Chapter 12: Control of Gene Expression Flashcards
Define operon
a group of genes that share a common promoter and are transcribed as a unit, producing a single mRNA molecules that encodes several proteins
T/F: Operons control the expression of genes
True
True/False: Operons are common in bacteria, archaea, and eukaryotes.
False. Operons are common in bacteria and archaea but not as common in eukaryotes
Define gene regulation
Encompasses the mechanisms and system that control the expression of genes
How does gene regulation help bacteria?
By providing internal flexibility, turning genes on and off in response to environmental changes
Define central dogma
Genetic information flows from DNA to RNA to proteins.
How does gene regulation help multicellular eukaryotic organisms?
By bringing about cellular differentiation
Define structural genes
Encode proteins used in metabolism or biosynthesis or that play a structural role in the cell.
Define regulatory genes
Either RNA or proteins, interact with other DNA sequences and affect the transcription or translation of those sequences
The products are regulatory genes are often…
DNA-bonding proteins or RNA molecules that affect gene expression
Define constitutive genes
Structural genes that encode essential cellular functions and are expressed continually and are not regulated
Define regulatory element
DNA sequences that are not transcribe, bit still affect the expression of DNA sequences to which they are physically linked
Control is involved in gene expression. What are the two types of control?
Positive control and negative control
Define positive control
Processes that stimulate gene expression
Define negative control
Processes that inhibit gene expression
At what levels can gene expression be controlled?
Any number of levels.
DNA/chromatin structure, transcription, mRNA processing, mRNA stability, translation, posttranslational modification
Why is transcription a particularly important level of gene regulation in both bacteria and eukaryotes?
Transcription is the first step in the process of information transfer from DNA to protein. For cellular efficiency, gene expression is often regulated early in the process of protein production
What is the strucutre of an operon?
A promoter and a regulator which bind to an operator site connected to 3 structural genes
Promoter - regualtor/operator - gene a / gene b / gene c
Define regulator gene
helps control the expression of the structural genes of the operon by increasing or decreasing their transcription
Define regulator proteins
Can bind to a region of the operon called the operator and affect whether transcription can take place
Define operator
A region of the operon that regulator proteins can bind to
What is the difference between a structural gene and a regulator gene?
A. Structural genes are transcribe into mRNA; regulator genes aren’t
B. Structural genes have complex structure; regulator genes have simple structures
C. Structural genes encode proteins that function in the structure of the cell; regulator genes carry out metabolic reactions
D. Structural genes encode proteins used in metabolism or biosynthesis or cell structure; regulator genes control the transcription of structural genes
D
D. Structural genes encode proteins used in metabolism or biosynthesis or cell structure; regulator genes control the transcription of structural genes
What are the two types of transcriptional control?
Postitive control and negative control
What is negative control regarding transcriptional control
A regulator protein is a repressor, binding to DNA and inhibiting transcription.
What is positive control regarding transcriptional control?
A regulatory protein is an activator, stimulating transcription
Define inducible operons
Which transcription is normally off (not taking place), something must happen to induce transcription, or turn it on
Define repressisble operons
Which transcription is normally on (taking place); something must happen to repress transcription or turn if off
Define inducer
A small molecule that bins to the repressor protein and transcription of a negative inducible is turned on
What 2 binding sites do regulator proteins contain?
- One that bins to DNA
- Another that binds to small molecules such as the inducer
How do inducers affect proteins?
When the protein binds with an inducer it’s shape changes and can no longer bind with DNA
Define allosteric proteins
Proteins that change shape upon binding to another molecule
What proteins do inducible operons usually control?
proteins that carry out degradative processes (proteins that break down molecules)
Define corepressor
A small molecule that binds to the repressor and makes it capable of binding to the operator
Is the lac operon a positive or negative control?
Positive.
The catabolite activator protein (CAP) binds to the promoter and increases the efficiency with which RNA polymerase can bind the promoter and transcribe the structural genes
The regulator protein that acts on a negative repressible operon is synthesized as
A: An active activator
B: an inactive activator
C: An active repressor
D: An inactive repressor
D
D: An inactive repressor
Define lactose
A major carbohydrate found in milk and can be metabolized by E. coli in the mammalian gut
What is the function of the protein lactose permease?
Permease helps lactose diffuse across the E. coli cell membrane
What is the function of B-Galactosidase?
Break down lactase into glucose and galactose. It also converts lactose into allolactose
Define allolactose
a compound that plays an important role in regulating lactose metabolism
Which lac gene encodes for permease?
lacY
Which lac gene encodes for B-galactosidase?
lacZ
Which lac gene encodes for thiogalactoside?
lacA
What is the function of thigalactoside?
Currently unknown
Define LacI
a regulator gene, transcribed into a short mRNA that is translated into a repressor
What role does lacP play in lactose regulation?
Promoter
What is lacO?
Operator for lactose regulation
How does the presence of lactose affect the lactose regulation?
- Lactose is converted into allolactose by B-Galactosidase
- The presence of allolactose keeps lacI from binding to lacO
- Transcription of lactose proteins (lacZ, lacY, and lacA) continues
How does the absence of lactose affect the lactose regulation?
- No lactose means no allolactose
- No allolactose means lacI binds to lacO
- The binding of lacO stops transcription for more lactose proteins (lacZ, lacY, and lacA)
In the presence of allolactose, the lac repressor
A: Binds to the operator
B: Binds to the promoter
C: Cannot bind to the operator
D: Binds to the regulator gene
C
C: Cannot bind to the operator
What does a partial-diploid do?
Helps define the roles of the different components of an operon
How do structural mutations affect the following:
lacZ
lacY
lacZ would not make B-galactosidase
lacY would not make permease
Are structural mutations linked or independent in lacZ and lacY genes?
Independent.
Meaning even if lacY was mutated and could not make permease lacZ could still make B-Galactosidase
How do regulator mutations (lacI) affect lacZ and lacY?
Both are affected. Even if both are present, mutations in lacI will keep either from forming their products
lacI+ is wild type where proteins function normally
lacI- is mutated type and proteins cannot function
Which type is dominant?
Wild type, lacI+
What is a superrepressor? (lacI^s)
Mutations that prevented transcription from taking place even in the presence of lactose
What is lacO^c vs. lacO+
lacO+ is wild type and can be turned on and off
lacO^c is the mutated type that cannot be turned off
Is lacO^c or lacO+ dominant?
lacO^c is dominant
Between lacI^s (superrepressor) and lacO^c (constitutive operator) which is dominant?
lacO^c is dominant, and even in the presence of lacI^s lac proteins will still be made
What happens if the promoter is mutated? (lacP is mutated into lacP-)
If the promoter cannot function no lac proteins will be made
Define catabolite repression:
When glucose is available, genes that participate in the metabolism of other sugars are turned off
Efficient transcription of the lac operon takes place only if _______ is present and _______ is absent
A. Glucose, Lactose
B. Lactose, Glucose
B. Lactose, Glucose
Efficient transcription of the lac operon takes places only if lactose is present and glucose is absent
Is catabolite repression a positive or negative control?
Positive
Define cAMP (cyclic AMP)
A modified nucleotide that is important in cellular signaling processes in both bacterial and eukaryotic cells
What is the relationships between cAMP and glucose?
High glucose = low cAMP
Results in little lac transcription
Low glucose = high cAMP
Results in lots of lac transcription
The lac operon is an…
inducible operon
Transcription does not normally take place and must be turned on
Some operons are repressible; what does this mean?
Transcription is normally turned on and must be repressed / turned off when not needed
Which kind of operon is the tryptophan (trp) operon?
Negative repressible operon
What are the 5 structural genes for trp?
trpE, trpD, trpC, trpB, and trpA
Define trpR
A regulator gene that encodes a repressor protein that is normally inactive. Regulates tryptophan.
Is transcription on or off when trp is low?
On
Is transcription on or off when trp is high?
Off
In the trp operon, what happens to the trp repressor in the absence of tryptophan?
A: It binds to the operator and represses transcription
B: It cannot bind to the operator, and transcription takes place
C: It binds to the regulator gene and represses transcription
D: It cannot bind to the regulator gene, and transcription takes place
B
B: It cannot bind to the operator, and transcription takes place
How does chromatin structure repress gene expression?
The DNA is wrapped so tightly around the histone proteins that other transcription factors cannot reach the DNA
Define chromatin-remodeling complexes:
Regulatory proteins and other transcription factors that alter the chromatin structure without altering the chemical structure of the histones directly
Histones have 2 domains. What are they?
- A globular domain that associates with other histones and the DNA
- A positively charged tail domain that interacts with the negatively charged phosphate groups on the DNA
How are tails of histones often modified?
by the addition or removal of phosphate groups, methyl groups, or acetyl groups
What is the ubiquitination modification to histones?
when a small molecule called ubiquitin is added or removed from the histones
Define histone code
The collection of different mechanisms that affect chromatin structure
How do histone codes affect gene expression?
by altering chromatin structure directly or sometimes by providing recognition sites for proteins that bind to DNA and regulate transcription
Define methylation
The addition of a methyl group
How does methylation affect histones?
the addition of methyl groups (CH3) to the tails of histone proteins can activate or repress transcription depending on the histone modified and which amino acids were affected
Define histone methyltransferases
Enzymes that add methyl groups to specific amino acids
Define demethylases
Enzymes that remove methyl groups from histones
True/False: Enzymes and proteins that modify histones do not bind to specific DNA sequences and must be recruited to specific chromatin sites
True
What 3 things serve to recruit histone-modifying enzymes to specific sites?
Sequence-specific binding proteins, preexisting histone modifications, and RNA molecules
Define acetylation
A type of histone modification that affects the chromatin structure through the addition of acetyl groups (CH3CO)
What effect does acetylation have?
Usually stimulates transcription by destabilizing chromatin structure
Define Acetyltransferase enzymes
add acetyl groups (increase transcription)
Define Deacetylases
remove acetyl groups (repress transcription)
Which amino acid does methylation usually affect?
Cytosine
How does methylation of cytosine affect the histone?
Methylation attracts deacetylases, deconstructing histones and allowing transcription
Define cofactors
other proteins that can repress or activate transcription recruited by transcription factors
Define general transcription factors
Bind to the promoter and are part of the basal transcript apparatus. These are the complex of RNA polymerase, transcription factors, and other proteins that assemble to carry out transcription.
Define coactivator
a protein that indirectly acts with the basal transcription apparatus at the core promoter to stimulate or stabilize transcription
basal transcription apparatus and core promoter are just part of the promoter in the operon
Many transcription factors stimulate transcription by interacting with
A: introns
B: Basal transcription apparatus
C: DNA polymerase
D: Nucleosomes
B
B: Basal transcription apparatus
Define enhancers
regulator elements that affects the transcription of distant genes
True/False: Enhancers are very rare
False. They are very abundant
Define silencers
A sequence that have an inhibitory effect on transcriptions of distance genes
Define insulator
Also called boundary elements,which are DNA sequences that block the effects of enhancers in a position-dependent manner
Ex: an insulator is in-between an enhancer and a promoter; the enhancer is blocked
How does the binding of transcription factors to enhancers affect transcription at genes that are thousands of base pairs away?
The DNA between the enhancers and the promoter loops out, so that transcription factors bound to the enhancer are able to interact directly with the basal transcription apparatus
Define response elements
A common regulatory sequence that typically contain the same consensus sequences at varying distances from the genes being regulated
How do transcription and translation differ time-wise in bacteria and eukaryotes?
Bacteria has transcription and translation simultaneously
Eukaryotes have transcription and the later translation
How does alternative splicing affect pre-mRNA?
allows pre-mRNA to be spliced in multiple ways, generating different proteins in different tissues or at different times in development
Are eukaryotic mRNAs or bacterial mRNAs more stable?
Eukaryotic
How does the stability of mRNA affect the synthesis of proteins?
The longer it is stable the more proteins are made
What 5 things affect the stability of mRNA?
- 5’ cap
- poly(A)tail
- 5’UTR
- Coding region
- Sequences in the 3’UTR
How does the poly(A)tail affect mRNA stability?
The poly(A)tail stabilizes the 5’ cap, which must be removed before the mRNA molecule can be degraded from the 5’ end.
What triggers RNA silencing?
Very small RNA molecules known as microRNA (miRNA) and small interfering RNAs (siRNA)
Define Dicer
an enzyme that cleaves and processes double-stranded RNA to produce single-stranded siRNAs or miRNAs which combine with proteins to form an RNA-induced silencing complex
Define RISC
A RNA-induced silencing complex formed by the Dicer enzyme
What are the 3 ways siRNAs and miRNAs regulate gene expression?
- Cleavage of mRNA
- Inhibition of translation
- Inhibition of transcription
How does cleavage of RNA take place?
mRNA is cleaved by a RISC containing siRNA or miRNA, after cleavage the mRNA degrades
How do siRNAs and miRNAs affect translation?
The more miRNAs and siRNAs are around the less translation there is
Transcriptional silencing which affects gene expression occurs in 3 steps involving siRNAs. What are these steps?
- siRNAs combine with RITS (RNA-induced transcriptional silencing)
- RITS attracts enzymes that methylate the tails of histone protein
- The addition of methyl groups to DNA keeps other proteins and enzymes from carrying out transcription since they can no longer bind to DNA
In RNA silencing, siRNAs and miRNAs usually bind to which part of the mRNA molecules that they control?
A. 5’ UTR
B. 5’ cap
C. 3’ poly(A)tail - my guess
D. 3’UTR
D
D. 3’UTR
Define epigenetics
The inheritance of variation above and beyond differences in DNA sequence
True/False: Epigenetics are often unstable.
False, epigenetics are mostly stable
How are epigentic effects brought about?
Through changes in chromatin strucutre
What are 3 molecular mechanisms that change chromatin structure to bring about epigenetics?
- Changes in patterns of DNA methylation
- Chemical modification of histone proteins
- RNA molecules that affect chromatin structure and gene expression
Where does changes in pattern of DNA methylation usually occur?
In cytosine, specifically CpG dinucleotides
Define CpG
Cytosine nucleotides that are immediately adjacent to guanine nucleotides
P = phosphate groups that connects C and G nucleotides
Define CpG Islands
DNa regions that have many CpG dinucleotides
How does epigenetics transfer through DNA methylation?
- Before replication, DNA is fully methylated at CpG dinucleotides
- During replication, new DNA strands are synthesized without methyl groups
- After replication, each new DNA molecule will have methylation on one strand but not the other: the DNA is hemimethylated
- Methyl groups attract methyltransferase enzymes, which add methyl groups to the unmethylated strand
- Resulting in fully methylated DNA
Define epigenetic marks
Types of modification that can alter chormatin structure and effect the transcription of genes
Define Paramutation
An interaction between two alleles that leads to a gertibale change in the expression of one of the alleles
What are 3 important features of paramutation?
- The newly established expression pattern of the converted allele is transmitted to future generation, even when the allele that brought about the alteration is no longer present
- The altered allele is now able to convert other alleles to the new phenotype
- There are no associated DNA sequence changes in the altered alleles
Define epigenome
The overall pattern of chromatin modifications in a genome
Gene regulation in bacteria cells:
a. Only occurs at the level of RNA processing
b. Is energy inefficient
c. Allows the bacteria to respond to environmental changes
d. Limits biochemical flexibility
c
c. Allows the bacteria to respond to environmental changes
What percentage of human genes can be regulated through RNA splicing?
95%
In vertebrates, the predominant DNA modification occurs at which base?
Cytosine
Genes that encode protein which are used in metabolism or biosynthesis are called _____ genes
structural
The DNA sequences that are capable of affecting transcription at distant promoters, sometimes tens of thousands of base pairs away, are referred to as…?
Enhancers
What is a molecular mechanism that underlies epigenetic phenotypes?
Modification of histone proteins
A mutations at the operator site prevents the regulator protein, which acts as a repressor, from binding. Constitutive expression results from the operon. This is an example of a(n) ___ operon.
Inducible
Many transcription factors regulate transcription by recruiting other proteins, called…?
cofactors
Unmethylated cytosines are usually near a DNA…?
promoter
Which E. coli strains with the lac genotypes will synthesize B-galactosidase, in the absence of lactose?
lacI-lacP+ lacO+ lacZ+ lacY-
What does the triple methylation of the fourth lysine in an H3 histone tail likely tell you about nearby genes?
That they are transcriptionally active
A researcher is studying histones in mouse cells that have just been acetylated. Which of these statements is TRUE of these histones?
The chromatin formed with these histones will likely appear open
A gene that encodes a protein which is continually expressed to help maintain essential cellular function would be considered…?
Constitutive
How does the availability of molecules such as elongation and initiation factors affect gene expression?
affects the rate of mRNA translation
_____ is initiated by double-stranded RNA molecules that are cleaved and processed
RNA interference
What is a stably inherited phenotype resulting from changes in chromatin without alterations in the DNA sequence?
Epigenetic trait
The observation that one histone mark may affect whether additional marks occur nearby is referred to as ______
crosstalk
Which level of gene control is matched appropriately to a regulatory mechanism?
posttranslational modification-activation of a protein by cleaving it
How would a scientist describe a double-stranded DNA molecule showing methylation on one strand but not the other?
hemi methylated
Would epigenetic changes brought about by methylation be inherited if methyltransferases were NOT present?
No. DNA is replicated in a semiconservative fashion
Enzymes called histone _____ add methyl groups to specific amino acids of histones. Other enzymes, called histone _____, remove methyl groups from histones
methyltransferases; demethylases
What determines whether the addition of a methyl group to a histone tail activates or represses transcription?
which histone is modified and the amino acid in the tail that gets methylated
In your experimental system, you notice that translation of the eukaryotic gene you are working with yields three different proteins. What might be the cause of this observation?
mRNA processing
Where are CpG islands commonly located in mammalian DNA?
promoter regions
What does the “p” stand for in “CpG”?
phosphate
Which statement describes an operon?
A. A gene cluster controlled by a single promoter that transcribes to a single mRNA strand
B. The processing of expos in mRNA that results in a single gene coding for multiple options
C. Protein modifications such as the addition of a function group, or alternate folding of the protein
D. mRNA modifications, such as the addition of a 5’-cap and 3’ poly-A tail and the removal on introns
E. Heritable changes in gene expression that occur without altering the DNA sequence
A
A. A gene cluster controlled by a single promoter that transcribes to a single mRNA strand
Which type of regulation doe the trp operon exhibit?
A. Positive regulation
B. Translational regulation
C. Protein modification
D. Negative regulation
D
D. Negative regulation
A mutation at the operator sire of an operon prevents the repressor from binding.
What effect will this mutation have on transcription in a repressible operon?
A. There will be a significant decrease in the operon’s activity
B. It will be impossible to turn on transcription of the structural genes
C. The operon will always be transcriptionally active
D. There will be no change in the operon’s activity
C
C. The operon will always be transcriptionally active
A mutation at the operator sire of an operon prevents the repressor from binding.
What effect will this, mutation have on transcription in an inducible operon?
A. There will be a significant decrease in the operon’s activity
B. The operon will always be transcriptionally active
C. It will be impossible to turn on transcription of the structural genes
D. There will be no chang in the operon’s activity
B
B. The operon will always be transcriptionally active
A mutant strain of E. coli produces B-galactosidase in the presence and in the absence of lactose
Where in the operon might the mutation in this strain occur, why? (multiple answers)
A. In the lacI gene, which leads to an inactive lac repressor
B. In the promoter region of the operon, where the mutation leads to the failure of the RNA polymerase to bind to the promoter
C. In the operator region, where the mutation leads to the failure of the operator to normally bind the repressor
D. Near the lacI gene, where the mutation leads to increased levels of lac repressor being made
E. In the CAP binding site, where the mutation leads to the inefficiency of RNA polymerase activity
F. In the operator region, which leads to increased binding of the lac repressor to the operator
A and C
A. In the lacI gene, which leads to an inactive lac repressor
C. In the operator region, where the mutation leads to the failure of the operator to normally bind the repressor
Which description applies to epigenetic gene regulation?
A. Heritable changes in gene expression that occur without altering the DNA sequences
B. Protein modification such as addition of a function group, or structural changes such as folding
C. A gene cluster controlled by a single promoter that transcribes to a single mRNA strand
D. Processing of exons in mRNA that results in a single gene coding for multiple proteins
E. mRNA modifications such as additions of a 5’ cap and 3’ poly-A tail and removal of introns
A
A. Heritable changes in gene expression that occur without altering the DNA sequences
Choose all of the statements that describe the benefits of combinatorial control of transcription in a eukaryotic multi-cellular organism (multiple answers)
A. An operon is able to initiate transcription
B. RNA reverts to DNA prior to transcription
C. mRNA synthesis occurs at an accelerated rate
D. RNA polymerase has selective access to specific genes for tissues specific effects
C and D
C. mRNA synthesis occurs at an accelerated rate
D. RNA polymerase has selective access to specific genes for tissues specific effects
Many molecules, including transcription factors, work together to transcribe genes and translate the information taken from the genes into proteins
What is a transcription factor?
A. A protein, such as RNA polymerase, that transcribes a specific DNA sequence
B. A nucleotide that binds to a specific DNA sequence to activate transcription
C. A protein that binds to a specific mRNA to prevent it from being translated
D. A protein that binds to a specific DNA sequence to regulate transcription
E. A nucleotide sequence that signals a ribosome to start protein translation
D
D. A protein that binds to a specific DNA sequence to regulate transcription
