Module 3

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An example of a gene product encoded by a regulatory gene is

repressor protein

E. coli bacteria are placed into a medium containing glucose and lactose. Which of the genes below do you expect to be turned on?

None of the above

After translation, eukaryotic proteins can be modified by

all of the above.

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

no effect gene

Ultraviolet light causes pyrimidine dimers to form in DNA. Some individuals are genetically incapable of repairing some dimers at "normal" rates. Such individuals are likely to suffer from

xeroderma pigmentosum

Regulation of gene expression using siRNAs is found in

eukaryotes only.

A _________ mutation changes a codon that specifies an amino acid into one that terminates translation.

nonsense

A class of mutations which results in multiple contiguous amino acid changes in proteins is likely to be the following

frameshift

Two formal terms used to describe categories of mutational nucleotide substitutions in DNA are called

transversions and transitions

E. coli lac operon control by lac I

negative inducible

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

It activates an activator protein.

The general term for a protein that binds to an operator.

repressor

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

negative inducible (binds= negative repressible)

unique-sequence DNA

gene-encoding sequence

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.

galactose, GAL3, GAL4, transcriptional activator

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

insertion or removal

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

promoter

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

constitutive

Which of the following two molecules of DNA has the lower melting temperature?
Why?

A DNA molecule with a higher percentage of G-C pairs will therefore have a higher Tm than that of DNA with more A-T pairs.

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

Mismatch: Enzymes excise incorrectly paired nucleotides from the newly synthesized strand and use the original nucleotide strand as a template when replacing them.

Direct: modified bases are changed back to their original structures.

Base excision: DNA repair that first excises modified bases and then replaces the entire nucleotide.

Nucleotide excision: removes bulky DNA lesions and other types of DNA damage.

Recent discoveries on causes of fragile-X syndrome, myotonic dystrophy, and Huntington disease indicate what type of genetic alteration?

change in trinucleotide repeats

What are the basic regulatory elements in a strand of DNA that allow for genes to be regulated? Are these different in eukaryotes and prokaryotes? If so, why?

DNA sequence that affects the transcription of other DNA sequences to which it is physically linked. Bacteria and eukaryotes use both positive and negative control mechanisms to regulate their genes. However, negative control is more important in bacteria, whereas eukaryotes are more likely to use positive control mechanisms.

The ____________________ stabilizes the 5' cap, which must be removed before the mRNA molecule can be degraded from the 5' end.

Poly(A) tail

A mutation in the gene for the yeast regulatory protein GAL4 causes yeast to grow poorly on galactose. What is the function of GAL4?

It is a transcription activator for the galactose-digesting enzyme gene.

Mutations which arise in nature, from no particular artificial agent are called

spontaneous mutation

What is a mutation?

a change in the DNA sequence

A mutant E. coli strain, grown under conditions that normally induce the lac operon, does not produce ß-galactosidase. What is a possible genotype of the cells?

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

A mutant E. coli strain, grown under conditions that normally induce the lac operon, produces high amounts of ß-galactosidase. What is a possible genotype of the cells?

lacI+ lacP+ lacOc lacZ+ lacY+ lacA+

What modification neutralizes the charges on histones that promote ionic interaction with DNA?

acetylation

The lac repressor binds to:

lactose and DNA.

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

inducer

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

Choose the type of control illustrated by GAL4 in the control of genes for yeast galactose-metabolizing enzymes

positive inducible

Name two mutagens which would be classified as base analogues.

5-bromouracil and 2-aminopurine

The region of a protein that is capable of holding on to a particular nucleotide sequence in order to affect proper gene regulation.

promoter

______________ is also known as RNA silencing and posttranscriptional gene silencing.

RNA interference

What symbols are used to describe constitutive mutations in the lac operon?

lacOc

____________________act as intermediaries between ______________________________ and specific _____ sequences to modify chromatin structure and activate transcription.

transcriptional activator protein, base

The ____________________ consists of modifications to histone proteins that affect the expression of DNA sequences.

histone code

When siRNAs are present, the rate of mRNA degradation_____________ and the rate of protein production ___________.

increases, decreases

telomeres

highly repetitive DNA

A promoter that affects only genes that are on the same piece of DNA is ____________-acting.

cis

Define RNA silencing (or interference). Explain how siRNAs arise and how they potentially affect gene expression. How are siRNAs different from the antisense RNA mechanism?

Process in which cleavage of double-stranded RNA produces small interfering RNAs (siRNAs) that bind to mRNAs containing complementary sequences and bring about their cleavage and degradation. siRNAs are produced by the cleavage and processing of double-stranded RNA. antisense RNA are small RNA molecule that base pairs with a complementary DNA or RNA sequence and affects its functioning.

What are the differences between neutral mutations and silent mutations?

neutral mutation: Changes the amino acid sequence of a protein but does not alter the function of the protein

silent mutation: Alters a codon, but the codon still specifies the same amino acid.

Explain why mutations in the lacI gene are trans in their effects, but mutations in the lacO gene are cis in their effects.

The lacI gene encodes the lac repressor protein, which can diffuse within the cell and attach to any operator. therefore affecting the expression of genes on the same or different molecules of DNA. The lacO encodes the operator. The binding of the lac repressor to the operator affects the binding of RNA polymerase to the DNA and therefore only affects the expression of genes on the same molecule of DNA.

Insulators can block the effects of enhancers only when

they lie between an enhancer and a promoter.

_____________ are complexes where, among other activities, a great deal of RNA degradation takes place.

P bodies

A constitutive gene is _______ regulated and is expressed ____________.

not, continually

What human condition is caused by unrepaired UV-induced lesions?

Xeroderma pigmentosum (XP)

These are factors that need not be adjacent to the genes they control. An example would be the lac operon's repressor protein.

initiation

One type of mutationinvolves the replacement of a pyrimidine with a purine. What general term is associated with this mutationalphenomena?

transversion

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?

SINES, LINES

Mutations in the promoter region of the b-globin gene indicate that some areas are more sensitive than others. When mutations occur in consensus sequences (modular elements such as GC box, CAAT box, TATA box) transcription ________________.

repressors

The process by which excessive numbers of a sex chromosome are corrected, often by methylating the X chromosome to form a Barr body.

dosage compensation

What role does RNA stability play in gene regulation? What controls RNA stability in eukaryotic cells?

The stability of mRNA influences gene expression by affecting the amount of mRNA available to be translated. The stability of mRNA is affected by the 5′ cap, the poly(A) tail, the 5′ UTR, the coding section, and sequences in 3′ UTR.

Why do insertions and deletions often have more drastic phenotypic effects than base substitutions do?

Base subs do not alter the reading frame. A single base change will only ater the amino acid that codon translates to. Insertion and deletions alter the frame causing the change of amino acids in every codon in every codon downstream causing drastic effects.

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

System of gene control in some bacterial operons in which glucose is used preferentially and the metabolism of other sugars is repressed in the presence of glucose because glucose enters glycolysis without further modification and therefore requires less energy to metabolize than do other sugars.

Degradation of a eukaryotic mRNA is generally preceded by shortening of the _____________.

Poly(A) tail

A _________________, which binds to a core promoter, consists of general transcription factors and RNA polymerase.

basal transcription apparatus

mRNAs are degraded by enzymes called ____________.

ribonucleases

What is the common influence of ultraviolet light on DNA?

pyrimidine dimer

The __________ is a type of _________ protein that binds to a region of DNA in the promoter of a gene called the _________ and prevents ______________ from taking place.

repressor, regulator, operator, transcription

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

AMES

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

chromatin-remodeling complex

Indicate the level of activity of the lac operon under the medium conditions listed below:

a) No lactose present, no glucose present
b) Lactose present, no glucose present
c) No lactose present, glucose present
d) Lactose present, glucose present

off, high, off, off.

Define gene regulation. What are three ways gene regulation can be controlled in a cell?

Mechanisms and processes that control the phenotypic expression of genes. Gene structure, transcription, mRNA processing, mRNA stability, translation, and protein modification.

A eukaryotic DNA sequence that affects transcription at distant promoters is called a(n) ________________.

enhancer

Explain two different ways that intragenic suppressors may reverse the effects of mutations.

producing a codon that specifies the same amino acid as that specified by the original codon OR suppressing a frameshift mutation.

List some important differences between bacterial and eukaryotic cells that affect the way in which genes are regulated.

a. Bacterial genes organized into operons, while Eukaryotic genes are not organized into operons and are transcribed from its own promoter.
b. In eukaryotic cells, DNA must be unwound from histone proteins prior totranscription occurring.
c. In eukaryotic cells, activators are more common than in bacterial cells.
d. In bacteria, transcription and translation can occur concurrently. In eukaryotes,the nuclear membrane separates transcription from translation (greater diversity)

Over the past decade, the most significant finding in biology has been the identification of miRNAs and siRNAs and their role in regulating the development of many multicellular organisms. Briefly describe the four different ways these small RNAs influence gene expression.

degrading mRNA: through slicer activity
inhibiting transcription: transcriptional silencing due to methylation of either histone proteinsor DNA sequences
inhibiting translation: binding of complementary regions with the mRNA molecule by miRNAs to prevent translation (premature termination)
silence genes:slicer-independent mRNA degradation stimulated by miRNA binding to complementary regions in the 3' UTR of the mRNA

List the different types of chromosome mutations and define each one.

chromosome rearrangements: Alter the structure of chromosomes
aneuploids: the number of chromosomes is altered
polyploids: one or more complete sets of chromosomes are added

What are three ways in which gene regulation is accomplished by modifying the structure of chromatin?

(1) the modification of histone proteins (2) chromatin remodeling
(3) DNA methylation.

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

(1) Alteration or modification of the gene structure at the DNA level
(2) Transcriptional regulation
(3) Regulation at the level of mRNA processing
(4) Regulation of mRNA stability
(5) Regulation of translation
(6) Regulation by post-translational modification of the synthesized protein

This structure forms when an extra X chromosome is methylated and largely inactivated. It is most commonly found in females.

barr body

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

Chromatin Remodeling

What is the difference between positive and negative control? What is the difference between inducible and repressible operons?

Positive: requires an activator protein (stimulate transcription at the operon)
Negative: requires repressor protein (turns off transcription at the operon) Inducible operon: requires an inducer molecule to stimulate transcription either by inactivating a repressor protein in a negative inducible operon or by stimulating the activator protein in a positive inducible operon.
repressible operon: (Transcription normally occurs) transcription is turned off either by the repressor becoming active in a negative repressible operon or by the activator becoming inactive in a positive repressible operon.

Why do extra copies of genes sometimes cause drastic phenotypic effects?

the expression of some genes is balanced with the expression of other genes; the ratios of their gene products, usually proteins, must be maintained within a narrow range for proper cell function. Extra copies of one of these genes cause that gene to be expressed at proportionately higher levels, thereby upsetting the balance of gene products.

repressor negative

slightly overlap

Nutritional mutations can be defined as

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

The lac repressor protein controls expression of the lac operon via ________________

binding to the lac operator site to repress expression

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.

LINES differ from retrotransposons in that LINES:

do not contain LTRs.

The following may be caused by mobile genetic elements except ________________

undergo mutation

Which of the following is TRUE for both prokaryotic and eukaryotic gene expression?

RNA polymerase binds to the promoter region to begin transcription.

In the previous diagram, if there is a mutation in P and I, which of the following is true?

These are mutations that are, respectively, cis and trans acting on lac operon expression.

highly methylated

heterochromatin

Which parts of the DNA region shown in the diagram encode proteins?

I, Z, Y, A

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

positive control

It is estimated that transposable elements compose approximately what percent of the human genome?

50

In what part of the mRNA does degradation generally begin?

at the 5' end with the removal of the poly(A) tail

Riboswitches were first discovered in 2002 and have been found in...

In all of the listed organisms

A class of mutations which results in multiple contiguous amino acid changes in proteins is likely to be the following

frameshift

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

translational termination is likely

Mutations in the lacI and lacO genes in the lactose system often lead to full production of the three structural genes related to the lac operon even with no lactose available to the organism. Such mutations would be called________.

consitutive

Parts of chromosomes that are not methylated for inactivation, but rather are less dense-staining and are likely active in transcription in the cell.

?

The process of error correction of mismatched bases carried out by DNA polymerases is called

proofreading

One type of mutation involves the replacement of a purine with a purine. What general term is associated with this mutational phenomena?

transition

Which of the following clusters of terms applies when addressing enhancers as elements associated with eukaryotic genetic regulation?

cis-acting, variable orientation, variable position

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

In the absence of glucose and in the presence of galactose, several genes are activated to enable yeast utilize galactose. The key regulator(s) of the yeast GAL system is/are the _______ protein(s).

All of the above

Alternative splicing is known to be important in the regulation of

the mammalian SV40 virus.

__________ mutations produce new traits and are usually dominant.

Gain-of-function

An insulator is also known as a __________________

boundary element

A catabolite-activating protein (CAP) exerts _____________control over the lac operon.

positive

When regions around genes become sensitive to the enzyme ______________ this is an indication that those regions are becoming ______________ active.

DNase I, transcriptionally

Transcriptional repression by methylation of DNA is most common in sequences called____________ islands.

cpG

siRNAs and miRNAs are produced by

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

An operon is controlled by a repressor. When the repressor binds to a small molecule, it binds to DNA near the operon. The operon is constitutively expressed if a mutation prevents the repressor from binding to the small molecule.

negative repressible

inactive through methylation

silent chromatin

It is possible for a repressor to negatively regulate the expression of an operon because

the repressor binding site overlaps the promoter site of the operon allowing it to physically block the binding of RNA polymerase.

Which of the following is NOT true regarding the differences in mRNA between prokaryotic cells and eukaryotic cells?

In eukaryotic cells, the transcription to mRNA and the translation from mRNA are coupled, while in prokaryotic cells transcription and translation are not coupled.

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