Biochem 2101 Clicker Questions

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At 20 torr O2, myoglobin will have __% of its O2 binding sites full

25%

What is the pH of a solution of the weak acid HA (pKa 5) when the ratio of conjugate acid to base is 100:1?

Van der Waals interactions are... always attractive always repulsive can be either attractive or repulsive

Rank the following proteins on the basis of their resistance to unfolding upon heating: Protein A (structure rich in covalent disulfide bonds) Protein B (stabilized by hydrogen bonds) Protein C (stabilized by van der waals interactions) Protein A > Protein B > Protein C Protein C > Protein B > Protein A Protein B > Protein C > Protein A Protein A > Protein C > Protein B

A - covalent bonds are much stronger than non-covalent and will there fore require more energy to break

Which two non-covalent (weak) interactions occur between non-polar groups? Hydrophobic interaction Van der Waals Electrostatic Hydrogen Bonds

A and B - Electrostatic is between charged particles and H-bonds occur in polar molecules

IgG (a protein) has a permanently attached carbohydrate - that means IgG is a (choose as many as apply)... A) glycoprotein B) hemoprotein C) conjugated protein D) allosteric protein E) kinase F) zymogen

A and C

An α-helix would be destabilized most by: A) an electric dipole spanning several peptide bonds throughout the alpha- helix. B) interactions between neighboring Asp and Arg residues. C) interactions between two adjacent hydrophobic Val residues. D) the presence of an Arg residue near the carboxyl terminus of the alpha helix. E) the presence of two Lys residues near the amino terminus of the alpha helix.

As CO binds to one or two subunits of a hemoglobin tetrameter, the affinity for O2 is __________ substantially in the remaining subunits. I.e. CO is an __________ of hemoglobin A) increased, allosteric activator B) increased, allosteric inhibitor C) decreased, allosteric activator D) decreased, allosteric inhibitor

How can my new knowledge of biochemistry help me get hair this nice? A) Break the strong disulfide bonds with a reducing agent, put my hair in the shape I want, then oxidize to re-form the disulfides. B) Break the strong disulfide bonds with an oxidizing agent, put my hair in the shape I want, then reduce to re-form the disulfides. C) Break the strong hydrogen bonds with an oxidizing agent, put my hair in the shape I want, then reduce to re-form the hydrogen bonds.

IDPs are _________ in bulky hydrophobic (Ile, Leu, Val) and aromatic (Trp, Tyr, and Phe) amino acids, which form and stabilize the hydrophobic cores of folded globular proteins A) depleted B) enriched

The melting point of fatty acids... A) Increases with chain length, increases with saturation B) Increases with chain length, decreases with saturation C) Increases with chain length, unaffected by saturation D) Decreases with chain length, increases with saturation E) Decreases with chain length, decreases with saturation

The pKa for COOH ⇌ COO- + H+ is ~2, so at pH 1 A) it will be mostly in the COOH form B) it will be mostly in the COO- form C) there will be approximately equal amounts of COOH and COO-

The pKa for NH3+ ⇌ NH2 + H+ is ~9.5, so at pH 1 A) it will be mostly in the NH3+ form B) it will be mostly in the NH2 form C) there will be approximately equal amounts of NH3+ and NH2

Which is true? A) chemical group will be in its more protonated form at a pH below its pKa B) chemical group will be in its less protonated form at a pH below its pKa C) chemical group will be more negatively charged at a pH below its pKa (compared to at higher pHs) D) chemical group will be fully protonated only at its pKa

Which mutation in myosin underlies FHC (Familial Hypertrophic Cardiomyopathy) : A) R403Q B) R403K

Which non-covalent force is entropic in nature? A) Hydrophobic interaction B) Van der Waals C) Electrostatic D) Hydrogen Bonds

because of an alpha helices dipole moment, As an example, this means that negatively charged ligands (ligand = another molecule that binds to a specific site on the protein) (e.g. phosphates) usually bind proteins near the _ -terminus of a helix. A) "N" B) "C"

At low pH, things (e.g. water, proteins, etc.) will tend to be... A) MORE protonated than at high pH B) LESS protonated than at high pH C) the SAME protonation compare to high pH

A) more protonated means more positively charged

Which has more favourable entropy? A) water molecule in "bulk" water? B) water molecule in a clathrate structure surrounding a hydrophobic molecule?

A) - water molecules are free to form transient H-bonds with other molecules. This allows many different forms of spatial orientation (more entropy, more random) - a clathrate structure is more limited in the spatial orientations it can take on because it cannot form H-bonds with surrounding non-polar molecules

In active tissues, there are more protons around, the pH is ________ and hemoglobin has ________ affinity for O2 compared to in the lungs. A) lower, lower B) lower, greater C) greater, lower D)greater, greater

A) - Things are more protonated at a lower pH - the H+ produced tends to decrease the pH of the blood plasma • hemoglobin can bind H+ (at a different site from the oxygen binding site) and transport it away

Which of these point mutants (all non-polar) is LEAST likely to wreck a protein ? A)Leucine —> Isoleucine B) Leucine —> Alanine C) Leucine —> Glycine D) Leucine —> Phenylalanine

A) Leucine and Isoleucine are very similar in size and will therefore be the least likely to wreck the protein

Which statement best describes the function of wool and silk? A) Wool is strong, but stretchy. Silk is strong, but not stretchy. B) Wool is strong, but stretchy. Silk is weak and stretchy. C) Wool is weak and stretchy. Silk is strong, but not stretchy. D) Wool is weak and stretchy. Silk is strong, but stretchy.

A) Silk is strong, but not stretchy becuase its secondary structure contains tightly packed beta sheats which are more rigid

Which has the stronger hydrogen bonds? A) antiparallel beta-sheet B) parallel beta-sheet

A) antiparallel because they form linear H-bonds which are stronger than bent ones

The amino acid composition of spider silk and silk from cocoons is quite different. Which do you think belongs to spider silk? A) ~37% glycine ~21% alanine ~4.5% serine no cysteine ~37.5% remaining AA B) ~45% glycine ~30% alanine ~12% serine no cysteine ~13% remaining AA

A) less glycine means less tight packing which allows the silk to be more flexible

What is special about water (pick as many as apply) ? It has an anomalously high melting temperature It has especially strong inter-molecular interactions The solid form is less dense than the liquid form It has an unusually high viscosity

All of the above

Compared to one grown at 37C, a bacterial colony grown at 25C could be expected to have... A) More stearic acid B) More linoleic acid C) Less linoleic acid D) More cholesterol E) Less cholesterol

What's easier to break? covalent bond non-covalent bond

Will changing the height of the cliff affect how often buffalo fall over it? Yes No

A GTPase activator protein (GAP) will... A) Prolong signal transduction B) Shorten signal transduction C) Enhance G-protein activation D) Prevent G-protein association with receptors E) Inhibit protein kinases

A hydropathy plot can be used to predict... A) Membrane spanning β-sheets B) Membrane spanning α-helices C) Any membrane associated protein D) Any membrane associated α-helix E) Membrane fluidity

A lyase enzyme catalyzes... A) Hydrolysis reactions B) Either cleavage of bonds resulting in creation of a double bond or addition of groups to double bonds C) Transfer of groups within a molecule D) Formation of new bonds by condensation reactions using ATP as an energy source E) Oxidation-reduction reactions (transfer of electrons)

At high O2 levels both Hemoglobin and Myoglobin have ~%100 full binding sites In the tissues (~30 torr), myoglobin will release ~___% of its O2 and ~___% A) 5% (Mb), 5% (Hb) B) 5% (Mb), 40% (Hb) C) 40% (Mb), 5% (Hb) D) 40% (Mb), 40% (Hb)

At neutral pH, do the charges on the C- and N-terminal groups of hemoglobin matter? A)No, they cancel. B) Yes, they do matter - they help to form ionic interactions that stabilize deoxyhemoglobin

Catalytic efficiency... A) = Vmax/[E] B) An indication of the number of reactions catalyzed at low [S] C) An indication of the number of reactions catalyzed at full saturation D) = slope of a Lineweaver-Burk plot E) Requires plotting an Eadie-Hofstee plot

Covalent catalysis involves A) Permanent attachment of a prosthetic group to an enzyme B) The formation of a modified enzyme intermediate C) Joining of two or more substrate molecules together to form a single product D) Nothing. Covalent bonds are permanent and therefore cannot be involved in enzymes reactions

How do Proteins "Know" What Tertiary Structure to Fold Into? A) There's special machinery in the cell that folds each protein chain into the right shape. B) The correct tertiary structure is somehow encoded into the amino acid sequence of the protein. C) None of the above.

How strong are disulfide bonds? A) disulfide bonds are about the same strength as hydrogen bonds B) disulfide bonds are about 100 times stronger than hydrogen bonds C) disulfide bonds are about 10 times as strong as an ionic bond D) disulfide bonds are about 10 times as strong as a van der waals bond

IDPs are ___________ in polar (Arg, Gly, Gln, Ser, Pro, Glu and Lys) and structure-breaking (Gly and Pro), disorder promoting amino acids A)depleted B)enriched

In the tissues (~30 torr), myoglobin will release ~___% of its O2 and hemoblogin will release ~___% A) 5% (Mb), 5% (Hb) B) 5% (Mb), 40% (Hb) C) 40% (Mb), 5% (Hb) D) 40% (Mb), 40% (Hb)

Sickle-cell anemia can be caused by mutation in hemoglobin: glu6->val6 , i.e A) from a hydrophobic residue to another hydrophobic residue B) from a charged residue to a hydrophobic residue C) from a negatively charged residue to a positively charged residue D) from a hydrophobic residue to a polar residue

Sphingolipids ALWAYS... A) Have a phosphate containing head-group B) Contain unsaturation C) Contain a carbohydrate head-group D) Contain either choline or ethanolamine E) Use ester linkages to connect groups to sphingosine

The amino acids glutamate and aspartate have a sidechain carboxyl group with a pKa of ~4. What is the predominant charge of the side chains at pH 2 ? A) -1 B) 0 C) +1

The pKa for NH3+ ⇌ NH2 + H+ is ~9.5 So, at pH 13 A) it will be mostly in the NH3+ form B) it will be mostly in the NH2 form C) there will be approximately equal amounts of NH3+ and NH2

The pKa for NH3+ ⇌ NH2 + H+ is ~9.5, so at pH 13 A) it will be mostly in the NH3+ form B) it will be mostly in the NH2 form C) there will be approximately equal amounts of NH3+ and NH2

What happens if you add mercaptoethanol and urea to IgG? A) The protein will break into 12 separate polypeptide chains. B) The protein will break into 4 separate polypeptide chains. C) The protein will break into 3 separate polypeptide chains. D) The protein will break into 2 separate polypeptide chains.

What is different about immunoglobulins compared to other proteins? A) they are composed of several structure domains B) they can have many different primary structures C) they can bind specifically to other proteins D) they are composed of beta-sandwich type domain folds

The equilibrium constant for the reversible ionization of water is.... A) Keq = [H2O] / [H+][OH-] B) Keq = [H+][OH-] / [H2O] C)Keq = [H2O]2 / [H+][OH-] D) Keq = [H+]/[OH-]

B) - products over reactants

Let's say you can make a protein that is totally unnatural in that it is made up of D-amino acids instead of L-amino acids. What do you think will happen if you treat it with a protease (e.g. a protease you purify from an animal source)? A) It will get chopped up into pieces B) Nothing

B) D-amino acids are stable for longer

At pH: 2, what is the predominant form: A- or HA? (i.e. same as the last question, but now we're just looking for an approximation) A) Mostly A- B) Mostly HA C) Bit of both

B) more protonated

Which of the following types of inhibitor can be identified kinetically A) Mechanism-based inhibitor B) Non-competitive inhibitor C) Transition state analogue D) Substrate analoge E) Suicide inhibitor F) All of the above

B) only reversible inhibitors can be identified kinetically

How would you expect glycine to look when it's in solution at pH 7? A) nonionic form B) zwitterionic form

B) zwitterionic form has a neutral charge. an amino acid in solution at neutral pH will be in zwitterionic form

There are a practically infinite number of possible primary structures. So, if two proteins found in nature have similar amino acid sequences, what is more likely: A) That probably happened by random chance. B) The proteins are probably related and had a common ancestor.

Both

A G-protein is activated when... A) An agonist binds to the G-protein B) GDP replaces GTP in the alpha-sub-unit C) GTP replaces GDP in the alpha-sub-unit D)An antagonist binds to the receptor E) The G-protein binds to a receptor

Immunoglobulin G's quaternary structure... A) ....is different for every antibody B) ...is a beta-sandwich domain fold C) ....is heterotetrameric D) ...contains only an antigen recognition region and no other functional domains

Last class you learned that each turn of an α-helix is comprised of 3.6 residues. Based on this, which two residues in the following helical sequence would wind up on the same face of the helix? MEQALKRN. A) M and E B) M and Q C) M and A D) M and K

Which statement is incorrect A) The Na and K voltage gated channels contain two gates B) Na voltage gated channels open quicker than K voltage gated channels C) The nicotinic acetylcholine receptor has a sodium selectivity filter D) Ion channels spontaneously inactivate E) There are ion selective binding sites in voltage gated channels

Which pair(s) are just different terms for the same thing? A) Hydrophobic interaction/van der Waals B) Hydrogen bond/Hydrophobic interaction C) Electrostatic interaction/ionic interaction D) Hydrogen Bonds/H-bond E) Hydrophobic interaction/H-bond F) van der waals interaction/London dispersion force

C , D and F

Enzymes enhance reaction rates by... A) Providing a different reaction pathway that has a more negative ΔG B) Selectively enhancing the forward reaction over the reverse reaction C) Providing a different reaction pathway that has a lower activation energy D) Binding to the substrate to make the ΔGo' more favourable

Many people with mild egg allergies are OK eating egg as along as it's well cooked. Can you think of why this might be? A) Cooking gets rid of the protein (lysozyme) that many people are allergic to. B) Cooking disrupts the primary structure of the lysozyme so it can no longer bind the antibody. C) Cooking disrupts the tertiary structure of the lysozyme, preventing the antibody from recognizing it.

The pKa for NH3+ ⇌ NH2 + H+ is ~9.5, so at pH 9.5 A) it will be mostly in the NH3+ form B) it will be mostly in the NH2 form C) there will be approximately equal amounts of NH3+ and NH2

Which is most true? A) All the residues in the N-terminal domain are conserved. B) All the residues in the N-terminal domain vary a lot. C) All regions of the N-terminal domain vary, but some regions vary a LOT more than others.

Which of the following is true about protein domains? A) Protein domains lose their three-dimensional structure when separated from the remainder of the polypeptide chain. B) Protein domains lose their function when separated from the remainder of the polypeptide chain. C) Protein domains often fold into stable globular units. D) protein must have more than one domain to be functional.

Which of the following sets of amino acids have ionizable sidechains? A) A,L,G,D B) R,K,E,D C) R,K,E,D,H D) G,P E) A,L,E,D,H

We are researching an enzyme found in small intestine (pH ~ 8). Which of the following buffers should we use? (on an exam we'd be likely to also ask you why) A) pKa 3.5 B) pKa 6.7 C) pKa 7.4 D) pKa 9.2

C) - a good buffer will be with in +/- 1 of the pH

At neutral pH... A) [H+]=[OH-] = 1.0 x 10-28 B) [H+]=[OH-] = 1.0 x 10-14 C) [H+]=[OH-] = 1.0 x 10-7 D) [H+]=[OH-] = 1.0 x 10-3.7

C) (-)log (1.0x10^-7)=7 pH of 7 is neutral

G (Gibb's free energy) of a protein when it's folded is about 1,000,000 kcal/mole (take it account all those weak interactions). A) G of an unfolded protein is about ________ B) 10,000 kcal/mol C) 100,000 kcal/mol D) 1,000,000 kcal/mol E) 10,000,000 kcal/mol

C) Free energy is about the same. despite all the interactions holding folded proteins together, there are an almost equal amount of interactions in unfolded proteins

Which point mutation listed below is LEAST likely to wreck protein function ? A) Leucine —> Tyrosine B) Leucine —> Serine C) Leucine —> Phenylalanine D) Leucine —> Tryptophan

C) Leucine and Phenylalanine are both non-polar. Point mutation between amino acids with similar polarity is the least likely to disrupt the protein function

Proteolytic cleavage of chymotrypsinogen to chymotrypsin A) Assembles the active site B) Stabilizes the R-state C) Assembles the substrate binding pocket D) Inactivates the enzyme E) Alters the pH optimum of the enzyme

C) forms the catalytic triad

What would happen if there were only 3.5 residues per turn in an alpha helix instead of 3.6? A) nothing - 3.6 to 3.5 is not a big change at all B) the coiled-coil would have more of a twist and be even stronger C) the coiled-coil would have less of a twist and would not be very strong at all

C) if there were only 3.5, the hydrophobic faces wouldnt line up so it would be weaker

Delta G is: The name of Dr. Berry's dog Positive for a spontaneous process ∆H - ∆S ∆H - T∆S Completely useless for Biochemistry

Which is true? A) Myoglobin is a monomer well suited for oxygen transport, while hemoglobin is a tetramer best suited for oxygen storage B) Myoglobin is a heterotetramer well suited for oxygen storage, while hemoglobin is a heteromonomer best suited for oxygen transport C) Myoglobin is a monomer well suited for oxygen storage, while hemoglobin is a homotetramer best suited for oxygen transport D) Myoglobin is a polypeptide well suited for oxygen storage, while hemoglobin is an oligomer best suited for oxygen transport

Which of the following is represents a spontaneous reaction? ΔH = -5, TΔS = -5 ΔH = +5, TΔS = -5 ΔH = +5, TΔS = +5 ΔH = -5, TΔS = +5

A helix has 3 residues per turn and is stabilized by inter-chain hydrogen bonds. What kind of a helix is it? A) 3-10 helix B) alpha helix C) pi helix D) polyproline helix

A protein in solution is more likely to maintain its native conformation when A) the number of hydrogen bonds within a protein is minimized. B) the shell of water becomes more ordered. C) the protein is least stable. D) its hydrophobic residues are largely buried in the protein interior.

Fibrous proteins all possess structural features that give them _______ A) frailty B) delicacy C) flimsiness D) strength

KM is... A) Representative of substrate affinity B) Obtained from the x-intercept of a Michaelis-Menten plot C) Obtained from the y-intercept of a Lineweaver-Burk plot D) A value determined from the ratio of the rate constants of each step of a reation E) An indication of the speed of a reaction

Myosin causes this process ATP + H2O —> ADP + Pi to happen much faster than it would otherwise, so myosin is an... A) epitope B) electrophile C) endergonic reaction D) enzyme

People with "pollen-food allergy" start out with hay fever, but then develop oral allergies to a defined group of foods (e.g. apple, pear, peach, nectarine, kiwi, cherry, hazel nuts). This tells us that these foods and pollen all share a common... A) immunoglobulin B) lymphocyte C) antigen D) epitope E) antibody

Sucrose consists of... A) 2 x Glucose B) 2 x Fructose C) 2 x Galactose D) Fructose and Glucose E) Galactose and Fructose F) Galactose and Glucose

The binding of a tiny (relative to myosin) molecule like ATP can cause such a large change in myosin protein structure/actin-binding because.... A) proteins are marginally stable B) proteins just barely fold C) the interactions that stabilize proteins are weak and non-covalent D) all of the above

The following characteristics are TRUE of polyclonal antibodies. Which of the characteristics is actually an ADVANTAGE of polyclonal over monoclonal antibodies? A) they have different amino acid sequences B) they recognize different regions of the target protein C) they bind the target protein with different affinities D) they're relatively easy to make

What is the strongest non-covalent interaction? A)Hydrophobic interaction B)Van der Waals C)Electrostatic D)Hydrogen Bonds

Which of the following are NOT found in thin filaments? A) troponin B) actin C) tropomyosin D) myosin

Which part of the myosin-actin /muscle contraction cycle does a corpse's proteins get stuck in during rigor mortis? A)ATP binds myosin, myosin releases actin B)ATP hydrolyses, myosin head goes into high energy conformation C)Myosin binds a different position on the actin filament, Pi is released D)Myosin undergoes a conformational change, releases ADP

Which statement about biological membranes is FALSE. A) All are self-sealing B) They are held together by weak non-covalent interactions C) Their lipids are asymmetrically distributed D) They consist entirely of lipids E) Different membranes contain different lipids

Which statement about domain folds is true? A) there are almost as many domain folds as their are proteins B) "domain fold" refers to the individual polypeptide chain in an oligomeric protein C) protein needs more than one domain to be functional D) domain folds represent a stable way to put together secondary structure elements into a stable 3D structure E) the domain fold will maximize the entropy of the protein chain

cis-Δ9,12 octadecadienoic acid is more commonly called... A) Palmitic acid B) Stearic acid C) Oleic Acid D) Linoleic acid E) α-linolenic acid F) Arachidonic acid

Even if a protein is able to sample a million different conformations per second, it would still take ________ to sample all the potential conformations and find the native conformation (the lowest energy conformation). A) a couple of hours B) many days C) about a year D) ~1036 years

D) Levinthals Paradox

Which amino acids are prevalent in the regions of proteins that contact DNA? (hint: DNA is negatively charged) A) K, D B) E, R C) E, H D) K, R E) E, D The truth is a lemon meringue!

D) Lysine and Argenine are positivley charged residues

At low pH (e.g. pH 1), the carboxyl will... A) ...be deprotonated and have a charge of -1. B) ...be deprotonated and have a charge of 0. C) ...be deprotonated and have a charge of +1. D) ...be protonated and have a charge of -1. E) ...be protonated and have a charge of 0. F) ...be protonated and have a charge of +1.

E - low pH is more protonated - carboxyl can either have a charge of -1 or 0 so 0 will be the more protonated (positive) option

If feed-forward stimulation occurs in an amplification cascade, the affected enzyme... A) Has its R-state stabilized B) Has its T-state stabilized C) Shows a leftward shift in its kinetic plot D) Shows a rightward shift in its kinetic plot E) A and C F) A and D G) B and C H) B and D

The concensus binding sequence (selectivity) for protein kinase A is Arg-Arg-X-Ser/Thr-Z where X is any small non-polar residue, Z is a large hydrophobic reside, and Ser/Thr is the phosphate acceptor. Which statement about the likely binding pocket(s) is correct? A) There is a single binding pocket that can accomodate all 5 residues B) There is a single binding pocket that is complementary to the Ser/Thr residue C) There are three binding pockets 2 identical ones for each Arg residue and one for the Ser/Thr D) There are 5 binding pockets, one for each residue E) There are 3 bindings pockets on the N-terminal side of the Ser/Thr, and 1 binding pocket on the C-terminal side of the Ser/Thr F) There are 3 binding pockets on the C-terminal side of the Sert/Thr and 1 binding pocket on the N-terminal side

Which statement is correct? A) GLUT1 allows active transport of glucose B) The Na-K ATPase is an example of a symporter C) GLUT1 is a uniporter and therefore does not show Michaelis-Menten kinetics D) The Na-K ATPase is electrogenic moving 3 Na into cells and 2K out of cells E) Both GLUT 1 and Na-K ATPase will give linear Lineweaver-Burk plots

Which of the following will have the fastest rate? A) A → B ∆G = -5 KJ/mol B) B → C ∆G = +5 KJ/mol C) C → D ∆G = -10 KJ/mol D) D → E ∆G = +10 KJ/mol E) Impossible to tell from provided information

E) delta G has nothing to do with rate! Rate is determined by the activation energy

All of the following forces are responsible for helping stabilize the tertiary structure of globular proteins, EXCEPT for... A) hydrogen bonds B) hydrophobic interactions C) van der waals interactions D) ionic interactions E) peptide bonds

E) peptide bonds are involved in the primary sequence of a protein.

At low pH (e.g. pH 1), the amino group will... A) ...be deprotonated and have a charge of -1. B) ...be deprotonated and have a charge of 0. C) ...be deprotonated and have a charge of +1. D) ...be protonated and have a charge of -1. E) ...be protonated and have a charge of 0. F)...be protonated and have a charge of +1.

F) - charge options for amino groups are +1 or 0 so +1 is the more protonated (positive) option

At pH 2, what is the ratio of base to acid? (for a carboxyl group with pKa =4) A) 100:1 B) 10:1 C) 2:1 D) 1:2 E) 1:10 F) 1:100 G) 1:1000

F: (1/100=0.01)

True (A) or False (B): There is a specific 3-base genetic code for the amino acid hydroxyproline so that it is incorporated into the protein during translation of the mRNA. True False

False: only the 20 standard amino acids can be translated genetically. The rest must undergo post-translational modification

Here's the sequence of part of a protein. Given what you know about amino acids and the 4 weak interactions, which amino acids do you think will be positioned in the interior of the protein (away from water)? A) ....TSNQQLIVQNIMFTN...

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