BIOC192 STUDY GUIDE - BIOCHEMISTRY PAPER SEM2

Lecture 1: Introduction to Proteins
Friday, 3 July 2015 7:14 p.m.

Learning Objectives
• Describe the properties of amino acids, and how they relate to protein structure and function.
• Give examples of amino acids containing non polar, polar, and ionisable side chains

Proteins
• Form nanostructures
• Form tiny molecular machines
• Help us grow, replicate, digest
• Make up our immune system
• Form muscle, hair and nails
• Are non-branching polymers that form macromolecules
• Only 20 amino acids used to make proteins

Amino Acids
• Are chiral (except for glycine)
• L means non-hydrogen group on the left
• D means non-hydrogen group on the right
• Amino acids in solution are zwitterions (NH3+ and COO-)
• Have a common backbone but different side chains, represented by 'R' group
• They therefore have different chemical properties and different functions




Non-Polar Amino Acids - often found in hydrophobic core of protein
• Alanine, Ala, A
• Valine, Val, V
• Leucine, Leu, L
• Isoleucine, Ile, I
• Glycine, Gly, G
• Cysteine, Cys, C
• Phenylalanine, Phe, F
• Tryptophan, Trp, W
• Methionine, Met, M
• Proline, Pro, P



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,Polar Amino Acids - partake in hydrogen bonding
Uncharged Polar Amino Acids
• Serine, Ser, S
• Threonine, Thr, T
• Tyrosine, Tyr, Y
• Asparagine, Asn, N
• Glutamine, Gln, O

Negatively Charged/Acidic Polar Amino Acids - can form ionic bonds
• Aspartic acid, Asp, D
• Glutamic acid, Glu, E

Positively Charged/Basic Polar Amino Acids - can form ionic bonds
• Lysine, Lys, K
• Arginine, Arg, R
• Histidine, His, H

Pka and pI
• The pKa value for an ionizable group on an amino acid or protein is the pH at which the group is 50%
ionized
• The pI, or isoelectric point is the pH at which the net charge on an amino acid (or protein) is zero

Modified Amino Acids
• Almost all amino acids start out as one of the basic 20
• They are “translated” from RNA into proteins at the ribosome
• Some amino acids are modified after they are added to a protein
• This is called “post-translational modification”

An example




Other Amino Acid Modifications
1. Phosphorylation
2. Glycosylation
3. Methylation
4. Adenylation

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, 4. Adenylation
5. Iodination
6. Metal binding

Notating Mutations
• Old way "valine for glutamate at position 6"
• New way "E6V"
○ First letter – wild type or native amino acid
○ Number – location of mutation from N-terminus
○ Second letter – mutated amino acid residue

Peptide Bonds, Peptides and Proteins
• Amino acids are covalently linked together by peptide bonds
• A short stretch of amino acids joined together is a peptide.
• A longer chain of amino acids joined together, usually with a defined biological function, is a protein.
• Amide bonds are peptide bonds between amino acids
• Condensation reaction forms high energy covalent bond

Amide Bonds




• 40% double bond character, leads to planarity
• Planar conformation maximizes π-bonding overlap
• Rotational barrier of ~80 kJ/mol
• Note the dipole, slightly positive nitrogen, slightly negative oxygen
• Predominately trans as hydrogen pointing down, on opposite side of oxygen, this position is more
energetically favourable
• ~10% that precede proline may be cis
• Other bonds in amino acids can rotate - this is important to enable proteins to fold into a biologically
active 3-D structure





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