Biochemistry 2280A Lecture Notes - Lecture 3: Amide, Post-Translational Modification, Threonine

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Biochem Lecture 3 September 13, 2013
Topic 2 continued
o Phosphorylation (post-translational modification) only happens to serine,
threonine and tyrosine
Is energetically favourable to replace the hydroxyl group with a phosphate
Not every serine/threonine/tyrosine gets phosphorylated, just some of them
Has a big impact on protein function
How do you determine in the lab that a specific serine/threonine/tyrosine is
phosphorylated and is it important?
Replace the amino acid that they think will get phosphorylated with a
different amino acid
Replace it with alanine (charge = 0)
Won’t fold properly = problems with function
Replace with an acidic amino acid, like aspartic acid (charge = -1)
Wouldn’t see a change because you replaced a negative with a
different negative
o Ka = equilibrium constant of a reaction
pKa = -logKa
o Calculating amino acid net charge: SEE LECTURE 3 PPT
Topic 3: Protein structure
o Proteins are linear polymers of amino acids
Size: 50 to >30,000 amino acids
Peptides formed through a condensation reaction (water is formed) and is a
covalent bond (shares electrons)
o The peptide bond
Resonance gives partial double bond between C=O and C=N
Limited rotation between the double bond = restricts the possible folding
patterns of the protein chain
Atoms involved (c=o and c=n) are coplanar
Residues: remaining part of amino acids after peptide bond is formed (minus
water
Peptides: small numbers of joined residues
Dipeptide, tripeptide etc. to polypeptide
Backbone: repeating part of polypeptide
N-C-C-N-C-C-N-C-C
Side chains: project from backbone
o Levels of protein structure
Proteins fold into many different shapes
Rules govern how proteins obtain their final form
Certain structural elements are found in many proteins
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Document Summary

Topic 2 continued: phosphorylation (post-translational modification) only happens to serine, threonine and tyrosine. Is energetically favourable to replace the hydroxyl group with a phosphate. Not every serine/threonine/tyrosine gets phosphorylated, just some of them. Has a big impact on protein function. Replace the amino acid that they think will get phosphorylated with a different amino acid. Replace it with alanine (charge = 0) Won"t fold properly = problems with function. Replace with an acidic amino acid, like aspartic acid (charge = -1) Wouldn"t see a change because you replaced a negative with a different negative: ka = equilibrium constant of a reaction. Pka = -logka: calculating amino acid net charge: see lecture 3 ppt. Topic 3: protein structure: proteins are linear polymers of amino acids. Peptides formed through a condensation reaction (water is formed) and is a covalent bond (shares electrons: the peptide bond. Resonance gives partial double bond between c=o and c=n.

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