CHEM 3375 Learning Curves Chapters: 1,2,3,4,5,6,7,10

In an acetic acid solution with a pH of 5.00, what is the ratio of acetate ion to acetic acid (not ionized)? The pKa of acetic acid is 4.76.

1.7

Cell fractionation separates particles based on _____.

size

Which of the following best defines the term bioinformatics?

an area of research focusing on the computerized analysis of biological data

What will the initial reaction velocity of an enzymatic reaction be when the substrate concentration is equal to 0.5 Km?

0.33 Vmax

IgG can bind to viruses that invade an organism. What happens next?

The Fc region of IgG binds to a macrophage, which destroys the virus.

Which of the following statements is false regarding water? a. The H-O-H bond angle is 109.5°, the angle of a perfect tetrahedron. b. The hydrogen atoms of a water molecule each share a pair of electrons with the central oxygen. c. The oxygen atom of one water molecule is attracted to the hydrogen of another water molecule. d. Each hydrogen atom in water has a partial positive charge.

The H-O-H bond angle is 109.5°, the angle of a perfect tetrahedron.

Which amino acid has the greatest tendency to form an α helix?

alanine

During muscle contraction _____. sarcomeres become progressively shorter thick and thin filaments slide past each other Z disks in neighboring I bands draw closer together all of the above

all of the above

Which two organic functional groups do all linear carbohydrates contain?

carbonyl and hydroxyl

Hsp70 is an example of a/an ________.

chaperone that binds hydrophobic regions of unfolded proteins

The reaction shown is a single-step reaction. What happens to the rate if the concentrations of both A and B are doubled? A + B → C

rate quadruples

Derivation of the Michaelis-Menten equation requires an assumption of a "steady state". Put simply, this means _____.

the ES complex formation is very rapid relative to product formation

N-linked oligosaccharides have an N-glycosyl bond to ___.

the amide nitrogen of Asn

The carbonyl of the first (#1) amino acid (amino end) of an α helix will hydrogen bond to the amine group of which amino acid?

#5

Assuming that the pKa values are not affected by peptide bond formation, calculate the net charge on Arg-Asp at pH 3.65.

+0.5

What is the net charge of histidine at pH = 1?

+2

What is the net charge of this oligopeptide at pH = 1?

+2

For the reaction in the previous question, calculate ΔG if [S] = 1 mM and [P] = 100 mM.

+5.9 kJ/mol

Which of the following is an example of an essential fatty acid, one that needs to be obtained from the diet because humans cannot synthesize it?

α-Linolenic acid

Which is an essential fatty acid? An essential fatty acid is necessary in the diet because humans cannot synthesize it.

α-linolenic acid

Most cells are microscopic, ranging from about 5-100 ____ in diameter, which can also be expressed as 0.005-0.1___.

μm; mm

Glycine has two ionizable groups with pKa values of 2.34 and 9.60. What is the average net charge of glycine at pH 9.60?

-0.5

Which of the following combinations of φ and ψ dihedral angles would be allowed in a poly-Alanine polymer?

-120°, + 120°

For the acid AH, if [A-]/[AH] is 4500 when pH is three times the pKa, what is the pKa for this acid?

1.8

Theoretically, if all of the antigen-binding sites on an IgM pentamer are occupied, how many antigens would be bound to the structure?

10

How many more hydrogen ions does a 1 L solution at pH = 3 have than a 1 L solution at pH = 5?

100x

Which fatty acid is expected to have the lowest melting point?

10:2(Δ3,6)

If a protein is composed of 100 amino acids, what would its approximate molecular weight be?

11 (kilodaltons)

What is the total number of possible peptide pentamers that could be formed from five different amino acids? (Assume that each amino acid is present only once per peptide.)

120

Given that an α helix has 3.6 residues per turn and the rise along the α helix axis is 5.4 Å, approximately how many amino acids would you find in a single contiguous α helix that is 210 Å long?

140

Which of the following correctly identifies the order of events that describe the mechanism of action of HIV protease?1. Formation of a tetrahedral intermediate.2. Attack of the carbonyl carbon by water.3. Protonation of the amino acid leaving group.

2,1,3

What is the pH of a 0.150 M solution of acetic acid at 25 °C? (pKa = 4.75)

2.8

Estimate the number of of amino acids in a typical α helix that is 30 Å long.

20

Which of the following structures is not an omega-3 (ω-3) polyunsaturated fatty acid (PUFA)?

20:4 (Δ5,8,11,13)

How many hydrogen bonds can form between guanine and cytosine?

3

The complementarity between the two strands is useful for determining base composition. If guanine makes up 14% of the nucleotides in a DNA sample, what percentage of nucleotides in this sample will be adenine?

36

Calculate the osmotic pressure of a solution at 300 K that is 0.500 M in sucrose and 0.500 M in KCl. (Note: 1 J/L = 1000 Pa = 1 kPa).

3750 kPa

What is the approximate ratio of product to substrate at pH 7.0 if ΔG'° at 298 K equals -1 kJ/mol?

3:2

Compare the linear structures of D-glucose and L-glucose. These two molecules have different configurations about ___ carbon atom(s).

4

Imagine a reaction mixture favors only the formation of dipeptides. If the mixture contains ample amounts of glycine and alanine, how many different dipeptides can possibly be formed?

4

Using the Henderson-Hasselbalch equation, calculate the percentage of an ammonia solution that would be in the ionic form at pH 9.40, assuming a pKa for the ammonium ion of 9.25.

41.5%

Glycine and alanine can form two possible dipeptides: gly-ala and ala-gly. How many possible disaccharides can be formed from two molecules of α-D-glucopyranose, using O-glycosidic bonds?

5

How many stereoisomers does D-ribose, an aldopentose, have?

8

What is the [OH-] in a 0.010 M sulfuric acid (H2SO4) aqueous solution at 25 °C?

5.0 x 10-13 M

At which pH would the net electric charge of tyrosine be zero, given that its -COOH group has a pKa of 2.20, its -NH3+ group has a pKa of 9.11, and its R group has a pKa of 10.07?

5.66

Lysine has three pKas of 2.18, 8.95 and 10.53. Calculate the pI of lysine.

9.74

Which statement describes the relationship between absorbance (A) and solute concentration (c) that follows the Lambert-Beer Law for an absorbing layer of fixed path length?

A is directly proportional to c.

Which of the following statements about the degradation of phospholipids and sphingolipids is incorrect?

A lysophospholipid is produced when a phospholipase removes both fatty acids.

A biochemist has some E. coli cells to suspend in a buffer. The biochemist has some buffer in the refrigerator, but decides it is hypotonic. What should the biochemist do?

Add some sucrose to the buffer.

Which type of chromatography has the potential to save many steps in a purification protocol?

Affinity chromatography because of its specificity for a protein.

Which of the following peptides would have a +1 charge at pH = 7?

Ala-Gly-Asn-Leu-Lys

Which is true about the melting temperature, Tm, for ribonuclease?

At Tm ribonuclease exhibits half the activity of a sample in its native conformation.

Consider the equation H2O → H+ + OH-. Which of the following statements is false? a. The H+ shown in this equation will immediately bind to a water molecule, forming a hydronium ion, H3O+. b. At equilibrium, the concentration of water molecules equals the concentration of H+ and OH-. c. This is a reversible reaction. d. The H+ and OH- molecules that form from the dissociation of water are very reactive.

At equilibrium, the concentration of water molecules equals the concentration of H+ and OH-.

What must occur for a polysaccharide to be branched?

At least one monosaccharide unit must be simultaneously bonded to three other monosaccharide units by glycosidic bonds.

Which of the following statements is false regarding the binding of 2,3-BPG to hemoglobin?

BPG blood levels decrease in individuals shortly after they move from sea level to high altitudes.

Which of the following statements is false regarding bacterial and animal cells?

Bacterial cells do not have a plasma membrane and have a cell wall instead.

Olive oil, beef fat, and butter are natural fats that differ in their fatty acid composition. Based on the properties of these fats, rank them on their C16 and C18 saturated fatty acid levels.

Beef fat > Butter > Olive oil

Describe what is occurring in the following reaction: C6H12O6 + 6O2 → 6CO2 + 6H2O + energy.

C6H12O6 is oxidized and O2 is reduced.

Which of the following is an advantage of using polysaccharides over lipids as a source of energy?

Carbohydrates are a quick source of energy compared to lipids because they are water soluble.

Why can the pKa value for an ionizable R group change when an amino acid becomes incorporated into a peptide?

Environmental factors can influence pKa. Ionizable R groups can interact with other peptide R groups. There can be a loss of charge to alpha-carboxyl and alpha-amino groups. all of the above

Which enzyme has the highest catalytic efficiency?

Enzyme A: Km = 2.5 µM; Vmax = 100 mM/min

Hydrolytic enzymes often have low activity at high pH and low pH, with their greatest activity at a neutral pH. Without a catalyst present, hydrolysis is more rapid at high and low pH values and very slow at neutral pH. How would you explain this apparent contradiction?

Enzymes employ both general acid and general base groups that are in their optimal protonation state at neutral pH.

In the IgG structure, the constant domains are found in the _________ portion(s) and the variable domains are found in the __________ portion(s).

Fab and Fc; Fab only

A nonapeptide was determined to have the following amino acid composition: two Lys, two Gly, two Phe, one each of His, Leu, and Met. When the native peptide was exposed to cyanogen bromide, a heptapeptide and a dipeptide were recovered. Incubation of the native peptide with trypsin gave a pentapeptide and a tetrapeptide. Cyanogen bromide cleaves at Met (C); whereas trypsin cleaves at Lys and Arg (C). Which sequence is compatible with this data?

Gly-Met-Leu-Lys-His-Phe-Gly-Phe-Lys

Why is it not a good idea to eat cotton?

Humans lack the enzyme that degrades (β1→ 4) linkages.

Which of the following statements regarding β conformation is false?

Interstrand H bonds are in-line for the parallel β sheet and not in-line for the antiparallel variant.

Which of the following statements is true with regard to the effect of solutes on osmolarity?

It depends on the number of solute particles.

Which of the following is true regarding troponin C?

It has 2 calcium-binding domains.

Which statement is true about insulin?

It has two chains joined by covalent bonds.

What is the purpose of dicyclohexylcarbodiimide (DCC) in peptide synthesis?

It is a coupling agent used to activate the carboxylic acid for reaction with amines

Which of the following statements is false regarding the antiviral drug oseltamivir? It prevents the release of viruses from the infected cell. It is a sugar analog. It inhibits viral sialidase by competing with the host cell's oligosaccharides for binding. It is a noncompetitive inhibitor of neuraminidase.

It is a noncompetitive inhibitor of neuraminidase.

Which of the following statements about platelet-activating factor is incorrect?

It is less water soluble than most glycerophospholipids.

What is the activity of a lysophospholipase?

It removes the second fatty acid from a glycerophospholipid after phospholipase A has removed the first one.

All of the following amino acids except _________ are classified as nonpolar aliphatic.

Lys

Rotation about which bond changes the dihedral angle designated φ?

N-Cα

Which of the following correctly matches the enzyme class with the type of reaction it catalyzes? ligase: cleavage of C—C, C—O, C—N, or other bonds by elimination, leaving double bonds Hydrolase: group transfer reaction Oxidoreductase: transfer of electrons Lyase: formation of C—C, C—S, C—O, and C—N bonds by condensation reactions

Oxidoreductase: transfer of electrons

Which active lipid is mismatched with its role?

PIP2; inactivates the hormone vasopressin

Which of the following properties of RNA suggest it or its related precursors may have been the first genes and catalysts?

RNA-like molecules can form abiotically. RNA molecules can catalyze their own formation. The process of RNA self-replication is not perfect, enabling the formation of RNA variants. all of the above

A scientist working with human cells accidentally incubated the cells in water instead of the phosphate-buffered saline solution she should have used. What effect, if any, will this have on the cells?

Since water is hypotonic compared to the cells, water will move into the cells and the cells will swell.

Carbonic acid, H2CO3, is an important buffering component in blood that helps stabilize pH. Given the following equation, H2CO3 → HCO3- + H+, what would you expect to happen if the pH of the blood decreases?

The H2CO3 concentration would increase and the HCO3- concentration would decrease.

Affinity chromatography can be used to purify proteins such as growth factor receptors. The ligand of the growth factor receptor can be linked to resin, and then an extract containing membrane proteins can be poured over the resin. If a high concentration of free ligand were poured over the resin next, what would you expect to happen?

The excess ligand will compete with the ligand attached to the resin, releasing the growth-factor receptor from the resin.

What defines an omega-3 fatty acid?

The fatty acid has a double bond between the third and fourth carbons from the methyl end of the molecule.

Which of the following statements is incorrect regarding a Lineweaver-Burk plot? It is a plot of 1/V0 versus 1/[S]. The line has an intercept of 1/Vmax on the 1/V0 axis. The line has an intercept of -1/Km on the 1/[S] axis. The line has a slope of Vmax / Km.

The line has a slope of Vmax / Km.

How are the melting points and water solubility of fatty acids affected by the length of the hydrocarbon chain?

The longer the fatty acid chain, the higher the melting point and the lower the solubility in water.

Which statement is true about the backbone bonds in a protein?

The peptide bond has restricted rotation, the N-Cα bond is restricted for proline, otherwise free rotation is only limited by steric constraints.

A solution is made by mixing 0.82 grams of sodium acetate, 1 mL of 12 M acetic acid (pKa=4.76) and water to give a final volume of 1 L. Select the answer that best evaluates the usefulness of this solution as a buffer.

The ratio of acid to conjugate base is close enough for this to be a good buffer.

In aqueous solution proteins will tend to fold and bury the hydrophobic amino acids toward the protein's interior. In the process, a great deal of conformational entropy is lost by the protein as it adopts a more ordered shape. If so much entropy is lost by the protein, why does it fold?

There is a larger entropic gain for the surrounding water molecules. (hydrophobic effect)

Which of the following statements is false regarding the Hsp70 family of proteins?

They actively promote the folding of the substrate protein.

Which of the following generalizations about globular proteins is incorrect? They tend to have a dense hydrophobic core. They generally have quaternary structure. The globular structure derives stability from hydrophobic interactions. Globular proteins have a more compact shape than fibrous proteins.

They generally have quaternary structure.

Which of the following statements is incorrect about mass spectrometry of lipid samples? It can be used to accurately determine the length of a hydrocarbon chain. To be analyzed, individual lipids must be fractioned out from complex lipid mixtures. It can be used to accurately determine the position of double bonds in a hydrocarbon chain. It can be used to create catalogs of all the lipids present in a specific cell type under particular conditions.

To be analyzed, individual lipids must be fractioned out from complex lipid mixtures.

The protein keratin is composed of two helical strands that wrap around each other in what is called a coiled coil. The two strands remain in contact with each other over the entire length of the protein via hydrophobic interactions. What amino acid might you predict occupies multiple sites along the entire length of the keratin sequence?

Val

Circular dichroism measures the difference between _____.

absorption of right circular polarized light vs. left circular polarized light

In the cation exchange chromatography of amino acids where the elution buffer is applied as a gradient from low pH to high pH, what is the order of elution (first to last) of a mixture of glycine, aspartate and arginine?

aspartate; glycine; arginine

Which of the following is not water soluble? ethanol butane glucose glyceraldehyde

butane

Which of the following refers to the aqueous solution inside of the cell, excluding organelles?

cytosol

Myosin can best be described as _____. a. a contractile protein of the muscle b. an actin-binding protein c. an ATPase d. all of the above e. both a contractile protein of the muscle and an actin-binding protein

d. all of the above

What effect would decreasing the column length have in column chromatography?

decreased resolution and separation of proteins

________ reactions require an input of energy and their ΔG values are ________.

endergonic ; positive

β turns are generally found on the ____ of a protein and often consist of ____ residues.

exterior; pro and gly

For which lipids are phosphoethanolamine or phosphocholine not common components?

gangliosides

A protein that binds to glutathione can be purified using an affinity column where the solid phase is a cellulose matrix covalently attached to the molecule glutathione. What should be included in the elution buffer for this experiment to remove the protein from the column?

glutathione

There is a ____ propensity for gastric ulcers in people in the type __ blood group because an H. pylori lectin binds an oligosaccharide in the glycoproteins and glycolipids of that blood group.

higher; O

Strong acids have ___ Ka values and ___ pKa values than weaker acids.

higher; lower

Consider the following atoms commonly found in chemical reaction mechanisms. Rank them from least to most electronegative.

hydrogen, carbon, nitrogen, oxygen

Which is not a constraint that affects the stability of the α-helix? interactions between side chains at the end of the helix and the helix dipole hydrophobic interactions between adjacent amide groups the intrinsic propensity of the R groups to form an α-helix the bulkiness of adjacent R groups the occurrence of Pro and Gly residues

hydrophobic interactions between adjacent amide groups

Which shape applies to a plot of the fraction of binding sites occupied with a ligand (Y) versus the concentration of ligand (L)?

hyperbolic

In eukaryotes, cardiolipin is found almost exclusively in the ___________, and it is synthesized in the _____________.

inner mitochondrial membrane; mitochondria

You have isolated a crude sample of two related peptides (Peptide A and Peptide B). To separate the two, what protein purification method would be most effective? Peptide A: Ala-Ala-Gly-Glu-Asp-Ser-Glu-Ala Peptide B: Ala-Ala-Gly-Lys-Arg-Ser-His-Ala

ion exchange chromatography

Each water molecule in liquid form at room temperature and atmospheric pressure forms ___ hydrogen bonds than water molecules in ice.

less

All the lipids present in a particular cell type under particular conditions is called the ________.

lipidome

Which of the following structures is specific to animal cells?

lysosome

What is the cellular site of glycerophospholipid degradation by phospholipases?

lysosomes

Which is not made of fibrous protein?

myoglobin

Thin filaments in muscle cells contain all of the following except _____. actin troponin myosin tropomyosin

myosin

The resin used for cation exchange is _______ charged. If a solution of Val, Lys, and Glu at pH = 7 are loaded onto a column with cation exchange resin, what order would the amino acids elute from the column if eluted with salt?

negatively; Glu, Val, Lys

Coenzyme Q (also called CoQ10 or ubiquinone) is a popular dietary supplement. In what type of reactions does coenzyme Q participate within a cell?

oxidation-reduction

Which element(s) is(are) reduced in the following reaction? C6H12O6 + 6O2 → 6CO2 +6H2O

oxygen

The oligopeptide below can best be classified as a _____.

pentapeptide

Which is not a common coenzyme?

peptidoglycan

If a scientist were interested in cleaving the phosphodiester bonds in the head group of a glycerophospholipid like phosphatidylinositol 4,5−bisphosphate, which phospholipase would be a good choice?

phospholipase D phospholipase C

The bonding of atoms of very different electronegativity is the source of ______.

polarity

Biological macromolecules are composed of monomeric subunits. Identify the macromolecule whose subunit is shown.

protein

If a disulfide bond connects two polypeptide chains in a protein, the highest level of protein organization this protein has is _____.

quaternary structure.

What is the name of the structure indicated by the bracket in the image of muscle below?

sarcomere

Comparing two weak acids, which one is the weaker?

the larger pKa

A single heavy chain of an immunoglobulin molecule has ________, whereas a single light chain of an immunoglobulin molecule has _______.

three constant domains and one variable domain; one constant domain and one variable domain

The purpose of adding β-mercaptoethanol during a protein electrophoresis (SDS-PAGE) experiment is _____.

to make sure all disulfides are reduced

Which of the following types of proteins are exceptions to the two simple rules of protein folding: (1) Hydrophobic residues are found buried in the interior of a protein; and (2) the number of hydrogen bonds and ionic interactions within the protein are maximized? globular proteins transmembrane proteins proteins with intrinsically disordered segments both b and c

transmembrane proteins proteins with intrinsically disordered segments both b and c

The lack of which vitamin leads to problems with collagen synthesis?

vitamin C

When amino acids react and join to each other, what molecule is lost?

water

Which of the following lipids is the most polar?

yellow (bottom)

ELISA is a very useful technique for quantifying specific proteins in a complex mixture. One of the components used in ELISA is a secondary antibody attached to the enzyme horseradish peroxidase (HRP). What is the purpose of the HRP in this assay?

HRP is an enzyme that can convert certain colorless substrates into colored products.

What distinguishes proteoglycans from glycoproteins?

Proteoglycans contain glycosaminoglycans; glycoproteins contain oligosaccharides.

The following molecule resembles a triacylglycerol, but is not. Why can this molecule not be classified as a triacylglycerol?

The chain on carbon 3 is not an ester linkage.

Why are salt bridges much stronger when they occur at the interior of a protein as compared to its surface?

The interior of the protein has a much lower dielectric constant than the solvent so there is no shielding of the charges.

Which of the following statements is true regarding the kinetic properties of allosteric enzymes?

The kinetic behavior of allosteric enzymes generally reflects cooperative interactions between multiple protein subunits.

Kinetic studies frequently use the initial rate method. Which statement does not apply to this method? a. The [S] is high enough that it changes little during the rate measurement. b. The length of the pre-steady state is evaluated. c. The [S] at which saturation occurs can be determined. d. How the rate depends on [S] can be evaluated when [E] is held constant.

The length of the pre-steady state is evaluated.

In order for a solute to be soluble in water, which situation must be true?

The water-solute interactions are more favorable energetically than water-water interactions.

In an SDS-PAGE experiment, a protein migrates much faster than expected relative to protein standards, based on its known molecular weight. What could cause this?

The protein had a very high intrinsic negative charge.

Free-energy funnels are used to explain the thermodynamics of protein folding. What can be said of a protein that has the following free-energy funnel?

The protein has folding intermediates with substantial stability on nearly every pathway leading to the native state.

An active protein was purified to homogeneity using gel filtration and analyzed for its amino terminal residue using dabsyl chloride as described in Chapter 3. After multiple tries, the researcher gave up because there appeared to be four different amino terminal residues in the protein. What would you conclude about this protein?

The protein was made of four unique subunits.

At a substrate concentration that is much greater than the Km for the reaction, which statement below is true (assuming the enzyme obeys Michaelis-Menten kinetics)?

The reaction velocity is Vmax

Which of the following statements is false regarding the reaction catalyzed by lysozyme?

There are two chemically reasonable mechanisms that could generate the observed product of lysozyme reaction, although recent data supports the SN1 model.

In which ways can dietary intake of trans fatty acids contribute to a higher incidence of cardiovascular disease?

They raise the levels of triacylglycerols and LDL cholesterol and lower HDL cholesterol levels.

Which is a distinguishing feature of living organisms?

They use, transform and extract energy from the environment. They can change (evolve) over time. They can self-replicate. all of the above

How might a researcher determine the overall monosaccharide composition of an oligosaccharide?

acid hydrolysis followed by HPLC

How are enzymes different than the average catalyst? They have a high degree of specificity for their substrates. They function under mild aqueous temperature and pH. Their catalytic power is often far greater than for synthetic or inorganic catalysts. all of the above

all of the above

What effect does the binding of CO2 and H+ to hemoglobin in the peripheral tissues have in the body? The tense form of hemoglobin is stabilized by the binding of CO2 and H+. Binding of H+ to hemoglobin serves as a buffer to regulate the pH of peripheral tissues. It facilitates the release of O2 in the peripheral tissues.

all of the above

Which apply to vitamin E? antioxidant contains a substituted aromatic ring and a long isoprenoid side chain found in eggs, vegetable oils and wheat germ all of the above

all of the above

Which is involved in the mechanism of catalysis of peptide bond hydrolysis by chymotrypsin? all of the above covalent catalysis transition-state stabilization general acid-base catalysis

all of the above

Which is true about a retrovirus? all of the above Its genome is composed of RNA. It incorporates a complementary DNA copy of its genome into the host genome. Reverse transcriptase is an important retroviral protein.

all of the above

Which of the following statements is true regarding syndecans and glypicans? Glypicans are attached to the membrane by a derivative of phosphatidylinositol. They both can be shed into the extracellular space. Syndecans have a single transmembrane domain and an extracellular domain with 3 to 5 chains of heparan sulfate or chondroitin sulfate. all of the above

all of the above

Which of the following terms best describes the structure shown below?

amphipathic

Describe the chemical steps, in order, that are involved in the conversion of β−carotene into retinoic acid.

cleavage, alcohol oxidation, aldehyde oxidation

The top lipid is an example of a(n) ___, while the bottom lipid is an example of a(n) ___.

sphingolipid; glycerophospholipid

Which does not contain a carbohydrate unit (is not a glycolipid)?

sphingomyelin

How can lipids be visualized after separation by thin-layer chromatography (TLC) on silica gel?

spray with rhodamine - lipid spots will fluoresce

Administration of which vitamin can prevent rickets, a disease in which the bones of children are softened and weakened?

vitamin D