Part 1 : Structure and function of Enzymes

Ch1. An introduction to enzymes

1.1 What are enzymes

Enzymes : apoenzyme + cofactor holoenzyme

Cofactor(prosthetic group) : coenzyme(organic) metal(inorganic)

1.3 Classification

EC : Type of rxn
Types of enzymatic reactions

EC1 Oxidoreductase EC2 Transferase EC3 Hydrolase EC4 Lyase

EC5 Isomerase
EC6 Ligase

1) oxidoreductase
EC : 1 e- donor e- acceptor serial #

e- donor AH

Trivial names A

Oxidase(oxygenase), dehydrogenase
Reductase , hydrogenase

B e- acceptor

BH

<e- donor> 1. 2. 3. 4. 5. 6. Alcohol Carbonyl -CH-CHPrimary amine Secondary amine NADH or NADPH 1. 2.

<e- acceptor> NAD+ or NADP+ Fe3+

3.

O2

99. others

* Ex) CH3-CH-COOH OH

CH3-C-COOH O

NAD+ E.C. 1.1.1.27

NADH + H+

(S)-lactate : NAD+ oxidoreductase(lactate DHase)

2) transferase
EC : 2 group transfered serial #

1.

-CH3 -CH2OH -COOH

1.

1-carbon group

2. 3.

details of transfered group

2.
3. 4.

Aldehyde or ketone
Acyl Glycosyl

1. alcohol 2. carboxyl 3. nitrogenous

acceptor of phosphate

7. Phosphate

Trivial names 2.1.1.

2.1.2. 2.7. .
HO O OH OH OH OH

: methyltransferase
: hydroxymethyl transferase : phosphotransferase (kinase)
O
-O-P-O

O
OH

O OH OH OH

ATP E.C. 2.7.1. 1

ADP

ATP : D-hexose-6-phosphotransferase(hexokinase)

3) Hydrolase
1. carboxyesterase thioseterase phosphoesterase

EC :

3 substrate

1. 2. 3.

esterase glycosidase peptidase

2. 3.

4) Lyase

EC :

1. 2.

C-C C-O C-N C-S

1. 2.

carboxyl aldehyde

type of group removed 3. bond broken 4.

3.

Ketoacid(-C-COOH) O

5) Isomerase EC :

5 Substrate
1.Amino acids 2.Hydroxy acids 3.carbohydrates

1. 2. 3. 4.

Type of reaction Racemization or epimerization cis-trans isomerization Intramolecular oxidoreductase Intramolecular transfer reaction

6) Ligase (synthetase): enzymes catalyzing the joining of two molecules with concomittant hydropysis of pyrophosphate bond in ATP or similar triphosphate. EC : 6 1. 2. C-O C-S C-N C-C

Description of bond being formed

Type bond synthesized

3. 4.

3.1. acid-ammonia(-CO-NH2) 3.2. acid-amino acid (-CO-NH-)

Homework 1-1 enzyme EC # ?

COOH

+ O2

COOH
O OH

Ch2. The structure of proteins

2.1 ~ 2.2
HOOC NH 2
S S H2N HOOC NH 2

:N

NH
COOH

Cystine

cf. cysteine

2.3 The basis of protein structure Primary (1) Secondary (2) Tertiary (3)

Quaternary (4)
cf. 3-dimensional structure

2.4 The determination of primary structure

cf. ninhydrin test (ninhydrin reaction)
O

R
OH

NH2-CH-COOH

OH O

+
OH

RCHO + CO2

Purple color

max = 570 nm (max = 440 nm for pro)

yellow

2.5 X-ray crystallography

2.5.1 Principle 1) Crystal lattice and Bragg condition

d1

d1 + d2 = d sin + d sin = n = 2d sin = n intensity

R B d2 d

2) Phase problem

Theoretical model building Isomorphous replacement

intensity phase Fourier Transformation

electron density map

2.5.2 Some result of X-ray crystallography

peptide bond -helix

-plated sheet

1 O 3 N
H

6 N
H7

9 N
H 10

10

11

12 N
H 13

13

14

15 N
H 16

16

Helix nomenclature
nm n : # of residue per helical turn m : # atoms, including H, in the ring that is closed by the hydrogen bond Residue of H-bond NH 2 3 4 5 n 2.2 3 3.6 4.4 nm 2.2 7 3 10 3.6 13 4.4 16 2.27 ribbon 310-helix -helix -helix

-keratin : right-hand -helix collagen : left-hand -helix

-helix

2.6 Protein structure in solution

spectrophotometry

Spectroscopy
spectrofluorometry

ESR

NMR Homework1-2 Pb 2.1 & Pb 2.2