metabolic biochemistry bibc 102 summer 2005. lecture 1 august 1, 2005 lehninger (4 th edition),...

Metabolic Biochemistry

BIBC 102

Summer 2005

Lecture 1

• August 1, 2005

• Lehninger (4th Edition), Chapter 3, 4, 6

Figure 4.2b

Figure 4.4a,b

Figure 4.4c

Figure 4.4d

Box 4-1

Figure 4.7a

Figure 4.7b

Figure 4.16sperm whale myoglobin

hydrophobic side chains in blue

space filling model with atoms represented as spheres with van der Waals radii

Figure 4.23a deoxy-hemoglobin

Figure 4.24b

Macromolecular Museum

KEGG

Kyoto Encyclopedia of Genes and Genomes

OMIMOnline Mendelian Inheritance in Man

Chapter 6

ENZYMES

Enzymes are catalysts: speed up the reaction

Enzymes have exquisite specificity:

a) selection of substrates (chemical nature, stereochemistry)

b) nature of the reaction catalyzed

Enzyme activity can be regulated

Apoenzyme

+

Co-enzymeCo-factorProsthetic groupMetal ion(s)

Active enzyme

The enzyme chymotrypsin with its active site and its substrate (red)

LNC 6-1

LNC 6-4

Dihydrofolate reductase with the substrates tetrahydrofolate (yellow)and NADP + (red)

EC3.4.17.1: hydrolase - peptidase (subclass) - metallocarboxypeptidase (sub-subclass) -

arbitrary assigned serial number

NOMENCLATURE

page from KEGG Metabolic Chart

Regulation of enzyme activity

1. At the level of gene expression and protein turnover

2. By covalent modifications of side chains

3. By binding of small molecules (ligands) that are not substrates

4.

allosteric mechanisms in multisubunit enzymes

ENZYME KINETICS

LNC Chapter 6

REACTANTS

SUBSTRATESPRODUCTS

kFirst order reactions: A P

kSecond order reactions: A + B P

1st order: ln[A] = ln[Ao] - kt or [A] = [Ao] exp(-kt)

2nd order: 1/[A] = 1/[Ao] + kt

TRANSITION STATE THEORY

A C

B D

A C

B D

A C

B D

A catalyst serves in at least two ways:it binds and aligns the substratesit facilitates the redistribution of electrons (charges)

• End of Lecture 1

• August 1, 2005