EXAM 4 QUESTIONS Flashcards
Define gene regulation.
What are the 3 ways gene regulation can be controlled in a cell?
Gene regulation is defined as the control of a gene’s transcript and its protein product.
It can be achieved by altering either the
1) Transcription of the gene (RNA level), (with repressors, enhancers…).
2) mRNA processing (alternative splicing)
3) Translation of the protein from that transcript,
4) Altering the structure of DNA such that transcription cannot occur.
5) mRNA stability (mRNA can be degraded)
Acetylation increases transcription.
Methylation decreases transcription.
Enhancers, Inducers, and repressors also help regulate gene expression.
How are miRNAs produced?
How do miRNAs function to affect production of proteins? Provide sufficient detail in your answer for full credit.
Look for this in SLIDES
The miRNAs are produced when the double stranded DNA transcribed into RNA, creates hairpin loop structure,
then miRNAs are cleaved by a dicer enzyme.
It can bind with RISC (RNA-induced silencing complex) or RITS (RNA-induced transcriptional silencing).
mRNA can be cleaved for degradation when miRNA is complementary to mRNA, or inhibit translation by binding mRNA when it is not complementary.
RITS complex can lead to chromatin remodeling by methylation, or alternative silence the mRNA.\
List at least 3 different types of DNA repair and briefly explain how each is carried out.
Photoreactivation:
Repairs dimers that were formed due to UV light mutagen. Blue light and Photoreactivation enzymes separate the dimers back into proper bases.
Base excision repair:
DNA glycosylase recognizes and excises the mismatched base.
AP endonuclease recognizes the lesion and nicks the DNA there.
DNA polymerase and ligase synthesize the new nucleotide and seal the gap, respectively.
In nucleotide excision repair, the same thing occurs as with base excision repair except that instead of just one base and nucleotide being removed, after the first one is removed and the DNA is nicked, then an excision endonuclease comes and removes a whole stretch of nucleotides. Then DNA polymerase synthesizes the new nucleotides and ligase seals the gap.
Lactose Absent -
Lactose Present +
csdcda
**Look this up!!!
The following table lists several genotypes associated with the lac operon in E. coli. For each, indicate with a “+” or “-” whether beta-galactosidase would be expected to be produced at induced levels.
(Assume that glucose is not present in the medium.)
- I+ O+ Z+ / F’ I+ O+ Z+
- I- Oc Z- / F’ I- Oc Z-
- I- Oc Z+ / F’ I- O+ Z+
- Is Oc Z- / F’ Is O+ Z+
- +, +
- -, -
- +, +
- -, -
Name at least 2 mechanisms involved in epigenetic regulation of gene expression.
DNA methylation
Chromatin Remodeling Complex
Histone Acetylation
Describe alternative splicing.
What is the ultimate result of the alternative splicing process?
Alternative Splicing refers to the process that involves removing introns and sometimes some exons from the mRNA transcript before translation.
There are sometimes many different ways that a transcript can be spliced, so that you can begin with two identical pre-splicing transcripts and end up different proteins yielded by each.
Alternative splicing contributes to diversity.
What is catabolite repression?
How does it allow a bacterial cell to use glucose in preference to other sugars?
catabolite repression =
The selective inactivation of an operon by a metabolic product of the enzymes encoded by the operon.
In the bacterial cell, the glucose inhibits lac gene expression:
The lac system uses CAP in a positive inducible system.
For the lac system to proceed, CAP must bind to cAMP.
The amount of functioning cAMP is inversely related to the amount of glucose in the cell.
Thus, even if there are high levels of lactose available, the lac system is expressed at high levels only when there is little to no glucose present.
We discussed cis regulatory elements (CREs) in transcriptional networks. What are CREs and how are they involved in gene regulation?
CREs are regulatory elements that can only affect the DNA they are located on and not other DNA strands. They have variable positions and variable operations.
Promoters are CREs located upstream of a transcription start site; they hold the site where transcription is initiated.
Enhancers & silencers are examples of CREs.
Enhancers are CREs that increase transcription of a gene, and can be located upstream, downstream, or within the genes they regulate.
Silencers are CREs that inhibit transcription of a gene.
A _________________, which binds to a core promoter, consists of general transcription factors and RNA polymerase.
basal transcription apparatus
Proteins that affect chromatin structure without altering histone chemical structure are called…
Chromatin remodeling complexes
The human condition _____ is caused by unrepaired UV-induced lesions
Xeroderma pigmentosum
A eukaryotic DNA sequence that affects transcription at distant promoters is called a(n)
enhancer
Within the control region of the tryptophan operon is a second of DNA that is sensitive to levels of tryptophan in the system.
What is the name of this region?
leader/attenuator region
Constitutive mutations may occur in various components of the lac operon.
Name 2 genes of the lac operon in which constitutive mutations could occur
LacI-, LacOc
Certain mutations in the regulator gene of the lac system in E. coli result in maximal synthesis of the lac proteins (B-galactosidase, etc.) even in the absence of the inducer (lactose).
Provide an explanation for this observation.
These mutations are constitutive mutations of the operator, such as lacOc or lacI-, which allows the lac operon system to be on all the time, regardless of the presence or absence of the lactose inducer.
Constitutive mutations are not regulated and are continually active to allow the synthesis of lac proteins.
What is the common influence of ultraviolet light on DNA?
Pyrimidine Dimer formation
E. coli lac operon control by lacI
negative inducible
In what part of the mRNA does degradation generally begin?
at the 3’ end with the removal of the Poly(A) tail
Two formal terms used to describe categories of mutational nucleotide substitutions in DNA:
transversions and transitions
A _________ mutation changes a codon that specifies an amino acid into one that terminates translation.
nonsense
Mutations which arise in nature, from no particular artificial agent are called _____ .
spontaneous mutation
Insulators can block the effects of enhancers only when….
they lie BETWEEN an enhancer and a promoter.
Regulatory proteins that bind DNA have common motifs that interact with sequences of DNA.
How do amino acids in DNA-binding proteins interact with DNA?
By forming Hydrogen Bonds with DNA bases
Which parts of the DNA region encode proteins?
I, Z, Y, A
The role of tautomerism in causing mutations relates to the fact that the process ultimately affects the:
hydrogen bonding properties of nitrogenous bases
Mutations that arise in nature, from no particular artificial agent, are called
Spontaneous mutations
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https://docs.google.com/document/d/1nTc7G1Omlnvhyux78oOIhXmJSrBr0wfb5oJqPbCKYCQ/edit?pli=1#
Name 2 mutagens which would be classified as base analogues.
5-bromouracil and 2-aminopurine
Which of the following terms best characterizes catabolite repression associated with the lactose operon in E. coli?
positive control
Regarding eukaryotic and prokaryotic genetic regulation, what process seems to be the most similar between the two?
transcriptional regulation
Which of the following are Epigenators?
Stress Starvation Inflammation All of the above None of the above
All of the above
TRUE or FALSE?
An epigenetic trait is a stable, mitotically but not meiotically heritable phenotype that results from changes in gene expression without alteration in the DNA sequence
False
TRUE or FALSE?
Antisense RNA can affect the translation of mRNA.
TRUE
What is the function of cAMP in regulation of the lac operon?
It activates an activator protein.
TRUE or FALSE?
Regulation of RNA transport through the nuclear membrane is as common in prokaryotes as in eukaryotes
False
TRUE or FALSE?
In a negative repressible operon, the regulator operon, the regulator protein is synthesized as an inactive repressor.
true
DNA methylation may be a significant mode of genetic regulation in eukaryotes. Methylation refers to ______
addition of methyl groups to the cytosine of CG doublets
Name two mutagens which would be classified as base analogues.
5-bromouracil and 2-aminopurine
How are miRNAs produced? How do miRNAs function to affect production of proteins? Provide sufficient detail in your answer for full credit.
The miRNAs are produced when double-stranded DNA is transcribed into RNA.
It creates hairpin loop structure, then miRNAs are cleaved by a dicer enzyme.
It can bind with RISC (RNA-induced silencing complex) or RITS (RNA-induced transcriptional silencing).
mRNA can be cleaved for degradation when miRNA is complementary to mRNA, or inhibit translation by binding mRNA when it is not complementary.
RITS complex can lead to chromatin remodeling by methylation, or alternative silence the mRNA.
A condition in which a gene or group of genes is expressed all the time
constitutive
Where would the lac repressor be bound in a (nonmutant) E. coli cell that is growing in low glucose and high lactose?
The repressor would not be bound.
This term describes genetic elements that affect other elements only when they are located adjacent to them. For example, the operator has this effect on its structural genes.
cis-acting
Highly repetitive DNA
telomeres
unique-sequence DNA
gene-encoding sequence
A constitutive gene is ____ regulated and is expressed ____.
not, continually
How does the availability of glucose in the environment affect the regulation of the lac operon?
What is the term describing this regulation, and how is it accomplished (short outline)?
When glucose is available in the environment, the lac operon is repressed.
This regulation is positive control.
Glucose inhibits adenyl cyclase conversion to cAMP.
No cAMP to bind to the CAP means RNA polymerase cannot bind to the complex and the DNA, so transcription is inhibited.
The ___________ can be used to quickly screen chemicals for their ability to be mutagenic (and hence potentially carcinogenic).
Ames test
Transcriptional repression by methylation of DNA is most common in sequences called ______islands.
CpG
The ______ is a type of _______ protein that binds to a region of DNA in the promoter of a gene called the _______ and prevents transcription from taking place in bacteria.
repressor, regulatory, operator
A(n) ________ can function at variable distances and in either orientation. However, it differs from an enhancer in that it cannot function downstream of the transcription starting point.
Upstream Activator Sequence (UAS)
To use RNAi (RNA interference) as a research tool, investigators introduce short synthetic ______ RNA into cells.
double-stranded, small interfering
Alternative RNA splicing is a method that apparently evolved for the production of many different polypeptides from the same pre-mRNA.
Provide an example of alternative splicing.
The drosophila protein Dscam has many sites that can be alternatively spliced (~38000)
How do enhancer elements differ from suppressor mutations?
Enhancer elements enable transcription of a gene to be increased.
Suppressor mutations cause transcription to be inhibited.
Which of the below is not true about the location of enhancers?
The position of the enhancer has no effect on gene regulation.
siRNAs and miRNAs are produced by
the cutting and processing of double-stranded RNA by Dicer enzymes
An example of a gene product encoded by a regulatory gene is
repressor protein
A mutant E. coli strain, grown under conditions that normally induce the lac operon, does not produce beta-galactosidase.
What is a possible genotype of the cells?
lacI+ lacP- lacO+ lacZ+ lacY+ lacA+
After translation, eukaryotic proteins can be modified by:
acetylation
the addition of phosphate groups
the removal of amino acids
the addition of methyl groups
all of the above
all of the above
A mutant E. coli strain, grown under conditions that normally induce the lac operon, produces high amounts of beta-galactosidase.
What is a possible genotype of the cells?
lacI+ lacP+ lacOc lacZ+ lacY+ lacA+
Which of the following terms best characterizes catabolite repression associated with the lactose operon in E. coli?
positive control
The role of tautomerism in causing mutations relates to the fact that the process ultimately affects the
hydrogen bonding properties of nitrogenous bases
In the lactose operon, the product of structural gene lacZ is capable of
splitting the beta-linkage of lactose
What term refers to a contiguous genetic complex that is under coordinate control?
operon
Regarding eukaryotic and prokaryotic genetic regulation, what process seems to be the most similar between the two?
transcriptional regulation
When transcriptional activators interact with DNA, is the resulting genetic control typically positive or negative?
positive
TRUE or FALSE?
Under a system of negative control, genetic expression occurs unless such expression is shut off by some form of regulator.
TRUE
What experimental results would indicate that the mutation lacIs is dominant to lacI+?
The observation that lacIs is a trans-acting superrepressor and represses the operator on both sides of the DNA sequence, while lacI+ still has variable regulation (for example: transcription is off when lactose is not present, but transcription is on when lactose is present.)
The observation that lacIs is a trans-acting superrepressor and represses the operator on both sides of the DNA sequence, while lacI+ still has variable regulation (for example: transcription is off when lactose is not present, but transcription is on when lactose is present.)
DNA repair
The molecular nature of transposable elements was first understood in E. coli due to the simplicity of the E. coli genome. Which of the following types of DNA contribute significantly to the genome complexity of other organisms?
LINES, SINES, LTR retrotransposons
This is the region of a gene where RNA polymerase binds to initiate transcription.
promoter
Since the binding of the _________ to the _________ prevents it from binding to _________ by causing a conformational change in its structure, it is called an _________ protein.
inducer,
repressor protein,
DNA,
allosteric
Highly methylated region of a chromosome that has become largely deactivated and can be seen as dense-regions when viewed using electron microscopy.
heterochromatin
Frameshift mutations are caused by the __________ or __________ of one or more nucleotides in DNA.
removal, insertion
Which of the following is NOT true regarding the differences in mRNA between prokaryotic cells and eukaryotic cells?
In eukaryotic cells, mRNA is spliced before translation, while in prokaryotic cells there is no mRNA splicing
In eukaryotic cells, the 5’ end of mRNA is modified with a cap, while in prokaryotic cells there is no cap.
In eukaryotic cells, the 3’ end of mRNA is modified with a tail, while in prokaryotic cells there is no tail.
In eukaryotic cells, the transcription to mRNA and the translation from mRNA are coupled, while in prokaryotic cells transcription and translation are not coupled.
in eukaryotic cells, the transcription to mRNA and the translation from mRNA are coupled, while in prokaryotic cells transcription and translation are not coupled
In what part of the mRNA does degradation generally begin?
3 prime end poly a tail.
An example of a gene product encoded by a regulatory gene is
repressor protein
Acridine orange is an alkylating agent?
FALSE
What is the Ames test and how does it work?
Can be used to quickly screen chemicals for their ability to be mutagenic (and hence potentially carcinogenic).
It implores mutagens of histadine in its mechanism (his-).
It also places the mutagens in a test tube that has liver cells because the liver cells will allow to mutagens to be expressed.
the test tubes are then plated, presence of colonies indicates that a mutagen is present, absence of colonies means that a mutagen is not present.
Under certain conditions, the rate of mutation of a particular gene may be determined in humans. What properties of the mutation would favor the most direct determination of mutation rate in humans? (Check all that apply)
Dominant
X-chromosome
Fully expressed
100% penetrance
(all but recessive)
T/F: Alternative RNA processes generate different mRNAs which can direct the synthesis of different polypeptides.
true
T/F: The CAAT (CAAT box) sequence appears to be critical to the promoters ability to facilitate transcription.
true
I P O Z Y A
Which parts of the DNA region encode proteins?
I, Z, Y, A
This process moves a nucleosome from the TATA box of a gene’s promoter so that transcription can occur. (short answer)
!!!!!!
chromatin remodeling
Proteins that affect chromatin structure without altering histone chemical structure are called…
Chromatin remodeling complexes
Parts of chromosome that are not methylated for inactivation but rather are less dense-staining and are likely active in transcription in the cell
Euchromatin
UV light causes pyrimidine to form in DNA. Some individuals are genetically incapable of repairing dimers at “normal” rates.
Such individuals likely suffer from..
Xeroderma pigmentosum
Transcription factors appear to be important molecules relating to the regulation of gene activity. Regarding eukaryotes, two general classes of transcription factors exist.
Briefly describe each.
One class assembles at promoter regions adjacent to the site of transcription. The other class binds at more distant regions (enhancers)
Recruitment of an activator to a promoter results in increased gene expression. Recruitment of a repressor leads to decreased gene expression.
Regulatory proteins that bind DNA have common motifs that interact with sequences of DNA. How do amino acids in DNA-binding proteins interact with DNA?
By forming hydrogen bonds with DNA bases
It’s possible for a repressor to negatively regulate the expression of an operon because….
Repressor binding site overlaps promoter site of operon allowing it to physically block binding of RNA polymerase.
Transcription factors are proteins with at least two functional ______.
domains
What term is used to refer to the process in which DNA can be introduced into host bacterial cells?
transformation
Two formal terms to describe mutational nucleotide substitution in DNA are called…
Transversions and transitions
Under the system of genetic control of the tryptophan operon
When there is no tryptophan in the medium, transcription of the trp operon occurs at high level
The general term for a non-polymerase protein that binds to an operator (fill in blank)
repressor
Degradation of a eukaryotic mRNA is generally preceded by shortening of the___
Poly A tail
These are factors that need not be adjacent to the genes they control. An example would be the lac operon’s regressor protein
trans-acting
Regulation of gene expression using siRNAs is found in
Prokaryotes only
Eukaryotes only
Both
Eukaryotes only
What modification neutralizes the charges on histones that promotes ionic interactions with DNA?
Phosphorylation
Polydenylation
Acetylation
Demethylation
Acetylation
A class of mutations which results in multiple contiguous amino acid changes in proteins is likely to be the following
Frameshift
PPPPPPPPPPPPP
What is meant by polycistronic mRNA? Give an example
Messenger RNA polymer that carries code for more than one polypeptide chain (ex. lactose and tryptophan operon)
One type of mutation involves the replacement of a purine with a purine. What general term is associated with this mutational phenomena?
transition
*replacing a purine with a pyrimidine or vice versa is called a transversion
A condition in which a gene or group of genes is expressed all the time.
constitutive expression
Name three types of consensus sequences or modular DNA sequences that exist upstream from the coding regions of some eukaryotic genes.
CAAT, TATA, GC repeats
When X rays penetrate cells, electrons are ejected from atoms of molecules. Stable molecules can be transformed into what types of hazardous materials?
Free radicals
When referring to attenuation in regulation of the tryptophan operon it would be safe to say that when there are high levels of tryptophan available to the organism
transcriptional termination is likely
E. coli bacteria are placed into a medium containing glucose and lactose. Which of the genes below do you expect to be turned on?
f-galactosidase Lac I Lac P Permease None of the above
None of the above
Which of the following is TRUE for both prokaryotic and eukaryotic gene expression?
RNA polymerase binds to the promoter region to begin transcription
Which of the following clusters of terms applies when addressing enhancers as elements associated with eukaryotic genetic regulation?
cis-acting, variable orientation, variable position
The ______ sequence is specific to many (but not all) eukaryotic promoters and often facilitates transcription.
CAAT, CG
The lac repressor protein controls expression of the lac operon via ________________
binding to the lac operator site to repress expression
Certain mutations in the regulator gene of the lac system in E. coli result in maximal synthesis of the lac proteins (B-galactosidase, etc.) even in the absence of the inducer (lactose).
Provide an explanation for this observation.
Certain mutations in the regulator gene of the lac system in E. coli result in maximal synthesis of the lac proteins (B-galactosidase, etc.) even in the absence of the inducer (lactose). Provide an explanation for this observation.
____________ mutations produce new traits and are usually dominant
Gain-of-function
