CHAPTER 11 Flashcards
(121 cards)
1
Q
is initially synthesized using a DNA template in the process called transcription; the enzyme that catalyzes the process is DNA-dependent RNA polymerase.
A
RNA
2
Q
All four ribonucleoside triphosphates
A
ATP, GTP, CTP, and UTP
3
Q
Required cofactor for RNA Synthesis
A
Mg2+
4
Q
A primer is not needed in RNA synthesis, but a DNA template is required
A
true
5
Q
As is the case with DNA biosynthesis, the RNA chain grows from the 5’ to the 3’ end. The nucleotide at the 5’ end of the chain retains its triphosphate group
A
true
6
Q
The enzyme uses one strand of the DNA as the template for RNA synthesis. The base sequence of the DNA contains signals for initiation and termination of RNA synthesis. The enzyme binds to the template strand and moves along it in the _________ direction
A
3’-to-5’ direction.
7
Q
the holoenzyme binds to and transcribes only the template strand
molecular weight about 500,000
A
RNA Polymerase
8
Q
the role of the _________ subunit is recognition of the promoter locus;
released after transcription begins
A
sigma
8
Q
The basics of transcription
A
RNA polymerase uses the template strand of DNA to make an RNA transcript that has the same sequence as the nontemplate DNA strand, with the exception that T is replaced by U.
If this RNA is mRNA, it can later be translated to protein.
8
Q
RNA Polymerase holoenzyme
A
a2bb’sigma
8
Q
RNA Polymerase core enzyme
A
a2bb’
8
Q
of the two DNA strands, the one that serves as the template for RNA synthesis is called the __________
other is called the ____________, the strand of DNA that contains the genetic code for a protei
A
template strand or antisense strand
coding (or nontemplate) strand or sense strand
8
Q
DNA sequence that provide direction for RNA polymerase
RNA polymerase needs to know which strand is template strand, which part to transcribe, and where first nucleotide of gene to be transcribed is
Fairly large nucleotide sequences
Bind to RNA polymerase and transcription factors
A
Promoter Sequence
8
Q
Simplest of organisms contain a lot of DNA that is not transcribed
A
true
8
Q
1 mRNA = 1 gene
A
true
8
Q
toward 5′ is upstream; toward 3′ is downstream.
A
true
8
Q
First phase of transcription is
A
initiation
9
Q
Initiation and Elongation in Transcription
Nucleotides in this region are numbered with reference to the base at the transcription start site, which is designated ________.
A
+1
9
Q
Two types of termination mechanisms:
controlled by specific sequences, termination sites
Termination sites characterized by two inverted repeats
A
intrinsic termination
9
Q
initiation begins when RNA polymerase binds to promoter and forms
A
closed complex
9
Q
DNA and RNA are synthesized in the 5′-to-3′ direction
A
true
9
Q
After initiation, DNA unwinds at promoter to form _______________ which is required for chain initiation
A
closed comple
9
Q
Initiation and Elongation in Transcription steps
A
Recognition of promoter by sigma holoenzyme subunit
binding of polymerase to DNA
migration to promoter
Rna polymerase will then form and unwind the closed promoter complex, to make it an open promoter complex
RNA polymerase initiates the mrna synthesis with purines, and continues to elongate. Sigma-sub unit will then be released
9
Q
RNA polymerase initiates the mrna synthesis with __________
A
purines
9
RNA polymerase catalyzes formation of ________________ bonds between the incorp. ribonucleotides
phosphodiester
9
enzyme relax supercoils in front of and behind transcription bubble
Topoisomerases
9
If the RNA polymerase followed the template strand around the axis of the DNA duplex, there would be no strain, and no supercoiling of the DNA would occur, but the RNA chain would be wrapped around the double helix once every 10 base pairs.
Why is this unlikely?
unlikely because it would be difficult to disentangle the transcript from the DNA complex.
9
How could topoisomerases help with transcription elongation
topoisomerases could remove the supercoils.
A topoisomerase capable of relaxing positive supercoils situated ahead of the advancing transcription bubble would “relax” the DNA. A second topoisomerase behind the bubble would remove the negative supercoils
9
Two types of termination mechanisms:
Other type of termination involves rho protein
termination sequences cause hairpin loop to form
Rho-dependent termination
9
how does the Rho-dependent termination work?
The rho-factor mechanism of transcription termination.
Rho (r) factor (a) attaches to a recognition site on mRNA and
(b) moves along it behind RNA polymerase.
(c) When RNA polymerase pauses at the termination site, rho factor unwinds the DNA:RNA hybrid in the transcription bubble,
releasing the nascent mRNA (d).
9
can refer to a change in DNA conformation during transcription, a type of locomotion in flatworms, or a hairstyling technique
“scrunching” phenomenon
9
_________ in the DNA sequence being transcribed can lead to an mRNA molecule that forms a hairpin loop. This is often used to terminate transcription.
Inverted repeats
9
In prokaryotes, transcription regulated by:
alternative sigma factors
enhancers
operons
transcription attenuation
10
organisms that exert control over which genes are expressed by producing different sigma-subunits that direct the RNA polymerase to different genes.
Alternative sigma factors
10
Control of transcription via different sigma subunits, shown by phage SPO1
the host RNA polymerase (tan) and σ-subunit (blue) transcribe the early genes of the infecting viral DNA.
One of the early gene products is gp28 (green), an alternative σ-subunit.
The gp28 directs the RNA polymerase to transcribe the middle genes, which produces gp33 and gp34.
The gp33 and gp34 direct the host’s RNA polymerase to transcribe the late genes.
10
Certain genes include sequences upstream of extended promoter region
DNA sequences that bind to a transcription factor and increase the rate of transcription
Upstream or downstream of genes
Bind to activator proteins
Amplifies Rna Pol
Short nucleotide sequences
Enhancers
10
genes for ribosomal production have 3 upstream sites, called the ______ sites
is a specific DNA sequence where the protein Fis (Factor for Inversion Stimulation) binds
Fis sites
10
enhancers are Bound by proteins called
transcription factors
10
protein Fis is a transcription factor.
true
10
The core promoter includes the 210 and 235 regions
true
11
Components of the lac operon
Structural genes
Promoter
Operator
Repressor
Inducer
Catabolite Activator Protein (CAP)
12
Components of the lac operon
These genes code for enzymes needed to break down lactose:
Encodes β-galactosidase, which breaks down lactose into glucose and galactose.
lacZ
13
Components of the lac operon
These genes code for enzymes needed to break down lactose:
Encodes lactose permease, a protein that helps transport lactose into the bacterial cell.
lacY
14
Components of the lac operon
These genes code for enzymes needed to break down lactose:
Encodes transacetylase, an enzyme with a less clear role in lactose metabolism.
lacA
15
Components of the lac operon
A region of DNA where RNA polymerase binds to start transcription of the structural genes.
Promoter
16
Components of the lac operon
A region of DNA where a repressor protein can bind to block transcription
Operator
17
Components of the lac operon
Components of the lac operon
A region of DNA where a repressor protein can bind to block transcription
Repressor
18
Components of the lac operon
A molecule that binds to the repressor, causing it to change shape and detach from the operator. In the case of the lac operon, the inducer is allolactose, a form of lactose.
Inducer
19
Components of the lac operon
A protein that, when bound to cAMP (cyclic AMP), enhances the transcription of the lac operon. cAMP levels are low when glucose is abundant and high when glucose is scarce.
Catabolite Activator Protein (CAP)
20
Regulation of the lac operon
Negative control
In the absence of lactose, the repressor protein binds to the operator, preventing RNA polymerase from transcribing the structural genes. This effectively turns off the lac operon. When lactose is present, it is converted to allolactose, which binds to the repressor, causing it to detach from the operator. This allows RNA polymerase to transcribe the structural genes, enabling the bacteria to utilize lactose.
21
Regulation of the lac operon
Positive control
When glucose levels are low, cAMP levels are high. cAMP binds to CAP, and the CAP-cAMP complex binds to a site near the promoter. This enhances the binding of RNA polymerase to the promoter, further increasing the transcription of the structural genes. This ensures that the lac operon is only fully activated when glucose is scarce and lactose is available.
22
a group of operator, promoter, and structural genes that codes for proteins
the control sites, promoter, and operator genes are physically adjacent to the structural gene in the DNA
the regulatory gene can be quite far from it
are usually not transcribed all the time
Operon
22
an inducible protein
beta-Galactosidase
23
beta-Galactosidase coded for by a structural gene
lacZ
24
structural gene ________ codes for transacetylase
lacA
24
structural gene ________ codes for lactose permease
lacY
25
expression of these three structural genes is controlled by the regulatory gene ______ that codes for a repressor
lacI
26
e produces a protein that
represses the lac operon by binding to the operator.
lacI
26
In the presence of an ________, the repressor cannot bind, and the operon genes are transcribed.
inducer
27
Operator and promoter together are the
control sites
27
is induced when E. coli has lactose as the carbon source
Binding Sites On the lac operon
27
Lac protein synthesis repressed by _________ (catabolite repression)
glucose
28
Negative numbers are assigned to base pairs in the _______ sites
regulatory sites.
29
Positive numbers indicate the _______ gene, starting with base pair +1.
structural
30
The _______ site is seen next to the RNA polymerase binding site
CAP binding
31
CAP forms complex with cAMP
Complex binds at CAP site
RNA polymerase binds at available binding site, and transcription occurs
a regulatory system that helps microorganisms adapt to their carbon and energy sources
Catabolite Repression
32
Components of the trp operon
Structural genes
Promoter
Operator
Repressor
Tryptophan (Corepressor)
Leader sequence
33
Components of the trp operon
The region where RNA polymerase binds to initiate transcription
Promoter
33
Components of the trp operon
These genes encode the enzymes necessary for tryptophan biosynthesis. There are five structural genes (trpE, trpD, trpC, trpB, and trpA) in E. coli that are transcribed as a single mRNA.
Structural genes
34
Components of the trp operon
A region of DNA where the repressor protein can bind to block transcription
Operator
35
Components of the trp operon
A protein that, when bound to tryptophan (the corepressor), binds to the operator and prevents transcription.
Repressor
35
Components of the trp operon
The amino acid tryptophan itself acts as the corepressor. High levels of tryptophan activate the repressor.
Tryptophan (Corepressor)
36
Trp operon codes for a leader sequence (trpL) and _________ polypeptides
five
37
Components of the trp operon
The amino acid tryptophan itself acts as the corepressor. High levels of tryptophan activate the repressor.
Leader sequence
38
In trp operon, The five proteins make up 4 different enzymes that catalyze the multistep process that converts ________ to tryptophan
chorisimate
39
The trp operon is primarily regulated by negative feedback:
true
39
Regulation of the trp operon
Derepression:
When tryptophan levels are low, the repressor is not bound to tryptophan. The repressor alone cannot bind to the operator efficiently. RNA polymerase can then transcribe the structural genes, leading to tryptophan synthesis.
40
Regulation of the trp operon
Repression:
When tryptophan levels are high, tryptophan binds to the repressor protein, changing its conformation. This allows the repressor-tryptophan complex to bind to the operator, blocking RNA polymerase from transcribing the structural genes. This effectively shuts down tryptophan production.
41
Alternative 2˚ structures Can Form in trp Operon
Pause structure
Terminator loop
Antiterminator structure
42
Alternative 2˚ structures Can Form in trp Operon
Alternative binding between regions 2 and 3
forming an anti-termination hairpin and enabling transcription to continue into the structural genes of the operon.
Antiterminator structure
42
Alternative 2˚ structures Can Form in trp Operon
binding between regions 1 and 2
when ribosome passes over Trp codons when Trp levels are high
can form alternative secondary structures (hairpins) depending on the availability of tryptophan
Pause structure
42
attenuation
When tryptophan levels are high, the ribosome quickly translates the leader sequence. This allows a specific hairpin loop (the terminator hairpin) to form in the mRNA, which signals RNA polymerase to stop transcription prematurely. This prevents the complete transcription of the structural genes.
High Tryptophan
43
Alternative 2˚ structures Can Form in trp Operon
binding between regions 3 and 4
a "terminator" hairpin that signals transcription termination and an "antiterminator" hairpin that allows transcription to continue
Terminator loop
43
The trp operon also employs a mechanism called _________, which provides finer control over tryptophan production. This mechanism works during transcription:
attenuation
44
attenuation
When tryptophan levels are low, the ribosome stalls at the tryptophan codons in the leader sequence because it's waiting for a tRNA charged with tryptophan. This stalling causes a different hairpin loop (the anti-terminator hairpin) to form in the mRNA. The anti-terminator loop prevents the terminator hairpin from forming, allowing RNA polymerase to continue transcribing the structural genes. This increases tryptophan production.
Low Tryptophan
45
Transcription in Eukaryotes
Three RNA polymerases are known
found in the nucleolus and synthesizes precursors of most rRNAs
RNA Polymerase I
46
Transcription in Eukaryotes
Three RNA polymerases are known
found in the nucleoplasm and synthesizes mRNA precursors
Most studied on the polymerases
Consists of 12 subunits
RPB- RNA Polymerase B
RNA Polymerase II
46
Transcription in Eukaryotes
Three RNA polymerases are known
found in the nucleoplasm and synthesizes tRNAs, other RNA molecules involved in mRNA processing and protein transport
RNA Polymerase III
47
How does Pol II Recognize the Correct DNA?
Four elements of the Pol II promoter allow for this phenomenon
48
Any protein regulator of transcription that is not itself a subunit of Pol II is a
transcription factor
49
General Transcription Initiation Factors
TFIIH recruitment; modulation of TFIIH
helicase ATPase, and kinase activities;
promoter melting
TFIIE
50
General Transcription Initiation Factors
TATA box recognition, positioning of
TATA box DNA around TFIIB and Pol II
TFIID-TBP
50
General Transcription Initiation Factors
Promoter melting; promoter clearance via phosphorylation of CTD
TFIIH
51
Transcription with Transcription Initiation Factors
TFIID (which contains the TATA-box binding protein, TBP) binds to the TATA box.
TFIIA and TFIIB then bind, followed by recruitment of RNA polymerase II and TFIIF.
TFIIH and TFIIE then bind to form the preinitiation complex (PIC).
Kinases phosphorylate the C-terminal domain of Pol II, leading to the open complex in which the DNA strands are separated.
RNA is produced during elongation as Pol II and TFIIF leave the promoter and the other general transcription factors behind.
Pol II dissociates during the termination phase, and the CTD is dephosphorylated. Pol II/TFIIF is then recycled to bind to another promoter.
52
begins by stopping RNA Pol; the eukaryotic consensus sequence for termination is AAUAAA
Termination
52
Gene Regulation
regulatory sequences that augment or diminish transcription, respectively
Enhancers and silencers
53
Chromatin remodeling
complexes.
(a) The remodeling complex binds to the chromatin in an ATP-independent manner.
(b) ATP is hydrolyzed and the chromatin structure is loosened. The remodeling complex is released in a manner that is not well understood as indicated by the question mark. Remodeling can take
multiple forms, such as sliding of the octamers or their removal and transfer. The end result is that the loosening of the chromatin allows the transcription
machinery to access the DNA.
53
Gene Regulation
brings enhancers into contact with transcription factors and polymerase
DNA looping
54
Eukaryotic Gene Regulation
are enhancers that respond to certain metabolic factors
all bind proteins (transcription factors) that are produced under certain cell conditions
Response elements
55
Transcription is regulated by modification of histone proteins in the chromatin. There are many sites for modification as shown, such as acetylation of lysines (acK), methylation of arginines (meR), methylation of lysines (meK) and phosphorylation of serines (PS).
true
55
Response elements
* heat shock element (HSE)
* glucocorticoid response element (GRE)
* metal response element (MRE)
* cyclic-AMP response element (CRE)
56
DNA-Binding domains have domains that are either:
* Helix-Turn-Helix (HTH)
* Zinc fingers
* Basic-region leucine zipper
56
As much as 98% of transcriptional output from human genomes may be comprised of
Linked to: regular transcription, gene silencing, replication, processing of RNA, RNA modification, translation, protein stabilization, protein translocation
Non-Coding RNAs
57
Most proteins that activate or inhibit RNA Pol II have two functional domains:
DNA-binding domain
transcription-activation domain
58
Structural Motifs in DNA-Binding Proteins
Many transcription factors contain this motif, such as CREB
Half of the protein composed of basic region of conserved Lys, Arg, and His
Half contains series of Leu
Leu line up on one side, forming hydrophobic pocket
Basic-Region Leucine Zipper Motif
58
Structural Motifs in DNA-Binding Proteins
Motif contains 2 cysteines and 2 His 12 amino acids later
Zinc binds to the repeats
Zinc Finger Motif
59
Structural Motifs in DNA-Binding Proteins
The amino acids listed show the progression down the helix. Note that the leucines line up along one side, forming a hydrophobic spine.
Helical Wheel Structure of Leucine Zipper
60
Transcription Activation Domains
acidic domains
glutamine-rich domains
proline-rich domain
61
tRNA, rRNA, and mRNA are all modified after transcription to give the functional form
Post Transcriptional RNA Modification
61
Post Transcriptional RNA Modification
trimming of leader and trailer sequences
addition of terminal sequences (after transcription)
modification of the structure of specific bases (particularly in tRNA)
62
Modification of tRNA
trimming, addition of terminal sequences, and base modification all take place
methylation and substitution of sulfur for oxygen are the two most usual types of base modification
63
Modification of mRNA
Includes the capping of the 5’ end with an N-methylated guanine that is bonded to the next residue by a 5’ -> 5’ triphosphate.
Also, 2’-O-methylation of terminal ribose(s)
63
Modification of rRNA
processing of rRNA is primarily a matter of methylation and trimming to the proper size
in prokaryotes, 3 rRNAs in one intact ribosome
in Eukaryotes, ribosomes have 80s, 60s, and 40s subunits
base modification in both prokaryotes and eukaryotes is primarily by methylation
64
mRNA Modification
tail that is usually100-200 nucleotides long, is added to the 3’ end before the mRNA leaves the nucleus
This tail protects the mRNA from nucleases and phosphatases
polyadenylate “tail”
65
Expressed DNA sequences are called
exons
65
Intervening DNA sequences that are not expressed are called
introns
66
These genes are often referred to as split genes
introns, exons
66
Ribozymes
require an external guanosine
example: pre-rRNA of the protozoan Tetrahymena
Group I ribozymes
67
The Splicing Reaction
Exons are separated by intervening intron
nucleophilic attack on exon
When the exons are spliced together, _________ in the intron
lariat forms
68
Ribozymes
display a lariat mechanism similar to mRNA splicing
no requirement for an external nucleotide
Group II ribozymes
69
discovered included those that catalyze their own self-splicing
More recently, ribozymes have been discovered that are involved in protein synthesis
Ribozymes
