Module 1 Biological Molecules

1. Module 1Biological Molecules F212 Molecules, biodiversity, food and health

2. Biological molecules Water Intro to biological molecules Proteins Carbohydrates Lipids Practical biochemistry Nucleic acids Enzymes Module 1 Topics

3. Learning Outcomes • describe how hydrogen bonding occurs between water molecules, and relate this, and other properties of water, to the roles of water in living organisms

4. Definitions • Covalent bond • Formed when atoms share electrons • Strong bonds • Hydrogen bond • Weak interaction that occurs when a negatively charged atom is bonded to a positively charged hydrogen

5. Water • 60 – 70 % of mammals • About 90% of plants • Life originated in water • Good solvent • What else do you know about little old dihydrogen monoxide (DHMO)

6. Water is a liquid • A polar molecule • Made up of two positively charged hydrogen atoms and one negatively charged oxygen • Covalent bonds form between oxygen and hydrogen with electrons shared between them. • Hydrogen bonds form between water molecules • Up to four may form clusters which break and reform all the time

7. Water molecule

8. Hydrogen Bonds in water Hydrogen bonds

9. Key features of water • Key features of water as a constituent of living organisms • Good solvent • High specific heat capacity • High latent heat of vaporisation • High cohesion • Reactive • Incompressibility

10. Learning Outcomes • To be able to • Define metabolism • State the functions of biological molecules • Name monomers and polymers of carbohydrates, fats, proteins and nucleic acids • Describe general features of condensation and hydrolysis reaction

11. Biological Molecules • Molecular biology • the study of structure and functioning of biological molecules. • Metabolism • sum total of all biochemical reactions in the body.

12. Nutrients and Health • To maintain a healthy body • Carbohydrates • Lipids • Proteins • Vitamins and minerals • Nucleic acid • Water • fibre

13. Key Biological Molecules • There are 4 key biological molecules • Carbohydrates • lipids • proteins • nucleic acids

14. Building blocks of life • 4 most common elements in the living organisms • hydrogen • carbon • oxygen • nitrogen

15. Biochemicals and bonds • Covalent bonds join atoms together to form molecules • Carbon is able to make 4 covalent bonds • Carbon can bond to form chains or rings with other atoms bonded to the chain • Carbon can also form double bonds • E.g. C=C or C=O

16. Polymers • “poly” means “many” = polymers • Macromolecules are made up of repeating subunits that are joined end to end, they are easy to make as the same reaction is repeated many times. • Polymerisation is the making of polymers.

17. Macromolecules

18. Metabolism • Metabolism is the sum of all of the reactions that take place within organisms • Anabolism • Build up of larger, more complex molecules from smaller, simpler ones • This process requires energy • Catabolism • The breakdown of complex molecules into simpler ones • This process releases energy

19. Condensation reactions • In a condensation reaction • A water molecule is released • A new covalent bond is formed • A larger molecule is formed by bonding together of smaller molecules

20. Hydrolysis Reactions • In hydrolysis reactions • A water molecule is used • A covalent bond is broken • Smaller molecules are formed by the splitting of a larger molecule

21. Hydrolysis and condensation OH HO CONDENSATION HYDROLYSIS O

22. Learning Outcomes • describe, with the aid of diagrams, the structure of an amino acids • describe, with the aid of diagrams, the formation and breakage of peptide bonds in the synthesis and hydrolysis of dipeptides and polypeptides

23. Introduction to protein • 50% of the dry mass of cells is protein • Important functions include • Cell membranes • Haemoglobin • Anti-bodies • Enzymes • Keratin (hair and skin) • collagen

24. Structure of proteins • All proteins are made up of the same basic components  amino acids • There are 20 different amino acids, which alter by having different residual groups (R groups) • A single chain of amino acids makes a polypeptide

25. Structure of an amino acid • Amino acids contain • Amine group (NH2) • Carboxylic acid group (COOH) Joined at the same C atom

26. Structure of an amino acid R group varies in different amino acids R O H C C N OH H H Amine group Carboxyl group

27. TEST TIME • Build an amino acid using the molymod models • Glycine is an amino acid where the R group is hydrogen – change you molecule into glycine • Build a dipeptide using the molymod models

28. Different Amino Acids • Glycine R group = H • Alanine R group = CH3 • Valine R group = C3H7 • You will be expected to learn how to draw the basic structure of an amino acid. Remember that each Amino acid has it’s own specific R group

29. Learning Outcomes • explain, with the aid of diagrams, the term ‘primary structure’ • explain, with the aid of diagrams, the term ‘secondary structure’ with reference to ‘hydrogen bonding’

30. Peptide bond R O H R O H N C C N C C H H H OH Peptide bond

31. Building a polypeptide • Peptide bonds are formed in condensation reactions • Primary structure • The primary structure of a polypeptide is its amino acid sequence • This is determined by the gene that codes for the polypeptide Peptide Bond Amino acid

32. Secondary Structure • Polypeptides become twisted or coiled • They fold into one of two structures • Alpha helix (right handed helix) • Beta-pleated sheet • Hydrogen bonds hold coils in place • Weak but give stability to the parts of a protein molecule. C O H N

33. Learning Outcomes • explain, with the aid of diagrams, the term ‘tertiary structure’ with reference to hydrophobic and hydrophilic interactions, disulphide bonds and ionic interactions

34. Tertiary Structure • Folding of the polypeptide to give a more complex 3-D shape, the shape is specific to the function of the polypeptide. • Examples • Hormone must fit into the hormone receptor in a target cell • Enzymes have a complementary active site to it’s substrate

35. Tertiary Structure - bonds • Four types of bond help to hold the folded proteins in their precise shape. • Hydrogen Bonds • Disulphide bonds • Ionic bonds • Hydrophobic interactions

36. Hydrogen Bonds • Between polar groups • Electronegative oxygen atoms of the –CO • Electropositive H atoms on either the –OH or –NH groups.

37. Disulphide bonds • Between sulfur-containing R groups of the amino acid cysteine. • Covalent bonds • Form strong links which make the tertiary protein structure very stable. • This bond can be broken by reducing agents

38. Ionic Bonds • Between R groups, which ionise to form positively and negatively charged groups that attract each other.

39. Hydrophobic Interactions • These are interactions between the non-polar side chains of a protein molecule. • The bond forms between non-polar, hydrophobic R groups on the amino acids. • Once the two hydrophobic molecules are close together the interaction is reinforced by Van der Waals attractions (which provide the weak bond).

40. Van der Waals attractions • Electrons are always in motion, and are not always evenly distributed about a molecule. • This results in areas of positive and negative charge, which are continuously changing, and enables molecules to “stick” to one another.

41. Denaturing Protein • The Polar R groups of proteins interact with water forming hydrogen bonds that face outwards, This creates a hydrophobic core to the molecule • When proteins are heated these bonds break, the tertiary structure changes and the protein does not function. • The destruction of shape or loss of function is denaturation.

42. Denaturing Proteins • Frying an egg

43. Learning Outcomes • explain, with the aid of diagrams, the term ‘quaternary structure’, with reference to the structure of haemoglobin

44. Quaternary Structure • Association of different polypeptide chains bonded together to form intricate shapes • Sometimes contain prosthetic groups, which are a permanent part of a protein molecule but not made of amino acids

45. Quaternary Structure • Globular protein • Molecules curl up into a “ball” shape • Examples – myoglobin, haemoglobin • Metabolic roles • Fibrous Proteins • Form long strands • Usually insoluble • Have a structural role • Examples – keratin, collagen

46. Haemoglobin • Function – oxygen carrying pigment found in red blood cells • Structure • 4 polypeptides • 2 x α-globin • 2 x β-globin • Each polypeptide has a 3o structure stabilised by hydrophobic interactions in the centre • In the middle each polypeptide in a haem group

47. OK so let’s summarise proteins

48. Protein structure and diversity • It is difficult to describe in a simple sentence the role of proteins. • when there is something to do, it is a protein that does it. • Therefore proteins are • important • numerous • very diverse • very complex, • able to perform actions and reactions under some circumstances

49. Some examples of proteins • Antibodies: • they recognise molecules of invading organisms. • Receptors: • part of the cell membrane, they recognise other proteins, or chemicals, and inform the cell... • Enzymes: • assemble or digest. • Neurotransmitters and some hormones: • Trigger the receptors... • Channels and pores: • holes in the cell membrane

50. Summary of levels of protein structure • Primary Structure • Amino acids linked in a linear sequence • Secondary Structure • folding or coiling of polypeptide • Tertiary structure • Folding of polypeptide by disulphide bonds, ionic bonds, hydrogen bonds or hydrophobic interactions • Quaternary structure • Two or more polypeptides bonded together