Biochemistry

Power to Understand What

We Are!!
Introduction to Biochemistry
 The word biochemistry was first introduced
by a Germen Chemist , Carl Neuberg in
1903.

“Chemistry of Life”
1. Biochemistry
 Definition: The chemistry of life
 The science concerned with:
 the chemical basis of life.
 the various molecules that occur in living cells
and organisms and with their chemical reaction.

 Anything more than a superficial comprehension of

life – in all its diverse manifestation - demands a
knowledge of biochemistry.
Biochemistry
Aim:
To describe and explain in molecular
terms of all chemical processes that
occur in living cells.
 Structure-function
 Metabolism and Regulation
 How life began ？
Biochemistry
 Significance: be essential to all life
sciences as the common knowledge
 Genetics; Cell biology; Molecular biology
 Physiology and Immunology
 Pharmacology and Pharmacy
 Toxicology; Pathology; Microbiology
 Zoology and Botany
Biochemistry
 Medical students who acquire a sound knowledge
of biochemistry will be in a strong position to
deal with two central concerns of the health
sciences:

1. the understanding and maintenance of health

2. the understanding and effective treatment of
disease

 Causes of cancers
 Molecular lesions causing various genetic diseases
 Rational design of new drugs
The use of biochemical tests:
 Biochemical investigations are involved in every branch of
clinical medicine.
 The results of biochemical tests may be of use in:
 diagnosis and in the monitoring of treatment.
 screening for disease or in assessing the prognosis.
 research into the biochemical basis of disease
 clinical trials of new drugs

 Biochemical investigations hold the key for:

 the diagnosis and prognosis of DMs, jaundice, myocardial
infarction, gout, pancreatitis, rickets, cancers, acid-base
imbalance etc.
 NB: Successful medical practice is unimaginable without
the service of clinical biochemistry laboratory.
 2. Organization of Life
• Elements
• Simple organic compounds (monomers)
• Macromolecules (polymers)
• Supramolecular structures
• Organelles
• Cells
• Tissues
• Organisms
Elements:
– Substances that can not be broken down into
simpler substances by chemical reactions.
– There are 110 different elements that are known to
man.
• Life requires about 25 of them.

• The living matter is composed of mainly six elements-Carbon,

Hydrogen, Oxygen, Nitrogen, Phosphorus and Sulphur.
(CHONPS).
– These elements together constitute more than 90% of the dry
weight of the human body.

• Several other functionally important elements are also

found in the cells.
– These include- Ca, K, Na, Cl, Mg, Fe, Cu, Co, Zn, F, Mo and Se.
Carbon-a unique element of life
• Carbon is the most predominant and versatile
element of life.

• It possesses as unique property to form infinite

number of compounds.

• This is attributed to the ability of carbon to

form:
 stable covalent bonds and C-C chains of unlimited length.

• It is estimated that about 90% of compounds

found in living system invariably contain carbon.
 Functional Groups:
• Groups of atoms that have unique chemical and
physical properties.

• Compounds that are made up solely of carbon

and hydrogen are not very reactive.

• One or more H atoms of the carbon skeleton may

be replaced by a functional group.

• Functional groups determine chemical &

physical properties of organic molecules.
Types of biomolecules
 Small molecules:
 Phospholipid, glycolipid, sterol,
 Vitamin
 Hormone, neurotransmitter
 Sugar
 Monomers:
 Amino acids
 Nucleotides
 Monosaccharides
 Polymers:
 Peptides, oligopeptides, polypeptides, proteins
 Nucleic acids, i.e. DNA, RNA
 Oligosaccharides, polysaccharides (including cellulose)
 Making and Breaking Polymers

 There are two main chemical mechanisms in

the production and break down of
macromolecules.
 Condensation or Dehydration Synthesis
 Hydrolysis

 In the cell these mechanisms are regulated

by enzymes.
 Relatively few monomers are used by cells to
make a huge variety of macromolecules

Macromolecule Monomers or Subunits

1. Carbohydrates 20-30 monosaccharides
or simple sugars

2. Proteins 20 amino acids

3. Nucleic acids (DNA/RNA) 4 nucleotides (A,G,C,T/U)

4. Lipids (fats and oils) ~ 20 different fatty acids

and glycerol.
 Structural hierarchy in the molecular organization of
cells

 Just like cells are building blocks of tissues, biomolecules

are building blocks of cells.
Similarities among all types of cells
 All cells use nucleic acids (DNA) to store information
 Except RNA viruses, but not true cells
(incapable of autonomous replication)
 All cells use nucleic acids (RNA) to access
stored information

 All cells use proteins as catalysts (enzymes) for chemical

reactions
 A few examples of RNA based enzymes, which may reflect
primordial use of RNA
 All cells use lipids for membrane components
 Different types of lipids in different types of cells
 All cells use carbohydrates for cell walls (if present),
recognition, and energy generation
 3. Cells
 Basic building blocks of life
 Smallest living unit of an organism

 A cell may be:

 an entire organism (unicellular) or
 it may be one of billions of cells that make up the organism
(multicellular).
 Grow, reproduce, use energy, adapt, respond to
their environment
 Many cannot be seen with the naked eye
 a typical cell size is 10µm; a typical cell mass is
1 nanogram.)
Cells May be Prokaryotic or Eukaryotic

 Prokaryotes (Greek: pro-before;

karyon-nucleus) include various
bacteria
 lack a nucleus or membrane-bound
structures called organelles

 Eukaryotes (Greek: eu-true; karyon-

nucleus) include most other cells
(plants, fungi, & animals)
 have a nucleus and membrane-bound
organelles
•Cell membrane & cell wall • Cell Membrane
•Nucleoid region contains the DNA • Nucleus
•Contain ribosomes (no membrane) • Cytoplasm with organelles
Characteristic Bio-membranes and
Organelles
•Plasma Membrane-Cell’s defining boundary
Providing a barrier and containing
transport and signaling systems.

•Nucleus – Cell’s information center

Double membrane surrounding the chromosomes and
the nucleolus. The place where almost all DNA
replication and RNA synthesis occur. The nucleolus is
a site for synthesis of RNA making up the ribosome

• Mitochondria- the power generators

Mitochondria (Greek: mitos-thread; chondros-granule):
Surrounded by a double membrane with a series of
folds called cristae. Functions in energy production
through metabolism. Contains its own DNA.
Endoplasmic Reticulum

 Found in all eukaryotic cells

 Folded membrane of sacs/tubules
 Continuous with nuclear membrane
 Site of synthesis of proteins and lipids
Endoplasmic reticulum (ER) – The transport
network for molecules
Rough endoplasmic reticulum (RER)
Covered with ribosomes
Gives granular or “rough” appearance
Site of protein synthesis

•Ribosomes
Protein and RNA complex responsible for
protein synthesis

•Smooth endoplasmic reticulum (SER)

A site for synthesis and metabolism of lipids.
Rough Endoplasmic Reticulum/RER
 Membrane bound ribosomes
 Found in RER
 Produce proteins mostly for secretion from cell
 Protein hormones, digestive enzymes

 Free ribosomes
 Found “free” in cytosol
 Produce proteins mostly used by cell
 Metabolism, structure
Nissl Bodies
 Rough endoplasmic reticulum in neurons
 Synthesize neurotransmitters

Nissl Bodies

Dr. Dimitri Agamanolis

neuropathology-web.org
RER
 Abundant in cell that secrete proteins
 Goblet cells of intestines (mucus)
 Plasma cells (antibodies)
 Pancreatic beta cells (insulin)
Smooth Endoplasmic Reticulum/SER
 Portions of ER without ribosomes

 Important for lipid/steroid synthesis

 Also detoxification of drugs and toxins

 Sarcoplasmic reticulum = SER in myocytes

 Stores calcium for muscle contraction
SER
 Lots of SER found in hepatocytes
 Synthesis of cholesterol/lipoproteins
 Many detoxification enzymes
 Cytochrome P450 family of enzymes

 Also found in steroid producing organs

 Adrenal glands
 Gonads
•Golgi apparatus -process and package the
macromolecules.
A series of stacked membranes. Vesicles
carry materials from the RER to the Golgi
apparatus. Vesicles move between the stacks
while the proteins are "processed" to a
mature form.

•Lysosomes-contain digestive enzyme

A membrane bound organelle that is
responsible for degrading proteins and
membranes in the cell.

•Cytoplasm
enclosed by the plasma membrane, liquid
portion called cytosol and it houses the
membranous organelles.
4. Chemical composition of a normal man
(weight 65 kg)

Constituent Percent (%) Weight (kg)

Water 61.6 40

Protein 17.0 11

Lipid 13.8 9

Carbohydrate 1.5 1

Minerals 6.1 4
Water: The Ideal Compound for Life

– Living cells are 60-90% water

– Water covers 3/4 of earth’s surface

– Water is the ideal solvent for chemical

reactions

– On earth, water exists as gas, liquid, and

solid
 Water
• Making up 60% or more of the weight of most organisms.

• Biological macromolecules assume specific shapes in

response to the chemical and physical properties of water.

• Biological molecules undergo chemical reactions in an

aqueous environment.

• Many of the weak interactions within and between

biomolecules are strongly influenced by the solvent
properties of water.
– such as membrane lipids, interact with each other in ways dictated
by the polar properties of water.
Fig.2 Fluid compartments of the body.
Volumes are for an average 70-kg person.
 Functions of Water in Human Body

• Transports nutrients and oxygen into cells

• Regulates body temperature
• Detoxifies
• Moisturizes the air in lungs
• Helps with metabolism
• Protects vital organ
• Helps organs to absorb nutrients
• Protects and moisturizes our joints 49
 Hydrolysis/ Energy Release
• Water is needed to separate (by hydrolysis) a
phosphate group from ATP or GTP to get energy.
• Without water hydrolysis is not possible.

• ATP +H2O = Energy + ADP + Inorganic Phosphate

• GTP +H2O = Energy + GDP + Inorganic Phosphate

• Water is the engine of metabolism.

• Participates in the biochemical break-down of
what we eat. 50
 Variation in Water Levels
Tissue type:
 lean tissues have higher fluid content than fat tissues.
Gender:
 males have more lean tissue and therefore more body
fluid.
Age:
 lean tissue is lost with age and body fluid is lost with it.

NB: Lean tissue is the muscle tissue without fat.

 Water
• A water molecule (H2O), is made up of
three atoms --- one oxygen and two
hydrogen.
 Polarity
• Many of water’s biological functions stem from
its chemical structure.

• Water is a polar molecule

– It has unequal charge distribution that results in
areas of δ- and δ+ charge (δ = partial)
– The oxygen in water is more electronegative than
the hydrogen
• The oxygen nucleus has a greater attraction for electrons
than the hydrogen nucleus, so the oxygen will have a δ-
charge, leaving the hydrogen with a δ+ charge
 Polarity of water causes hydrogen bonding

 Water molecules are held together by H-bonding

 Partially positive H attracted to partially negative O atom.

 Individual H bond are weak, but the cumulative effect of

many H bonds is very strong.

 H bonds only last a fraction of a second, but at any

moment most molecules are hydrogen bonded to others.
Unique properties of water caused by H-bonds
– Cohesion: Water molecules stick to each other. This
causes surface tension.
• Film-like surface of water is difficult to break.
• Used by some insects that live on water surface.
• Water forms beads.

– Adhesion: Water sticks to many surfaces.

Capillary Action: Water tends to rise in narrow tubes.
This is caused by cohesion and adhesion (water
molecules stick to walls of tubes).
Examples: Upward movement of water through plant
vessels and fluid in blood vessels.
Unique properties of water caused by H-bonds
– Expands when it freezes.
• Ice forms stable H bonds, each molecule is bonded to four
neighbors (crystalline lattice).
– Water does not form stable H bonds.

• Ice is less dense than water.

• Ice floats on water.

• Life can survive in bodies of water, even though the earth

has gone through many winters and ice ages
 Unique properties of water caused by H-bonds
– Stable Temperature: Water resists changes in
temperature because it has a high specific heat.
• Specific Heat: Amount of heat energy needed to raise 1 g of
substance 1 degree Celsius
– Specific Heat of Water: 1 calorie/gram/oC

• High heat of vaporization: Water must absorb large amounts of

energy (heat) to evaporate.
– Heat of Vaporization of Water: 540 calorie/gram.
• Evaporative cooling is used by many organisms to regulate body
temperature.
– Sweating
– Panting
Unique properties of water caused by its polarity
– Universal Solvent: Dissolves many (but not all)
substances.
Two Types of Solutes:
A. Hydrophilic: “Water loving” dissolve easily in water.
• Ionic compounds (e.g. salts)
• Polar compounds (molecules with polar regions)
• Examples: Compounds with -OH groups (alcohols).
• “Like dissolves in like”
B. Hydrophobic: “Water fearing” do not dissolve in water
• Non-polar compounds (lack polar regions)
• Examples: Hydrocarbons with only C-H non-polar bonds, oils,
gasoline, waxes, fats, etc.
 References
DM Vasudevan, Sreekumari S. Text Book of Biochemistry
for Medical Students, 7th Edition. Jaypee Brothers Medical
Publishers Ltd. New Delhi

Murray R.K et al. Harper's illustrated Biochemistry 30th

edition .
Pamela C.C, and Richard A.H., Lippincott's Illustrated
Reviews: Biochemistry 6th edition, J.B.
 Thomas M. Devlin. Text Book of Biochemistry with
Clinical Correlations. 7th Edition, Wiley-Liss Publication,
USA

 Marks' Essential Medical Biochemistry, 4th Edition Copyright

Lippincott Williams & Wilkins.
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