Principles of science- protein

what is meant by a protein structure hierarchy

-primary, secondary, tertiary, quaternary(eg 2 beta and 2 alpha globin polypeptides with a heme group)

• what type of amino acids are mammalian proteins

• how many amino acids

• what is the peptide bond classified by

• how many amino acids makes a protein

• shape of peptide bond

• mammalian proteins are alpha amino acids

• 20 amino acids

• carboxyl group reacts with amino group to form a peptide bond and lose a water molecule

• catalysed by peptidyl transferase (28s ribozyme-ribonucleic acid enzymes)

• within a polypeptide chain, individual amino acids = residues

• when >50 amino acids are in a polypeptide is a protein

• peptide bond is planar (partial double bond between carbonyl O and N)

bonding determining protein structure

• covalent primary

• hydrogen secondary

• hydrophobic+VDW tertiary

• electrostatic within tertiary helps maintain

• VDW/ electrostatic quaternary

alpha helix

• what runs parallel to the helix axis

• what winds around the axis

• what does htis lead to

• how many amino acid residues per complete turn

beta sheets

• what orientation do H bonds run to the chain direction

• alpha helix- H bonds run parallel to helix axis. alpha carbon backbone winds around an axis so that each carbonyl O atom is H bonded to each amino N of the amino acid located 4 residues closer to C terminus

• The standard alpha helix has approximately 3.6 amino acid residues per complete turn

• beta sheets- H bonds run perpendicular to chain direction

• parallel and antiparallel

types of r groups

nonpolar, polar, electrically charged

cysteine

can form disulphide bonds as it has an SH group

examples of tertiary proteins

-catalase

-triose phosphate isomerase

-actin

tertiary domain

the smallest stable unit of a tertiary structure. a domain is defined as that region of a polypeptide chain that can fold into an autonomous stable tertiary structure

domain shuffling- when domains have been switched around between proteins through evolution

quaternary

1. haemoglobin- needs to deliver oxygen tissues. needs high enough affinity to pick up oxygen but low enough to release it.

2. t state- oxygen unbound

3. r state- oxygen bound. so that the 3 other units have higher affinity

4. small changes in oxygen concentration can dramatically affect binding to haemoglobin giving a sigmoidal curve of oxygen binding

collagen

• what type of protein

• what is the general structure

• extracellular fibrous protein but not an alpha helix

• 3 helical chains that wind around a central axis

• general structure is Gly-X-Y where X can be any amino acid especially proline lysine or hydroxyproline

• Glycine is small so glycines from each chain fit at the centre of each helix

• H bonds between the chains