Introductory Biochemistry
Instructors
• Dr. Nafez Abu Tarboush
• Dr. Mamoun Ahram
Recommended textbooks
• Biochemistry; Mary K. Campbell and Shawn O.
Farrell, Brooks Cole; 6th edition
Recommended electronic web address
• NCBI Bookshelf:
(http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=
Books)
• The Medical Biochemistry Page:
(http://web.indstate.edu/thcme/mwking/home.html)
• Biochemistry, Garret and Grishan, Second Ed.:
http://web.virginia.edu/Heidi/home.htm
Outline
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Introduction (MA)
Acid, base, and pH (MA)
Macromolecules and carbohydrates (MA)
Lipids (MA)
Nucleic acids and nucleotides (MA)
Amino acids (NA)
Polypeptides and protein structure (NA)
Protein analysis (NA)
Protein structure-function relationship (NA)
Enzymes (NA)
Enzymes (cofactors) (MA)
Mid-term (preliminary)
Sunday, July 1
Introduction into biochemistry
&
Chemical composition of living organisms
Dr. Mamoun Ahram
Lecture 1
Reference
• Campbell and Farrell, Page 35-43
What is biochemistry?
• Biochemistry is the chemistry of living organisms
• It seeks to describe the structure, organization, and
functions of living matter in molecular terms
Understanding life
• Know the chemical structures of biological molecules
• Understand the biological function of these
molecules
• Understand interaction and organization of different
molecules within individual cells and whole biological
systems
• Understand bioenergetics (the study of energy flow
in cells)
Biochemistry and medicine
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diagnose and monitor diseases
design drugs (new antibiotics, chemotherapy agents)
understand the molecular bases of diseases
The chemical elements
Chemical elements in living creatures
• Living organisms on Earth are composed mainly of 31
elements
Abundant elements
• Four primary elements: carbon,
hydrogen, oxygen, and nitrogen
– 96.5% of an organism's weight
• The second groups includes sulfur
and phosphorus
• Most biological compounds are
made of only SIX elements: C, H, O,
N, P, S
Others…
• Minor, but essential,
elements
– Mostly metals
Dalton
• The atomic weight of an atom, or the molecular
weight of a molecule, is its mass relative to that of a
hydrogen atom
– Specified in Daltons
• One Dalton equals to the mass of a hydrogen atom
CHEMICAL BONDS
Types of chemical bonds
• There are two types of chemical bonds between
atoms:
– an ionic bond is formed when electrons are donated
by one atom to another (example: NaCl)
– a covalent bond is formed when two atoms share a
pair of electrons
Important properties of bonds
• Bond strength (amount of energy that must be
supplied to break a bond)
• Bond length: the distance between two nuclei
• Bond orientation: bond angles determining the
overall geometry of atoms
The three-dimensional structures of molecules are
specified by the bond angles and bond lengths for
each covalent linkage
COVALENT BONDS
Properties of covalent bonds
• Bond strength: The strongest bonds
• Bond length: variable
• Bond orientation: specific bond angles determining
the overall geometry of atoms
The three-dimensional structures of molecules are
specified by the bond angles and bond lengths for
each covalent linkage
Single and double bonds
• Most are single bonds
• Some are double bonds
Single vs. double bonds
• O, N, S, P, and C atom
allow double bonds
• Double bonds are shorter
and stronger
• A single covalent bond
allows rotation of a
molecule
Polarity of covalent bonds
• Covalent bonds in which the electrons are shared
unequally in this way are known as polar covalent
bonds
Examples
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Oxygen and hydrogen
Nitrogen and hydrogen
Not carbon and hydrogen
Oxygen and nitrogen atoms are
electronegative
• Water is an excellent example
of polar molecules
NON-COVALENT INTERACTIONS
What are they?
• Reversible and relatively weak
• Electrostatic interactions, hydrogen bonds, and van
der Waals interactions
Electrostatic interactions
(charge-charge interactions)
• Formed between two charged particles
• These forces are quite strong in the absence of water
Hydrogen bonds
• The hydrogen atom in a hydrogen bond is partly
shared between two relatively electronegative atoms
Donor and acceptor
van der Waals interactions
• The distribution of electronic charge
around an atom changes with time
• The strength of the attraction is
affected by distance
Hydrophobic interactions
• Not true bonds
CARBON
Why is carbon important?
• It can form single, double, or triple bonds
• Different geometries
– Rotation
• Stable
• Internediate electronegativity
– Hydrophilic vs. hydrophobinc
• Chains and rings
– backbone
• Versatile three-dimensional structure
WATER
Polarity of water
• Water accounts for about
70% of a cell's weight
• In the water molecule,
oxygen is more
electronegative than
hydrogen; therefore, the
oxygen side of the
molecule has a negative
charge and the other side
has a positive charge
Hydrogen bonds
• Each water molecule can
form hydrogen bonds
through its two H atoms
to two other water
molecules, producing a
network
Properties of water
• Polar molecule
– Bent, not linear, the charge distribution is asymmetric
• An excellent solvent
– It weakens electrostatic forces and hydrogen bonding
– Small size
• Highly cohesive
– Networks of hydrogen bonds
• Reactive
– Nucleophile
• Ionization
ORGANIC COMPOUNDS AND
FUNCTIONAL GROUPS
Functional groups
• Groups of atoms attached to carbon skeleton
– Usually hydrophilic
Functional groups
• Hydroxyl group (-OH)
– -Alcohols. eg. ethanol, sugars, phenol
– -Dissolve in water (sugars)
• Carbonyl group (C=O)
– aldehyde
– ketone
• Carboxyl group (-COOH)
– Carboxylic acids
• formic acid, acetic acid, amino acids
Functional groups
• Amino group (-NH2)
– Amines. eg. amino acids
• Sulfhydryl group (-SH)
– Thiols
• Phosphate group
– Phosphate is formed by dissociation of an acid
called phosphoric acid (H3PO4)