PROTEINS

FOLDED POLYPEPTIDES

2007 Paul Billiet ODWS

PRIMARY STRUCTURE
The sequence of amino acids
MIL1 sequence: >gi|7662506|ref|NP_056182.1| MIL1 protein [Homo sapiens] MEDCLAHLGEKVSQELKEPLHKALQMLLSQPVTYQAFRECTLETTVHASGWNKILVPLVLLRQML LELTRLGQEPLSALLQFGVTYLEDYSAEYIIQQGGWGTVFSLESEEEEYPGITAEDSNDIYILPS DNSGQVSPPESPTVTTSWQSESLPVSLSASQSWHTESLPVSLGPESWQQIAMDPEEVKSLDSNGA GEKSENNSSNSDIVHVEKEEVPEGMEEAAVASVVLPARELQEALPEAPAPLLPHITATSLLGTRE PDTEVITVEKSSPATSLFVELDEEEVKAATTEPTEVEEVVPALEPTETLLSEKEINAREESLVEE LSPASEKKPVPPSEGKSRLSPAGEMKPMPLSEGKSILLFGGAAAVAILAVAIGVALALRKK length: 386amino acids
Anne-Marie Ternes

PRIMARY STRUCTURE

The numbers of amino acids vary (e.g. insulin 51, lysozyme 129, haemoglobin 574, gamma globulin 1250) The primary structure determines the folding of the polypeptide to give a functional protein Polar amino acids (acidic, basic and neutral) are hydrophilic and tend to be placed on the outside of the protein. Non-polar (hydrophobic) amino acids tend to be placed on the inside of the protein

2007 Paul Billiet ODWS

Infinite variety
The number of possible sequences is infinite An average protein has 300 amino acids, At each position there could be one of 20 different amino acids = 10390 possible combinations Most are useless Natural selection picks out the best

2007 Paul Billiet ODWS

SECONDARY STRUCTURE
The folding of the N-CC backbone of the polypeptide chain using weak hydrogen bonds

Text 2007 Paul Billiet ODWS Science Student

SECONDARY STRUCTURE

This produces the alpha helix and beta pleating The length of the helix or pleat is determined by certain amino acids that will not participate in these structures (e.g. proline)

Text2007 Paul Billiet ODWS

Dr Gary Kaiser

TERTIARY STRUCTURE
The folding of the polypeptide into domains whose chemical properties are determined by the amino acids in the chain

MIL1 protein

2007 Paul Billiet ODWS Anne-Marie Ternes

TERTIARY STRUCTURE

This folding is sometimes held together by strong covalent bonds (e.g. cysteine-cysteine disulphide bridge) Bending of the chain takes place at certain amino acids (e.g. proline) Hydrophobic amino acids tend to arrange themselves inside the molecule Hydrophilic amino acids arrange themselves on the outside

2007 Paul Billiet ODWS

Chain B of Protein Kinase C

Max Planck Institute for Molecular Genetics

QUATERNARY STRUCTURE
Some proteins are made of several polypeptide subunits (e.g. haemoglobin has four)

Protein Kinase C
Max Planck Institute for Molecular Genetics

Text 2007 Paul Billiet ODWS

QUATERNARY STRUCTURE
These subunits fit together to form the functional protein Therefore, the sequence of the amino acids in the primary structure will influence the protein's structure at two, three or more levels

2007 Paul Billiet ODWS

Result
Protein structure depends upon the amino acid sequence This, in turn, depends upon the sequence of bases in the gene

2007 Paul Billiet ODWS

PROTEIN FUNCTIONS
Protein structure determines protein function Denaturation or inhibition which may change protein structure will change its function Coenzymes and cofactors in general may enhance the protein's structure

2007 Paul Billiet ODWS

Fibrous proteins
Involved in structure: tendons ligaments blood clots (e.g. collagen and keratin) Contractile proteins in movement: muscle, microtubules (cytoskelton, mitotic spindle, cilia, flagella)

2007 Paul Billiet ODWS

Globular proteins
most proteins which move around (e.g. albumen, casein in milk) Proteins with binding sites: enzymes, haemoglobin, immunoglobulins, membrane receptor sites

2007 Paul Billiet ODWS

Proteins classified by function

CATALYTIC: enzymes STORAGE: ovalbumen (in eggs), casein (in milk), zein (in maize) TRANSPORT: haemoglobin COMMUNICATION: hormones (eg insulin) and neurotransmitters CONTRACTILE: actin, myosin, dynein (in microtubules) PROTECTIVE: Immunoglobulin, fibrinogen, blood clotting factors TOXINS: snake venom STRUCTURAL: cell membrane proteins, keratin (hair), collagen

2007 Paul Billiet ODWS