Transcript Bab1-Biokimia-Pendahuluan

BIOKIMIA:
Pendahuluan
Prof. Dr.sc.agr. Ir. Suyadi, MS.
Tata Tertib Kuliah
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Tepat waktu, toleransi maks. 15 menit
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HP tidak diaktifkan
Hadir minimal 70%  boleh ujian
Paham bahasa Indonesia & Inggris
Baca salah satu / dua buku acuan
Pakaian rapi
Kerjakan Tugas, Mid, & Ujian
Ujian bisa lisan
Tujuan Perkuliahan
• Mengenalkan dan memahamkan dasar
biokimia : Kosakata (istilah dan struktur
kimia), tatabahasa (reaksi-reaksi kimia),
struktur kalimat (Jalur metabolisme) dan
arti (keterkaitan metabolik)
Buku Acuan
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Trudy McKee and James McKee. 2003. Biochemistry:
The Molecular Basis of Life. Third edition. McGraw-Hill,
Boston.
Lehninger, Nelson,
& Cox. 1997. Principles of
nd
Biochemistry.2 edition. Worth Publishers.
Albert L. Lehninger. 1995. Dasar-dasar Biokimia. (Alih
bahasa: Maggy Thenawidjaja). Penerbit Erlangga,
Jakarta.
Koolman J. dan K-H.Roehm. 1994. Atlas Berwarna dan
Teks BIOKIMIA (aliha bahasa: Inawati-Wanandi I, 2001).
Penerbit Hipokrates, Jakarta.
David S. Page. 1995. Prinsip-prinsip Biokimia. Penerbit
Unair, Surabaya.
Soeharsono. 1982. Biokimia I dan II. Gadjah Mada
University Press, Yogyakarta.
Ngili, Y. 2010. Biokimia Dasar. Penerbit Rekayasa,
Bandung.
Dari rumput menjadi daging dan susu
Fresh grass
hay
Silage
Dari pakan konsentrat menjadi daging dan telur
Dari makanan menjadi manusia
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.“
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-dimensional
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?
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First to reveal the chemical
composition of living organisms.
History of
Biochemistry
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
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
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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.
• Physiology: in relation with the all process of maco- and
micro molecules in cellular-, tissue or organ levels to
give an output
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:
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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
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Group transfer reactions
Oxidation-reduction reactions
Rearrangements (isomerizations)
Cleavage reactions
Condensation reactions
Biomolecules – Structure
Anabolic
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Building block
Simple sugar
Amino acid
Nucleotide
Fatty acid
Catabolic
• Macromolecule
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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
• P
2.1
3.0
• H
2.1
• Na
0.9
• K
0.8
3.0
2.5
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
TUGAS...!