Chem make up Exam

supercoiled

A _____ DNA molecule is more compact than its relaxed form.

intron

A noncoding region within a gene is known as a(n):

Stem-loop structures in the RNA would be destabilized.

A student separated some RNA from yeasts. What would be a result of dialyzing this sample against the buffer without Mg2+ and Ca2+?

urea

Agents such as ______________________ and guanidine hydrochloride denature proteins by disrupting the noncovalent interactions.

left-handed helices.

Although the right-handed double helix is the most well-known DNA structure, DNA can also form:

intrachain hydrogen bonds between the carbonyl oxygen of a residue and the amide hydrogen of the fourth residue away.

An α helix is a coil stabilized by:

-COO-

At a pH of 12, what is the charged groups present in glycine?

Double-helical DNA can be supercoiled.

Choose the feature of DNA structure that was NOT deduced by Watson and Crick from the DNA diffraction patterns.

ATT - ATA

Choose the point mutation.

strand separation - heating to 95°C; hybridization of primers - cooling to 54°C; DNA synthesis - heating to 72°C

Choose the right temperature for each step of the PCR cycle (the cycles have to be in the right order).

degenerate

Codons that specify the same amino acid are termed:

hydroxyproline

Collagen contains _____________________, a modified amino acid. Write the full name.

alternative splicing

Due to what mechanism do many genes encode more than one protein?

amino acid.

Each three-base codon encodes a specific:

Glycine

Every third residue in the protein collagen is ____________________.

broadest

How can the helix diameter for DNA in the A form be described as compared to other DNA forms?

Ribose contains 4 chiral carbon atoms, whereas deoxyribose contains 3.

How many chiral carbon atoms do ribose and deoxyribose contain in nucleic acids?

5 to 3

In DNA replication, the new strand always grows in the _____ direction.

Shine-Dalgarno sequence

In bacterial mRNA, the initiating AUG codon is preceded several nucleotides away by a purine-rich sequence called the _____, which base-pairs with a complementary sequence in an rRNA.

pyrimidine-rich tract

Introns nearly always begin with GU and end with AG that is preceded by the _______.

peptide bonds

Multiple amino acids connected by ............ ................

Ramachandran

Name of the plot that allows one to investigate the likely orientation of certain amino acid pairs.

mRNA.

Proteins are synthesized in vivo by the translation of

rRNA and proteins.

Ribosomes are composed of:

same sticky ends

The DNA fragment was inserted into the specific plasmid. What do plasmid and the DNA fragment have in common?

Sanger dideoxy

The MOST common type of DNA sequencing is the _____ method.

are polar.

The amino acids Tyr, Asn, and Thr:

The original data are not correct.

The base composition of the DNA includes 28% G and 26% A. How much T would be in the RNA synthesized from this DNA template?

A-U.

The base pair that would be found in RNA is:

van der Waals interactions.

The chemical forces that contribute to the stability of the DNA due to the base stacking present in the DNA helix are:

U instead of T.

The difference in RNA bases compared with DNA bases is that RNA contains:

DNA ligase.

The enzyme that catalyzes the formation of a phosphodiester linkage at a break in a DNA strand is:

AAGCTT

The first three bases of the six-base recognition cleavage site of HindIII are AAG. What is the complete sequence of this 6-bp site?

deoxycytidine

The nucleoside that is composed of a D-deoxyribose linked to a cytosine base is called:

a portion of the mRNA of the gene.

The probe used to isolate a gene from a genomic library is often:

annealing.

The process of DNA renaturation after melting is called:

salt counter-ions reducing electrostatic attractions between protein molecules.

The salting in of proteins can be explained by:

Tm

The temperature at which half of the DNA helical character is lost is referred to as:

proline

This amino acid residue disrupts the α helix because its side chain contains a unique ring structure that restricts bond rotations.

B

Under physiological conditions, most DNA is in the form of a _______ form helix.

GCATATGC

What DNA sequence contains a palindromic inverted repeat such as those recognized by restriction enzymes? (Note: Only one strand is shown.)

This technique allows the creation of proteins with unique characteristics and activities.

What advantage can be gained by splicing together portions of two different genes?

histidine

What amino acid has an ionizable R group with a pKa near neutral pH?

a TATA box at about -25 and often a CAAT box at about -75

What are the common promoter regions found in eukaryotic genes?

β-glycosidic

What bonds link bases to sugars in nucleotides?

a primer

What component is strongly required by DNA polymerases but is NOT needed by RNA polymerase?

DNA polymerase

What enzyme catalyzes the step-by-step addition of deoxyribonucleotide units to a DNA strand on the basis of template DNA?

reverse transcriptase

What enzyme is capable of synthesizing DNA from an RNA template?

none

What group (or atom) of the nucleotide base is esterified to a phosphate group to bind that nucleotide to the next one?

The sequence of the target needs to be known so that complementary primers can be synthesized.

What is NOT a feature of PCR?

reverse transcriptase

What is NOT included in the PCR mixture?

In the lysogenic pathway, viral DNA is integrated in the E. coli genome, while in the lytic pathway, phage DNA multiplies without insertion.

What is the difference between lytic and lysogenic pathways that λ phage uses for multiplying?

ψ

What is the name of the angle of rotation about the bond between the α carbon and the carbonyl carbon atoms?

GAC

What is the nucleotide sequence on the DNA coding strand that yields the GUC codon for valine?

TAG

What is the nucleotide sequence on the DNA template strand that yields the CUA codon for leucine?

secondary

What level of protein structure is composed of α helices, β sheets, and turns?

Lys, Arg

What pair of amino acids is positively charged at a neutral pH?

Arg and Lys

What residues are hydrolyzed during trypsin digestion?

exons

What sequences in eukaryotes link together to form mRNA after splicing?

To begin synthesis, DNA polymerases require a primer with a free 5-OH group that is already bound to the template strand.

What statement about DNA replication is INCORRECT?

A nucleotide is a nucleoside with a phosphate ester linked to the sugar.

What statement about nucleosides is CORRECT?

A bacterial cell always has plasmids.

What statement about plasmids is FALSE?

Polyacrylamide gels are used to separate mixtures of larger fragments than agarose gels can separate.

What statement about polyacrylamide gels and agarose gels is FALSE?

A restriction enzyme recognizes any sequence as long as it is palindromic.

What statement about the palindromic sequence is FALSE?

tRNA contains an anticodon sequence that serves as the template recognition site.

What statement is CORRECT concerning the adaptor molecule tRNA?

asparagine

Which amino acid has the one-letter abbreviation N?

mRNA

Which molecules are used as a template in translation?

amplification of the restriction fragment-probe duplex

Which step is NOT included in the technique called Southern blotting?

They are not degenerate and have single codons.

Why are Met and Trp codons often used to design DNA probes from amino acid sequences?

β-mercaptoethanol

_____ can be added prior to gel electrophoresis to fully denature proteins and break the disulfide bonds.