in the genetic code, a triplet is…

A

a sequences of 3 bases (codon) is needed to specify one AA

75
Q

in the genetic code, universal means

A

the same in viruses, prokaryotes, eukaryotes

76
Q

all 64 codons have

A

assigned meanings

77
Q

how many code for AAs?

A

61

78
Q

termination signals

A

UAA, UAG, UGA

79
Q

start codon

A

AUG (also codes for methionine or met)

80
Q

does transcription occur in prokaryotes?

A

yes and in the cytosol - is coupled to translation

81
Q

amino acids must be activated by…

A

tRNA and aminoacyl-tRNA synthetases

82
Q

what does ATP do in AA activation?

A

provides energy for bond formation of adding AA to tRNA

83
Q

where on the tRNA is the AA added to?

A

3’ end

84
Q

carboxyl group of the AA is

A

linked to the 3’-OH of tRNA

85
Q

where does the polypeptide chain start?

A

N-terminus, ending at C-terminus

86
Q

in prokaryotes, initiation requires

A
  • tRNA fmet anticodon which pairs with AUG in mRNA
  • AUG (initiation codon of mRNA)
  • small ribosomal subunit
  • large ribosomal subunit
  • initiation factors (IFs)
  • GTP, Mg2+
87
Q

what is fmet?

A

modified methionine in which a formaldehyde group has been added to the AA

88
Q

the components of prokaryotic initiation form….

A

the initiation complex

89
Q

how many sites does tRNA use on the ribosome during chain elongation?

A

P (peptidyl), A (aminoacyl), E (exit) sites

90
Q

what does chain elongation require?

A
  • elongation factors
  • GTP and Mg2+
  • enzyme peptidyl trasferase forms peptide bond (e.g. RNA acting as an enzyme)
91
Q

chain termination requires

A

stop codons (UAA, UAG, UGA) of mRNA
release factor (RF)
GTP

92
Q

why is the genetic code redundant?

A

b/c more than one codon can code for the same AA (e.g. Leu, Ser and Arg are coded for by 6 triplets

93
Q

61 different sense codons don’t require…

A

61 diff tRNAs (usually abt ~45)

94
Q

some tRNAs can recognize more than one codon b/c…

A

of variations allowed in H bonding

95
Q

tRNAs contain…

A

inosine that can pair with U, C, or A
- e.g. tRNA carrying phenylalanine matches codons UUU and UUC

96
Q

protein degradation can be caused by

A

subcellular organelles lysosomes, macromolecular structures proteosomes and in euks: ubiquitinylation

97
Q

what is ubiquitinylation?

A

ubiquitinylation becomes bonded to ubiquitin, targeting a protein for destruction

98
Q

what does the 3’-OH at the end of a new DNA chain do?

A
  • acts as a nucleophile
  • phosphorus adjacent to the sugar is attacked and then added to the growing chain
99
Q

dna polymerase iii carries out the…

A

synthesis and linking of new DNA strands

100
Q

RNA primer is removed by….

A

DNA polymerase 1

101
Q

dna is unwound and opened by (x) at the (y) forming a (z)

A

enzyme helicase, origin of replication, replication bubble

102
Q

what enzyme can lay a primer without having a 3’ end present?

A

rna primase

103
Q

what is the main replicating enzyme?

A

dna polymerase iii

104
Q

new strand of dna must be made in the (x) direction

A

5’ to 3’

105
Q

new nucleotides are added to the (x) end?

A

3’ end

106
Q

what takes out the rna primer in the lagging strand?

A

dna polymerase I

107
Q

what shows that dna replication is complete?

A

no rna primers + okazaki fragments are sealed by ligase, making covalent bonds

108
Q

which enzyme carries out transcription?

A

rna polymerase

109
Q

where does transcription take place in eukaryotes?

A

nucleus

110
Q

where does transcription take place in prokaryotes?

A

cytoplasm

111
Q

what does the +1 in the dna strand during transcription mean?

A

start/initiation site for transcription

112
Q

which of the two dna strands is transcribed into the mRNA sequence (template or coding strand)?

A

template strand

113
Q

what is the coding strand?

A

strand with the same “code” sequence as mRNA

114
Q

purpose of the TATA box?

A

region that rna polymerase knows to bind to and start the process of transcription (~10 nucleotides downstream)

115
Q

what is a 5’ cap?

A

methane group added to the 5’ end

116
Q

what is a poly-A tail?

A

AAAAAAA added to 3’ end

117
Q

could translation and transcription occur simultaneously in eukaryotes?

A

no b/c mRNA has to leave nucleus

118
Q

purpose of 3’ poly A tail at ends of mRNA in eukaryotes?

A

not necessary in prokaryotes; prevents the degradation of actual mRNA sequence

119
Q

why would a eukaryotes need a 5’ cap?

A

to allow for the ribosome to know which end of the mRNA to start process of translation

120
Q

which site does the first tRNA bind to first?

A

P-site

121
Q

after the p-site, tRNA moves to…

A

A site

122
Q

what is translocation?

A

tRNA shifting from A site back to P site, and when it no longer is holding an AA, moves to E site to Exit

123
Q

what is an anticodon?

A

3 nucleotides sequence on tRNA that is complementary to mRNA codon

124
Q

if mRNA codon is 5’ CGU 3’, what is the tRNA anticodon?

A

3’ GCA 5’

125
Q

can tRNA be reused?

A

yes

126
Q

can more than one codon code for the same AA?

A

yes

127
Q

what are polyribosomes?

A

many ribosomes attached to 1 mRNA strand
- all of them are making copies of the same protein (making many of the same protein at once)

128
Q

which enzyme binds to transcribes the template strand?

A

RNA polymerase

biochem (11 decks)

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