Introductory Biochemistry

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Theodore Edwards
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1 Introductory Biochemistry

2 Instructors Dr. Nafez Abu Tarboush Dr. Mamoun Ahram

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

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

5 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)

6 Mid-term (preliminary) Sunday, July 1

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

8 Reference Campbell and Farrell, Page 35-43

9 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

10 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)

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

12 The chemical elements

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

15 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

16 Others Minor, but essential, elements Mostly metals

17 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

18 CHEMICAL BONDS

19 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

21 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

22 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

Properties of water Polar molecule Bent,

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

47 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

48 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)

Introduction into Biochemistry. Dr. Mamoun Ahram Lecture 1

Introduction into Biochemistry Dr. Mamoun Ahram Lecture 1 Course information Recommended textbooks Biochemistry; Mary K. Campbell and Shawn O. Farrell, Brooks Cole; 7 th edition Instructors Dr. Mamoun