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
• 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
• 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
• 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)