Biochemistry Quiz 1

Which statement about DNA structure is INCORRECT?

It is a branched polymer with a flexible backbone.

The DNA backbone is built of repeating sugar–phosphate units.

Each DNA strand has directionality due to identical orientation of the sugar–phosphate units.

Each sugar is connected to two phosphate groups through different linkages.

Its structure is a double helix composed of two intertwined strands.

What makes water a versatile solvent?

stabilization of large molecular complexes

ease of breaking different bonds

irreversible breakage of different bonds

simultaneous formation of a large number of hydrogen bonds

stabilization by large molecular complexes

Which statement about covalent bonds is INCORRECT?

A covalent bond is formed by the sharing of a pair of electrons between adjacent atoms.

If more than one electron pair is shared, then a covalent bond becomes stronger.

Existence of several resonance structures of nearly equal energies decreases stability of a compound.

Some molecules possess several patterns of covalent bonding.

The key properties of a bond are length and energy.

What is the energy of an ionic interaction?

the product of a proportionality constant and charges of two atoms divided by the product of the dielectric constant and the distance between atoms

the product of the dielectric constant and a sum of two charges divided by the product of the proportionality constant and the distance between charges

the product of the dielectric constant and the distance between atoms divided by the product of the proportionality constant and charges of two atoms

the product of the dielectric constant and two charges subtracted from the product of the proportionality constant and the distance between charges

the difference between the proportionality constant and charges of two atoms multiplied by the dielectric constant

What is the reason for the existence of the hydrophobic effect?

the tendency of water molecules to make a bond with hydrophobic proteins

the tendency of polar molecules to self-associate in the presence of an aqueous solution

the tendency of nonpolar molecules to self-associate in the presence of an aqueous solution

the inability of charged molecules to dissolve in water

the property of nucleic acids to dissolve in water

Which statement about noncovalent bonds is CORRECT?

Five fundamental noncovalent bonds differ in their geometry, strength, and specificity.

In the strongest hydrogen bonds, all their components lie along a straight line.

The transient asymmetry in the electronic charge distribution of one atom can induce a complementary asymmetry in the neighboring atoms due to hydrophobic interactions.

The release of water from more ordered structures is unfavorable.

Very strong repulsive forces become dominant at distances greater than the van der Waals contact distance.

Which statement about ionic interactions in the formation of the DNA double helix is CORRECT?

Separation of negatively charged phosphate groups with distances greater than 10 Å prevents unfavorable interactions.

Only favorable ionic interactions take place when two strands of DNA come together.

Ionic interactions cause the formation of the double helix.

Disposition of negatively charged phosphate groups with distances greater than 10 Å provides only favorable interactions.

Some unfavorable ionic interactions take place when two strands of DNA come together.

Which statement about the role of hydrogen bonds in DNA double helix formation is INCORRECT?

The hydrophobic effect contributes to the favorability of base stacking.

Hydrogen bonds contribute greatly to the overall process of double helix formation.

There are more hydrogen bonds with water than bonds between the bases in single-stranded DNA.

When two single strands come together, hydrogen bonds with water are broken and new hydrogen bonds between the bases of two DNA strands are formed.

Hydrogen bonds contribute greatly to the specificity of bases binding.

Which statement about nonpolar interactions in the formation of the DNA double helix is INCORRECT?

Van der Waals interactions are nearly optimal in a double-helical structure.

Nonpolar surfaces of the bases are moved into contact with each other due to a more complete base stacking.

Nucleotide bases tend to stack even in single-stranded DNA molecules.

The separation distance of the planes of adjacent bases needs to be adjusted for the favorable van der Waals contacts.

Surface complementarity maximizes the formation of hydrogen bonds and van der Waals interactions while minimizing the nonpolar surface area exposed to the aqueous environment.

What is FALSE regarding the laws of thermodynamics?

Energy can be neither created nor destroyed.

The local decrease in enthalpy will increase the entropy of the surroundings.

Heat is a manifestation of the kinetic energy associated with the random motion of molecules.

Within chemical systems, potential energy is related to the likelihood that atoms will store energy in some form.

Ordered structures can be formed within a system only if the entropy of the surroundings will proportionally increase.

The heat content of a system is called:

entropy.

enthalpy.

kinetic energy.

potential enthalpy.

kinetic entropy.

Why does a spontaneous chemical process always increase the entropy of the universe?

The system entropy will increase if and only if the entropy of surroundings is greater than the ratio of the heat transferred to the surroundings and their temperature.

The total entropy will increase if and only if the product of temperature and the change in system entropy is lower than zero.

The total entropy will increase if and only if the change in enthalpy is lower than zero.

The system enthalpy will increase only when the change in temperature is greater than zero.

The total entropy will increase if and only if the entropy of a system is greater than the ratio of the heat transferred to surroundings and their temperature.

How was the fact that formation of the double helix does not violate the second law of thermodynamics experimentally confirmed?

in a water bath monitoring the change in entropy to check whether it remains constant

in a water bath monitoring the change in heat to sustain a constant temperature in the bath

in a water bath monitoring the change in entropy to sustain a constant temperature in the bath

in a water bath monitoring the free energy to sustain constant heat content in the bath

in a water bath monitoring the change in heat to sustain constant Gibbs energy in the bath

A proton exists in a solution as:

H+.

a water molecule.

a deprotonated water molecule.

a hydronium ion.

H2O+

What is the direct consequence of the bent shape of a water molecule?

Water is highly cohesive.

Distribution of charge is asymmetric.

Hydrogen atoms possess a net negative charge.

The oxygen atom possesses a net positive charge.

The water molecule is able to form hydrogen bonds.

Why are free interactions of water molecules in bulk water more favorable than more ordered interactions with nonpolar compounds?

The total entropy in such interactions increases because the Gibbs free energy is positive.

The total entropy in such interactions decreases because the Gibbs free energy is negative.

The enthalpy of the ordered state is lower than the enthalpy of the bulk state.

The total entropy in such interactions increases because the Gibbs free energy is negative.

The total entropy in such interactions decreases because the Gibbs free energy is positive.

What is the concentration of hydroxide ions [OH–] in an aqueous solution with pH 9?

10–9 M

10–14 M

105 M

9 M

10–5 M

Which statement about acid–base relations is CORRECT?

If [H+] is higher than 10–3, pH is above 3.

If [OH–] is 10–9, pH is 7.

If [H+] is lower than 10–9, pH is below 9.

If [OH–] is higher than 10–3, pH is below 3.

If [OH–] is 10–7, pH is 7.

Which component of DNA bases is the most susceptible to hydroxide ions?

proton of N-1 atom of guanine base

proton of O atom of guanine base

proton of N-3 atom of thymine base

proton of O atom of adenine base

proton of N-1 atom of adenine base

What is a pKa value in an acid–base reaction?

the equilibrium constant for proton dissociation

concentration of hydrogen ions in the solution

a quantitative measure of the strength of an acid in the solution

the equilibrium constant for the dissociation of water

concentration of hydroxide ions in the solution

What is pKa of a buffer solution (pH = 5.05) containing 0.2 M sodium acetate and 0.1 M acetic acid?

4.75

0.2

0.3

4.45

1.58

Which statement is INCORRECT if the buffer capacity is not consumed upon addition of a strong acid to the solution?

There are more protonated forms of the buffer compound than deprotonated ones.

When hydrogen ions are added to this buffer solution they remain free.

The pH differs from the pKa value of the buffer's base component.

There are more deprotonated forms of the buffer compound than protonated ones.

Such a buffer is not actually a buffer and cannot mitigate the pH changes.

By which factor will the 1 M buffer sodium acetate (pKa = 4.75) increase the amount of acid required to produce a drop of pH from 7.4 to 7.3 in comparison with pure water where a respective change in [H+] is equal to 1 × 10–8 M?

5,600

60

60,000

1

600

Consider the conventional description of bonds in a Fischer projection. What is the CORRECT statement about the bonds in a Fischer projection?

Horizontal bonds project behind the page away from the viewer.

A solid wedge with the broad end away from the carbon atom denotes a bond coming away from the viewer.

The bonds to the central atom are represented by lines from that atom to the substituents.

Vertical bonds project behind the page away from the viewer.

A dashed wedge with its broad end at the carbon atom represents a bond going toward the viewer.

The structure of DNA described by Watson and Crick includes:

a triple helix.

a triple helix composed of three intertwined strands.

base pairs that are stacked on the inside of the double helix.

a sugar-phosphate backbone that lies on the inside of the helix.

base pairs that are stacked on the outside of the triple helix.

What did Watson and Crick suggest to be significant about the base-pairing found in the DNA helix?

It allowed the DNA to twist in a helix.

The DNA could be circular.

It was a good base for the mechanism of copying genetic information.

Only one of the strands could act as a template.

The DNA sequence was determined by the sequence of RNA.

What gives proteins such a dominant role in biochemistry?

rigidity of the peptide backbone

ability to act as a blueprint

ability to self-replicate

ability to spontaneously fold into complex three-dimensional structures

usage of 40 different building blocks

What is the concentration of hydrogen ions in a urine sample that has a pH of 6?

10–6 M

10–8 M

106 M

10–14 M

6 M

Order the type of interactions by the bond strength in descending value.

hydrogen bonds, covalent bonds, van der Waals interactions

covalent bonds, van der Waals interactions, hydrogen bonds

van der Waals interactions, covalent bonds, hydrogen bonds

covalent bonds, hydrogen bonds, van der Waals interactions

hydrophobic interactions, hydrogen bonds, electrostatic interactions

Which of the following is a hydrogen bond donor?

the N in H- - -N—HD

the S in S—H- - -O

the O and P in P—O- - -H

the H in O—H- - -O

the O in O—H- - -NN

hat is the [A–]:[HA] ratio when a weak acid is in a solution one pH unit below its pKa?

1:1

1:10

10:1

2:1

1:2

Using the Henderson–Hasselbalch equation, calculate the pH of a buffer solution made from 0.20 M CH3COOH and 0.05 M CH3COO– that has pKa = 4.7.

5.3

4.1

2.5

0.4

5.0

What are the primary chemical components present in a phosphate buffer at pH = 7.4?

H3PO4 and PO43–

H2PO4– and PO43–

HPO42– and PO43–

H2PO4– and HPO42–

H3PO4 and HPO42–

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

hydrogen bonds.

van der Waals interactions.

hydrophobic interactions.

salt bridges.

charge repulsive forces.

Single-stranded nucleic acids can adopt complex structures through long-range interactions such as

Watson–Crick base pairing.

nonstandard hydrogen bonding.

hydrophobic effect.

hypochromic effect.

van der Waals interactions.

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

the 3-hydroxyl (3-OH) group

the 5-hydroxyl (5-OH) group

N-1 in purines and N-9 in pyrimidines

N-9 in purines and N-1 in pyrimidines

none

What bonds link bases to sugars in nucleotides?

ester

α-glycosidic

β-glycosidic

phosphodiester

ether

Approximately how many base pairs are in the human genome?

about 3 × 1011

about 3 × 107

about 3 × 108

about 3 × 109

about 3 × 1010

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

What is the technique on which the Watson–Crick model was based?

absorbance spectrophotometry

electron microscopy

X-ray diffraction

radioactive labeling

spectrofluorometry

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

broadest

narrowest

intermediate

broader than the Z form but narrower than the B form

broader than the B form but narrower than the Z form

Ribosomes are composed of:

DNA.

rRNA.

proteins.

DNA and rRNA.

rRNA and proteins.

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

Th.

Tm.

T0.5.

TDNA.

T50.

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

A instead of T.

U instead of G.

U instead of T.

A instead of U.

C instead of T.

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

triple strands.

straight chains.

branched chains.

left-handed helices.

tight globules.

What is NOT a key property that enable proteins to participate in a wide range of functions?

Proteins have a high molecular weight.

Proteins contain different functional groups.

Some proteins are quite rigid, whereas others display considerable flexibility.

Proteins are linear polymers built of different amino acids.

Proteins can interact with one another and with other biological macromolecules to form complex assemblies.

What does an α-amino acid consist of?

carbonyl group, α carbon, amino group, oxygen atom, distinctive R group

carboxylic acid group, α carbon, amino group, hydrogen atom, distinctive R group

carboxylic acid group, ε carbon, nitro group, hydrogen atom

alcohol group, α carbon, amino group, nitrogen atom, distinctive R group, hydrogen atom

carboxylic acid group, δ carbon, imine radical, hydrogen atom, distinctive R group

What isomers of amino acids are found in proteins and what absolute configuration do they have?

L isomer; R absolute configuration

D and L isomers; R absolute configuration

L isomer; S absolute configuration

D isomer; S absolute configuration

L and D isomers; S absolute configuration

In an acidic solution (pH = 1), what is the ionization state of an amino acid?

The amino group is deprotonated; the carboxyl group is protonated.

The amino group is not dissociated; the carboxyl group is not dissociated.

The amino group is protonated; the carboxyl group is deprotonated.

The amino group is protonated; the carboxyl group is not dissociated.

The amino group is deprotonated; the carboxyl group is not dissociated.

Choose the correct groups for Thr, Lys, His, Met, respectively, on the basis of general chemical characteristics.

polar but uncharged; negatively charged; positively charged; hydrophobic

polar but uncharged; positively charged; positively charged; hydrophobic

positively charged; hydrophobic; polar but not charged; positively charged

negatively charged; hydrophobic; positively charged; polar but not charged

positively charged; positively charged; polar but not charged; negatively charged

Which amino acid has the one-letter abbreviation K?

histidine

asparagine

alanine

valine

lysine

The amide bond is a linkage between the:

β-amino group of one amino acid and the α-amino group of another amino acid.

β-carboxyl group of one amino acid and the β-amino group of another amino acid.

δ-carboxyl group of one amino acid and the α-carboxyl group of another amino acid.

α-amino group of one amino acid and the ε-amino group of another amino acid.

α-carboxyl group of one amino acid and the α-amino group of another amino acid.

What is the amino-terminal residue and what is the carboxyl-terminal residue in the sequence of amino acids Gly-Tyr-Gly-Phe-Leu?

Leucine is N-terminal and glycine is C-terminal.

Glycine is N-terminal and leucine is C-terminal.

Tyrosine is N-terminal and leucine is C-terminal.

Phenylalanine is N-terminal and leucine is C-terminal.

There are no N-terminal and C-terminal residues in the sequences of amino acids.

A protein with a molecular weight of 75 550 g mol–1 has a mass of:

75,550 Da or 755.5 kDa.

7555 Da or 75.55 kDa.

75,550 Da or 75.55 kDa.

755,500 Da or 7.555 kDa.

7,555,000 Da or 75550 kDa.

Knowledge of the amino acid sequences is important for several reasons. What is NOT one of those reasons?

Amino acid sequences determine the three-dimensional structures of proteins.

The sequence of a protein reveals much about its evolutionary history.

Knowledge of the sequence of a protein can help to prevent mutations.

Changes in the amino acid sequence can lead to abnormal protein functioning and disease.

The sequence of a protein is necessary to determine its function.

What is the configuration of peptide bonds in proteins?

Almost all peptide bonds are in the cis configuration.

Almost all peptide bonds are in the trans configuration.

Half of all peptide bonds are in the trans configuration and the other half are in the cis configuration.

Approximately one third are in the trans configuration and rest are in the cis configuration.

Approximately one third are in the cis configuration and rest are in the trans configuration.

An α helix is a coil stabilized by:

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

intrachain nitrogen bonds between the carbonyl nitrogen of a residue and the amide nitrogen of the second residue away.

extrachain oxygen bonds between the carbonyl oxygen of a residue and the amide nitrogen of the fifth residue away.

intrachain nitrogen bonds between the carbonyl nitrogen of a residue and the amide nitrogen of the sixth residue away.

extrachain hydrogen bonds between the carbonyl hydrogen of a residue and the amide oxygen of the third residue away.

A β sheet is formed by linking two or more β strands lying next to one another through:

nitrogen bonds.

oxygen bonds.

ionic bonds.

disulfide bridges.

hydrogen bonds.

Why are porins considered to be "inside out" relatives to proteins that function in aqueous solution?

Porins are positively charged while usual proteins are negatively charged.

Porins interact with the neighboring alkane chains while usual proteins interact with alkene chains.

Porins function in outer membranes while usual proteins function in inner membranes.

Porins function only in bacteria while usual proteins function in all organisms.

Porins have a reverse distribution of hydrophobic and hydrophilic amino acids.

What are the interactions that associate the two helices in α-keratin?

hydrogen bonds and electrostatic forces

van der Waals forces and covalent interactions

electrostatic forces and metallic bonds

van der Waals forces and ionic interactions

metallic bonds and van der Waals forces

What is the simplest sort of quaternary structure?

a monomer

a dimer consisting of two different subunits

a dimer consisting of two identical subunits

a trimer consisting of two identical subunits and one diverse subunit

a tetramer consisting of two identical subunits and diverse subunits

What is a structure of the hemoglobin molecule?

α2 dimer

β2 dimer

α2β1 trimer

α1β2 trimer

α2β2 tetramer

What disrupts the noncovalent interactions in proteins?

guanidinium sulfide

β-mercaptoethanol

uric acid

urea

ammonia

In the ribonuclease experiments performed by Anfinsen, β-mercaptoethanol reduced:

all incorrectly paired bonds and stabilized the protein structure.

all bonds and destroyed the protein structure.

all charged residues, and the protein was unable to take part in signaling.

all bonds, and the unfolded protein molecules became tangled up with one another to form aggregates.

incorrectly paired disulfide bonds, allowing them to reform with the correct pairing until the most stable conformation of the protein had been obtained.

What is the term for a molecule that contains both positive and negative charges but overall has a neutral charge?

enantiomer

amino acid

racemate

zwitterion

amphipath

Which amino acid forms disulfide bonds?

histidine

methionine

proline

serine

cysteine

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

histidine

serine

aspartic acid

lysine

tyrosine

What plot type allows one to investigate the likely ϕ and ψ angles of the peptide backbone?

Hill

Lineweaver–Burk

Hanes–Woolf

Ramachandran

Michaelis–Menten

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

primary

secondary

tertiary

quaternary

supersecondary

The overall three-dimensional structure of a single polypeptide is referred to as _____ structure.

primary

secondary

tertiary

quaternary

supersecondary

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

–NH3+

–COO–

–NH2+

–NH+

–CO–

The amino acids Tyr, Asn, and Thr:

have aromatic rings.

are negatively charged at pH = 7.0.

are positively charged at pH = 7.0.

have double bonds in side chains.

are polar.

Which individual won a Nobel Prize for his or her landmark work in sequencing the protein insulin?

Pauling

McClintock

Gilbert

Maxam

Sanger

The term quaternary with respect to protein structure stands for:

a repeating structure stabilized by intrachain hydrogen bonds.

the ability to form all four kinds of noncovalent bonds.

a multisubunit structure.

a linear sequence of four amino acids.

the only four amino acids that can form hydrogen bonds.

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

Lys, Arg

Tyr, Arg

Cys, Met

Leu, Pro

Asp, Glu

What is NOT a modification acquired by proteins?

cleavage and trimming of the protein

addition of carbohydrate groups

phosphorylation of certain groups

hydrolysis of all protein

addition of acetyl groups

What amino acid residue would MOST likely be buried in the interior of a water-soluble globular protein?

Asp

Ser

Phe

Lys

Gln