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MCB3020 > Exam 2 > Flashcards

Exam 2 Flashcards

1
Q

transcription

A

the synthesis of RNA complementary to a DNA template

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2
Q

translation

A

the ribosomal synthesis of proteins based on triplet codons present in mRNA

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3
Q

messenger RNA, or mRNA

A

an RNA molecule that encodes a protein

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4
Q

RNA polymerase

A

an enzyme that produces an RNA complementary to a template DNA strand

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5
Q

RNA products of transcription in bacteria can be

A

monocistronic or polycistronic

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6
Q

Core polymerases

required for the elongation phase

A

αI, αII, β, β’, ω

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7
Q

In bacteria, the RNA polymerase is made up of

A

Core polymerase and sigma factor

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8
Q

holoenzyme

A

the core polymerase and sigma factor when together

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9
Q

sigma factor

A

helps the core enzyme detect the promoter, which signals the beginning of the gene. A single bacterial species can make several

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10
Q

“housekeeping” sigma factor in Escherichia coli

A

sigma-70

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11
Q

promoter

A

a noncoding DNA regulatory region immediately upstream of a structural gene that is needed for transcription initiation

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12
Q

sigma-70

what does it do

A

recognizes consensus sequences at the -10 and -35 positions, relative to the start of the RNA transcript (+1). Keeps essential genes and pathways operating

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13
Q

phases of transcription

A

initiation, elongation, termination

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14
Q

initiation of transcription

A

RNA pol holoenzyme binds to the promoter followed by melting of the helix and synthesis of the first nucleotide of the RNA

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15
Q

elongation of transcription

A

sequential addition of ribonucleotides from nucleoside triphosphates (the RNA chain is extended)

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16
Q

termination of transcription

A

RNA pol detaches from the DNA after the transcript is made

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17
Q

RNA polymerase holoenzyme forms a loosely bound ____ with DNA

initiation of transcription

A

closed complex

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18
Q

the closed complex must become an open complex through

initiation of transcription

A

the unwinding of one helical turn

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19
Q

RNA polymerase in the open complex becomes ____ to DNA to begin transcription

initiation of transcription

A

tightly bound

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20
Q

the first ribonucleoside triphosphate of the new RNA chain is

initiation of transcription

A

usually a purine (A or G)

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21
Q

the original RNA polymerase continues to move along the template, synthesizing RNA at

elongation of transcription

A

~45 bases/sec

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22
Q

the unwinding of DNA ahead of the moving complex forms a

elongation of transcription

A

17-bp transcription bubble

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23
Q

positive supercoils ahead are removed by

elongation of transcription

A

DNA topoisomerases

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24
Q

all bacterial genes use one of two known transcription termination signals:

A

Rho-dependent and Rho-independent

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25
Q

Rho-dependent

A

relies on a protein called Rho and a strong pause site at the 3’ end of the gene

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25
Q

Rho-independent

A

requires a GC-rich region of RNA, as well as 4-8 consecutive U residues

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25
Q

Rifamycin B

effect on transcription

A

selectively binds to the bacterial RNA pol and inhibits transcription initiation

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25
Q

antibiotics

fundamental criteria

A

must kill or retard the growth of a pathogen, and they must not harm the host - selectivity

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25
Q

Actinomycin D

effect on transcription

A

nonselectively binds to DNA and inhibits transcription elongation

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26
Q

RNA differences to DNA

A
  • usually single-stranded
  • contains ribose sugar
  • uracil replaces thymine
  • often folds back on itself to form complex hairpins and other secondary structures
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26
Q

RNA stability is measured

A

in terms of half-life

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26
Q

average half-life of mRNA

A

1-3 minutes

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27
Q

rRNA (ribosomal RNA)

A

an RNA molecule that includes the scaffolding and catalytic components of ribosomes

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28
Q

tRNA (transfer RNA)

A

an RNA that carries an amino acid to the ribosome. The anticodon on the tRNA base-pairs with the codon on the mRNA. Shaped like a clover leaf (in 2D) and a boomerang (in 3D)

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29
Q

sRNA (small RNA)

A

a non-protein-coding regulatory RNA molecule that modulates translation or mRNA stability; can base-pair with target mRNA or other RNA sequences; 100-200 nucleotides; encoded by intergenic sequences

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30
Q

tmRNA (transfer messenger RNA)

A

a molecule resembling both tRNA and mRNA that rescues ribosomes stalled on damaged mRNAs lacking a stop codon

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31
Q

catalytic RNA

A

also called ribozyme. An RNA molecule that is capable of catalyzing reactions

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32
Q

central dogma

A

theory stating that genetic information flows only in one direction, from DNA, to RNA, to protein, or RNA directly to protein. RNA viruses can use reverse transcriptase to make DNA from RNA

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33
Q

codons

A

nucleotide triplets. An mRNA molecule can be thought of a sentence and codons represent individual words, or amino acids

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34
Q

there are __ possible codons

A
  • there are 64 possible codons
  • 61 specify amino acids (includes the start codons)
  • 3 are stop codons
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35
Q

functional regions of tRNA:

A

anticodon and 3’ (acceptor) end

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36
Q

anticodon

A

hydrogen bonds with the mRNA codon
specifying an amino acid

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37
Q

3′ (acceptor) end

A

binds the amino acid

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38
Q

aminoacyl-tRNA synthetase

A

an enzyme that condenses a specific amino acid with the 3’ OH group of the correct tRNA, thereby charging the tRNA

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39
Q

each cell has ____ aminoacyl t-RNA synthetases

A

20, one for each amino acid

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40
Q

each aminoacyl t-RNA synthetase must

A

recognize its own tRNA but not bind to any other tRNA. Each tRNA has its own set of interaction sites that match only the proper synthetase

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41
Q

ribosome

A

a large enzyme, composed of RNA and protein subunits, that translates mRNA into protein

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42
Q

ribosomal subunits

A

30S (small subunit) and 50S (large subunit) and combine to form the 70S ribosome

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43
Q

70S ribosome binding sites

A

A (acceptor) site, P (peptidyl-tRNA) site, and E (exit) site

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44
Q

A (acceptor) site

A

the region of a ribosome that binds an incoming charged tRNA

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45
Q

P (peptidyl-tRNA) site

A

the region of a ribosome that contains the growing protein attached to a tRNA

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45
Q

E (exit) site

A

the region of a ribosome that holds the uncharged, exiting tRNA

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45
Q

peptidyltransferase

A

a ribozyme that catalyzes the formation of peptide bonds. Part of the 23S rRNA of the large ribosomal subunit

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46
Q

____ rRNA serves as a molecular clock

A

16S. Genes for ribosomal RNA are highly conserved in many different species due to their slow rate of undergoing mutations

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47
Q

Shine-Dalgarno sequence

A

(ribosome-binding site). In bacteria, a stretch of nucleotides upstream of the start codon in an mRNA that hybridizes to the 16S rRNA of the ribosome, correctly positioning the mRNA for translation.

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48
Q

the Shine-Dalgarno sequence is located _ of the start codon in Escherichia coli

A

4-8 bases upstream

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49
Q

start codons

A

AUG (90%), GUG (8.9%), UUG (1%). Code for N-formyl-methionyl-tRNA (fMet-tRNA)

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50
Q

Streptomycin

effect on translation

A

inhibits 70S ribosome formation

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51
Q

Tetracycline

effect on translation

A

inhibits aminoacyl-tRNA binding to the A site

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52
Q

Chloramphenicol

effect on translation

A

inhibits peptidyltransferase

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53
Q

Erythromycin

effect on translation

A

causes abortive translocation

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54
Q

translocation

A

the energy-dependent movement of a ribosome to the next triplet codon along an mRNA

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55
Q

coupled transcription and translation

A

ribosomes will bind to the 5’ end of the mRNA and begin translating protein before RNA polymerase has even finished making an mRNA molecule

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56
Q

coupled transcription and translation occurs near __

A

the nucleoid

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57
Q

translation of fully transcribed mRNA occurs at __

A

the cell poles

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58
Q

polysome

A

once a ribosome begins translating mRNA and moves beyond the ribosome-binding site, another ribosome can immeditaly jump onto that site. Closely packed and arranged helically along mRNA

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59
Q

step after translation for many proteins

A

a protein must be modified after translation to achieve an approriate 3D structure or to regulate its activity

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60
Q

a healthy cell “cleans house”

A

by degrading damaged or unneeded proteins by specific devices such as proteases or proteasomes

61
Q

N-formyl group

protein structure modification after translation

A

may be removed by methionine deformylase to leave just methionine on the polypeptide. This can escape immunorecognition because fMet peptides are produced only be bacteria and mitochondria

62
Q

addition of phosphoryl or methyl groups

protein structure modification after translation

A

can change the activity of signal transduction

63
Q

adenylation

protein structure modification after translation

A

covalent attachment of adenosine 5’ monophosphate, can regulate the activity of enzymes such as glutamine synthetase

64
Q

acetylation

protein structure modification after translation

A

can serve multiple functions, including protein stabilization and regulation of protein activity

65
Q

lipidation

protein structure modification after translation

A

covalent attachment of lipids to proteins and provides hydrophobic tail that anchors lipoproteins to the cytoplasmic membrane or to the outer membrane in Gram-negative organisms

66
Q

glycosylation

protein structure modification after translation

A

covalent addition of monosaccharides or polysaccharides to generate glycoprotein

67
Q

mass spectrometry

A

an analytical technique that measures the mass of molecules and to assess posttranslational modifications. Molecules are ionized and sorted according to their mass-to-charge (m/z) ratio

68
Q

chaperones

A

a protein that helps other proteins fold into their correct tertiary structure

69
Q

heat-shock proteins (HSPs)

A

name of original chaperones. A chaperone protein whose synthesis is induced by a high-temperature stress. More resistant to heat denaturation than the average protein is

70
Q

trigger factor (TF)

A

acts as a ribosome-associated chaperone and is the first chaperone to interact with nascent polypeptide

71
Q

GroEL structure

A

forms a stacked ring structure with a hollow center

72
Q

GroES structure

A

cap-like structure that fits over one end of GroEL

73
Q

GroEL and GroES complex

A

facilitate protein folding; protein enters central cavity of GroEL, and the GroES cap helps create a controlled environment for folding

74
Q

DnaK and DnaJ complex

A

do not form rings, act as clamp-like chaperones

75
Q

DnaK

A

also known as Hsp70, can bind to exposed hydrophobic regions on unfolding or misfolded proteins, preventing their aggregation and assisting in proper folding

76
Q

DnaJ

A

often works with DnaK, helps recruit substrates and regulate DnaK’s ATPase activity

77
Q

degrons

A

degradation signal in many normal proteins that dictate the stability of a protein

78
Q

N-terminal rule

A

type of degron; tendency of the N-terminal amino acid (leucine, phenylalanine, tryptophan, or tyrosine) of a protein to influence protein stability; cleaved by ClpAP protease

79
Q

protease

A

enzyme that catalyzes proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurring the formation of new protein products.

80
Q

N-terminal signal sequences

A

a specific amino acid sequence on the amino terminus of proteins that directs them to the endoplasmic reticulum (of a eukaryote) or the cell membrane (of a prokaryote)

81
Q

signal recognition particle (SRP)

A

a receptor that recognizes the signal sequence of peptides undergoing translation. The complex attaches to the cell membrane of prokaryates (or rough ER of eukaryotes), where it docks the protein-ribosome complex to the membrane for protein membrane insertion or secretion

82
Q

FtsY

A

shuttles the complex delivered by SRP to the transmembrane SecYEG secretion machinery (translocon)

83
Q

SecA-dependent general secretion pathway

A

common mechanism in bacteria for translocating certain proteins from the cytoplasm to the periplasm. Essential for proper localization of periplasmic proteins

84
Q

SecB

A

piloting protein that captures the completed pre-secretion protein and prevents aggregationg and misfolding

85
Q

SecA

A

takes pre-secretion protein from SecB; is an ATPase associated with the SecYEG translocon

86
Q

SecYEG translocon

A

protein complex embedded in the bacterial inner membrane that serves as a channel for protein translocation across the membrane

87
Q

twin arginine translocase (TAT)

A

transport complex that assembles on demand to ship fully folded proteins across the cell membrane to the periplasm; powered by the proton motive force

88
Q

type I protein secretion

A

moves certain products directly from the cytoplasm to the environment; typically found in Gram-negative bacteria

89
Q

ABC transporter

A

short for ATP-binding cassette transporter; membrane protein complex that plays a crucial role in the active transport of various molecules across biological membranes; simplest of protein secretion systems; make up type I protein secretion

90
Q

type I systems all have three protein components

A
  1. an outer membrane channel
  2. an ABC transporter protein at the inner membrane
  3. a periplasmic protein lashed to the inner membrane
91
Q

cells do not express every gene at maximal level under all conditions for a number of reason

A
  • physical space limitations
  • energy and resource conservation
  • contradictory functions
92
Q

gene regulation occurs at multiple, often interwoven levels

A
  • alteration of DNA sequence
  • control of transcription
  • control of mRNA stability
  • translational control
  • posttraslational control
93
Q

control at the DNA level is ___

A

the most drastic and least reversible

94
Q

control at the protein level is ___

A

the most rapid and most reversible

95
Q

transcriptional regulators (activators and repressors)

A

regulatory proteins that control gene transcription by binding to specific DNA sequences; activity influenced by ligand molecules whic can bind and modulate their function

96
Q

two-component signal transduction system (TCS)

A

a message relay system composed of a sensor kinase protein and a response regulator protein that regulates gene expression in response to a signal (usually extracellular)

97
Q

sensor kinase

A

a transmembrane protein that phosphorylates itself from ATP in response to an extracellular signal and transfers the phosphoryl group to a receiver protein

98
Q

alternative sigma factors (RpoS, or σS)

A

can recognize and bind to specific promoter sequences, directing RNA polymerase to transcribe specific sets of genes in response to certain conditions; in many Gram negative cells

99
Q

riboswitch

A

a secondary structure with some mRNA transcripts that can interact with metabolites or antisense RNA molecules, change structure, and affect production or translation of mRNA by folding into 3D structures; found upstream of coding sequence;

100
Q

second messenger

A

a regulatory molecule produced in response to primary signal; typically affect expression of numerous genes

101
Q

___ is a major site of regulatory control in bacterial cells

A

transcription initiation

102
Q

___ control initiation of transcription at gene promoters

A

DNA-binding regulatory proteins

103
Q

regulatory proteins

A

a protein that can bind DNA and modulate transcription in response to a metabolite; controls transcription initiation

104
Q

the sequence of DNA affects the ___

A

binding affinity of regulatory proteins

105
Q

repressor

A

a regulatory protein that can bind to a specific DNA sequence and inhibit transcription of genes; prevent gene expression (repression) by binding to DNA sequences called operators

106
Q

activators

A

a regulatory protein that can bind to a specific DNA sequence and increase transcription of genes; stimulate gene expression by contacting an RNA polymerase positioned at a nearby promoter

107
Q

operators

A

a region of DNA to which the repressor protein binds; usually located near promoters

108
Q

inducer

A

ligand that stimulates transcription of genes by changing the DNA-binding properties of a regulatory protein; binds to a repressor protein making it lose the ability to bind the operator and blocks transcription; binds to an activator protein making it gain the ability to bind the DNA and the RNA polymerase to stimulate transcription

109
Q

response regulator

A

a cytoplasmic protein that is phosphorylated by a sensor kinase and modulates gene transcription depending on its phosphorylation state; controlled by covalent modifications

110
Q

Jacques Monod and François Jacob

A

French scientists who proposed the revolutionary idea that genes could be regulated in 1961; noticed that enzymes used to metabolize lactose in E. coli were inducible, whereas those for glucose were constitutive

111
Q

lactose

A

disaccharide sugar made of glucose and galactose that can be used as a carbon and energy source

112
Q

lactose metabolism requires two components:

A
  • lactose permease (LacY): imports (transports) lactose into the cell
  • β-galactosidase (LacZ): cleaves lactose into the monosaccharides glucose and galactose
113
Q

lac operon promoter

A

PlacZYA; serves as binding site for RNA polymerase to initiate transcription

114
Q

lac operon operator

A

lacO; DNA sequence upstream of promoter and serves as binding site for lac repressor

115
Q

lactose operon repressor

A

LacI; regulatory protein situated immediately upstream of the operon

116
Q

in the ___ LacI binds as a tetramer to the operator region and ___ transcription by preventing open complex formation by RNA polymerase

A

absence of lactose, represses

117
Q

in the ___ of lactose, β-galactosidase (LacZ)
cleaves and rearranges lactose to make ___

A

presence and inducer allolactose

118
Q

allolactose

A

inducer; binds to LacI and reduces its affinity for the operator

119
Q

cyclic AMP (cAMP)

A

governs the level of lacZYA transcription in E. coli by binding to a dimeric regulator called CRP; accumulates when a cell is starved for carbon

120
Q

cAMP-CRP complex

A

binds to a DNA sequence located 60bp upstream; causes DNA to bend, allowing CRP to interact directly with alpha subunit of RNA polymerase bound at the PlacZYA promoter to activate transcription

121
Q

maximum expression of the lactose operon requires ___ and ___

A

removal of the lactose repressor (LacI) and the binding of an activated cAMP-CRP complex

122
Q

catabolite repression

A

an operon enabling the catabolism of one nutrient is repressed by the presence of a more favorable nutrient; ex: glucose is favored over lactose

123
Q

diauxic growth

A

a biphasic cell growth curve caused by depletion of the favored carbon source and a metabolic switch to the second carbon source

124
Q

inducer exclusion

A

the ability of glucose to cause metabolic changes that prevent the cellular uptake of less favorable carbon sources that could cause unnecessary induction; glucose transport by phosphotransferase system inhibits LacY and prevents lactose from entering

125
Q

aporepressors

A

genes encoding biosynthetic enzymes typically regulated by inactive repressors; becomes active when corepressor binds to it

126
Q

corepressor

A

binds to aporepressors and the complex binds to an operator sequence upstream of a target gene or operon to turn transcription off

127
Q

trp operon

A

codes for enzymes involved in biosynthesis of the amino acid tryptophan

128
Q

aporepressor protein (TrpR)

A

when tryptophan levels exceed cellular needs, excess binds to this inactive TrpR and converts it into an active repressor

129
Q

regulon

A

collection of coregulated operons that are scattered around the bacterial chromosome

130
Q

protease ClpXP

A

orchestrates the stationary phase-dependent accumulation of σS by modulating its degradation

131
Q

when cells enter stationary phase degradation of σS ___

A

stops

132
Q

anti-sigma factor

A

proteins that inhibit activity not by degradation, but instead by binding directly to specific sigma factors and blocking their access to the RNA polymerase; release is important for spore formation and flagella construction

133
Q

anti-anti-sigma factor

A

can neutralize anti-sigma factors

134
Q

attenuation

A

a regulatory mechanism in which translation of a leader peptide affects transcription of an operon’s downstream structural genes

135
Q

asRNA (cis-antisense RNA)

A

molecules are transcribed from
the nontemplate strands of mRNA-encoding genes; affects RNA stability; 700-3000 nucleotides

136
Q

Guanosine tetraphosphate (ppGpp)

A

a second messenger that allows cells to handle abrupt changes in nutrient availability by switching from rapid growth to slower growth.

137
Q

stringent response

A

nutrient scarcity leaves many ribosomes idle

138
Q

Cyclic di-GMP (c-di-GMP)

A

a second messenger used by E. coli cells to
transition between a motile, single-cell (planktonic) state and an adhesive multicellular (biofilm) state

139
Q

autoinducer

A

a membrane-permeable second messenger that allows cells to regulate gene expression based on the density of cells in the environment

140
Q

quorum sensing

A

mechanism that bacteria use to coordinate gene expression in response to changes in population density; first discovered in Aliivibrio fischeri

141
Q

LuxI (in V. fischeri)

A

synthesizes autoinducer, which diffuses into extracellular medium

142
Q

LuxR regulatory proteins (in V. fischeri)

A

autoinduce reenters the cells and binds to these proteins when threshold levels are reached

143
Q

LuxR-autoinducer complex

A

activates transcription of luciferase genes that confer luminescence

144
Q

Pseudomonas aeruginosa quorum sensing

A

forms a biofilm in the lungs of cystic fibrosis
patients and secretes virulence factors like proteases only when it can overwhelm its host and avoid immune responses with high cell densities

145
Q

Vibrio harveyi quorum sensing

A

uses three different, but converging, quorum-sensing systems; separate autoinducers for each system may be made by other microbial species

146
Q

competent cells

A

can import free DNA fragments and integrate them into their genomes by recombination

147
Q

competence stimulation peptide (CSP)

A

autoinducer produced by competent cells; activates a phosphorylation cascade that ultimately actives ComX, an alternative sigma factor used specifically to transcribe genes that establish competency

148
Q

benefits of taking up foreign DNA

A
  • imported DNA can be used as a food source
  • can repair damaged chromosomes
  • drive genome evolution
149
Q

Agrobacterium tumefaciens which causes crown gall disease

A
  • can transfer genes across biological domains
  • contains a tumor inducing Ti plasmid that can be transferred via conjugation to plant cells
150
Q

F factor replication origins:

A
  • oriV: used in nonconjugating cells
  • oriT: used during DNA transfer
151
Q

tra genes

A

responsible for several aspects of conjugation, including pilus formation and DNA export

152
Q

relaxase

A

plasmid codes this protein for DNA transfer and unwinds DNA

153
Q

the entire chromosome takes about ___ to transfer

A

100 minutes

154
Q

generalized transduction

A

can transfer any gene from a donor to a recipient cell

155
Q

specialized transduction

A

can transfer only a few closely linked to the phage insertion site between cells

156
Q

Vibrio cholerae

A

gram-negative, extends a type IV pilus, which can actively take up free DNA in the environment

157
Q

Transposable elements transpose by one of two mechanisms:

A
  • replicative transposition: transposable element jumps from one site to another
  • nonreplicative transposition: transposable element is copied, one copy remains in original site
158
Q

homologs

A

genes with shared ancestry have sequence similarity, or homology

159
Q

orthologs

A

homologs found in different species, same function

160
Q
A

MCB3020 (2 decks)

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