PROTEINS FOLDED POLYPEPTIDES © 2016 Paul Billiet ODWS

PRIMARY STRUCTURE The sequence of amino acids MIL1 sequence: >gi|7662506|ref|NP_056182.1| MIL1 protein [Homo sapiens] MEDCLAHLGEKVSQELKEPLHKALQMLLSQPVTYQAFRECTLETTVHASGWNKILVPLVLLRQMLLELTRLGQEPLSALLQFGVTYLEDYSAEYIIQQGGWGTVFSLESEEEEYPGITAEDSNDIYILPSDNSGQVSPPESPTVTTSWQSESLPVSLSASQSWHTESLPVSLGPESWQQIAMDPEEVKSLDSNGAGEKSENNSSNSDIVHVEKEEVPEGMEEAAVASVVLPARELQEALPEAPAPLLPHITATSLLGTREPDTEVITVEKSSPATSLFVELDEEEVKAATTEPTEVEEVVPALEPTETLLSEKEINAREESLVEELSPASEKKPVPPSEGKSRLSPAGEMKPMPLSEGKSILLFGGAAAVAILAVAIGVALALRKK length: 386amino acids kachkeis.com/ img/essay2_pic0.jpg

PRIMARY STRUCTURE The numbers of amino acids vary (e.g. insulin 51, lysozyme 129, haemoglobin 574, gamma globulin 1250, titin 34 350) 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. © 2016 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. © 2016 Paul Billiet ODWS

SECONDARY STRUCTURE The folding of the N-C-C backbone of the polypeptide chain using weak hydrogen bonds student.ccbcmd.edu/.../ images/alphahelix.jpg © 2016 Paul Billiet ODWS

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) student.ccbcmd.edu/.../ images/betasheet.jpg © 2016 Paul Billiet ODWS

TERTIARY STRUCTURE The folding of the polypeptide into domains whose chemical properties are determined by the amino acids in the chain MIL1 protein kachkeis.com/ img/essay2_pic0.jpg © 2016 Paul Billiet ODWS

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. © 2016 Paul Billiet ODWS

Chain B of Protein Kinase C www.bioinfo.org.cn/ lectures/quaternary.gif

QUATERNARY STRUCTURE Some proteins are made of several polypeptide subunits (e.g. haemoglobin has four) Protein Kinase C www.bioinfo.org.cn/ lectures/quaternary.gif © 2016 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. © 2016 Paul Billiet ODWS

Result Protein 3-D structure depends upon the amino acid sequence This, in turn, depends upon the sequence of bases in the gene. © 2016 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. © 2016 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). © 2016 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. © 2016 Paul Billiet ODWS

Proteins classified by function CATALYTIC: enzymes e.g. rubisco STORAGE: ovalbumen (in eggs), casein (in milk), zein (in maize) TRANSPORT: hemoglobin COMMUNICATION: hormones (e.g. 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. PIGMENTS: e.g. Rhodopsin, melanin © 2016 Paul Billiet ODWS