1. Conformationally changed Stability
Section 2 – Protein structure, binding and conformational change
Proteins
Varied
Specific
Conformationally changed
Stability

2. Proteins
Basically they are composed of amino acids joined together but there are 4 levels to their structure:
Primary
Secondary
Tertiary
Quaternary

3. Basic amino acid structure
Amino group
Residue or Side chain
Carboxylic acid group
 carbon

4. Essential amino acids
Histidine, Isoleucine, Leucine, Lysine, Methionine,
Phenylalanine, Threonine, Tryptophan, Valine
Non-essential amino acids
Alanine, Arginine, Asparagine, Aspartic acid, Cysteine,
Glutamic acid, Glutamine, Glycine, Proline,
Serine, Selenocysteine, Tyrosine

5. Proteins
21 amino acids
Based on functional group (R group)
Properties will be in relation to the functional groups
Functional groups give 5 main amino acid groupings
Positively charged, basic
Negatively charged, acidic
Polar
Hydrophobic, non-polar
Other (special cases)(uncharged polar)

7. Positively charged
Arginine (+NH2)

8. Negatively charged
Aspartic acid (loses H+ on OH)

9. Polar (uncharged)
Serine

10. Hydrophobic
Tyrosine
Phenylalanine

11. Other (special cases)
Glycine

12. Bonding between amino acids in the polypeptide chain
Carboxylic acid end/amide end of adjacent aa producing water
Covalent peptide bond is a strong chemical bond
Bond formed due to dehydration synthesis

13. Primary Structure
Depends on the sequence of amino acids in the polypeptide chain.
This is predetermined by the DNA of an organism.
Only specific sequences will bring about correct function.
Many amino acids joined together by peptide bonds give a polypeptide chain.

14. Secondary Structure
Is related to how the polypeptide chain is folded.
It is mainly concerned with hydrogen bonds between C=O and N-H groups.
There are 2 common types of folding (with turns):
-helix
-sheet

15. H bonds between
N-H groups and C=O groups.
Producing helices

16. amino acid chains can either be parallel or antiparallel but are arranged in sheets

18. Turns in alpha helix or beta sheets

19. Tertiary Structure
Relates to the folding of the alpha helices and beta sheets.
This is maintained by hydrophobic interactions, H bonds, covalent disulphide bonds, ionic bonds and van der Waals interactions between side chains.

20. Quaternary Structure
This is where 2 or more polypeptide subunits are joined together (more H bonds, ionic bonds and disulphide bridges).
This also can incorporate a prosthetic non protein group such as in Haemoglobin
Haemoglobin
4 polypeptide subunits and 4 haem groups

21. R group interactions can be influenced by temperature and pH
Functions of Protein
Catalytic (enzymes) - speed up chemical reactions.
Structural - cell membrane, tissues, etc.
Messenger (hormones) - chemical messengers within cells and between cells
Carriers - proteins transporting chemicals into and out of cells.

22. Hydrophobic interactions
Occur between non-polar R groups along the length of the polypeptide. Folding of these regions occurs so that they form a central hydrophobic core, separating non-polar hydrophobic R groups from aqueous solution while the polar hydrophilic R groups are expressed on the outside of the structure, free to interact in aqueous solution. Hydrophobic sections of proteins are classically found embedded in the phospholipid bilayer of a cell, while the hydrophilic polar parts are free to interact with the extracellular and intracellular solutions.

23. Hydrophobic protein domains
Adenylate Cyclase is part of G protein cascade
Adenylate cyclase: a protein that is part of the G protein signalling cascade.
Hydrophobic domains: embedded in plasma membrane.
Hydrophilic domains: free to interact in the aqueous intracellular environment. They convert ATP to cAMP, a second messenger.

24. Ionic bonds
Charge dependent attraction occurring between oppositely charged polar R groups, e.g. between the amino acids arginine and aspartic acid.
pH affects ionic bonding and results in denaturation of the protein at extremes of pH as the H+ and OH– ions in solution interact with the charge across the ionic bond.

25. Hydrogen bonds
Hydrogen bonding is a weak polar interaction that occurs when an electropositive hydrogen atom is shared between two electronegative atoms.
Hydrogen bonding is charge dependent.
pH affects hydrogen bonding and results in denaturation of the protein at extremes of pH as the H+ and OH– ions in solution interact with the charge across the hydrogen bond.

26. Ionic and hydrogen bonds

27. Van der Waals interactions
Weak intermolecular force between adjacent atoms.
Geckos and Van der Waals forces.

28. Disulfide bridges
Covalent bonds that form between adjacent cysteine amino acids.
These can occur within a single polypeptide (tertiary structure) or between adjacent polypeptides (subunits, quaternary structure).