Chapter 12: Control of Gene Expression Flashcards
Why is gene expression control necessary?
- Certain genes are necessary for the entire lifespan of an organism
- Other genes are needed at specific stages of development
- Other genes are needed to react to the environment
What are the 5 different levels at which genes may be controlled? What does it act on?
- Alteration of structure (compact DNA)
- Transcription (relaxed DNA)
- mRNA processing (pre-mRNA)
- RNA stability and translation (processed mRNA)
- Posttranslational modifications (inactive protein)
Which levels of gene control may primarily occur in Eukaryotes?
- Alteration of structure
- mRNA processing
What molecules are an example of a molecule that can control translation?
siRNA
Genes may be separated into two broad categories, what are they?
- Structural genes
- Regulatory genes
What do structural genes encode for?
- Enzymes, proteins, or molecules that are not really involved in the regulation of transcription
- Do not interact with DNA
What is the function of regulatory genes?
- Capacity to bind DNA, impacting the transcription and activation of other genes
- Possess features (motifs) that allow them to interact directly with the DNA
Name three examples of structural motifs that are capable of binding DNA
- Helix-turn-helix
- Zinc fingers
- Leucine zippers
What does polycistronic mean?
- In bacteria, not all genes possess their own promoter
- Multiple genes may be controlled by a single promoter
What is an operon?
- Polycistronic gene
- Transcriptional unit that includes a series of structural genes, a promoter, and an operator
- Group of genes that are transcribed as a unit, producing a single mRNA that encodes for several proteins
What does an operon include?
- Structural genes
- Promoter
- Operator
What encodes a regulator protein? What does it bind to?
- Separate regulator gene, with its own promoter
- The regulatory protein may bind directly the operator region of DNA
Which organisms contain operons?
Largely contained within Prokaryotes and bacteria
Are genes in an operon regulated differently or in the same way?
In the same way, as they are taking part in a given process
What occurs if there is no inducer present in an operon?
- Regulator protein is a repressor that binds to the operator
- Prevents transcription of the structural genes
What occurs if there is an inducer present in an operon?
- Binds to the regulator
- Makes the regulator unable to bind to the operator
- Allows transcription to take place
Are the regulator proteins (inducer or repressor) present in the first or second step?
Only in the second step
What is a negative operon?
When the regulator protein is attached to the DNA, the state of transcription is OFF
What is a positive operon?
When the regulator protein is attached to the DNA, the state of transcription is ON
What is an inducible operon?
Induces transcription from off to on
What is a repressible operon?
Represses transcription from on to off
What is the regulatory protein in negative inducible operons? What occurs to transcription?
- Active repressor turns off transcription
- Substrate from transcription makes the repressor inactive
- Transcription is turned ON
What is the regulatory protein in positive inducible operons? What occurs to transcription?
- Inactive activator turns transcription off
- Substrate from transcription makes the activator active
- Transcription is turned ON
What is the regulatory protein in negative repressible operons? What occurs to transcription?
- Inactive repressor turns transcription on
- Product from transcription makes the repressor active
- Transcription is turned OFF
What is the regulatory protein in positive repressible operons? What occurs to transcription?
- Active activator turns transcription on
- Product from transcription makes the activator inactive
- Transcription is turned OFF
Why is lactose metabolism necessary in bacteria?
- Most bacteria prefer to utilize glucose as a carbon source
- If glucose is not present in sufficient quantities, lactose is utilized
What is the function of permease?
Actively transports lactose into the cell
What is the function of B-galactosidase?
- Converts lactose into allolactose
- Converts allolactose into glucose and galactose
What is the function of transacetylase?
Neutralization of other compounds that may enter the cell alongside lactose
What does the LacZ gene encode?
B-galactosidase
What does the LacY gene encode?
Permease
What does the LacA gene encode?
Transacetylase
What occurs to the lac operon in the absence of lactose?
The regulator protein (repressor) binds to the operator and inhibits transcription
What kind of operon is the lac operon?
Negative inducible
What occurs to the lac operon when lactose is present?
- Some of it is converted into allolactose (inducer), which then binds to the regulator protein, making it inactive
- The regulator protein cannot bind to the operator, and the structural genes are transcribed and translated
How is allolactose produced to induce the expression of genes in the lac operon if there is no lactose present?
The operons are “leaky” as they are never entirely turned off, but instead function at a very low rate
How do the operator and promoter regions relate to each other in the lac operon?
The operator overlaps the promoter at the 5’ end of the first structural gene
Why is transcription blocked when the repressor binds to the operator region of the lac operon?
The RNA polymerase is physically blocked by the repressor protein, and cannot reach the gene for transcription
Gene cloning uses ____________ to produce blue and white screening.
B-galactosidase
What does a blue colony signify?
- B-galactosidase is intact
- The gene is undisrupted
- There is no insert that is breaking the open reading frame
What does a white colony signify?
- B-galactosidase is split in two
- Insert is present in the middle
- Possesses the gene cloned within the plasmid
What system occurs at the same time as the lac operon to produce the proper energy balance within the cell?
Catabolite activator protein (CAP)
What does the CAP system sense?
The levels of the end-product of lactase metabolism, glucose
What occurs to the CAP system when glucose is low?
- Causes the cell to synthesize cAMP, which readily binds CAP
- CAP-cAMP complex binds DNA and increases the efficiency of polymerase binding
- High rates of transcription and translation of structural genes, and the production of glucose from lactose
What occurs to the CAP system when glucose is high?
- Levels of cAMP are low, and cAMP is less likely to bind to CAP
- RNA polymerase cannot bind to DNA as efficiently so transcription is at a low rate
What type of regulator is the CAP system? What is its primary function?
- Positive control and catabolite repression
- Binds to the promoter of the lac operon and stimulates transcription
What does the binding of the cAMP-CAP complex to DNA produce?
A sharp bend in DNA that activates transcription solely when glucose is low
What kind of operon is the trp operon?
Negative repressible operon
What is the function of the trp operon?
- Controls the biosynthesis of tryptophan
- Tryptophan is a rate-limiting amino acid in bacteria, as it is limited in the environment
Which level of control is almost exclusively found in Eukaryotes?
Alteration of gene structure (epigenetics)
What is chromatine?
- Complex of DNA and histone proteins
- DNA (negatively charged) wraps around histone proteins (positively charged)
Give examples of common histone tail modifications.
- K (lysine) acetylation
- K (lysine) methylation
- Phosphorylation
- Ubiquitylation
What does H3K9me3 signify?
- H3 = Histone H3
- K9 = Lysine 9
- me3 = trimethylation
Is it possible to contain both activating and repressive marks on the same nucleosome?
Yes
What may change the histone code?
- Cell type
- Tissue type
- Environment (ex: identical twins raised separately have very different epigenomes, but identical genomes)
What is histone acetylation catalyzed by? What is it removed by?
- Catalyzed by acetyltransferases (HATs)
- Removed by deacetylases (HDACs)
What is histone methylation catalyzed by? What is it removed by?
- Catalyzed by methyltransferases (HMTs)
- Removed by demethylases (HDMs)
What is the consequence of histone acetylation?
- The addition of acetyl groups to lysine residues REMOVE the positive charge on lysine, decreasing their interaction with negative DNA
- Increases the accessibility of DNA
What is the consequence of histone methylation?
- Does not affect the charge
- Functions as signal molecules for code readers (modifiers)
What is the function of code readers?
- Detect methylation
- Either release or compact the DNA
- The number of methyl groups may differ whether they cause activation or repression
What does H3Kme2 cause? What about H3Kme3?
- H3Kme2: activation/repression
- H3Kme3: repression
How does the histone code differ from the genome code?
- Histone code is extremely dynamic
- Genome of a species takes millions of years to evolve
How does histone methylation and DNA methylation differ?
- Histone methylation occurs on the histone proteins
- DNA methylation occurs directly on the DNA at cytosine residues
What results from the transfer of a methyl group to DNA?
5-methyl-cytosine residues
DNA methylation does not alter _________, and is catalyzed by what?
base pairing DNA methyltransferases (DNMTs)
Is DNA methylation considered epigenetic control? Why or why not?
It is considered epigenetic control, as it does NOT create mutations, but instead changes the conformation of DNA
What kind of signals does DNA methylation provoke?
- Found in transcriptionally silent regions
- ALWAYS signals repression by compacting the DNA and rendering genes inaccessible
Is DNA methylation maintained?
- Yes, through DNA replication
- Epigenetics is heritable, but the level of heritability is unknown
Are acetyl groups present when the FLC gene is activated? Why?
- Yes they are
- There is no plus charge on histones because of the presence of acetyl groups
- FLC gene is accessible
What does the FLC gene encode for?
Regulator protein that represses flowering, which inhibits flowering to take place
What does the FLD gene encode for?
- Histone deacytelase enzyme that removes acetyl groups and restores chromatin structure
- Inhibits the transcription of FLC taking place
- Flowering is not suppressed, and so it takes place
Are acetyl groups present when the FLD gene is activated? Why?
- No, because FLD encodes for a deacytelase enzyme
- The positive charges on histone allows the compaction of DNA
Why do promoters possess many different response elements?
Because they must demonstrate flexibility through these elements, and respond to many different conditions
What is GRE? What is MRE?
- GRE: steroid-receptor protein
- MRE: methyl-regulatory element
What response element responds to heat and other stress?
Heat-shock element
What is the function of an insulator?
Blocks the action of an enhancer on a promoter when the insulator lies between the enhancer and the promoter
Why are insulators necessary?
- In genes that are physically close in space, and the DNA was in an open conformation
- If there was no insulator present in this situation, the elements binding to the promoter of one gene would affect the other
- To keep the signal inputs to a single side of the DNA
What is a constitutive gene?
A constitutive gene is not regulated and is expressed continually
What are the two possible modifications to DNA that alter its structure?
- DNA methylation
- Changes in chromatin
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 difference between a structural gene and a regulator gene?
- Structural genes encode proteins
- Regulator genes control the transcription of structural genes
What operons usually control proteins that carry out degradative processes?
Inducible operons
In a negative inducible operon, the regulator protein is synthesized as A) an active activator B) an inactive activator C) an active repressor D) an inactive repressor
C) an active repressor
In a negative repressible operon, the regulator protein is synthesized as A) an active activator B) an inactive activator C) an active repressor D) an inactive repressor
D) an inactive repressor
What operons usually control enzymes that carry out biosynthesis of molecules needed in the cell?
Repressible operons
In a positive inducible operon, the regulator protein is synthesized as A) an active activator B) an inactive activator C) an active repressor D) an inactive repressor
B) an inactive activator
In a positive repressible operon, the regulator protein is synthesized as A) an active activator B) an inactive activator C) an active repressor D) an inactive repressor
A) an active activator
What compound is responsible for the induction of the lac operon?
Allolactose
In the presence of allolactose, the lac operon repressor A) binds to the operator B) binds to the promoter C) cannot bind to the operator D) binds to the regulator gene
C) cannot bind to the operator
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) It cannot bind to the operator and transcription takes place
What are the three major differences between gene regulation in prokaryotes and eukaryotes?
1) Many prokaryotic genes are transcribed into a single RNA molecule, while most eukaryotic genes have their own promoters and are transcribed separately
2) Chromatin structure affects gene expression in eukaryotes
3) The nuclear membrane separates transcription and translation in eukaryotes in time and space
Most transcriptional activator proteins affect transcription by interacting with A) introns B) the basal transcription apparatus C) DNA polymerase D) nucleosomes
B) the basal transcription apparatus
What are enhancers?
Regulatory elements that may be located some distance from the gene
What occurs if an insulator lies between an enhancer and a promoter?
It blocks the action of the enhancer
What occurs if an insulator lies outside the region between the enhancer and promoter?
No effect
How does the binding of regulatory proteins to enhancers affect transcription at genes that are thousands of base pairs away?
The DNA between the enhancer and promoter loops out, so that transcription activators bound to the enhancer are able to interact directly with the basal transcription apparatus
How is the transcription of eukaryotic genes coordinated (e.g. heat shock proteins) if they are not organized into an operon?
They share short regulatory sequences in their promoters or enhancers (response elements)
What controls sex determination in Drosophila melanogaster?
Alternative splicing of the dsx pre-mRNA
What causes female Drosophila melanogaster?
1) When X:A = 1, the activated Sxl gene produces a protein that causes tra pre-mRNA to be spliced to produce Tra protein
2) Tra and Tra-2 proteins direct female-specific splicing of dsx pre-mRNA
3) Produces proteins causing the embryo to develop into a female
What causes male Drosophila melanogaster?
1) When X:A = 0.5, the Sxl gene is not activated, and the Sxl protein is not produced
2) tra pre-mRNA is spliced at an upstream site, producing a non-functional Tra protein
3) Without Tra, the male-specific splicing of dsx pre-mRNA produces male Dsx proteins that cause the embryo to develop into a male
What does RNA silencing lead to?
- Degradation of mRNA
- Or, the inhibition of translation or transcription
What is the major difference between siRNAs and miRNAs concerning their origin?
- siRNAs are NOT encoded in the genome (arise from a virus or pathogen)
- miRNAs are encoded by a gene within the genome
What is the major difference between siRNAs and miRNAs concerning their ultimate function?
- siRNAs degrade mRNA by cleavage
- miRNAs lead to the inhibition of translation
How are siRNAs produced?
1) Double-stranded RNA is recognized by Dicer, which cleaves them into siRNAs
2) siRNAs combine with RISC, and pair with complimentary sequences of mRNA from the originator (ex: virus)
3) The complex then cleaves and degrades the mRNA that “should not be there”
How are miRNAs produced?
1) Hairpin structure is created from an RNA molecule (encoded within the genome), which is detected and cleaved into miRNAs by Dicer
2) miRNAs combine with RISC and pair imperfectly with mRNA, coming from ANOTHER gene within the genome
3) Leads to the inhibition of translation
How may certain siRNAs inhibit translation?
- By methylating histone proteins or DNA
- siRNAs may interact with DNA itself, changing the chromatin structure
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
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 D) 3' UTR
D) 3’ UTR
Regulation by small RNAs occurs in eukaryotes or bacteria?
Both
What are three types of molecular mechanisms that alter chromatin structure and underlie many epigenetic phenotypes?
1) Changes in patterns of DNA methylation
2) Chemical modifications of histone proteins
3) RNA molecules that affect chromatin structure and gene expression
A mutation at the operator prevents the regulator protein (repressor in a repressible operon) from binding. What effect will this mutation have?
The operon will never be turned off, and transcription will take place all the time
A mutation at the operator prevents the regulator protein (repressor in an inducible operon) from binding. What effect will this mutation have?
The result will be constitutive expression, and transcription will take place all the time
A mutation prevents the catabolite activator protein (CAP) from binding to the promoter in the lac operon. What will the effect of this mutation be on the transcription of the operon?
RNA polymerase will bind the lac promoter poorly, significantly decreasing the transcription of the lac structural genes
How do amino acids in DNA-binding proteins interact with DNA?
A) By forming covalent bonds with DNA bases
B) By forming hydrogen bonds with DNA bases
C) By forming covalent bonds with DNA sugars
B) By forming hydrogen bonds with DNA bases
What is the difference between a structural gene and a regulator gene?
A) Structural genes are transcribed into mRNA, but regulator genes aren’t.
B) Structural genes have complex structures; 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; regulator genes control the transcription of structural genes.
D) Structural genes encode proteins; regulator genes control the transcription of structural genes.
What is the effect of high levels of glucose on the lac operon?
A) Transcription is stimulated.
B) Little transcription takes place.
C) Transcription is not affected.
D) Transcription may be stimulated or inhibited, depending on the levels of lactose.
B) Little transcription takes place.
What are some of different processes that affect gene regulation by altering chromatin structure?
Three general processes are the modification of histone proteins (e.g. methylation and acteylation of histones), chromatin remodelling, and DNA methylation.
Which is not a mechanism of epigenetic change?
A) DNA methylation
B) Alteration of a DNA base sequence in a promoter
C) Histone acetylation
D) Nucleosome repositioning
B) Alteration of a DNA base sequence in a promoter
