Introductory Biochemistry
Instructors Dr. Nafez Abu Tarboush Dr. Mamoun Ahram
Recommended textbooks Biochemistry; Mary K. Campbell and Shawn O. Farrell, Brooks Cole; 6 th 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)