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Introductory Biochemistry

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; 6 th edition. Recommended electronic web address. NCBI Bookshelf:

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Introductory Biochemistry

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  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: (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

  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. 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

  17. 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

  18. Others… • Minor, but essential, elements • Mostly metals

  19. 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

  20. Chemical bonds

  21. 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

  22. 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

  23. Covalent bonds

  24. 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

  25. Single and double bonds • Most are single bonds • Some are double bonds

  26. 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

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

  28. 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

  29. Non-covalent interactions

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

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

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

  33. Donor and acceptor

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

  35. Hydrophobic interactions • Not true bonds

  36. Carbon

  37. 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

  38. Water

  39. 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

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

  41. 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

  42. Organic compounds and functional groups

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

  44. 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

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