Protein function biomedical science, Slides of Anatomy

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4BICH001W Biochemistry

Amino Acids & Protein Function

Dr Paul Curley (C2.13)

e-mail: [email protected]

Amino Acids and Proteins

Learning outcomes:

1. To know the general structure of amino acids.
2. To know how amino acids can be linked together by peptide bonds.
3. To understand what is meant by primary, secondary, tertiary and quaternary structures of proteins and know some of the most common secondary structures.
4. Understand the importance of protein 3D structure for biological function.

There are a huge number of possible amino acids, but only 20 are genetically encoded and transcribed in protein synthesis… Figs. Mathews, van Holde, and Ahern Biochemistry 3 rd

1. Primary structure The amine group of one amino acid can react with the carboxyl group of another to join two amino acids together. In organic chemistry, this would be called an amide. In biochemistry, the bond linking two amino acids is called a peptide bond (hence peptides… polypeptides…): Figs. Mathews, van Holde, and Ahern Biochemistry rd

Figs. Mathews, van Holde, and Ahern Biochemistry 3 rd edition. Peptide (and protein) sequences are written from the N-terminus to the C-terminus…

http://users.rcn.com/ jkimball.ma.ultranet/ BiologyPages/L/ Lysozyme.html e.g. Lysozyme – structure stabilised by 4 disulphide bonds…

A protein’s 3D structure is absolutely essential for it to carry out its biological function... Proteins do NOT simply consist of a randomly coiled chain of amino acids – they usually have a very well defined structure.

2. Secondary structure Associations between amino acids ( particularly hydrogen bonds between the C=O and N-H of different peptide bonds) can lead to formation of a number of simple and stable repetitive conformations. The best known of these are the  -helix and the  -strand (or b- sheet).

From Biochemistry 2nd Ed. by Garrett and Grisham

C

N

Bacteriorhodopsin Myoglobin It is common to show -helices as spirals or cylinders…

Sucrose membrane transporter protein from Salmonella typhimurium Human Retinol (in blue) binding prote It is common to show -sheets as broad arrows… Sucrose (^) Retinol

Stabilisation of protein tertiary structure / protein folding? Amino acid side-chains can interact in a variety of ways in order to stabilise complex and specific three-dimensional structures. These include:

• (^) Hydrogen bonding (e.g. Asn (N), Gln (Q), Ser (S), Thr (T))
• (^) Hydrophobic interactions (e.g. Ile (I), Leu (L), Val (V))
• (^) Electrostatic interactions (e.g. Arg (R), Asp (D), Glu (E), Lys (K))

One of the most important observation

in all of modern biology is that a

protein’s three-dimensional structure

determines its biological function…