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What are amino acids?

➢They act as: enzymes (catalysts), metabolic intermediates, carriers
of energy and waste products, and hormones.
➢ Building blocks of proteins

Amino Acids ➢ Among all possible amino acids, only 20 are usually found in
proteins
ENGR. JEREMI AH EMI ER VI L L AN U EVA ➢ All 20 naturally occurring amino acids in pure form are white,
CHEMI CAL ENGI NEERI NG DEPARTMEN T crystalline, high-melting solids.
ADAMSON U NI VERSI TY

What are amino acids? General Structure

➢ Proteins are the most abundant macromolecules in living cells. ➢ Any organic molecule with at least one
They play a vital role in almost every biological process. CARBOXYL group (organic acid) and at least one
➢ One way to link amino acids together – PEPTIDE BOND AMINO group (organic base)

➢ Protein structure and function is defined by the sequence and type ➢ At physiological pH (~7.4), amino acids exist as
of amino acids. zwitterions – positive and negative charge on
the same molecule. Dependent on the pKa of
the group.

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Stereochemistry Stereochemistry
➢ Every compound has a mirror image ➢ Superimposable mirror images: ACHIRAL
➢ Sometimes mirror images of a molecule are superimposable in ➢ Examples: two plain mugs, you can turn the
space with the original object. mirror image of the plain mug in space to make
➢ Non-superimposable mirror images: CHIRAL it superimposable.
➢ Greek word cheir: “hand”
➢ Have no plane of symmetry
➢ General rule: Carbon atom with 4 different atoms or groups
bonded to it.
➢ Example: hand or foot

Enantiomers Enantiomers
➢ Non-superimposable mirror images ➢ Each amino acid except glycine has
2 enantiomers.
➢ Most amino acids (except glycine) have four different groups
attached to the a-carbon. Chiral center. ➢ The enantiomers are classified
based on the ability to rotate
➢ Glycine – R is hydrogen. Therefore the mirror images ARE polarized light – optically active.
superimposable and NOT chiral. Also a plane of symmetry exists. ➢ Rotate light in either (+) or (-)
direction.
➢ Called D or L enantiomers.
➢ Racemic mixture – optically
inactive

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Enantiomers
➢ Both D and L amino acids exist in
nature but only L amino acids are
used as building blocks for proteins.
➢ D-amino acids are found in a few
rare bacteria in the cell walls.
Example: Thalidomide
➢ A sedative given to women in late 1950s and
early 1960s to help morning sickness.
➢ Mixture of R- and S- forms
➢ R- form is effective
➢ S- form caused severe birth defects, including
appendage
➢ Can racemize in vivo – both forms can
interconvert
➢ All 20 amino acids
Amino Acids
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Examples
➢ Different flavors tasted depending
on the chirality of one carbon in
carvone.
➢ (+) spearmint
➢ (-) caraway
➢ Taste receptors can tell the
difference in 3-D structure of small
molecules.
➢ Taste buds are chiral environment.
Example: Conversion of L to D with age
➢ Part of ageing process may include isomerization of the amino acid
aspartic acid (aspartate) from L to D in proteins in teeth and eyes.
➢ Isomerized proteins are less biologically active
➢ Scientists are identifying the enzymes that change D back to L to
try and slow the ageing process.
have both three letter
and one letter abrv.
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Side chains (R group) Classification of amino acids

➢ The “R” group side chains on amino acids ➢ Group 1: Non-polar side chains
are VERY important (hydrophobic)
➢ Reasons: ➢ Group 2: Polar, uncharged side
➢ Determine the properties of the amino chains
acid itself (polar, nonpolar, acidic or basic) ➢ Group 3: Charged Side Chains
➢ Determine the properties of the proteins ➢ Acidic Side chains
the contain those amino acids. ➢ Basic Side chains
➢ Dictate what a protein can and cannot do
and how it folds.

Group 1: Non-polar (hydrophobic) Group 1: Non-polar (hydrophobic)

➢ Side chains of Group 1 amino acids are mainly hydrocarbons – very ➢ Aliphatic hydrocarbons
unreactive amino acids. ➢ Glycine (G, Gly)
➢ 2 subgroups: Aliphatic hydrocarbons and Aromatic hydrocarbons ➢ R group is hydrogen
(have benzene rings) ➢ Found in flexible parts of
➢ These amino acids will tend to be buried (away from water) 0in 3-D proteins
structure of proteins. ➢ Not chiral
➢ Can be modified by addition
of a fatty acid (myristate – 14
Carbon)

Group 1: Non-polar aliphatic

➢ Aliphatic hydrocarbons
➢ Alanine (A, Ala)
➢ The model amino acid
➢ R group is –CH3 (methyl)
➢ Valine (V, Val)
Leucine (L, Leu)
Isoleucine (I, Ile)
Extended aliphatic chains
Can be branched

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Group 1: Non-polar aliphatic Group 1: Non-polar aliphatic

➢ Methionine (M, Met) ➢ Proline (P, Pro)
➢ Contains sulfur ➢ Only imino acid
➢ Can interact and bind with ➢ Affects protein folding
metal ions ➢ Often found at bends in protein
➢ Often found in metalloproteins 3-D structures
➢ Hydroxylation of proline
important for the structure of
collagen.

Group 1: Non-polar aromatic

➢ Phenylalanine (F, Phe) and Tryptophan (W, Trp)
➢ Fluorescent
➢ UV absorbing at 250-300 nm – can be useful to identify proteins
in a mixture
➢ Tryptophan is converted to serotonin
➢ Serotonin – has a sedative effect, gives a pleasant feeling
➢ Very low levels of serotonin associated with depression
➢ Extremely high levels produce a manic state
➢ Contains an indole ring

Group 2: Neutral Polar Side chains Group 2: Neutral Polar Side chains
➢ Polar residues are also buried on the surface of proteins. ➢ Serine (S, Ser) and Threonine (T,
Thr)
➢ They form H-bonds with other polar residues in the protein or with
water. ➢ Polarity contributed by the
hydroxyl group (-OH)
➢ Example: Serine can both donate as well as accept a hydrogen ➢ Sugars attach to Ser and Thr to
bond. form glycoproteins
➢ Ser and Thr can have
phosphates attached – regulates
the activity of some proteins.

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Group 2: Neutral Polar Side chains
➢ Tyrosine (Y, Tyr)
➢ Fluorescent – absorbs UV light
at 280 nm (easy to identify)
➢ Can be phosphorylated (have
phosphates attached)
➢ Derived from phenylalanine
➢ Converted to catecholamines –
includes epinephrine
(adrenaline)
Group 2: Neutral Polar Side chains
➢ Asparagine (N, Asn) and
Glutamine (Q, Gln)
➢ Classified as amides
➢ Neither acidic nor basic
➢ Forms H-bonds
➢ Asn can be modified with
sugars to form glycoproteins
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Group 2: Neutral Polar Side chains
➢ Adrenaline
➢ “fight or flight” hormone
➢ causes release of glucose and
other nutrients into the blood
and stimulates brain function
Group 2: Neutral Polar Side chains
➢ Cysteine (C, Cys)
➢ Sulfhydryl side chain (-SH)
which gives polarity.
➢ Can oxidize to form disulfide
bonds that strengthen protein
structure
➢ Disulfide bonds are covalent
but reversible upon reduction
Group 3: Charged Amino Acids
➢ Acidic Side Chains
➢ Glutamate or Glutamic Acid (E,
Glu)
➢ Aspartate or Aspartic Acid (D,
Asp)
➢ Always negatively charged at
physiological pH (~7.4)
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Group 3: Charged Amino Acids

➢ Basic Side Chains
➢ All gain a proton at physiological pH (positively charged)
➢ Lysine (K, Lys)
➢ Arginine (R, Arg)
➢ Histidine (H, His)