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 AhramLecture 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)