MolGen4500 Module 4

Which of these is a level of regulation in eukaryotes? Transport Processing Post-translational Transcriptional Operon

1,2,3,4,

Fill in the blanks in the "level of transcription" column of this table with: + for high levels of transcription, and - for minimal levels of transcription of the lac operon. Consider regulation by both the lac repressor and CAP (catabolite activator protein). The strain is wild type, with no partial diploidy. Please label your answer with numbers 1-4 based on the chart below. Medium conditions Level of transcription 1 high glucose, no lactose 2 no glucose, high lactose 3 high glucose, high lactose 4 no glucose, no lactose

1- 2+ 3- 4-

Name two mutagens which would be classified as base analogues. (multiple choice)

5-bromouracil and 2-aminopurine

What is catabolite repression? How does it allow a bacterial cell to use glucose in preference to other sugars?

A process where the presence of glucose inhibits transcription of genes in the presence of other sugars. The genes for the other sugars are suppressed so only enzymes produced in the presence of glucose are utilized. Glucose presence varies inversely with CAMP levels, so when glucose is high, CAMP is low, and CAP is unable to bind to CAMP, therefore transcription cannot take place.

What modification neutralizes the charges on histones that promotes ionic interactions with DNA? Phosphorylation Polydenylation Acetylation Demethylation

Acetylation

Which of the following are Epigenators? Stress Starvation Inflammation All of the above None of the above

All of the above

Describe alternative splicing. What is the ultimate result of the alternative splicing process?

Alternative splicing is the process where all of the introns are removed from the mRNA strand but different exons can be left in and different ones removed. This results in different proteins being translated from the same original DNA sequence.

The ___________ can be used to quickly screen chemicals for their ability to be mutagenic (and hence potentially carcinogenic).

Ames test

List at least three different types of DNA repair and briefly explain how each is carried out.

Base excision repair Nucleotide excision repair Direct repair Base excision repair occurs this way: 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. Direct repair occurs by directly repairing the base instead of removing and replacing it.

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

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. Enhancers and silencers are examples of CREs. Enhancers increase transcription of a gene. Silencers inhibit transcription of a gene.

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.

What is a mutation?

Change in DNA sequence

Proteins that affect chromatin structure without altering histone chemical structure are called...

Chromatin remodeling complexes

Transcriptional repression by methylation of DNA is most common in sequences called ______islands.

CpG

Name at least two mechanisms involved in epigenetic regulation of gene expression.

DNA methylation Chromatin Remodeling Complex Histone Acetylation

Strand discrimination during the process of ______ is based on DNA methylation in E. coli

DNA repair

In what part of the mRNA does degradation generally begin? (multiple choice)

Degradation of poly-A tail from 3'

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)

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.

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

Regulation of gene expression using siRNAs is found in Prokaryotes only Eukaryotes only Both

Eukaryotes only

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

Regulation of RNA transport through the nuclear membrane is as common in prokaryotes as in eukaryotes

False

A class of mutations which results in multiple contiguous amino acid changes in proteins is likely to be the following Base analogue Transition Transversion Recombinant Frameshift

Frameshift

What is the function of cAMP in regulation of the lac operon?

It activates an activator protein.

Degradation of a eukaryotic mRNA is generally preceded by shortening of the___

Poly A tail

Fill in the blanks in the "strain genotype" Include lacI, lacP, lacO, lacZ, and lacY. Strain Genotype Lactose absent Lactose present 1 ? - + 2 ? + + 3 ? - -

lacI+ lacP+ lacO+ lacZ+ lacY+ lacI+ lacP+ lacOc lacZ+ lacY+ lacIs + lacP+ lacO+ lacZ+ lacY+ or 3) could be: I+ P- O+ Z+ Y+ I got full credit for 3) I+ P- O+ Z+ Y+ (1 and 2 the same as above)

If produces HIGH amounts of beta-galac.:

lacI+ lacP+ lacOc lacZ+ lacY+ lacA+

A ____ mutation changes a codon that specifies an amino acid into one that terminates translation. (multiple choice)

nonsense

When transcriptional activators interact with DNA, is the resulting genetic control typically positive or negative?

positive

siRNAs and miRNAs are produced by (multiple choice)

the cutting and processing of double-stranded RNA by Dicer enzymes

Insulators can block the effects of enhancers only when (multiple choice)

they lie between an enhancer and a promoter

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

Match each number with the closest type of DNA:

unique-sequence DNA gene-encoding sequence

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.) Genotype No lactose With lactose a I+ O+ Z+ / F' I+ O+ Z+ ________ ________ b I- Oc Z- / F' I- Oc Z- ________ ________ c I- Oc Z+ / F' I- O+ Z+ ________ ________ d Is Oc Z- / F' Is O+ Z+ ________ ________

+, + -, - +, + -, -

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.) Genotype No lactose With lactose a I+O+Z+/F'I-O+Z+ ________ ________ b I-OcZ+/F'I-O+Z- ________ ________ c IsOcZ+/F'I+O+Z+ ________ ________ d I-O+Z+/F'I-O+Z+ ________ ________

-,+ +,+ +,+ +,+

Mutations in the lacI and lacO genes in the lactose system often leads to full production of the three structural genes related to the lac operon even with no lactose available to the organism. Such a mutation would be called _____.

Constituitive

I P O Z Y A Which parts of the DNA region encode proteins?

I, Z, Y, A

Where would the lac repressor be bound in a (nonmutant) E. coli cell that is growing in low glucose and high lactose? *Shows picture*

The repressor would not be bound.

DNA methylation may be a significant mode of genetic regulation in eukaryotes. Methylation refers to what?

addition of methyl groups to the cytosine of CG doublets

This process moves a nucleosome from the TATA box of a gene's promoter so that transcription can occur. (short answer)

chromatin remodeling

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

A condition in which a gene or group of genes is expressed all the time

constitutive

A condition in which a gene or group of genes is expressed all the time.

constitutive expression

Transcription factors are proteins with at least two functional ______.

domains

To use RNAi (RNA interference) as a research tool, investigators introduce short synthetic ______ RNA into cells.

double-stranded, small interfering

Regarding eukaryotic and prokaryotic genetic regulation, what process seems to be the most similar between the two? (multiple choice)

transcriptional regulation

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 (TA told me this is the right answer) ^ That's probably what they were looking for, but I got credit for radioactive isotopes.

Define gene regulation. What are the three 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 transcription of the gene (RNA level), the translation of the protein from that transcript, or by altering the structure of DNA such that transcription cannot occur.

(I = lac repressor gene: Z, Y, A = lac operon structural genes: P = lac promoter: O = lac operator) Reference: Ref 16-2 Which parts of the DNA region shown in the diagram encode proteins?

I, Z, Y, A

Which of the below is not true about the location of enhancers?

The position of the enhancer has no effect on gene regulation.

Two formal terms to describe mutational nucleotide substitution in DNA are called...

Transversions and transitions

Antisense RNA can affect the translation of mRNA

True

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 what?

addition of methylation groups to the cytosine of CG doublets

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

The role of tautomerism in causing mutations relates to the fact that the process ultimately affects the: (multiple choice)

hydrogen bonding properties of nitrogenous bases

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

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

Which of the following terms best characterizes catabolite repression associated with the lactose operon in E. coli?

positive control

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.

Nutritional mutations can be defined as

Those mutations which do not allow an organism to grown on minimal medium, but do allow the organism to grow on complete medium

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)

A constitutive gene is ____ regulated and is expressed ____. (fill in blank)

not, continually

How can the expression of a gene be drastically altered by the presence of comparatively small numbers of RNA molecules? What is the term for this class of gene regulation?

Small RNA molecules are called siRNAs and miRNAs, and they affect RNA stability. They can cleave mRNA with a slicer enzyme and cause degradation, they inhibit translation, silence transcription, and cause degradation without a slicer present.

Mutations that arise in nature, from no particular artificial agent, are called Natural mutation induced mutation cosmic mutation chromosomal aberrations spontaneous mutations

Spontaneous mutations

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 drosophilia protein Dscam has many sites that can be alternitively spliced(~38000)

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

Constitutive mutations may occur in various components of the lac operon. Name two genes of the lac operon in which constitutive mutations could occur

LacI-, LacOc

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) TA pretty much said this question is on exam

Operon is controlled by a repressor. When repressor bind to small molecule, it's released from binding to DNA near operon. The operon is never expressed if a mutation prevents the repressor from binding to the small molecule

Negative inducible

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

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.)

(I = lac repressor gene: Z, Y, A = lac operon structural genes: P = lac promoter: O = lac operator) Reference: Ref 16-2 Where would the lac repressor be bound in a (nonmutant) E. coli cell that is growing in low glucose and high glucose? O I, P, O P and O The repressor would not be bound P

The repressor would not be bound

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

Under a system of negative control, genetic expression occurs unless such expression is shut off by some form of regulator.

True

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.

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 human condition _____ is caused by unrepaired UV-induced lesions

Xeroderma pigmentosum

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

Acridine orange is an alkylating agent

false

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

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? (multiple choice)

lacI+ lacP+ lacOc lacZ+ lacY+ lacA+

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? (multiple choice)

lacI+ lacP- lacO+ lacZ+ lacY+ lacA+

How are miRNAs produced? How do miRNAs function to affect production of proteins? Provide sufficient detail in your answer for full credit.

miRNAs are produced by being transcribed from genes that are not their (the miRNAs) targets. This double stranded RNA molecule, which can be formed from long hairpin loops, are then cleaved by DICER. The RNA fragments can then go on to complex with RISC, where the entire complex can bind to other mRNAs to prevent translation and ribosomal binding. This prevents or inhibits the production of certain proteins and serves as a form of translational regulation. Unlike siRNAs, miRNAs are known to imperfectly base pair with their targets and are synthesized from the host genome rather than a viral source. RITS is also involved in production of proteins and can aid in the methylation of DNA, thus preventing its transcription and subsequent gene expression.

What term refers to a contiguous genetic complex that is under coordinate control?

operon

This is the region of a gene where RNA polymerase binds to initiate transcription.

promoter

Frameshift mutations are caused by the __________ or __________ of one or more nucleotides in DNA.

removal, insertion

The general term for a non-polymerase protein that binds to an operator (fill in blank)

repressor

An example of a gene product encoded by a regulatory gene is (multiple choice)

repressor protein

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

In the lactose operon, the product of structural gene lacZ is capable of (multiple choice)

splitting the beta-linkage of lactose

A mutation that occurs naturally without exposure to known mutagen is called a

spontaneous mutation

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

List four levels at which gene control can take place in eukaryotes.

transcription (with repressors, enhancers...) translation mRNA processing (alternative splicing) mRNA stability (mRNA can be degraded) gene structure

Genetic regulation in eukaryotes can take place at a variety of levels from transcriptional to post-translational. At what level is genetic regulation considered most likely in prokaryotes? intron processing capping transcriptional polyadenylation of the 3' end of the mRNAs exon processing

transcriptional