question

pKa (chapter 3)

answer

measure of the tendency of a group to give up a proton (acidity); tendency decreases tenfold as pKa increases by one unit

question

thioester bond (1)

answer

compounds with functional group C-S-CoA-C (eg, in acetyl-CoA)

question

zwitterion (3)

answer

dipolar ion with both positive and negative groups but overall neutral charge; can act as either an acid or base

question

Isoelectric point (pI) (chapter 3)

answer

the characteristic pH at which the net electric charge is zero

question

SDS - Sodium Dodecyl Sulfate (chap 3)

answer

detergent used to unfold proteins and give them uniform negative charge

question

SDS Page (3)

answer

chromatography used to separate proteins based on mass. light proteins travel fast than heavier ones

question

PCR - Polymerase chain reaction (3)

answer

copies DNA multiple times to increase sample size

question

Isoelectric focusing (chapt 3)

answer

procedure used to determine the isoelectric pt (pI) of a protein. Protein migrates through gel until pH = pI (net charge = 0)

question

Two-Dimensional Electrophoresis (3)

answer

combines isoelectric focusing and SDS electrophoresis; separates proteins by both molecular weight and pI

question

specific activity (3)

answer

number of enzyme units per mg of total protein (a measure of enzyme purity)

question

activity (3)

answer

total units of a certain enzyme in a solution

question

Peptide bonds (chapter 4)

answer

C-N bond with double bond character due to resonance (C-N bond cannot rotate, and is planar)

question

Edman degredation (3)

answer

used in the sequencing of polypeptides; labels and removes ONLY the amino-residue from a polypeptide. carried out in a machine called a sequenator

question

? in peptide bonding (chapter 4)

answer

angle around the ?-carbon - amide nitrogen bond

question

? in peptide bonding (chapter 4)

answer

angle around the ?-carbon - carbonyl carbon bond

question

Ramachandran Plot (4)

answer

shows favoreable ?-? angle combinations. 3 main "wells" for ?-helices, ?-sheets, and left handed ?-helices

question

Levinthal's Paradox (4)

answer

protein folding cannot be a completely random, trial and error process

question

chaperonins (4)

answer

elaborite protein complexes required for the folding of a number of cellular proteins that do not fold spontaneously

question

Henderson-Hasselbach Equation (2)

answer

pH = pKa + log([A-]/[HA])

question

which amino acids are not found in ?-helices? (4)

answer

glycine and proline. glycine is too flexible, proline is too rigid to rotate.

question

which amino acids are commonly found in ? turns? (4)

answer

glycine, because it is small and flexible, and proline because it forms cis conformation in tight turns.

question

?-mercaptoethanol (4)

answer

breaks disulfide bonds

question

circular dichroism (4)

answer

technique that measures the amount of helical structures in macromolecule (protein is denatured)

question

Acid Dissasociation constant Ka (2)

answer

quantitative measure of the strength of an acid in solution

question

Size-exclusion chromatography (3)

answer

Separates proteins according to size. Large proteins emerge from the column before small ones (counterintuitive result). The solid phase consists of beads with engineered pores or cavities of a particular size. Large proteins cannot enter the cavities, and so take a short (and rapid) path through the column, around the beads. Small proteins enter the cavities, and migrate through the column more slowly as a result

question

Affinity chromatography (3)

answer

based on the binding affinity of a protein. The beads in the column have a covalently attached chemical group. A protein with affinity for this particular chemical group will bind to the beads in the column, and its migration will be retarded as a result

question

HPLC, or high-performance liquid chromatography.

answer

pumps speed the movement of the protein molecules down the column, as well as higher-quality chromatographic materials that can withstand the crushing force of the pressurized flow. By reducing the transit time on the column, HPLC can limit diffusional spreading of protein bands and thus greatly improve resolution.

question

cation-exchange chromatography (3)

answer

solid matrix (stationary phase) has negatively charged groups. In the mobile phase, proteins with a net positive charge migrate through the matrix more slowly than those with a net negative charge. The two types of protein can separate into two distinct bands.

question

Induced fit

answer

conformational changes (in either ligand or protein) that can occur upon ligand binding in order for tighter binding of ligand. ex: HbA

question

porphin

answer

organic compound that is aromatic and heterocyclic, consisting of 4 pyrole rings joined by 4 methine (=CH-) groups to form a larger macrocycle ring. Ex: hemoglobin

question

hemoglobin, HbA (5)

answer

sigmoidal curve (positive cooperativity); four subunits bind four O2; binding one O2 increases affinity for binding the other three (heme-heme interaction)

question

ligand (5)

answer

any molecule that binds reversibly to a protein

question

myoglobin, Mb (5)

answer

hyperbolic curve; one subunit binds one O2; higher affinity for oxygen than HbA, binds oxygen dropped by HbA in low oxygen environments (myo = muscle)

question

Hill plot (5)

answer

turns sigmoid into straight lines. slope = n (# of binding sites). allows measurement of cooperative binding sites.

question

Hill number, n/nH (chapter 5)

answer

provides a measure of the degree of cooperativity between states. nH 1.0, positive cooperativity, binding of first ligand makes binding of second MORE likely. nH = 1.0, not a cooperative system

question

Hemoglobin "Tense-state"

answer

low pH, high CO2, high 2,3-BPG

question

PO2 (5)

answer

about 13 kPa in lungs, 4 kPa in tissues

question

Bohr effect (5)

answer

effect of H+ and CO2 on the binding and release of O2 from Hb. O2 binds well at higher pH and low CO2.

question

2,3-bisphosphoglycerate (5)

answer

decreases affinity of Hb for O2, stabilizing T-state

question

antibodies or immunoglobulins, Ig (chapter 5)

answer

bind bacteria, viruses, or large molecules identified as foreign and target them for destruction

question

ELISA (enzyme-linked immunosorbent assay) (5)

answer

allows for rapid screening and quantification of the presence of an antigen in a sample.

question

epitope (antigenic determinant) (5)

answer

where individual antibodies or t-receptors bind on antigen

question

1) competitive inhibitors 2) uncompetitive inhibitors 3) mixed inhibitors (chapter 6)

answer

1) Km increases, no effect on Vmax, same y-intercept, increasing slope, increased substrate can overcome 2) Vmax decreases, y-intercepts increase, constant slope, increased substrate cannot overcome 3) Km increases, Vmax decreases, y-intercepts increase, slope increases, increased substrate cannot overcome

question

?Gb - binding energy (6)

answer

major source of free energy used by enzymes to lower the activation energies of reactions

question

michealis-menton equation (6)

answer

V0 = Vmax [S] / (Km + [S])

question

Km in michaelis-menten (6)

answer

Km = [S] when V0 = 0.5(Vmax)

question

Kcat (6)

answer

rate limiting step in any enzyme catalyzed reaction and saturation. Kcat = Vmax / Et

question

chymotrypsin (6)

answer

cleaves proteins on C-terminal end of Phe, Trp, and Tyr

question

mutarotation (7)

answer

conversion from ? to ? forms of sugar at the anomeric carbon

question

ionophore (11)

answer

hydrophobic molecule that binds to ions and carries them through cell membranes disrupting concentration gradients.

question

ethanol fermentation (14)

answer

pyruvate --> acetylaldehyde --> ethanol. uses pyruvate decarboxylase and alcohol dehydrogenase. NADH --> CO2 (TPP) + NAD+

question

what enzyme is used in converting pyruvate to oxaloacetate? (14)

answer

pyruvate carboxylase (in mitochondria). cofactors include biotin (carries activated biocarbonate). ATP is used.

question

pyruvate dehydrogenase complex enzymes (14)

answer

1) Pyruvate dehydrogenase, 2) dihydrolipoyl transacetylase, 3) dihydrolipoyl dehydrogenase

question

stimulates gluconeogenesis / inhibits glycolysis (14)

answer

acetyl-CoA, glucagon

question

stimulates glycolysis / stimulates glycolysis (14)

answer

ADP, AMP, insulin

question

sum for gluconeogenesis (14)

answer

2 pyruvate + 4ATP + 2GTP + 2NADH + 2H+ + 4H2O --> glucose + 4ADP + 2GDP + 2NAD + 6Pi

question

ultimate electron acceptor of oxidative decarboxylation in the TCA cycle

answer

O2

question

Hexokinase IV (glucokinase)

answer

inhibited by fructose 6-phosphate and G6P. found in hepatocytes and ?cells of pancreas; buffers blood glucose

question

PFK -1

answer

activated by AMP, F26BP.

question

pyruvate kinase

answer

allosterically inhibited by high ATP; activated by F1,6-BPase

question

pyruvate carboxylase

answer

activated by acetyl-CoA

question

carnitine shuttle (17, p. 634)

answer

transports free fatty acids across inner mitochondrial membrane. 3 enzymatic reactions: 1) esterification to CoA (acyl CoA synthetases) 2) transesterification to carnitine (folllowed by transport) 3) transesterification back to CoA

question

electron carriers for the electron transport chain (19)

answer

1) coenzyme Q - ubiquinone 2) cytochromes (heme prosthetic groups)

question

plastocyanin (19)

answer

carries electrons from photosystem II to photosystem I

question

amylose chain (20)

answer

?-1,4-linkages that produce a coiled helix similar to an ?-helix. has a reducing end and a non-reducing end

question

anomeric carbon (20)

answer

carbon that is cyclized. always the same as the aldo or keto carbon in the linear form.

question

mobilization of fatty acids

answer

stimulated by hormones glucagon and epinephrine

question

promoter

answer

identifies the start of a gene, which strand is to be copied, and the direction in which to copy it.

question

operator

answer

site of repressor binding

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