Quiz 1 - chapter 1 -3, BCH3025 Exam 1, Questions 5, BCH3025 Exam 1, BCH3025 Exam 1

The dimensions of living cells are limited, on the lower end by the minimum number of biomolecules necessary for function, and on the upper end by the rate of diffusion of solutes such as oxygen. Except for highly elongated cells, they usually have lengths and diameters in the range of: A) 0.1 m to 10 m. B) 0.3 m to 30 m. C) 0.3 m to 100 m. D) 1 m to 100 m. E) 1 m to 300 m.

0.3 micro meters to 100 micro meters

What fraction of ligand binding sites are occupied () when [ligand] = Kd? Show your work.

0= [L]/[L]+Kd thus = Kd/Kd+Kd = 1/2

In the binding of oxygen to myoglobin, the relationship between the concentration of oxygen and the fraction of binding sites occupied can best be described as: A) hyperbolic. B) linear with a negative slope. C) linear with a positive slope. D) random. E) sigmoidal.

A

The energy that is released by the hydrolysis of ATP by actin is used for: A) actin filament assembly. B) actin filament disassembly. C) actin-myosin assembly. D) actin-myosin disassembly. E) muscle contraction.

A

Which of the following generalizations concerning motor proteins is correct? A) They convert chemical energy into kinetic energy. B) They convert chemical energy into potential energy. C) They convert kinetic energy into chemical energy. D) They convert kinetic energy into rotational energy. E) They convert potential energy into chemical energy.

A

Both prokaryotic and eukaryotic cells possess what?

A plasma membrane.

Which one of the following has the cellular components arranged in order of increasing size? A) Amino acid < protein < mitochondrion < ribosome B) Amino acid < protein < ribosome < mitochondrion C) Amino acid < ribosome < protein < mitochondrion D) Protein < amino acid < mitochondrion < ribosome E) Protein < ribosome < mitochondrion < amino acid

Amino acid < protein < ribosome < mitochondrion

Explain why most multicellular organisms use an iron-containing protein for oxygen binding rather than free Fe2+. Your answer should include an explanation of (a) the role of heme and (b) the role of the protein itself.

Ans: (a) Binding of free Fe2+ to oxygen would result in the formation of reactive oxygen species that can damage biological structures. Heme-bound iron is less reactive in this regard. (b) Binding of oxygen to free heme can result in irreversible oxidation of the Fe2+ to Fe3+ that does not bind oxygen. The environment of the heme group in proteins helps to prevent this from occurring.

a) What is the effect of pH on the binding of oxygen to hemoglobin (the Bohr Effect)? (b) Briefly describe the mechanism of this effect.

Ans: (a) The affinity decreases with decreasing pH. (b) At lower pH (i.e., higher H+ concentration) there is increasing protonation of protein residues such as histidine, which stabilizes the low affinity conformation of the protein subunits.

Although the myosin molecule "walks" along actin in discrete steps, you are aboe to make smooth motions using your muscles. Explain how this is possible.

Ans: A given muscle consists of many bundled muscle fibers, each of which contains many myofibrils, each of which contains many thick and thin filaments. Furthermore when a muscle contracts, the myosin molecules move asynchronously. Thus, the individual steps of individual myosin molecules are masked by the millions of other myosin molecules taking steps at different times.

What is the role of ATP and ATP hydrolysis in the cycle of actin-myosin association and disassociation that leads to muscle contraction?

Ans: ATP binding to myosin results in a conformational change that causes dissociation of actin from the myosin. ATP hydrolysis results in a change of orientation of the myosin relative to the actin filament, which allows movement to the next actin subunit. This is followed initially by release of the phosphate hydrolysis product and weak binding of the myosin to this actin subunit, and, subsequently, by tight binding and release of the ADP hydrolysis product.

Describe briefly the basic structure of an IgG protein molecule.

Ans: An IgG protein contains two copies of a large polypeptide (heavy chain) and two copies of a small polypeptide (light chain). structure contributes significantly to the tertiary structure of domains of both chains. Disulfide bonds link the heavy chains to one another and to the light chains. The chains are arranged in a Y-shaped structure where the two arms are linked to the base by a protease sensitive ("hinge") region.

Describe how you would determine the Ka (association constant) for a ligand and a protein.

Ans: An experiment would be carried out in which a fixed amount of the protein is incubated with varying amounts of ligand (long enough to reach equilibrium). The fraction of protein molecules that have a molecule of ligand bound is then determined. A plot of this fraction () vs. ligand concentration [L] should yield a hyperbola. The value of [L] when = 0.5 is equal to 1/Ka.

Why is it likely that the immune system can produce a specific antibody that can recognize and bind to any specific chemical structure?

Ans: As a result of genetic recombination mechanisms, antibody-producing B cells are capable of producing millions of different antibodies with different binding specificities.

How does BPG binding to hemoglobin decrease its affinity for oxygen?

Ans: BPG binds to a cavity between the subunits. It binds preferentially to molecules in the low-affinity T state, thereby stabilizing that conformation.

Describe the cycle of actin-myosin association and disassociation that leads to muscle contraction.

Ans: First, ATP binds to myosin and a cleft in the myosin molecule opens, disrupting the actin-myosin interaction so that the bound actin is released. Second, ATP is hydrolyzed, causing a conformational change in the protein to a "high-energy" state that moves the myosin head and changes its orientation in relation to the actin thin filament. Myosin then binds weakly to an F-actin subunit closer to the Z disk than the one just released. Third, as the phosphate product of ATP hydrolysis is released from myosin, another conformational change occurs in which the myosin cleft closes, strengthening the myosin-actin binding. Fourth, this is followed quickly by a "power stroke" during which the conformation of the myosin head returns to the original resting state, its orientation relative to the bound actin changing so as to pull the tail of the myosin toward the Z disk. ADP is then released to complete the cycle. (See Fig. 5-31, p. 178.)

What is the relationship between G-actin and F-actin?

Ans: G-actin is a monomeric protein that can polymerize to form a long polymeric filament known as F-actin.

Explain how the effects of sickle cell disease demonstrate that hemoblobin undergoes a conformational change upon releasing oxygen.

Ans: In Hemoglobin S, the wild-type glutamate at residue 6 of the B-chain is replaced by valine. When oxygen is bound, both Hemoglobin A and Hemoglobin S are soluble, but in the deoxy- form. Hemoglobin S (but not Hemoglobin A) becomes very insoluble, due to exposure of the hydrophobic valine residue. This exposed "patch" causes aggregation of deoxy-Hemoglobin S into long insoluble fibrous aggregates, resulting in distorted shapes of the red blood cells (and leading to the symptoms of the disease). (See p. 168-169 and Fig. 5-20.)

Describe briefly the two principal models for the cooperative binding of ligands to proteins with multiple binding sites

Ans: In the concerted model, binding of a ligand to one site on one subunit results in an allosteric effect that converts all of the remaining subunits to the high-affinity conformation. As a result, all of the subunits are either in the low- or high-affinity conformation. In the sequential model, each subunit is changed individually to the high affinity conformation. As a result, there are many possible combinations of low- and high-affinity subunits.

Describe the concept of "induced fit" in ligand-protein binding.

Ans: Induced fit refers to the structural adaptations that occur when a ligand binds to a protein. This often involves a conformational change in the protein that alters the binding site to make it more complementary to the ligand.

Why is carbon monoxide (CO) toxic to aerobic organisms?

Ans: It binds to heme with a higher affinity than oxygen, and thus prevents oxygen from binding to hemoglobin.

For the binding of a ligand to a protein, what is the relationship between the Ka (association constant), the Kd (dissociation constant), and the affinity of the protein for the ligand?

Ans: Ka = 1/Kd. The larger the Ka (and hence the smaller the Kd), the higher the affinity of the protein for the ligand.

Describe briefly the structure of myosin.

Ans: Myosin contains two copies of a large polypeptide (heavy chain) and four copies of a small polypeptide (light chain). The helix contributes significantly to the structure of the heavy chains. At their carboxyl termini, the heavy chains are wrapped around each other in a fibrous left-handed coil. At their amino termini, they each have a globular domain with which the light chains are associated.

What is the chemical basis for the specificity of binding of an immunoglobin antibody to a particular antigen?

Ans: Specific binding results from complementarity between the chemical properties (such as size, charge, and hydrophobicity) of the antigen and the antigen-binding site of the antibody.

What is the concept of "induced fit" as it applies to antigen-antibody binding?

Ans: The conformations of the antigen and antigen-binding site of the antibody are influenced by each other and change as binding occurs. These conformational changes increase the chemical complementarity of the sites and result in tighter binding.

Explain briefly why the relative affinity of heme for oxygen and carbon monoxide is changed by the presence of the myoglobin protein.

Ans: The geometry of binding O2 and CO to heme is slightly different. In myoglobin there is a histidine residue that does not interact with the heme iron, but can interact with a ligand that is bound to the heme. It does not affect O2 binding but because of steric hindrance, it may prevent CO binding. As a result the relative affinity of protein-bound heme for CO and O2 is only 200, compared to 20,000 for free heme.

Explain why the structure of myoglobin makes it function well as an oxygen-storage protein whereas the structure of hemoglobin makes it function well as an oxygen-transport protein.

Ans: The hyperbolic binding of oxygen to the single binding site of myoglobin results in a high affinity even at the relatively low partial pressures of O2 that occur in tissues. In contrast, the cooperative (sigmoidal) binding of O2 to the multiple binding sites of hemoglobin results in high affinity at high partial pressures such as occur in the lungs, but lower affinity in the tissues. This permits hemoglobin to bind O2 in the lungs and release it in the tissues.

What properties of antibodies make them useful biochemical reagents? Describe one biochemical application of antibodies (with more than just the name of the technique).

Ans: The important properties are the high specificity of protein recognition, and the high affinity of the antibody-antigen association. These make possible immunoaffinity chromatography, immunocytochemistry, enzyme-linked immunosorbent assay (ELISA), and immunoblotting, all of which are described on pp. 173-175.

Describe how immunoaffinity chromatography is performed.

Ans: The specific antibody is covalently attached to an inert supporting material, which is then packed into a chromatography column. The protein solution is passed through the column slowly; most proteins pass directly through, but those for which the antibody has specific affinity are adsorbed. They can subsequently be eluted by a buffer of low pH, a salt solution, or some other agent that breaks the antibody-antigen association.

Which amino acid has a net negative charge at pH 7.0?

Aspartate.

An allosteric interaction between a ligand and a protein is one in which: A) binding of a molecule to a binding site affects binding of additional molecules to the same site. B) binding of a molecule to a binding site affects binding properties of another site on the protein. C) binding of the ligand to the protein is covalent. D) multiple molecules of the same ligand can bind to the same binding site. E) two different ligands can bind to the same binding site.

B

An individual molecular structure within an antigen to which an individual antibody binds is as a(n): A) antigen. B) epitope. C) Fab region. D) Fc region E) MHC site.

B

During muscle contraction, hydrolysis of ATP results in a change in the: A) conformation of actin. B) conformation of myosin. C) structure of the myofibrils. D) structure of the sarcoplasmic reticulum. E) structure of the Z disk.

B

The predominant structural feature in myosin molecules is: A) a structure. B) an helix. C) the Fab domain. D) the light chain. E) the meromyosin domain.

B

When oxygen binds to a heme-containing protein, the two open coordination bonds of Fe2+ are occupied by: A) one O atom and one amino acid atom. B) one O2 molecule and one amino acid atom. C) one O2 molecule and one heme atom. D) two O atoms. E) two O2 molecules.

B

Which of the following parts of the IgG molecule are not involved in binding to an antigen? A) Fab B) Fc C) Heavy chain D) Light chain E) Variable domain

B

Which of the following is true about energy from sunlight? A) All organisms obtain their energy directly from the radiant energy of sunlight. B) Photosynthetic cells use light energy to drive electrons from one molecule to another. C) Photosynthetic cells use light energy to product CO2 that can be used as energy by non-photosynthetic cells. D) Photosynthetic cells absorb light energy and use it to break down compounds such as starch and sucrose.

B) Photosynthetic cells use light energy to drive electrons from one molecule to another.

A monoclonal antibody differs from a polyclonal antibody in that monoclonal antibodies: A) are labeled with chemicals that can be visualized. B) are produced by cells from the same organism that produced the antigen. C) are synthesized by a population of identical, or "cloned," cells. D) are synthesized only in living organisms. E) have only a single polypeptide chain that can recognize an antigen.

C

In hemoglobin, the transition from T state to R state (low to high affinity) is triggered by: A) Fe2+ binding. B) heme binding. C) oxygen binding. D) subunit association. E) subunit dissociation.

C

The fundamental cause of sickle-cell disease is a change in the structure of: A) blood. B) capillaries. C) hemoglobin. D) red cells. E) the heart.

C

Which of the following is not correct concerning 2,3-bisphosphoglycerate (BPG)? A) It binds at a distance from the heme groups of hemoglobin. B) It binds with lower affinity to fetal hemoglobin than to adult hemoglobin. C) It increases the affinity of hemoglobin for oxygen. D) It is an allosteric modulator. E) It is normally found associated with the hemoglobin extracted from red blood cells.

C

Which of the following is not correct concerning cooperative binding of a ligand to a protein? A) It is usually a form of allosteric interaction. B) It is usually associated with proteins with multiple subunits. C) It rarely occurs in enzymes. D) It results in a nonlinear Hill Plot. E) It results in a sigmoidal binding curve.

C

The amino acid alanine contains all groups except.... A) an amino group B) a methyl group C) an ester group D) a carboxyl group

C) an ester group.

L-alanine and D-alanine...

C) are enantiomers.

Which of the following is NOT a macromolecule composed of many subunits? A) proteins. B) DNA. C) proteome. D) polysaccharides.

C. proteome.

What is the difference between phototrophs and chemotrophs?

Their energy source.

A prosthetic group of a protein is a non-protein structure that is: A) a ligand of the protein. B) a part of the secondary structure of the protein. C) a substrate of the protein. D) permanently associated with the protein. E) transiently bound to the protein.

D

Carbon monoxide (CO) is toxic to humans because: A) it binds to myoglobin and causes it to denature. B) it is rapidly converted to toxic CO2. C) it binds to the globin portion of hemoglobin and prevents the binding of O2. D) it binds to the Fe in hemoglobin and prevents the binding of O2. E) it binds to the heme portion of hemoglobin and causes heme to unbind from hemoglobin

D

The amino acid substitution of Val for Glu in Hemoglobin S results in aggregation of the protein because of ___________ interactions between molecules. A) covalent B) disulfide C) hydrogen bonding D) hydrophobic E) ionic

D

The interactions of ligands with proteins: A) are relatively nonspecific. B) are relatively rare in biological systems. C) are usually irreversible. D) are usually transient. E) usually result in the inactivation of the proteins.

D

At the center of all 20 standard amino acids is what is termed the a-carbon that is covalently bonded with 4 other chemical groups. Which of these four chemical groups is not a normal component of all amino acids?

D) A methyl group

Supramolecular complexes of proteins, nucleic acids, and polysaccharides are NOT held together by...

D) covalent bonds.

Myoglobin and the subunits of hemoglobin have: A) no obvious structural relationship. B) very different primary and tertiary structures. C) very similar primary and tertiary structures. D) very similar primary structures, but different tertiary structures. E) very similar tertiary structures, but different primary structures.

E

Which of the following statements about protein-ligand binding is correct? A) The Ka is equal to the concentration of ligand when all of the binding sites are occupied. B) The Ka is independent of such conditions as salt concentration and pH. C) The larger the Ka (association constant), the weaker the affinity. D) The larger the Ka, the faster is the binding. E) The larger the Ka, the smaller the Kd (dissociation constant).

E

If heat energy is absorbed by the system during a chemical reaction, the reaction is said to be A) at equilibrium. B) endergonic. C) endothermic. D) exergonic. E) exothermic.

Endothermic

Exergonic and endergonic reactions differ in that...

Exergonic reactions produce less free energy than the reactants; endergonic reactions produce products with more free energy than the reactants.

Under what conditions is a carbon atom a chiral center?

If it has four different substituent groups.

l

Larger proteins move faster in the gel than smaller proteins.

Current theories describing the evolution of multicellular organisms from inorganic molecules...

NOT TRUE: Enzymes did not appear until after the first cells appeared.

Paralogs and orthologs differ in that...

Paralogs exist in the same species and orthologs exist in different species.

Which one of the following is not among the four most abundant elements in living organisms? A) Carbon B) Hydrogen C) Nitrogen D) Oxygen E) Phosphorus

Phosphorus

Which group or groups on a protein contribute most to its overall acid-base properties?

The R groups on the protein.

The titration curve of the amino acid glycine reveals a pK1 of 2.34, a pI of 5.97, and a pK2 of 9.60. When dissolved in water, which ionic species is most likely to predominate at pH = 5.97? a) NH3+-CH2-COO- b) NH2-CH2-CH2-COOH c) NH2-CH2-COO- d) NH3+-CH2-COOH

a) NH3+-CH2-COO-

All of the amino acids that are found in proteins, except for proline, contain a(n) a) amino group b)ester group c) carboxyl group d) carbonyl group

a) amino group

A protein retained on an affinity chromatography column is usually eluted off the column by...

adding the protein's free ligand.

Synthetic pathways are...

anabolic.

Carbon...

atoms can form covalent bonds with up to four other atoms.

Because proteins can absorb light maximally at 280 nm, they can be identified and quantified in solution by using a spectrophotometer. Which of the following is true about the absorption of light by proteins? A) All amino acids absorb light equally b) Absorbance of 280 nm light by proteins increases with the concentration of the protein c) Absorbance of 280 nm light by proteins increases with the concentration of the protein d) Proteins absorb infrared light

b) Absorbance of 280 nm light by proteins increases with the concentration of the protein

Which of the two amino acids contain sulfur atoms? a) Threonine and Serine b) Cysteine and Methionine c) Methionine and Threonine d) Cysteine and Serine

b) Cysteine and Methionine

Under what conditions is a carbon atom a chiral center? a) If it has no stereoisomers b) If it has four different substituent groups c) If it is symmetric d) If the molecule that it belongs to can be superimposed on its mirror image after rotation

b) If it has four different substituent groups

In a solution of pH below the isoelectric point (pI) of an amino acid, the amino acid will: a) be zwitterionic b) be positively charged c) not contain any charge d) be negatively charged

b) be positively charged

Of the 20 standard amino acids, only ___________ is not optically active. The reason is that its side chain __________ a) proline; forms a covalent bond with the amino group b) glycine; is a hydrogen atom c) glycine; is unbranched d) alanine; is a simple methyl group

b) glycine; is a hydrogen atom

At the centre of all 20 standard amino acids is what is termed the α-carbon that is covalently bonded with four other chemical groups. Which of these four chemical groups is not a normal component of all amino acids? a) a side chain (R group) b) an amino group c) A methyl group d) a carboxyl group

c) A methyl group

Peptide bonds, which covalently links two amino acids, result from a) hydrogen bonds between amino acids b) the oxidation of amino acids c) the condensation of amino acids d) the hydrolysis of amino acids

c) the condensation of amino acids

The three-dimensional structure of macromolecules is formed and maintained primarily through noncovalent interactions. Which one of the following is not considered a noncovalent interaction? A) carbon-carbon bonds B) hydrogen bonds C) hydrophobic interactions D) ionic interactions E) van der Waals interactions

carbon-carbon bonds

The bacterium E. coli requires simple organic molecules for growth and energy—it is therefore a A) chemoautotroph. B) chemoheterotroph. C) lithotroph. D) photoautotroph. E) photoheterotroph.

chemo heterotroph.

Which of the following statements about aromatic amino acids is correct? a) Histidine's ring structure results in its being categorized as aromatic or basic, depending on pH b) The major contribution to the characteristic absorption of light at 280 nm by proteins is the phenylalanine R group c) All are strongly hydrophilic d) On a molar basis, tryptophan absorbs more ultraviolet light than tyrosine

d) On a molar basis, tryptophan absorbs more ultraviolet light than tyrosine

Humans maintain a nearly constant level of hemoglobin by continually synthesizing and degrading it. This is an example of a(n): A) dynamic steady state. B) equilibrium state. C) exergonic change. D) free-energy change. E) waste of energy.

dynamic steady state

Stereoisomers that are nonsuperimposable mirror images of each other are known as A) anomers. B) cis-trans isomers. C) diastereoisomers. D) enantiomers. E) geometric isomers

enantiomers.

Stereoisomers....

have different configurations.

What functional groups are present on this molecule? A) ether and aldehyde B) hydroxyl and aldehyde C) hydroxyl and carboxylic acid D) hydroxyl and ester E) hydroxyl and ketone

hydroxyl and aldehyde

Absorbance of 280 nm light by proteins...

increases with the concentration of the protein.

Enzymes are needed in the cell to increase the...

rate of a chemical reaction.

The 3D structure (native conformation) of proteins is determined primarily by...

it's amino acid sequence.

Human hemoglobin and infulenza virus RNA polyperase are...

multisubunit proteins.

In eukaryotes, the nucleus is enclosed by a double membrane called the: A) cell membrane. B) nuclear envelope. C) nucleolus. D) nucleoplasm. E) nucleosome

nuclear envelope

The macromolecules that serve in the storage and transmission of genetic information are: A) carbohydrates. B) lipids. C) membranes. D) nucleic acids. E) proteins.

nucleic acids.

In a bacterial cell, the DNA is in the: A) cell envelope. B) cell membrane. C) nucleoid. D) nucleus. E) ribosomes.

nucleoid

Cysteine residues play an important role in the structure of many proteins by...

providing covalent links between parts of a protein molecule or between two different protein chains.

SDS

separate the subunits of a multisubunit protein.

The enzyme fumarase catalyzes the reversible hydration of fumaric acid to l-malate, but it will not catalyze the hydration of maleic acid, the cis isomer of fumaric acid. This is an example of: A) biological activity. B) chiral activity. C) racemization. D) stereoisomerization. E) stereospecificity.

stereo specificity.

Diastereomers

stereoisomers that are NOT mirror images.

Three dimensional folding of a polypeptide is referred to as....

tertiary structure.

The four covalent bonds in methane (CH4) are arranged around carbon to give which one of the following geometries? A) linear B) tetrahedral C) trigonal bipyramidal D) trigonal planar E) trigonal pyramidal

tetrahedral

An open system is one...

that exchanges both matter and energy with its surroundings.

Peptide bonds, which covalently link two amino acids, results from...

the condensation of amino acids.

A major change occurring in the evolution of eukaryotes from prokaryotes was the development of: A) DNA. B) photosynthetic capability. C) plasma membranes. D) ribosomes. E) the nucleus.

the nucleus.

The isoelectric point, or pI, of an amino acid or protein is...

the pH at which the amino acid or protein has no net charge.

A dynamic steady state results when...

the rate of intake or synthesis of a molecule equals the rate of its disappearance.

Cells couple thermodynamically ____________ reactions to the __________ of ATP.

unfavorable, hydrolysis