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MB207 Molecular Cell Biology
2. Cell Chemistry and Biosynthesis
Cell Chemistry and Biosynthesis
 Chemistry of life:
- based majority on carbon compounds, organized into
macromolecules that are require for cells growth and
function.
- cells are 70% water (life depends almost exclusively
on chemical reactions that take place in aqueous
solution)
- cell chemistry is enormously complex: even the
simplest cell is vastly more complicated in its
chemistry than any other chemical system known.
Chemical component of a cell
• Matter is made of combinations of elements.
Substances that cannot be broken down or converted into other
substances by chemical means ie. Hydrogen or carbon
• Smallest particle of an element is an atom
• A molecule may consist of atoms of a single element or of different
elements.
• These elements are connected by chemical bonds that hold atoms
together.
Cell are made from a few types of atoms
 Cells are made from atoms.
- Atom is the smallest particle of an
element
- consisting of a +ve charged
nucleus (protons and neutrons),
surrounded by a cloud of
-ve charged electrons.
- There are 92 naturally occurring
elements, differing in protons
and electrons in its atoms.
 Atom
- electron (held in a series of orbitals
electrostatic attraction to the
nucleus)
- protons (positively charged, gives
the atomic number)
- neutron (uncharged)
Atomic nucleus


Living organisms are made up of 4 main elements: C, H,
N & O. This composition differs markedly from that of the
nonliving inorganic environment.
Chemical bonds :
1) Covalent bonds (sharing of electrons) - strongly bonding
2) Non-covalent bonds: ionic, hydrogen bond, Van der
Waals attraction and hydrophobic strength
70% of a cell’s weight is water
Representations of a water molecule
Covalent bond and ionic bond
2 types of chemical bonds between atoms:
a. Covalent bond: formed when 2 atoms have a pair of electrons
b. Ionic bond: formed when electrons are donated by 1 atom to another
Cl2 & CO2 : examples of covalent
bonds formation
Chlorine molecule formed by
2 atoms sharing 1 pair of
electrons
Carbon dioxide molecule formed
from 2 oxygen atom each sharing
2 pairs of electrons with a carbon
atom
Sodium Chloride: ionic bond formation
Four types of noncovalent interactions help
to bring molecules together in cells
Ionic bond
Van der Waals interactions
Hydrogen bond
• Interactions between two
oppositely charged ions.
• interactions between two
atoms that occur only if the
atoms are very close to one
another and are oriented
appropriately.
• polar interactions of a
electropositive hydrogen
that is shared by two
neighboring
electronegative atoms.
Hydrophobic forces
• Pushing of non-polar surfaces out of the
hydrogen-bonded water network.
Ionic
Van der Waals
Hydrophobic
forces
~100 kcal/mole ~3 kcal/mole
~ 5 kcal/mole
~1 kcal/mole
~3 kcal/mole
electrons
shared
water-water
full charge
transfer
fluctuating
not a bond per
se
organic-water
can attract Hbond
induced dipole
entropy driven
organicorganic
strong in dry
crystal
at close range
only
only works in
water
weak,
orientation
sensitive
weak in water
weak
weak
Covalent
strong
Hydrogen
Strong
Covalent
Weak
>
ionic
>
hydrogen
>
van der Waals
Cells contain 4 major families of
small organic molecules
 Are carbon-based compounds having molecular weights in the range 100 to
1000 and contain up to 30 or so carbon atoms.
Function:
monomer subunits - to construct polymeric macromolecules eg. proteins,
nucleic acids, and large polysaccharides of the cell.
energy sources - are broken down and transformed small molecules in
intracellular metabolic pathways.
1) Sugar (2%)  polysaccharides
2) Fatty acids (2%)  Fats, lipids,
phospholipids (membrane)
3) Amino Acids (15%)  polypeptides,
proteins
4) Nucleotides (7%)  nucleic acids
Others (4%) + H2O (70%)
Cells contain four major families of small
organic molecules
Sugars
 Simplest - monosaccharides.
 General formula [CH2O]n where n is a number between 3 – 8.
 Polysaccharides are large molecules composed of individual sugar
units.
 Can exist in either 2 forms, D-form and L-form, which are mirror
images of each other.
 Exist in either a ring or and open-chain form.
Open –chain form: aldosugars or ketosugars
 Main functions:
• Energy source
• Mechanical support
e.g. cellulose
• Covalently linked to protein
and lipid
 glycoprotein or glycolipids
Condensation and hydrolysis of disaccharide
Fatty Acids
 Is a long, unbranched hydrocarbon
chain with a carboxyl group at one end.
 Amphipathic; carboxyl group renders
one end polar whereas the hydrocarbon
tail is nonpolar.
 Variable but usually even number of
carbon atoms ranging from 12 to 20
carbon atoms per chain.
 Main functions:
• long-term energy storage
• Act as structural components e.g.
the major building block in cell
membranes
• as "messengers" (hormones) that
play roles in communications within
and between cells
Saturated fatty acids
Unsaturated fatty acids
Phospholipid structure and the orientation
of phospholipids in membranes
Nucleotides
• Nitrogen-containing ring compound linked to a five-carbon sugar.
• Ribose: ribonucleotides
Deoxyribose: deoxyribonuleotides
• Pyrimidines: cytosine, thymine and uracil
• Purines: guanine and adenine
• Main functions:
• Subunits for DNA & RNA, storage of genetic information
• Short term carriers of chemical energy, e.g. ATP
• Coenzyme & specific signaling molecules in the cells e.g. cAMP
The assembly of macromolecules
Energy is needed for the assembly of
macromolecules, where can cells
obtain such energy?
Cell Metabolism
- Organized by enzymes
Chemical reactions:
(1) catabolic pathways;
(2) anabolic or biosynthetic pathways
Catalysis & the use of energy by cells
A set of enzyme-catalyzed reactions generates a metabolic pathway
Cell metabolism
Catabolism
Breaks large molecules into smaller molecules; usually
releases energy.
Anabolism
Builds large molecules from smaller ones; usually
consumes energy.
The Carbon Cycle
How cells obtain energy from food???
- To produce ATP, NADH
Food Molecules Are Broken Down in 3 Stages:
a. Digestion (enzymatic breakdown of food molecules into
monomer subunits)
b. Partial breakdown of simple molecules to provide some energy
in the cytoplasm (Different metabolism pathways)
c. Complete oxidation through respiration at the mitochondria to
provide more energy
Metabolism of Food
& Energy production
1) Break down of large
macromolecules to simple
subunits (amino acids,
simple sugars, fatty acids &
gylcerol)
2) Further breakdown to Acetyl
CoA, production of limited amount
of ATP and NADH (Glycolysis and
Kreb Cycle)
3) Complete oxidation of Acetyl
CoA to H2O & CO2, production of
large amount of NADH and ATP in
mitochondria.
The 3 stages of cellular metabolism from
food to waste products in animal cells
1st stage: Breakdown of large macromolecules to simple subunits
outside cells
Outside
cell
Digestion
2nd stage : Oxidation begin
Cytosol
1st stage
Outside cells
2nd stage: Breakdown of simple subunits to acetyl CoA
accompanied by production of limited amounts of ATP and NADH
Cytosol
Glycolysis
Mitochondrial
3rd stage
Mitochondrial
Glycolysis
Glucose
Pyruvate
ATP
Pyruvate
dehydrogenase
NADP
3rd stage
Cytosol
CO2 + Carbon acetyl group
+ coenzyme A
Aceyl CoA
Citric acid cycle
ATP
Oxidation phosphorylation
CO2
ATP
ATP
O2 + H2O mitochondrion
Waste products
2nd stage
Cytosol + mitochondrial
3rd stage:
Complete
oxidation of
acetyl CoA to
H2O and CO2
accompanied
by production
of large
amounts of
NADH and
ATP
Mitochondrial
Waste product