BIO 172 Exam 3 Discussions

Approximately what percentage of the human genome actually codes for proteins?

2.5%

In order to Sanger sequence a strand of template DNA, dATP, dTTP, dCTP, dGTP, ddGTP, DNA polymerase and primers with the sequence 5'-TACGA-3' were added to a test tube. Assume ddGTP is labeled with a red fluorescent tag. If DNA templates with the sequence below were added to the test tube, how many red fragments of different lengths would you have at the end of the sequencing process? 3'-ATGCTACGCTACGATTCATGCAAACG-5'

6

What is an inducer molecule?

A molecule that can prevent a repressor protein from inhibiting transcription.

In terms of gene expression, what is a repressor molecule?

A molecule that does not allow transcription to occur.

Assume you have a mutation that affects gene expression in the Lac operon. This mutation leads to no/low gene expression when glucose levels are low and lactose levels are high. What mutation could explain this expression pattern?

A mutation in the LacI gene, such that the repressor protein is made but it is unable to bind lactose

In an E.coli mutant beta-galactosidase is expressed at high levels whether or not lactose levels are high. What can explain this phenotype?

A mutation in the LacI protein which prevents binding to DNA.

What is meant by the term homologous chromosomes?

A pair of chromosomes, each carrying the same set of genes.

DNA methylation patterns can be inherited from cell generation to the next because...

An enzyme called DNA methyltransferase recognizes hemimethylated DNA and methylates the other strand

Replica plating was used to find mutant E. coli that cannot utilize lactose as a food source because

Bacteria with the desired mutation will not grow on lactose only plates

Why isn't the Lac operon expressed at high levels in the presence of both glucose and lactose?

Because glucose suppresses cAMP levels.

Enhancers are

DNA sequences to which regulatory transcription factors bind

One difference between DNA sequencing and PCR is:

DNA sequencing uses dideoxy nucleotides, while PCR does not

What is a nucleosome?

DNA wrapped around a group of histone proteins

Which types of receptor is membrane-associated?

G-protein couple receptor, ligand-gated ion channel, receptor kinase

The CORRECT sequence of steps in the eukaryotic cell cycle is:

G1, S phase, G2, mitosis, cytokinesis.

What regulatory transcription factor most likely recruit to an enhancer?

HATS

How does addition of a nonhydrolyzable form of GTP affect G-protein coupled receptor signaling?

It activates the pathway

What is the function of the enzyme beta-galactosidase?

It cleaves lactose into glucose and galactose.

You are studying regulation of the SDC-2 gene by another gene called LET-34 in the eukaryote C. elegans. You find that in cells that lack the LET-34 gene (it is deleted), SDC-2 mRNA levels are unchanged, but protein levels are higher. What can you conclude about LET-34?

It could be a miRNA gene or code for a protein that binds the 3' UTR of the SDC-2 mRNA

Which of the following is not considered a DNA regulatory sequence in the lac operon? (CRP-cAMP binding site, LacZ gene, Operator, Promoter)

LacZ

Assume there is a mutation in the operator, such that the repressor protein cannot bind to it. How would this mutation affect transcription of the LacZ and LacY genes?

LacZ and LacY transcription will be regulated only by glucose levels and will be high, when glucose levels are low

If there were a mutation in CRP that prevented it from binding to cAMP, what effect would this have on lacZ gene expression?

LacZ would never be expressed at high levels

What modification takes place when lactose is present in a bacterial cell?

Lactose induces a conformational change in the repressor protein.

What is one common feature between G-protein coupled receptor signaling and steroid hormone receptor signaling?

Ligand binding leads to conformational change in both types of receptors

methylation

Methyl groups are most often added to guanine-cytosine base pairs because they are held by three hydrogen bonds, and this decreases the probability of gene expression.

what is a difference between siRNA and miRNA?

Only siRNA can work at the level of transcriptional control.

microRNA (miRNA) and small interfering RNA (siRNA) are incorporated into a protein complex called

RISC (RNA induced silencing complex)

Fill in the blank: ______________results in chemical modifications to RNA bases, which can lead to changes in the amino acid sequence of the protein

RNA editing

What process can lead to the production of multiple proteins from the same primary transcript?

RNA editing

Which process can lead to the production of multiple proteins from the same primary transcript?

RNA editing

What mechanism of gene regulation is used only in eukaryotes and not in prokaryotes?

Regulation of chromatin structure by modifying histones

What modes of gene regulation is used in both prokaryotes and eukaryotes?

Regulatory proteins binding to specific DNA elements

What does the term "shotgun sequencing" refer to?

Sequencing many randomly created pieces of the genome, and then assembling the sequences into a finished product.

The transcription factor CREB is phosphorylated by a kinase in response to a signal the cell receives. The kinase hydrolyzes ATP and transfers a phosphate group to CREB. Phospho-CREB will bind specific DNA sequences and activate transcription of target genes. Therefore, target gene expression is low in the absence of a signal and high in the presence of the signal. What will happen to target gene expression if you add a non-hydrolyzable analog of ATP to the cells?

Target gene expression will be low both in the presence and in the absence of the signal.

What region of an mRNA plays a role in mRNA stability?

The 3' UTR.

Why does addition of a ddNTP terminate synthesis of the growing DNA chain?

The 3' carbon in the ddNTP lacks a hydroxyl group

The DPY-27 protein in nematode larvae is 340 amino acids long, but in adults it is 270 amino acids long. What could cause this difference?

The DPY-27 mRNA is edited in adults, but not in larvae

Runner is a protein that can be used for cellular movement. The runner protein in white blood cells is 140 amino acids long while the runner protein in skin cells is 110 amino acids long. What can account for this difference?

There is alternate splicing of the runner mRNA.

What is a potential outcome from RNA editing?

There is an introduction of an early termination codon.

What characteristic of genes would classify them as belonging to the same operon?

They are under the control of the same promoter and operator sequence.

How do miRNAs regulate a specific mRNA?

Through complementary base pairing with the mRNA.

What is a major role for the 3' UTR in mRNA?

Translational regulation.

What is a similarity between dideoxy sequencing and Illumina sequencing?

Use of nucleotides labeled with different colors

In a mutant mouse cell line, normal amounts of HOX-3 mRNA are produced, but the mRNA is shorter than normal. In addition, no functional HOX-3 protein is produced. What is consistent with these observations?

a change in splicing

centromere

a constriction on the chromosome, the point where sister chromatids are held together.

Inactivation of a protein that was previously activated by phoshorylation requires

a phosphatase

Translation can be controlled by

a protein binds to the 3' UTR of an mRNA to control the efficiency of translation; the ribosome is phosphorylated in response to viral invasion; a miRNA binds to the an mRNA to inhibit translation

What is a miRNA?

a small regulatory RNA that forms a hairpin structure

RNA splicing provides an opportunity for regulating gene expression because:

a spliceosome in one cell can "see" as an intron what another spliceosome in another cell "sees" as an exon, allowing different proteins to be produced from the same primary transcript.

What do kinases do?

add phosphate groups to other molecules

What is one explanation for the lack of correlation between the number of genes in an organism and organismal complexity?

alternative splicing

Positive regulation of transcription requires what to help RNA polymerase bind?

an activator protein

The signaling cell and the responding cell are one in the same in

autocrine signaling

correctly list the types of cellular communication from shortest to longest distance travelled by the signaling molecule to reach its responding cell?

autocrine, paracrine, endocrine

Sequence assembly is accomplished by aligning the fragments:

by using a complex computer program.

example of a second messenger in a signaling pathway

cAMP

A G-protein coupled receptor activates adenylyl cyclase, which produces cAMP. Therefore, cAMP levels are low in the absence of a signal and high in the presence of a signal. What would happen to cAMP levels if you added a nonhydrolyzable form of GTP?

cAMP levels will be high both in the presence and in the absence of a signal

During the G0 phase of the cell cycle,

cells are performing activities specific for their cell functions.

Epigenetic mechanisms of gene regulation include:

chemical modifications to DNA.

In DNA methylation in mammals, which nitrogenous base is most frequently methylated?

cytosine

type of signaling that usually involves the circulatory system and acts over long distances?

endocrine signaling

A constitutively active gene is

expressed continuously

The human body contains approximately 200 major cell types. They look and function differently from one another because each:

expresses a different set of genes.

Proteins which bind to a gene's promoter to recruit factors necessary to recruit RNA Pol and start transcription are called

general transcription factor

The CRP-cAMP complex binds the lactose operon when:

glucose levels are low and cAMP levels are high.

Positive and negative transcriptional regulation differ in that:

in positive regulation, the binding of a regulatory protein to the DNA is necessary for transcription to occur; in negative regulation, such binding prevents transcription.

The number of genes in an organism's genome is not a perfect indication of the organism's complexity because

individual polypeptides can interact to form multiple types of protein complexes, post translational modifications can increase the types of proteins produced by a single gene, alternative splicing can increase the number of proteins made from a single pre-mRNA

For the lactose operon, lactose is a(n):

inducer

A type of RISC complex can be found in the nucleus. The function of this complex is likely to be

inhibition of transcription

Packaging of DNA into chromatin...

inhibits transcription by blocking RNA Polymerase from accessing DNA

Why is an open reading frame more difficult to find in a eukaryote than a prokaryote?

introns

In the presence of glucose, Beta g

is not produced

A G-protein is inactive when

it is bound to GDP

A G-protein is active when

it is bound to GTP

Which gene encodes the protein beta-galactosidase?

lacZ

One difference between DNA sequencing and PCR is

need for a heat-resistant DNA polymerase

Chromatin remodeling refers to the process by which

nucleosomes are repositioned to expose different stretches of DNA to the nuclear environment.

Chromatin remodeling refers to the process by which:

nucleosomes are repositioned to expose different stretches of DNA to the nuclear environment.

In E. coli, lactose binds with the lactose operon ...

operator, preventing RNA polymerase from being recruited. This prevents the lacZ and lacY genes from being transcribed.

Regulation of STAT activity was described in lecture. Based on the model, what would be the outcome if the STAT genes contained a mutation that makes the STAT protein unable to bind DNA?

phosphorylated STAT protein dimers would accumulate in the nucleus, but transcription would not be activated

what steps in a signal transduction pathway involves signal amplification?

phosphorylation cascade

Complete the following sentence: Acetylation of histones neutralizes the _____________ charges on histones, therefore phosphate groups on DNA are __________ attracted to them.

positive, less

In using the shotgun approach to genome sequencing, the sequenced fragments originate from:

random sites scattered across the genome.

Whole genome sequencing is often approached by a shotgun sequencing technique in which large genomes are:

randomly digested, short fragments are sequenced, and the overlapping sequences are assembled in order.

what are the steps in cell signaling in the correct order?

receptor activation, signal transduction, response, termination

An operon is a:

region of DNA consisting of the promoter, the operator, and coding sequences for structural proteins.

Gene Htz1 is expressed at high level in yeast cells. While studying regulation of Htz1 gene expression you find a protein, Wzt1, which binds to the Htz1 mRNA in the cytoplasm. Which does Wzt1 do to regulate Htz1 expression?

regulate translation of Htz1

siRNA is a type of _____ RNA.

regulatory

What do phosphatases do?

remove phosphate groups from other molecules

What occurs during S phase?

replication of DNA

Fill in the blanks. In prokaryotes, regulatory proteins called _______________ bind to DNA sequences called _________________ to regulate expression of genes.

repressors, operators

The gene E01G4.3 is regulated by a short RNA. You notice that when the short RNA is not present, both mRNA levels and protein levels of E01G4.3 increase. This short RNA is likely to be a

siRNA

Eukaryotic cells use several mechanisms to inhibit transcription of transposable elements. What can be used to achieve this?

siRNAs

what immediately follows receptor activation in a signaling pathway?

signal transduction

If the lac operon were constitutively expressed,

the cell would be wasting energy.

cytokinesis

the division of the parent cell into two daughter cells.

Where does the signal bind to the receptor?

the ligand binding site

What happens to the repressor protein when lactose is present?

the repressor protein is unable to bind to DNA

Negative transcriptional regulation means that

there is a regulatory factor that turns off transcription.

Which of the protein domains is present in a G-protein coupled receptor, but not in a steroid hormone receptor?

transmembrane domain