Chemistry and Biochemistry Part 3

1. Chemistry and BiochemistryPart 3 For Advanced Diploma students of the WEA Hunter Academy of Complementary Health (c) WEA Hunter Academy of Complementary Health. Created by John Radvan. Reproduction or transmission without the express permission of the author is prohibited.

2. Chapter 5 AMINO ACIDS AND PROTEINS

3. Proteins • Most abundant component of cell • Proteins are made from chains of amino acids • 300 amino acids out there, 20 of biological importance

4. Amino Acid Structure

5. Four groups of amino acids • Split into four groups. Each group will look at an amino acid group. Note the structure and any unique features using p50-52 as a guide. • Draw all the 20 amino acids up on the board (each group draw your own amino acids) • Then share what you learned with everyone else • It’s a symposium!!!

6. Peptide formation • Peptide = joined amino acids • Examine the process in Fig5.4 p54 • C-terminus = end of the chain with a free carboxyl group • N-terminus = end of the chain with a free amino group

7. Primary Structure

8. Primary Structure • Differences in peptide organisation = differences in overall function (function follows form!) • Dipeptide = 20 x 20 = 400 possibilities • Tripeptides = 203 = 8000 possibilities • 20n (where n is number of residues) = number of possible combinations • Primary structure determines the secondary and tertiary structure

9. Primary Structure - effects • Sometimes small differences have large effects – have a look at the handout I gave you: • Insulin example p594 (paragraph 3 ‘Another example...’) • Slight differences – strikingly similar effects • Vasopressin/Oxytocin and Hemoglobin (last paragraph) • Slight differences – dangerously different effects

10. Secondary Structure • Pattern repetition is the key here • Proteins fold and align themselves • Two common secondary structures (Fig 5.6) • α-helix – where a single chain twists to a right handed coil spring by H-bonds parallel to the coils axis • β-pleated sheet – resembles a folded piece of paper by H-bonds between the chain backbones (either intra- or inter-molecularly)

11. Tertiary Structure (Fig 5.7) • This is the 3D arrangement of the protein chain • Tertiary Structures are stabilised in five ways: • Covalent bonds – disulfide bond (S-S) occurs when there are two cysteine residues in the chain/s (also see Fig 5.8) • Hydrogen bonds – either between polar groups on side chains or a side chain and the backbone

12. Tertiary Structure (Fig 5.7) • Ionic bonds – simple attraction between ionized atoms on the side chains • Hydrophobic interaction – nonpolar groups turn inwards toward each other in aqeous solution, this is a weak bond but over a large surface area so they are collectivelystrong • Metal Ion Coordination (not in textbook)– a metal ion (eg Mg2+) can attract two side chains forming a bridge (where they would normally repel).

13. Quatenary Structure • Applies only to proteins with more than one polypeptide chain, these fit together to make a bigger protein • Determines how different subunits of a protein fit together • Held together by hydrogen bonds, ionic bonds, and hydrophobic interactions (just like tertiary structures)

14. Quaternary - Haemoglobin • Four chains of globins: two alpha chains of 141 amino acid residues, and two beta chains of 146 residues • Each globin chain surrounds a heme unit which has an Fe2+ ion • Proteins that have parts that are not amino acids are called conjugated proteins – the non-amino acid part is called the prosthetic group (this is the ‘heme’ in this example) • See video link on Engage Online

15. Protein Denaturation • Firstly, use the section ‘Environmental Conditions’ beginning on p57 to define denature. • Then using your text, write down a list of all the different ways that proteins can be denatured. • I am going to post your finished list on Engage Online for an activity I would like you to do – to find one article each on Google Scholar that involves one of the denaturing agents.

16. Chaperonins • Exciting recent discovery! • Read the section ‘How proteins fold in cells’ and draw or reproduce a diagram that helps you to understand how chaperonins work. • Write a paragraph explaining the process to yourself. • Read ‘When proteins go bad’ to learn about Mad Cow Disease (Creutzfeldt-Jakob disease in humans).