BIOKIMIA Osfar sjofjan

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

3 Tata Tertib Kuliah Tepat waktu, toleransi maks. 15 menit Tidak Berisik
HP tidak diaktifkan Hadir minimal 80% Paham bahasa Indonesia & Inggris Baca salah satu / dua buku acuan Kerjakan Tugas, Mid, & Ujian

4 RPKPS MTK BIOKIMIA Mtk ini akan membahas tentang sel sebagai unit dasar kehidupan (hewan dan tanaman), pengertian metabolisme, struktur dan fungsi protein dan enim, bioenergetika dan metabolisme karbohidrat dan lemak, biosintesis protein dan asam amino, struktur dan fungsi dan replikasi makromoolekul informasi genetik, biokimia komunikasi intraselulair dan ekstraselulair, biosintesis mineral dan vitain. Aplikasi Ilmu biokimia ternak menyiasai perubaan nutrisi dan lingkungan serta strategi produksi susu, telur dan daing serta olahannya.

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

6 Filosofi Pembelajaran
Menjelaskan, bukan mengindoktrinasi Menunjukkan hal yang perlu diketahui dan yang tidak perlu diketahui Menghargai pertanyaan tentang hal yang belum diketahui Mempelajari semua hal adalah tidak mungkin, tetapi yang lebih penting adalah mengorganisir hal yang kita ketahui agar dapat digunakan 29 Jan 2006

7 STRATEGI PERKULIAHAN / PRAKTIKUM
Metode perkuliahan akan banyak menggunakan ceramah dikombinasikan dengan metode diskusi dan tugas membuat makalah serta pengembangan softskill mahasiswa (komunikasi lisan, etika dan berpikir analitis)

8 STRATEGI PERKULIAHAN / PRAKTIKUM
Berbagai instruksi instruksional akan digunakan dalam perkuliahan tersebut yaitu membuat tugas terstruktur / makalah topik perkuliahan, mahasiswa mencari bahan dengan referensi terbaru yang dilampirkan bersamaan tugas terstruktur / makalah yang dikumpulkan pada tengah dan akhir semester sebagai salah satu komponen bobot penilaian

9 TUGAS Mahasiswa ditugaskan untuk membaca setiap bacaan perkuliahan sebelum perkuliahan dilaksanakan Tugas materi perkuliahan berikutnya diberikan tiap akhir pertemuan kuliah sebelumnya Tugas terstruktur berupa makalah dan dipresentasikan pada perkuliahan sesuai jadwal yang disepakati Tugas praktikum terdiri laporan sementara dan laporan akhir praktikum. Laporan sementara dikumpulkan tiap akhir praktikum, sedangkan laporan akhir dikumpulkan setelah semua materi praktikum selesai dilaksanakan

10 KRITERIA PENILAIAN Nilai diberikan terhadap mahasiswa apabila telah memenuhi ketentuan kehadiran kuliah yaitu 80% bagi mahasiswa baru dan 80% bagi mahasiswa mengulang Kehadiran Praktikum 100 % Pembobotan Penilaian (A,B+ … E) dilakukan menggunakan acuan Sesuai Buku Pedoman Pendidikan Fpt UB

11 MONEV MTK Biokimia Kuiz / Tugas Terstruktur : 10 % UTS : 30 %
Praktikum : 30 % UAS : 30 %

12 Staf Pengajar Prof. Dr. Ir Kusmartono
Prof. Dr. Ir. Suyadi, M.Agr.DSc. MS Dr. Ir. Osfar Sjofjan, M.Sc Dr. Ir. Gatot Ciptadi, DESS Dr. Ir. Eko Widodo, M.Agr.Sc. M.Sc Dr. Ir. Marjuki, M.Sc Dedes Armeningtiyas, S.Pt. MP Artharini Irsyammawati, S.Pt. MP Achadiah S.Pt. MP Rini Dwi Wahyuni, S.Pt. MP Firman Djaya, S.Pt. MP 29 Jan 2006

13 What is biochemistry? Definition:
Webster’s 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.“

14 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.

15 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?

16 History of Biochemistry
First to reveal the chemical composition of living organisms. The biologically most abundant elements are only minor constituents of the earth’s 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 # unpaired e’s Fractional amount H 1 2/3 O 2 1/4 N 3 1/70 C 4 1/10

17 The lightest elements form the strongest bonds in general.
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.

18 History of Biochemistry
Then to identify the types of molecules found in living organisms. Amino Acids Nucleotides Carbohydrates Lipids

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

20 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.

21 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.

22 (1) ENERGY, which it must know how to:
Life needs 3 things: (1) ENERGY, which it must know how to: Extract Transform Utilize

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

24 (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

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

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

27 How does an enzyme do it, thermodynamically?

28 How does an enzyme do it, mechanistically?

29 The Versatile Carbon Atom is the Backbone of Life

30 Chemical Isomers Interconversion requires breaking covalent bonds

31 Stereoisomers: Chemically identical Biologically different!

32 Stereoisomers: Chemically identical Biologically different!

33 Biochemical Transformations Fall into Five Main Groups
Group transfer reactions Oxidation-reduction reactions Rearrangements (isomerizations) Cleavage reactions Condensation reactions

34 Biomolecules – Structure
Anabolic Building block Simple sugar Amino acid Nucleotide Fatty acid Macromolecule Polysaccharide Protein (peptide) RNA or DNA Lipid Catabolic

35 Biosynthesis Requires Simple Molecules to Combine Covalently in Many Ways…

36 1. Relative electronegativities of the two atoms
Bond strength includes dependence on 1. Relative electronegativities of the two atoms High electronegativity = High affinity for electrons P 2.1 H 2.1 Na 0.9 K 0.8 O 3.5 Cl 3.0 N 3.0 C 2.5

37 2. The number of bonding electrons

38 Common Bond Strengths Approx. Avg. Triple: 820 kJ/mole
Double: kJ/mole Single: 350 kJ/mole

39 Common Functional Groups

40 Important Biological Nucleophiles: Electron-rich functional groups

41 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