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

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

Flashcards in Exam 2: Ch 4 -- Translation, DNA Replication, Repair, Recombination, and Viruses Deck (107):
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translation

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

in cytoplasm

2

3 types of RNA used in translation

mRNA

tRNA

rRNA

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mRNA

carries genetic information transcribed from DNA in a linear form

read in sets of 3 nt sequences called codons

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each codon specifies an ...

AA

5

tRNA

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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rRNA

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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post-translational processing

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

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how many codons

64

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how many stop codons

3

UAA, UGA, UAG

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most aas are encoded for by more than one ...

codon

only Met and Trp have a single codon

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which aas have 6 codons

leu, ser, arg

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degenerate

a particular aa can be specified by multiple codons

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start codon

AUG-Met

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reading frame

sequence of codons from start to stop

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aminoacyl-tRNA synthetase

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

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how many tRNAs in bacteria vs eukaryotes

30-40

vs

50-100

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more tRNAs than...

aas

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

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many tRNAs can pair with more than one codon

explains how there are more codons than tRNA

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acceptor stem

3' end of the unlooped aa with sequence CCA

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wobble

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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example of wobble

phenylalanine codon UUU and UUC and recognized by tRNA GAA

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inosine

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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cognate

compatible tRNAs

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aminoacyl-tRNA synthetase rxn

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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how is aminoacylation driven toward activation

hydrolysis of phosphoanhydride bond in released PPi

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how do aminoacyl-tRNA synthetases recognize their cognate tRNAs

interact with anticodon loop and acceptor stem

interact with other regions

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proofreading of aminoacyl-tRNA synthetases

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

ribosome

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rate of elongation by a ribosome

3-5 aa added per second

100-200 aa proteins made in a minute or less

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ribosome structure

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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Svedberg unit

rRNA and ribosomal subunits

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

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tRNAiMet

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

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eukaryotic translation initiation factors (eIFs)

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

34

what is the start codon

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

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Kozak sequence

5'-ACCAUGG-3'

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elongation factor (EF)

proteins that mediate elongation in translation

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translocation

movement of the ribosome one codon at a time along mRNA

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steps of elongation

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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release factor (RF)

2 types

eRF1

eRF3

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eRF1

eukaryotic release factor 1

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

41

eRF3

GTP binding protein that works with eRF1

cleaves peptidyl-tRNA to release the completed protein

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ribosome recycling

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

43

2 factors that increase rate a cell can synthesize a protein

simultaneous translation of a single mRNA by multiple ribosomes

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

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polyribosome

translation of a single mRNA by multiple ribosomes

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

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GTPase superfamily

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

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nonsense mutation

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

forms nonfunctional proteins

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nonsense mutations in E. coli

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

changes anticodon to complement codon of mutated mRNA

48

conservative DNA replication

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

49

semiconservative DNA replication

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

50

primer

short preexisting RNA or DNA strand beginning chain growth

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DNA polymerase

uses a DNA primer to start chain growth

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

5' --> 3' direction

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helicase

enzyme that unwinds parental DNA beginning at replicatino origins

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pimase

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

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replication fork

DNA region where proteins come together to carry out replication

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leading strand

replicated continuously from a single RNA primer in the 5'---> 3' direction

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lagging stand

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

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PCNA

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

known as a sliding clamp

58

daughter strands of DNA grow _________

bidirectionally

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

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ORC

6 subunit protein - orgin recognition comples

binds to each origin and associated with other proteins

60

primary mechanism for regulating DNA replication

controlling initiation

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S-phase cyclin dependent kinase

regulates activation of MCM helicase, which initiates replication

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mutation

change in normal DNA sequence

63

1st line of defense of preventing mutations

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

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point mutation

change in a single base pair in DNA sequence

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missense

point mutation that changes the codon for an aa

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silent mutation

point mutation that does not change aa sequence

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one of the most frequent point mutations

deamination of a cytosine base converts it into uracil

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DNA excision repair system

segment of damaged DNA excised

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

69

most common type of point mutation in humans

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

70

base excision repair

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

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depurination

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

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mismatch excision repair

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

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nt excision repair

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

ex. thymine-thymine dimers are repaired

74

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

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

2 things that cause ds breaks in DNA

ionizing radiation

anti-cancer drugs

76

ds breaks can lead to

gross chromosomal rearrangements

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2 systems to repairs ds breaks

homologous recombination

non homologous end joining (NHEJ)

78

NHEJ

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

can NHEJ join broken ends of different chromosomes together?

yes, leads to translocations

80

BRCA genes participate in what repair system

homologous recombination

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homologous recombination

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

82

DNA recombination in meiosis

regions of homologous chromosomes crossover to create genetic diversity

83

viruses

obligate intracellular parasites

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

84

virion

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

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

4, 200

86

surface of a virion

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

determines host range

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host range

group of cell types a virus can infect

88

bacteriophage

virus that only infects bacteria

89

poliovirus affects cells in the

intestine

motor neurons in spinal cord causing paralysis

90

HIV-1 affects...

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

neurons and glia

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capsid

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

nucleocapsid

capsid + enclosed nucleic acid

93

how is the nucleocapsid arranged

helical structure in a groove inside a protein tube - rodlike

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

94

envelope

external membrane covering the nucleocapsid

phospholipid bilayer and a few viral glycoproteins

95

plaque assay

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

when does a plaque develop

when a single virion infects a single cell

virus replicates and then lyses the cell to release progeny virions

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virus clone

the progeny virions in a plaque

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lytic cycle

adsorption

penetration

replication

assembly

release

99

lytic cycle: adsorption

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

100

lytic cycle: penetration

viral genome crosses plasma membrane

viral proteins inside capsid can also enter in some cases

101

lyric cycle: replication

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

lytic cycle: assembly

viral proteins and replicated genomes associate to form progeny virions

103

lytic cycle: release

infected cell is lysed or disintegrates gradually

104

rabies

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

105

temperate phages

establish nonlytic association with a host cell that does not kill

106

lysogeny

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

part of temperate phages

107

retroviruses

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

RNA genome is a template for forming DNA by reverse transcriptase