Biochem final exam

The study of biochemistry attempts to explain

biological processes at the molecular and cellular level

The \__________ differentiates amino acids from one another.

side chains attached to the central carbon

If the concentration of aspartate in the cell decreased, what would be the predicted outcome?

decreased concentration of fumarate

Plasmids are small, circular DNA molecules that are used in which of the following?

gene cloning

A hydrogen bond can best be described as a

weak noncovalent interaction.

Given a DNA sequence of 3'-CAT-5', what is the complementary sequence in mRNA?

5'-GUA-3'

Bioinformatics shows that 98% of human DNA is identical to that of chimpanzees. If human DNA contains 3.2 billion nucleotides, how many nucleotides are different between the two species?

64 million

In DNA the phosphate groups are on the outside of the helix. Why does this stabilize the structure?

ionic interactions with the solvent

What is the cause of the overall negative charge of a molecule of DNA?

the phosphate backbone

Highly conserved gene sequences that encode proteins with the same function in different organisms are called \__________ genes.

orthologous

The DNA double helix is stabilized by the interactions between nucleotides because of \__________ between nucleotides.

pi-pi stacking

What side products of pyruvate are being converted into alcohol and carbon dioxide by yeast?

CO2 and NAD+

A requirement for a covalent bond to form between two atoms is that

there are unpaired electrons on each atom.

The correct name for the VSEPR arrangement around a carbon in methane is

tetrahedral

Cell signaling and cell membranes are examples of functions performed by which biomolecule?

fatty acid

The figure below shows an example of which functional group?

phosphoryl

Triacylglycerols are neutral molecules made of

three fatty acid esters covalently linked to glycerol.

Vitamin B2 is a metabolite. Lack of vitamin B2 can lead to blurred vision and a swollen tongue. Vitamin B2 has such a strong effect on health because metabolites

are the catalysts that drive biochemical reactions necessary for life-sustaining processes

Which of the following is the correct solar energy reaction that takes place on the sun?

4 H --\> 4He

What is the final molecule made from the oxidation of H2O by solar energy?

glucose

The difference between an oxidation reaction and a reduction reaction is that oxidation is the \__________ and reduction is the \__________.

loss of electrons; gain of electrons

Which of the following is an example of a system?

a test tube with reaction components

A hot pack on your arm is an example of what kind of system?

closed

The combustion of gasoline is considered exothermic because heat is

transferred from the system to the surroundings

The change in entropy of a system is a function of a change in

enthalpy and temperature

If a reaction has a deltaH \> 0and a deltaS < 0, then \__________ and the reaction is \__________ at all temperatures.

deltaG \> 0; nonspontaneous

If the equilibrium constant (Keq) is greater than 1, which direction will the reaction proceed?

spontaneously to products

Under what conditions could a biological reaction spontaneously proceed to reactants if the deltaG knot \> 0?

Product concentrations are greater than reactant concentrations.

The transfer of a phosphate from ATP to another molecule produces a(n)

highly reactive intermediate

Under steady-state conditions in a mammalian cell, the adenine nucleotide concentrations are [ATP] \= 3.3 mM, [ADP] \= 1.2 mM, and [AMP] \= 0.2 mM. What is the energy charge of this cell?

0.83

Organisms on Earth cannot easily exist at 0° C temperatures below because at that temperature

ice crystals form in the organism.

A hydrogen bond can form between a hydrogen atom on a(n)

electronegative donor group and another electronegative atom

The interaction between an amino group and a carboxylate group is best characterized as

ionic interactions

The interaction between nonpolar molecules is best characterized as

van der Waals interactions

How do plants, fungi, and bacteria avoid the damaging effects of a hypotonic environment?

rigid cells walls

Calculate the pH of a solution that contains 3.9 10^-4 M H+.

3.41

Weak acids have a high pKa because the

HA concentration is high

Given a solution with pH \> pKa, what are the relative concentrations of A- and HA?

\[HA] < [A-]

A molecule with hydrophobic and hydrophilic properties is best described as

amphipathic

The figure below shows part of the primary structure of DNA. Identify the nucleoside.

C

Which form(s) of DNA exhibit(s) a right-handed helical structure?

A-DNA and B-DNA

Chargaff's rule is that the amount of

A \= T and the amount of C \= G

The DNA double helix is considered to be a \__________ structure.

secondary

Predict the complementary strand of the following DNA sequence: 5'-ATCTGAATCT-3'

5' - AGATTCAGAT - 3'

The K+ ion concentration in a DNA sample is increased from 50 mM to 100 mM. The Tm will

increase

DNA strands containing 20 base pairs, 40 base pairs, and 60 base pairs were denatured and the results were graphed below. Identify the curve from the 60 base pair DNA strand.

C

A double helix that crosses itself in a right-handed twist is referred to as a

negative supercoil

Calculate the linking number for a B-DNA strand that contains 735 total base pairs.

70

Predict how type I topoisomerases change the supercoil region.

Lk \= -1

Predict how type II topoisomerases change the supercoil region.

Lk \= -2

During eukaryotic DNA condensation, nucleosomes are packed together to form

chromatin

Less condensed, gene-rich chromatin is referred to as

euchromatin

Two identical copies of replicated DNA that remain attached until cell division are referred to as

sister chromatids

Polycistronic genes that contain a coding sequence for proteins that are only involved in one biochemical process are called

operons

In the eukaryotic cell, the coding sequences on a gene are referred to as

exons

The mixing and matching of novel genes in eukaryotic cells occurs through

exon shuffling

Deletions or insertions into the genome cause a polymorphism called

short tandem repeats

When a gene sequence is cloned using mRNA, which enzyme is used to seal the single-strand gaps left behind in the second strand of DNA?

DNA ligase

When DNA is sequenced, which analytical technique is used to separate the chain-terminated DNA fragments?

gel electrophoresis

In the second temperature phase of PCR, why does the temperature vary from 55C to 65C?

G-C content

Identify the phase of PCR amplification where DNA is denatured and the strands are separated.

A

This method of analyzing RNA transcripts relies on a predetermined collection of complementary DNA sequences.

gene-expression microarrays

Which method of analyzing RNA transcripts is considered to be an unbiased approach because it does not use a predetermined collection of complementary DNA sequence?

RNA-seq

The chirality of naturally occurring amino acids in proteins is

L

Using the pKas shown, what is the isoelectric point of the amino acid tyrosine?

5.5

What are the three-letter and one-letter abbreviations for the amino acid tyrosine?

Tyr, Y

Which linear sequence of bonded atoms can be found in the backbone of polypeptides?

C-C-N-C

The peptide bond

has a mix of single and double bond characters

The peptide bond is stronger than the ester bond. What structural feature of the peptide bond gives it additional bond strength?

Resonance structures give the peptide bond some double bond character

Use the table below to determine how many possible RNA sequences could code for the dipeptide Pro-Ala.

16

Using the table below, determine the kind of gene mutation illustrated.ATG_AAT_CAC ATG_AAG_CAC

missense mutation

All of the following are types of protein secondary structure EXCEPT

β-helixes

Which statement regarding protein secondary structures is correct?

Protein α-helices and β-strands differ in that α-helices are stabilized by intrahelical hydrogen bonds, whereas β-strands are stabilized by hydrogen bonds across adjacent strands.

What is the minimum number of amino acids needed to make one turn of an α-helix?

4

Which of the following statements about -sheet structures is true?

The individual strands of all -sheet structures are connected by turns, helices, or loops.

What is a difference between parallel and antiparallel β-sheet secondary structures?

Parallel β-sheets require a larger loop connecting together the individual peptide strands in the sheet.

How many β-turns or β-loops are required to construct a β-sheet composed of four antiparallel strands?

3

Which class of protein structures does the protein shown below fit into?

predominantly β-sheet

The common protein fold shown below is the \__________ fold.

α/β barrel

The protein fold known as the Rossman fold is found in proteins that commonly bind

nucleotides

Protein tertiary structures

are often disrupted by the either very low pH or very high pH values as a result of alterations in the ionization states of acidic or basic amino acids.

At the interface between subunits of a protein with quaternary structure, which of the following interactions between amino acid side chains would contribute to the stability of the dimer?

glutamate-lysine

In multi-subunit proteins, such as hemoglobin, the different subunits are usually bound to one another by all of the following EXCEPT

peptide bonds

Which gives rise to a favorable enthalpic (S) driving force for protein folding?

The decrease in ordered water molecules as hydrophobic amino acids pack together.

Of the three proposed models of globular protein folding, which one describes the initial formation of all secondary structures, followed by the arrangement of those secondary structures into a final tertiary structure?

framework model

Why is the process of purifying proteins from cells considered challenging?

There are 10,000 to 100,000 proteins in one sample

When preparing to isolate proteins from plant cells, the first step in preparing the cell homogenate would be

enzymatic treatment

After centrifugation, the purity of the protein is determined by

specific activity

After centrifugation, there is a 10% decrease in activity and a 75% decrease in total protein. What is purification of the target protein?

3.6-fold

Calculate the specific activity when 500 mg of protein has an activity of 18,000 units

9000 units/mg protein

The advantage of using a native PAGE gel compared with an SDS-PAGE gel is that the native PAGE gel

gives information on the charge or conformation of the protein

Two-dimensional polyacrylamide gel electrophoresis separates proteins based on

pI and molecular weight

In isoelectric focusing, a protein with a pH below the pI would

migrate toward the cathode

Which enzyme or reagent cleaves a peptide at the carboxyl side of a methionine residue?

cyanogen bromide

A polypeptide was digested by trypsin and chymotrypsin. Use the following information to determine the polypeptide sequence.

LMYKWDERMGFCE

In tandem mass spectrometry, the first mass spectrometer

uses electrospray ionization to select peptide fragments

Which technique ionizes polypeptides by releasing them from a small metallic capillary at high voltage?

ESI

Which technique ionizes polypeptides by embedding the tryptic fragments into a light-absorbing matrix and exposing it to a laser?

MALDI

In tandem mass spectrometry, the second mass spectrometer

determines the mass of peptide subfragments

In solid-phase peptide synthesis, which reagent is used to remove the peptide from the solid resin support?

HF