Biochemistry 2288A Lecture Notes - Steric Effects, Covalent Bond, Beta Sheet

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Published on 20 Nov 2012
Department
topic
pages
introduction
1-6, 11-22, 26-35
1. central dogma
2. amino acids
3. protein structure
3. protein function
5. enzyme catalysis
6. protein purification
72-73
121-140
120, 138-143
89-92, 99-103,
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
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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
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