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.

Introduction into biochemistry&

Chemical composition of living organisms

Dr. Mamoun AhramLecture 1

Reference

• Campbell and Farrell, Page 35-43

)أال له الخلق واألمر(

AnatomyPhysiology and

biochemistry

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)