Course Title: Biochemistry Credit units: 4 Instructors: All members of faculty from Department of Biochemistry Biochemistry can be defined as the science concerned with the chemical basis of life. Since cell is the structural unit of living systems, a

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Course Title BiochemistryCredit units
4Instructors All members of faculty from
Department of Biochemistry Biochemistry can be
defined as the science concerned with the
chemical basis of life. Since cell is the
structural unit of living systems, a functional
definition of biochemistry can be the science
concerning with the chemical constituents of
living cells and with the reactions and processes
that they undergo.
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Course Description This course seeks to
describe the structure, organization, and
functions of living matter in molecular terms.
Three principal areas will be covered (1) the
structural chemistry of the components of living
matter and the relationship of biological
function to chemical structure, (2) metabolism,
the chemical reactions that occurs in living
matter, and (3) molecular genetics which provides
introduction on how genetic material is
replicated, recombined and maintained, how the
genetic information is flowed from DNA to
protein, and how these processes are regulated.
The different subjects covered in this course
will be taught by different members of faculty
whose research interest is in line with the
covered subject. This course is offered as an
introductory course of biochemistry and is
intended for undergraduate students.Textbook
Lehninger, Principles of Biochemistry, 5th
edition, 2008Reference Harper, Biochemistry,
25th edition, 2000.
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????MD2010
Biochemistry (School year 2008) Date
Topics (Chapters) Instructor
2/24 1. Introduction (1-2)
??? 2/26 2. Amino Acids, Peptides,
and Proteins (3)(I) ?? 3/03 3. Amino Acids,
Peptides, and Proteins (3)(II) ?? 3/05 4. The
Three Dimensional Structure of Proteins(I) (4)
?? 3/10 5. The
Three Dimensional Structure of Proteins(II)
(4) ?? 3/12 6. Protein Function (5)
??? 3/17 7. Enzymes (I) (6)
??? 3/19 8. Enzymes (II) (6)
??? 3/24 9. Principles of Bioenergetics
(13) ??? 3/26 10.
Carbohydrates and Glycobiology (I) (7)
??? 3/31 11. Carbohydrates and
Glycobiology (II) (7)
??? 4/064/10 First Examination
??/???/??? 4/02 12. Nucleotides
and Nucleic Acids (8)
??? 4/07 13. Lipids (10)
??? 4/09 14. Biological Membrane and Transport
(I)(11) ??? 4/14 15. Biological
Membrane and Transport (II)(11)
??? 4/16 16. Glycolysis and the Catabolism of
Hexoses (14,15)
??? 4/21 17. The Citric Acid Cycle (16)
??? 4/23 18. Oxidative Phosphorylation
(19)
??? 4/28 19. Carbohydrate Biosynthesis (20)
??? 5/045/08 Second Examination
???/???
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4/30 20. Fatty Acid Catabolism (17)
??? 5/05 21. Lipid Biosynthesis(I)
(21) ??? 5/07 22. Lipid Biosynthesis(II)
(21) ??? 5/12 23. Amino Acid Catabolism
(18) ??? 5/14 24. Biosynthesis of Amino Acids
and Nucleotides (22)
??? 5/19 25. Integration of Metabolism
(23) ??? 5/255/29 Third Examination
???/??? 5/21 26. Genes and
Chromosomes (24) ??? 5/26 27. DNA Metabolism
(I) (25) ??? ? 5/28 28.
DNA Metabolism (II) (25) ??? 6/02 29. RNA
Metabolism (26) ??? 6/04 30. Protein
Metabolism (27) ??? 6/09 31. Regulation of
Gene Expression (28) ??? 6/11 32. DNA-Based
Information Technologies (9) ??? 6/16 33.
Biosignaling(I) (12) ??? 6/18 34. Biosignaling
(II)(12) ??? 6/226/26 Final Examination
???/???/???
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Biochemistry is a Science Dealing with the
Chemistry of Living Matter

• We know quite well what is chemistry
• But what is living matter?
• Life is characterized by
• High degree of complexity
• Extraction, transformation, and systematic use of
  energy to create and maintain structures and to
  do work
• Ability to sense and respond to changes in
  surrounding
• A capacity for fairly precise self-replication
  while allowing enough change for evolution

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Life is Complex

• Living organisms have
• internal structures with defined functions
• large number of different compounds
• macromolecules that are capable of highly
  specific interactions

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Six Kingdoms of Life

• Living things are placed in kingdoms on the
  basis of similarities and differences at the
  organism, cellular, and molecular levels

Six kingdoms
Cellular organization Unicellular
prokaryote Unicellular prokaryote Unicellular
eukaryote Uni- or Multicellular
eukaryote Multicellular eukaryote Multicellular
eukaryote

• Archaea
• Bacteria
• Protista
• Fungi
• Plantae
• Animalia

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Cell The Universal Building Block

• Living organisms are made of cells
• Simplest living organisms are singe-celled
• Larger organisms consists many cells with
  different functions
• Not all the cells are the same

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Bacterial, Plant, and Animal Cells are Different

• The internal structure and properties of cells
  from organisms in different kingdoms are rather
  different

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Components of Bacterial Cell

• Structure Composition Function
• Cell wall Peptidoglycan Mechanical support
• Cell membrane Lipid protein Permeability
  barrier
• Nucleoid DNA protein Genetic information
• Ribosomes RNA protein Protein synthesis
• Pili Protein Adhesion, conjugation
• Flagella Protein Motility
• Cytoplasm Aqueous solution Site of metabolism

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Eukaryote Cells More Complexity

• Have nucleus by definition
• protection for DNA site of DNA metabolism
• selective import and export via nuclear membrane
  pores
• some cells become anuclear (red blood cells)
• Have membrane-enclosed organelles
• Mitochondria for energy in animals, plants and
  fungi
• Chloroplasts for energy in plant
• Lysosome for digestion of un-needed molecules
• Spatial separation of energy-yielding and energy
  consuming reactions helps cells to maintain
  homeostasis and stay away from equilibrium

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Cytoplasm and Cytoskeleton

• Cytoplasm is highly viscous solution where many
  reactions take place
• Cytoskeleton consists of microtubules, actin
  filaments, and intermediate filaments
• cell shape
• transport paths
• movement

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The three types of cytoskeletal filaments
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Chemical Foundations

• The four most abundant elements in living
  organisms are H, O, N, and C.
• Elements H, O, N, P, S are also common
• Metal ions (e.g. K, Na, Ca, Mg, Zn, Fe)
  play important roles in metabolism
• Together, about 30 elements are essential for
  life

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Biomolecules
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Biomolecules are compounds of carbon with a
variety of functional groups

• Cells contain a universal set of small molecules
  which include common amino acids, nucleotides,
  sugars and their phosphorylated derivatives, and
  mono-, di-, and tricarboxylic acids.
• Macromolecules are the major constituents of
  cells. The four major macromolecules are
  proteins, nucleic acids, polysaccharides and
  lipids.
• Three-dimensional structure is described by
  configuration and conformation. Stereoisomers and
  optical isomers have different biological
  properties.
• Interactions between biomolecules are specific.
  Macromolecules have unique binding pockets. Only
  certain molecules fit in well and can bind.

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