PPT Review (Exam 1)

Question 1

What are the thermodynamic terms?

Answer 1

• E: energy
• H: Enthalpy
• S: Entropy
• G: Free energy
• Hf: heat of formation

Question 2

How do you convert between KJ/mol and Kcal/mol?

Answer 2

1 calories = 4.18 Joules

Question 3

What does it mean when ▲S>0?

Answer 3

It means that the reaction is favorable and is often spontaneous

Question 3

What does it mean when ▲H>0?

Answer 3

It means that the reaction releases heat and is exothermic

Question 4

How do you calculate ▲G’ from ▲G°’?

Answer 4

▲G’ = ▲G°’ + RTln([Products]/[Reactants])

R = 8.315

T = Absolute Temperature (Kelvin)

Question 5

What does it mean when ▲G° is positive or negative? What about when it is equal to 0?

Answer 5

• When ▲G° > 0, that means the reaction is not spontaneous (endergonic)
• When ▲G° < 0, that means the reaction is spontaneous (exergonic)
• When ▲G° = 0, the reaction is at equilibrium

Question 6

What are the four organic elements?

Answer 6

Carbon, Hydrogen, Oxygen, and Nitrogen

Question 7

What properties of water make it a great solvent for life?

Answer 7

polarity, ionization, hydrogen bonding

Question 8

How do you get pH from pKa?

Answer 8

pH = pKa +log([A-]/[HA])

Question 9

How do you calculate pH from [H+]? How about pOH from [OH-]?

Answer 9

pH = -log[H+]

pOH = -log[OH-]

Note: pH + pOH = 14, so you can use this to check your work on problems to see if you did something wrong

Question 10

What is the Henderson-Hasselbach Equation?

Answer 10

pH = pKa + log([H+]/[HA])

Note: you can use either [H+] or [A-] as their concentrations will be equal if you only put in one acid

Question 11

What are the key steps in calculating pH?

Answer 11

• First, determine if it is a strong acid (strong base) or a weak acid
• Write down the equation
• Consider pKa/Ka values—how efficient is the dissociation?
• Calculate the [H+] ([OH-]) concentration
• Calculate the –log[H+]

Question 12

The first law of thermodynamics states that-
A. The total amount of energy in the universe always stays the same
B. The total amount of energy in the universe always decreases
C. Every process increases the total energy in the universe
D. The total energy change of the system and the surroundings is always a positive number.

Answer 12

A. The total amount of energy in the universe always stays the same

Question 13

The second law of thermodynamics states that-
A. The total amount of energy of the universe is constant
B. The total amount of energy of the universe always decreases
C. Every process involves an INCREASE in the entropy of the universe
D. Every process involves a DECREASE in the entropy in the universe.

Answer 13

C. Every process involves an INCREASE in the entropy of the universe

Question 14

Which of the following best approximates the pH of the cytosol in a living human cell?
A. 3
B 5
C 7
D 9
E 11

Answer 14

C. 7

Question 15

Which of these statements about hydrogen bonds is not true?
A. Individual hydrogen bonds are much weaker than covalent bonds.
B. Hydrogen bonds account for the anomalously high boiling point of water.
C. Individual hydrogen bonds in aqueous water exist for many seconds and sometimes for minutes.
D. In liquid water, the average water molecule forms hydrogen bonds with 3 to 4 other water molecules.

Answer 15

C. Individual hydrogen bonds in aqueous water exist for many seconds and sometimes for minutes.

Question 16

A reaction, under particular conditions, has ∆G < 0. What does this tell you about the reaction?
A. Product formation is accompanied by a gain of entropy in the system.
B. Product formation is accompanied by a loss of enthalpy in the system.
C. Product formation is thermodynamically favored.
D. Product formation is thermodynamically unfavored.
E. Product formation will occur at a reasonable rate even without catalysis.

Answer 16

C. Product formation is thermodynamically favored.

Question 17

Which of the following best approximates the standard free-energy change accompanying hydrolysis of ATP?
A. 6 kJ/mol
B. 10 kJ/mol
C. 30 kJ/mol
D. 60 kJ/mol
E. 100 kJ/mol

Answer 17

C. 30 kJ/mol

Question 18

Which one of the following has the cellular components arranged in order of increasing size?
A. Amino acid < protein < mitochondrion < ribosome
B. Amino acid < protein < ribosome < mitochondrion
C. Amino acid < ribosome < protein < mitochondrion
D. Protein < amino acid < mitochondrion < ribosome
E. Protein < ribosome < mitochondrion < amino acid

Answer 18

B. Amino acid < protein < ribosome < mitochondrion

Question 19

The three-dimensional structure of macromolecules is formed and maintained primarily through non-covalent interactions. Which one of the following is not considered a non-covalent interaction?
A. carbon-carbon bonds
B. hydrogen bonds
C. hydrophobic interactions
D. ionic interactions
E. van der Waals interactions

Answer 19

A. carbon-carbon bonds

Question 20

Which one of the following is not among the four most abundant elements in living organisms?
A. Carbon
B. Hydrogen
C. Nitrogen
D. Oxygen
E. Phosphorus

Answer 20

E. Phosphorus

Question 21

The four covalent bonds in methane (CH4) are arranged around carbon to give which one of the following geometries?
A. linear
B. tetrahedral
C. trigonal bipyramidal
D. trigonal planar
E. trigonal pyramidal

Answer 21

B. tetrahedral

Question 22

Which of the following groups cannot participate in a hydrogen bond?
A. O-H
B. N-H2
C. C=O
D. C-H

Answer 22

D. C-H (Non-Polar)

Question 23

The fact that some pure solutions of hydrocarbons do not readily evaporate at room temperature is a result of-
A. London dispersion forces.
B. The hydrophobic effect.
C. Extensive hydrogen bonding.
D. The existence of permanent dipoles.
E. All of the answers are correct.

Answer 23

A. London dispersion forces.

Question 24

The pKa of formic acid is 3.75. The pKa of acetic acid is 4.76. This means that -
A. Formic acid is a stronger acid
B. Acetic acid is a stronger acid
C. Formic acid dissociates less than acetic acid
D. Formic acid and acetic acid will be equally dissociated if they are in solutions of the same pH.
E. A and D are correct

Answer 24

A. Formic acid is a stronger acid

Question 25

The greatest buffering capacity of weak acids is when-
A. They are almost completely dissociated
B. They are almost completely undissociated
C. They are half dissociated
D. The ratio between [A-] and [HA] is very high
E. None of the answers is correct

Answer 25

C. They are half dissociated

Question 26

Consider an acetate buffer, initially at the same pH as its pKa (4.76). When sodium hydroxide (NaOH) is mixed with this buffer, the:
A. pH remains constant.
B. pH rises more than if an equal amount of NaOH is added to an acetate buffer initially at pH 6.76.
C. pH rises more than if an equal amount of NaOH is added to unbuffered water at pH 4.76.
D. ratio of acetic acid to sodium acetate in the buffer falls.
E. sodium acetate formed precipitates because it is less soluble than acetic acid.

Answer 26

D. ratio of acetic acid to sodium acetate in the buffer falls.

Question 27

Which amino acids absorb UV light (? nm)

Answer 27

Only Phe, Tyr, and Trp absorb UV, Absorbance at 280 nm is utilized to quantify proteins

Question 28

Which one can form disulfide bond bridges?

Answer 28

Cysteine

Question 29

How do you calculate pI?

Answer 29

pI = ½ (pK1 + pK2)

Question 30

How does Urea denature proteins?

Answer 30

Urea will distorts the 3-dimensional structure by interfering with non-covalent interactions that stabilize the protein’s conformation

Question 31

How does DTT denature proteins?

Answer 31

DTT will reduces the disulfide bonds in the RNAse, making the enzyme completely inactive. The activity at the end of the step-1 will be 0%

Question 32

Which of the following statements about aromatic amino acids is correct?
A. All are strongly hydrophilic.
B. Histidine’s ring structure results in its being categorized as aromatic or basic, depending on pH.
C. On a molar basis, tryptophan absorbs more ultraviolet light than tyrosine.
D. The major contribution to the characteristic absorption of light at 280 nm by proteins is the phenylalanine R group.
E. The presence of a ring structure in its R group determines whether or not an amino acid is aromatic.

Answer 32

C. On a molar basis, tryptophan absorbs more ultraviolet light than tyrosine.

Question 33

Which of the following statements about cystine is correct?
A. Cystine forms when the —CH2—SH R group is oxidized to form a —CH2—S—S—CH2— disulfide bridge between two cysteines.
B. Cystine is an example of a nonstandard amino acid, derived by linking two standard amino acids.
C. Cystine is formed by the oxidation of the carboxylic acid group on cysteine.
D. Cystine is formed through a peptide linkage between two cysteines.
E. Two cystines are released when a —CH2—S—S—CH2— disulfide bridge is reduced to —CH2—SH.

Answer 33

A. Cystine forms when the —CH2—SH R group is oxidized to form a —CH2—S—S—CH2— disulfide bridge between two cysteines.

Question 34

Amino acids are ampholytes because they can function as either a(n):
A. acid or a base.
B. neutral molecule or an ion.
C. polar or a nonpolar molecule.
D. standard or a nonstandard monomer in proteins.
E. transparent or a light-absorbing compound.

Answer 34

A. acid or a base.

Question 35

Titration of valine by a strong base, for example NaOH, reveals two pK’s. The titration reaction occurring at pK2 (pK2 = 9.62) is:
A) —COOH + OH- → —COO- + H2O.
B) —COOH + —NH2 → —COO- + —NH2+.
C) —COO- + —NH2+ → —COOH + —NH2.
D) —NH3+ + OH- → —NH2 + H2O.
E) —NH2 + OH- → —NH- + H2O.

Answer 35

D) —NH3+ + OH- → —NH2 + H2O.

Question 36

For amino acids with neutral R groups, at any pH below the pI of the amino acid, the population of amino acids in solution will have:
A. a net negative charge.
B. a net positive charge.
C. no charged groups.
D. no net charge.
E. positive and negative charges in equal concentration.

Answer 36

B. a net positive charge.

Question 37

The formation of a peptide bond between two amino acids is an example of a(n) ______________ reaction.
A. cleavage
B. condensation
C. group transfer
D. isomerization
E. oxidation reduction

Answer 37

B. condensation

Question 38

The peptide alanyl-glutamyl-glycyl-alanyl-leucine has:
A. a disulfide bridge.
B. five peptide bonds.
C. four peptide bonds.
D. no free carboxyl group.
E. two free amino groups.

Answer 38

C. four peptide bonds.

Question 39

An octapeptide composed of four repeating glycylalanyl units has:
A. one free amino group on an alanyl residue.
B. one free amino group on an alanyl residue and one free carboxyl group on a glycyl residue.
C. one free amino group on a glycyl residue and one free carboxyl group on an alanyl residue.
D. two free amino and two free carboxyl groups.
E. two free carboxyl groups, both on glycyl residues.

Answer 39

C. one free amino group on a glycyl residue and one free carboxyl group on an alanyl residue.

Question 40

At the isoelectric pH of a tetrapeptide composed of three positively charged amino acids:
A. only the amino and carboxyl termini contribute charge.
B. the amino and carboxyl termini are not charged.
C. the total net charge is zero.
D. there are four ionic charges.
E. It is positively charged.

Answer 40

C. the total net charge is zero.

Question 41

Which of the following refers to particularly stable arrangements of amino acid residues in a protein that give rise to recurring patterns?
A. Primary structure
B. Secondary structure
C. Tertiary structure
D. Quaternary structure
E. None of the above

Answer 41

B. Secondary structure

Question 42

By adding SDS (sodium dodecyl sulfate) during the electrophoresis of proteins, it is possible to:
A. determine a protein’s isoelectric point.
B. determine an enzyme’s specific activity.
C. determine the amino acid composition of the protein.
D. preserve a protein’s native structure and biological activity.
E. separate proteins exclusively on the basis of molecular weight.

Answer 42

E. separate proteins exclusively on the basis of molecular weight.

Question 43

One method used to prevent disulfide bond interference with protein sequencing procedures is:
A. cleaving proteins with proteases that specifically recognize disulfide bonds.
B. protecting the disulfide bridge against spontaneous reduction to cysteinyl sulfhydryl groups.
C. reducing disulfide bridges and preventing their re-formation by further modifying the —SH groups.
D. removing cystines from protein sequences by proteolytic cleavage.
E. sequencing proteins that do not contain cysteinyl residues.

Answer 43

C. reducing disulfide bridges and preventing their re-formation by further modifying the —SH groups.

Question 44

All of the following are considered “weak” interactions in proteins, except:
A. hydrogen bonds.
B. hydrophobic interactions.
C. ionic bonds.
D. peptide bonds.
E. van der Waals forces.

Answer 44

D. peptide bonds.

Question 45

In an aqueous solution, protein conformation is determined by two major factors. One is the formation of the maximum number of hydrogen bonds. The other is the:
A. formation of the maximum number of hydrophilic interactions.
B. maximization of ionic interactions.
C. minimization of entropy by the formation of a water solvent shell around the protein.
D. placement of hydrophobic amino acid residues within the interior of the protein.
E. placement of polar amino acid residues around the exterior of the protein.

Answer 45

D. placement of hydrophobic amino acid residues within the interior of the protein.

Question 46

Which of the following best represents the backbone arrangement of two peptide bonds?
A. Cα—N—Cα—C—Cα—N—Cα—C
B. Cα—N—C—C—N—Cα
C. C—N—Cα—Cα—C—N
D. Cα—C—N—Cα—C—N
E. Cα—Cα—C—N—Cα—Cα—C

Answer 46

D. Cα—C—N—Cα—C—N

Question 47

In the α-helix the hydrogen bonds:
A. are roughly parallel to the axis of the helix.
B. are roughly perpendicular to the axis of the helix.
C. occur mainly between electronegative atoms of the R groups.
D. occur only between some of the amino acids of the helix.
E. occur only near the amino and carboxyl termini of the helix.

Answer 47

A. are roughly parallel to the axis of the helix.

Question 48

In an α-helix, the R groups on the amino acid residues:
A. alternate between the outside and the inside of the helix.
B. are found on the outside of the helix spiral.
C. cause only right-handed helices to form.
D. generate the hydrogen bonds that form the helix.
E. stack within the interior of the helix.

Answer 48

B. are found on the outside of the helix spiral.

Question 49

The major reason that anti-parallel ß-stranded protein structures are more stable than parallel b-stranded structures is that the latter:
A. are in a slightly less extended configuration than antiparallel strands.
B. do not have as many disulfide crosslinks between adjacent strands.
C. do not stack in sheets as well as antiparallel strands.
D. have fewer lateral hydrogen bonds than antiparallel strands.
E. have weaker hydrogen bonds laterally between adjacent strands.

Answer 49

E. have weaker hydrogen bonds laterally between adjacent strands.

Question 50

Determining the precise spacing of atoms within a large protein is possible only through the use of:
A. electron microscopy.
B. light microscopy.
C. molecular model building.
D. Ramachandran plots.
E. x-ray diffraction.

Answer 50

E. x-ray diffraction.

Question 51

Which of the following statements concerning protein domains is true?
A. They are a form of secondary structure.
B. They are examples of structural motifs.
C. They consist of separate polypeptide chains (subunits).
D. They have been found only in prokaryotic proteins.
E. They may retain their correct shape even when separated from the rest of the protein.

Answer 51

E. They may retain their correct shape even when separated from the rest of the protein.

Question 52

Experiments on denaturation and renaturation after the reduction and reoxidation of the —S—S— bonds in the enzyme ribonuclease (RNase) have shown that:
A. Folding of denatured RNase into the native, active conformation, requires the input of energy in the form of heat.
B. Native ribonuclease does not have a unique secondary and tertiary structure.
C. The completely unfolded enzyme, with all —S—S— bonds broken, is still enzymatically active.
D. The enzyme, dissolved in water, is thermodynamically stable relative to the mixture of amino acids whose residues are contained in RNase.
E. The primary sequence of RNase is sufficient to determine its specific secondary and tertiary structure

Answer 52

E. The primary sequence of RNase is sufficient to determine its specific secondary and tertiary structure

Question 53

Q. Name four factors (bonds or other forces) that contribute to stabilizing the native structure of a protein, and describe one condition or reagent that interferes with each type of stabilizing force.

Answer 53

Among forces that stabilize native protein structures are (a) disulfide bonds, (b) hydrogen bonds, (c) hydrophobic interactions, and (d) ionic interactions. Agents that interfere with these forces are (a) mercaptoethanol or dithiothreitol, (b) pH extremes, (c) detergents and urea, and (d) changes in pH or ionic strength, respectively.

Question 54

Each of the following reagents or conditions will denature a protein. For each, describe in one or two sentences what the reagent/condition does to destroy native protein structure.
(a) urea
(b) high temperature
(c) detergent
(d) low pH

Answer 54

(a) Urea acts primarily by disrupting hydrophobic interactions. (b) High temperature provides thermal energy greater than the strength of the weak interactions (hydrogen bonds, electrostatic interactions, hydrophobic interactions, and van der Waals forces, breaking these interactions. (c) Detergents bind to hydrophobic regions of the protein, preventing hydrophobic interactions among several hydrophobic patches on the native protein. (d) Low pH causes protonation of the side chains of Asp, Glu, and His, preventing electrostatic interactions.

Question 55

Q. Draw the resonance structure of a peptide bond, and explain why there is no rotation around the
C—N bond.

Answer 55

The intermediate resonance structure imparts a partial double bond characteristic to the C—N bond, thereby prohibiting rotation.

Question 56

Q. Draw the hydrogen bonding typically found between two residues in an α-helix.

Answer 56

Hydrogen bonds occur between every carbonyl oxygen in the polypeptide backbone and the peptide —NH of the fourth amino acid residue toward the amino terminus of the chain.

Question 57

Q. Explain what is meant by motifs in protein structure.

Answer 57

Motifs are particularly stable arrangements of elements of secondary structure (e.g., α helix and ß conformation), including the connections between them, which are found in a variety of proteins.

Question 58

A B C D E
__________________________________________________________________
(Tyr-Lys-Met) (Gly-Pro-Arg) (Asp-Trp-Tyr) (Asp-His-Glu) (Leu-Val-Phe)
Which one of the above tripeptides:
____(a) is most negatively charged at pH 7?
____(b) will yield DNP-tyrosine when reacted with l-fluoro-2,4-dinitrobenzene and hydrolyzed in acid?
____(c) contains the largest number of nonpolar R groups?
____(d) contains sulfur?
____(e) will have the greatest light absorbance at 280 nm?

Answer 58

(a) D
(b) A
(c) E
(d) A
(e) C

Question 59

Briefly describe the five major groupings of amino acids and name the amino acids that fall in those categories

Answer 59

Amino acids may be categorized by the chemistry of their R groups: (1) nonpolar aliphatics; (2) polar, uncharged; (3) aromatic; (4) positively charged; (5) negatively charged.

Non-Polar: Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, and Tryptophan

Polar, uncharged: Cysteine, Tyrosine, Serine, Threonine, Asparagine, Glutamine

Aromatic: Phenylalanine, Tyrosine, Tryptophan

Positively Charged: Arginine, Histidine, Lysine

Negatively Charged: Glutamate and Aspartate