Biokimia dan

Biosintesis Sel
DONO INDARTO, dr., M.Biotech.St., Ph.D

Tujuan Pembelajaran
1. Menjelaskan dasar biokimia dan biosintesis sel
2. Menjelaskan protein sebagai materi penting dalam
kehidupan

Topik Pembelajaran
1. Komponen kimia sel
2. Struktur dan fungsi protein
3. Struktur dan aksi kerja enzim
4. Metabolisme energi seluler

Terminologi
1. Biokimia
2. Biomolekul
3. Biosintesis
4. Bioenergetika

I. Komponen Kimia Sel

Organisms are composed of matter that
takes up space and has mass

 Cells Are Made From a Few Types of

Atoms
Element substance that cannot
be broken down to other substances
by chemical reactions

Atom smallest particle of an

element

Molecules groups of atoms

Atomic weight mass of atom
relative to that of hydrogen atom
(protons + neutrons)

Molecular weight sum of the

atomic weights of all of the atoms in
compound

Figure 2-1

Subatomic Particles

Atoms are composed of subatomic particles

Relevant subatomic particles include:
Neutrons (no electrical charge)
Protons (positive charge)
Electrons (negative charge)

 Neutrons and protons form the atomic nucleus

Electrons form a cloud around the nucleus
Neutron mass and proton mass are almost identical
and are measured in daltons
Cloud of negative
charge (2 electrons)

Electrons
Nucleus

(a)

(b)

The Chemical Components of A Cell

Basic Element: Atom, protons, Neutrons, Electrons
Atomic Weight, Molecular Weight
Avgadros number (6x1023 molecules), Mole (1 mole=
6x1023 molecules), Molar solution (1M=1mole/liter)
Electron shells (2,8,8,18,18)

1 gram of hydrogen
6 x 1023 atoms
Avogadro number
89 naturally found elements:
-differ in number of protons
and electrons in their atoms
- C, H, N, O 96.5% of the
living organisms weight

Figure 2-2

Chemical elements in the

nonliving world
-differs significantly from
the composition of the
Living word

Figure 2-3

 The Outermost Electrons Determine

Atom Interactions
Living organisms:
- only electrons have rearrangements

Electrons:
-continuous movement around the
nucleus;
- exist in certain states (orbitals);

Electron shell:
-orbital of certain type with set number
of electrons in it;
-innermost shell holds maximum of 2
electrons;
-the second shell has max of 8
electrons;
-the third shell max 8
-4th and 5th shells max 18

Figure 2-4

Electrons mostly fill the

orbitals in order:
- most stable in the innermost shells;
- If outermost shell is filled :
atom is very stable and chemically
unreactive;
-Unfilled outermost shells:
atoms less stable and chemically
reactive;
interact with other atoms by gaining
or losing electrons to fill the outermost
shell

Electrons mostly fill the

orbitals in order:

red unfilled outermost shells

yellow filled shells (unreactive)
Figure 2-4

Covalent Bond and Ionic Bond

Ionic bond: electron transfer
Covalent bond: electron sharing

Electron exchange between atoms:

2 types of chemical bonds
1. Transfer of electron from one atom to another:
Ionic bond
2. Two atoms share a
pair of electrons:
Covalent bond
(can be polar)
Valence number of electrons needed
to fill the outermost shell

Figure 2-5

Sodium Chloride: ionic bond formation

The geometry of covalent bonds

 Different Types of Covalent Bonds

Single

Single bond - sharing of 2 electrons

Figure 2-9

one donated by each atom

Double bond sharing of 4 electrons

Double

2 donated by each atom:

-shorter, stronger and more rigid

Polar bond different atoms

attract shared electrons with
different strength

Nonpolar between the same atoms

Polar
Figure 2-10

Nonpolar

 Water Is the Most Abundant Substance in

Cells
Water is the biological medium on Earth
All living organisms require water more than any other
substance
Most cells are surrounded by water, and cells themselves are
about 70-95% water
The abundance of water is the main reason the Earth is
habitable

The Water Environment

70% of cell is water
Hydrogen bond
Hydrophilic and hydrophobic
Acid and base
Proton and hydroxyl
Non-covalent interactions in water: Ionic bonds,
hydrogen bonds, van der waals attractions, hydrophobic
force

 The water molecule is a polar molecule:

The opposite ends have opposite charges
Polarity allows water molecules to form
hydrogen bonds with each other
Hydrophilic - molecules with polar bonds
that can form hydrogen bonds with H2O
and will readily dissolve in water
Hydrophobic uncharged molecules
that do not make hydrogen bonds with
H2O

Acid
Donate a proton

Base
Absorb a proton or donate OHNH3+H2O->NH4++OHNaOH->Na++OH-

Ionic bonds in Water

Hydrogen bond
Polar interaction: a
elecgtropositive hydrogen is
shared by two neighboring
electornegative atoms

Chapter 2

Some Polar Molecules Are Acids and

Bases

Water is in a state of dynamic equilibrium in which water

molecules dissociate at the same rate at which they are
being reformed

Chapter 2

Some Polar Molecules Are Acids and

Bases

An acid is any substance that increases the H3O+ concentration

of a solution
A base is any substance that reduces the H3O+ concentration
of a solution (raises OH- concentration)

Figure 2-13

II. Struktur dan Fungsi Protein

Hemoglobi
n

Aktin

Proteins
1. Most diverse and complex macromolecules
in the cell
2. Used for structure, function and
information
3. Made of linearly arranged amino acid
residues
folded up with active regions

Review
Central Dogma

DNA

5 ATG GAC CAG TCG GTT TAA GCT 3

3 TAC CTG GTC AGC CAA ATT CGT 5
transcription

RNA

5 AUG GAC CAG UCG GUU UAA GCU 3

translation

Protein

aa - aa - aa - aa - aa - aa - aa

Protein Structure

via condensation

Amino Acids
Building blocks for polymers called proteins
Contain an amino group, NH2, and a carboxylic
acid, COOH
Can form zwitterions: have both positively
charged and negatively charged groups on same
molecule
20 required for humans

Chapter 15

46

Peptide Bond
Connect amino acids from carboxylic
acid to amino group
Produce amide linkage: -CONH Holds all proteins together
Indicate proteins by 3-letter abbreviation

Chapter 15

47

Protein Structure
Primary Structure

Sequence of Amino Acids

Amino acids need to be in correct order for
protein to function correctly
Similar to forming sentences out of words

Chapter 15

49

Structure of -amino acids

2. Structure of Amino Acid Monomers

Consist of an asymmetric carbon covalently
bonded to:
Hydrogen
Amino group
Carboxyl (acid) group
Variable R group specific to each amino acid

Protein folding is dependent on

the amino acid R groups
R

General Structure

H2N

COOH

There are 20 amino acids.

Their properties are determined by the R group.

There are 20 amino acids.

Nonpolar or hydrophobic (9)
Polar (hydrophillic), but uncharged (6)
Polar (hydrophillic), but charged (5)

Nonpolar
ring

(Hydrophobic)

sulfur

Protein Structure
Primary Structure

Importance of Proteins
Main catalysts in biochemistry: enzymes (involved in
virtually every biochemical reaction)
Structural components of cells (both inside and outside
of cells in tissues)
Regulatory functions (if/when a cell divides, which
genes are expressed, etc.)
Carrier and transport functions (ions, small molecules)

Types of Proteins
1) Enzymes catalyzes covalent bond breakage or
formation
2) Structural collagen, elastin, keratin, etc.
3) Motility actin, myosin, tubulin, etc.
4) Regulatory bind to DNA to switch genes on or off
5) Storage ovalbumin, casein, etc.
6) Hormonal insulin, nerve growth factor (NGF), etc.
7) Receptors hormone and neurotransmitter
receptors
8) Transport carries small molecules or irons
9) Special purpose proteins green fluorescent
protein, etc.

Levels of Protein Structure

Primary Structure - amino acid sequence in a
polypeptide
Secondary Structure - local spatial arrangement of a
polypeptides backbone atoms (without regard to side
chain conformation)
Tertiary Structure - three-dimensional structure of entire
polypeptide
Quaternary Structure - spatial arrangement of subunits
of proteins composed of multiple polypeptides (protein
complexes)

Primary Structure
1. Unique sequence of amino acids in a protein
2. Slight change in primary structure can alter
function
3. Determined by genes
4. Condensation synthesis reactions form the
peptide bonds between amino acids

Secondary Structure
1. Repeated folding of proteins polypeptide
backbone
2. Stabilized by H bonds between peptide
linkages in the proteins backbone
3. 2 types, alpha helix, beta pleated sheets

Pleated Sheets

Chapter 15

67

Alpha Helix

Chapter 15

68

Tertiary Structure
1. Irregular contortions of a protein due to
bonding between R groups
2. Weak bonds:
H bonding between polar side chains
ionic bonding between charged side chains
hydrophobic and van der Waals interactions

3. Strong bonds:
disulfide bridges form strong covalent linkages

Tertiary Structure
Spatial relationships
of amino acids
relatively far apart in
protein chain
Globular proteins:
compact spherical
shape

Chapter 15

70

Intermolecular Forces in
Proteins

Hydrogen bonding
Ionic bonds
Disulfide linkages
Dispersion forces

Chapter 15

71

Quaternary Structure
Results from interactions among 2 or more
polypeptides

Quaternary Structure
Structure when
two or more amino
acid sequences are
brought together
Hemoglobin has
four units arranged
in a specific
pattern

Chapter 15

75

Factors That Determine Protein

Conformation
Occurs during protein synthesis within cell
Depends on physical conditions of environment
pH, temperature, salinity, etc.

Change in environment may lead to denaturation of protein

Denatured protein is biologically inactive
Can renature if primary structure is not lost

III. Struktur dan Aksi Kerja

Enzim

Enzymes
Biological catalysts produced by cells
Nearly all are proteins
Enormous catalytic power
Reactions occur at lower temperatures and at higher rates

Ordinarily highly specific

Chapter 15

79

Trypsin catalyses hydrolysis of peptide bonds on

the carboxyl side of Lysine and Arginine

Helps to break down proteins in intestine

Fig.22.1,p.554

Classification of Enzymes
Enzymes are commonly named after the reaction or reactions
they catalyze
example: lactate dehydrogenase, acid phosphatase

Enzymes are classified into six major groups

oxidoreductases: oxidation-reduction reactions

transferases: group transfer reactions
hydrolases: hydrolysis reactions
lyases: addition of groups to a double bond, or removal of groups to
create a double bond
isomerases: isomerization reactions
ligases: the joining to two molecules

Terms in Enzyme Chem

apoenzyme: the protein part of an enzyme
cofactor: a nonprotein portion of an enzyme that is involved in
a chemical reaction; examples are metallic ions such as Zn 2+
and Mg2+
coenzyme: an organic cofactor; an example is heme
substrate: the compound or compounds whose reaction an
enzyme catalyzes
active site: the specific portion of the enzyme to which a
substrate binds during reaction

Cofactors
Something other than polypeptide chain required by
enzyme
May be metal
Iron in hemoglobin

May be organic cofactor

Coenzyme

Apoenzyme: does not have cofactor

Chapter 15

85

Terms in Enzyme Chem

activation: any process that initiates or increases the activity
of an enzyme
inhibition: any process that makes an enzyme less active or
inactive
competitive inhibitor: an substance that binds to the active
site of an enzyme thus preventing binding of substrate
noncompetitive inhibitor: any substance that binds to a
portion of the enzyme other than the active site and thus
inhibits the activity of the enzyme

Enzyme Activity
Enzyme activity: a measure of how much a reaction rate
is increased
We examine how the rate of an enzyme-catalyzed
reaction is affected by

enzyme concentration
substrate concentration
temperature
pH

Substrate Concentration and Reaction Rate

The rate of reaction increases as substrate
concentration increases (at constant
enzyme concentration)
Maximum activity occurs when the
enzyme is saturated (when all enzymes
are binding substrate)
The relationship between reaction rate
and substrate concentration is
exponential, and asymptotes (levels off)
when the enzyme is saturated

Temperature and Enzyme Activity

Enzymes are most active at an optimum temperature (usually
37C in humans)
They show little activity at low temperatures
Activity is lost at high temperatures as denaturation occurs

pH and Enzyme Activity

Enzymes are most active at optimum pH
Amino acids with acidic or basic side-chains have the proper
charges when the pH is optimum
Activity is lost at low or high pH as tertiary structure is disrupted

Optimum pH for Selected Enzymes

Most enzymes of the body have an optimum pH of about 7.4
However, in certain organs, enzymes operate at lower and higher
optimum pH values

Mechanism of Action
Lock-and-key model
the enzyme is a rigid three-dimensional body
the enzyme surface contains the active site

Mechanism of Action
Induced-fit model
the active site becomes modified to accommodate the
substrate

Induced-Fit Model of
Enzymes
Explains how enzyme works
Substrate: reacting substance
Active site: where chemical
reaction takes place and where
substrate fits

Chapter 15

94

Inhibition of Enzymes
Lets cell control
when an enzyme
works
Inhibitor binds to
allosteric site
Prevents substrate
from binding

Chapter 15

95

Reversible Inhibitors (Competitive

Inhibition)
A reversible inhibitor goes on and off, allowing the
enzyme to regain activity when the inhibitor leaves
A competitive inhibitor is reversible and has a structure
like the substrate
- it competes with the substrate for the active site
- its effect is reversed by increasing substrate
concentration

Competitive Inhibition
the induced-fit model explains competitive inhibition
the inhibitor fits into the active site, preventing the substrate
from entering

Reversible Inhibitors
(Noncompetitive Inhibition)
A noncompetitive inhibitor has a structure that
is different than that of the substrate
- it binds to an allosteric site rather than to the
active site
- it distorts the shape of the enzyme, which
alters the shape of the active site and prevents
the binding of the substrate
The effect can not be reversed by adding more
substrate

Noncompetitive Inhibition
the mechanism of noncompetitive inhibition

 Enzyme assays useful in medical diagnosis

Enzyme

Body Fluid

Disease Diagnosed

Alanine aminotransferase (ALT)

Acid phosphatase
Alkaline phosphatase (ALP)
Amylase

Serum

Hepatitis
Prostate cancer
Liver or bone disease
Pancreatic disease

Serum
Serum
Serum
Aspartate aminotransferase (AST) Serum,
Cerebrospinal
fluid
Lactate dehydrogenase (LDH)
Serum
Creatine phosphokinase (CK)
Serum
Phosphohexose isomerase (PHI)
Serum

Heart attack or
hepatitis
Heart attack
Heart attack
Heart attack

III. Metabolisme Energi Seluler

Four Major Small Organic Molecules

Metabolism
Series of coordinated reactions that keeps cells alive
Catabolism: reactions that break down molecules for
energy
Anabolism: synthesize molecules of living systems

Chapter 15

103

Sugar [(CH2O)n, carbohydrates]

Glucose

Disaccharide
Condensation and hydrolysis

Fatty Acids

Phospholipid (amphipathic)