Bio 172 Exam 3 Practice Problems

You are cloning a gene in the lab, and you wish to use restriction enzymes that recognize palindromic DNA sequences. Single strands of DNA representing restriction site sequences are shown below. Which of the below restriction sites is not a palindrome?

5' ACGGCA 3'

is: 5' AATATT 3'

restriction enzymes

cut stretches of DNA at specific sites known as recognition sequences

ato separate the template strands in PCR, you need ___. To separate the template strands in cellular DNA replication you need ___.

heat; helicase

You run a PCR reaction for 5 cycles starting with a single DNA duplex. How many copies of your sequence will you synthesize?

32

electrophoresis separates DNA fragments on a gel according to

size

if you performed a PCR reaction but accidentally only added one of the two primers, what would the product be?

only one DNA strand will be synthesized

what is the correct order of steps when performing molecular cloning?

cut DNA with restriction enzyme, ligation, transformation, antibiotic selection

What is the correct order of steps in a PCR reaction?

Denature the DNA, anneal DNA primers, extend the chain with DNA polymerase

a long string of codons for amino acids, uninterrupted by a stop codon is called

an open reading frame

the C-value paradox explains

the disconnect between genome size and organismal complexity

DNA sequences that can replicate and inset themselves randomly into new places in the genome are called

transposable elements

Using current DNA sequencing technology, it is possible to sequence an entire chromosome (250 million nucleotides) as one long molecule

false

the technique of Sanger sequencing takes advantage of the fact that dideoxynucleotides (nucleotides in which the 3' hydroxyl group is absent) act as

chain terminators

You discover a new bacterium and you wish to sequence its genome using shotgun sequencing. Among the many DNA sequences, you obtain the four fragments shown below.

1. TAGCTTACGGT

2. ATACGTCCGAT

3. ATGCATTAG

4. CGGTACGTATA

The order the fragments would have been found in the original bacterial genome is

3-1-4-2

One difference between PCR and DNA sequencing is

PCR needs two different primers, which DNA sequencing only needs one primer

what is responsible for pulling apart the double stranded DNA when running a PCR reaction?

heat

a constitutively active gene is

expressed continuously

positive transcriptional regulation means that

there is a regulatory factor that turns on transcription

in negative regulation

a regulatory molecule (protein) binds to the DNA near the gene in order to prevent transcription

which of the following genes might not be constitutively expressed?

the gene encoding stress hormone

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. Which of the following mutations could explain this expression pattern?

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

The CRP-cAMP complex binds the lactose operon when

glucose levels are low and cAMP levels are high

the lacZ and lacY genes are transcribed when

lactose is present and glucose levels are low

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

a mutation in the operator which prevents Lacl binding to it

negative transcriptional regulation means that

there is a regulatory factor that turns off transcription

an operon is a

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

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

a molecule that does not allow transcription to occur

the E coli Trp operon is regulated by the Trp repressor. When Trp levels are high in the cell, Trp binds to the repressor and this allows the repressor to bind to the operator. What would be the result if the repressor was mutated in such a way that it could no longer bind Trp?

expression of the structural genes in the operon would be high regardless of Trp levels in the cell

what is a inducer molecule?

a molecule that can prevent a repressor protein from inhibition transcription

You are observing levels of beta galactosidase production in bacteria under different environmental conditions. You record the following results:

High glucose, high lactose High

High glucose, low lactose Low

Low glucose, high lactose High

What could account for the result observed above?

the bacteria have a mutation in the gene that codes for CRP, such that CRP does not need to bind to cAMP to be actiated

cAMP binds to the CRP protein and activates the protein. In other words, cAMP regulates CRP

posttranslationally

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

which gene encodes the protein beta-galactosidase?

lacZ

an operator is

a regulatory region in DNA; the binding site for the repressor

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

what is true regarding polycistrony

-expression of polycistronic genes can be controlled by DNA binding proteins

-polycistronic mRNA is found only in prokaryotes

-more than one protein can be translated from a single mRNA

-each of the genes on a polycistronic mRNA contains a start and stop codon

-

false: polycistronic DNA is controlled by multiple promoters

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

lactose induces a conformational change in the repressor protein

what is an inducer molecule?

a molecule that can prevent a repressor protein from inhibiting transcription

in prokaryotes, regulatory proteins called __ bind to DNA sequences called ___ to regulate expression of genes

repressors; operators

what is a nucleosome?

DNA wrapped around a group of histone proteins

What about gene regulation in correct?

genes can be regulated at transcription, post translational, translational, and chromatin structure level

false: genes are regulated only in prokaryotes

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

cytosin

Which of the following about DNA methylation is true?

-DNA methylation patterns can be copied following DNA replication

-DNA methylation is associated with condensed chromatin

-most DNA methylations are reset during gametogenesis

false: DNA methyltransferases add methyl groups to histones

which of the following has a an inhibitory effect on transcription?

methylation of cytosines in DNA

transgenerational epigenetic inheritance

can happen in both plants and animals; genomic imprinting

what is true?

histone acetylation correlates with active transcription

which of the following can lead to changes in chromatin structure and is often associated with activation of transcription?

addition of acetyl groups to lysines located in the histone tail

epigenetic mechanisms of gene regulation include

chemical modifications to DNA

which of the following is an example of epigenetics?

-genomic imprinting in mammals

-methylation of DNA leading to gene silencing

-DNMTs recognize and methylate hemimethylated DNA

false: mutation

Praeder-Willi syndrome is a genetic disease, caused by a mutation in a gene subject to genomic imprinting. Disease only develops if the mutation is inherited from the father. What can you conclude from these observations?

the allele inherited from the mother is not expressed

which of the following statements is true regarding epimutations in the SUPERMAN gene in the plant Arabidopsis thaliana?

-DNA methylation keeps the gene silent

-the silent state of the gene is heritable from one plant generation to the next

-the DNA sequence of the gene is not changed

false: the silent state of the gene is heritable from one plant generation to the next

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

regulation of chromatin structure by modifying histones

which of the following components of gene regulatory mechanisms is used in eukaryotes?

-alternative splicing

-regulatory proteins binding to DNA sequences

-histone methylation

-DNA methylation

not used: operons

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

RISC (RNA induced silencing complex)

posttranslational modifications include

addition of phosphate groups to amino acid side chains in the protein

which of the following is considered translational control of protein synthesis?

-controlling when a protein is synthesized

-controlling the location of where a protein is synthesized

-controlling the rate of protein synthesis

not: controlling the primary protein sequence

When comparing the expression of the LIN-28 gene in two different cell types, you notice that both cell types make the same amount of mRNA. They also produce the same amount of protein, but the protein is much shorter in one cell type than in the other. Which of the following regulatory mechanisms is consistent with these observations?

RNA editing

if a cell is exposed to high temperatures and a large amount of protein misfolding will kill the cell, why is modifying ribosomal activity a good strategy for cell preservation?

it would prevent a large number of misfolded proteins from accumulating within the cell

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

inhibition of transcription

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

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

miRNA

Which is an example of a post translational event?

-insertion of an integral membrane protein into the plasma membrane

-protein folding

-addition of copper cofactor to an enzyme

not: removal of introns

what is a miRNA

a small regulatory RNA that forms a hairpin structure

which of the following is an example of posttranslational modification of a protein?

-phosphorylating proteins

-adding a covalent functional groups such as a carbohydrate

-marking proteins for degradation

not: changing the mRNA codon sequence

translation can be controlled by which mechanisms?

-the ribosome is phosphorylated in response to viral invasion

-a miRNA binds to the mRNA to inhibit translation

-a protein binds to the 3' UTR of an mRNA to control the efficiency of translation

A chaperone responsible for proper folding of an enzyme is missing from a cell. What might happen to that enzyme?

it could be tagged with ubiquitin

what is a major role for the 3' UTR in mRNA

translational regulation

GLD-1 is an RNA binding protein which binds to the 3' UTR of the MES-3 mRNA. If GLD-1 is not functional, MES-3 mRNA levels do not change, but MES-3 protein levels increase. The size of the MES-3 protein does not change, only its quantity. What is the function of GLD-1?

inhibits translation

what is the major function of the mRNA 5' cap?

initiation of translation

___ results in chemical modifications to RNA bases, which can lead to changes in the amino acid sequence of the protein

RNA editing

siRNA is a type of ___ RNA

regulatory

miRNAs function ___, siRNAs function ___

in the cytoplasm; either in the nucleus or in the cytoplasm

alternative splicing is very common in eukaryotes. Which of the following, when sequences, would provide evidence of alternative splicing?

cDNA

what is siRNA?

small interfering RNA, an example of a short regulatory RNA

proteasomes

help to regulate protein levels

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. Which of the following is consistent with these observations?

-a change in splicing

-a mutation in a gene (other than HOX-3) that produces a protein that binds to the HOX-3 3'UTR

-a mutation in a miRNA which binds to the HOX-3 mRNA

A G protein is active when

it is bound to GTP

Which type of receptor is membrane associated?

-receptor kinase

-ligand gated ion channel

-G protein coupled receptor

which of the following types of signaling depends on direct cell-cell contact?

juxtacrine

which of the following is true of G protein coupled receptor signaling?

-G protein hydrolyzes GTP to GDP to become inactive

-G protein is inactive when bound to GDP

-non hydrolyzable analog of GTP would cause the G protein to be permanently activated

false: the signal indirectly responsible for g protein activation is hydrophobic

in paracrine signaling, the signal affects only

target cells close to the cell from which it was secreted

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

it activates the pathway

What is a key difference between cell signaling by cell surface receptor and cell signaling by an intracellular receptor?

cell surface receptors bind polar signaling molecules; intracellular receptors bind nonpolar signaling molecules

second messengers

-are degraded in order to terminate a cellular signaling response

-plays a role in activation of intracellular signal transduction

-amplify the effects of the signal

-are small intracellular molecules that participate in signal transduction

-include cAMP and Ca++

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

autocrine signaling

which type of receptor undergoes a conformational change upon ligand binding?

-receptor kinase

-G protein coupled receptor

-intracellular receptor

-ligand gated ion channel

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

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

transmembrane domain

In communication between cells, the ___ produces the signaling molecule, also know as the ___; the ___ produces the ___, to which the signaling molecule binds

signaling cell; ligand; responding cell; receptor

when a ___ reaches its ___, there is a specific means of receiving it and acting on the message. this task is the responsibility of specialized proteins called ___.

signaling molecule; target cell; receptors

where does the signal bind to the receptor?

the ligand binding site

what do kinases do?

add phosphate groups to other molecules

which is true about a hydrophilic signaling molecule

-its effect is transduced across the cell but the signal never enters the cell itself

-they may bind G protein coupled receptors

how is signal transduction in a phosphorylation cascade terminated?

phosphatases remove phosphate groups from proteins

signaling pathways must be terminated. Termination of signaling can include which of the following?

-secondary messengers are degraded

-detachment of signaling molecule from the receptor

-phosphatases

-GTP hydrolysis by G proteins

not: ATP hydrolysis by receptor tyrosine kinases

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

You are studying a signaling pathway that involves a receptor, a G-protein, and a kinase in the lab. What would you expect if you replace all available ATP with non-hydrolyzable ATP?

kinase target proteins would not get phosphorylated

a steroid hormone uses a receptor protein that has two binding sites, one is a ligand binding site and the other is a DNA binding site. what type of receptor is this?

an intracellular receptor

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

autocrine, paracrine, endocrine

what is true about receptors in signaling pathways

some receptors are transmembrane proteins, some others are intracellular proteins