Chapter 3 (Protein structure and function)



Chapter 3 Proteins

Protein structure (pages 125- 148; figures 3-1 to 3-28, 3-35)

1. The Shape and structure of proteins

- primary, secondary, tertiary, quaternary structure of proteins

- primary structure – sequence of amino acids; peptide bond

- secondary structures – α-helix and β-sheet; hydrogen bonds

- tertiary structure – noncovalent bonds; folding of proteins into a conformation of lowest energy

- quaternary structure – noncovalent bonds

2. Protein domain arrangements (module)

- “In-line” – e.g. fibronectin type I, immunoglobulin

- “plug-in” – e.g. SH2 domain, kringle

3. Proteins can be classified into many families

4. Sequence searches can identify close relatives

- Generally a 30% identity suggests relatedness

5. Domain shuffling

6. Quaternary structure of proteins

- Weak bonds

- “head to head” arrangement – dimmers

- Single binding site

- “head to tail” arrangement – multimers

- 2 binding sites

- Ring – neuraminidase

- Filaments – actin

7. Proteins that have elongated, fibrous shapes

- Fibrous proteins

- e.g. alpha-keratin – intracellular

- collagen – extracellular

- Elastic fibers

- e.g. elastin – extracellular

8. Disulfide bonds stabilize extracellular proteins

- form in the ER

Protein function (pages 152-178; figures 3-36 to 3-67)

9. Selective binding of proteins to other molecules

- Binding may be weak or tight

- Specificity

- Weak bonds – ionic (electrostatic), hydrogen, van der Waals, hydrophobic

- Binding site

10. Surface conformation of a protein determines its chemistry

- Interaction of neighboring parts of the polypeptide chain may restrict the access of

water molecules to the protein’s binding site

- Clustering of neighboring polar amino acid side chains can alter their reactivity e.g. clustering of negatively charged side chains increases affinity of a positively charged ion

11. The equilibrium constant measures binding strength

12. cAMP binding proteins – brings about conformational changes

- DNA binding proteins

- Enzymes (e.g. PKA)

- Ion channels

13. Serine proteases – “catalytic triad” – chemistry at an active site

14. SH2 domain – example of conserved binding sites

- Protein protein interactions – surface string, helix-helix, surface-surface

15. Antibody molecules – specificity and affinity of binding sites

16. Equilibrium constant (K); Vmax; Km

- Turnover number = Vmax/enzyme concentration

17. Transition state; catalytic antibodies

- Stabilization of a transition state by an antibody creates an enzyme

18. Lysozyme – example of acid-base catalysis

- Distortion of bound substrate

- Negatively charged Asp attacks the C1 of the distorted sugar; Glu donates a proton to the oxygen in the glycosidic bond; water molecule displaces the Asp

19. General strategies for enzyme catalysis

- Carbamoyl phosphate synthetase - molecular tunnels that connect active sites

Glutamine ( NH3 ( carboxyphosphate ( carbamate ( carbamoyl phosphate

- Pyruvate dehydrogenase complex – multienzyme complex

- Aspartate transcarbamoylase – allosteric transition

- Protein kinases/protein phosphatases – protein phosphorylation

- Cdk – integrating protein

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