Exam 5 - Study Guide (BIOL 305)

Describe riboswitches

- Allosteric mRNA leader binds effector - Effector molecule binds an aptamer that induces change in expression platform

Describe gene regulation in prokaryotes.

- Attenutation controls gene expression - Expression of several genes is coordinated with operons - A single RNA polymerase is utilized

Describe gene regulation in eukaryotes.

- Chromatin structure plays a role - mRNAs are transported from nucleus to cytoplasm - Genes products depend on alternative splicing - Posttranscriptional mRNA processing regulates genes - Three RNA polymerases are utilized

Describe Antisense RNAs

- RNA complementary to the mRNA may control stability of the mRNA - RNA complementary to the MRNA may inhibit translation - Transcribed from the opposite template strand as target RNA

Describe regulatory small RNAs

- RNA complementary to the mRNA may inhibit translation - Often complementary to the ribosome binding site

Describe Attenuation

- Relies on coupling of transcription and translation - Small leader peptide synthesized - Part of regulation of amino acid biosynthetic operons

Describe gene regulation in both prokaryotes and eukaryotes

- Transcription is controlled by proteins that bind to specific DNA sequences - Similar DNA-binding domains are found in many DNA-binding proteins (e.g. helix-turn-helix domain)

At which of the following level(s) can gene expression be regulated in eukaryotes?

- initiation of transcription - transcript splicing transcript splicing - export of mRNA from the nucleus to the cytoplasm - stability of the mRNA stability of the mRNA - frequency of protein synthesis - localization of the protein to a particular cellular - modification of the protein

In an RNA-Seq experiment, the typical length of a sequence read is ______ and about one _______ reads will be obtained.

150 nt; billion

Fifteen different strains of bacteria are auxotrophic for maltose and their mutations do not complement each other. The mutations in these bacteria map to the same DNA region using transformation of random fragments of genomic DNA. Only two different enzymes participate in the maltose biosynthetic pathway, and the genes for both are within a single operon. What does this data suggest?

All the strains have mutations that prevent transcription of the operon.

________ is a derivative that forms when lactose is present; inside an E. coli cell it acts as a(n) _______ for production of the lactose-utilization enzymes.

Allolactose; inducer

E. coli co-transformed with luxA mutant and luxB mutant plasmids, is this bioluminescent or not bioluminescent?

Bioluminescent

E. coli transformed with 9 kb V. fischeri lux operon fragmentis, is this bioluminescent or not bioluminescent?

Bioluminescent

Wild-type V. fischeri cells, is this bioluminescent or not bioluminescent?

Bioluminescent

What would be the phenotype of a null mutation in the gene encoding Lac repressor?

Constitutive expression of the lac operon

How is glucose involved in catabolite repression of the lac operon?

Glucose causes cAMP levels to decrease, which leads to decreased CRP binding and the lac operon is repressed even when lactose is present.

Cells of which bacterial genotype would be able to utilize lactose as an energy source?

I+oc Z+Y−/ F′ (I+o+ Z− Y+)

Sequenctation, quenching, and competitions re all mechanisms of ____ leading to interferent with the function of an activator

Indirect repression

Two enzymes are necessary for lactose utilization. One of these is ________, which allows lactose to pass into the cell.

Lac permease

E. coli co-transformed with two luxR- mutant plasmids, is this bioluminescent or not bioluminescent?

Not bioluminescent

E. coli transformed with luxI- mutant plasmid, is this bioluminescent or not bioluminescent?

Not bioluminescent

Wild type E. coli cells, is this bioluminescent or not bioluminescent?

Not bioluminescent

An untranslated region at the 5' end of a bacterial mRNA.

RNA leader sequence

Some corepressors prevent ________ from binding to the promoter.

RNA polymerase

Termination of transcription may be dependent or independent of the _______ protein factor.

Rho (ρ)

As a general principle of gene regulation through operons, regulatory genes encode

Trans-acting proteins that interactive with cis-acting DNA elements

_______ factors are proteins that bind to enhancers to either increase or decrease the level of transcription from a ______ level.

Trans-acting; basal

How does tryptophan, the end product of the trp operon, function in the regulation of the operon

Trp binds to and changes the conformation of re repressor, which can then bind DNA and block transcription of the gene

How does tryptophan, the end product of the trp operon, function in the regulation of the operon?

Trp binds to and changes the conformation of the repressor, which can then bind DNA and block transcription of the operon.

These two enzymes are always present in small amounts; adding lactose to the growth medium, however, results in ________ in these two enzymes.

a 1000-fold increase

F′ lac plasmids were constructed with combinations of mutations in the lactose-utilization genes. Inserting one of these plasmids into an E. coli cell produces ________ for the genes of interest.

a partial diploid

RNA-seq can be used to examine gene regulation by comparing the mRNAs in a wild-type strain to those in a strain with a mutation in ________.

a regulatory protein

Which of the following is an example of a reporter gene? a.) The lacZ coding sequence under the control of a prokaryotic promoter b.) A human protein expressed under the control of a prokaryotic promoter c.) The linkers that are attached to RNA molecules to perform RNA-Seq d.) The DNase I enzyme used to digest DNA for a footprint essay

a.) The lacZ coding sequence under the control of a prokaryotic promoter

Bind to enhancers

activators

The Lac repressor cannot bind the operator when bound to

allolactose

A protein that changes its conformation upon binding to another molecule, such as a repressor that binds to an inducer.

allosteric protein

Proteins whose conformations change when they are bound to an effector molecule are called

allosteric proteins

The amino acid arginine can be synthesized by __________ pathway that requires seven enzymes. Wild-type bacteria should __________ production of these enzymes if arginine is present in the environment.

an anabolic; repress

A crucial step In the regulation of most bacterial genes occurs

at transcription initiation

A crucial step in the regulation of most bacterial genes occurs

at transcription initiation

Premature termination of transcription in response to translation of an RNA leader.

attenuation

Bind to promoters

basal factors

A crucial step in the regulation of many genes is the__________ to DNA at the promoter.

binding of RNA polymerase

Small RNAs can regulate gene expression by

binding of target RNAs and inhibiting translation.

How does a positive regulator affect transcription by RNA polymerase in prokaryotes?

by interacting with RNA polymerase to increase the frequency of transcription initiation

How do negative regulators such as the Lac repressor prevent RNA polymerase from initiating transcription?

by physically blocking the DNA binding site of RNA polymerase

Which statement describes regulation by transcriptional repression? a.) An amino acid binds to the operator, blocking the repressor, allowing transcription to proceed. b.) A sugar, such as lactose, acts as an inducer and binds to a repressor to prevent transcription. c.) An amino acid binds a repressor so that the repressor binds to the operator and prevents transcription. d.) An inducer binds to a positive regulator so that the regulator binds to DNA and prevents transcription.

c.) An amino acid binds a repressor so that the repressor binds to the operator and prevents transcription.

Which of the following is correct regarding sigma factor? a.) It forms an open complex. b.) It forms mRNA. c.) It recognizes the promoter region. d.) It is involved in the termination of replication.

c.) It recognizes the promoter region.

In the absence of tryptophan, the TrpR repressor

cannot bind to the operator

A preferred sugar prevents transcription of a sugar-metabolizing operon.

catabolite repression

The term ______ indicates that a mutation affects adjacent genes of the same DNA molecule.

cis

A strain that synthesizes curtain enzymes regardless of environmental conditions.

constitutive mutant

By contrast, in a lacI+ oc Z+ cell with a lacI+ o+ Z− plasmid, β-galactosidase _______ in the absence of lactose, suggesting that mutations to the lac o gene are cis-acting.

continued to be produced

Which of the following is an example of a reporter gene? a.) The linkers that are attached to RNA molecules to perform RNA-Seq b.)The DNase I enzyme used to digest DNA for a footprint assay c.) A human protein expressed under the control of a prokaryotic promoter d.) The lacZ coding sequence under the control of a prokaryotic promoter

d.) The lacZ coding sequence under the control of a prokaryotic promoter

Which of the following is not part of the lac operon? a.) lacZ b.) lacP c.) lacA d.) lacI e.) laco

d.) lacI

Repressors are trans-acting factors that _______ transcription initiation by recruiting ______.

decrease; corepressors

One assumption underlying RNA-Seq is that the number of reads of a particular sequence is _______ to the number of those mRNAs in the cells.

directly proportional

After RNA polymerase moves away from the promoter, it releases the sigma (σ) subunit and proceeds with _______.

elongation

Lactose is a disaccharide composed of _______.

glucose and galactose

The lac operon is highly expressed when

glucose is low and lactose is present.

E. coli prefers to use ______ as an energy source, but when this monomer is depleted, the bacterium will ______ for lactose utilization.

glucose; produce proteins

A complex of two different subunits

heterodimer

A complex of two identical subunits

homodimer

Activators are trans-acting factors that ________ transcription by stabilizing RNA polymerase binding to the promoter or recruiting ________.

increase; coactivators

Stimulation of transcription by a specific molecule.

induction

Translational regulation can occur at _____.

initiation, elongation or release of mRNA

Transcriptional regulation of gene expression can occur at _______.

initiation, elongation or termination

The lacI− and oc mutations have the same effect on the lac operon, namely that expression of the operon genes _______.

is always occurring

A type of dimerization domain

leucine zipper

Transcription and translation can be coupled in bacteria but not eukaryotes because

no nuclear membrane exists in prokaryotes.

Another type of coactivator are chromatin remodelers that remove _______ from the promoter.

nucleosomes

Alterations to DNA sites such as promoters and operators can act

only in cis

Coactivators ______ chromatin structure. One type of coactivator are Histone acetyl transferase (HAT) enzymes that _______ particular amino acids of _______ tails.

open; acetylate; histone

A cluster of genes transcribed together into a single mRNA and regulated as a group.

operon

Alters a protein's activity, stability, or localization.

phosphorylation

Because bacterial mRNAs lack _______, directional cDNA libraries are constructed with different _________ on the ends of each cDNA strand.

poly-A tails; adapters

Control of gene expression can occur at the protein level through _________.

posttranslational modification and protein stability

A crucial step in the regulation of most bacterial genes is the binding of the RNA polymerase holoenzyme to DNA at the ______.

promoter

Basal factors bind to the

promoter

Binding of basal factors and RNA polymerase to the________ results in a basal level of ________.

promoter; transcription

A mechanism of indirect repression in which a repressor binds to an activator that is bound to an enhancer

quenching

A mutation in a ribosome binding site in the lac operon would likely result in

reduction in the amount of LacZ, LacY, or LacA protein.

The transition from transcriptional initiation to elongation involves

release of sigma factor

A gene fusion where the regulatory region of one gene is fused to the open reading frame of another gene whose protein product is easy to detect.

reporter gene

Prevention of gene expression by a specific protein that binds to an operator.

repression

Mutations in the lacI site alter the ________, whereas mutations in the lac o site alter the ______.

repressor protein; DNA base sequence of the operator

RNA-Seq experiments are useful for studying the ______ of cells to different environmental stimuli, such as ______.

responses; heat shock

V. fischeri senses the density of V. fischeri cells in the environment by

secretion of a molecule that can then be internalized and bound to a receptor in the cytoplasm

Initiation of transcription by RNA polymerase involves the binding of which of the following subunits to the core enzyme?

sigma

Bacterial RNA polymerase is composed of several subunits. The _______ subunit must be present for transcription initiation to occur.

sigma (σ)

The sigma factor that mediates a global heat-shock response in E. coli is

sigma 32

Regulation of gene expression can occur during events of transcription, or after transcription. Posttranscriptional controls may alter the ______ of mRNA, the efficiency of ribosome binding, or the stability of the _______ product.

stability; polypeptide

Anabolic pathways involved in the synthesis of essential molecules are usually regulated in response to

the end product of the pathway

The term ______ indicates that a mutation acts more globally, affecting any appropriate DNA target site in a cell.

trans

The first stage of control of gene expression occurs at ________.

transcriptional initiation

A result of heterochromatin formation

transcriptional silencing

RNA-Seq refers to a type of study in which cDNA is sequenced to determine the _______ for a particular cell type or organism.

transcriptome

In bacteria, _____ of an mRNA transcript can begin while transcription is still taking place.

translation

A type of DNA binding domain

zinc finger

The other enzyme is _________, which splits the bond between the monosaccharide components of lactose.

β-galactosidase