BIOKIMIA

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BIOKIMIA

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

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Jadual SAP
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Jadual SAP
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Jadual SAP
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Buku Acuan

• John Moore and Richard Langley. 2008.Biochemistry
  for Dummies. (soft copy available)
• David L. Nelson and Michael M. Cox.
  2004.Lehninger Principles of Biochemistry. W.H.
  Freeman Co. (soft copy available)
• Jeremy M. Berg, John L. Tymoczko, and Lubert
  Stryer. 2002. Biochemistry. W.H. Freeman Co.
  (soft copy available)
• Trudy McKee and James McKee. 2003. Biochemistry
  The Molecular Basis of Life. Third edition.
  McGraw-Hill, Boston.
• 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

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Penilaian

• Total Nilai Ujian Mid Tugas dari 4 dosen
  dibagi 4
• (Rata-rata dari Nilai Dosen I II III IV)
• Pengharkatan
• A gt rata-rata kelas 1,5 x stdev
• B lt rata-rata kelas 1,5 x stdev
• gt rata-rata kelas 0,5 x stdev
• C lt rata-rata kelas 0,5 x stdev
• gt rata-rata kelas 0,5 x stdev
• D lt rata-rata kelas 0,5 x stdev
• gt rata-rata kelas 1,5 x stdev
• E lt 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 memahamkan bahasa biokimia
  Kosakata (istilah dan struktur kimia), tatabahasa
  (reaksi-reaksi kimia), struktur kalimat (Jalur
  metabolisme) 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 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.

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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.

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Features of Living Organisms

• A high degree of chemical complexity and
  microscopic organization
• Systems for extracting, transforming, and using
  energy from the environment
• A capacity for precise self-replication and
  self-assembly
• Mechanisms for sensing and responding to
  alterations in their surroundings
• Defined functions for each of their components
  and regulated interactions among them
• A history of evolutionary change

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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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Cellular Foundations
eukaryotes (Greek eu, true, and karyon,
nucleus)
prokaryotes (Greek pro, before)
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Three Distinct Domains of Life
Aerobic anaerobic
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Organisms Classification according to how they
obtain the energy and carbon
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The organic compounds from which most cellular
materials are constructed

• Amino Acids
• Nucleotides
• Carbohydrates
• Lipids

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Structural hierarchy in the molecular
organization of cells
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Molecular Bonds
Between monomeric subunits
covalent bonds - Protein - Poysacharides -
Polypeptides
Supramolecular complexes
noncovalent interactions - hydrogen bonds - ionic
interactions - hydrophobic interactions - van der
Waals interactions
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Chemical Foundations

• 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.
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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.
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Biomolecules Are Compounds of Carbon
Each carbon atom can form single bonds with up to
four other carbon atoms. Two carbon atoms also
can share two (or three) electron pairs, thus
forming double (or triple) bonds.
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The number of bonding electrons
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Geometry of carbon bonding
Free rotation around each single bond
Carbon atom are arranged tetrahedrally
Double bonds are shorter and do not allow free
rotation
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Common Functional Groups
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Several common functional groups in a single
biomolecule.
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Molecule structure
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Chemical IsomersInterconversion requires
breaking covalent bonds
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Stereoisomers Chemically identical
Biologically different!
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Stereoisomers Chemically identical
Biologically different!
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Interactions between Biomolecules Are
Stereospecific
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Physical Foundations
Living cells and organisms - must perform work
to stay alive and to reproduce themselves -
require the input of energy

• The Flow of Electrons Provides Energy for
  Organisms
• Oxidation reduction reactions
• one reactant is oxidized (loses electrons)
• as another is reduced (gains electrons)

The first law of thermodynamics in any physical
or chemical change, the total amount of energy in
the universe remains constant, although the form
of the energy may change
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Free Energy (G)
To bring about the synthesis of macromolecules
from their monomeric units, free energy (G) must
be supplied to the system (the cell). DG DH
TDS DG free energy change DH enthalpy
change (reflecting the kinds and numbers of
chemical bonds and noncovalent interactions
broken) T the absolute temperature (in degrees
Kelvin) DS enthropy change (describing the
change in the systems randomness) A
process tends to occur spontaneously only if G is
negative. Endergonic energy-requiring
reactions Exergonic Reactions that liberate
free energy
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Energy coupling
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enzymesbiocatalysts
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enzymesbiocatalysts
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The central role of ATP in metabolism
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Genetic Foundations

• Genetic information is encoded in the linear
  sequence of four deoxyribonucleotides in DNA
• The flow of information known as Central Dogma of
  Biology
• Replication Transcription - Translation

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DNA Replication
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Transcription
Translation
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Evolutionary Foundations
Role of mutation in evolution
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A possible RNA world scenario
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Landmarks in the evolution of life on Earth.
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Evolution of eukaryotes through endosymbiosis.
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END