Biochemistry

Protein Biochemistry

Structure and Function

Educational Aims and Objectives

Text:

Champe, Harvey & Ferrier (2007) Biochemistry (4th Edition) Lippincott

Suggested Additional Reading:

Berg Tymoczko & Stryer, (2006) Biochemistry (6th Edition) Freeman

Hames & Hooper (2005) Biochemistry 3rd Edition, Taylor & Francis [Instant Notes Series]

Aim: To present an overview of the structure/function relationships inherent to proteins.

Objectives: Upon successful completion of this lecture course, students shall be able to:

1. Classify proteins according to their function.

2. Recognise the structures of the 20 amino acids commonly found in proteins, know the properties of
their side-chains (variable radicals) and how these properties affect protein structure.

3. Recognise the structure of the peptide bond, and explain how its properties influence protein folding.

4. Describe the mechanisms of (and evidence for) protein folding.

5. Know the four (4) levels of protein structure.

6. Define and describe the periodic structures found in proteins.

7. Explain what is meant by protein denaturation.

8. Recognise the significance of fibrous proteins, and identify the three major fibrous proteins.

9. Explain the biomechanical significance of fibrous proteins in health and disease.

Topics:

1. Protein classification and amino acids.

2. Peptide bonds and polymerisation.

3. Periodic structures and protein folding.

4. Collagen structure and function.

5. Elastin, fibrin and IVD proteins.

1. Protein Classification and Amino Acids

Aim: To review protein classification and amino acid structure.

Objectives: To understand the relationship between structure and function. To understand the
properties of individual amino acids and how these may affect whole proteins.

Key Words: Protein, function, catalysis, storage, transport, locomotion, immunity, signalling,
structure, neutral aliphatic, aromatic, sulphur-containing, imino acids, dicarboxylic amino
acids, basic amino acids.

Reading: Lecture notes. Chapter 1 pp. 1-12 in text.

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2. Peptide Bonds and Polymerisation

Aim: To review amino acid polymerisation and peptide bond geometry.

Objectives: To understand the vectorial linking of amino acids to form peptides. To understand the
role of the peptide bond in stabilising protein conformations.

Key Words: Condensation reaction, residue, peptide bond, peptide, polypeptide, N-terminal, C-
terminal, main chain, side chain, disulphide bonds.

Reading: Lecture notes. Chapter 2 pp. 13-24 in text.

3. Periodic Structures and Protein Folding

Aim: To review the common periodic structures found in proteins. To review levels of protein
structure. To review the forces influencing protein folding.

Objectives: To understand the functional significance of alpha-helical, beta sheet and superhelical
structures in proteins. To understand the progression of levels of protein structure and
the factors determining protein folding.

Key Words: Alpha-helix, pitch, beta-sheet, antiparallel, superhelix, primary, secondary, tertiary and
quaternary levels of structure, bovine ribonuclease, stabilisation.

Reading: Lecture notes. Chapter 2 pp. 13-24 in text.

4. Collagen - Structure and Function

Aim: To present an overview of collagen structure and function.

Objectives: To understand how collagen’s molecular structure affects its biomechanical roles.

Key Words: Collagen, triple helix, fibres, tropocollagen, glycine, hydroxylation, scurvy, Vitamin C,
fibroblasts, self-assembly, collagenases.

Reading: Lecture notes. Chapter 3 pp. 43-52 in text

5. Elastin, Fibrin and Proteoglycans

Aim: To review the structures and functions of elastin, fibrin and proteoglycans.

Objectives: To understand the relationship between molecular structure and biomechanical function
in the above three proteins.

Key Words: Elastin, ligaments, blood vessels, desmosine, fibrinogen, fibrin, fibrinopeptides,
haemostasis, proteoglycans, chondroitin sulphate, link protein, ground substance.

Reading: Lecture notes; Chapter 3 pp. 43-52 in text; Chapter 14 pp. 157-172 in text.

Tutor’s Notes:

1. "Lecture notes" refers to your own notes made in the course of formal instruction and does not
imply any commitment on the part of the tutorial staff to provide a written record of the work
undertaken.

2. The reading listings are guidelines, not tramlines! Additional student directed reading is desirable,
and can be achieved by use of the key word listing, together with the index in your chosen
textbook.