NOTHING IS REAL! EXAM 1 REVIEW

Question 1

Antigens are recognized with high affinity by antibodies because

Answer 1

the sequences of three hypervariable loops are selected in an immune response to exquisitely complement the 3D shape of the antigen.

Question 2

kcat is what type of parameter?

Answer 2

Kinetic rate constant independent of enzyme or substrate concentration

Question 3

Change in Km

Answer 3

noncompetitive (mixed)

Question 4

Change in Km and Vmax

Answer 4

uncompetitive

Question 5

change Vmax

Answer 5

competitive

Question 6

The assigned reading “Therapeutic monoclonal antibodies,” describes several types of engineered antibody molecules that have been developed for therapeutics. Which of the names below DOES refer to a type of therapeutic monoclonal antibody?

Answer 6

Fab, BiTE, scFv

Question 7

Twelve domains compose an IgG molecule. Of these domains,

Answer 7

all have two or more cysteine residues.

Question 8

Ig chains

Answer 8

4: 2 heavy 2 light

Question 9

Ig fold (Domain)

Answer 9

-sandwich of 2 antiparallel B-sheets
-disulfide bond linkage
-hydrophobic residues
-connected to each other by loops = flexible

Question 10

Substrate enzyme interactions

Answer 10

-hydrophobic to hydrophobic
-H bonding
-coloumbic

Question 11

KI

Answer 11

-dissociation constant
-analogous to KD
-low=more affinity

Question 12

Cheng-Prusoff

Answer 12

relationship btw Ki and IC50

Question 13

The development of an allosteric drug is attractive because

Answer 13

it is possible to consider ACTIVATING an enzyme target in treating a disease.

Question 14

Darunavir

Answer 14

interacts with polypeptide backbone and catalytic asp residues from each subunit of HIV protease

Question 15

The basis for selectivity of certain NSAIDS, such as celecoxib, for COX-2 over COX-1 is

Answer 15

the spatial complementarity between the inhibitor and COX-1 is poor

Question 16

HIV protease

Answer 16

-homodimer
-heme group
-aspartic

Question 17

Aspirin vs everything else on COX

Answer 17

acetylates SERINE residue near active site to block access

Question 18

Mech-based inhibitors

Answer 18

-2-thioxanthines on MPO

Question 19

TX2 on MPO

Answer 19

covalently bonded to heme via thioether bond

Question 20

NSAIDs

Answer 20

block prostaglandin

Question 21

COX-2 vs COX-1

Answer 21

small Valine residue
steric hinderance

Question 22

Allosteric inhibitor kinetics

Answer 22

typically mixed

Question 23

Allosteric inhibition

Answer 23

increase Km

Question 24

Cytochrome inhibitor

Answer 24

-increase bioavailability/plasma levels of drug
-drug more potent

Question 25

CYP3A4

Answer 25

-monoxygenase -membrane bound -activity and dosing of drugs

Question 26

cytochrome catalytic activity

Answer 26

-insertion of OH from O2 -metabolism of fatty acids -produce vitamin A and D -detoxification

Question 27

G is positive

Answer 27

NEED energy

Question 28

SLC transporters

Answer 28

-large family -most bio substrates -NO energy

Question 29

electrochemical transporters

Answer 29

-SLC (uni,sym,antiport)

Question 30

SLC2

Answer 30

-glucose by uniport

Question 31

SGLT (SLC5)

Answer 31

Na+/glucose -Na+ provides energy to move glucose across gradient -SYMPORT

Question 32

ATP hydrolysis

Answer 32

-P-type (Na/K+ ATPase) -ABC

Question 33

ABC

Answer 33

-energy -lipids -P-glycoprotein

Question 34

P-glycoprotein

Answer 34

hydrolysis of ATP drives NBDs apart and converts TMDs back

Question 35

The A-form DNA helix

Answer 35

often occurs in formation of DNA-RNA hybrid helix.

Question 36

B-DNA

Answer 36

-longer -skinnier -smaller diameter -C'2 endo -bigger pitch and twist

Question 37

B-form major groove

Answer 37

wider and shallower -highly accessible

Question 38

Intercalators

Answer 38

-mod DNA locally -mutagens -stretch base pairs apart -TOTO -small molecules in mostly minor grooves

Question 39

positive supercoiling

Answer 39

-left -overwound -hard to unwind good for bad condititons

Question 40

topologically strained DNA

Answer 40

greater activity for transcription etc

Question 41

TOP 1

Answer 41

1. cuts one strand 2. controlled rotation 3. re-ligate -NO ENERGY -REMOVES supercoiling

Question 42

TOP 2

Answer 42

1. Cuts both strands 2. Moves other strand through opening in cut strand 3. re-ligate -LK change by 2 -gyrase (adds negative) -NEEDS ENERGY

Question 43

TOP inhibitors

Answer 43

-trap complex of enzyme + DNA -inhibit re-ligation -topotecan and irinotecan

Question 44

Nucleosome

Answer 44

DNA wrapped around histone octamer

Question 45

Energy required to deform DNA

Answer 45

from electrostatic interactions between DNA backbone and histone side chains

Question 46

HTH

Answer 46

-2 helices w short turn -second helix binds major groove -first helix stabilizes

Question 47

Zinc Fingers

Answer 47

-a-helix binds -ALSO recognizes RNA -4 cys or 2 cys+2his -tandem

Question 48

bZIP

Answer 48

-leucine every 7th a-helix -dimers -arg and lys basic region binds major groove -phosphate baxkbone and H bonding

Question 49

HLH

Answer 49

-2 a-helix connected by loop -4helix dimer -extension of one a-helix binds major groove

Question 50

CREB domains

Answer 50

-DBD (bzip): binding -Activation domain (Q1 and2): interact with TFs -protein interaction domain (KID): histone acetyltransferases

Question 51

TBP TATA binding protein

Answer 51

B-sheet -MINOR GROOVE -bends TATA box -binding directs assembly of initiation complex

Question 52

Steroid nuclear receptors

Answer 52

-bind steroid then bind to DNA to activate transcription -DBD-hinge-LBD