Exam 2 Flashcards
(168 cards)
1
Q
transcription
A
the synthesis of RNA complementary to a DNA template
2
Q
translation
A
the ribosomal synthesis of proteins based on triplet codons present in mRNA
3
Q
messenger RNA, or mRNA
A
an RNA molecule that encodes a protein
4
Q
RNA polymerase
A
an enzyme that produces an RNA complementary to a template DNA strand
5
Q
RNA products of transcription in bacteria can be
A
monocistronic or polycistronic
6
Q
Core polymerases
required for the elongation phase
A
αI, αII, β, β’, ω
7
Q
In bacteria, the RNA polymerase is made up of
A
Core polymerase and sigma factor
8
Q
holoenzyme
A
the core polymerase and sigma factor when together
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
10
Q
“housekeeping” sigma factor in Escherichia coli
A
sigma-70
11
Q
promoter
A
a noncoding DNA regulatory region immediately upstream of a structural gene that is needed for transcription initiation
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
13
Q
phases of transcription
A
initiation, elongation, termination
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
15
Q
elongation of transcription
A
sequential addition of ribonucleotides from nucleoside triphosphates (the RNA chain is extended)
16
Q
termination of transcription
A
RNA pol detaches from the DNA after the transcript is made
17
Q
RNA polymerase holoenzyme forms a loosely bound ____ with DNA
initiation of transcription
A
closed complex
18
Q
the closed complex must become an open complex through
initiation of transcription
A
the unwinding of one helical turn
19
Q
RNA polymerase in the open complex becomes ____ to DNA to begin transcription
initiation of transcription
A
tightly bound
20
Q
the first ribonucleoside triphosphate of the new RNA chain is
initiation of transcription
A
usually a purine (A or G)
21
Q
the original RNA polymerase continues to move along the template, synthesizing RNA at
elongation of transcription
A
~45 bases/sec
22
Q
the unwinding of DNA ahead of the moving complex forms a
elongation of transcription
A
17-bp transcription bubble
23
Q
positive supercoils ahead are removed by
elongation of transcription
A
DNA topoisomerases
24
Q
all bacterial genes use one of two known transcription termination signals:
A
Rho-dependent and Rho-independent
25
Rho-dependent
relies on a protein called Rho and a strong pause site at the 3' end of the gene
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Rho-independent
requires a GC-rich region of RNA, as well as 4-8 consecutive U residues
25
Rifamycin B
| effect on transcription
selectively binds to the bacterial RNA pol and inhibits transcription initiation
25
antibiotics
| fundamental criteria
must kill or retard the growth of a pathogen, and they must not harm the host - selectivity
25
Actinomycin D
| effect on transcription
nonselectively binds to DNA and inhibits transcription elongation
26
RNA differences to DNA
* 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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RNA stability is measured
in terms of half-life
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average half-life of mRNA
1-3 minutes
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rRNA (ribosomal RNA)
an RNA molecule that includes the scaffolding and catalytic components of ribosomes
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tRNA (transfer RNA)
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)
29
sRNA (small RNA)
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
30
tmRNA (transfer messenger RNA)
a molecule resembling both tRNA and mRNA that rescues ribosomes stalled on damaged mRNAs lacking a stop codon
31
catalytic RNA
also called *ribozyme*. An RNA molecule that is capable of catalyzing reactions
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central dogma
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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codons
nucleotide triplets. An mRNA molecule can be thought of a sentence and codons represent individual words, or amino acids
34
there are __ possible codons
* there are 64 possible codons
* 61 specify amino acids (includes the start codons)
* 3 are stop codons
35
functional regions of tRNA:
**anticodon** and **3' (acceptor) end**
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anticodon
hydrogen bonds with the mRNA codon
specifying an amino acid
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3′ (acceptor) end
binds the amino acid
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aminoacyl-tRNA synthetase
an enzyme that condenses a specific amino acid with the 3' OH group of the correct tRNA, thereby charging the tRNA
39
each cell has ____ aminoacyl t-RNA synthetases
20, one for each amino acid
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each aminoacyl t-RNA synthetase must
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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ribosome
a large enzyme, composed of RNA and protein subunits, that translates mRNA into protein
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ribosomal subunits
**30S** (small subunit) and **50S** (large subunit) and combine to form the **70S** ribosome
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70S ribosome binding sites
A (acceptor) site, P (peptidyl-tRNA) site, and E (exit) site
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A (acceptor) site
the region of a ribosome that binds an incoming charged tRNA
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P (peptidyl-tRNA) site
the region of a ribosome that contains the growing protein attached to a tRNA
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E (exit) site
the region of a ribosome that holds the uncharged, exiting tRNA
45
peptidyltransferase
a ribozyme that catalyzes the formation of peptide bonds. Part of the 23S rRNA of the large ribosomal subunit
46
____ rRNA serves as a molecular clock
16S. Genes for ribosomal RNA are highly conserved in many different species due to their slow rate of undergoing mutations
47
Shine-Dalgarno sequence
(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.
48
the Shine-Dalgarno sequence is located _ of the start codon in *Escherichia coli*
4-8 bases upstream
49
start codons
AUG (90%), GUG (8.9%), UUG (1%). Code for **N-formyl-methionyl-tRNA (fMet-tRNA)**
50
Streptomycin
| effect on translation
inhibits 70S ribosome formation
51
Tetracycline
| effect on translation
inhibits aminoacyl-tRNA binding to the A site
52
Chloramphenicol
| effect on translation
inhibits peptidyltransferase
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Erythromycin
| effect on translation
causes abortive translocation
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translocation
the energy-dependent movement of a ribosome to the next triplet codon along an mRNA
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coupled transcription and translation
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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coupled transcription and translation occurs near __
the nucleoid
57
translation of fully transcribed mRNA occurs at __
the cell poles
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polysome
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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step after translation for many proteins
a protein must be modified after translation to achieve an approriate 3D structure or to regulate its activity
60
a healthy cell "cleans house"
by degrading damaged or unneeded proteins by specific devices such as proteases or proteasomes
61
N-formyl group
| protein structure modification after translation
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
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addition of phosphoryl or methyl groups
| protein structure modification after translation
can change the activity of signal transduction
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adenylation
| protein structure modification after translation
covalent attachment of adenosine 5' monophosphate, can regulate the activity of enzymes such as glutamine synthetase
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acetylation
| protein structure modification after translation
can serve multiple functions, including protein stabilization and regulation of protein activity
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lipidation
| protein structure modification after translation
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
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glycosylation
| protein structure modification after translation
covalent addition of monosaccharides or polysaccharides to generate glycoprotein
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mass spectrometry
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
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chaperones
a protein that helps other proteins fold into their correct tertiary structure
69
heat-shock proteins (HSPs)
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
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trigger factor (TF)
acts as a ribosome-associated chaperone and is the first chaperone to interact with nascent polypeptide
71
GroEL structure
forms a stacked ring structure with a hollow center
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GroES structure
cap-like structure that fits over one end of GroEL
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GroEL and GroES complex
facilitate protein folding; protein enters central cavity of GroEL, and the GroES cap helps create a controlled environment for folding
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DnaK and DnaJ complex
do not form rings, act as clamp-like chaperones
75
DnaK
also known as Hsp70, can bind to exposed hydrophobic regions on unfolding or misfolded proteins, preventing their aggregation and assisting in proper folding
76
DnaJ
often works with DnaK, helps recruit substrates and regulate DnaK's ATPase activity
77
degrons
degradation signal in many normal proteins that dictate the stability of a protein
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N-terminal rule
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
protease
enzyme that catalyzes proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurring the formation of new protein products.
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N-terminal signal sequences
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
signal recognition particle (SRP)
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
FtsY
shuttles the complex delivered by SRP to the transmembrane SecYEG secretion machinery (translocon)
83
SecA-dependent general secretion pathway
common mechanism in bacteria for translocating certain proteins from the cytoplasm to the periplasm. Essential for proper localization of periplasmic proteins
84
SecB
piloting protein that captures the completed pre-secretion protein and prevents aggregationg and misfolding
85
SecA
takes pre-secretion protein from SecB; is an ATPase associated with the SecYEG translocon
86
SecYEG translocon
protein complex embedded in the bacterial inner membrane that serves as a channel for protein translocation across the membrane
87
twin arginine translocase (TAT)
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
type I protein secretion
moves certain products directly from the cytoplasm to the environment; typically found in Gram-negative bacteria
89
ABC transporter
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
type I systems all have three protein components
1. an outer membrane channel
2. an ABC transporter protein at the inner membrane
3. a periplasmic protein lashed to the inner membrane
91
cells do not express every gene at maximal level under all conditions for a number of reason
* physical space limitations
* energy and resource conservation
* contradictory functions
92
gene regulation occurs at multiple, often interwoven levels
* alteration of DNA sequence
* control of transcription
* control of mRNA stability
* translational control
* posttraslational control
93
control at the DNA level is ___
the most drastic and least reversible
94
control at the protein level is ___
the most rapid and most reversible
95
transcriptional regulators (activators and repressors)
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
two-component signal transduction system (TCS)
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
sensor kinase
a transmembrane protein that phosphorylates itself from ATP in response to an extracellular signal and transfers the phosphoryl group to a receiver protein
98
alternative sigma factors (RpoS, or σS)
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
riboswitch
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
second messenger
a regulatory molecule produced in response to primary signal; typically affect expression of numerous genes
101
___ is a major site of regulatory control in bacterial cells
transcription initiation
102
___ control initiation of transcription at gene promoters
DNA-binding regulatory proteins
103
regulatory proteins
a protein that can bind DNA and modulate transcription in response to a metabolite; controls transcription initiation
104
the sequence of DNA affects the ___
binding affinity of regulatory proteins
105
repressor
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
activators
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
operators
a region of DNA to which the repressor protein binds; usually located near promoters
108
inducer
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
response regulator
a cytoplasmic protein that is phosphorylated by a sensor kinase and modulates gene transcription depending on its phosphorylation state; controlled by covalent modifications
110
Jacques Monod and François Jacob
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
lactose
disaccharide sugar made of glucose and galactose that can be used as a carbon and energy source
112
lactose metabolism requires two components:
* **lactose permease (LacY):** imports (transports) lactose into the cell
* **β-galactosidase (LacZ):** cleaves lactose into the monosaccharides glucose and galactose
113
lac operon promoter
PlacZYA; serves as binding site for RNA polymerase to initiate transcription
114
lac operon operator
lacO; DNA sequence upstream of promoter and serves as binding site for lac repressor
115
lactose operon repressor
LacI; regulatory protein situated immediately upstream of the operon
116
in the ___ LacI binds as a tetramer to the operator region and ___ transcription by preventing open complex formation by RNA polymerase
absence of lactose, represses
117
in the ___ of lactose, β-galactosidase (LacZ)
cleaves and rearranges lactose to make ___
presence and inducer allolactose
118
allolactose
inducer; binds to LacI and reduces its affinity for the operator
119
cyclic AMP (cAMP)
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
cAMP-CRP complex
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
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maximum expression of the lactose operon requires ___ and ___
removal of the lactose repressor (LacI) and the binding of an activated cAMP-CRP complex
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catabolite repression
an operon enabling the catabolism of one nutrient is repressed by the presence of a more favorable nutrient; ex: glucose is favored over lactose
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diauxic growth
a biphasic cell growth curve caused by depletion of the favored carbon source and a metabolic switch to the second carbon source
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inducer exclusion
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
aporepressors
genes encoding biosynthetic enzymes typically regulated by inactive repressors; becomes active when corepressor binds to it
126
corepressor
binds to aporepressors and the complex binds to an operator sequence upstream of a target gene or operon to turn transcription off
127
trp operon
codes for enzymes involved in biosynthesis of the amino acid tryptophan
128
aporepressor protein (TrpR)
when tryptophan levels exceed cellular needs, excess binds to this inactive TrpR and converts it into an active repressor
129
regulon
collection of coregulated operons that are scattered around the bacterial chromosome
130
protease ClpXP
orchestrates the stationary phase-dependent accumulation of σS by modulating its degradation
131
when cells enter stationary phase degradation of σS ___
stops
132
anti-sigma factor
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
anti-anti-sigma factor
can neutralize anti-sigma factors
134
attenuation
a regulatory mechanism in which translation of a leader peptide affects transcription of an operon’s downstream structural genes
135
asRNA (cis-antisense RNA)
molecules are transcribed from
the nontemplate strands of mRNA-encoding genes; affects RNA stability; 700-3000 nucleotides
136
Guanosine tetraphosphate (ppGpp)
a second messenger that allows cells to handle abrupt changes in nutrient availability by switching from rapid growth to slower growth.
137
stringent response
nutrient scarcity leaves many ribosomes idle
138
Cyclic di-GMP (c-di-GMP)
a second messenger used by E. coli cells to
transition between a motile, single-cell (planktonic) state and an adhesive multicellular (biofilm) state
139
autoinducer
a membrane-permeable second messenger that allows cells to regulate gene expression based on the density of cells in the environment
140
quorum sensing
mechanism that bacteria use to coordinate gene expression in response to changes in population density; first discovered in Aliivibrio fischeri
141
LuxI (in V. fischeri)
synthesizes autoinducer, which diffuses into extracellular medium
142
LuxR regulatory proteins (in V. fischeri)
autoinduce reenters the cells and binds to these proteins when threshold levels are reached
143
LuxR-autoinducer complex
activates transcription of luciferase genes that confer luminescence
144
Pseudomonas aeruginosa quorum sensing
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
Vibrio harveyi quorum sensing
uses three different, but converging, quorum-sensing systems; separate autoinducers for each system may be made by other microbial species
146
competent cells
can import free DNA fragments and integrate them into their genomes by recombination
147
competence stimulation peptide (CSP)
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
benefits of taking up foreign DNA
* imported DNA can be used as a food source
* can repair damaged chromosomes
* drive genome evolution
149
Agrobacterium tumefaciens which causes crown gall disease
* can transfer genes across biological domains
* contains a tumor inducing Ti plasmid that can be transferred via conjugation to plant cells
150
F factor replication origins:
* oriV: used in nonconjugating cells
* oriT: used during DNA transfer
151
tra genes
responsible for several aspects of conjugation, including pilus formation and DNA export
152
relaxase
plasmid codes this protein for DNA transfer and unwinds DNA
153
the entire chromosome takes about ___ to transfer
100 minutes
154
generalized transduction
can transfer any gene from a donor to a recipient cell
155
specialized transduction
can transfer only a few closely linked to the phage insertion site between cells
156
Vibrio cholerae
gram-negative, extends a type IV pilus, which can actively take up free DNA in the environment
157
Transposable elements transpose by one of two mechanisms:
* replicative transposition: transposable element jumps from one site to another
* nonreplicative transposition: transposable element is copied, one copy remains in original site
158
homologs
genes with shared ancestry have sequence similarity, or homology
159
orthologs
homologs found in different species, same function
160
