BIOKIMIA

Prof. Sabirin Matsjeh Prof. Prapto Yudono Dr. Ngadiman Dr. Donny Widianto

Jadual & SAP

No. Topik Kuliah Pendahuluan : 1. - Konsep dasar biokimia - Reaksi-reaksi biokimia 2. Tanggal 29-08-2006 05-09-2006 Dosen Prof. Prapto Yudono Prof. Sabirin Matsjeh

3.

4.

5.

6.

Air dan Buffer Karbohidrat I - Tinjauan umum - Monosakarida - Disakarida - Polisakarida Karbohidrat II - Reaksi monosakarida - Ikatan glikosida - Fungsi karbohidrat Asam Amino dan Protein I - Tinjauan umum - Asam Amino - Biosintesis asam amino Asam Amino dan Protein II - Peptida - Struktur protein - Fungsi asam amino dan protein - Biosintesis protein

12-09-2006

Prof. Prapto Yudono

19-09-2006

Prof. Prapto Yudono

26-09-2006

Prof. Sabirin Matsjeh

03-10-2006

Prof. Sabirin Matsjeh

Jadual & SAP

No. Topik Kuliah Ujian Sisipan 7. 8. Tanggal Jadual Fak. 07-11-2006 Dosen Topik 1 s/d 6 Dr. Ngadiman Lipida I - Tinjauan umum - Asam lemak jenuh & tak jenuh - Reaksi asam lemak Lipida II - Fungsi asam lemak dan lipid - Biosintesis asam lemak Asam nukleat I - Tinjauan umum - Nukleosida dan nukleotida Asam nukleat II - Struktur DNA dan RNA - Informasi genetik

9. 10. 11. 12.

14-11-2006 21-11-2006 28-11-2006

Dr. Ngadiman Dr. Donny Widianto Dr. Donny Widianto Dr. Donny Widianto

Enzim 05-12-2006 - Tinjauan umum - Klassifikasi enzim - Koenzim dan kofaktor - Mekanisme dan kinetika kerja enzim - Penghambatan

Jadual & SAP

No. Topik Kuliah 13. Metabolisme I - Tinjauan umum - Jalur metabolisme 14. Metabolisme II - Bioenergetika - Kontrol metabolisme 15. Ujian Akhir Tanggal Dosen

12-12-2006
19-12-2006 Jadual Fak.

Dr. Ngadiman
Dr. Ngadiman Topik 8 s/d 14

Buku Acuan
Trudy McKee and James McKee. 2003. Biochemistry: The Molecular Basis of Life. Third edition. McGraw-Hill, Boston. Lehninger, Nelson, & Cox. 1997. Principles of Biochemistry.2nd edition. Worth Publishers. Albert L. Lehninger. 1995. Dasar-dasar Biokimia. (Alih bahasa: Maggy Thenawidjaja). Penerbit Erlangga, Jakarta. David S. Page. 1995. Prinsip-prinsip Biokimia. Penerbit Unair, Surabaya. Soeharsono. 1982. Biokimia I dan II. Gadjah Mada University Press, Yogyakarta.

Penilaian
Total Nilai Ujian + Mid + Tugas dari 4 dosen dibagi 4 (Rata-rata dari Nilai Dosen I + II + III + IV) Pengharkatan A : > rata-rata kelas + 1,5 x stdev B : < rata-rata kelas + 1,5 x stdev & > rata-rata kelas + 0,5 x stdev C : < rata-rata kelas + 0,5 x stdev & > rata-rata kelas 0,5 x stdev D : < rata-rata kelas 0,5 x stdev & > rata-rata kelas 1,5 x stdev E : < rata-rata kelas 1,5 x stdev

Tata Tertib Kuliah

Tepat waktu, toleransi maks. 15 menit Tidak Berisik HP tidak diaktifkan Hadir minimal 70% Paham bahasa Indonesia & Inggris Baca salah satu / dua buku acuan Kerjakan Tugas, Mid, & Ujian

Tujuan Perkuliahan
Mengenalkan dan memahamkan bahasa biokimia : Kosakata (istilah dan struktur kimia), tatabahasa (reaksireaksi kimia), struktur kalimat (Jalur metabolisme) dan arti (keterkaitan metabolik)

What is biochemistry?
Definition:
Websters dictionary: Bios = Greek, meaning life The chemistry of living organisms; the chemistry of the processes incidental to, and characteristic of, life. WebNet dictionary: Biochemistry is the organic chemistry of compounds and processes occuring in organisms; the effort to understand biology within the context of chemistry.

What is biochemistry?
Understanding biological forms and functions in chemical terms Biochemistry aims to understand how the lifeless molecules interact to make the complexity and efficiency of the life phenomena and to explain the diverse forms of life in unifying chemical terms.

Issues addressed by biochemistry

What are the chemical and three-deminsional structure of biomolecules? How do biomolecules interact with each other? How does the cell synthesize and degrade biomolecules? How is energy conserved and used by the cell? What are the mechanisms for organizing biomolecules and coordinating their activities? How is genetic information stored, transmitted,

and expressed?

History of Biochemistry
First to reveal the chemical composition of living organisms. The biologically most abundant elements are only minor constituents of the earths crust (which contains 47% O, 28% Si, 7.9% Al, 4.5% Fe, and 3.5% Ca).

The six principle elements for life are: C, H, N, O, P, and S.

99% of a cell is made of H, O, N, and C Element H O N # unpaired es 1 2 3 Fractional amount 2/3 1/4 1/70

1/10

Most of the elements in living matter have relatively low atomic numbers; H, O, N and C are the lightest elements capable of forming one, two, three and four bonds, respectively.

The lightest elements form the strongest bonds in general.

History of Biochemistry
Then to identify the types of molecules found in living organisms.

Amino Acids

Nucleotides Carbohydrates Lipids

History of Biochemistry
Then to understand how the biomolecules make life to be life.

Relationship between Biochemistry and other subjects

Organic chemistry, which describes the properties of biomolecules. Biophysics, which applies the techniques of physics to study the structures of biomolecules. Medical research, which increasingly seeks to understand disease states in molecular terms. Nutrition, which has illuminated metabolism by describing the dietary requirements for maintenance of health.

Relationship between Biochemistry and other subjects

Microbiology, which has shown that single-celled organisms and viruses are ideally suited for the elucidation of many metabolic pathways and regulatory mechanisms. Physiology, which investigates life processes at the tissue and organism levels. Cell biology, which describes the biochemical division of labor within a cell. Genetics, which describes mechanisms that give a particular cell or organism its biochemical identity.

Life needs 3 things:

(1) ENERGY, which it must know how to:

Extract Transform Utilize

Life needs 3 things: (2) SIMPLE MOLECULES, which it must know how to:

Convert Polymerize Degrade

(3) CHEMICAL MECHANISMS, to:

Harness energy Drive sequential chemical reactions Synthesize & degrade macromolecules Maintain a dynamic steady state Self-assemble complex structures Replicate accurately & efficiently Maintain biochemical order vs outside

Trick #1: Life uses chemical coupling to drive otherwise unfavorable reactions

Trick #2: Life uses enzymes to speed up otherwise slow reactions

How does an enzyme do it, thermodynamically?

How does an enzyme do it, mechanistically?

The Versatile Carbon Atom is the Backbone of Life

Chemical Isomers Interconversion requires breaking covalent bonds

Stereoisomers: Chemically identical Biologically different!

Stereoisomers: Chemically identical Biologically different!

Biochemical Transformations Fall into Five Main Groups

Group transfer reactions Oxidation-reduction reactions Rearrangements (isomerizations) Cleavage reactions Condensation reactions

Biomolecules Structure
Anabolic

Building block Simple sugar Amino acid Nucleotide Fatty acid

Catabolic

Macromolecule
Polysaccharide Protein (peptide) RNA or DNA Lipid

Biosynthesis Requires Simple Molecules to Combine Covalently in Many Ways

Bond strength includes dependence on

1. Relative electronegativities of the two atoms
High electronegativity = High affinity for electrons

O Cl N C

3.5 3.0 3.0 2.5

P H Na K

2.1 2.1 0.9 0.8

2. The number of bonding electrons

Common Bond Strengths

Approx. Avg.
Triple: 820 kJ/mole

Double: 610 kJ/mole Single: 350 kJ/mole

Common Functional Groups

Important Biological Nucleophiles:

Electron-rich functional groups

In summary
Tetrahedral carbon has versatile bonding properties Compounds with many atoms may exist in many isomeric forms Interconversion requires breaking chemical bonds Large molecules are built from small ones by making new chemical bonds