PROTEINS FOLDED POLYPEPTIDES © 2007 Paul Billiet ODWSODWS

Understandings The sequence and number of amino acids in the polypeptide is the primary structure. The secondary structure is the formation of alpha helices and beta pleated sheets stabilized by hydrogen bonding. The tertiary structure is the further folding of the polypeptide stabilized by interactions between R groups. The quaternary structure exists in proteins with more than one polypeptide chain. Copyright Pearson Prentice Hall

Polypeptides --linear chain of Amino Acids Polypeptides are polymers of amino acids A protein consists of one or more polypeptides

IB Assessment Statment Explain the four levels of protein structure, indicating the significance of each.

PRIMARY STRUCTURE The sequence of amino acids © Anne-Marie Ternes

Amino Acid Monomers Amino acids are organic molecules with carboxyl (--COOH) and amino groups (--NH 2 ) Amino acids differ in their properties due to differing side chains, called R groups Cells use 20 amino acids to make thousands of proteins Amino group Carboxyl group  carbon

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 ODWSODWS

All living organisms using the same 20 Amino Acids. Below are 9 nonpolar/ hydrophobic amino acids Isoleucine (Ile) Methionine (Met) Phenylalanine (Phe) Tryptophan (Trp) Proline (Pro) Leucine (Leu) Valine (Val) Alanine (Ala) Nonpolar Glycine (Gly)

Asparagine (Asn) Glutamine (Gln)Threonine (Thr) Polar Serine (Ser) Cysteine (Cys) Tyrosine (Tyr) All living organisms using the same 20 Amino Acids. Below are 6 polar/ hydrophilic amino acids

LE 5-17c Electrically charged Aspartic acid (Asp) Acidic Basic Glutamic acid (Glu) Lysine (Lys)Arginine (Arg) Histidine (His) All living organisms using the same 20 Amino Acids. Below are 5 VERY polar/ hydrophilic amino acids

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 = possible combinations Most are useless Natural selection picks out the best © 2007 Paul Billiet ODWSODWS

Polar vs. Nonpolar Amino Acids & Protein Function

SECONDARY STRUCTURE The folding of the N-C-C backbone of the polypeptide chain using weak hydrogen bonds © Science Student © Text 2007 Paul Billiet ODWSODWS

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) © Dr Gary Kaiser © Text2007 Paul Billiet ODWSODWS

TERTIARY STRUCTURE The folding of the polypeptide into domains whose chemical properties are determined by the amino acids in the chain MIL1 protein © Anne-Marie Ternes © 2007 Paul Billiet ODWSODWS

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 ODWSODWS

Disulfide bonds of tertiary structures of proteins Covalent bonds can form between two adjacent cysteine amino acids. The bond is covalent. The covalent bond stabilises the tertiary shape of a protein.

© Max Planck Institute for Molecular Genetics Chain B of Protein Kinase C

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 ODWSODWS

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 ODWSODWS

Result Protein structure depends upon the amino acid sequence This, in turn, depends upon the sequence of bases in the gene © 2007 Paul Billiet ODWSODWS

QUATERNARY STRUCTURE In some cases proteins consist of nonpoly-peptide (non-protein) chain called a prosthetic group Example: haemoglobin is linked to a heme group (iron contain molecule) Proteins with a prosthetic group are called conjugated proteins. © 2007 Paul Billiet ODWSODWS

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 ODWSODWS

Hemoglobin-- What characteristic of hemoglobin allows it to be considered a protein with quaternary structure? A. It contains many beta sheets. B. It consists of polypeptide subunits and heme groups. C. It allows bonding to oxygen atoms. D. It contains histidine (His) residues.

Protein Channels What structure is labelled X? A. DNA B. Beta pleated sheet C. Alpha helix D. Prosthetic group

Protein Channels Which part of this protein channel is Hydrophilic/ Polar? Explain why.

IB Assessment Statement Outline the difference between fibrous and globular proteins with references to two examples of each protein type

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 ODWSODWS

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 ODWSODWS

IB Assessment Statement State four functions of proteins, giving a named example of each

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 ODWSODWS