Biochem Chapter 6

Front 1

Class of Enzymes

Back 1

1. Oxidoreductases
2. Transferases
3. Hydrolases
4. Lyases
5. Isomerases
6. Ligases

Front 2

prochiral

Back 2

molecules that can be converted from achiral to chiral in a single step

Front 3

multiple ___-_________ interactions between an enzyme and substrate are important & help confer the high degree of __________

Back 3

non-covalent; specificity

Front 4

Chemotrypsin

Back 4

proteolytic enzyme, a protease, a proteinse

-doesn't have a high specificity
*cleaves peptide, amine, and ester bonds

Front 5

sometimes enzymes need help in the form of ________

Back 5

cofactors

-expand the chemical repertoire of the enzymes
*repertoire = pieces that it knows

Front 6

Types of Cofactors

Back 6

1) Metal ions

2) Coenzymes
-cosubstrates & prosthetic groups

Front 7

Reaction of enzyme & cofactor

Back 7

apoenzyme (inactive) + cofacter <---> holoenzyme (active)

apoenzyme = enzyme by itself
holoenzyme = enzyme + cofactor

Front 8

Example of an Enzyme that uses NAD+/NADH

Back 8

NAD+/NADH = cofactor

alcohol dehydrogenase, ADH

ethanol + NAD+ --> Acetaldehyde + NADH + H+

Front 9

Isergonic

Back 9

Free energy (G) is the SAME before and after reaction

Front 10

What is the top of the "hill" in a reaction called?

Back 10

ephemeral transition state

Front 11

How do enzymes work?

Back 11

3 main strategies:

1) General acid-base catalysis
2) Covalent Catalysis
3) Metal-Ion Catalysis

Front 12

General Acid VS General Base

Back 12

Acid = donate proton

Base = accepts proton

Front 13

General Acid-Base Catalysis Enzymes assist in...

Back 13

the formation of the Enol form of a substrate molecule (from ketone the form)

**a proton is transferred between the enzyme and the substrate
**enzymes can use acid-catalysis, base catalysis, or both

Front 14

Residues that function as general acid catalysts

Back 14

Asp, Glu, His, Lys, Cys, Tyr, Arg

**7 AA's that have R values!

Front 15

What can dramatically affect the activity of General-Acid Base enzymes?

Back 15

pH; b/c their catalytic function depends on their state of protonation or deprotonation

-low rate, low pH
-high rate, ~physiological pH
-low rate, high pH

*temp too high = denature enzyme

Front 16

Covalent Catalysis occurs when

Back 16

a group on the enzyme temporarily becomes covalently linked to the substrate or part of the substrate/intermediate

*happens during formation of the transition state

Front 17

Protein groups that can act as covalent catalysts

Back 17

Ser, Tyr , Cys, Lys, His

*nucleophiles in their basic form

Front 18

Example of a Covalent Catalysis

Back 18

primary amine (RNH2) reacts with substrate to form intermediate = Schiff base (imine)

Front 19

Metal-Ion Catalysis

Back 19

mediates oxidation-reduction rxns or by promoting the reactivity of other groups in the enzyme's active site through electrostatic effects

1) Fe(II), Fe (III), Cu(II), Mn(II), & Co(II) usually catalytic
2) Na+, K+, Ca+ usually structural
3) Mg2+ and Zn2+ can be either catalytic or structural

Front 20

Chrymotrypsin uses..

Back 20

BOTH general acid-base and covalent catalysis

Front 21

Catalytic _____ of Chymotrypsin

Back 21

Triad

Asp 102, His 57, Ser195
*known as a serine protease b/c Ser essential for catalysis

*not next to eachother in sequence but next to eachother in space b/c way protein folds

Front 22

Enzyme Substrate interactions are maximized where?

Back 22

The Transition state

Front 23

mimicking the transition state leads to

Back 23

excellent inhibitors

Front 24

LBHBs

Back 24

low barrier hydrogen bonds

-Aspartate IS important in triad
-neither Asp or His own the H between them

*could test this w/ site directed mutagensis by changing D102A

Front 25

What are important when substrate is binding to enzyme?

Back 25

proximity and orientation

Front 26

Which two of these together will react the fastest?

intermolecular, intramolecular, unimolecular, and bimolecular.

Back 26

Intramolecular and unimolecular

Front 27

what do kinases do?

Back 27

transfer of phosphoryl groups: (PO3)2-

Front 28

What three proteins descended from the same common ancestor?

Back 28

Chymotripson, trypsin, and elastase

*have different specificity pockets

-dissimilar structures overall, but convergent (similar) active site architectures

Front 29

convergent evolution

Back 29

a phenomenon whereby unrelated proteins evolve similar characteristics (similar solution to common problems)

Front 30

what does the prefix pro- and suffix -ogen indicate?

Back 30

inactive precursor

Front 31

Activation of chymotrypsin

Back 31

Chymotrypsinogen (inactive) -1-> π chymotrypsin (active) -2-> δ chymotrypsin (active) -3-> α chemotrypsin (active)

1 trypsin cuts at Arg 15 and forms 1 active strip
2 chymotrypsin removes Ser14 Arg 15 segment
3 chymotrypsin removes Thr147 Asn148 segment

*2 & 3 are autoactivation steps

Front 32

α chemotrypsin

Back 32

three polypeptide sequence fold together and form active chymotrypsin structure

Front 33

Chymotrypsin and ________ have the same Asp-His-Ser active site and oxyanion hole

Back 33

Subtilisin

**these two have NO sequence similarities or overall structural similarity

Front 34

Clotting Cascade

Back 34

Prothrombin ---> Thrombin via Xa factor

Fibrinogen --> Fibrin via Thrombin (after it is produced in above rxn)

*Cross-linked Fibrin clots will be formed

Front 35

Dicoumarol and warfarin resemble ________ in structure?

Back 35

Vitamin K

Front 36

Where does out Vitamin K come from?

Back 36

bacteria in our gut make the Vit K we need

Front 37

The Gla domain of prothrombin contain a lot of

Back 37

Glu residues

Front 38

Dicoumarol and warfarin are

Back 38

anticoagulents

-dicoumarol in hay and warfarin used as arodenticide

-These compounds inhibit (prevent) Vit K form carrying out its role in the γ-carboxylation rxns of Glu residues in the Gla domain of prothrombin

-γ-carboxyglutamate residue now contains 2 carboxyl groups instead of 1

Front 39

γ-carboxyglutamate residues are

Back 39

bind to Ca2+ much better, which helps localize prothrombin to phospholipid membranes of blood platelets after injury, which brings prothrombin into close proximity to two proteins that activate it

Front 40

Where can Dicoumarol and warfarin be found?

Back 40

Dicoumarol = in hay; it is a derivitive of coumarin (which is responsible for the pleasant smell of freshly cut hay)

warfarin = rodenticide

Front 41

K. P. Link did what?

Back 41

the important of regulating or limiting protease activity

*ISOLATED dicoumarol and DEVELOPED warfarin which inhibit Vit K therefore prothrombin

Front 42

Catalyst

Back 42

substance that participates in the reaction yet emerges at the end in it's original form

-living systems use catalysts called ENZYMES to increase the rate of chemical reactions

Front 43

Most enzymes are

Back 43

PROTEINS

but few are made of RNA (ribozymes)

Front 44

active site

Back 44

the area (cleft) of an enzyme where hydrolysis of polypeptide substrates takes place

Front 45

isozymes

Back 45

Multiple enzymes catalyzing the same reaction

Front 46

Difference btwn enzymes and nonbiological catalysts?

Back 46

1. enzymes can act under mild conditions while chemical catalysts require extremely high temps and pressures for optimal performance

2. Specificity- most enzymes are highly specific for their substrates

3. Activities of enzymes are regulated so organism can respond to changing conditions or follow genetically determined developmental programs

Front 47

An enzyme lowers the height of the activation barrier by

Back 47

lowering the energy of the transition state

Front 48

Coenzymes

Back 48

organic molecules which may be derived from vitamins

1) cosubstrates = enter & exit the active site as substrates do

2) prosthetic groups = a tightly bound coenzyme that remains in the active site between reactions

Front 49

enzymes that use covalent catalysis undergo...

Back 49

a two-part reaction process, so the rxn coordinate diagram contains TWO activation barriers with the intermediate btwn them