BIOl 4880 Unit 1-3
Carbohydrates could be described as polyhydroxy ethers and esters.
False
Which statement is TRUE regarding coupled reactions? a. The coupled reactions must have different intermediates. b. The free energy of the endergonic reaction must be greater in magnitude than the free energy of the exergonic reaction. c. The standard free energy changes of the coupled reactions are additive and the coupled reactions must share a common intermediate. d. The standard free energy changes of the coupled reactions are multiplicative.
The standard free energy changes of the coupled reactions are additive and the coupled reactions must share a common intermediate.
Which statement concerning protein domains is TRUE? a. They are examples of structural motifs. b. They are a form of secondary structure. 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.
They may retain their correct shape even when separated from the rest of the protein.
Complex carbohydrates are built by linking simple sugars via glycosidic bonds.
True
Is this statement True/False? Most reaction steps in biochemistry involve an unshared electron pair (i.e. are not radical-based reactions).
True
Plants, as a kingdom, have many more estimated metabolites than humans.
True
True/False for the entire statement: When the K'eq is 1, the \DeltaΔG'o must therefore be zero. Starting with all components at 1 M, the reaction will remain at equilibrium.
True
True/False to entire statement: Catabolic reactions break down macromolecules resulting in the extraction of stored chemical energy. Relative to catabolic reactions anabolic reactions in general will require a greater net input of energy, e.g. via ATP.
True
True/False. In the "Lock and Key" model, protein and ligand do not influence each other.
True
True/False. Proline is a special case and can take up a cis configuration around the peptide bond.
True
Studies of peptide bonds show that:
peptide bonds are essentially planar, with no rotation about the C-N axis
Check all the types of chemicals that are part the human metabolome. - Xenobiotics - Non-nutritive chemicals in diet - Microbiome - Environmental
- Xenobiotics - Non-nutritive chemicals in diet - Microbiome - Environmental
The pKa of lysine's carboxyl group, amino group, and side chain are 2.2, 9.0, and 10.5, respectively. If lysine is in a pH 13 solution, what is the net charge on each lysine molecule? a. -2 b. +2 c. 0 d. +1 e. -1
-1
CHECK ALL THE ANSWERS THAT APPLY TO THIS STATEMENT: Which property(ies) of water contributes to the fitness of the aqueous environment of living organisms -high heat of vaporization -the very low molecular weight of water -high specific heat -cohesion of liquid water due to hydrogen bonding -the density of water being greater than the density of ice
-high heat of vaporization -high specific heat -cohesion of liquid water due to hydrogen bonding -the density of water being greater than the density of ice
Protein P has a binding site for ligand L. Using the concentrations given calculate the Ka (nM). [PL] = 20 nM [P] = 5 nM [L] = 10 nM a. 0.04 nM b. 4 nM c. 0.4 nM d. 0.0004 nM
0.4 nM
What is the EXPECTED biological concentration ranges (uM) for CORE BIOLOGICAL METABOLOME in humans? a. 1 to 10,000 uM b. 10-4 to 100 uM c. 10-12 to 10-8 uM d. 10-8 to 0.1 uM
10-4 to 100 uM
he pH of a solution of 0.1 M NaOH is: a. 0.1 b. 1.0 c. 12.8 d. 14 e. 13
13
What is the pH of a 0.1 mM solution of HCl at 37 deg C? a. 1 b. 4 c. 3 d. 0.1
4
Check all the amino acids that are GENERALLY favorable (helix formers) in alpha helices. - Pro - Ala - Trp - Gly
Ala
A hydronium ion: a. is a hydrated hydrogen ion. b. All of the answers are correct. c. has the structure H3O+. d. is the usual form of one of the dissociation products of water in solution. e. is a hydrated proton.
All of the answers are correct.
Hydrophobic interactions make important energetic contributions to: a. membrane structure. b. All of the answers are correct. c. binding of a hormone to its receptor protein. d. three-dimensional folding of a polypeptide chain. e. enzyme-substrate interactions.
All of the answers are correct.
Which of the following statements is false regarding oligomerization? a. A monomeric enzyme only contains a polypeptide chain with tertiary structure. b. A multienzyme complex is comprised of different enzymes catalyzing sequential reactions in the same pathway and are bound together. c. A multifunctional enzyme is a single polypeptide chain with multiple enzymatic activitie. d. All of the other statements are true (ergo none are false). e. An oligomeric enzyme has 2+ polypeptide chains associated with noncovalent forces.
All of the other statements are true (ergo none are false).
If a protein is not folded correctly or becomes partially unfolded, what could NOT be a consequence? a. The protein may be degraded by the proteasome. b. The protein may be remodeled by a chaperone. c. All of these consequences are possible. d. The protein may be refolded. e. The protein may form an inactive aggregate that leads to disease.
All of these consequences are possible.
Which of the following could potentially form a H bond? Assume distance is close enough to form said H bond. a. Met methyl-R group with carbonyl on backbone b. Pro amide-R group with carbonyl on backbone c. Asn amide-R group with carbonyl on backbone d. Val methyl-R group with carbonyl on backbone
Asn amide-R group with carbonyl on backbone
For the reaction A → B, the Keq' is 104. If a reaction mixture originally contains 1 mmol of A and no B, which statement must be TRUE? a. ΔG'° for the reaction will be large and positive. b. At equilibrium, there will be far more B than A. c. The reaction requires coupling to an exergonic reaction in order to proceed. d. The reaction will proceed toward B at a very high rate. e. The rate of the reaction is very slow.
At equilibrium, there will be far more B than A.
For the reaction A → B, the Keq' is 10-6. If a reaction mixture originally contains 1 mmol of A and 1 mmol of B, which statement must be TRUE? a. The rate of the reaction is very slow. b. At equilibrium, there will be still be equal levels of A and B. c. The reaction will proceed toward B at a very high rate. d. At equilibrium, the amount of A will greatly exceed the amount of B. e. ΔG'° for the reaction will be large and positive.
At equilibrium, there will be still be equal levels of A and B.
Match these vitamins with the appropriate coenzyme derivative. Updated question 08/28 to fix previous duplicate issue.
Biotin- Biocytin Vitamin B6- PLP Vitamin B12- Cobalamin Pantothenate- Coenzyme A Riboflavin- FAD/FMN Niacin- NAD Vitamin B1- TPP Folic Acid- THF n/a- SAM
Which compound would result in the formation of a clathrate structure? a. NH3 b. CH3CH2OH c. CH2O d. Glucose e. CH4
CH4
This question deals with chemical groups transferred (first blank) and reaction type (second blank) for coenzymes. Biocytin (Biotin) transfers _______ and therefore part of a _______reaction.
CO2; carboxylation
Which of the following is not an inorganic ion that serves as cofactors for enzymes? a. Fe b. Mg c. K d. Ca e. Cu
Ca
Which of the following chemical types in the human metabolome has the LEAST EXPECTED VARIABILITY in human populations? a. Micriobiome-related chemicals b. Supplements and pharmaceuticals c. Core biological metabolites d. Non-nutritive chemicals in diet
Core biological metabolites
Protein P has a binding site for ligand L. Using the concentrations given, calculate the fraction of bound sites (\thetaθ) rounded to the nearest two decimal places. [PL] = 40 nM [Total P] = 45 nM [L] = 100 nM a. 0.50 b. 0.89 c. 0.80 d. 0.67
Correct Answer: 0.89
In a highly basic solution, pH = 11, the dominant form of glycine is: a. NH2—CH2—COOH. b. NH2—CH2—COO-. c. NH3+—CH2—COOH. d. NH2—CH3+—COO-. e. NH3+—CH2—COO-
Correct Answer:NH2—CH2—COO-.
Which pairs of bonds within a peptide backbone show free rotation around both bonds? a. Cα—C and N—Cα b. N—Cα and N—C c. C=O and N—C d. C=O and N—Cα e. N—C and Cα—C
Cα—C and N—Cα
Which pairs of bonds within a peptide backbone show free rotation around both bonds? a. N—C and Cα—C b. C=O and N—C c. C=O and N—Cα d. Cα—C and N—Cα e. N—Cα and N—C
Cα—C and N—Cα
Select all the types of events / "stimuli" that CAN result in changes to an organisms metabolome?
Development Genetics Drugs Pollutants
Check all the types of chemicals that are part the human metabolome. Environmental Non-nutritive chemicals in diet Xenobiotics Microbiome
Environmental Non-nutritive chemicals in diet Xenobiotics Microbiome
If chemical reactions will eventually reach an equilibrium state, what is the purpose of enzymes in a biological system? a. Enzymes prevent the formation of unstable reaction intermediates. b. Enzymes slow down chemical reactions. c. Enzymes alter the equilibrium state between reactants and products. d. Enzymes speed up chemical reactions without being used up in the process. e. Enzymes are consumed to speed up chemical reactions.
Enzymes speed up chemical reactions without being used up in the process.
Which statement is TRUE about oxidation-reduction reactions? a. Every oxidation must be accompanied by a reduction. b. They usually proceed through homolytic cleavage. c. Dehydrogenases typically remove two electrons and two hydrides. d. During oxidation a compound gains electrons. e. There are four commonly accessed oxidation states of carbon.
Every oxidation must be accompanied by a reduction.
All of the statements below describe factors that contribute to the bent shape of a water molecule. a. the lack of a dipole moment in a water molecule b. the unavailable electron pairs on the oxygen atom c. the electronegativity difference between hydrogen and oxygen d. the unequal electron sharing between hydrogen and oxygen
False
Catalytic sites bind and orient substrate(s) while binding sites reduce chemical activation energy.
False
Do all nucleophiles react with ALL electrophiles?
False
Metabolites are large-molecular-weight (>1000 Da) organic and inorganic chemicals.
False
Metabolites are usually distributed uniformly throughout an organism.
False
Metal ions such as hydrogen, carbon, nitrogen, and oxygen play important roles in metabolism.
False
Starch and glycogen are simple carbohydrates comprised of few sugar units.
False
True/False. Absolute and sterochemical enzyme specificity are relatively low specificity while group and linkage are relatively high specificity.
False
True/False. The peptide bond is a resonance hybrid of two canonical structures. This resonance is spread across the alpha carbon and amide oxygen.
False
True/False: Hydrogen bonds stabilize the helical structure of the alpha helix. When unfolding, the hydrogen bonds remain intact.
False
True/False: In general oxidoreductases, transferases, and hydrolases are the minority of biochemical reactions (<25% total) while ligases, lyases, and isomerases are the majority of biochemical reactions (>75%).
False
Phosphoric acid is tribasic, with pKa's of 2.14, 6.86, and 12.4. The ionic form that predominates at pH 3.2 is: a. H2PO4-. b. None of the answers is correct. c. PO43-. d. HPO42-. e. H3PO4.
H2PO4-.
Adenine binding to thymine in DNA is an example of which of: a. Hydrogen bond (complementarity) b. Covalent bonding c. Ionic interactions d. A racemic mixture e. Transcription
Hydrogen bond (complementarity)
Which statement about hydrogen bonds is NOT true? a. Hydrogen bonds are strongest when the three atoms in the bond are in a straight line. b. Hydrogen bonds are highly directional. c. Hydrogen bonds are capable of holding molecules in a specific geometric arrangement. d. Hydrogen bonds are strongest when the oxygen atom is perpendicular to the hydrogen donor. e. Hydrogen bonds place a hydrogen ion directly between two partial negative charges.
Hydrogen bonds are strongest when the oxygen atom is perpendicular to the hydrogen donor.
Which statement is TRUE about the properties of aqueous solutions? a. A pH change from 8.0 to 6.0 reflects a decrease in the proton concentration ([H+]) by a factor of 100. b. Hydrogen bonds form readily in aqueous solutions. c. The pH can be calculated by adding 7 to the value of the pOH. d. Charged molecules are generally insoluble in water.
Hydrogen bonds form readily in aqueous solutions.
Which statement is TRUE about the properties of aqueous solutions? a. Hydrogen bonds form readily in aqueous solutions. b. The pH can be calculated by adding 7 to the value of the pOH. c. Charged molecules are generally insoluble in water. d. A pH change from 8.0 to 6.0 reflects a decrease in the proton concentration ([H+]) by a factor of 100.
Hydrogen bonds form readily in aqueous solutions.
Of the following bonds, which have freedom of rotation? I. N - Calpha II. Calpha - C III. C - N IV. R - Calpha a. II, III, and IV b. All of them c. I and IV d. I, II, and III e. I, II, and IV
I, II, and IV
Which group of amino acids would be MOST likely to be found in the core of protein that is folded into a three-dimensional structure and soluble in water? a. F, Y, and W b. N, Y, and K c. M, S, and Y d. I, M, and V e. V, T, and R
I, M, and V
Check all the amino acids that are GENERALLY favorable in beta strands
Ile Phe Cys Val
The dipole moment in a water molecule Which statement about hydrogen bonds is NOT true? a. Individual hydrogen bonds are much weaker than covalent bonds. b. The strength of a hydrogen bond depends on the linearity of the three atoms involved in the bond. c. Hydrogen bonds account for the anomalously high boiling point of water. d. In liquid water, the average water molecule forms hydrogen bonds with three to four other water molecules. e. Individual hydrogen bonds in liquid water exist for many seconds and sometimes for minutes.
Individual hydrogen bonds in liquid water exist for many seconds and sometimes for minutes.
The dipole moment in a water molecule Which statement about hydrogen bonds is NOT true? a. Individual hydrogen bonds in liquid water exist for many seconds and sometimes for minutes. b. Individual hydrogen bonds are much weaker than covalent bonds. c. Hydrogen bonds account for the anomalously high boiling point of water. d. The strength of a hydrogen bond depends on the linearity of the three atoms involved in the bond. e. In liquid water, the average water molecule forms hydrogen bonds with three to four other water molecules.
Individual hydrogen bonds in liquid water exist for many seconds and sometimes for minutes.
What does the molecule SDS do to proteins?
It denatures large portions of proteins and distributes a large negative charge throughout the protein.
Which statement concerning the process of spontaneous folding of proteins is FALSE? a. It may be defective in some human diseases. b. It may involve initial formation of local secondary structure. c. It may involve a gradually decreasing range of conformational species. d. It may be an essentially random process. e. It may involve initial formation of a highly compact state.
It may be an essentially random process.
At pH 7.0, converting a glutamic acid to -carboxyglutamate, will have what effect on the overall charge of the protein containing it? a. It will become more negative. b. It will become more positive. c. It will stay the same. d. There is not enough information to answer the question. e. The answer depends on the salt concentration.
It will become more negative.
Below are binding affinities for four different ligands and Protein P (P + L <----> PL). Select the ligand with the highest binding affinity. a. Ligand D, Ka = 104 M-1 b. Ligand B, Kd = 10-15 M c. Ligand C, Ka = 1013 M-1 d. Ligand A, Kd = 10-2 M
Ligand B, Kd = 10-15 M
Below are binding affinities for four different ligands and Protein P (P + L <----> PL). Select the ligand with the highest binding affinity. a. Ligand D, Ka = 102 M-1 b. Ligand B, Kd = 1014 M c. Ligand C, Ka = 1015 M-1 d. Ligand A, Kd = 10-5 M
Ligand C, Ka = 1015 M-1
Which mutation would be MOST likely to result in amyloid formation? Gln -> Glu Lys -> Phe Trp -> Ile Tyr ->His Lys -> Arg
Lys -> Phe
What is the systematic characterization of the entire collection of small molecules in a given cell under a specific set of conditions called? a. Genomics b. Metabolomics c. Systems biology d. Proteomics e. Lipidomics
Metabolomics
Cell Biology Review: Which organelle is found in both plant and animal cells? a. Glyoxysome b. Starch Granule c. Mitochondrion d. Chloroplast e. Plasmodesma
Mitochondrion
Which method would be most useful to solve the structure of a small, soluble protein that does not easily form a repeating structure?
NMR
Which statement BEST describes why niacin is required in the mammalian diet? a. Niacin is a precursor of nicotinamide adenine dinucleotide (NAD), which is a coenzyme required by many oxidoreductase enzymes. b. Niacin is a precursor of thiamine pyrophosphate, which is a coenzyme required by many transferases. c. Niacin is a precursor of flavin adenine dinucleotide (FAD), which is a coenzyme required by many ligases. d. Niacin is a component of coenzyme A, which is involved in many transferase reactions. e. Niacin is not actually required in the mammalian diet.
Niacin is a precursor of nicotinamide adenine dinucleotide (NAD), which is a coenzyme required by many oxidoreductase enzymes.
Which statement is TRUE for the reaction A + B ↔ C + D if its Keq for the reaction is 104? a. The value of ΔG'° will be large and positive. b. None of the statements is true. c. All of the statements are true. d. When the reaction has reached equilibrium, there will be significantly more A and B than C and D in solution. e. The formation of A and B will proceed at a high rate.
None of the statements is true.
Why can only some amino acids be used to measure protein concentration based on absorption of UV light? a. Only some amino acids are strongly hydrophilic. b. Only some amino acids are aromatic. c. Only some amino acids are positively charged. d. Only some amino acids are negatively charged. e. Only some amino acids are strongly hydrophobic.
Only some amino acids are aromatic.
Which of the following is not an inorganic ion that serves as cofactors for enzymes? a. Pb b. Cu c. Ni d. Mn e. Fe
Pb
Amino acid residues commonly found in the middle of β turn are: a. Ala and Gly. b. those with ionized R-groups. c. Pro and Gly. d. hydrophobic. e. two Cys.
Pro and Gly.
Place the following general functions in the macromolecule category it fits with BEST. Answers only go with one category
Proteins- Speeds up biochemical reactions Correct answer:Binds and transport substances Lipids- Store energy as (most often) ampipathic/hydrophobic molecules Most abundant (by number of molecules) component of membranes Polysaccharides- provides structural support in membranes as long change (ether-linked) polymers Stores energy in hydroxyl rich molecules Nucleic Acids- Most directly involved in heritability Correct answer:Stores genetic info
Which statement is TRUE regarding the actual free-energy change for a reaction? a. None of the statements is true. b. The actual free energy varies depending on the standard free energy and the concentration of reactants and products. c. The actual free-energy change varies depending on the pathway by which the reaction occurs. d. When the standard free energy is large and positive, the reaction will never occur. e. All of the statements are true.
The actual free energy varies depending on the standard free energy and the concentration of reactants and products.
Which of the following is NOT true regarding phi/psi angles in a polypeptide? a. The conformation in which both phi and psi are 0 degrees is highly favored. b. psi is angle around alpha carbon-carbonyl carbon bond c. Both the phi and psi angles are defined as being +/- 180 degrees when the polypeptide backbone is fully extended and all peptide groups are in the same plane. d. phi is angle around alpha carbon-amide nitrogen bond
The conformation in which both phi and psi are 0 degrees is highly favored.
Which statement about protein-ligand binding is correct?
The larger the Ka, the smaller the Kd (dissociation constant).
The average molecular weight of the 20 standard amino acids is 138, but biochemists use 110 when estimating the number of amino acids in a protein of known molecular weight. Why? a. The number 110 takes into account the relatively small size of nonstandard amino acids. b. The number 110 is based on the fact that the average molecular weight of a protein is 110,000 with an average of 1000 amino acids. c. The number 110 reflects the higher proportion of small amino acids in proteins, as well as the loss of water when the peptide bond forms. d. The number 138 represents the molecular weight of conjugated amino acids. e. The number 110 reflects the number of amino acids found in the typical small protein, and only small proteins have their molecular weight estimated this way.
The number 110 reflects the higher proportion of small amino acids in proteins, as well as the loss of water when the peptide bond forms.
Which statement is TRUE about the pKa values for ionizable R-group of amino acids within a polypeptide? a. The pKa values for R-groups are 1 pH unit higher than free amino acids. b. The pKa values for R-groups do not change from free amino acids. c. The pKa values for R-groups vary depending on the local environment of the side chain. d. The pKa values for R-groups depend on how close the R-group is to the N- or C-terminus of the polypeptide. e. The pKa values for R-groups are 1 pH unit lower than free amino acids.
The pKa values for R-groups vary depending on the local environment of the side chain.
ΔG'° for the hydrolysis of ATP is -30.5 kJ/mol. What effect will doubling ATP concentration have on the value of ΔG'° for ATP hydrolysis? a. Make the value of ΔG'° more positive. b. Make the value of ΔG'° less negative. c. There will be no change in the value of ΔG'°. d. Make the value of ΔG'° less positive. e. Make the value of ΔG'° more negative.
There will be no change in the value of ΔG'°.
Which statement is NOT an appropriate description for van der Waals interactions? a. They are highly specific. b. An individual van der Waals interaction does not contribute significantly to the stability of a protein. c. They involve dipole-dipole interactions. d. They can involve hydrophobic amino acids. e. Their strength depends on the distance between the two interacting atoms.
They are highly specific.
Chitin and cellulose are two polysaccharide-based polymers that are essentially insoluble in water. What is the best reason for this? a. Polymers of these molecules pack so tightly together that there is no geometric space left for water. b. They form many internal hydrogen bonds, leaving no sites for bonding to water. c. Because beta-glycosidic linkages are nonpolar and alpha linkages are polar. d. Because there are no enzymes that can break the beta linkages. e. Because the linear polymer cannot make hydrogen bonds.
They form many internal hydrogen bonds, leaving no sites for bonding to water.
Place the elements in the correct category essential for human life. (hint 4 are not used)
Tier 1- Hydrogen Carbon Oxygen Nitrogen Tier 2- Sulfur Sodium Phosphorous Tier 3- Iron Manganese Copper Unused- Helium Lithium Lead Aluminum
According to what I taught you, general covalent bonds are where both atoms contribute one electron each whereas a coordinate covalent bond generally one atom contributes both electrons.
True
Is this statement True/False? Curved arrows ( ) represent the movement of electron pairs wheras a singleheaded (fishhook-type) arrow is used for movement of a single electron (as in a free radical reaction).
True
True/False. Researchers have shown that protein stability can be enhanced by engineering "extended" disulfide bonds.
True
True/False: Hydrogen bond interactions with water and protein can contribute to stability (e.g. rhodopsin).
True
True/False: Peptide bonds are formed through a nucleophilic addition-elimination reaction. In this reaction the amine group is the nucleophile and the carbonyl (part of a carboxyl group) is the electrophile.
True
True/False: The "conformational selection" model allows for the most conformational flexibility of the 3 models.
True
Which statement about buffers is True? a. A buffer composed of a weak acid of pKa = 5 is stronger at pH 4 than at pH 6. b. When pH = pKa, the weak acid and salt concentrations in a buffer are equal. c. At pH values lower than the pKa, the salt concentration is higher than that of the acid. d. The strongest buffers are those composed of strong acids and strong bases. e. The pH of a buffered solution remains constant no matter how much acid or base is added to the solution.
When pH = pKa, the weak acid and salt concentrations in a buffer are equal.
Which statement about Gibbs free energy is FALSE?
When the reactants are in excess of their equilibrium concentrations, the conversion of product to reactant is more likely to occur.
A D-amino acid would interrupt an α helix made of L-amino acids. Another naturally occurring hindrance to the formation of an α helix is the presence of: a. a nonpolar residue near the carboxyl terminus. b. a Pro residue. c. two Ala residues side by side. d. a positively charged Lys residue. e. a negatively charged Arg residue.
a Pro residue.
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 positive charge. b. no charged groups. c. no net charge. d. positive and negative charges in equal concentration. e. a net negative charge.
a net positive charge.
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. positive and negative charges in equal concentration. b. no charged groups. c. a net negative charge. d. no net charge. e. net positive charge.
a net positive charge.
Water can act as ___________ in biological reactions. Check all that are correct. - an enzyme - a product - a solvent - a reactant
a product a solvent a reactant
A reaction that has a ΔG'o of 25kJ/mol is likely to have which property?
a small equilibrium constant
Which of the following is NOT TRUE about electrophiles? a. accepts an electron pair from a nucleophile to form a chemical bond b. electrophiles are Lewis acids c. a electrophile becomes attracted to a full or partial negative charge d. all molecules or ions with a free pair of electrons or at least one pi bond can act as electrophiles
all molecules or ions with a free pair of electrons or at least one pi bond can act as electrophiles
Which of the following is a main role of protein-bound metals? a. stability b. ligand binding c. all of the other answers d. electron transfer e. catalysis
all of the other answers
Proteins can be denatured by a. urea. b. all of the other answers. c. organic solvents. d. extreme heat or cold. e. pH extremes.
all of the other answers.
All of the amino acids that are found in proteins, except for proline, contain a(n) _____ group. a. amino b. ester c. carboxyl d. carbonyl e. thiol
amino
his question deals with chemical groups transferred (first blank) and reaction type (second blank) for coenzymes. Pyridoxal phosphate (PLP) transfers _______ and therefore part of a _____________ reaction.
amino groups; transfer of amino groups
Molecules that have both hydrophobic and hydrophilic character are called: a. hyperbaric b. amphipathic c. isotonic d. osmolar e. colligative
amphipathic
A protein with a high percentage of aspartate and glutamate residues would be BEST purified and concentrated with which type of column? a. anion exchange (i.e. positive charged residues on stationary phase) b. affinity chromatography (i.e. positive charged residues on stationary phase) c. reverse-phase chromatography d. cation exchange (i.e. negative charged residues on stationary phase) e. size-exclusion chromatography
anion exchange (i.e. positive charged residues on stationary phase)
One of the enzymes involved in glycolysis, aldolase, requires Zn2+ for catalysis. Under conditions of zinc deficiency, when the enzyme may lack zinc, it would be referred to as the: a. apoenzyme. b. coenzyme. c. holoenzyme. d. prosthetic group. e. substrate.
apoenzyme
In an α helix, the R groups on the amino acid residues: a. generate the hydrogen bonds that form the helix. b. cause only right-handed helices to form. c. are found on the outside of the helix spiral. d. stack within the interior of the helix. e. alternate between the outside and the inside of the helix.
are found on the outside of the helix spiral.
In the α helix, the hydrogen bonds: a. occur only near the amino and carboxyl termini of the helix. b. occur only between some of the amino acids of the helix. c. are roughly parallel to the axis of the helix. d. occur mainly between electronegative atoms of the R groups. e. are roughly perpendicular to the axis of the helix.
are roughly parallel to the axis of the helix.
The interactions of ligands with proteins: a. are usually transient. b. are relatively nonspecific. c. usually result in the inactivation of the proteins. d. are usually irreversible. e. are relatively rare in biological systems.
are usually transient.
The structure below is a molecule used in the sweeteners Equal® and NutraSweet®. When heated, the peptide bond will hydrolyze into methanol and which two amino acids? a. glutamic acid and histidine b. aspartic acid and tryptophan c. aspartic acid and phenylalanine d. asparagine and tyrosine e. glutamic acid and phenylalanine
aspartic acid and phenylalanine
The uncommon amino acid selenocysteine has an R group with the structure —CH2—SeH (pKa 5). In an aqueous solution, pH = 7.0, selenocysteine would: a. be nonionic. b. be found in proteins as D-selenocysteine. c. not be optically active. d. be a fully ionized zwitterion with no net charge. e. never be found in a protein.
be a fully ionized zwitterion with no net charge. never be found in a protein.
A good transition-state analog: a. is too unstable to isolate. b. must be almost identical to the substrate. c. binds to the enzyme more tightly than the substrate. d. binds covalently to the enzyme. e. binds very weakly to the enzyme.
binds to the enzyme more tightly than the substrate.
A protein with a high percentage of lysine and arginine residues would be BEST purified and concentrated with which type of column? a. affinity chromatography b. cation exchange (i.e. negative charged residues on stationary phase) c. reverse-phase chromatography d. anion exchange (i.e. positive charged residues on stationary phase) e. size-exclusion chromatography
cation exchange (i.e. negative charged residues on stationary phase)
Which factor is LEAST likely to result in protein denaturation? a. disruption of weak interactions by boiling b. exposure to detergents c. changing the salt concentration d. mixing with organic solvents such as acetone e. altering net charge by changing pH
changing the salt concentration
A complex organic molecule that is necessary for enzyme function but is NOT permanently associated with the enzyme is a: a. cofactor. b. coenzyme. c. prosthetic group. d. metal ion. e. holofactor.
coenzyme.
The formation of a peptide bond between two amino acids is an example of a(n)________ reaction
condensation
Cell Biology Review: In a typical animal cell, which of the following compartments is the largest (percentage of cell volume? a. cytosol b. mitochondria c. Peroxisomes d. Glyoxysome e. nucleus
cytosol
What name is given to the nucleotide found in DNA and not in RNA? a. guanine b. uracil c. deoxycytosine d. deoxyuridylate e. deoxythymidylate
deoxythymidylate
Proteins often have regions that can fold and function as an independent entity from the whole protein. These regions are called: a. domains. b. peptides. c. sites. d. subunits. e. oligomers.
domains.
This question deals with chemical groups transferred (first blank) and reaction type (second blank) for coenzymes. Lipoate (or lipoic acid) transfers _____________and therefore part of a ____________reaction.
electrons and acyl groups; dehydrogenation, acyl group transfer
This question deals with chemical groups transferred (first blank) and reaction type (second blank) for coenzymes. Coenzyme (CoQ) transfers ___________ and therefore part of a _________ reaction.
electrons; redox
The MOST important contribution to the stability of a protein's conformation appears to be the: a. sum of free energies of formation of many weak interactions among the hundreds of amino acids in a protein. b. entropy increase from the decrease in ordered water molecules forming a solvent shell around it. c. stabilizing effect of hydrogen bonding between the carbonyl group of one peptide bond and the amino group of another. d. maximum entropy increase from ionic interactions between the ionized amino acids in a protein. e. sum of free energies of formation of many weak interactions between its polar amino acids and surrounding water.
entropy increase from the decrease in ordered water molecules forming a solvent shell around it.
The peptide alanylglutamylglycylalanylleucine has: a. a disulfide bridge. b. two free amino groups. c. four peptide bonds. d. no free carboxyl group. e. five peptide bonds.
four peptide bonds.
The three-dimensional conformation of a protein may be strongly influenced by amino acid residues that are very far apart in sequence. This relationship is in contrast to secondary structure, where the amino acid residues are:
generally near each other in the sequence
Phenotype is the set of observable characteristics of an individual resulting from the interaction of its___________ with the environment.
genotype
Polysaccharides are comprised of monosaccharides linked by _________ bonds.
glycosidic
Cell Biology Review: Which of the following organelles is not matched with its corresponding function? a. nucleolus, ribosome production b. ribosome, protein synthesis c. nucleus, DNA replication d. golgi apparatus, sugar synthesis e. chloroplasts, photosynthesis
golgi apparatus, sugar synthesis
The reaction ATP → ADP + Pi is an example of a(n) _____ reaction. a. internal rearrangement b. free radical c. oxidation/reduction d. homolytic cleavage e. group transfer
group transfer
Proline residues are infrequently found in _____ due to their _____. a. helices; large positive charge that disrupts the repeating structure b. turns; decreased flexibility as an amino acid c. sheets; large positive charge that disrupts the repeating structure d. helices; decreased ability to serve as hydrogen-bond donors
helices; decreased ability to serve as hydrogen-bond donors
Biological buffering systems include: a. phosphate b. bicarbonate and phosphate c. histidine d. bicarbonate e. histidine, bicarbonate, and phosphate
histidine, bicarbonate, and phosphate
This question deals with chemical groups transferred (first blank) and reaction type (second blank) for coenzymes. Nicotinamide adenine dinucleotide (NAD(P)+) transfers_______ and therefore part of a ________ reaction.
hydride (electrons + proton); redox
Which force plays the GREATEST role in stabilizing biological structures in membranes? a. hydrophobic interactions that increase solvent entropy b. van der Waals interactions, because of the attraction between transient dipoles c. covalent interactions, because they are very stable interactions d. hydrogen bonding, because it a strong non-covalent bond e. electrostatic interactions between oppositely charged ions
hydrophobic interactions that increase solvent entropy
The role of an enzyme in an enzyme-catalyzed reaction is to: a. increase the rate at which substrate is converted into product. b. make the free-energy change for the reaction more favorable. c. ensure that the product is more stable than the substrate. d. ensure that all of the substrate is converted to product. e. bind a transition state intermediate, such that it cannot be converted back to substrate.
increase the rate at which substrate is converted into product.
Dissolving a nonpolar solute in water________ the order of the solvent and________ the dynamic interplay among water molecules that occurs in pure water.
increases; decreases
An average protein will NOT be denatured by: a. heating to 90°C. b. urea. c. pH 10. d. a detergent such as sodium dodecyl sulfate. e. iodoacetic acid.
iodoacetic acid.
The amino acid proline is unique because the R group: a. is cyclical. b. has a phosphate attached. c. is positively charged. d. None of the answers is correct. e. is attached to the carboxylic acid carbon.
is cyclical.
The term specificactivity differs from the term activity in that specific activity: a. is the activity (enzyme units) in a milligram of protein. b. is measured only under optimal conditions. c. refers only to a purified protein. d. refers to proteins other than enzymes. e. is the activity (enzyme units) of a specific protein.
is the activity (enzyme units) in a milligram of protein.
Cell Biology Review: What is the initial fate of a protein with no sorting signal? a. it remains in the nucleus b. it is excreted extracellularly c. it is directed to the mitochondria d. none of the other answers e. it remains in the cytosol
it remains in the cytosol
Cell Biology Review: Chemical analysis indicates that the cell membrane is composed mainly of a. lipids and proteins b. lipids and starch c. proteins and starch d. proteins and cellulose e. proteins and mitochondria
lipids and proteins
For the following reaction, ΔG'° = +29.7 kJ/mol. L-Malate + NAD+ → oxaloacetate + NADH + H+ The reaction as written: a. can occur in a cell only if it is coupled to another reaction for which ΔG'° is positive. b. can occur only in a cell in which NADH is converted to NAD+ by electron transport. c. can never occur in a cell. d. cannot occur because of its large activation energy. e. may occur in cells at some concentrations of substrate and product
may occur in cells at some concentrations of substrate and product.
Protein S will fold into its native conformation only when protein Q is also present in the solution. However, protein Q can fold into its native conformation without protein S. Protein Q, therefore, may function as a ____________ for protein S.
molecular chaperone
Proteins in their functional, folded conformation are called _____ proteins. a. native b. inherent c. unique d. natural e. intrinsic
native
The polarity of water will result in oxygen containing a partial ________ charge and hydrogen a partial __________ charge.
negative; positive
Amino acids without ionizable R-groups can act as a zwitterion in a(n) _____ solution. a. nonpolar b. basic c. neutral d. acidic e. boiling
neutral
Which of the following is NOT TRUE about nucleophiles? a. all molecules or ions with a free pair of electrons or at least one pi b. bond can act as nucleophiles c. a nucleophile becomes attracted to a full or partial positive charge d. nucleophiles are Lewis acids e. donates an electron pair to an electrophile to form a chemical bond
nucleophiles are Lewis acids
Proteins are amino acids linked by __________ bonds.
peptide
Which interactions are NOT considered "weak" in proteins?
peptide bonds
Studies of peptide bonds show that: primary structure of all proteins is similar, although the secondary and tertiary structure may differ greatly. a. peptide bonds in proteins are unusual, and unlike those in small model compounds. b. peptide bonds are essentially planar, with no rotation about the C—N axis. c. at pH 7, many different peptide bond conformations are equally probable. d. peptide bond structure is extraordinarily complex.
peptide bonds are essentially planar, with no rotation about the C—N axis.
A prosthetic group of a protein is a nonprotein structure that is:
permanently associated with a protein.
You set up an experiment to record the height of every student in biology. What are you most directly measuring? a. Transcriptome b. Epigenetics c. Phenotype d. Genome e. Metabolome
phenotype
This question deals with chemical groups transferred (first blank) and reaction type (second blank) for coenzymes. Adenosine triphosphate (ATP) transfers _________ and therefore part of a___________reaction.
phosphates; phosphoryl group transfer
Which enzymes are NOT among the six internationally accepted classes of enzymes? a. hydrolases b. polymerases c. ligases d. oxidoreductases e. transferases
polymerases
Proteostasis is the cellular process by which: a. proteins are synthesized. b. proteins are degraded. c. proteins are modified. d. proteins are folded. e. protein levels are maintained (i.e. balancing synthesis, folding, modification, and degradation).
protein levels are maintained (i.e. balancing synthesis, folding, modification, and degradation).
The first step in two-dimensional gel electrophoresis generates a series of protein bands by isoelectric focusing. In a second step, a strip of this gel is turned 90 degrees, placed on another gel containing SDS, and electric current is again applied. In this second step: a. proteins with similar isoelectric points become further separated according to their molecular weights. b. the individual bands become visualized by interacting with protein-specific antibodies in the second gel. c. the individual bands become stained so that the isoelectric focus pattern can be visualized. d. the proteins in the bands separate more completely because the second electric current is in the opposite polarity to the first current. e. the individual bands undergo a second, more intense isoelectric focusing.
proteins with similar isoelectric points become further separated according to their molecular weights.
The Henderson-Hasselbalch equation: a. employs the same value for pKa for all weak acids. b. is equally useful with solutions of acetic acid and of hydrochloric acid. c. does not explain the behavior of di- or tri-basic weak acids. d. allows the graphic determination of the molecular weight of a weak acid from its pH alone. e. relates the pH of a solution to the pKa and the concentrations of acid and conjugate base.
relates the pH of a solution to the pKa and the concentrations of acid and conjugate base.
Cell Biology Review: Prokaryotic and eukaryotic cells generally have which of the following features in common? a. nucleoid b. a membrane-bound nucleus c. a cell wall made of cellulose d. similar size and complexity e. ribosomes
ribosomes
Which type of structure refers to particularly stable arrangements of amino acid residues in a protein that give rise to recurring patterns? a. tertiary structure b. primary structure c. None of the answers is correct. d. secondary structure e. quaternary structure
secondary structure
A protein is highly unlikely to have both and angles equal to zero degrees due to: a. steric hindrance between the side chain and the peptide backbone. b. polarity differences between adjacent side chains. c. steric hindrance between adjacent side chains. d. too few van der Waals contacts for proper folding. e. hydrophobic interactions between adjacent side chains.
steric hindrance between the side chain and the peptide backbone.
Thr and/or Leu residues tend to disrupt an α helix when they occur next to each other in a protein because: a. the R group of Thr can form a hydrogen bond. b. covalent interactions may occur between the Thr side chains. c. electrostatic repulsion occurs between the Thr side chains. d. an amino acids like Thr is highly hydrophobic. e. steric hindrance occurs between the bulky Thr side chains.
steric hindrance occurs between the bulky Thr side chains.
The concept of "induced fit" refers to the fact that: a. enzyme-substrate binding induces movement along the reaction coordinate to the transition state. b. substrate binding may induce a conformational change in the enzyme, which then brings catalytic groups into proper orientation. c. enzyme-substrate binding induces an increase in the reaction entropy, thereby catalyzing the reaction. d. when a substrate binds to an enzyme, the enzyme induces a loss of water (desolvation) from the substrate. e. enzyme specificity is induced by enzyme-substrate binding.
substrate binding may induce a conformational change in the enzyme, which then brings catalytic groups into proper orientation.
Long-range interactions between residues on a single polypeptide chain could BEST be classified as _____ structure. a. primary b. tertiary c. globular d. quaternary e. secondary
tertiary
When the ribosome forms a peptide bond, which two atoms form a covalent bond? a. the amino nitrogen and carboxylic acid carbon b. the carbon and the amino nitrogen c. It depends on the amino acids being joined. d. the amino nitrogen and the carbon e. the carbon and the carboxylic acid carbon
the amino nitrogen and carboxylic acid carbon
I need to calculate the pH of a weak acid. I know the concentration of the acid and its conjugate base, and my solution is at 30°C. Using the Henderson-Hasselbalch equation, what else do I need? a. the total H+ concentration (i.e., free and bound to the acid) b. the Kd for H+ of the acid c. the free-energy change for release of the H+ d. All that is needed has been given. e. the pKa of the acid
the pKa of the acid
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. the completely unfolded enzyme, with all —S—S— bonds broken, is still enzymatically active. c. the primary sequence of RNase is sufficient to determine its specific secondary and tertiary structure. d. the enzyme, dissolved in water, is thermodynamically stable relative to the mixture of amino acids whose residues are contained in RNase. e. native ribonuclease does not have a unique secondary and tertiary structure.
the primary sequence of RNase is sufficient to determine its specific secondary and tertiary structure.
What is the actual function of a buffer system such as acetate/acetic acid? a. to maintain the solution at neutral pH b. to maintain a constant pH in the event that the concentration of an acid or alkali increases c. to keep the solution within one pH unit of the pKa d. to ensure that the solution has no free H+ or OH⎼ within a specific range e. to maintain the solution at the pKa
to maintain a constant pH in the event that the concentration of an acid or alkali increases
Biological oxidation-reduction reactions always involve: a. transfer of hydrogens. b. formation of water. c. mitochondria. d. direct participation of oxygen. e. transfer of electron(s).
transfer of electron(s).
Which pair of amino acids can be used to measure the concentration of proteins based on the absorption of UV light?
tyrosine and tryptophan
What compound is a side-product of a peptide bond formation?
water
According to the Henderson-Hasselbalch equation, when is the pH equal to the pKa? a. when the concentration of acid is close to zero. b. when the concentration of the conjugate base is equal to the concentration of the acid. c. when the pH approaches 7 d. None of the answers is correct. e. when the concentration of the conjugate base is equal to the ionization constant for water
when the concentration of the conjugate base is equal to the concentration of the acid.
Which method would be MOST useful to the atomic resolution structure of a protein that happens to easily form repeating structure?
x-ray crystallography
Which statement is TRUE with respect to the change in free energy for a given reaction? a. All of the statements are true. b. ΔG provides no information about the rate of the reaction. c. None of the statements is true. d. ΔG is linearly proportional to the rate of the reaction. e. ΔG is a logarithmic function of the equilibrium constant.
ΔG provides no information about the rate of the reaction.
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. —NH2 + OH- —NH- + H2O. b. —NH3+ + OH- —NH2 + H2O. c. —COOH + OH- —COO- + H2O. d. —COOH + —NH2 —COO- + —NH2+. e. —COO- + —NH2+ —COOH + —NH2.
—NH3+ + OH- —NH2 + H2O.