CHMI-2227EL Study Guide - Midterm Guide: Macromolecule, Histidine, Glutamic Acid
27 Jun 2018
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Biochemistry - Mid-Term Review 2018.02.05.
Intro to Amino Acids
- All proteins are composed of 20 amino acids
-AA are composed of an amino group (NH2), carboxyl group (COOH) a hydrogen atom and a
distinctive side chain group (R), all attached to a carbon atoms (the alpha carbon) from the
organic chemistry nomenclature
-All AA are called alpha-amino acids because they have a primary amino group, and a
carbonyl group
-Only proline, a cyclic amino acid, is the exception, it is called an imino acid but still
commonly referred to as an alpha-amino
-When placed in neutral solution, pH 7, the amino group exists as
NH3+ and the carboxyl group as COO-, here it is depolarized and
called a zwitterion (german for hybrid ion)
-This is because the NH2 group will act as a base, and the COOH
group will act as an acid
-The additional carbons in an R group are called, beta (β), gamma
(γ) , delta (δ), and epsilon (ε) and so forth proceeding
out from the alpha (α) carbon
Classification of Amino Acids
-Non-polar Amino Acids
-1) Glycine (Gly, G)
-The simplest AA
-It only has one hydrogen atom as its side chain
-2) Alanine (Ala, A)
-It has a methyl group as its side chain
-3) Valine (Val, V)
-It has 3 carbon branched side chain
-Side chain is like a V
-4) Leucine (Leu, L)
-Has a 4-carbon branched side chain, with 2 methyl
groups off of second carbon (y-shape)
-5) Isoleucine (Ile, I)
-Has a 4-carbon branched side chain, with an ethyl and a methyl branch off of first
carbon
-6) Methionine (Met, M)
-Ethyl group with a thiol group and then a methyl group
-Hydroxy Amino Acids
-Have alcoholic functional groups
-7) Serine (Ser, S)
-Alcohol group off of one carbon chain
-8) Threonine (Thr, T)
-Alcohol group off of 1st carbon in a 2 carbon chain
-9)Cysteine (Cys, C)
-Has a thiol group (SH) off of one carbon chain
-Acidic Amino Acids
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-Carboxylic acid chain (COO- when deprotonated)
-10) Aspartic Acid (Asp, D (think of it as AsparDic))
-Contains a carboxyl group off of methyl chain
-11) Glutamic Acid (Glu, E)
-Contains a carboxyl group off of an ethyl chain
-Basic Amino Acids
-12) Arginine (Arg, R)
-Contains a guanidino group (this is a carbon surrounded by 3 amino groups, C(-NH,
=NH2, -NH2)), off of a propyl chain
-13) Lysine (Lys, K)
-Has a butyl chain with an amino group at the end (butylammonium group)
-14) Histidine (His, H)
-Has a imidazole ring (a C=CH-N=CH-NH ring) off of a methyl chain
- Secondary Amino Acid (Imino Acid)
-15) Proline (Pro, P)
-Has a heterocyclic pyrrolidine ring (C-NH2+-CH2-CH2-CH2 ring)
-Amidic Amino Acid
-16) Asparagine (Asn, N)
-Has an ether and amino group off of methyl chain
-17) Glutamine (Gln, Q)
-Has an ether and amino group off of an ethyl chain
-Aromatic Amino Acids
-18) Phenylalanine (Phe, F)
-Has a phenyl group off of a methyl group
-19) Tyrosine (Tyr, Y)
-Has a phenolic group (phenyl group with alcohol attached) off of
a methyl chain
-20) Tryptophan (Trp, W)
-Only amino acid with a double ring
-Bicyclic Indole group (a cyclohexene ring (2 double bonds) and
a (C-C=C-NH-CH=) ring, off of a methyl group
-Aromatic Amino acids absorb light in the near-UV region
- of the spectrum
-This characteristic is frequently used for analytical detection of
proteins by measuring their absorption at 280 nm
Modified Amino Acids in Proteins
-Other uncommon amino acids are found in several proteins, but not coded for DNA
-These uncommon amino acids are derived from the common 20 amino acids and are
produced by modification of the parent amino acid after the protein is synthesized
(this is called post translational modification)
-Among these amino acids:
-5-hydroxylysine
-4-hydroxyproline
-These are both important structural
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components of connective tissue proteins, like collagen
-When there is insufficient hydroxylation of collagen there is a vitamin C deficiency
called Scurvy
-γ-Carboxyglutamic Acid
-A calcium bonding amino acid residue found in prothrombin (blood clotting
protein)
-In vitamin K deficiency, there is insufficient carboxylation of glutamic acid in
prothrombin, may lead to hemorrhage
Stereochemistry of Amino Acids
-With the exception of glycine, amino acids have a carbon (the
alpha carbon) with 4 different substituents bonded to it, making it
chiral and optically active (they rotate the plane of polarized light)
-Amino acids exist as stereoisomeric pairs, called enantiomers
-By convention, the mirror image pairs of amino acids are called:
-D - Dextrorotary (Latin, dexter = right)
-L - Levorotary (Latin, laevus = left)
-All amino acids found in proteins are of L-configuration, however D-
amino acids occur in bacterial cell walls and some antibodies
-When reading Fischer clockwise, in L position: CO (COO-) H R (R-
GROUP) N (NH3+)
Acid Base Properties of Amino Acids
-Amino acids are amphoteric molecules, as they possess both acidic and basic groups
-Low pH: At high concentrations of H+, the carboxylic group (COO-)
will accept a proton and have an overall positive charge (+1)
-High ph: At low concentrations of H-ion (high pH), the amino group will
lose its proton and become negatively charged (-1)
-Intermediate pH: here amino acids contain positive and negative
charges (dipolar ion) as it will have dipole moments
-If the pH of the medium the amino acid is in varies, each ionizable group
will vary between charged and neutral, here the amino acids will exist as
different molecular species with different net charged
-There is a unique pH at which the # of - charged ions = # of +
charged ions in an AA, this is called the isoelectric point (pI)
-pI>pH = amino acid is positive
-pI<pH = amino acid is negative
-pH = pI = amino acid neutral
-the isoelectric point or pI can be calculated from the pK values:
-pI = (pKa1 + pKa2) / 2
-where pKa1 (carboxyl group pKa) and pKa2 (amino group pKa)
-Most amino acids have a pKa1 ~ 2 and pKa2 ~ 8 to 10
-The isoelectric point or pI can be determined by subjecting the amino acid to subjecting the
amino acid to electrophoresis in buffers of varying pH
Weak Acids and Bases
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