kulbiokim2006b1

8/3/2019 KulBiokim2006B1

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BIOKIMIAProf. Sabirin MatsjehProf. Prapto YudonoDr. Ngadiman

Dr. Donny Widianto


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Jadual & SAP

No. Topik Kuliah Tanggal Dosen

1. Pendahuluan :- Konsep dasar biokimia- Reaksi-reaksi biokimia

29-08-2006 Prof. Prapto Yudono

2. Air dan Buffer 05-09-2006 Prof. Sabirin Matsjeh3. Karbohidrat I

- Tinjauan umum

- Monosakarida- Disakarida- Polisakarida


4. Karbohidrat II- Reaksi monosakarida- Ikatan glikosida- Fungsi karbohidrat


5. Asam Amino dan Protein I- Tinjauan umum- Asam Amino- Biosintesis asam amino

26-09-2006 Prof. Sabirin Matsjeh

6. Asam Amino dan Protein II- Peptida

- Struktur protein- Fungsi asam amino dan protein- Biosintesis protein

03-10-2006 Prof. Sabirin Matsjeh


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Jadual & SAP

No. Topik Kuliah Tanggal Dosen

7. Ujian Sisipan Jadual Fak. Topik 1 s/d 6

8. Lipida I- Tinjauan umum- Asam lemak jenuh & tak jenuh- Reaksi asam lemak

07-11-2006 Dr. Ngadiman

9.Lipida II- Fungsi asam lemak dan lipid- Biosintesis asam lemak


10. Asam nukleat I- Tinjauan umum- Nukleosida dan nukleotida

21-11-2006 Dr. Donny Widianto

11. Asam nukleat II

- Struktur DNA dan RNA- Informasi genetik


12. Enzim- Tinjauan umum- Klassifikasi enzim- Koenzim dan kofaktor- Mekanisme dan kinetika kerja enzim

- Penghambatan



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Jadual & SAP

No. Topik Kuliah Tanggal Dosen13. Metabolisme I

- Tinjauan umum- Jalur metabolisme


14. Metabolisme II- Bioenergetika- Kontrol metabolisme


15. Ujian Akhir Jadual Fak. Topik 8 s/d 14


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Buku Acuan

Trudy McKee and James McKee. 2003.Biochemistry: The Molecular Basis of Life.Third edition. McGraw-Hill, Boston.

Lehninger, Nelson, & Cox. 1997. Principles ofBiochemistry.2nd edition. Worth Publishers.

Albert L. Lehninger. 1995. Dasar-dasarBiokimia. (Alih bahasa: Maggy Thenawidjaja).Penerbit Erlangga, Jakarta.

David S. Page. 1995. Prinsip-prinsip Biokimia.Penerbit Unair, Surabaya.

Soeharsono. 1982. Biokimia I dan II. GadjahMada University Press, Yogyakarta.


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Penilaian

Total Nilai Ujian + Mid + Tugas dari 4 dosen dibagi 4(Rata-rata dari Nilai Dosen I + II + III + IV)

PengharkatanA : > 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


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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


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Tujuan Perkuliahan

Mengenalkan dan memahamkanbahasa biokimia : Kosakata (istilah danstruktur kimia), tatabahasa (reaksi-

reaksi kimia), struktur kalimat (Jalurmetabolisme) dan arti (keterkaitan

metabolik)


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What is biochemistry?

Definition: Websters dictionary: Bios = Greek,

meaning life The chemistry of living

organisms; the chemistry of the processesincidental to, and characteristic of, life.

WebNet dictionary: Biochemistry is theorganic chemistry of compounds and

processes occuring in organisms; the effortto understand biology within the context ofchemistry.


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What is biochemistry?

Understanding biological forms andfunctions in chemical terms Biochemistry aims to understand how

the lifeless molecules interact tomake the complexity and efficiency of

the life phenomena and to explain the

diverse forms of life in unifyingchemical terms.


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Issues addressed by biochemistry

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

and expressed?


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History of Biochemistry First to reveal the chemical composition of living organisms.

The six principleelements for lifeare: C, H, N, O,P, and S.

The biologically mostabundant elements are onlyminor constituents of theearths crust (which

contains 47% O, 28% Si,7.9% Al, 4.5% Fe, and 3.5%

Ca).

99% of a cell is made of H, O, N, and C

Element # unpaired es Fractional amount

H 1 2/3

O 2 1/4

N 3 1/70

C 4 1/10


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

The lightest elements form thestrongest bonds in general.


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History of Biochemistry

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

Amino Acids

Nucleotides

Carbohydrates

Lipids


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


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Relationship betweenBiochemistry and other subjects

Organic chemistry, which describes theproperties 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 formaintenance of health.

R l ti hi b t


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Relationship betweenBiochemistry and other subjects

Microbiology, which has shown that single-celledorganisms and viruses are ideally suited for theelucidation of many metabolic pathways andregulatory mechanisms.

Physiology, which investigates life processes atthe 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.


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(1) ENERGY, which it

must know how to:

Extract

Transform

Utilize

Life needs 3 things:


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Life needs 3 things:

(2) SIMPLE MOLECULES,

which it must know how to:

Convert

Polymerize Degrade


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(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

T i k #1 Lif h i l


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Trick #1: Life uses chemicalcoupling to drive otherwiseunfavorable reactions

Trick #2: Life uses enzymes to


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Trick #2: Life uses enzymes tospeed up otherwise slowreactions


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How does an enzyme do it,

thermodynamically?


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How does an enzyme do it,

mechanistically?


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The Versatile Carbon Atom is the

Backbone of Life

Chemical Isomers


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Chemical IsomersInterconversion requiresbreaking covalent bonds

Stereoisomers:


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Stereoisomers:Chemically identicalBiologically different!

Stereoisomers:


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Stereoisomers:Chemically identicalBiologically different!

Biochemical Transformations


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Biochemical TransformationsFall into Five Main Groups

Group transfer reactions Oxidation-reduction reactions

Rearrangements(isomerizations)

Cleavage reactions

Condensation reactions


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BiomoleculesStructure

Building block

Simple sugar

Amino acid

Nucleotide

Fatty acid

Macromolecule

Polysaccharide Protein (peptide)

RNA or DNA

Lipid

Anabolic

Catabolic


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Biosynthesis

Requires

Simple

Molecules to

Combine

Covalently in

Many Ways


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1. Relative electronegativities of the two atoms

O 3.5

Cl 3.0

N 3.0

C 2.5

P 2.1

H 2.1

Na 0.9

K 0.8

Bond strength includes dependence on

High electronegativity = High affinity for electrons


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2. The number of bonding electrons

C B d


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Common BondStrengths

Approx. Avg.

Triple: 820 kJ/mole

Double: 610 kJ/mole

Single: 350 kJ/mole

Common Functional


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Common FunctionalGroups


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ImportantBiological

Nucleophiles:

Electron-rich

functional

groups


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In summary

Tetrahedral carbon has versatilebonding properties

Compounds with many atoms mayexist in many isomeric forms

Interconversion requires breaking

chemical bonds Large molecules are built from small

ones by making new chemical bonds

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