Download BIOKIMIA

BIOKIMIA: Pendahuluan
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
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.
Tata Tertib Kuliah
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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:
– 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-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
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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
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.
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
• 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