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)