Introductory Biochemistry

Instructors Dr. Nafez Abu Tarboush Dr. Mamoun Ahram Dr. Said Ismail

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 (Ahram) Introduction Acid, base, and pH Macromolecules and carbohydrates Lipids Amino acids Polypeptides and proteins structure Protein analysis

Outline (Abu Tarboush) Protein structure-function relationship (part I: fibrous proteins) Protein structure-function relationship (part II: globular proteins) Enzymes (introduction) Enzymes (kinetics) Enzymes (mechanism of regulation) Enzymes (cofactors)

Outline (Ismail) Nucleic acids structure Replication, synthesis, and repair of DNA Transcription, synthesis of RNA Translation, synthesis of proteins Regulation of Gene Expression Oncogenes and tumor suppressor & cancer Recombinant DNA Technology Gene Therapy Stem cell technology

Office hours Location: Faculty of Medicine, first floor Time: Daily 2-4 Note: If I am not in my office, then try the lab in the third floor. Simply ask for me.

Dr. Mamoun Ahram Lecture 1 Introduction into biochemistry & Chemical composition of living organisms Dr. Mamoun Ahram Lecture 1

Reference Campbell and Farrell, Page 35-43

(ألا له الخلق والأمر) Physiology and biochemistry Anatomy

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) Sulfhydryl group (-SH) Amines. eg. amino acids Sulfhydryl group (-SH) Thiols Phosphate group Phosphate is formed by dissociation of an acid called phosphoric acid (H3PO4)