Biochem Final

covalent catalysis

when enzymes derive much of their rate acceleration from formation of covalent bonds between enzyme and substrate

nucleophilic

the side chains of amino acids in proteins offer a variety of \_________ centers for catalysis

amines, carboxylates, aryls, alkyl hydroxyls, imidazoles, and thiols

what are six examples of nucleophilic centers

general acid base catalysis

what is the most abundant form of catalysis

specific acid-base catalysis

acid base catalysis that involves H+ or OH- that diffuses into the catalytic center

general acid-base catalysis

acid-base catalysis that involves a proton transfer in the transition state (ionizable groups on the protein provide the H+ transferred in the transition state)

metal ion catalysis

metalloenzymes bind metal very tightly or require the metal ion to maintain its stable and native state. The metals stabilize the increased electron density or negative charge that develop during the catalysis reaction

general acid base catalysis

what type of catalysis does serine proteases use

serine, histidine, aspartic acid

what three amino acids are in the catalytic triad

burst kinetics

the serine protease mechanism involves what type of kinetics

orients histidine

what is the function of aspartic acid in the serine protease mechanism

acts as a general acid and base

what is the function of histidine in the serine protease mechanism

forms covalent bond with peptide to be cleaved

what is the function of serine in the serine protease mechanism

tetrahedral oxyanion intermediate

what type of intermediate is made in the serine protease mechanism

aspartic acid; histidine; serine

\_______ positions an immobilized \____ in the active site which acts as an active site base and abstracts a proton from \__________

oxyanion hole

tetrahedral intermediates are stabilized by a pair of amide groups called the \_____________. These are found on serine and glycine

somewhere in the pathway

where are allosteric effectors usually produced

feedback inhibition

A method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway.

sigmoid (S shaped)

what does the kinetics of allosteric regulation look like

cooperative

binding of one substrate molecule to a protein molecule in allosteric regulation makes it easier for additional substrate molecules to bind to protein, therefore, substrate binding is \_____________--

no

do feedback inhibitors (final product) resemble the starting product it inhibits?

oligomeric

allosteric enzymes typically have an \______________ organization aka they are composed of more than one polypeptide chain and each subunit has a binding site for substrate and a distinct binding sire for effectors

confirmational changes

regulatory effects exerted on the enzyme's activity are achieved by \____________________ occurring in the protein when effector metabolites bind

MWC model

model that says proteins exist in two states: R (relaxed) and T (taut). T confirmation is greatly favored when no ligands present but substrate binds to R more when it is around. Substrate binding is cooperative. Equilibrium between conformational states

R;T

in the MWC model, allosteric activators bind only to the \________ state and allosteric inhibitors only bind to the \____ state

KNF model

allosteric regulation model that relies on the idea that ligand binding triggers a confirmational change in the protein. If oligomeric- one subunit confirmational change can trigger anothers. It is sequential model.

serine, threonine, tyrosine

what three amino acids are phosphorylated

kinases

what type of enzyme does phosphorylation

phosphatases

what type of enzyme does reverse phosphorylation/ removes phosphoryl groups

true

t/f: kianses and phosphatases themselves are targets of regulation

intrasteric control

kinases are often regulated by \____________ in which a regulatory subunit has a pseudosubstrate sequence that mimics the target sequence which lacks the phosphorylatable residue (-OH group)

catalytic domain and regulatory domain

protein kinase A has what two subunits

carboxylation

what is the addition of a carboxyl group called

acetylation

what is the addition of an acetyl group called

glycosylation

what is the attachment of a sugar molecule to the protein or addition of ubiquitin to free amino group called

adenylation, uridylation, ADP-ribosylation

what three covalent modifications to enzymes require nucleoside triphosphates (ATP, UTP)

oxygen transport and oxygen transport

what are hemoglobin (blood) and myoglobin (muscle) used for respectively

michaelis-menten

myoglobin (Mb) displays \____________ O2 binding curves which resemble allosteric enzyme substrate saturation

sigmoid

hemoglobin (Hb) displays \___________ O2 binding curves which obeys classic substrate saturation behavior

no

are Hb and Mb enzymes

heme

a polphyrin ring system complexing an iron ion as its prostetic group

quarternary

oxygen binding by Hb induces \_____________ structure change

salt bridges

\_____________ that stabilize deoxy-Hb are broken in oxy-Hb

H+, CO2, Cl-, 2,3 BPG

what four things promotes dissociation of oxygen from hemoglobin

2,3 BPG

what is an allosteric inhibitor of hemoglobin

higher; lower

fetal hemoglobin has a \______affinity for O2 because it has a \__________ affinity for BPG

flavoproteins (1-2); coenzyme Q (1-2); cytochromes (1); iron-sulfur (1); protein-bound copper (1)

what are the five different electron carriers in the ETC and how many electron transfers do they carry out

FMN, Fe-S

what prosthetic groups does complex one have

FAD, Fe-S

what prosthetic groups does complex two have

Hemes, Fe-S

what prosthetic groups does complex three have

Hemes, CuA, CuB

what prosthetic groups does complex four have

complex 1

which complex in ETC accepts electrons from NADH and is thus the primary link between TCA and ETC/OP

complex 2

which complex includes succinate dehydrogenase (succinate --\> fumarate), providing a direct link between TCA and ET

complex 3

which complex in ETC is the where UQH2 is the substrate

complex 4

which complex in ETC reduces oxygen

NADH dehydrogenase

complex one is called what

succinate dehydrogenase

complex two is called what

ubiquinone-cytochrome c oxidoreductase

complex three is called what

cytochrome c oxidase

complex IV is called what

ATP synthase

proton diffusion through \_________________ drives ATP synthesis

transmembrane channel that H+ move through

the Fo complex of ATP synthase forms what

O (open)

the _ site in ATP synthase has low affinity for ligands and is thus inactive

L (loose)

the _ site in ATP synthase has loose affinity for ligands and is thus inactive

T (tight)

the _ site in ATP synthase has high affinity for ligands and is thus active

ATP-ADP translocase

what enzyme mediates the movement of ATP and ADP across the mitochondrial membrane. It is a coupled process, in which ATP is moved out concomitantly with ADP's movement in

1H+; 3H+; 4H+

Every ATP transported out costs \______ and one ATP synthesis about \______. Thus, synthesis and exporting 1 ATP require \__________

10

the electron transport chain yields \________ H+ pumped out per electron pair from NADH to oxygen

6

for electrons entering as succinate (FADH2) about \_________H+ pumped per electron pair to oxygen

10/3.7 \= 2.7ATP

what is the phosphate/oxygen ratio for mitochondrial electron transport of ATP/NADH

6/3.7 \= 1.6ATP

what is the phosphate/oxygen ratio for mitochondrial electron transport of ATP/FADH2

nitrogen of amino and oxygen of hydroxyl

what two can act as a nucleophile in metabolic reactions?

pH\= pKa + log(A-/HA)

what is the henderson hasselback equation

Pyrrolysine

what amino acid is found in methanogenic archaea and bacteria but not humans, is polar with a weak basic side chain, is identified as the 22nd AA, and its abbreviation is Pyl or O

the lysine residues are neutral which eliminate electrostatic repulsion between the R groups

poly-lysine is a random coil when the pH is less than 11, while it forms an a-helix if the pH is raised to greater than 12. This is because at pH 12:

proline and hydroxyproline

\_________ and \_________ acts as helix breakers due to their unique structure, which fixes the value of the Ca-N-C bond angle

Lys and Asp

an electrostatic interaction might occur within a protein between which of the following amino acid pairs at typical physiological pH

cooperativity, stability, bringing catalytic sites together, genetic economy and efficiency

what are the structural and functional advantages of quarternary structure

amino acid sequence

all the information necessary for folding of the peptide chain into its native structure is contained in the \______ of the peptide

hydrophobic interactions, ionic bonds, van der Waals forces, hydrogen bonds

secondary and higher orders of structure are determined by:

tertiary structure

the folding of a single polypeptide chain in three-dimensional space

amphiphilic helix

the outward face of a(n) \_________________ consists mainly of polar and charged residues, whereas the inner face contains mostly nonpolar, hydrophobic residues

true

t/f: a chemical property of carbohydrates is the existence of at least one and often two or more asymmetric centers

true

t/f: a chemical property of carbohydrates is the ability to exist in either linear or ring structures

true

t/f: a chemical property of carbohydrates is the capacity to form polymeric structure via glycosidic bonds

no

is trehalose a reducing sugar

serine

which amino acid can be modified with carbohydrate

sugar esters, amino sugars, sugar acids, sugar alcohols, deoxy sugars, acetals/ketals

monosaccharides can be converted to several derivative forms. What are six of these derivatives

OH up, H down

what is a reducing sugar

OH and CH2OH

what is a nonreducing sugar

epimer

two sugars that differ in stereochemistry at only one carbon

hydrogen bonds

what is the strongest type of bonding that occurs between water and the polar functional groups on non-ionic polar solutes

glycine; is a hydrogen atom

of the 22 amino acids, only \____________ is not optically active. The reason is that its side chain\_______________

No

is pH 7 always neutral

alzheimers, parkinsons, cystic fibrosis, creutzfeldt-jakob

what 4 diseases are caused by protein misfolding

cyclization, oxidation, dehydration

what are the three steps of green fluorescent protein (GFP)

22%

what is true adenosine in a circular double-stranded DNA genome that is determined by chemical means to be 28% of guanosine?

2'-OH

which -OH group in ribonucleotides makes the 3'-phosphodiester bond susceptible to nucleophilic cleavage during alkaline hydrolysis

DNA library

a set of cloned fragments that collectively represent the genes of a particular organism

40

what is the linking number in a relaxed circular DNA duplex of 400 bp

writhe + twist

linking number (L) \=