BIOC2000 Lecture Notes - Lecture 13: Aromatic Amino Acids, Selenocysteine, Peptide Bond
Lecture 13: An introduction to
protein structure and folding
Proteins are made up of covalently linked bonds
All amino acids comprise of:
- N terminal amino group – positively charged at neutral pH
- C terminal carboxyl group – negatively charged
- alpha C with single H
Only the nature of the R group differs between amino acids
Amino acids
Amino acids have a full name, a
three letter code and a one-letter
code.
e.g. Glycine, Gly, G
There are actually 21 ‘genetically
encoded’ amino acids - ones DNA
instruct ribosome to put into
proteins. There are other non-
genetically encoded amino acids used in the course of metabolism but
they are not put into proteins.
Most textbooks say 20 amino acids because selenocysteine (Sec, U) is rare,
only found in about 20 human proteins. Selenocysteine is the same as
cysteine but instead of sulphur in side chain, there is selenium.
Gly was discovered first because the R group of Gly is just a H – simplest
amino acid. Threonine was discovered last of the ‘main 20’, even though it
is not the most complex; Sec was last to be discovered.
* Do not worry about classification but have general idea of the properties of
each amino acid
There is overlap – the aromatic amino acids are also very hydrophobic so
they could be classified together with leucine, valine etc.
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Amino acid properties
Neutral: Amino acids are zwitterions thus each amino acid has at least 2
pKa values (one for amine group, one for carboxyl group).
Exceptions are:
- positively charged amino acids – Lys, Arg, His
- negatively charged amino acids – Asp, Glu
These are amino acids with an ionisable side chain so they carry a net
positive or negative charge at neutral pH – these amino acids have 3 pKa
values.
Important because they can form electrostatic interactions with one
another, e.g. in a protein a –vely charged Glu next to a +vely charged Lys
will form a favourable electrostatic interaction.
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Isoelectric point (pI): the pH at which the amino acid has 0 net charge.
Amino acids will be least soluble at this pH.
In the primary structure of a protein, amino acids are linked
by polypeptide bonds
Peptide bond: A peptide bond (amide bond) is a covalent chemical bond
formed between two molecules when the carboxyl group of one molecule
reacts with the amino group of the other molecule, releasing a molecule of
water (H2O).
The number of peptide bonds in a protein is 1 less than the number of
amino acid residues.
e.g. 50 residue protein has 49 peptide bonds
Chains up to about 50 resides are peptides, longer chains are proteins.
These numbers vary between textbooks, just know that short proteins are
peptides.
Peptide bond resonance
Resonance structure has significant implications for the formation of H
bonds.
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Document Summary
Lecture 13: an introduction to protein structure and folding. Proteins are made up of covalently linked bonds. N terminal amino group positively charged at neutral ph. C terminal carboxyl group negatively charged. Only the nature of the r group differs between amino acids. Amino acids have a full name, a three letter code and a one-letter code. e. g. glycine, gly, g. There are actually 21 genetically encoded" amino acids - ones dna instruct ribosome into proteins. There are other non- genetically encoded amino acids used in the course of metabolism but they are not put into proteins. Most textbooks say 20 amino acids because selenocysteine (sec, u) is rare, only found in about 20 human proteins. Selenocysteine is the same as cysteine but instead of sulphur in side chain, there is selenium. Gly was discovered first because the r group of gly is just a h simplest amino acid.
