exam 2 study materials

what is a heme? (ch5)

protein bound prosthetic group

where is heme found? (ch5)

many oxygen transporting proteins, as well as in cytochromes that participate in oxidation reduction

which variable reflects fractional occupancy on a binding graph? (ch5)

Y axis

which variable reflects ligand concentration on a binding graph? (ch5)

X axis

what does a hyperbolic binding curve indicate? (ch5)

saturation of binding sites

what does P + L ⇌ PL represent in protein ligand binding? (ch5)

a reversible binding interaction

what is the primary factor that determines where a ligand binds on a protein? (ch5)

shape complimentary of the binding site

the Bohr effect is best described as… (ch5)

oxygen binding increasing with pH

at which pH does hemoglobin release the most oxygen? (ch5)

7.2

what is the role of carbonic anhydrase in tissues? (ch5)

convert CO₂ and water to bicarbonate and acid

the sigmoidal oxygen binding curve of hemoglobin is primarily due to… (ch5)

cooperative binding among subunits

hemoglobin is best suited for oxygen transport because… (ch5)

it transitions between high and low affinity states

myoglobin and the subunits of hemoglobin have… (ch5)

very similar tertiary structures, but different primary structures

an allosteric interaction between a ligand and a protein is one in which… (ch5)

binding of a molecule to a binding site affects binding properties of another site on the protein

which statement is not correct concerning 2,3-bisphosphoglycerate (BPG)? (ch5)

it increases the affinity of hemoglobin for oxygen

the amino acid substitution of Val for Glu in hemoglobin S results in aggregation of the protein because of ___ interactions between molecules. (ch5)

hydrophobic

patients with chronic hypoxia (low O₂ levels) due to decreased lung function may adapt by increasing their circulating BPG levels. predict which outcome will be true for such a patient. (ch5)

P₅₀ for O_{2 will be increased}

an individual molecular structure within an antigen to which an individual antibody binds is an… (ch5)

epitope

which generalization concerning motor proteins is correct? (ch5)

they convert chemical energy into kinetic energy

the energy that is released by the hydrolysis of ATP by actin is used for… (ch5)

actin filament assembly

the binding site of a protein is complementary to a specific ligand due to which characteristic of the binding site? (ch5)

its size, its shape, its charge, its hydrophobicity

which molecule binds most strongly to heme iron? (ch5)

CO

a significant contribution to the change in hemoglobin affinity for oxygen from pH 7.2 to pH 7.6 is due to a change in protonation state of which amino acid side chain? (ch5)

His

the binding of oxygen to hemoglobin stabilizes the ___ state of the protein due to interactions between ___ residues in the center of the multisubunit complex. (ch5)

R, His

sickle cell anemia is often lethal in childhood, yet the gene for sickle cell hemoglobin persists in the human population. which statement best describes why this is the case? (ch5)

individuals with sickle cell anemia trait are protected from malaria infection, while individuals with normal hemoglobin are not

small molecules attached to larger protein structures that elicit an immune response are referred to as… (ch5)

haptens

the fab regions of an antibody are made of which protein chain? (ch5)

both a light chain and a heavy chain containing variable and constant regions

myosin moves relative to actin filaments by using energy derived from the hydrolysis of what molecule? (ch5)

ATP

nerve impulses control muscle contractions by releasing which ion? (ch5)

Ca²⁺

individual contractile units in muscle fibers are called… (ch5)

sarcomeres

myosin obtains its high tensile strength due to its composition of… (ch5)

alpha helices supercoiled around each other in a left handed coiled coil

during muscle contraction, the ___ of myofibrils contract and the ___ move closer together due to the movement of myosin thick filaments along actin thin filaments. (ch5)

I bands, Z disks

what role do vitamins like B12 serve in enzyme function? (ch6)

coenzymes

enzyme names often reflect… (ch6)

the reaction they catalyze

what happens to the reaction rate when an enzyme is added? (ch6)

it increases the rate by lowering activation energy

which diagram part represents kinetics in a reaction energy graph? (ch6)

energy of activation

what is the correct sequence of enzyme catalysis? (ch6)

enzyme + substrate → product

classify the enzymes catalyzing the following reactions according to the 6 classes: (ch6)

isomerase

a good transition state analog… (ch6)

binds to the enzyme more tightly than the substrate

which enzymes are not among the seven internationally accepted classes of enzymes? (ch6)

polymerases

for enzymes in which the slowest (rate-limiting) step is the reaction, ES →k₂→ P, K_m becomes equivalent to… (ch6)

the dissociation constant K_d for the ES complex

the steady state assumption, as applied to enzyme kinetics implies: (ch6)

the ES complex is formed and broken down at equivalent rates

the concept of induced fit refers to the fact that: (ch6)

substrate binding may induce a conformational change in the enzyme, which then brings catalytic groups into proper orientation

which of the following contains a new stereocenter upon cyclization of glucose? (ch7)

carbon 1

which carbon determines the D or L designation of a sugar? (ch7)

the last stereocenter furthest from the carbonyl

alpha and beta forms of glucose are called? (ch7)

anomers

what is a trios carbohydrate? (ch7)

a carbohydrate with 3 carbon atoms

what kind of projection is used to draw linear forms of sugars? (ch7)

fischer

which of the following is true of sucrose? (ch7)

it contains an acetal linkage

what term describes the sugar derived from animals that includes both alpha and beta D-glucose units? (ch7)

maltose

which component is required to form an acetal from a hemiacetal? (ch7)

another alcohol

what is formed when two monosaccharides form a disaccharide through glycosidic bonding? (ch7)

glycoside

which functional group forms when a hemiacetal reacts with an alcohol? (ch7)

acetal

which arrow correctly identifies the atom that will become the anomeric carbon? (ch7)

A

in an ___, the carbonyl group is at the end of the carbon chain, but in an ___, the carbonyl can be at any other position. (ch7)

aldose, ketose

following complete hydrolysis of a sample of glycogen and a sample of cellulose, which is true? (ch7)

both samples consist of a mixture of alpha-D-glucose and beta-D-glucose

during which process are chemical bonds not broken? (ch7)

interconverting between two conformations

to posses optical activity, a compound must be: (ch7)

asymmetric

which pair is anomeric? (ch7)

alpha-D-glucopyranose and beta-D-glucopyranose

when forming a disaccharide maltose from two glucose monosaccharides: (ch7)

water is eliminated and a hemiacetal is converted to an acetal

which compound is not a reducing sugar? (ch7)

sucrose

which of these monosaccharides is not an aldose? (ch7)

fructose

when drawing a haworth perspective formula from a fischer projection, which statement is true regarding anomers? (ch7)

it is alpha if the hydroxyl group on the anomeric carbon is on the opposite side of the ring as the C-6

starch and glycogen are both polymers of? (ch7)

alpha-D-glucose

which is a heteropolysaccharide? (ch7)

glycosaminoglycan

which pair is epimeric? (ch7)

D-glucose and D-mannose

which monosaccharide is not a hexose? (ch7)

ribose

what is the correct linkage designation for the glycosidic bond between the two monosaccharide rings? (ch7)

(beta1-4)

when the linear form of a glucose cyclizes, the product is an… (ch7)

hemiacetal

the reference compound for naming D and L isomers of sugars is: (ch7)

glyceraldehyde

which pair is interconverted in the process of mutarotation? (ch7)

alpha-D-glucopyranose and beta-D-glucopyranose

when two carbohydrates are epimers… (ch7)

they differ only in the configuration around one carbon atom

these two monosaccharides can be best described as… (ch7)

epimers

D-glucose is called a reducing sugar because it undergoes an oxidation-reduction reaction at the anomeric carbon. one of the products of this reaction is… (ch7)

D-gluconate

based on the form of the cyclic sugar in a haworth projection, which fischer projection formula could have formed this structure? (ch7)

A

which statement about starch and glycogen is false? (ch7)

both serve primarily as structural elements in cell walls

from the abbreviated name of the compound Gal(beta1-4)Glc, we know that… (ch7)

C-4 of glucose is joined to C-1 of galactose by a glycosidic bond

which of the following is involved in DNA sequencing? (ch8)

complementary base pairing

what makes GC bonds stronger than AT bonds? (ch8)

triple hydrogen bonds

which base pair is not found in DNA? (ch8)

uracil

what is the total height of one complete turn of B-DNA? (ch8)

36A

which technique relies on the principle of nucleotide complementarity? (ch8)

PCR

large K_a means

strong binding

small K_b means

strong binding

for the Hill equation, n = 1 means

no cooperativity

for the Hill equation, n > 1 means

positive cooperativity

for the Hill equation, n < 1 means

negative cooperativity

low pH in the tissues means O₂ is released, what state is it in?

T state

high pH in the lungs means O₂ is binding, what state is it in?

R state

O₂ is released in the

T state

O₂ is binding in the

R state

if K_eq > 1 then

more products than reactants

K_eq < 1 then

less products more reactants

in Michaelis-menten, what influences the rate

the substrate

the michaelis-menten equation is

V₀=V_max[s]/K_m+[s]

this is an

aldehyde

this is a

ketone

in the concerted enzyme theory diagram…

once a ligand binds, all are changed, all or nothing

in the sequential enzyme theory diagram…

only affects conformation of the bound ligand, one at a time, based on individual subunit and how it changes

in hemoglobin, which ‘sections’ (alpa 1, beta 2 etc) interact the most?

alpha 1 and beta 1 interact more strongly with each other