1. Introductory Biochemistry

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

3. Recommended textbooks
Biochemistry; Mary K. Campbell and Shawn O. Farrell, Brooks Cole; 6th edition

4. Recommended electronic web address
NCBI Bookshelf: (
The Medical Biochemistry Page: (
Biochemistry, Garret and Grishan, Second Ed.:

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

6. 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)

7. 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

8. 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.

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

10. Reference
Campbell and Farrell, Page 35-43

11. (ألا له الخلق والأمر)
Physiology
and
biochemistry
Anatomy

12. 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

13. 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)

14. Biochemistry and medicine
diagnose and monitor diseases
design drugs (new antibiotics, chemotherapy agents)
understand the molecular bases of diseases

15. The chemical elements

16. Chemical elements in living creatures
Living organisms on Earth are composed mainly of 31 elements

18. 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

19. Others…
Minor, but essential, elements
Mostly metals

20. 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

21. Chemical bonds

22. 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

24. 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

25. Covalent bonds

27. 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

28. Single and double bonds
Most are single bonds
Some are double bonds

29. 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

30. Polarity of covalent bonds
Covalent bonds in which the electrons are shared unequally in this way are known as polar covalent bonds

31. 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

32. Non-covalent interactions

33. What are they? Reversible and relatively weak
Electrostatic interactions, hydrogen bonds, and van der Waals interactions

34. Electrostatic interactions (charge-charge interactions)
Formed between two charged particles
These forces are quite strong in the absence of water

35. Hydrogen bonds
The hydrogen atom in a hydrogen bond is partly shared between two relatively electronegative atoms

36. Donor and acceptor

37. van der Waals interactions
The distribution of electronic charge around an atom changes with time
The strength of the attraction is affected by distance

38. Hydrophobic interactions
Not true bonds

39. Carbon

40. 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

41. Water

42. 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

43. Hydrogen bonds
Each water molecule can form hydrogen bonds through its two H atoms to two other water molecules, producing a network

44. 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

45. Organic compounds and functional groups

46. Functional groups Groups of atoms attached to carbon skeleton
Usually hydrophilic

50. 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

51. 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)