KULIAH BIOKIMIA FAKULTAS KEDOKTERAN

UNIVERSITAS HASANUDDIN

STAFF PENGAJAR
1. Prof.Dr.Rosdiana Natzir.,PhD.,SpBiok.( Ketua)
2. Dr. Ika Yustisia.,MSc( Sekr.Bagian)
3. Dr.Nurdin Mappewali.,SpBiok.
4. Dr. Marhaen Hardjo.,PhD ( malaysia )
5. Dr. Andi BauDilam A..,MBSc ( Koord.Lab)
6. Dr.Sahrijuita.,Mkes.,Sp.THT.
7. Dr.I;hamuddin.,Msi. (Sekr.Biomed I )
8. DR.dr.Agnes K. ( purnabakti )
9. Dr. Yangki H (purnabakti).

Prentice Hall c2002 Chapter 1 1

 Principles of

BIOCHEMISTRY

2
 Introduction to Biochemistry

Adenovirus: Viruses consist of a nucleic

acid molecule surrounded by a protein coat

Prentice Hall c2002 Chapter 1 3

 1.1 Biochemistry Is a Modern Science

Urea was synthesized by heating the inorganic

compound ammonium cyanate (1828)
This showed that compounds found exclusively
in living organisms could be synthesized from
common inorganic substances

Prentice Hall c2002 Chapter 1 4

 Two notable breakthroughs in the
history of biochemistry

(1) Discovery of the role of enzymes as

catalysts
(2) Identification of nucleic acids as
information molecules

Flow of information: from nucleic acids to proteins

DNA RNA Protein

Prentice Hall c2002 Chapter 1 5

 1.2 The Chemical Elements of Life

Only six nonmetallic elements: oxygen, carbon,

hydrogen, nitrogen, phosphorous, and sulfur
account for >97% of the weight of most organisms
These elements can form stable covalent bonds
Water is a major component of cells
Carbon is more abundant in living organisms than
it is in the rest of the universe

Prentice Hall c2002 Chapter 1 6

 Fig 1.1 Periodic Table of the elements

Important elements found in living cells are

shown in color
The six abundant elements are in red
(CHNOPS)
Five essential ions are in purple
Trace elements are in dark blue (more
common) and light blue (less common)

Prentice Hall c2002 Chapter 1 7

Prentice Hall c2002 Chapter 1 8
 Functional groups in biochemistry

Functional groups - specific parts of molecules

involved in biochemical reactions
Figure 1.2 shows the general formulas of:
(a) Organic compounds
(b) Functional groups
(c) Linkages common in biochemistry
(R represents an alkyl group (CH3CH2)n-)
Prentice Hall c2002 Chapter 1 9
 Fig 1.2 (a) General formulas

Prentice Hall c2002 Chapter 1 10

 Fig 1.2(b) General Formulas

Prentice Hall c2002 Chapter 1 11

 Fig 1.2 (c) General Formulas

Prentice Hall c2002 Chapter 1 12

 1.3 Many Important Biomolecules
are Polymers

Biopolymers - macromolecules created by

joining many smaller organic molecules
(monomers)
Condensation reactions join monomers
(H2O is removed in the process)
Residue - each monomer in a chain

Prentice Hall c2002 Chapter 1 13

 Molecular mass

Molecular weight is more correctly termed the

relative molecular mass (Mr) - the molecular
mass relative to 1/12 mass of a carbon atom (12C)
Mr is a relative quantity and is dimensionless
A typical protein may have an Mr = 38,000
The absolute molecular mass of this protein =
38,000 daltons (1 dalton = 1 atomic mass unit)

Prentice Hall c2002 Chapter 1 14

 A. Proteins

Proteins are composed of 20 common amino acids

Each amino acid contains:
(1) Carboxylate group (-COO-)
(2) Amino group (-NH2)
(3) Side chain (R) unique to each amino acid

Prentice Hall c2002 Chapter 1 15

 Fig 1.3 Structure of an amino acid
and a dipeptide
(a) Amino group (blue), carboxylate group (red)
(b) Dipeptides are connected by peptide bonds

Prentice Hall c2002 Chapter 1 16

 Polypeptides

Polypeptides - amino acids joined end to end

Conformation - the three dimensional shape of
a protein which is determined by its sequence
Active site - a cleft or groove in an enzyme that
binds the substrates of a reaction

Prentice Hall c2002 Chapter 1 17

 Fig 1.4 Egg white lysozyme

(a) Free enzyme

(b) Enzyme, bound substrate in active site cleft

Prentice Hall c2002 Chapter 1 18

 B. Polysaccharides

Carbohydrates, or saccharides, are

composed primarily of C,H and O
Polysaccharides are composed of saccharide
monomers
Most sugar structures can be represented as
either linear (Fischer projection) or cyclic

Prentice Hall c2002 Chapter 1 19

 Fig 1.5 Representations of the
structure of ribose

Prentice Hall c2002 Chapter 1 20

 Fig 1.6 (a) Glucose, (b) Cellulose

Glycosidic bonds
connecting glucose
residues are in red

Prentice Hall c2002 Chapter 1 21

 C. Nucleic Acids

Polynucleotides - nucleic acid biopolymers

are composed of nucleotide monomers
Nucleotide monomers are composed of:
(1) A five-carbon sugar
(2) A heterocyclic nitrogenous base
(3) Phosphate group(s)

Prentice Hall c2002 Chapter 1 22

 Fig 1.7 Deoxyribose

Deoxyribose lacks a hydroxyl group at C-2.

It is the sugar found in DNA.

Prentice Hall c2002 Chapter 1 23

 Nitrogenous bases

Major Purines:
Adenine (A)
Guanine (G)
Major Pyrimidines
Cytosine (C)
Thymine (T)
Uracil (U)
Prentice Hall c2002 Chapter 1 24
 Fig 1.8 Adenosine Triphosphate (ATP)

Nitrogenous base (adenine), sugar (ribose)

Prentice Hall c2002 Chapter 1 25

 Fig 1.9 Structure of a dinucleotide

Residues
are joined
by a
phosphodi
ester
linkage

Prentice Hall c2002 Chapter 1 26

Fig 1.10 Short segment
of a DNA molecule

Two polynucleotides
associate to form a
double helix
Genetic information is
carried by the sequence
of base pairs

Prentice Hall c2002 Chapter 1 27

 D. Lipids and Membranes

Lipids are rich in carbon and hydrogen, but

contain little oxygen
Lipids are not soluble in water
Fatty acids are the simplest lipids: long chain
hydrocarbons, a carboxylate group at one end
Fatty acids are often components of
glycerophospholipids

Prentice Hall c2002 Chapter 1 28

Fig 1.11 Structures of (a) glycerol 3-phosphate, (b) a
glycerophospholipid

Prentice Hall c2002 Chapter 1 29

 Fig 1.12 Model of a membrane lipid

Hydrophilic (water-loving)
head interacts with H2O
Hydrophobic (water-
fearing) tail

Prentice Hall c2002 Chapter 1 30

Fig 1.13 Structure of a biological membrane

A lipid bilayer with associated proteins

Prentice Hall c2002 Chapter 1 31

 1.4 The Energetics of Life

Photosynthetic organisms capture sunlight

energy and use it to synthesize organic
compounds
Organic compounds provide energy for all
organisms

Prentice Hall c2002 Chapter 1 32

 Energy Flow

Prentice Hall c2002 Chapter 1 33

 Metabolism and energy

Metabolism - collection of reactions by

which organic compounds are synthesized
and degraded
Bioenergetics - study of the changes in
energy during metabolic reactions

Prentice Hall c2002 Chapter 1 34

 Free energy (DG)

Free energy change (DG) can predict the equilibrium

concentrations and direction of a reaction where:
DH = enthalpy change, DS = entropy change, T = temp
When DG<0, the reaction will proceed spontaneously
in the direction written
When DG>0, the reaction requires energy to proceed

DG = DH - TDS
Prentice Hall c2002 Chapter 1 35
 1.5 Biochemistry and Evolution

Prokaryotes - do not have a membrane-

bounded nucleus
Eukaryotes - possess nucleus and other
complex internal structures
Prokaryotes and eukaryotes appear to have
evolved from a common ancestor over three
billion years ago

Prentice Hall c2002 Chapter 1 36

 1.6 The Cell is the Basic Unit of Life

Plasma membrane - surrounds aqueous

environment of the cell
Cytoplasm - all materials enclosed by the
plasma membrane (except the nucleus)
Cytosol - aqueous portion of the
cytoplasm minus subcellular structures
Bacteriophage or phage - viruses that
infect prokaryotic cells
Prentice Hall c2002 Chapter 1 37
1.7 Prokaryotic Cells: Structural Features

Prokaryotes, or bacteria are usually single-

celled organisms
Prokaryotes lack a nucleus (their DNA is
packed in a nucleoid region of the cytoplasm)
Escherichia coli (E. coli) - one of the best
studied of all living organisms
E. coli cells are ~0.5mm diameter, 1.5mm long

Prentice Hall c2002 Chapter 1 38

 Fig. 1.14 E. coli cell

Prentice Hall c2002 Chapter 1 39

 1.8 Eukaryotic Cells: Structural Features

Eukaryotes: plants, animals, fungi, protists

Have a membrane-enclosed nucleus containing
the chromosomes
Are commonly 1000-fold greater in volume than
prokaryotic cells
Have an intracellular membrane network that
subdivides the interior of the cell

Prentice Hall c2002 Chapter 1 40

 Fig 1.15 (a) Eukaryotic cell (animal)

Prentice Hall c2002 Chapter 1 41

 Fig 1.15(b) Eukaryotic cell (plant)

Prentice Hall c2002 Chapter 1 42

 A. The Nucleus
Nuclear envelope and endoplasmic
reticulum of a eukaryotic cell

Prentice Hall c2002 Chapter 1 43

 B. Endoplasmic Reticulum and
Golgi Apparatus

Endoplasmic reticulum - network of

membrane sheets and tubules extending from
the nucleus
Golgi apparatus - responsible for modification
and sorting of some biomolecules.

Prentice Hall c2002 Chapter 1 44

 Golgi apparatus

Prentice Hall c2002 Chapter 1 45

 C. Mitochondria and Chloroplasts
Mitochondria are the main sites of energy
transduction in aerobic cells.

Prentice Hall c2002 Chapter 1 46

Chloroplasts - sites of photosynthesis in plants,
green algae

Prentice Hall c2002 Chapter 1 47

 D. Specialized Vesicles

Lysosomes - contain specialized digestive

enzymes
Peroxisomes - carry out oxidative reactions in
animal and plant cells
Vacuoles - fluid-filled vesicles, used as storage
sites for water, ions and nutrients such as glucose

Prentice Hall c2002 Chapter 1 48

 E. The Cytoskeleton

A protein scaffold is required for support, internal

organization and movement of a cell
Actin filaments form ropelike threads
Microtubules are rigid fibers packed into bundles
- Serve as an internal skeleton
- Form the mitotic spindle during mitosis
- Form movement structures (e.g. cilia, flagella)
Prentice Hall c2002 Chapter 1 49
Fig 1.16

Fluorescently labeled:
(a) Actin filaments

(b) Microtubules

Prentice Hall c2002 Chapter 1 50

1.9 A Picture
of Living Cell

Fig 1.17 Cytosol

of an E. coli cell.
Magnification:
Top 106X
Bottom 107X
(shows water,
other small
molecules)
Prentice Hall c2002 Chapter 1 51
 1.10 Biochemistry is Multidisciplinary

Various disciplines contribute to

understanding biochemistry:
Physics Genetics
Chemistry Physiology
Cell biology Evolution

Prentice Hall c2002 Chapter 1 52

 Textbook organization

Horton is organized into four sections:

1. PART ONE: Introduction
2. PART TWO: Structure and Function of
Biomolecules
3. PART THREE: Metabolism and
Bioenergetics
4. PART FOUR: Biological Information Flow
Prentice Hall c2002 Chapter 1 53