Course
Code
Credit hours
Lecture
Lecturer
:
:
:
:
:
BIOCHEMISTRY
SY10102
2
2 h/week
Associate Prof. Dr. Jualang Azlan Gansau and Mr. Wilson Yong Thau Lym
Synopsis
The course is designed to review the biochemistry of the fundamental cellular components underlying the
mechanism of life. The physio-chemical characteristics of biomolecules and the role of proteins, lipids,
carbohydrates, and nucleic acids in cells function will be considered. Enzymology, especially enzyme
kinetics (including enzyme inhibition and activation) and the effect of cofactors and coenzymes (vitamins)
will be discussed. Bioenergetics, especially the structure of the mitochondrion, tricarbocyclic acid cycle,
electron transport and oxidative phosphorylation as well as photosynthesis will be explained briefly.
Essential pathways of intermediary metabolism such as glycolysis, glycogenesis, glycogenolysis,
gluconeogenesis, hexose monoposphate shunt, -oxiadation of fatty acids, lipogenesis, catabolism of
ketogenic and glycogenic amino acids and the urea cycle will be considered. Chemistry as well as the
roles of DNA and RNA in protein biosynthesis will also be discussed.
Assessments
Quiz
Mid semester exam
Final exam
: 15%
: 40%
: 45%
Course Contents
Week
1
2
3
Lecture Topics
Introduction, Synopsis.
Biochemistry and organization of cells
a. Biomolecules
b. Origin of life
c. Prokaryotes and eukaryotes
d. Five kingdoms
e. Commond ground for all cells
f. How cells use energy
Water:
a.
b.
c.
d.
e.
f.
The solvent for biochemical reactions
The polar nature of the water molecule
H-bond
Acids and bases
Self-dissociation of water and pH scale
Titration curves
Buffers
Amino
a.
b.
c.
d.
e.
f.
g.
Acid and Peptides
Amino acids: general formula and 3-D structure
The structure and properties of amino acids
Titration curve of the amino acids
The peptide bond
Small peptides and physiological interest
The anabolism of amino acids
Essential amino acids
3-D Structure of Proteins
a. The structure of proteins determines their function
b. Primary structure
c. Secondary structure
d. Tertiary structure
e. Quaternary structure
Protein
a.
b.
c.
d.
4
Remarks
JAG
WYTL
WYTL
(Quiz)
Purification and Characterization Techniques
Purification
Column chromatography
Electrophoresis
Determining the primary structure of a protein
Enzymes
a. As biological catalysts
b. Catalysis: kinetics, thermodynamic reactions
c. Enzyme kinetics
d. Formation of enzyme-substrate complex (1st step in enzymatic
reaction)
e. The Michaelis-Menten approach of enzyme kinetics
f. Inihihition of enzymatic reaction
g. Allosteric enzyme
h. Zymogens
i. Active site event in enzyme
WYTL
j.
k.
Lipids
a.
b.
c.
d.
e.
f.
g.
h.
5
6
7
8
9
Type of catalytic mechanisms
Active site and transition states
Definition of lipid
Chemical nature of the lipid type
The nature of biological membranes
Membrane proteins
The Fluid Mosaic model of membrane structure
Membrane function
Lipid-soluble vitamins
Postaglandins and leukotrienes
Lipid Metabolism
a. Lipid digestion, absorption and transport
b. Fatty acid oxidation
c. Ketone bodies
d. Fatty acid biosynthesis
e. Regulation of fatty acid metabolism
f. Membrane lipid synthesis
g. Cholesterol metabolism
Amino
a.
b.
c.
d.
e.
f.
g.
Acid Metabolism
Intercellular protein degradation
Amino acid deamination
The urea cycle
Brakedown of amino acids
Amino acid biosynthesis
Othe product of amino acids metabolism
Nitrogen fixation
Mid-Term Exam
MID-SEMESTER BREAK
Nucleic Acids
a. Level structure of in nucleic acids
b. The covalent structure of polynucleotides
c. The structure of DNA
d. Denaturation of DNA
e. The principles kinds of RNA and their structure
Nucleic Acid Replication
a. The flow of genetic information in the cell
b. DNA replication
c. DNA polymerase reaction
d. Proofreading and repair
e. DNA replication in Eukaryotes
Transcription of the Genetic Code: The Biosynthesis of RNA
a. Transcription in prokaryotes
b. Regulation of transcriptions in prokaryotes
c. Transcription in eukaryotes
d. Regulation of transcriptions in eukaryotes
e. Post-transcription modification of RNA
f. Ribozymes: RNA as an enzyme
WYTL
(Quiz)
WYTL
WYTL
JAG
10
Protein
a.
b.
c.
d.
e.
f.
g.
h.
i.
j.
k.
l.
Synthesis: Translation of the Genetic Message
The process of translating the genetic message
The genetic code
Amino acid activation
Translation in prokaryotes
Translation in eukaryotes
Post-translation modification of proteins
Protein degradation
Methods for working with nucleic acids
Recombinant DNA and cloning
PCR
DNA libraries
DNA fingerprinting
JAG
(Quiz)
The Importance of Energy Change and Electron Transfer in Metabolism
a. Energy and change
b. The criterion and spontaneity
c. Std states and std free energy change
d. Thermodynamics
e. The nature of metabolism (oxidation and reduction)
f. The role of CoA
11
12
13
Carbohydrates
a. Structure and stereochemistry
b. Monosaccharide
c. Oligosaccharides
d. Polysaccharides
e. Glycoproteins
f. Reaction of monosaccharide
Glycolysis
a. Overview
b. The reaction of glycolysis
c. Anaerobic reactions of pyruvate
d. Energy consideration in glycolysis
e. Control of glycolysis
f. Metabolism of hexoses other than glucose
g. The pentose phosphate pathway
Glycogen Metabolism and Gluconeogenesis
a. Glycogen breakdown
b. Glycogen synthesis
c. Control of glycogen metabolism
d. Gluconeogenesis
e. Other carbohydrates biosynthetic pathways
The Citric Acid Cycle
a. The role of the CAC in metabolism
b. Overview
c. Energetics and control of the CAC
d. The glyoxylate cycle
e. CAC catabolism
f. CAC anabolism
JAG
JAG
(Quiz)
JAG
15
Electron Transport and Oxidative Phosporylation
a. The role of electron transport in metabolism
b. Mechanism
Photosynthesis
a. Chloroplast and chlorophyll
b. The light reaction
c. The dark reaction
d. An alternative pathway for carbon fixation
Final Exam
JAG
(Quiz)
JAG
References
Campbell and Farrell’s. Biochemistry 5th Edition. The Thomson Corp.
Alberts, B., Bray, D., Lewis, J., Raff, M.m Roberts, K., Watson, J 1994. Molecular Biology of the Cell.
3rd Edition, Garland Publishing Inc.
Conn, E. E., Stumpf, P.K., Bruening, G., Doi, R.H. 1995. Asas Biokimia. Dewan Bahasan dan Pustaka,
Kuala Lumpur.
Lehninger, A.L., Nelson, D.L. Cox, M. M. 1993. Principles of Biochemistry 2nd Edu. Worth Publisher.
Voet, D., Voet., J. G 1997. Biochemistry John Wiley and Sons, New York.
Zubay, G.L., Parson, W.W., Vance, D.E.
1995. Principles of Biochemistry., W.C. Brown Publisher,
United Kindgom.