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Biochemistry 2288A
Derek Mc Lachlin

topic pages introduction 1-6, 11-22, 26-35 1. central dogma 2. amino acids 72-73 3. protein structure 121-140 3. protein function 120, 138-143 5. enzyme catalysis 89-92, 99-103, 6. protein purification 140-143, 146-148, 152-153 164-167 PEPTIDE BOND amino acids are connected by a covalent peptide bond > between the alpha amino group of one and the alpha carboxyl group of another in a condensation reaction once incorporated, each individual amino acid unit is called an amino residue (because water has been lost) the amino acid chain is elongated by the further addition of amino acids to the C-terminal > results in a polar molecule with a free amino group on one end (N- terminal) and a free carboxyl group on the other (C-terminal) each polypeptide has a unique order of amino acids - amino acid sequence conventionally written with N-terminus on the left and C-terminus on the right > results in a 'polypeptide backbone' of repeating NCC-NCC-NCC- units > side chains of residues project outwards from the backbone the properties of the side chains of individual residues gives characteristics to the polypeptide chain > some side chains are hydrophilic/hydrophobic, etc due to resonance from the C=O and C-N bond the peptide bond exhibits characteristics of a double bond > restricts movement around the C-N peptide bond 6 involved atoms are coplanar restriction limits the number of conformations the chain can take/ constrains flexibility and limits folding patters proteins can fold in many ways but are constrained by various sets of weak non-covalent bonds that form within proteins PRIMARY STRUCTURE > sequence of residues making up the protein chain > residues linked by covalent bonds only minimum size of a protein sequence is 50 residues - anything smaller is just a peptide average molecular weight of a residue is 110Da no theoretical largest size largest protein so far discovered has 30 000 residues SECONDARY STRUCTURE > describes local folding patterns of the polypeptide backbone > stabilized by H-bonds between the C=O and N-H groups on the polypeptide backbone a-helix > helical arrangement of a single polypeptide chain > H-bonds between C=O and N-H groups 4 residues further on the chain - C=O and N-H groups are oriented parallel to the helical axis all C=O and N-H groups are bonded > very rigid cylinder precise measurements: - 3.6 residues/turn - 0.54 nm/ turn side chains project outwards and contact the solvent > ends up looking like a bottle brush b-sheet > polypeptide chain folds back on itself so strands lie side by side forming a beta sheet > stabilized by H-bonds between C=O and N-H groups of neighbouring b- strands - forms a rigid structure can fold back parallel or antiparallel - produces parallel or antiparallel beta sheet side chains project alternately upward and downward from the polypeptide backbone a-helix and b-sheet are the most common but there are any other possible secondary structures > many polypeptide chains have different regions that take on different folding patterns some proteins are made up of many different folding patterns structural determinants include - steric hindrance (between large side chains or charge repulsion between similarly charged side chains) - presence of proline (the imino acid; the presence of the cyclic side chain constrains bond angles and prevents it from forming a-helix or beta- sheets; also missing an H so cannot form H-bonds) - presence of other chemical groups that interact with each other TERTIARY STRUCTURE > describe how secondary structures fold together - 3D arrangement of the protein chain incl. a-helices, b-sheets, etc > stabilized by 4 weak forces acting between side chains or between side chains and the polypeptide backbone ( often distant in sequence) four weak forces are: hydrophobic interaction/bonds (most important) > proteins are most stable when hydrophobic components are buried on the inside away from water with the hydrophilic components facing out - more hydrophobic residues are facing inwards while hydrophilic residues face outwards on the surface ionic bonds > between side chains hydrogen bonds van de Waal's forces ALSO disulfide bonds > the one covalent bond involved in tertiary structures > bond forms
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