Lecture 9- Substrate binding

Question 1

Nucleophilic substitution

Answer 1

Swap functional groups

Question 2

Nucleophilic addition

Answer 2

Add functional groups

Question 3

Carbonyl condensation

Answer 3

Change # of carbons

Question 4

Elimination

Answer 4

Change (increase) bond order

Question 5

Oxidation-reduction

Answer 5

Move electrons

Question 6

Oxidoreductases

Answer 6

Oxidation-reduction;

-Move electrons

Question 7

Transferases

Answer 7

Move functional group (group transfer); PHOSPHATE and METHYL GROUP

Question 8

Hydrolases

Answer 8

Hydrolysis reactions (transfer of functional groups to water)

Question 9

Lysases

Answer 9

Addition or removal of groups to form double bonds

Question 10

Isomerases

Answer 10

Isomerization (intramolecular group transfer)

Question 11

Ligases

Answer 11

Ligation of two substrates at the expense of ATP hydrolysis

Question 12

Oxidoreductases activated carriers/coenzymes

Answer 12

NADH, NADPH, FADH2, FMNH2

Question 13

NADH, NADPH building blocks

Answer 13

[Oxidoreductases]
Building blocks: Vitamin B3** and Adenine;
Carrying a single electron (follow the H)

Question 14

In CATABOLIC reactions, dehydrogenases do what to their substrate and use what

Answer 14

Oxidize, NAD+

Question 15

In ANABOLIC reactions, dehydrogenases do what to their substrate and use what

Answer 15

Reduce, NADPH

Question 16

Transferases activated carriers/coenzymes

Answer 16

ATP, Pyridoxal phosphate (moves phosphate/ Vitamin B6), SAM**, Tetrahydrofolate, 5’deoxyadenosylcobalamin

Question 17

Transferases ATP and pyridoxal phosphate

Answer 17

Transfers PHOSPHATE GROUP;

Building blocks: Adenosine Triphosphate and Vitamin B6

Question 18

Transferases SAM**, Tetrahydrofolate, 5’-deoxyadenosylcobalamin

Answer 18

Transfer of METHYL group;
Building blocks: Methionine and Adenine
[Note: SAME is the primary methyl donor in cells]

Question 19

Adenosine Triphosphate

Answer 19

Usually the gamma-phosphate is removed, but the B+gamma phosphates can be removed as pyrophosphate

Question 20

Vitamin B6

Answer 20

Refers to 6 molecules:

Pyridoxine, pyridoxal and pyridoxine; plus their phosphate derivatives

Question 21

Vitamin 9

Answer 21

Glutamate derivative;
Forms of interest:
-Solid as Folic Acid
-Bioavailable after reduction as Tetrahydrofolate
-Donates a methyl from Methyltetrahydrofolate

Question 22

Vitamin B12

Answer 22

Can take many forms:
-Sold as Cyanocobalamin
-Metabolically active as 5’Deoxyadenosylcobalamin or Methylcobalamin
==> Unusual bc contains a metal (COBALT)

Question 23

FADH2, FMNH2 building blocks

Answer 23

Vitamin B2 (and Adenine)

Question 24

Hydrolases

Answer 24

BREAK a chemical bond by ADDING WATER across it (via hydrolysis)

Question 25

Isomerases

Answer 25

REARRANGE order of atoms in a molecule (isomerization)

Question 26

Lyases

Answer 26

BREAK chemical bond WITHOUT WATER

Question 27

Ligases

Answer 27

Paste two pieces together (MAKE chem bond), uses ATP

Question 28

Activators/coenzymes

Answer 28

TPP, CoASH, lipoamide, biotin

Question 29

TPP building blocks

Answer 29

``` Vitamin B1 (+2 phosphates); Also uses redox chemistry (can help oxidize substrates) ```

Question 30

CoASH (COenzyme A) building blocks

Answer 30

Vitamin B5 and Adenine

Question 31

Lipoamide building blocks

Answer 31

Fatty acid derivative and Lysine

Question 32

Biotin

Answer 32

(=Vitamin B7); +/- CO2 GROUP | Biotin + Lysine--> Biocytin the version found in enzymes

Question 33

Ag-Ab binding site

Answer 33

Target=Ag

Question 34

Receptor-ligand binding site

Answer 34

Target=ligand

Question 35

Enzyme-Substrate binding site

Answer 35

Target=substrate

Question 36

Apoenzymes

Answer 36

Incomplete, inactive, and lack cofactor/enzyme | - Coenzymes (Biotin, CoA, pyridoxal phosphate)

Question 37

Holoenzymes

Answer 37

Whole, active contain cofactor/enzyme | -Metals (Zn, Mg, K, Mn)

Question 38

KA

Answer 38

=1/KD - Affinity or association constant - Coming together

Question 39

KD

Answer 39

=1/KA - Dissociation constant - Breaking apart - Dissociation constant for ESn complex - Equal to the concentration of ligand where 1/2 the available binding sites are full - When the receptor is half-saturated**

Question 40

Measuring KD

Answer 40

Y= [S]/ KD + [S] <

Question 41

Possible values for Y (fractional saturation)

Answer 41

0

Question 42

Y=0

Answer 42

No ligand bound

Question 43

Y=1

Answer 43

Receptor is saturated

Question 44

Y=0.5

Answer 44

Receptor is half-saturated; | Note: definition of [S]=KD

Question 45

Y v [S] graph for

Answer 45

Hyperbolic curve

Question 46

Linear Plot (Scatchard Plot)

Answer 46

Slope: -1/KD Y-intercept: -1/KD X-intercept: [E]T

Question 47

Cooperativity

Answer 47

Binding of each subsequent (sites are no longer independent) ligand influences the affinity (strength of interaction) of the next ligand (each ligand influences the next) to bind an active site

Question 48

The "perfectly cooperative binder" (n>1)

Answer 48

"Angle sign"= Sn/KD +Sn | n= number of binding sites (aka nH or alphaH)

Question 49

Cooperative binder of n>1 graph

Answer 49

Slope is positive= (nH) | Y-intercept: log (1/KD)

Question 50

nH=1

Answer 50

No cooperatively (Sites are independent)

Question 51

nH>1

Answer 51

Positive cooperativity (Affinity increases)

Question 52

0 < nH <1 (decimal)

Answer 52

Negative cooperativity (Affinity decreases)