Dr. Madushani Silva
(MBBS)
North Colombo Teaching Hospital – Ragama
Biochemistry
 Chemistry of living organisms.
 The study of biology at the molecular level.
Biochemistry has become the foundation for
understanding all biological
processes.
It has provided explanations for the causes of many
diseases in humans,
animals and plants
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What is Biochemistry ?

Biochemistry is the application of chemistry to the
study of biological processes at the cellular and
molecular level.
A.
Studying the structure and behavior of the complex
molecules found in biological material and
B.
the ways these molecules interact to form cells, tissues and
whole organism
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Elements
• Make up all matter.
• 92 occur in nature.
• Identified by names or chemical symbols (abbreviations of
modern or Latin names).
• Identified by number (based on structure of subunits or
atoms).
• Described and organized in periodic table.
Periodic Table
Molecules and Compounds
Molecules
• Formed when two or more atoms unite on the basis of
their electron structures
• Can be made of like atoms or atoms of different elements
Compounds
• Composed of two or more elements
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)
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Linking Monomers
Cells link monomers by a process
called dehydration synthesis
(removing a molecule of water)
Remove
H
H2O Forms
Remove OH
This process joins two sugar monomers
to make a double sugar
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Breaking Down Polymers
 Cells break down
macromolecules by
a process called
hydrolysis (adding
a molecule of
water)
Water added to split a double sugar
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Molecular Organisation of a cell
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Water
About 60-90 percent of
an organism is water
Water is used in
most reactions in
the body
Water is called
the universal
solvent
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Biomolecules
 Carbohydrates
 Lipids
 Proteins
 Nucleic acid
Biomolecules – Structure
Anabolic
 Building block
 Macromolecule
 Simple sugar
 Polysaccharide
 Amino acid
 Protein (peptide)
 Nucleotide
 RNA or DNA
 Fatty acid
 Lipid
Catabolic
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Sugars
 Carbohydrates most abundant organic
molecule
found in nature.
 Initially synthesized in plants from a
complex series
of reactions involving photosynthesis.
 Basic unit is monosaccharides.
 Monosaccharides can form larger
molecules e.g. glycogen, plant starch or
cellulose.
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Functions
 Store energy in the form of starch
(photosynthesis in plants) or glycogen (in
animals and humans).
 Provide energy through metabolism pathways
and cycles.
 Supply carbon for synthesis of other
compounds.
 Form structural components in cells and
tissues.
 Intercellular communications
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Carbohydrates
 Composed of carbon, hydrogen, and oxygen.
 Sugars
 Monosaccharides
 Ex. Glucose
 Disaccharides
 Ex. Sucrose
 Polysaccharides
 Ex. Glycogen, Peptidoglycan
Carbohydrate - Glucose
www.palaeos.com
Carbohydrate - Sucrose
www.chm.bris.ac.uk
Monosaccharides -Polysaccharides
Glucose - Cellulose
Glycosidic bonds connecting
glucose residues are in red
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Carbohydrate - Peptidoglycan
www.biologie.uni-hamburg.de
Carbohydrate - Glycogen
www.elmhurst.edu
Fatty acids - Lipids
 Are monocarboxylic acid contains even number C atoms
 Two types: saturated (C-C sb) and unsaturated (C-C db)
 Fatty acids are components of several lipid molecules.
 E,g. of lipids are triacylglycerol, steriods (cholestrol, sex
hormones), fat soluble vitamins.
Functions
 Storage of energy in the form of fat
 Membrane structures
 Insulation (thermal blanket)
 Synthesis of hormones
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Lipids
 Fatty Acids
 The building
blocks of lipids.
biology.clc.uc.edu
courses.cm.utexas.edu
Triglyceride
Glycerol
Fatty Acid Chains
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Lipids
 Examples are:
 Waxes
 Fats and oils
 Phospholipids
 Steroids
Phospholipid Cell Membrane.
www.williamsclass.com
Structure of a biological membrane
• A lipid bilayer with associated proteins
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Steroids
The carbon skeleton of
steroids is bent to form
4 fused rings
Cholesterol is the
“base steroid” from
which your body
produces other
steroids
Cholesterol
Estrogen
Testosterone
Estrogen &
testosterone are also
steroids
Synthetic Anabolic Steroids are variants of testosterone
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Proteins
 Made up of polymers
of amino acids.
 “beads on a string.”
 20 primary amino
acids exist.
 A polymer of 3 or
more amino acids
forms a polypeptide.
Amino acids - Proteins:
 Amino acids:
•
Building blocks of proteins.
•
R Group (side chains) determines the
chemical properties of each amino acids.
•
Also determines how the protein folds and
its biological function.
•
Functions as transport proteins, structural
proteins, enzymes, antibodies, cell
receptors.
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Proteins
 Primary Structure
 Linear sequence of amino acids.
 Secondary Structure
 Form helices or sheets due to their structure.
 Tertiary Structure
 A folded protein.
 Quaternary Structure
 2 or more polypeptide chains bonded together.
Protein
Structure
www.denizyuret.com
Proteins as Enzymes
 Many proteins act as biological catalysts or enzymes
Thousands of different enzymes exist in the body
Enzymes control the rate of chemical reactions by
weakening bonds, thus lowering the amount of
activation energy needed for the reaction ->
Catalysator
-> No not interfere with the equilibrium of reaction
-> Enzymes are reusable !!!!
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Enzymes
 Are proteins.
 Are considered
biological catalysts.
 Speed up a chemical
reaction without being
altered.
 Names often end in “ase.”
 Ex. Lipase,
carbohydrase.
 Act on a substrate.
 Proteins, including
enzymes, can be
denatured.
Enzymes:
• Active site - a cleft or groove in an enzyme that binds the
substrates of a reaction
The nature and arrangement of amino acids in the
active site make it specific for only one type of
substrate. (accepts just one enaniomer)
Egg white lysozyme
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Nucleic Acids
 DNA and RNA.
 (DNA - deoxyribonucleic acid,
 RNA - ribonucleic acid).
 Is the “hereditary molecule.”
 Contains genes that code for a certain product.
 DNA is translated into RNA which is used to produce a
protein or other product.
Nucleic Acid Structure
 DNA nucleotides
 Building blocks of DNA.
 RNA nucleotides
 Building blocks of RNA.
Nucleic Acid Structure
 DNA
 Nitrogenous base
 Deoxyribose
 Phosphate group
 RNA
 Nitrogenous base
 Ribose
 Phosphate group
www.microbelibrary.org
Nitrogenous Bases
 Adenine (A)
 Guanine (G)
 Cytosine (C)
 Thymine (T) – only DNA
 Uracil (U) – only RNA
DNA and RNA
Nitrogenous Bases
 A and G
 Purines (doublering structures)
 C, T, and U
 Pyrimidines
(single-ring
structures)
hyperphysics.phy-astr.gsu.edu
DNA Structure
 Nucleotides bond between
sugar and phosphate
groups to form long
polymers.
 Double-stranded DNA
 - The two nucleotide
polymers bind
at the nitrogenous
bases.
 Bonding forces cause the
double-stranded polymer to
form a double helix.
www.genome.gov
DNA Structure
 James Watson (left) and Francis Crick (right)
discovered the double-helix structure of DNA and
its process of replication in the 1950s.
www.achievement.org
DNA Replication
 Occurs during cell division.
 Both strands of the double-helix unwind and replicate
a complimentary strand.
 The parent strand and new daughter strand form a
new double-helix.
 DNA polymerase is one enzyme used in replication
process.
Macromolecules
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Macromolecules
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Life needs 3 things:
(1) ENERGY, which it must
know how to:

Extract
 Transform
 Utilize
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Glycolysis: the preferred way for the
formation of ATP
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Life needs (2) SIMPLE MOLECULES,
which it must know how to:
 Convert
 Polymerize
 Degrade
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Life needs (3) CHEMICAL
MECHANISMS, to:
 Harness energy






Drive sequential chemical reactions
Synthesize & degrade macromolecules
Maintain a dynamic steady state
Self-assemble complex structures
Replicate accurately & efficiently
Maintain biochemical “order” vs outside
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Trick : Life uses enzymes to speed up
otherwise slow reactions
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Biochemical Reactions
Metabolism: total sum of the chemical reaction happening in a
living organism (highly coordinated and purposeful activity)

a.
b.
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:
a. acquisition & utilization of energy
b. Synthesis of molecules needed for cell structure and
functioning (i.e. proteins, nucleic acids, lipids, & CHO
c. Removal of waste products
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Even though thousands of pathways sound very
large and complex in a tiny cell:
 The types of pathways are small
 Mechanisms of biochemical pathways are simple
 Reactions of central importance (for energy
production & synthesis and degradation of major cell
components) are relatively few in number
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Energy for Cells
 Living cells are inherently unstable.
 Constant flow of energy prevents them from becoming
disorganized.
 Cells obtains energy mainly by the oxidation of bio-
molecules (e- transferred from 1 molecule to another
and in doing so they lose energy)
 This energy captured by cells & used to maintain
highly organized cellular structure and functions
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