Proteins and Enzymes 2

Proteins and Enzymes 2

• Proteins are large molecules composed of several hundred amino acids
• The linear sequence of amino acids in a peptide is referred to as the primary structure of the protein
• A polypeptide chain is not linear and folds into a biologically active shape
• The biologically active form is known as the native conformation
• The biological functions of many proteins can be explained on the basis of their comformations or shaped
• e.g. an enzyme folds to form an active site that can recognise substrate molecules

• The properties of the peptide bond has considerable impact on the shape and function on proteins
• The peptide bond is planar, electron resonance gives 40% double bond character. The peptide bond may be regarded as the average of two extreme resonance forms
• Some properties of the double bond are a result of its double bond character:
  • The peptide bond is described as rigid and planar
  • Rotation around the peptide bond no possible

• Peptide bonds have a trans comformation
• Steric hindrance between side chain groups favours the trans conformation
• Since the peptide bond is rigid, only two free movements exist in a polypeptide chain
• Rotation about the aC-N bond is called the phi torsion angle
• Rotation about the aC-C bond is called the psi torsion angle

• Protein conformation depends on psi and phi rotation. The flexibility of these bonds allows the primary sequence to fold into its native comformation
• Rotation is limited by:
  • Steric hindrance: bulky groups, e.g. side chains cannot approach each other
  • The rigidity of the peptide bond ultimately restricts movement
  • Favourable interacions, e.g. hydrogen bonds, with other regions of the polypeptide chain

• Secondary protein structure can be defined as the three dimensional arrangement of the primary amino acid structure
• The alpha-helix is a secondary structure that results when consecutive amino acid residues have similar phi and psi torsion angles: psi = -57 degrees, phi = -47 degrees
• The alpha-helix is a single helix 
• 3.6 amino acid residues are required for one complete turn of the helix
• Each backbone carbonyl oxygen is hydrogen bonded to the peptide nitrogen of the fourth residue along (towards C terminus), this is a favourite interaction that stabilises the helix
• Although hydrogen bonds are weak, they hold the helix structure together
• Side chains are arranged on the outside of the helix

• Receptors are proteins rich in alpha-helices. They usually contain a trans-membrane domain composed entirely of alpha-helices
• A beta sheet is a secondary protein structure in which several strands (called beta strands) of the peptide backbone are hydrogen bonded to themselves
• The beta-sheet is an elongated, reasonably flat sheet-like structure
• Inter-strand hydrogen bonds between backbone carbonyl oxygen and amide nitrogens stabilise the beta-sheet
• In the beta-sheet, side chain interactions (mostly hydrophobic interactions between small groups) can provide additional stabilisation

• Antiparallel beta-sheet: Optimally hydrogen bonded, linear hydrogen bonds (better overlap = stronger bond), 2-15 strands possible (average 6)
• Parallel beta-sheet: Hydrogen bonds distorted, sheet less stable, no more than 5 strands encountered
• Avidin is a protein commonly found in egg whites that is entirely composed of a beta-sheet
• The beta turn occurs between beta strands. Hydrogen bonding stabilises a 180 degree change in direction

• Fibrous proteins contain only alpha-helix secondary protein structure. They have a simple, elongated structure resembling threads or fibres. They provide mechanical support in skin, tendons and bones. They are physically durable, chemically inert and water insoluble. Structure maintained by hydrogen bonding within the alpha-helix.
• Hair is composed mostly of alpha-keratin, a double coil of alpha-helices. Many double coils are packed together to form a strand of hair

• Tertiary protein structure refers to the three dimensional (spatial) arrangement of secondary structure
• Tertiary proteins, e.g. enzymes, usually contain an assortment of secondary features
• Therefore fibrous proteins are usually classified as secondary proteins
• Receptors also have tertiary structure. The trans-membrane domain is usually attached to a cytoplasmic domain (i.e. a mixture of secondary structure)
• The precise structure of membrane-bound receptors is extremely difficult to determine

• Globular proteins are teritary proteins with greater structural diversity than fibrous proteins. All enzymes are globular proteins.
• Water soluble
• Compact, roughly spherical
• Tightly folded peptide chains
• Hydrophobic interior, hydrophilic surface
• Structure maintained by covalent and hydrogen bonding, non-covalent crosslinks and hydrophobic interactions
• Possess indents or clefts - active site
• Enzymes

• Proteins are most stable in water with their hydrophobic side chains tucked into the protein interior 
• Non-polar substances will always minimise their contact with water
• Non-polar side chains aggregate, causing the protein to fold with non-polar side chains inside and polar side chains outside the protein in contact with water
• Efficient packing maximises van der Waals interactions between non-polar residues and excludes water from the interior of the protein
• Structure controls function: enzymes must be water soluble to function in cells
  • Val, Leu, Ile, Met, Phe and Ala are rarely on protein exteriors

• Proteins are arranged so virtually all possible hydrogen bonds are formed
• Polar side chains forced into the protein interior can neutralise their polarity by forming hydrogen bonds of electrostatic interactions
• Folding of a protein occurs to allow formation of all possible hydrogen bonds and hydrophobic interactions: stabilises protein tertiary structure

• Disulfide bonds are covalent cross links that form between adjacent cysteine residues and help stabilise the conformations of some proteins
• A covalent bond is very strong compared to H-bond or van der waals
• Disulfide links are especially common in proteins that are secreted from cells

• In the laboratory, heating a chemical reaction usually increases the rate fo the reaction. Enzymes however function poorly at extremes of temperature or pH
• The tertiary structure of an enzyme is responsible for biological activity
• Tertiary structure is maintained by weak interactions (mostly hydrogen bonds and van der Waals forces)
• Variations of pH or temperature disrupt the stabilising interactions, causing changes to the tertiary structure. The protein is said to be denatured
• Enzymes have evolved to function (i.e. maximum stabilisation of tertiary structure) at physiological conditions: pH 7.4 and 37 degrees

• Quaternary structure refers to proteins that are composed of more than one polypeptide strand
• Haemoglobin is composed of 4 globular protein subunits; two identical alpha units containing 141 amino acids, and two identical beta units containing 146 amino acids. Each subunit contains an iron atom, vital for the transport of oxygen in the blood
• Insulin, a hormone that controls glucose metabolism, consists of two peptide chains linked and maintained in the biologically active conformation by three disulfide bridges