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Cellular and Molecular Biology > Exam 2: Ch 4 -- Translation, DNA Replication, Repair, Recombination, and Viruses > Flashcards

Exam 2: Ch 4 -- Translation, DNA Replication, Repair, Recombination, and Viruses Flashcards

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1
Q

translation

A

process where nt sequence of mRNA is used as a template to join aas in a pp chain in the correct order

in cytoplasm

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2
Q

3 types of RNA used in translation

A

mRNA

tRNA

rRNA

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3
Q

mRNA

A

carries genetic information transcribed from DNA in a linear form

read in sets of 3 nt sequences called codons

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4
Q

each codon specifies an …

A

AA

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5
Q

tRNA

A

deciphers codons in mRNA

each aa has its own subset of tRNAs, which bind the aa and carry it to the growing end of the pp

contains anticodon that base-pairs with the complementary codon in mRNA

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6
Q

rRNA

A

associates with a set of proteins to form ribosomes

move along an mRNA to catalyze assembly of aas into proteins

large and small subunit

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7
Q

post-translational processing

A

pp chain undergoes additional folding, modifications, and association with other pps

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8
Q

how many codons

A

64

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9
Q

how many stop codons

A

3

UAA, UGA, UAG

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10
Q

most aas are encoded for by more than one …

A

codon

only Met and Trp have a single codon

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11
Q

which aas have 6 codons

A

leu, ser, arg

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12
Q

degenerate

A

a particular aa can be specified by multiple codons

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13
Q

start codon

A

AUG-Met

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14
Q

reading frame

A

sequence of codons from start to stop

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15
Q

aminoacyl-tRNA synthetase

A

catalyze chemical linkage between a tRNA and its aa forming an aminoacyl-tRNA

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16
Q

how many tRNAs in bacteria vs eukaryotes

A

30-40

vs

50-100

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17
Q

more tRNAs than…

A

aas

so many aas have more than 1 tRNA they can bind to

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18
Q

many tRNAs can pair with more than one codon

A

explains how there are more codons than tRNA

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19
Q

acceptor stem

A

3’ end of the unlooped aa with sequence CCA

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20
Q

wobble

A

unstandard pairing between bases

3rd base in mRNA codon and first base in tRNA anticodon

ex. antibodon with G in first (wobble) position on tRNA can pair with C or U in 3rd position on mRNA

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21
Q

example of wobble

A

phenylalanine codon UUU and UUC and recognized by tRNA GAA

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22
Q

inosine

A

deaminated product of adenine

found in tRNA wobble position and can recognize mRNA codons with A, C, or U in the 3rd wobble position

4/6 codons for Leu are recognized by tRNA with anticodon 3’-GAI-5’ b/c of inosine

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23
Q

cognate

A

compatible tRNAs

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24
Q

aminoacyl-tRNA synthetase rxn

A

aa linked to tRNA by a high-engergy bond and is said to be “activated”

energy of this bond drives formation of peptide bonds

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25
Q

how is aminoacylation driven toward activation

A

hydrolysis of phosphoanhydride bond in released PPi

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26
Q

how do aminoacyl-tRNA synthetases recognize their cognate tRNAs

A

interact with anticodon loop and acceptor stem

interact with other regions

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27
Q

proofreading of aminoacyl-tRNA synthetases

A

checks fit in aa binding pocket

if wrong aa, bound synthetase catalyzes removal of aa from tRNA

error rate in E. coli is 1/50,000 codons

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28
Q

the ______ is the most abundant RNA-protein complex in the cell

A

ribosome

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29
Q

rate of elongation by a ribosome

A

3-5 aa added per second

100-200 aa proteins made in a minute or less

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30
Q

ribosome structure

A

3 (bacteria) or 4 (eukaryotic) different rRNA molecules and up to 83 proteins

2 subunits

small subunit has 1 molecule of rRNA

large subunit has 1 molecule of large rRNA and 5.8s rRNA

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31
Q

Svedberg unit

A

rRNA and ribosomal subunits

measure of the sedimentation rate of macromolecules centrifuged under standard conditions (a measure of size)

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32
Q

tRNAiMet

A

binds at appropraite site on small ribosomal subunit (P site) to begin synthesis of a pp chain

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33
Q

eukaryotic translation initiation factors (eIFs)

A

mediate small and large ribosomal subunits assembling around an mRNA that has an activated initiator tRNAiMet positioned at start codon of P site

bind GTP and hydrolysis to GDP functions as proofreading

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34
Q

what is the start codon

A

first AUG (Met) downstream from the 5’ end in mRNA

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35
Q

Kozak sequence

A

5’-ACCAUGG-3’

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36
Q

elongation factor (EF)

A

proteins that mediate elongation in translation

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37
Q

translocation

A

movement of the ribosome one codon at a time along mRNA

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38
Q

steps of elongation

A

tRNAiMet attached to P site, new tRNA attaches to A site and GTP hydrolyzed to GDP

3’ end of tRNA in A site is close to 3’ end of tRNAiMet and a peptidyltransferase rxn is catalyzed by large rRNA subunit

ribosome translocates and empty tRNA moved to E site and tRNA with pp chain moved from A site to P site

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39
Q

release factor (RF)

A

2 types

eRF1

eRF3

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40
Q

eRF1

A

eukaryotic release factor 1

looks like a tRNA and binds A site when it reaches stop codon

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41
Q

eRF3

A

GTP binding protein that works with eRF1

cleaves peptidyl-tRNA to release the completed protein

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42
Q

ribosome recycling

A

post-termination complex is bound to ABCE1, which uses ATP hydrolysis energy to separate the ribosomal subunits and release mRNA

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43
Q

2 factors that increase rate a cell can synthesize a protein

A

simultaneous translation of a single mRNA by multiple ribosomes

rapid recycling of ribosomal subunits after they disengage from the 3’ end of an mRNA

44
Q

polyribosome

A

translation of a single mRNA by multiple ribosomes

forms circle-like structure, where finished ribosomes start process again quickly

45
Q

GTPase superfamily

A

switch proteins that cycle between GTP-bound active form and GDP-bound inactive form

hydrolysis of GTP causes a conformational change

used in initiation, elongation, and translocation

46
Q

nonsense mutation

A

inactivates a gene by changing a base pair in a normal codon to the stop codon

forms nonfunctional proteins

47
Q

nonsense mutations in E. coli

A

can be suppressed by a second nonsense mutation in a tRNA gene

changes anticodon to complement codon of mutated mRNA

48
Q

conservative DNA replication

A

2 daughter strands form a new dsDNA and parental dsDNA remains intact

49
Q

semiconservative DNA replication

A

parental strands permanently separated and each forms a dsDNA with the daughter strand base-paired to it

50
Q

primer

A

short preexisting RNA or DNA strand beginning chain growth

51
Q

DNA polymerase

A

uses a DNA primer to start chain growth

adds deoxynucleotides to free hydroxyl group at 3’ end of primer

5’ –> 3’ direction

52
Q

helicase

A

enzyme that unwinds parental DNA beginning at replicatino origins

53
Q

pimase

A

a special RNA polymerase that forms a short RNA primer to the unwound template strands

54
Q

replication fork

A

DNA region where proteins come together to carry out replication

55
Q

leading strand

A

replicated continuously from a single RNA primer in the 5’—> 3’ direction

56
Q

lagging stand

A

a new primer is needed every few hundred bases and is elongated discontinuously in Okazaki fragments

57
Q

PCNA

A

homotrimeric protein that has a central hole that daughter dsDNA passes through

known as a sliding clamp

58
Q

daughter strands of DNA grow _________

A

bidirectionally

two replication forks assemble at the same origin and move in opposite directionss

59
Q

ORC

A

6 subunit protein - orgin recognition comples

binds to each origin and associated with other proteins

60
Q

primary mechanism for regulating DNA replication

A

controlling initiation

61
Q

S-phase cyclin dependent kinase

A

regulates activation of MCM helicase, which initiates replication

62
Q

mutation

A

change in normal DNA sequence

63
Q

1st line of defense of preventing mutations

A

DNA polymerase itself

3’ –> 5’ exonuclease activity of some DNA polymerases

polymerase pauses, 3’ end of growing chain transferred to exonuclease site and incorrect base is removed

64
Q

point mutation

A

change in a single base pair in DNA sequence

65
Q

missense

A

point mutation that changes the codon for an aa

66
Q

silent mutation

A

point mutation that does not change aa sequence

67
Q

one of the most frequent point mutations

A

deamination of a cytosine base converts it into uracil

68
Q

DNA excision repair system

A

segment of damaged DNA excised

gap filled by DNA polymerase and ligase using complementary DNA as a template

69
Q

most common type of point mutation in humans

A

C to T caused by deamination of 5-methyl C to T

70
Q

base excision repair

A

problem is recognizing which is the mutant DNA strand to make a repair

DNA glycosylase flips thymine out of helix then hydrolyzes the bond creating an AP (apruinic) site using endonuclease

DNA polymerase replaces missing base and ligase fills gap

occurs before DNA replicatino

71
Q

depurination

A

loss of guanine or adenine from DNA resulting from hydrolysis of glycosylic bond

72
Q

mismatch excision repair

A

eliminates base-pair mismatches and insertions or deletions of one or a few nts accidentally introduced by DNA polymerase

must determine which strand is the mutant strand

occurs after DNA replication

73
Q

nt excision repair

A

fix DNA regions containing chemically modified bases (chemical adducts) that distort the normal shape of DNA locally

ex. thymine-thymine dimers are repaired

74
Q

why is DNA damage in higher eukaryotes repaired much faster in regions of the genome being actively transcribed

A

shared subunits in transcription and DNA repair (transcription-coupled repair)

RNA polymerase is stalled at a lesion on DNA, protein CSB is recruited to RNA polymerase which opens the helix and TFIIH fixes it

75
Q

2 things that cause ds breaks in DNA

A

ionizing radiation

anti-cancer drugs

76
Q

ds breaks can lead to

A

gross chromosomal rearrangements

77
Q

2 systems to repairs ds breaks

A

homologous recombination

non homologous end joining (NHEJ)

78
Q

NHEJ

A

error-prone dominant mechanism for repairing ds breaks

rejoin nonhomologous ends of 2 DNA molecules

results in loss of several base pairs at joining point

could form mutagenic deletions

79
Q

can NHEJ join broken ends of different chromosomes together?

A

yes, leads to translocations

80
Q

BRCA genes participate in what repair system

A

homologous recombination

81
Q

homologous recombination

A

damaged sequence is copied from an undamaged copy of the same chromosome of a diploid organism, or sister chromatid

82
Q

DNA recombination in meiosis

A

regions of homologous chromosomes crossover to create genetic diversity

83
Q

viruses

A

obligate intracellular parasites

use a host cell’s machinery to synthesize viral proteins and to replicate the viral genome

84
Q

virion

A

infectious virus particle

consists of nucleic acid and an outer shell of protein that both protects the viral nucleic acid and functions in the process of host-cell infection

85
Q

simplest viruses contain only enough RNA/DNA to code for ___ proteins, while the most complex can code ___ proteins

A

4, 200

86
Q

surface of a virion

A

contains many copies of 1 type of protein that binds specifically to a receptor protein on a host cell

determines host range

87
Q

host range

A

group of cell types a virus can infect

88
Q

bacteriophage

A

virus that only infects bacteria

89
Q

poliovirus affects cells in the

A

intestine

motor neurons in spinal cord causing paralysis

90
Q

HIV-1 affects…

A

cells essential for the immune response called CD4+ T-lymphocytes - causes AIDS

neurons and glia

91
Q

capsid

A

protein coat the encloses the nucleic acid of virion

composed of multiple copies of 1 protein of a few different proteins coded by a single viral gene

92
Q

nucleocapsid

A

capsid + enclosed nucleic acid

93
Q

how is the nucleocapsid arranged

A

helical structure in a groove inside a protein tube - rodlike

icosahedron solid - spherical object build of 20 faces of equilateral triangles (head)

94
Q

envelope

A

external membrane covering the nucleocapsid

phospholipid bilayer and a few viral glycoproteins

95
Q

plaque assay

A

number of infectious viral particles in a sample

culture dilute sample of viral particles on a plate covered with host cells

count number of local lesions (plaques)

96
Q

when does a plaque develop

A

when a single virion infects a single cell

virus replicates and then lyses the cell to release progeny virions

97
Q

virus clone

A

the progeny virions in a plaque

98
Q

lytic cycle

A

adsorption

penetration

replication

assembly

release

99
Q

lytic cycle: adsorption

A

virion binds multiple copies of capsid protein to specific receptors on cell surface

100
Q

lytic cycle: penetration

A

viral genome crosses plasma membrane

viral proteins inside capsid can also enter in some cases

101
Q

lyric cycle: replication

A

viral mRNAs are produced with the aid of host cell machinery (DNA virus) or viral enzymes (RNA virus)

mRNAs translated by host cell machinery

102
Q

lytic cycle: assembly

A

viral proteins and replicated genomes associate to form progeny virions

103
Q

lytic cycle: release

A

infected cell is lysed or disintegrates gradually

104
Q

rabies

A

virion adsorbed by endocytosis and release of progeny virions occurs by budding from plasma membrane

105
Q

temperate phages

A

establish nonlytic association with a host cell that does not kill

106
Q

lysogeny

A

integrated viral DNA (prophage) is replicated as part of the cell’s DNA from one generation to the next

part of temperate phages

107
Q

retroviruses

A

enveloped viruses with a genome consisting of 2 identical strands of RNA

RNA genome is a template for forming DNA by reverse transcriptase

Cellular and Molecular Biology (34 decks)

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