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- Central alpha carbon is sp3 hybridized, so all alpha amino acids have a tetrahedral
geometry.
- All amino acids, except glycine (because it has two H groups), are chiral
o The stereocenter is at the alpha carbon
o The stereochemistry is designated D- or L-
o There is preference for L-amino acids in proteins.
o L- amino acids have the R-group on the left.
o Isoleuicine and threonine have an additional stereocenter at the beta carbon.
- Stereochemistry of amino acids promotes the formation of the secondary structure of proteins
(alpha helix and beta sheet), which, in turn, is a determinant of the overall structure of the
protein, and the overall structure determines function.
C. Properties of Amino Acid Side Chains: Classes of alpha-amino acids
- Amino Acids with Nonpolar Aliphatic Side Chains
o Glycine, alanine, valine, leucine, and isoleucine
o They all have aliphatic side chains. Aliphatic just means they are straight chains as
opposed to aromatic rings
o Aliphatic side chains are hydrophobic because they are made of chains of
hydrocarbons.
o The more hydrophobic amino acids, such as isoleucine, are usually found within the
core of a protein molecule, where they are shielded from water.
- Amino Acids with Positively Charged (Basic) Side Chains. (ALSO POLAR)
o Histidine, lysine and arginine
o Lysine (side chain pKa = 10) and arginine (pKa =12.5) are the more basic amino
acids (histidine side chain pKa= 6)
o Because lysine and arginine are so basic, their side chains are almost always
positively charged at physiological pH.
o Arginine has a guanidine group, which is the most basic amino acid de to the
resonance stabilization of the protonated side chain.
o Unique behavior of histidine
The imidazole ring in histidine loses its proton at about pH 6.
When incorporated into proteins, its pKa ranges from 6.5-7.4
The value of pKa for an ionizable side chain is sensitive to proximity of other
charged groups
Because the histidine side chain has a pKa near physiological pH, it is often
involved in proton transfers during enzymatic catalysis.
o Basic amino acids are strongly polar so they are usually found on the surface of
proteins or in substrate binding clefts.
- Amino Acids with Negatively Charged (Acidic) Side Chains (ALSO POLAR)
o Aspartic acid (pKa = 3.9) and glutamic acid (pKa=4.2)
o The side chain pKa values are so low that the negatively charged form of the side
chain typically predominates under physiological conditions, even when they are
incorporated into protein
o Therefore we usually refer to them as aspartate and glutamate (the conjugate bases
rather than the acids)
o They are very hydrophilic and tend to be on the surface of a protein.
C. Peptides
- Always write the N-terminal residue to the left and the C-terminal residue to the right
- In the structure of a peptide, we distinguish between the side chains and the main chain (or
peptide backbone), which is composed of the atoms that make up the peptide bonds- namely,
the alpha-NH, the alpha-C, and the alpha-C=O groups of each amino residue in the peptide
- Because proinsulin is not an active hormone, it can be produced and stored in the pancreas at
high concentrations, whereas similar high levels of active insulin would be toxic.
5.5: From Gene Sequence to Protein Function
- The degree of similarity between protein sequences is determined from a procedure called
alignment.
- Primary sequence analysis can be used to predict protein function because similarities in
aligned sequences are correlated with similarities in protein structure and function
- With at least 25% amino acid sequence identity, two proteins will have similar structure, and
very likely similar function.
- Gene sequence analysis can be used to identify protein variants associated with human
disease or resistance to certain treatment
- The sequence logo the type size used to represent the one-letter code of the amino acid is
correlated with the relative frequency of an amino acid at a given position.
- Basically, we know that the amino acid sequence for a protein is determined by the sequence
of DNA in the gene that codes that protein.
- We also know that bacteria have this piece of extrachromosomal DNA called plasmids.
Plasmids are capable of autonomous replication in a bacterial cell.
- This is good because what scientists can do is cut open that plasmid at a desired spot, and
splice in a gene encoding the protein they want to make more of.
- E.coli is a bacteria that we can insert plasmid (expression vectors), which are on the order of
2-10 kilobases in length.
- A selection marker is usually a protein that confers resistance to an antibiotic that is
included in the cell growth medium
o Only those cells that have taken up the vector, and are thereby capable of expressing
the desired protein, will survive in the growth medium.