Introduction to HGP from 1990, completed in 2003

BIOCHEMISTRY
Biochemistry
 The chemistry of life
 The science that deals with the chemical basis of
life.
 The science concerned with different molecules
that occur in living cells and organisms and their
interactions.
Essential / important to all life sciences
• Genetics; Cell biology; Molecular biology
• Physiology and Immunology
Genome - the genetic material of an organism
• Pharmacology and Pharmacy
Polymers and Monomers
• Toxicology; Pathology; Microbiology
• Zoology and Botany  Each of these types of molecules are polymers
that are assembled from single units called
Two notable breakthroughs monomers.
(1) Discovery of the role of enzymes as catalysts
 Each type of macromolecule is an assemblage of
(2) Identification of nucleic acids as information a different type of monomer.
molecules
Macromolecule Monomer
Flow of information: from nucleic acids to proteins  Carbohydrates Monosaccharide

DNA RNA Protein  Lipids Not always polymers;

Hydrocarbon chains

Some historic events  Proteins Amino acids

 In 1937， Krebs for the discovery of the Citric  Nucleic acids Nucleotides
Acid Cycle-won the Nobel Prize in Physiology or
Medicine in 1953 How do monomers form polymers?

 In 1953，Watson & Crick for the discovery of the  In condensation reactions (also called
“DNA Double Helix” -won the Nobel Prize in dehydration synthesis), a molecule of water is
Physiology or Medicine in 1962 removed from two monomers as they are
connected together.

Anabolic
Building block Macromolecule
 Simple sugar  Polysaccharide
 Amino acid  Protein (peptide)
 Nucleotide  RNA or DNA
 Fatty acid  Lipid

Catabolic
Principles of Biochemistry Carbon can form immensely diverse compounds, from
simple to complex.
 Cells (basic structural
units of living organisms) are
highly organized and constant
source of energy is required to
maintain the ordered state.
 All organisms use the
same type of molecules:
carbohydrates, proteins, lipids &
nucleic acids.
 Living processes contain
thousands of chemical pathways. Precise Methane with 1 Carbon DNA with tens of Billions of
regulation and integration of these pathways are atom Carbon atoms
required to maintain life.
 Instructions for growth, reproduction and
developments for each organism is encoded in
their DNA.
 Just like cells are building blocks of tissues,
biomolecules are building blocks of cells.
 Animal and plant cells contain approximately
10,000 kinds of biomolecules.
 Water constitutes 50-95% of cells content by
weight.
 Ions like Na+, K+ and Ca2+ may account for another
1%.
 Almost all other kinds of biomolecules are
organic (C, H, N, O, P, S).
 Organic compounds are compounds composed
primarily of a Carbon skeleton.

Biomolecules
are
compounds
of carbon
with a variety
of functional
groups
Types of biomolecules  All cells use carbohydrates for cell walls (if
present), and energy generation
Small molecules:
How much biochemistry do you need to know for this
 Lipid, phospholipid, glycolipid, sterol,
course?
 Vitamin
1. You are expected to learn the structure and
 Hormone, neurotransmitter
functions of these organic compounds:
 Carbohydrate, sugar
 Carbohydrates
Monomers:  Lipids
 Proteins
 Amino acids
 Nucleic Acids
 Nucleotides
2. You will be expected to learn the basic
 Monosaccharides
biochemical processes of major cell functions,
Polymers: such as respiration, protein synthesis and so on.
 Peptides, oligopeptides, polypeptides, proteins Importance
 Nucleic acids, i.e. DNA, RNA
• Biochemistry is used to learn about the biological
 Oligosaccharides, polysaccharides (including processes which take place in cells and
cellulose) organisms.
Chemical composition of a normal man (weight 65 kg) • Biochemistry may be used to study the
properties of biological molecules, for a variety of
Constituent Percent (%) Weight (kg) purposes. For example, a biochemist may study
the characteristics of the keratin in hair so that a
Water 61.6 40 shampoo may be developed that enhances
curliness or softness.
Protein 17.0 11 • Biochemists find uses for biomolecules. For
example, a biochemist may use a certain lipid as
a food additive.
Lipid 13.8 9
• Alternatively, a biochemist might find a
Carbohydrate 1.5 1 substitute for a usual biomolecule. For example,
biochemists help to develop artificial sweeteners.
Minerals 6.1 4 • Biochemists can help cells to produce new
products. Gene therapy is within the realm of
biochemistry. The development of biological
machinery falls within the realm of biochemistry.
Structural hierarchy in the molecular organization of
• Biochemists find uses for biomolecules. For
cells
example, a biochemist may use a certain lipid as
a food additive.
• Alternatively, a biochemist might find a
substitute for a usual biomolecule. For example,
biochemists help to develop artificial sweeteners.
• Biochemists can help cells to produce new
products. Gene therapy is within the realm of
biochemistry. The development of biological
machinery falls within the realm of biochemistry.

THE BIOCHEMISTRY OF WATER

Similarities among all types of cells The Chemical Structure Of Water

 All cells use nucleic acids (DNA) to store

information
Except RNA viruses, but not true cells
 All cells use nucleic acids (RNA) to access
stored information
 All cells use proteins as catalysts (enzymes) for
chemical reactions
Different types of lipids in different types of
cells
 Oxygen atom is more electronegative that
hydrogen atom  electrons spend more time
 around oxygen atom than hydrogen atom 
result is a polar covalent bond.
 Creates a permanent dipole in the molecule.
 Can determine relative solubility of molecules
“like dissolves like”.
Hydrogen bonds
 Due to polar covalent bonds  attraction of
water molecules for each other.
 Creates hydrogen bonds = attraction of one
slightly positive hydrogen atom of one water
molecule and one slightly negative oxygen atom
of another water molecule.
 Hydrogen bonds give water a high melting point
 Density of water decreases as it cools  water
expands. As it freezes  ice results from an open
lattice of water molecules  less dense, but
more ordered.
 Hydrogen bonds contribute to water’s high
specific heat (amount of heat needed to raise the
temperature of 1gm of substance 1oC) – due to
the fact that hydrogen bonds must be broken to
increase the kinetic energy (motion of molecules)
and temperature of a substance  temperature
fluctuation is minimal.
 Water has a High heat of vaporization – large
amount of heat is needed to evaporate water
because hydrogen bonds must be broken to
change water from liquid to gaseous state.
Universal solvent
 Water can interact with and dissolve other polar
compounds and those that ionize (electrolytes)
because they are hydrophilic.
 Do so by aligning themselves around the
electrolytes to form solvation spheres – shell of
water molecules around each ion.
 Solubility of organic molecules in water depends
on polarity and the ability to form hydrogen
bonds with water.
Hydrophobic interactions
 Nonpolar molecules are not soluble in water
because water molecules interact with each
other rather to nonpolar molecules
 Nonpolar molecules are excluded and
associate with each other (known as the
hydrophobic effect)
 Nonpolar molecules are hydrophobic.
 Molecules such as detergents or surfactants are
amphipathic (have both hydrophilic and
hydrophobic portions to the molecule).
PROPERTIES OF WATER
1. Water exists in three states ( Liquid – aquatic
environment outside us and inside us), solid (ice) and gas
(steam)
2. Surface Tension – the property of the surface of a
liquid that allows it to resist an external force, due to the
cohesive nature of the water molecules.
3. Cohesion – water molecules stick to each other held
together by H-bonds.
4. Adhesion – water molecules stick to unlike surfaces
such as glass or plastic due to H-bonds between water
and other polar compounds.
5. High Specific Heat – water can absorb or release large
amounts of heat energy with little temp change. E.g.
Water stabilizes temp. in cells and ecosystems
6. High Heat of Vaporization – many H-bonds must be
broken before water can evaporate.
7. Lower Density of Ice – water molecules in an ice crystal
are further apart because of H bonding.
8. Water is Polar – a good solvent; surrounds ions and
other polar molecules. E.g. Transport of nutrients in
organisms- plasma, cytoplasm, and xylem.
9. Medium for Chemical Reactions:
hydration/dehydration reactions.
Those molecules that are not soluble in water are
hydrophobic (water hating or fearing).
1. Hydrophobic molecules – repel water. Amphipathic
molecules -have both hydrophilic and hydrophobic
properties
• Acids and Bases Must Be Balanced in Cells
– An acid is a chemical substance that donates a
H+ to a solution; a base accepts the H+
– The pH scale indicates the acidity or alkalinity of
a solution
– Cell chemistry is very sensitive to changes in pH
  A suspension differs from a solution because the
particles of a suspension are much larger and do not
stay suspended indefinitely.
– The particles in a typical suspension have an
average diameter greater than 1000 nm.
– By contrast, the particle size in a solution is
usually about 1 nm.
– A solution is a homogeneous mixture.
– Suspensions are heterogeneous because at
least two substances can be clearly identified.

The difference between a solution and suspension is

easily seen when the type of mixture is filtered.

The small size of the solute The particles of a

particles in a solution allows suspension can be
them to pass through filter removed by filtration.
paper.

Explain why a mixture of sand and water can be

separated by filtration, but a mixture of salt and water
cannot.

A mixture of sand and water is a suspension, and a

mixture of salt and water is a solution. The particles in
the sand mixture are much larger than the ions in the salt
mixture. The sand particles are too large to pass through
filter paper; the ions are not.

COLLOIDS

What distinguishes a colloid from a suspension and a

solution?

 A colloid is a heterogeneous mixture containing

particles that range in size from 1 nm to 1000 nm.
– The particles are spread, or dispersed,
throughout the dispersion medium, which
can be a solid, liquid, or gas.

The first substances to be identified as colloids were

glues.

THE COLLOIDAL STATE OF MATTER

Why are some sunsets red?

The atmosphere contains particles of water and dust.

As sunlight passes through the particles, it is scattered.
However, not all wavelengths are scattered to the same
extent.

SUSPENSIONS

What is the difference between a suspension and a

solution?
 Colloids have particles smaller than those in
A suspension is a mixture from which particles settle
suspensions and larger than those in solutions.
out upon standing.
 – These intermediate-sized particles cannot be – The particles can clump together to form
retained by filter paper as are the larger heavier aggregates and settle out from
particles of a suspension. the dispersion.
– They do not settle out with time.
EMULSIONS
THE TYNDALL EFFECT
 An emulsion is a colloidal dispersion of a liquid in
 You cannot see a beam of sunlight unless the a liquid.
light passes through particles of water (mist) or – An emulsifying agent is essential for the
dust in the air. formation of an emulsion and for
– These particles scatter the sunlight. maintaining the emulsion’s stability.
– Similarly, a beam of light is visible as it – Oils and greases are not soluble in water.
passes through a colloid. – However, oils and greases readily form a
 The scattering of visible light by colloidal particles colloidal dispersion if soap or detergent is
is called the Tyndall effect. added to the water.
– One end of a large soap or detergent
molecule is polar and is attracted to
water molecules.
– The other end of the soap or detergent
molecule is nonpolar and is soluble in oil
or grease.
– Soaps and other emulsifying agents thus
Flashlight
allow the formation of colloidal
Solution Colloid Suspension
dispersions between liquids that do not
– Suspensions also exhibit the Tyndall ordinarily mix.
effect.
This table summarizes the properties of solutions,
– The particles in solutions are too small to
colloids, and suspensions.
scatter light.

What would be the ideal conditions to see a red sunset?

 A misty or foggy evening would be ideal for

seeing a red sunset. There would be a large
number of particles to scatter the sunlight.

BROWNIAN MOTION

 Flashes of light, or scintillations, are seen when

colloids are studied under a microscope.
– Colloids scintillate because the particles
reflecting and scattering the light move
erratically.
 The chaotic movement of colloidal particles,
which was first observed by the Scottish botanist
Robert Brown (1773–1858), is called Brownian
motion.
 Brownian motion is caused by collisions of the
molecules of the dispersion medium with the
small, dispersed colloidal particles.
– These collisions help prevent the colloidal
particles from setting.
COAGULATION
A suspension differs from a solution because the
particles of a suspension are much larger and do
not stay suspended indefinitely.
Colloids have particles smaller than those in
suspensions and larger than those in solutions.
suspension: a mixture from which some of the
particles settle out slowly upon standing
colloid: a mixture whose particles are intermediate
in size between those of a suspension and a solute
solution

 Colloidal particles also tend to stay suspended Tyndall effect: scattering of light by particles in a
because they become charged by adsorbing ions colloid or suspension, which causes a beam of light
from the dispersing medium onto their surface. to become visible
– Adsorption means to adhere to a surface.
 All the colloidal particles in a particular colloidal Brownian motion: the chaotic movement of
system will have the same charge, although the colloidal particles, caused by collision with particles
colloidal system is neutral. of the solvent in which they are dispersed
– The repulsion between the like-charged
particles prevents the particles from emulsion: the colloidal dispersion of one liquid in
forming heavier aggregates that would another
have a greater tendency to settle out.
 A colloidal system can be destroyed or
coagulated by the addition of electrolytes.
– The added ions neutralize the charged
colloidal particles.