Foundations of
Biochemistry
Doba Jackson, Ph.D.
Dept. of Chemistry & Biochemistry
Huntingdon College
Biological organisms have extroordinary
properties that distinguish them from
other forms of matter
• High degree of chemical complexity
and organization (muscle tissue)
• System for extracting energy from
the environment (bird)
• The ability to self-replicate (zebra)
• Ability to sense changes in the
surroundings and respond
• Defined functions of each
component and regulated
interactions
•
The ability to adapt with time (evolution)
Three stages of Life’s
development
• Chemical Evolution- Simple chemicals reacted
early in life’s existence to form biological polymers
(DNA, RNA, Proteins, complex Carbohydrates).
• Biochemical Evolution- Self-organization of
biological polymers to form a living system.
• Biological Evolution- Changes within living
systems to form the complex degree of differences
in modern life forms.
Chemical Foundations
“What are the common chemical
principals important to all cells”
Only 30 of the 90 naturally
occuring elements are found in
biological systems
Components of macromolecules:
the ABC’s of Biochemistry
Proteins
Nucleic Acids
Lipids
Carbohydrates
Biomolecules
are hydrocarbons
You
must remember
all of these
with attached
functionalfunctional
groups!!!!!groups
What do these have in common?
Hydrocarbons
What do these have in common?
All have carbon-oxygen bonds
What do these have in common?
All have carbon-nitrogen bonds
What do these have in common?
All have carbon-sulfur bonds
What do these have in common?
All have carbon-phosphate bonds
Some Definitions
• Chiral center- a carbon atom with four different
a substituents (ie.- asymmetric carbon)
• Enantiomers- pairs of stereoisomers that are
mirror images of each other.
• Diastereomers- pairs of stereoisomers that are
not mirror images of each other.
Enantiomers
4 substituents
Same molecule
3 substituents
Example: 2,3 disubstituted butanes
Stereoisomers distinguisable by
taste
Aspartate
Phenylalanine
Summary of chemical
foundations
• Only 30 of the 90 naturally occuring elements are
found in biological systems
• 99.9% of biomolecules are considered organic
compounds
• Most biomolecules have more than one functional
group
• Conformation, configuration, and constitution are all
important factors for determination of biological
activity
Hierarchy in the molecular
organization
Atoms, macromolecules and supramolecular
complexes are held in place by non-covalent
interactions
Atoms are held
together by covalent
interactions
Why do biological reactions occur so fast?
Enzymes provide a easier path for a chemical or a pair of
chemicals to reach their transition state by selective
binding and stabilization
- DNA exist as a double helix
- Each strand is separated and
replicated independently
- DNA strands are long and very thin
(some DNA strands may approach a
meter in length however all DNA has a
with of 10 Ǻ.
Evolutionary Foundations
Three stages of Life’s
development
• Chemical Evolution- Simple chemicals reacted
early in life’s existence to form biological polymers
(DNA, RNA, Proteins, complex Carbohydrates).
• Biochemical Evolution- Self-organization of
biological polymers to form a living system.
• Biological Evolution- Changes within living
systems to form the complex degree of differences
in modern life forms.
Mutation & Evolution
Stanley Miller’s 1953 experiment
Small Organic &
Biological molecules
Some Organic molecules from
Stanley Miller’s Experiment
Small Organic Molecules
O
H3C
OH
H 3C
N
Acetonitrile
Acetate
Small Biological Molecules
O
O
H2N
NH
HN
OH
Glycine (Gly)
O
Uracil
O
H
H
H
OH
OH
OH
OH
D-Ribose
RNA world: Why must RNA
had to exist before DNA
• RNA is less stable than DNA- More
susceptible to hydrolysis
• RNA can adopt more unique structures
• RNA can serve as a template for RNA
synthesis
• RNA can serve as an enzyme (catalyst)