1. Dr. Amina R ELGezeery Biochemistry Dept King Saud University

2. Continuous Assessment Tests (CAT) Two Tests --------------------------40 Marks Two Quiz --------------------------10 Marks Final----------------------------------50 Marks Dates for CAT: – 1st CAT: … Saturday 22 Dhu-Al-Qadah 1431 – 2nd CAT: Saturday ……… 5 Muharram 1432 Time: 12-1.00 Lecture Room: To be announced

3. Ref.Books Biochemistry by Lehninger: Pronciples of Biochemistry by DL. Nelson and MI. Cox -Biochemistry : Lippincott illustrated reviews. By : Champe P.C & Harvey R.A

4. Biochemistry can be defined as the science concerned with the chemical basis of life The cell is the structural unit of living systems. Thus, biochemistry can also be described as the science concerned with the chemical constituents of living cells and with the reactions and processes they undergo. Biochemistry

5. The Aim of Biochemistry Is to Describe &Explain, in Molecular Terms, All Chemical Processes of Living Cells

6. Biochemistry describes in molecular terms the structures,mechanisms, and chemical processes shared by all organisms and provides organizing principles that underlie life in all its diverse forms, principles we refer to collectively as the molecular logic of life. Biochemistry provides important insights and practical applications in medicine, agriculture, nutrition, and Industry.

7. Outline of lectures 1-6

8. What is matter ?

9. What is matter made of ?

10. Common Elements

11. What are elements made of ?

12. Atomic Structure

13. Structure of an Atom

14. Elements in Living and Non- Living Materials

15. Living and Non-living

16. Distinctive Properties of Living Systems Systems

17. Properties of Life

19. The hirerarchy in the molecular organization of cells

21. Organization Organismal level

23. The Levels of organization in cells

24. Structural hierarchy in the molecular organization of cells In this plant cell, the nucleus is an organelle containing several types of supramolecular complexes, including chromosomes. Chromosomes consist of macromolecules of DNA and many different proteins. Each type of macromolecule is made up of simple subunits—DNA of nucleotides (deoxyribonucleotides), for example.

26. Biomolecules Four major classes :

28. Polymers ands Monomers  Each of these types of biomolecules are polymers that are assembled from single units called monomers.

29. Biomolecule Carbohydrates Lipids Proteins Nucleic acids Monomer Monosaccharide Not always polymers; Hydrocarbon chains Amino acids Nucleotides

30. How do monomers form polymers?? In condensation reactions (also called  dehydration reaction), a molecule water is removed from two monomers and they are connected together.

31. Synthesis of Polymer Dehydration

32. Hydrolysis

33. 5 60.3 25.5 10.5 2.4

35. The four most abundant elements in living organisms, in terms of percentage of total number of atoms, are hydrogen, oxygen, nitrogen, and carbon, which together make up more than 99% of the mass of most cells. They are the lightest elements capable of forming one, two, three, and four coavelent bonds, respectively;. Thus they can react with each other to form a large number of different coavelent compounds.

36. Strengths of Bonds Common in Biomolecules

37. Organic substances are made of Carbon

39. Examples of ring & long chain carbon compounds

43. Biomolecules Are Compounds of Carbon with a Variety of Functional Groups -The chemistry of living organisms is organized around carbon, which accounts for more than half the dry weight of cells. Why carbon is special? -Carbon can form single bonds with hydrogen atoms, and both single and double bonds with oxygen and.nitrogen atoms -the ability of carbon atoms to form very stable carbon–carbon single bonds. Each carbon atom can form single bonds with up to four other carbon atoms. Two carbon atoms also can share two (or three) electron pairs, thus forming double (or triple) bonds.

44. Versatility of carbon bonding. Carbon can form covalent single, double, and triple bonds (in red), particularly with other carbon atoms. Triple bonds are rare in biomolecules.

45.  Carbon atom posses a significant property; capacity to bond with each other. ( since a carbon atom may either accept or donate four electrons to complete an outer octet, it can form covalent bonds with other four carbon atoms )  In this way covalently linked carbon atoms can form linear or branched or cyclic backbones of different organic molecules.

46. - The four single bonds that can be formed by a carbon atom are arranged tetrahedrally, with an angle of about 109.5 between any two bonds (Fig.) and an average length of 0.154 nm. - There is free rotation around each single bond, unless very large or highly charged groups are attached to both carbon atoms, in which case rotation may be restricted. -A double bond is shorter (about 0.134 nm) and rigid and allows little rotation about its axis. - Thus organic molecules with many single bonds can assume a number of different shapes, called conformation, depending on the degree to which each single bond is rotated.

47. Geometry of carbon bonding. (a) Carbon atoms have a characteristic tetrahedral arrangement of their four single bonds. (b) Carbon–carbon single bonds have freedom of rotation, as shown for the compound ethane (CH3OCH3). (c) Double bonds are shorter and do not allow free rotation. The two doubly bonded carbons and the atoms designated A, B, X, and Y all lie in the same rigid plane.

48.  As a result, organic biomolecules have characteristic size and three dimensional conformation.  The three dimensional conformation of biomolecules is important in many aspects of biochemistry, eg. :  - In the reaction between the catalytic site of an enzyme and its substrate, the two molecules must fit each other.  - Also hormone and receptor.  - Replication of DNA.

49. . To these carbon skeletons are added groups of other atoms, called functional groups, which confer specific chemical properties on the molecule. It seems likely that the bonding versatility of carbon was a major factor in the selection of carbon compounds for the molecular machinery of cells during the origin and evolution of living organisms. No other chemical element can form molecules of such widely different sizes and shapes or with such a variety of functional groups.