BCH480 All quizzes/Test Questions

The repeating structure of chitin can be classified as a: a. (1-->4)-beta-N-acetylglucosaminopyranan b. (1-->4)-alpha-glucosaminopyranan c. (1-->4)-beta-glucosaminofuranan d. (1-->4)-alpha-N-acetylglucosaminofuranan

(1-->4)-beta-N-acetylglucosaminopyranan

Which of the following structures is a zwitterion? a. H2N-CH2-COO- b. +H3N-CH2-COO- c. H2N-CH2-COOH d. All of these are zwitterions e. +H3N-CH2-COOH

+H3N-CH2-COO-

At neutral pH the net charge on a nucleotide diphosphate is: Select one: a. -2 b. depends on which nucleotide c. -3 d. 0 e. -1

-3

The hydrolysis of ATP to ADP + P yields approximately ____ kJ/mol, under standard state conditions. a. +21 b. -7.5 c. -21 d. -3.14 e. -30.5

-30.5

Hydrochloric acid is considered a strong acid. Thus, a 1M solution of HCl should have a pH of approximately: a. 0.1 b. 0 c. 1 d. 2 e. not enough information to determine the pH of this solution

0

List and briefly describe TWO of the three chemical/physical reasons that the hydrolysis of a phosphoanhydride bond in ATP is so energetically favorable.

1. The phosphate molecule released when ATP becomes ADP + P can be stabilized by several resonance structures. Because of this, the products are lower in energy than the reactant. 2. The entropy of ADP and P is higher than that of ATP. The reaction will spontaneously occur because of the system's desire to reach a higher state of disorder.

Assume that the pH of lemon juice is about 3.1and the pH of tangerine juice is about 4.06. You estimate that there are about ____ times as many hydronium ions in the lemon juice as the tangerine juice. a. Not enough information to determine. b. 0.1 c. 10 d. 0.9 e. 100

10

Which of the following nucleotides does not have a high energy bond? Select one: a. Uridine 5' diphosphate b. Adenosine 3' diphosphate c. All have a high energy bond(s) d. CTP e. 3'-5'-cyclic GMP

3'-5'-cyclic GMP

How many H-bonds can each water molecule in solution participate in?

4

In a classical alpha helix, carbonyl oxygens hydrogen bond with the backbone amide hydrogens belonging to the amino acid _____________ the chain. a. 3 residues toward the C terminus along b. 4 residues toward the N terminus along c. 4 residues toward the C terminus along d. 2 residues toward the C terminus along e. 3 residues toward the N terminus along

4 residues toward the C terminus along

You have used Sanger sequencing with fluorescent readout to determine the sequence of the following single stranded DNA, where "xxxxxxx" is the stretch of nucleotides to which the primer binds: 5'- ACATGCAGTTAxxxxxx-3'. In addition to the polymerase and dNTPs, you have added the following ddNTPs at low concentration, which are labeled with the following fluorescent dyes: red-ddATP; green-ddCTP; yellow-ddGTP; blue-ddTTP. What is the sequence of the first 'yellow' band to migrate down the capillary past the detector (not including the primer sequence)? Select one: a. 3'- TAACTG -5' b. 3'- ACATG -5' c. 5'- TG -3' d. 5'- ATTG -3' e. 5'- TAACTG -3'

5'-TAACTG-3'

You put a piece of single stranded DNA of sequence 5' GGCACTATCGGXXXXXXX-3' in a test tube in a suitable buffer for sequencing, and include the polymerase, a primer that anneals to the region indicated by XXXXXXX, and only the following nucleotide triphosphates: dATP, dCTP, dGTP, and ddTTP, where d stands for deoxy and dd stands for dideoxy). After you have let the reaction run to completion you find that the primer has been extended by how many nucleotides (i.e., how many nts have been added to the primer strand)? Select one: a. 4 and 6 nts b. 5 and 8 nts c. 5nts d. not enough information to tell e. 4nts

5nts. The chain would be terminated at the "A" in the original sequence, i.e., when the ddT was incorporated in the new strand. Since there is no dTTP present, the chain could not be extended beyond nt 5.

DNA pol III has all of the following roles in prokaryotic DNA replication EXCEPT: Select one: a. The pol III holoenzyme is made up of 10 different subunits b. It possesses 3' to 5' exonuclease activity for proofreading c. It is responsible for incorporating most of the nucleotides in the lagging strand d. A pol III holoenzyme synthesizes the entire leading strand prior to aiding in the synthesis of the lagging strand e. It is more processive and faster than Pol I

A pol III holoenzyme synthesizes the entire leading strand prior to aiding in the synthesis of the lagging strand

As Angstrom person, you are examining the structure of a piece of DNA. You note that the sugars along the backbone have their C3' carbons puckered up above the ring, toward the nucleobase. You deduce that this stretch of DNA is in its _______. Select one: a. B-form b. anti form c. syn form d. Z-form e. A-form

A-form

Which of the following sequences is least likely to form an alpha helix because of its amino acid composition? a. ANPRW b. not enough information to determine c. HKSFA d. EADAQ e. SFANR

ANPRW

If you wanted to buffer a solution at pH 5, which of the following acid/conjugate base pairs would be your best choice? a. Lactic acid/ Na lactate (pKa is 3.9) b. Succinic acid/ Na succinate (pKa is 4.2) c. Acetic Acid/ Na acetate (pKa is 4.8) d. H2CO3/ NaHCO3- (pKas are 3.8 and 10.4) e. NaH2PO4-/ Na2HPO4(2-) (pKas are 2.1, 7.2, 12.4)

Acetic Acid/ Na acetate (pKa is 4.8)

A common feature of all of the different head group components found attached to the phosphate on membrane phospholipids is: a. they are all hydrophobic to better interact with lipid bilayer b. they are all alcohols c. they are all charged d. they typically attach via an amide linkage

All of the groups attached to the phosphate are alcohols, forming an ester linkage. Some of the groups are charged, but not all. All of the groups are polar. They are all alcohols.

Important 'landmark' features of all tRNAs include all EXCEPT: Select one: a. Anticodon loop b. the T- ψ- C loop c. dihydrouridine, or D, loop d. the so-called variable loop e. All of these are important elements in the tRNA structure

All of these are important elements in the tRNA structure

Alpha keratin and collagen are both important structural proteins owing to their strong fibrous architecture. Briefly compare and contrast the secondary and quaternary structures of alpha keratin versus collagen.

Alpha keratin's core forms a classic right-handed alpha helical secondary structure. Alpha helices from two of these alpha keratin monomers then wrap around each other in a left-handed super helix. On the other hand, collagen's secondary structure is composed of the left handed collagen helix, and three strands of this protein wrap around each other in a right handed super helix.

You are trying to separate a mixture of lysine, valine, and aspartate using anion exchange chromatography at pH 7. List the order of elution and explain why they elute in this order.

Anion exchange chromatography binds to the negative portions of molecules. Thus lysine, having the highest positive charge, will have the lowest affinity and will pass through first. Valine is intermediate, and aspartate is the most negatively charged and will be retained the longest.

If you are Angstrom person and you're poking around a protein folding funnel, what do you find at the bottom of the funnel, and what would you find stuck in little crevices halfway up the side of the funnel wall?

At the bottom of the funnel you find the protein folded into its native, final, lowest energy structure. (Temporarily) stuck in the crevices along the wall are mis-folded or partially folded intermediates that are in a local energy minimum, but have not fully folded into their final lowest energy conformation.

"Optical tweezers" are extraordinarily useful tools for biochemists/biophysicists who are undertaking single molecule experiments. Optical tweezers enable the investigator to 'grab' both ends of a protein or peptide and pull with any given tension, and simultaneously visualize how far the peptide extends. Suppose you set up optical tweezers on a stretch of alpha helical peptide that was 50 amino acids long and applied increasing tension until there was a detectable and rather abrupt 'stretch' or lengthening of the peptide (without breaking the peptide chain). If you used a 50 amino acid long beta strand and did the same experiment, what do you expect the results to be, and why?

Because beta strands are already almost fully extended, very little stretch would be evident along a single strand.

"Optical tweezers" are extraordinarily useful tools for biochemists/biophysicists who are undertaking single molecule experiments. Optical tweezers enable the investigator to 'grab' both ends of a protein or peptide and pull with any given tension, and simultaneously visualize how far the peptide extends. Suppose you set up optical tweezers on a stretch of alpha helical peptide that was 50 amino acids long and applied increasing tension until there was a detectable and rather abrupt 'stretch' or lengthening of the peptide (without breaking the peptide chain). If you used a single strand of proline/lysine/glycine rich collagen helix in the same experiment, what would you expect the results to be, and compare the stretch to both the alpha helix and the beta strand experiment.

Because the collage helix is more extended than the alpha helix, you would see less stretch. Compared to a beta strand, however, you would see some lengthening of the collagen sequence.

The psi and phi bond angles exhibited in an amino acid within a peptide chain describe the path of the peptide backbone in three dimensional space. The phi angle describes the rotation about the ______ bond, while the psi angle describes the rotation about the _____ bond. a. N(amide)-C(carbonyl); C(carbonyl)- N(amide) b. C(alpha)-C(carbonyl); C(alpha)-N(amide) c. C(alpha)-C(carbonyl); C(alpha)-C(beta) d. C(alpha)-C(carbonyl); N(amide)-C(carbonyl) e. C(alpha)-N(amide); C(alpha)-C(carbonyl)

C(alpha)-N(amide); C(alpha)-C(carbonyl)

In what form will the carboxyl group and amino group of an amino acid predominately exist at pH = 13? a. COOH and NH2 b. not enough information to determine c. COO- and NH3+ d. COO- and NH2 e. COOH and NH3+

COO- and NH2

The van der Waals radius of a Na+ ion is about 0.95 angstroms, and the van der Waals radius of a K+ ion is about 1.33 angstroms. Briefly explain at the molecular level why a sodium ion doesn't pass easily through an open potassium channel pore.

Cations are hydrated in solution, with the water oxygens (partially negatively charged) interacting with the positively charged ion. But the ions are stripped of their waters as they enter an ion channel pore, and this is energetically unfavorable. To compensate, the potassium channel 'replaces' the lost water interactions with the ion with favorable contacts with protein chain oxygens, which are arranged in the correct geometry. While the geometry of these replaced contacts is perfect for potassium, they are wrong for sodium, so sodium cannot enter the potassium pore in an energetically favorable way.

In dilute solution, fructose mostly adopts a ________ configuration, made possible by formation of an intramolecular _____ linkage. a. D-fructofuranose; hemiketal b. L-fructopyranose; hemiacetal c. L-fructofuranose; hemiketal d. D-fructopyranose; hemiacetal

D-fructofuranose; hemiketal

You have been converted into Angstrom person, 0.1nm tall, and you are marveling at two short stretches of dsDNA in front of you. One is in A-form and one is in B-form. Describe one aspect of the sugars of the two forms that is different between the two, and one aspect about the positioning of the base pairs that is different between the two molecules. Make sure you indicate which characteristic belongs to which kind of DNA!

Difference in sugars: A-form: pucker is C3' endo B-form: pucker is C2' endo Difference in positioning of bps: A-form: base pairs are tilted with respect to the helix axis B-form: base pairs are perpendicular to the helix axis

Why is there limited rotation about the peptide bond between two amino acids?

Due to resonance structures, there is a partial double bond character which prevents free rotation as would be seen in a single bond.

You have a peptide of sequence EVLYRNQIMSKFAIT . Describe the product(s) you expect if you digest with trypsin.

EVLYR NQIMSK FAIT

(T/F) Although the nature of the lipid that tethers the protein to a membrane is different between farnesyl anchors and palmitoyl anchors, the chemical linkage to the cysteine side chain is the same.

False

T/F. The difference between the Ca2+ ATPase pump and bacteriorhodopsin is that the calcium pump requires the input of energy to pump Ca2+, while bacteriorhodopsin does not require input of energy to pump H+

False

T/F: The amino acids that have the highest side chain pKas (serine and threonine, side chain pKa =~13) should also have the highest pIs.

False

True or False. The entropy of pure water goes to zero when it freezes at 0 degrees C.

False

True or false. A simple electrospray ionization mass spectrometer analysis of an unknown protein gives molecular mass from which you can deduce directly the primary sequence of the protein.

False

T/F By definition, amino acids in the same protein sector would necessarily be located in the same domain.

False, amino acids in a protein sector are linked by a common function or evolutionary adaptation, but they do not have to belong to the same domain.

T/F Because there is a keto group on carbon 2 of the ketohexoses, they can only form furanose ring structures.

False. Aldoses can form pyranoses or furanoses and the ketoses (all the ones we talk about have keto at carbon 2) likewise can form either pyranoses or furanoses

True or False. The overall structures of human alpha-lactalbumin and actin are strikingly similar, as determined by x-ray crystallography. This similarity allows us to deduce that these two proteins carry out similar functions.

False. Although often proteins of similar structure possess similar function, many proteins in nature exhibit similarity of structure but disparity of function.

T/F. Domains in proteins are always composed of a stretch of contiguous amino acids in the peptide chain.

False. domains are often made up of a contiguous stretch of amino acids, but they can be made up of, e.g., a stretch of amino acids, the strand then exits the domain (perhaps to form another domain), and then the strand returns to complete the domain

Compared to A-DNA, the base pairs in B-DNA are positioned: Select one: a. farther toward the minor groove b. tilted up about 20 degrees on the long axis c. farther toward the major groove d. closer together to give a smaller pitch

Farther toward the major groove

From the list below, the most common amino acid one finds in a beta-turn is ______ because ______ . a. Y; it makes a hydrogen bond interaction with I on the other side b. V; it makes a hydrophobic interaction with the F on the other side c. G; its lack of a bulky side chain is amenable to the tight turn d. K; it makes a salt bridge with the D on the other side e. S; it forms a disulfide across the turn to stabilize it

G; its lack of a bulky side chain is amenable to the tight turn

Which of the following molecules contains an acid anhydride bond? Select one: a. RNA b. DNA c. cAMP d. GDP e. all of these have acid anhydride bonds

GDP

Which of the following peptides would be the most likely to acquire an N-terminal myristoyl lipid anchor? Select one: a. THISISIT b. VLIHGLEQN c. MEMEME d. GETREAL e. RIGHTHERE

GETREAL

RNA virus particles often have a rigid capsid enclosure just big enough to house the viral RNA genome coding for viral proteins necessary for the next round of infection. With this in mind, why do many viruses employ a strategy in which the active form of one or more of their proteins is a homodimer rather than a monomer?

Genomic economy. It requires less RNA genomic sequence to code for a smaller monomer that dimerizes into a larger functional unit than to code for the entire larger functional unit. Since the virus package has finite space, using less RNA to code for essential proteins is advantageous.

Which of the following statements is FALSE? a. Lys and Arg are positively charged at pH 7 b. Ile is more hydrophobic than Ala c. Y is more polar than F d. M and C contain sulfur e. Glu and Gln are acidic amino acids

Glu and Gln are acidic amino acids

Complete the comparison: Ribulose is to Ribose what Fructose is to ____________:

Glucose

Which of the weak forces is the most important in earliest structural organization as a protein is folding? a. hydrophobic interactions b. electrostatic interactions c. not enough information to tell d. van der Waals e. H-bonding

H-bonding

In the pyruvate kinase reaction, the high energy molecule phosphoenolpyruvate (PEP) donates its phosphate to ADP to make ATP. What event immediately following the transfer of the phosphate group makes this reaction energetically favorable?

Immediately following the phosphoryl transfer from PEP to ADP to make ATP, the enol-pyruvate tautomerizes spontaneously to keto-pyruvate, effectively pushing the reaction forward by removing the immediate product of the reaction.

Peptidoglycan can be thought of as an array of parallel strands of the repeating amino disaccharide (NAG-NAM) that are crosslinked via peptide cross-bridges. Using what you know about the structure of peptidoglycan, explain why the spacing between the poly(NAG-NAM) strands is greater or smaller in Gram positive versus Gram negative bacteria.

In Gram positive bacteria, the peptide linkage between adjacent carbohydrate strands includes an 'extra' pentaglycine peptide segment between the AEKA lysine on one strand with the AEKA D-alanine on the next strand. this would separate the strands by the equivalent length of 5 glycine residues.

Consider a micelle made up of amphiphilic (also called amphipathic) molecules that is floating in an aqueous solution. Describe the nature of the weak force(s) that contribute to the formation of the micelle itself and the weak force(s) that exist between the micelle and its aqueous environment. In each case, you should state which of the weak forces plays a role, and a brief definition/description of each of the kinds of weak forces you are talking about.

In a micelle, the hydrophobic tails aggregate via hydrophobic interactions, i.e., to avoid interactions with aqueous solution which would enhance ordering of water into clathrate structure surrounding the hydrophobic region. The polar/charged ends of the molecules interact with the aqueous solvent via hydrogen bonding and/or ionic interactions. Here, the polar portion of the molecule with an electronegative element bound to H will interact with with water O (or water H can interact with micelle electronegative element). A charged part of the amphiphilic molecule can also interact via charge-charge forces with ions in the solvent.

What makes carbon such an abundant element in biomolecules? a. It forms only single bonds. b. It can form up to five bonds by sharing its electrons. c. It forms stable covalent bonds by electron pair sharing. d. It provides low bond energy. e. It does not usually bond to other carbons, allowing a more diverse combination of elements.

It forms stable covalent bonds by electron pair sharing.

All of the statements about structural complementarity are true EXCEPT: a. It is the basis of many biological functions. b. It is the interaction of a biological macromolecule and its ligand. c. It produces strong irreversible interactions. d. It is the means of recognition in bimolecular interactions. e. Weak chemical forces mediate it.

It produces strong irreversible interactions.

You are Angstrom person, swimming around in a living cell with lots of different reactions going on. You keep noticing that there is a bossy little guy running around barking orders to enforce the rules of the equilibrium constants for all of the different reactions. You can't quite read the name on his cape, but you suspect his name might be: a. Fauntleroy b. Joe c. Donald d. LeChatlier e. Napoleon

LeChatlier

The isoelectric point of lysine is about pH 9.4. If the pKa's of lysine's three ionizable groups are about 2.0, 9.0, and 10.5, describe what each of lysine's ionizable groups would look like (in terms of charge/relative protonation) at the isoelectric point.

Lysine's alpha carboxy will be fully deprotonated to COO-. Both the alpha amino and the epsilon amino groups will be partially deprotonated, with the alpha amino group being more deprotonated than the side chain amino group, since the pKa of the alpha group is around 9, below the pI, while the epsilon group's pKa is 10.5, above the pI.

All of the statements below about metabolism are true EXCEPT: a. Metabolism is an ordered reaction pathway by which cellular chemistry proceeds. b. Metabolism is characterized by single reactions with large energy releases. c. Metabolism produces and/or utilizes ATP. d. Metabolism has two components: anabolism and catabolism. e. Metabolism is an organized transformation of energy.

Metabolism is characterized by single reactions with large energy releases

During normal "Watson-Crick" base pairing, the purine nucleobases form hydrogen bonds at which of their ring nitrogens? Select one: a. N7 b. Both N1 and N3 c. N1 d. N3 e. Both N3 and N7

N1

To determine the stereochemistry around the chiral carbon, which of the following represents the correct relative priorities of the groups attached to the alpha-carbon of cysteine? a. COO- > NH3+ > CH2SH > H b. COO- > H > CH2SH > NH3+ c. NH3+ > COO- > CH3 > H d. NH3+ > COO- > CH2SH > H e. NH3+ > CH2SH > COO- > H

NH3+ > CH2SH > COO- > H

You have fractionated a mixture of the amino acids phe, leu, lys, pro by cation exchange chromatography and separated the fractions coming off the column into 10 tubes. When you measure the absorbance of the tubes in a UV-vis spectrophotometer set at 280nm, you find that only one tube has significant absorbance. Assuming that nothing went technically wrong with the experiment, what is the reason that you only detect material in one tube?

Only the phe absorbs light at 280nm, so there's probably other amino acids in other fractions, you just haven't detected them by A280 measurements.

Explain the following observation based on what you know about the energetics of active and facilitated membrane transport: A proton pump, which uses energy from an external source, actively pumps protons from one side of a membrane to another. You simultaneously observe that Mg2+ ions, originally equal in concentration on both sides of the membrane, begin flowing through a Mg2+ ion channel (not an active transport pump) in the opposite direction as the protons. Why do the Mg2+ ions spontaneously flow in the opposite direction as the protons, forming a new Mg2+ gradient across the membrane?

Passive diffusion is driven by both charge and concentration gradients. As protons are pumped from one side to the other, the positive charge accumulates in the compartment in which the protons are being pumped. The Mg2+ ions that are in that compartment then flow to the other side to leave the excessive positive charge environment into a more negatively charged environment. Therefore, the active transport of the protons leads to passive transport of Mg2+ up a concentration gradient. In fact, this phenomenon happens in chloroplasts during the light reactions of photosynthesis!

When describing protein structure, we can talk about primary, secondary, tertiary, and quaternary structure. Briefly define each of these.

Primary-amino acid sequence Secondary-local interactions (e.g., forming alpha helices and beta sheets) Tertiary-overall 3D organization/shape Quaternary-multimeric subunit organization

Which enzyme at the prokaryotic DNA replication fork degrades the RNA primer from the Okazaki fragments and replaces it with DNA? Select one: a. Pol I b. beta sliding clamp c. DNA ligase d. gyrase e. helicase

Pol I

Which of the following peptides would be the most likely to acquire a prenyl (farnesyl or geranylgeranyl) anchor? Select one: a. AINTMEPICKA b. RIGHTCALL c. None of these would get a prenyl anchor d. ICANTICANT e. PICKME

RIGHTCALL

Which of the following is FALSE about the chemical synthesis of peptides? a. The incoming activated amino acid has a blocking agent on its amino group to limit the addition to one amino acid per cycle b. All of these are true about chemical synthesis of peptides c. Each successive amino acid in the sequence is when the activated amino acid reacts with the growing peptide bound to a solid support d. Similar to the biosynthesis of proteins within cells, chemical synthesis can easily produce peptides of thousands of amino acids long

Similar to the biosynthesis of proteins within cells, chemical synthesis can easily produce peptides of thousands of amino acids long

Phopsphoric acid (H3PO4) is a polyprotic acid whose protons have characteristic pKa's of 2.1, 7.2, and 12.4. Assume you are Angstrom person swimming and sightseeing in a solution of phosphoric acid whose pH is around 3.1. As you look around you in the solution, describe qualitatively how many H3PO4 and HPO4(2-) species you see.

Specifically at pH 3.1, the only ionization event that is predominant is H3PO4 --> H2PO4(-) . So, you would see a few H3PO4 molecules (most have been ionized to H2PO4(-) ), and since you're still several pH units away from the next ionization, you would see almost no HPO4(2-) ions.

An RNA-dependent DNA polymerase that carries the RNA template with it to synthesize repeats at the 3'-ends of chromosomes is called: Select one: a. telomerase b. DNA polymerase gamma c. DNA ligase d. DNA polymerase alpha e. topoisomerase

Telomerase

a) What are the respective roles of the 5′-exonuclease and 3′-exonuclease activities of DNA polymerase I? b) What might be a feature of an E. coli strain that lacked DNA polymerase I 3′-exonuclease activity?

The 5' nuclease activity is important for trimming off the primer sequence on the Okazaki fragments and also in some DNA repair mechanisms. The 3' nuclease activity is important for proofreading, where the enzyme can backtrack and remove an erroneously incorporated nucleotide. In a strain of E. coli that lacks the proofreading (3' exonuclease) activity, one could expect that the mutation rate in the bacterial genome would increase.

"Optical tweezers" are extraordinarily useful tools for biochemists/biophysicists who are undertaking single molecule experiments. Optical tweezers enable the investigator to 'grab' both ends of a protein or peptide and pull with any given tension, and simultaneously visualize how far the peptide extends. Suppose you set up optical tweezers on a stretch of alpha helical peptide that was 50 amino acids long and applied increasing tension until there was a detectable and rather abrupt 'stretch' or lengthening of the peptide (without breaking the peptide chain). At the molecular scale, what happened in the alpha helix when the peptide finally stretched out?

The Hydrogen bonds along the alpha helix gave way and the chain stretched because is was no longer coiled.

Why is glucose oxidizable under relatively mild conditions (to gluconic acid), but fructose is not?

The aldehyde present on glucose in its linear conformation is readily oxidized to a carboxylic acid, producing gluconic acid. Fructose, however, does not have an aldehyde, but instead a ketone. Ketones are not readily oxidizable, and if that happened, it would result in cleavage of the sugar. Individual hydroxyls on fructose (or any other sugar) can be oxidized, but this requires much stronger oxidizing conditions.

Hydrogen bonding and base stacking interactions are both important for double stranded DNA structure. Compare and contrast the relative contributions of these two weak forces toward overall stability of the dsDNA double helix and for the specificity of base pairing between the two antiparallel strands.

The base stacking interactions are the main energetic stabilizing force that holds the helix together. The pi-pi interactions between the bases exclude water and thus entropically favor the close interactions of each successive pair of bases in the helix. However, base stacking is not specific and does not dictate which bases interact with which other bases. On the other hand, the hydrogen bonding between each base pair does not contribute as much to the overall stability of the helix, but it is what determines that G's base pair with C's and A's base pair with T's, so they are responsible for the specificity of pairing of complementary bases across the two strands.

Consider the hypothetical protein procrastinase (some of us have a higher expression level than others!). You are studying the protein sequences of procrastinase from human, mouse, and frog, and these sequences from the same 12 amino acid segment of the protein are aligned and shown below: Human ...V-C-K-A-E-F-S-G-V-F-T-R... Mouse ....L-C-K-A-D-Y-S-W-I-L-P-Q... Frog ....L-C-R-A-E-F-T-N-H-T-I-H... In further experiments you learned that some part of this segment of the protein is important for binding to the metabolite citrate, which is a tricarboxylic acid and the carboxylates are completely deprotonated at neutral pH. In the Human sequence above, which residue(s) is/are the most likely to be part of this specific citrate binding pocket, and why?

The basic amino acids seen in all three sequences at position 3 would indicate that this residue could be involved in binding of the negatively charged citrate. The human sequence also has an arginine at the end, but since this is not conserved, it probably does not play a role in a specific binding pocket.

T/F. A residue with an overall positive average BLOSUM62 score is more likely to be highly conserved or invariant in a protein sequence than a residue with a negative score.

The best answer is "False", since a more positive score indicates the greater likelihood of each substitution. Amino acids that are rarely seen substituted give more strongly negative scores for most of the other amino acids. Therefore, an amino acid that can be interchanged with a bigger selection of alternate amino acids is less likely to be highly conserved or invariant.

Christian Anfinsen's famous experiments in which he denatured and then renatured purified ribonuclease protein provided evidence that all the information required for a protein to fold correctly was contained within the amino acid sequence. What alternative conclusion(s) would he have drawn if his experiments showed it was not possible to renature ribonuclease (or any other protein) after denaturation? i.e., If it were the case that it was impossible to renature a pure, isolated protein in vitro, then what conclusion would he have drawn about how proteins must get to their native conformation in vivo?

The big discovery by Anfinsen was that all of the information required to fold properly is contained within their amino acid sequence. If this were not the case, then simply trying to renature a protein by itself would not work, and alternatively, a protein must require external factors (like chaperones) to help it fold. Another possibility would have been that proteins can ONLY fold incrementally, i.e., that as the protein is "born", it folds into local structures that are not accessible by trying to renature a completely denatured protein.

An alpha helix establishes a dipole, with the positive side toward the N-terminus of the helix, and the negative side toward the C-terminus. This is because: a. There tend to be more lysines and arginines toward the C terminus b. The C-terminus is always oriented toward the negatively charged domain of the protein c. There tend to be more aspartates and glutamates toward the C-terminus d. The carbonyl O's are oriented toward the C-terminus of the helix, while the amide H's toward the N-terminus

The carbonyl O's are oriented toward the C-terminus of the helix, while the amide H's toward the N-terminus

Often biochemists seek to disrupt living cells gently to obtain intracellular complexes that have not been 'treated too roughly'. One way to do this is to abruptly change the medium in which the cells are growing to a medium that is hypotonic, i.e., very low in salt/ion content compared to the inside of cells. Why should this cause cells to lyse?

The concentration of salt/ions will be higher in the cell than outside the cell. Thus, water will rush into the cell to try and obtain equilibrium. The cell will swell and lyse.

Consider the hypothetical protein procrastinase (some of us have a higher expression level than others!). You are studying the protein sequences of procrastinase from human, mouse, and frog, and these sequences from the same 12 amino acid segment of the protein are aligned and shown below: Human ...V-C-K-A-E-F-S-G-V-F-T-R... Mouse ....L-C-K-A-D-Y-S-W-I-L-P-Q... Frog ....L-C-R-A-E-F-T-N-H-T-I-H... Even if you know nothing more about the protein than the sequences shown, if you had to predict which amino acid residue(s) in the human sequence is/are most likely to be critical for protein function, what would it/they be? Support your answer using the sequence data.

The cysteine and alanine at positions 2 and 4 are conserved between all species, suggesting a critical function. One could argue that the other N-terminal amino acids whose variation with 'similar' amino acids could also be essential for the function of procrastinase.

All of the statements about the nature of the hydrogen bond are true EXCEPT: a. The more linear the bond, the stronger the interaction. b. The donor is a hydrogen atom bonded to a carbon. c. The acceptor is an electronegative atom containing a nonbonding pair of electrons. d. It is a type of non-covalent bond. e. A hydrogen bond is stronger than van der Waals forces.

The donor is a hydrogen atom bonded to a carbon.

Explain briefly how the glycosaminoglycan moieties in cartilage contribute to cartilage's shock absorbing capacity.

The highly charged glycosaminoglycans decorating the lateral protein chains in cartilage readily coordinate water molecules when they are not under mechanical stress. Under stress, the bound water molecules are physically expelled from the arrays of glycosaminoglycans, damping the shock. Upon relaxation of the mechanical stresses, water is reabsorbed.

The methyl group on thymine in DNA plays an important role in preventing mutation, although the presence of the methyl group does not chemically stabilize the nucleobase in any way. Explain chemically how and why the methyl group is important to maintain the integrity of an organism's DNA genome.

The methyl group is important to distinguish a 'real' thymine from a uracil that is formed by deamination of a cytosine. Both the imposter uracil and the real thymine base pair the same, but the uracil would constitute a mutation (should be a C). The DNA repair machinery looks for uracils and removes them, replacing them with a cytosine.

Describe how the aggregation of non-polar molecules (or parts of molecules) in an aqueous solution decreases the disorder of the system?

The non polar molecules impart ordering on the water molecules surrounding them, decreasing the disorder/randomness of the system.

The HIV-1 protease is essential to the virus during its replication cycle since it processes viral polyproteins into their active, functional individual proteins. The HIV-1 protease is active as dimer of two differentially processed monomers of nearly the same size. What is the advantage to the virus of having the active form of the protease be a dimer?: a. all of these are advantages to the virus b. the individual monomers are small enough to evade immune detection c. the viral protease has increased substrate specificity as a dimer d. the subunits can bind very tightly together e. the amount of RNA required to code for the monomer is less than for a dimer-sized single protein

The only truly correct answer is that less genomic space is required to make the fully functional protease from two (small) identical monomers. The amount of RNA required to code for the monomer is less than for a dimer-sized single protein

Why is a triacylglycerol not as good a choice for a membrane component than, e.g., a glycerophospholipid?

The phospholipids that predominate in lipid bilayers are much more polar than triacylglycerols. This is because the phosphate group itself is highly charged, and the molecules that are esterified to the phosphate group are typically charged and/or polar.

Normally, a carbon-nitrogen single bond would display free rotation, but in a peptide bond, rotation is severely restricted between the carbonyl carbon and the amide nitrogen. Briefly explain why this is.

The resonance structure of the peptide bond imparts a partial double-bond character. Because of this, rotation is restricted.

Why are membranes with a higher proportion of unsaturated fatty acids more fluid and flexible than those with a higher proportion of saturated fatty acids?

The saturated fatty acids on phospholipids are capable of interacting in more stable and regular arrays than when unsaturated fatty acids, which are kinked at the site(s) of unsaturation, constitute some or all of the aliphatic tails in the lipid bilayer.

Consider the hypothetical protein procrastinase (some of us have a higher expression level than others!). You are studying the protein sequences of procrastinase from human, mouse, and frog, and these sequences from the same 12 amino acid segment of the protein are aligned and shown below: Human ...V-C-K-A-E-F-S-G-V-F-T-R... Mouse ....L-C-K-A-D-Y-S-W-I-L-P-Q... Frog ....L-C-R-A-E-F-T-N-H-T-I-H... Which part of the sequence appears to be more likely to have a critical role in procrastinase's structure and/or function, the N-terminal side or the C-terminal side? Explain how/why the sequence data support your answer.

The sequence is conserved and/or replaces amino acids with similar amino acids on the N-terminal side. The C-terminal side of the sequence contains very different amino acids in the different species, suggesting that these residues are not important for any conserved function.

An empirical survey of the amino acid sequences of homologous proteins from different organisms (BLOSUM62) shows that there are biases for which amino acids typically substitute for others. Explain in the context of overall protein structure and the weak forces that dictate structure why glutamate is very rarely substituted with a leucine in a homologous protein.

The side chains for glutamate and leucine are roughly the same size, so steric considerations do not play a large role. However glutamate, since it has an acidic side chain, is negatively charged at physiological pH. Therefore, it may be involved in an electrostatic interaction (e.g., with a K or R) that helps stabilize protein structure. Leucine, on the other hand, is hydrophobic and would not interact well with other charged residues. It would instead try to cluster with other hydrophobic residues and could thus disrupt the protein structure.

If you were asked to draw out a tetrapeptide of the sequence AEKA, you could do it unambiguously using some usual conventions of amino acid and peptide structural representation. However, the AEKA tetrapeptide that is critical for making the cross bridges in peptidoglycan of bacterial cell walls has two fundamental differences from the tetrapeptide you would have drawn. What are these differences?

The two striking differences between a 'normal' AEKA peptide and the one in peptidoglycan are 1) that the peptide bond between the glutamate and the lysine is via the glutamate's side chain carboxyl, not its alpha carboxyl; and 2) that the last alanine is the D-isomer instead of the otherwise nearly universal L-isomer configuration that is common to almost all amino acids in our biosphere.

Immunoglobulins are important components of the immune system. Schematically, the are made of two identical heavy chains, joined by several disulfides, and two identical light chains, each of which is joined to one heavy chain by several disulfides. If you divide a sample of immunoglobulin into two tubes, one is treated with the reducing agent beta mercaptoethanol, and one is not, then subject both of the samples to SDS-polyacrylamide gel electrophoresis (SDS-PAGE), what would you see when you visualize each lane?

The whole immunoglobulin held together by disulfides will migrate as a single large MW band. After reduction with BME, you get two bands on the gel, a larger MW band corresponding to the heavy chains, and a faster migrating smaller MW band corresponding to the light chains.

Old-time pirates who spent months at sea with little fresh fruit or vegetables often suffered from loose teeth, bleeding gums, and thin fragile skin because: a. Their India pale ales were not carbonated b. Their captains were too intoxicated c. Their prolines were not hydroxylated d. Their glucosamines were not acetylated e. Their glycines were not carboxylated

Their prolines were not hydroxylated Lack of fresh foods leads to vitamin C deficiency. Vitamin C is essential in the hydroxylation of prolines to construct the collagen helices that are important in connective tissue. The pirates had scurvy! Arrrrggghh, shiver me timbers!

Glycosaminoglycans' chemical characteristics are important for the shock absorbing characteristics of cartilage because: Select one: a. Their lipid content promotes association with protein cores b. Their hydrophobic nature makes them slippery c. Their uniform negative charge promotes full hydration and extension of the proteoglycan strands d. All of these are relevant characteristics of cartilage glycosaminoglycans

Their uniform negative charge promotes full hydration and extension of the proteoglycan strands

Which of the following does NOT help to explain the high energy of hydrolysis of a phosphoanhydride bond? a. The entropy is higher in ADP + P than in ATP b. There are more resonance structures available in ATP than in ADP + P c. The electrostatic repulsions are minimized upon hydrolysis d. All of these contribute to the high delta G of hydrolysis of ATP

There are more resonance structures available in ATP than in ADP + P

You are looking at two proteins from different microorganisms isolated from the shower floors of two rival rugby teams. You overexpress and purify both proteins and solve the crystal structure of each at high resolution. As you compare the structures, you see that they look quite different, but they both contain a nearly identical Adenine (ATP/ADP/AMP) nucleotide binding pocket. From this observation, you can deduce: a. Hydrolysis of a nucleotide suggests a similar biological function b. The proteins do not catalyze the same reaction in the different organisms c. There is not enough information to predict the two proteins' function d. The proteins catalyze the same reaction in the different organisms

There is not enough information to predict the two proteins' function. The take home message from the different protein structures we looked at was that sometimes similar looking proteins have different functions, and sometimes similar looking proteins have different functions. We also specifically looked at actin and hexokinase, two proteins that have completely different functions, but they both can bind ATP in similar binding pockets. Therefore the best answer is "we don't know". Just because they both have a nucleotide binding pocket does not necessarily imply they have a similar function.

What is the experimental strategy used to selectively isolate and purify eukaryotic mRNAs away from the rest of the RNAs that are normally present in a cell? Why does this same procedure not work for other types (non-mRNAs) of eukaryotic RNAs nor for prokaryotic mRNAs?

To isolate eukaryotic mRNAs, you run them across a solid support (chromatography column or beads) to which oligo dT has been attached. The (dT)n sequence hybridizes to the poly A tails of eukaryotic mRNAs and retains them on the column. After washing the rest of the cell debris away, the mRNAs can be eluted separately from the rest of the cellular material. This does not work for other types of RNA in a eukaryotic cell (besides mRNAs), or for prokaryotic mRNAs because they are not poly-adenylated, so there is nothing for the oligo dT sequence to hybridize to.

(T/F) A:T and G:C base pairs have nearly identical widths, making the dimensions of the outside of the dsDNA helix fairly homogeneous, regardless of the sequence of nucleotides inside.

True

(T/F) Hydrogen bonds and electrostatic bonds are both manifestations of a favorable charge-charge interaction, but electrostatic interactions are omnidirectional, whereas H-bonds are sensitive to orientation.

True

(T/F)During each cycle of a PCR protocol, the newly synthesized dsDNA must be thermally denatured.

True

T/F. If you had access to the measurements for the phi and psi angles for several successive amino acid residues in a peptide chain you could predict with some certainty whether the peptide adopts an alpha helix or a beta strand.

True

True or False. In liquid water, H-bonds last on the order of picoseconds, while in frozen water, the lifetime of an H-bond is much longer.

True

True or False. The mathematical reason, according to the Henderson-Hasselbalch equation, that the pKa is the pH at which half the weak acid is ionized to its conjugate base is because log([A-]/[HA]) = log(1) = 0.

True

At the interior of a globular protein you would be likely to find ______ , and you would be unlikely to find _______ residues. a. E; K b. A; L c. Q; F d. V; N

V;N

Which of the following amino acids is the most nonpolar? a. S b. Q c. A d. W e. K

W

The important characteristics of water that make it so well suited to living systems include all of the following EXCEPT: a. Water is a good solvent for salts because it increases ions' attraction for one another b. All of these are properties of water make it well suited for life systems. c. Ability to form networks of H-bonds d. Small but significant tendency to form hydrogen (hydronium) ions and hydroxide ions e. Ability to orient around hydrophobic/nonpolar molecules to promote hydrophobic interactions

Water is a good solvent for salts because it increases ions' attraction for one another

(2pts) Water is well suited to biological systems for a number of reasons, including its ability to interact with a variety of solutes. Considering ONLY entropic effects, compare and contrast what happens when an ionic substance (e.g., NaCl) and a hydrophobic compound (e.g., hexane) are dissolved/dispersed in water.

When water solvates crystalline ionic compounds, it increases entropy by dispersing the ions randomly in solution, far more entropic than when organized in a crystal lattice. When a hydrophobic substance is introduced, it causes formation of an organized clathrate cage of water around the molecule, thus decreasing entropy.

A single fragment of dsDNA was isolated from an EcoRI digest of eukaryotic genomic DNA for cloning. It was mixed with a plasmid vector which was linearized by digestion, also with EcoRI, so that the sticky ends could anneal. DNA ligase was then added to the mixture. List all possible (desired and undesired) products of the ligation reaction.

You could get the new DNA fragment inserted in the plasmid as desired, but in both orientations/directions. You could also get multiple copies of the new DNA inserted in tandem. You could also get a re-closed plasmid without an insert, and finally, you could get two or more plasmids ligated together via their sticky ends.

Consider a reaction S --> P, for which the standard state delta G is +15kJ/mol. This means that if you put some S into a test tube and wait long enough for the reaction to go to equilibrium, you will find: a. all of the S has been converted to P b. can't determine because don't know the Keq c. none of the S has been converted to P d. most of the S has been converted to P e. a small amount of S has been converted to P

a small amount of S has been converted to P

You have at your disposal two beakers of solutions of Na lactate and lactic acid, each at 50mM concentration. If you wanted to buffer a solution at pH 3.6, about how much lactic acid solution would you add compared to the sodium lactate? (The pKa of lactic acid is 3.9.) a. about twice as much as sodium lactate b. less than half as much as sodium lactate c. about the same amount d. more than half as much as sodium lactate e. about ten times as much as sodium lactate

about twice as much as sodium lactate

Many reactions in biochemistry are coupled to the hydrolysis of an ATP to ADP + P. To estimate the delta G of such a coupled pair of reactions, you should: a. subtract the smaller delta G from the larger delta G b. sum the delta G's and subtract the delta S's c. add the delta G's for both reactions together d. consider only the delta G of the more exergonic reaction

add the delta G's for both reactions together

Which of the following molecules is capable of adopting the syn conformation (be careful of the nomenclature)? Select one: a. guanine b. uridylic acid c. cytosine d. thymine e. adenosine

adenosine

Which of the following amino acids does not contain an alpha amino group as well as an alpha carboxyl group? a. lysine b. all of these has an alpha amino group and an alpha carboxyl group c. arginine d. proline e. histidine

all of these has an alpha amino group and an alpha carboxyl group

Individual amino acids all have _____ and ______ functional groups which can react in a head-to-tail fashion with another amino acid to form a/an _____ bond. a. carboxyl; amide; anhydride b. amide; carboxyl; peptide c. ester; amino; amide d. amino; anhydride; ester e. amine; carboxyl; peptide

amine; carboxyl; peptide

Sphingomyelins are all of the following EXCEPT: a. made up of sphingosine with an amide-linked fatty acid and esterified phosphorylcholine/ethanolamine b. all of these are true of sphingolipids c. important components of membranes d. are a subset of the ether glycerophosphlipids e. members of the phospholipids

are a subset of the eth glycerophospholipids

Phosphoric acid has three dissociable protons whose pKas are 2.1, 7.2, and 12.4. Where would you estimate phosphoric acid's isoelectric point to be? a. below pH 1 b. around pH 9.8 c. around pH 7.2 d. around pH 4.1 e. above pH 13

below pH 1

In our biosphere, most amino acids are stereochemically "L", or more precisely, in the "S" configuration, except for cysteine, which is naturally in the R configuration. If you were able to precisely swap out the sulfur in a molecule of R-cysteine and replace it in the same position with an oxygen, it would: a. convert it to D-threonine b. convert it to L-cysteine c. convert it to R-serine d. convert it to S-serine

convert it to S-serine

Which of the choices below is NOT a usual lipid anchor for a protein? a. geranylgeranylation at the N terminus b. farnesylation at a cys residue c. palmitoylation on a cys residue d. GPI anchor at the C-terminus

geranylgeranylation at the N terminus

Which equation defines a system at equilibrium? a. delta G°' = delta G b. deltaG > 0 c. delta G°' = 0 d. delta G = RT ln([products]/[reactants]) e. delta G = 0

delta G = 0

All are true about deltaG EXCEPT: a. delta G is negative for endergonic reactions. b. delta G is affected by pH. c. delta G depends on the concentrations of products and reactants. d. delta G is affected by temperature. e. A positive or negative deltaG indicates which direction a reaction will go.

delta G is negative for endergonic reactions

A molecule with a high phosphoryl transfer potential, like PEP, would be expected to be able to: a. catalyze an unfavorable reaction to go forward b. donate a phosphate to 1,3BPG c. donate a phosphate to ADP d. make an engine run more efficiently if added to the gasoline e. accept a phosphate from ATP

donate a phosphate to ADP

Experimentally, one can use calorimetry to directly measure: a. change in pressure, delta P b. total free energy change, delta G c. expected number of days you need to stay on a diet to lose x kilograms d. enthalpy change, delta H e. change in volume, delta V

enthalpy change, delta H

Enthalpy change, delta H, is: a. not a usual thermodynamic state function. b. the sum of heat absorbed and work. c. equal to the heat transferred at constant pressure and volume. d. determined by pressure change at a constant temperature. e. a measure of the disorder of a system.

equal to the heat transferred at constant pressure and volume

Which of the following processes has the highest positive change in entropy? a. changing conformation of a protein b. evaporation/sublimation of CO2 from dry ice c. melting of ice d. freezing of water

evaporation/sublimation of CO2 from dry ice

If you want to overproduce a eukaryotic protein in E. coli, the eukaryotic cDNA must be cloned in a(n) ________________ that contains__________ and __________. Select one: a. none of the above b. hybridization complex; promoter; transition start site c. mRNA; introns; exons d. mRNA; ribosomal-binding site; promoter e. expression vector; promoter; ribosomal-binding site

expression vector; promoter; ribosomal-binding site

Which amino acid contains an imidazole ring? a. proline b. histidine c. phenylalanine d. tyrosine e. tryptophan

histidine

The basic structure of the alpha helix is stabilized primarily by: a. ionic interactions b. randomizing the solvent water molecules c. hydrogen bonds d. hydrophobic interactions

hydrogen bonds

Which of the following would best help you determine whether the sequence of amino acids in a protein would encode transmembrane segments? Select one: a. a Rorschach plot b. a hydropathy plot c. an energy plot d. a Lineweaver-Burk plot e. a Ramachandran plot

hydropathy plot

Originating ultimately from basic biochemical precursors like carbon dioxide, water and ammonia, the complex biomolecules are made in which sequence? macromolecules, building blocks, metabolites, supramolecular complexes

metabolites, building blocks, macromolecules, supramolecular complexes

Z-DNA was first discovered unexpectedly in early crystallographic structure determinations of short DNA oligomers, but evidence suggests it exists in living cells, too. We would most expect to find Z-DNA in any of the following sequences/situations, EXCEPT: Select one: a. repeating purine-pyrimidine sequences b. near promoters of transcriptionally active DNA c. in relaxed plasmid DNA isolated from a bacterium d. in regions of DNA where there is high negative torsion/ underwinding of the helix

in relaxed plasmid DNA isolated from a bacterium

The entirety of information required for a protein to fold into its native conformation is contained in: a. its amino acid sequence b. the charges on specific amino acid side chains c. its amino acid composition d. its ability to form intermediate molten globules during translation e. the location of strategically placed disulfide bonds

its amino acid sequence

Even though the building blocks have fairly simple structures, macromolecules are exquisitely organized in their intricate three-dimensional architecture known as: a. Lewis structure b. primary sequence c. native conformation d. natural configuration e. structural maturation

native conformation

Considering the thermodynamics of living systems, we can assume that living systems are: a. closed systems exchanging only energy with surroundings b. open systems exchanging only matter from surroundings c. open systems exchanging matter and energy with surroundings d. isolated systems that are completely insulated from surroundings

open systems exchanging matter and energy with surroundings

Consider histidine, whose side chain's pKa is ~6.0. With this knowledge, we can expect what about this amino acid's isoelectric point? a. not enough information to determine relationship of pI and pKa b. pI > side chain pKa c. pI < side chain pKa d. pI = side chain pKa

pI > side chain pKa

The genome of which of the following organisms might NOT follow Chargaff's rules? Select one: a. Thermus aquaticus, a bacterium that lives in Yellowstone hot springs b. Dire wolf, and extinct canine species c. human cytomegalovirus, a double stranded DNA virus that latently infects most humans d. parvovirus, a single stranded DNA virus that infects mammalian hosts e. ALL genomes obey Chargaff's rules that [A] + [G] = [C] + [T]

parvovirus, a single stranded DNA virus that infects mammalian hosts

All of the following exhibit high energy of hydrolysis EXCEPT: a. phosphoanhydrides. b. acyl phosphates (mixed anhydrides). c. acid anhydrides. d. phosphate esters. e. enol phosphates.

phosphate esters

A common characteristic of intercalating agents is: Select one: a. ability to H-bond with individual bases b. specific high affinity binding to the sugar part of the backbone c. planar aromatic rings conducive to pi-pi interactions with bases d. ability to decrease the pitch of a DNA helix

planar aromatic rings conducive to pi-pi interactions with bases

Autonomously-replicating non-chromosomal DNA molecules found in bacteria that harbor genes that are advantageous for the fitness of the bacterium are called: Select one: a. Hoogsteen pairs b. ncDNAs c. plasmids d. stress response granules

plasmids

Which of the following amino acids does not contain a primary amino group? a. histidine b. arginine c. proline d. all of these has a primary amino group e. lysine

proline

In a typical eukaryotic plasma membrane a. all of the above are true. b. oligosaccharides generally face inward, away from the extracellular environment. c. lipids can freely flip from the cytosolic side to the external side within the bilayer. d. proteins and lipids can move laterally along the bilayer.

proteins and lipids can move laterally along the bilayer

Thermodynamics does NOT: a. allow the determination of whether a reaction is energetically favorable. b. describe the flow and interchange of heat, energy, and matter. c. provide information on the rate of a reaction. d. consider energy flow and entropy production. e. consider the effect of concentration on net energy change of a reaction.

provide information on the rate of a reaction

The following components are required to clone a library of eukaryotic genomic DNA fragments EXCEPT: Select one: a. a plasmid b. one or more restriction endonucleases c. purified mRNA d. all of the above would be required e. DNA ligase

purified mRNA

Viruses are not living, but they act as cellular parasites in order to: a. reproduce. b. grow in size. c. gain genetic information. d. protect themselves. e. all are true

reproduce

Translation takes place on/in the: a. nucleus b. DNA parent strand c. DNA polymerases d. smooth endoplasmic reticulum e. ribosomes

ribosomes

Useful when cloning blunt ended DNA, linkers are: Select one: a. short synthetic dsDNA oligonucleotides containing a restriction site that can be ligated onto DNA b. affinity tags incorporated into the synthetic DNA c. enzymes that integrate foreign DNA into plasmids by recombination d. name of spacer DNA located between the promoter and the actual gene e. proteins that attach cloning sites to a sequence of DNA

short synthetic dsDNA oligonucleotides containing a restriction site that can be ligated onto DNA

DNA ____________ is analogous to overtwisting or undertwisting a coiled phone cord so that it is torsionally stressed. Select one: a. hairpin turn b. supercoiling c. buoyant density d. secondary structure

supercoiling

In bacteria, DNA replication on the lagging strand is: Select one: a. synthesized in a 3' to 5' direction b. synthesized first as Okazaki fragments c. synthesized continuously d. accomplished primarily by DNA Pol I. e. carried out primarily by Pol delta then Pol alpha

synthesized first as Okazaki fragments

Explain why we see more varieties of base-pairing and unusual hydrogen bonding in tRNA than we see in 'regular' dsDNA. Then give plausible reasons why the anticodon loop and the acceptor stem -CCA sequence are not base paired to any other nucleotides in the tRNA sequence.

tRNAs are single stranded and the RNA strand can thus fold upon itself in a greater variety of conformations than are available in simple dsRNA or dsDNA structures. The bases in the anticodon will need to base pair with the codons on the mRNA, so it is appropriate for this region not to be stably sequestered in an intramolecular structure that would prevent it from base pairing with the mRNA. The anticodon stem is where the amino acid is attached for use in protein synthesis. This region also needs to be free and available for charging with an amino acid, and during translation, this amino acid will react with the growing peptide chain to extend the chain by one amino acid.

The steric/energetic barrier to pyrimidine nucleosides assuming the syn conformation is: Select one: a. the C2 oxo group clashing with ribose b. the C4 oxo group clashing with ribose c. the C5 methyl group clashing with ribose d. the C4 amino group clashing with ribose e. the C2 amino group clashing with ribose

the C2 oxo group clashing with ribose

You have a peptide of sequence EVLYNQIMSKFAIT . Describe the product(s) you expect if you treat this peptide with Edman's reagent, phenyl isothiocyanate. a. the PTH derivative of M plus a 6 and a 7 residue peptide b. the PTH derivatives of T and E plus a 12 residue peptide c. the PTH derivative of E plus a 13 residue peptide d. the PTH derivative of T plus a 13 residue peptide

the PTH derivative of E plus a 13 residue peptide

Gangliosides and cerebrosides can be differentiated chemically by: a. the degree of glycosylation b. the presence of a cis vs. trans double bond in the sphingosine backbone c. the type of linkage with their associated fatty acids d. the phosphorous content

the degree of glycosylation

Consider the (L)-enantiomer of D-glucose (in standard Haworth structure). Which of the following is NOT true: a. none of these are true statements b. the hydroxyl on C4 is up c. the hydroxyl on C5 is up d. the hydroxyl on C2 is up e. the hydroxyl on C3 is down

the hydroxyl on C5 is up

All the common sugars are referenced by D- or L- to the chirality of glyceraldehyde. With that in mind, what does L-glucose look like compared to D-glucose? a. the D- or L- designation only refers to the stereochemistry of C-5 b. the position 2 hydroxyl is on the left in L-glucose, right in D-glucose c. the position 1 hydroxyl is on the left in L-glucose, right in D-glucose d. the position 6 hydroxyl is on the left in L-glucose, right in D-glucose e. the position 3 hydroxyl is on the left in L-glucose, right in D-glucose

the position 2 hydroxyl is on the left in L-glucose, right in D-glucose

What gives proteins such a dominant role in biochemistry? a. their ability to self-replicate b. All of the these are reasons that proteins have a dominant role c. their ability to spontaneously fold into complex three-dimensional structures d. the ability to act as a genetic blueprint e. the variation in protein sizes

their ability to spontaneously fold into complex three-dimensional structures

Common reasons that producing a recombinant fusion (chimeric) protein may be useful include all EXCEPT: Select one: a. to increase solubility of a protein b. to attach a fluorescent domain to facilitate tracking of the protein c. to attach an affinity tag to facilitate purification of the protein d. to facilitate unfolding and denaturation of the protein

to facilitate unfolding and denaturation of the protein

According to the fluid mosaic model of membranes, phospholipids can readily and spontaneously move in all directions in the membrane EXCEPT: Select one: a. laterally b. rotationally c. transversely to the opposite leaflet d. molecules can spontaneously move in all these directions because the membrane is fluid

transversely to the opposite leaflet

A sea creature whose plasma membranes are richer in ________ can more likely live in or migrate to an area of low temperature. a. All of the above b. arachidonic acid c. unsaturated fatty acids d. saturated fatty acids

unsaturated fatty acids

Which of the following is NOT a characteristic of prokaryotic replication of a circular chromosome? Select one: a. torsional stress and supercoiling ahead of the replication fork is relieved by DNA gyrase b. after initiation, replication proceeds in both directions c. replication originates at oriC d. primase lays down a single primer on the leading strand to initiate the leading strand synthesis e. unwinding of the duplex DNA is caused by Pol III plowing through the dsDNA ahead of it like a wedge

unwinding of the duplex DNA is caused by Pol III plowing through the dsDNA ahead of it like a wedge

Rank the following bonds in order of increasing bond strength: van der Waals, ionic, hydrogen bond, covalent single bond

van der Waals, hydrogen bond, ionic, covalent single bond

Mobile genetic elements that are supramolecular complexes of nucleic acid encapsulated in a protein coat, and in some instances, surrounded by a membrane envelope are called: a. viruses b. nucleosomes c. plasmids d. ribosomes e. all are true

viruses

Because the intra- and intermolecular interactions of non-ionic polar solutes like sugar are _____ than the ______ bonding interactions with H2O molecules, sugar is readily dissolved in water. a. stronger; hydrophobic b. weaker; ionic c. stronger; electrostatic d. weaker; hydrogen e. stronger; hydrogen

weaker; hydrogen