Focus
biomolecules.
Biological structure
➢ Interaction, organization, and coordination of biomolecules
➢ Chemical and 3D structures of biomolecules
➢ Synthesis and degradation of biomolecules
Metabolism
➢ Energy production, utilization and conservation
➢ Anabolism vs. catabolism
Genetic information
➢ Transmission, expression and storage of genetic
information
Principles
➢ Cells, the basic structural units of all living organisms are
highly organized. A constant source of energy is required to
maintain a cell’s ordered state
➢ Living processes consist of thousands of chemical reactions
– precise regulation and integration of these reactions are
required to maintain life
➢ Certain fundamental reaction pathways, such as the
energy – generating conversion of glucose to pyruvic acid,
known as glycolysis are found in almost all organism
➢ All organism use the same type of molecules – eg.
Biomolecules which =include carbohydrates, lipids ,
proteins and nucleic acids – composed of 6 elements, C, H,
O, N, S, P
➢ The instruction for growth, development, and
reproduction are encoded in each organism’s nucleic acid
➢ Influence on diverse discipline such as medicine, nutrition,
pharmacology, environmental studies, fisheries and
agriculture
Introduction
➢ Complex living organism originate with simple elements, C,
H, and O combine to make up many biomolecules such as
carbohydrates. The addition of N and S make amino acid
that combine to form protein. Added P provides the
ingredients for DNA and RNA production.
➢ A collecting interacting molecule encased in a suitable
membrane becomes the cell-the basic unit of life
➢ Biochemistry is the study of living organism composed of
➢ Organic chemistry is the study of compounds of carbon
and hydrogen and their derivatives called organic
compounds
➢ These are being classified according to their functional
group.
Functional groups in Biomolecules
Functional groups – specific parts of molecules involved in
biochemical reactions
Table below shows the general formulas of:
➢ Organic compounds
➢ Functional groups
➢ Linkages common in biochemistry
➢ R – represents an alkyl group (CH3CH2)n)
General Formulas
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
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
➢ The absolute molecular mass of this protein = 38,000
daltons (1dalton = 1 atomic mass unit)
Biomolecules
▪ Protein
➢ Composed of 20 common amino acids
➢ Used in the synthesis of long, complex polymers
(polypeptides), transport, structural, enzyme, contains
peptide bond between amino acid and carboxyl group
➢ Each amino acid contains:
• Carboxylate group (-COO- )
• Amino group (-NH2)
• Side chain ® unique to each amino acid
➢ Dipeptides are connected by peptide bonds
➢ Polypeptides – amino acids joined end to end by a peptide
bond
➢ 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
• Carbohydrates (Polysaccharides)
➢ Carbohydrates, or saccharides are
composed primarily of C, H, and O
➢ Polysaccharides are composed of
saccharide monomers (simple sugar)
➢ Most sugar structures can be represented
as either linear (Fischer projection) or cyclic
(Haworth structure)
➢ energy source and structural component,
intracellular communications;
➢ described as polyhydroxy aldehyde and
ketone
Representation of the structure of mono-, di- and polysaccharides
• Nucleic Acids (Nucleotides)
➢ largest molecules in living organism,
composed of nucleotides which is
composed of five carbon sugar phosphate
group and nitrogenous base;
➢ two types of nucleic acid – DNA –repository
of organic genetic information and RNA –
involved in the expression of the
information in protein synthesis
➢ N-bases are Purine – adenine (A) and
guanine (G)and pyrimidine – thymine (T),
cytosine (C), uracil (U)
Adenosine Triphosphate
Biochemical processes
Life appears to be an exception to one such rule known as
the second law of thermodynamics which stipulate that in any
system the degree of disorder can only increase
➢ Metabolism: total sum of the chemical reaction
happening in a living organism (highly
coordinated and purposeful activity)
✓ Anabolism – energy requiring
biosynthetic pathways
✓ Catabolism – degradation of fuel
molecules and the production of
energy for cellular function
➢ All reactions are catalyzed by enzymes
➢ The primary functions of metabolism are:
✓ Acquisition and utilization of energy
✓ Synthesis of molecules needed for all
structure and functioning
✓ Removal of waste products
Biochemical Reaction
➢ ▪ Even though thousand of reactions sound very large and
complex in a tiny cell;
✓ The number of types of reaction is small
✓ Mechanism of biochemical reactions are simple
✓ Reactions of central importance (for energy
production and synthesis and degradation of
major cell components) are relatively few in
number
Biochemical processes are:
➢ Nucleophilic substitution reaction (one atom or group
substituted for another)
A: + B-X ---------------- A-B + X:
➢ Elimination reaction (double bond is formed when atoms
in a molecule is removed)
Alkyl halide ----------------- alkene + A-B
➢ Isomerisation ( involve intramolecular shift of atoms or
groups)
Aldose ----------- ketose sugar
➢ Oxidation reduction reaction
✓ Transfer of e- from a donor (reducing agent) to
an eacceptor (oxidizing agent)
✓ when reducing agent donate e- oxidized
✓ When oxidizing agent accept e- reduced
✓ Oxidation has occurred if a molecule gains O2 or
lose H +
✓ Reduction has occurred if a molecule losses O2
or gain H
➢ Hydrolysis (cleavage of double bond by water)
➢ Cleavage if a covalent bond by H2O eg. Digestion of many
food molecules
Energy (capacity to do work)

➢ Living cells are inherently unstable, only a

constant flow of energy prevent them from
becoming disorganized;

➢ the ultimate source of energy used by all life on

earth is the sun

➢ Photosynthesis – organism capture light energy

to transfer CO2 into sugar and other
biomolecules which are consumed by the
organism and source them as energy source and
structural materials

➢ Cells use energy to maintain their complex

structure and activation through oxidation of
biomolecules

➢ In energy transferring reaction, electron are

transferred from one molecule to another and
electron lose energy which is captured an used
to maintain highly organized cellular structures
and functions

Biological order

➢ The complex structure of cells requires the following high

internal order
✓ synthesis of biomolecules
▪ cellular components are synthesized in
vast array of chemical reactants
▪ integrated into carefully regulated
pathways that involve numerous steps

✓ Transport across membranes – cell membranes

regulate the passage of ions and molecules from
one compartment to another
▪ eg. Plasma membrane – responsible
for the transport of certain substances
such as nutrients for a relatively
disorganized environment into the
precisely ordered cellular interior

✓ Cell movement – organized movement

✓ Waste removal – all living cells produce waste
products.
▪ Eg. Animal cells convert food molecule,
such as sugar and amino acids into CO2
(diffuse out of the cell and extruded
through respiratory system), H2O
(excreted though kidney)and NH3
(convert to urea