Bioc-401 Elements of Biochemistry (Ch. 1, 2, 4, 5, 6, & 7)

True or False: As the pH of a solution decreases below the pKa, the weak acid become more protonated (more HA and less A-)

True

Characterizes the internal composition of a living cell:

slighty basic

pH slightly above 7

Match the +/- delta H,S,G to the following

Lower entropy

Higher entropy

Endothermic

Exothermic

Endergonic

Exergonic

+delta H: Endothermic

-delta H: Exothermic

+delta S: greater entropy

-delta S: lower entropy

+delta G: Endergonic

-delta G: Exergonic

Enthalpy (H)

equivalent to the heat content of the system

Entropy (S)

measure of how the energy is dispersed within that system. (measure of the system's disorder or randomness because the more way's a system components can be arranged, the more dispersed its energy). Essential Biochemistry 4th Edition Pratt & Cornely.

Which of the following is NOT associated with AMP?

provides coupled energy for most anabolic reactions

FEEDBACK: ATP is the energy currency for substrate-level phosphorylation and most biological/biochemical actions. AMP possesses too low of a free energy term-6change (ΔG° = -9.2 kJ/mol) to help drive forward other biochemical reactions.

In the image below, which components are part of the adenosine substrate?

d & e

A chemical reaction is identified as exothermic when

heat is lost from the system

FEEDBACK: Exothermic reactions result in the loss of heat from a system (surrounding gains that heat) and endothermic reactions result in the gain of heat by the system (loss of heat from the surrounding). When you grab a hot pan the heat leaves the pan (system) and enters you (surrounding). Considering the pan, it is an exothermic process because the pan is losing heat to its surrounding (YOU). Considering you, it is an endothermic process because you are gaining heat from the surroundings (pan).

Protein synthesis is a process that requires building covalent bonds between amino acids. Which of the following would logically be coupled to protein synthesis?

hydrolysis of ATP

FEEDBACK: Protein synthesis is an anabolic process where bonds are formed, a reduction reaction. This requires an input of energy (endergonic) to construct new bonds. In order to energetically produce bonds, an exergonic process must be coupled with this. The hydrolysis of ATP releases 30.5 kJ/mol at standard conditions. It is the hydrolysis of ATP that "fuels" many biochemical processes.

Which of the following describes a carbon atom in a hydrocarbon molecule? (Choose all correct answers)

can be bonded to hydrogen, oxygen, neon, and argon

are tetravalent (form 4 bonds)

if singly bonded, they don't rotate about the bond axis

can be sp3 hybridized

form polar bonds when bonded with oxygen

are tetravalent (form 4 bonds)

can be sp3 hybridized

form polar bonds when bonded with oxygen

True or False: In the production of potassium chloride from elemental potassium and chlorine gas, the chlorine molecules are reduced to chloride ions.

True

Which of the following amino acids has a side chain that contains a carboxyl group?

glutamic acid

Which of the chemical components of lysine would be mostly deprotonated at a pH equal to 9.9?

α-carboxyl

side chain

α-hydrogen

α-carbon

α-amino

α-carboxyl

α-amino

FEEDBACK: The pKa of a weak acid is the pH when the weak acid is 50% ionized (deprotonated). By looking at the pKa values of the α-carboxyl, the α-amino and the side chains, whichever pKa is closest to the actual pH then that represents the group which is near 50% ionization.

True or False: In a titration of glycine, the equivalence point in the titration represents equal concentrations of the carboxyl (-COOH) and carboxylate (-COO-) groups

False

FEEDBACK: The pKa values represent on a titration curve where the concentrations of the protonated and deprotonated forms are equal. In the case of carboxyl groups, at a pH = pKa, [carboxyl] = [carboxylate]. The equivalence point on a titration curve is denoted by a rapid change in pH values. This occurs when the concentration of the titrated acid is equal to the concentration of base added (for titration). This would imply that nearly 100% of the weak acid has been titrated (deprotonated).

Chaperone proteins are commonly associated with

folding of newly synthesized proteins.

True or False: The release of free energy in a biochemical reaction is commonly associated with catabolic reactions.

True

True or False: The cellular digestion of triglycerides (fats) to produce usable energy, commonly in the form of ATP is considered a catabolic process.

True

True or False: All living organisms fundamentally have the same molecular composition.

True

FEEDBACK: All living organisms have the same basic molecular composition; proteins made from amino acids, nucleic acids made from nucleotides, lipids produced from varying composition of nonpolar hydrocarbons and carbohydrates made from a similar basal monosaccharide composition (CH2O).

True or False: Water self-ionizes into hydrogen atoms and oxygen atoms.

False

FEEDBACK: The self-ionization of water molecules in solution produces hydrogen ions (hydronium ions: H3O+) and hydroxide ions (OH-). H2O → H+ + OH-

The loss of electrons in a chemical process is commonly known as

oxidation

Which of the amino acids would be classified as polar, charged (ionized/hydrophilic) amino acids?

aspartate

methionine

lysine

alanine

phenylalanine

aspartate

lysine

True or False: In a titration of glycine, the equivalence point in the titration represents equal concentrations of the carboxyl (-COOH) and carboxylate (-COO-) groups.

False

FEEDBACK: The pKa values represent on a titration curve where the concentrations of the protonated and deprotonated forms are equal. In the case of carboxyl groups, at a pH = pKa, [carboxyl] = [carboxylate]. The equivalence point on a titration curve is denoted by a rapid change in pH values. This occurs when the concentration of the titrated acid is equal to the concentration of base added (for titration). This would imply that nearly 100% of the weak acid has been titrated (deprotonated).

Which of the chemical components of histidine would be nearly 50% ionized at a pH equal to 9.2

α-amine

FEEDBACK: The pKa of a weak acid is the pH when the weak acid is 50% ionized (deprotonated). By looking at the pKa values of the α-carboxyl, the α-amino and the side chains, which ever pKa is closest to the actual pH then that represents the group which is near 50% ionization.

Which of the following amino acids is not incorporated into proteins as an L-enantiomer?

glycine

FEEDBACK: All amino acids are incorporated into proteins within humans as L-enantiomers. Glycine has a hydrogen as the side chain which means that there are two substituents of the α-carbon, making it achiral. An achiral glycine would not have L- nor D-enantiomers.

Which of the following intermolecular attractions would be associated with interactions between two cysteine residues?

disulfide bridges

True or False: The internal structure of a myoglobin protein excludes water due to a highly compact structure and a high concentration of nonpolar amino acids.

True

FEEDBACK: The internal environment of the globins are all nonpolar amino acids, except for two histidines which function to hold the heme ring in place.

The range of fraction oxygenation of myoglobin ranges in vertebrate muscle from

0-100%

Which of the protein filaments below consists of three helical polypeptides stabilized by H-bonding?

Collagen

Which of the following has the largest diameter?

microtubules

In contracting muscle fibers, where does hydrolysis of ATP occur?

In the myosin head subunits

The equilibrium concentrations of products and reactants are dependent upon

change in free energy

FEEDBACK: The concentrations of reactants and products at equilibrium are not affected by catalysis. At equilibrium ΔGo is zero and as such, there is no net change in concentrations of reactants and products. The relative concentrations of reactants and products is dependent upon the free energy differences between them. If ΔGo is negative, then product formation is preferred and the equilibrium constant would be larger.

The chemical structure along a reaction pathway that has the higest free energy is known as the

transition state

True or False: Weak attractions, such as hydrogen bonding and ionic attractions, allow an enzyme to loosely bind with the substrate.

True

In an enzyme-catalyzed reaction, the activation energy directly affects the

rate of a reaction

Feedback: An enzyme cannot affect the equilibrium, concentrations of reactants and products at equilibrium, nor the change in free energy. An enzyme only reduces the activation energy of BOTH the forward and reverse reactions, which merely changes the rates of BOTH the forward and reverse reactions equally. A reaction will proceed faster to products as long as the concentration of reactants is greater. An enzyme-catalyzed reaction simply proceeds faster to equilibrium than a non-catalyzed reaction. An enzyme-catalyzed reaction can also proceed forward as long as either reactant concentrations remain higher or product concentrations are lower (by eliminating products through other reactions).

Alanine is the substrate for a certain aminotransferase. What is the resulting product of alanine losing an amine?

pyruvate

When writing out a chemical mechanism, curved arrows represent

the movement of an electron pair.

In most serine proteases the serine residue within the active site is made very reactive because

Histidine removes a H+ from serine producing a very reactive oxide

Feedback: The active site of a serine protease contains serine, histidine and aspartate amino acids. During the hydrolysis of a peptide bond, the serine is made very reactive by the removal of a serine proton (H+) through an acid/base reaction. The deprotonated serine is now an oxide (-O-), which is a very strong base/nucleophile. The carboxyl carbon of the peptide bond can readily undergo nucleophilic attack by the serine oxide side chain.

Which of the following expressions best describes the rate by which the enzyme substrate complex dissociates without product formation?

k -1[ES]

Feedback: The enzyme substrate complex ( ES ) has two fates:

1. continue towards product formation, or

2. dissociate back into substrate and free enzyme.

If no product formation is perceived, the enzyme-substrate complex would fall back to substrate and free enzyme by the rate law equation:

v = k-1 [ES]

If a biochemist were to employ the following equation, what would they be solving for?

initial reaction rate

Feedback: The equation listed is the Michaelis-Menten equation which says that the initial rate of an enzyme-catalyzed reaction is determined by Km (Michaelis constant) and the theoretical maximum velocity (Vmax). The Michaelis constant describes the concentration of substrate needed to produce a velocity = 1/2Vmax, which really describes the relative affinity of an enzyme for a substrate. The higher the Km of an enzyme for a substrate, the lower the affinity and consequently more substrate is needed to produce a reaction. If Km is very low, this means the enzyme has a high affinity and little substrate is needed to produce the reaction.

Methanol in the body is metabolized by liver alcohol dehydrogenase (LADH) into the toxic product formaldehyde. In the event of methanol poisoning, ingesting ethanol (grain alcohol) causes LADH to produce acetylaldehyde and the metabolism of methanol is reduced. What form of inhibition does the ethanol represent here?

competitive-reversible

Feedback: Competitive, reversible inhibition is affected by substrate concentrations. The substrate and competitive, reversible inhibition compete for the active site and when substrate concentrations increase, the inhibitor binds less often and therefore its affect is diminished. Noncompetitive and irreversible inhibitors are not affected by substrate concentrations because in noncompetitive inhibition the inhibitor binds to an allosteric site and an irreversible inhibitor doesn't dissociate and therefore renders the enzyme ineffective.

Which of the following statements regarding enzyme inhibition is incorrect?

Competitive inhibition occurs when a substrate competes with an enzyme for binding with an inhibitor.

Feedback: Competitive, reversible inhibition is affected by substrate concentrations. The substrate and competitive, reversible inhibition compete for the active site and when substrate concentrations increase, the inhibitor binds less often and therefore its affect is diminished. Noncompetitive and irreversible inhibitors are not affected by substrate concentrations because in noncompetitive inhibition the inhibitor binds to an allosteric site and an irreversible inhibitor doesn't dissociate and therefore renders the enzyme ineffective.

Which of the following amino acids has the lowest molecular weight?

glycine

For the biochemical reaction W + X Y + Z, which of the following would indicate that in a cell the reaction would proceed toward the formation of more W + X?

Positive ΔG

Serine and aspartate are residues that are part of the "catalytic triad" in serine proteases. What is the third residue that makes up this triad?

His

Which of the following is the preferred unit for expression the energy gained or lost in biochemical reactions?

Joules

Which of the following has the greatest negative standard free energy for hydrolysis of the phosphate group?

ATP

Which of the following is NOT included in the Henderson-Hasselbalch equation?

Km

Which of the following would always be true for a six-carbon molecule being used to produce two three-carbon molecules?

Positive ΔS