Lesson 1: PROTEIN CHEMISTRY (c) hydroxyl groups

What Are Proteins? (d) S-containing groups.

1. Large molecules
2. Made up of chains of amino acids linked together in AMINO ACIDS
a long chain. 1. All 20 AAs, except glycine have at least one
3. Amino acids are linked by a peptide bond or amide asymmetric or chiral carbon atoms.
bond. 2. Glycine, the simplest amino acid is optically
4. Are found in every cell in the body inactive.
5. Are involved in most of the body’s functions and 3. Amino acids in proteins are L-configurated.
lifeprocesses 4. Only L-amino acids are manufactured in cells and
6. Name derived from Greek word Proteios, w/c assembled into proteins.
means “holding first place” o L-amino acid refers to an stereoisomer of a
Structure of Proteins particular amino acid whose amino group is on
the left side in its Fisher projection. (-NH2 is to
 Made up of chains of amino acids; classified by
the left of the α-carbon)
number of amino acids in a chain
o Peptides: fewer than 50 amino acids  L-α glycine, the only achiral amino acid. It is
o Dipeptides: 2 amino acids achiral because of the identical H attached
o Tripeptides: 3 amino acids to penultimate carbon.
o Polypeptides: more than 10 amino acids  L-α alanine, its C2 is an asymmetric carbon
o Proteins: more than 50 amino acids because there are 4 different groups
 Typically 100 to 10,000 amino acids linked attached to it. These are -COOH, -H,
together. Amino acids are composed of CH3 and –NH2.
carbon, hydrogen, oxygen, and nitrogen  L-α-valine, its C2 is an asymmetric carbon
AMINO because there are four different groups
attached to it. These are –COOH, -H, -
 Organic compound containing two functional CH(CH3)2 and –NH2
ACIDS groups: an amino group (-NH₂) and
Absence of a chiral carbon makes glycine optically
carboxyl group (-COOH).
inactive while alanine & valine have both chiral
 building blocks of proteins. centers and are therefore optically active.
 Most of the amino acids found in protein except
proline are alpha-amino acids.
 Alpha – because the amino group is attached to α
carbon atom, adjacent to the carboxyl group.

General Formula of Amino Acids

NOTE:
1. The R group is different for each amino acid and it
is the group that defines the amino acid.
2. Amino acid side chain is not restricted to alkyl
groups, may contain
(a) open-chain, cyclic or aromatic HC groups
(b) additional amino or carboxyl groups
Classification of Amino Acids According tO Human Non-polar side chains (Hydrophobic)
Body Needs 1. Glycine – simplest AA, optically inactive (absence
1. Essential amino acids - are amino acids which of chiral C)
organisms need to ingest because it is necessary for
nutrition and cannot be synthesized in the body, also
known as: indispensable amino acid.
o Examples: phenylalanine, valine, threonine,
methionine, arginine (required for the young,
but not for adults), tryptophan, histidine,
isoleucine, lysine & leucine. PVT MAT HILL
2. Non-essential amino acids – are amino acids which can
be synthesized by the human body. There are 11
nonessential amino acids: alanine, arginine,
asparagine, aspartic acid, cysteine, glutamic acid,
glutamine, glycine, proline, serine, and tyrosine. 2. Alanine
Classification of Amino Acids According to Side
Chain Polarity
1. Non-polar Amino Acids - R is alkyl hydrophobic
group which can’t hydrogen bond w/ H2O. There
are 9 non-polar amino acids:
Ala Trp
Gly Phe
Ile Pro
Leu Val
Met

2. Polar neutral amino acids - R contains polar 3. Valine

hydrophilic group so can form hydrogen bond with
H₂O. In those amino acids, R may contain:

OH - in ser, thr, tyr

SH in cys
Amide group in gln, asn

3. Polar, positively charged amino acids are the basic

amino acids:

Lys 4. Leucine
Arg
His

4. Polar, negatively charged amino acids are the

acidic amino acids:

Asp
Glu
5. Isoleucine
9. Tryptophan

6. Proline – an imino acid

Polar Nuetral Amino Acidschains (Hydrophilic)

1. Serine

7. Methionine 2. Threonine

3. Tyrosine

8. Phenylalanine
 4. Cysteine Polar, positively charged amino acids (Basic Amino Acids)

1. Lysine
 Has an additional –NH2 on its side chain, can
H-bond with water.

2. Histidine
 TRIVIA: Histidine is the precursor of histamine.
Histamine is a vasodilator w/c causes swelling
conditions during allergy.
3. Arginine
 Basic amino acids are positively charged
because in a solution at physiological pH, the 2
5. Glutamine amino grps. are protonated while the carboxyl
grp is deprotonated. -NH3⁺, -NH3⁺ , -
COO⁻ Net charge= +
 Acidic amino acids are negatively charged
because in a solution at physiological pH, 2
carboxyl groups are deprotonated while 1
amino group is protonated.
 -COO⁻, -COO⁻, NH3⁺ Net charge= -
 Has guanidine, –N(H)-C=NH NH2 on its side
chain.

6. Asparagine Interaction Exhibited by R-groups of Amino Acids

1. HYDROPHOBIC INTERACTION- exhibited by
amino acid if the R-group is mainly hydrocarbon
such as in ala, val, phe, leu, ile.

2. Ionic Interaction - exhibited by acidic amino acid

after deprotonation and by basic amino acid upon
protonation. Example: lys + asp

3. Hydrogen bonding - exhibited by –OH & -SH

containing amino acids. Formed from
electronegative atoms (F>O>N) with electropositive
Polar, negatively charged amino acids (Acidic Amino hydrogen.
Acids)
1. Aspartic acid 4. Disulfide bond – a strong covalent bond formed
 Has an additional –COOH on its side chain, can when two molecules of cysteine are oxidized to
H-bond with water. cystine unit.

2. Glutamic acid
 Has an additional –COOH on its side chain, can 5. Stacking interaction or pi-pi complexation – a weak
H-bond with water. attractive, noncovalent interaction between
aromatic rings. Aromatic amino acids are phe, trp,
tyr
Acid-Base Properties of Amino Acids
o pI
 Amino acids has both a basic amino group and an  Lys- 9.74
acidic carboxylic group. (amphoteric property)  Glu- 3.08
 They are acids when they are proton donors  Ala- 6.11
 They are bases when they are proton
acceptors. At physiological pH (7.38) which is a Peptide Bond
neutral pH, the carboxylic group lose proton while  also known as amide bond
the amino group accepts a proton to form zwitterion  is a chemical bond formed between two molecules
or dipolar ions. when the carboxyl group of one molecule of amino
o Zwitterion is a molecule that has (+) charge on acid reacts with the amino group of the other
one atom and a (-) charge on another atom, molecule, releasing a molecule of H2O.
thus its net charge is 0.  is a strong bond due to the double bond character
 At lower pH value, zwitterion’s carboxyl grp. is of the C-N bond as a consequence of pi electron
protonated to form a positively charged amino acid. delocalization.
 At higher pH value, zwitterion’s Positively charged  Links amino acids in a dipeptide, tripeptide and
amino acid amino group is deprotonated to form a polypeptides.
negatively charged amino acid.
Peptide Bond Formation
Isoelectric Point (pI)  is a dehydration synthesis reaction (also known as
 Is the pH at which amino acid exists in its zwitterion a condensation reaction
form.  Mnemonic device for writing structural formula of
 At isoelectric point, almost all amino acids in a peptides.
solution are in its zwitterion form.

Electrophoresis
 A method used to separate amino acids in an
electrical field.
 The (+)ly charged AAs move toward the negative
electrode (Cathode)
 The (-)ly charged AAs move toward the positive
electrode (anode).
 An amino acid at its pI does not migrate.
o Example: A mixture of lys, glu and ala buffered
at pH 6 was electrolyzed. Which of the amino
acids will migrate to the cathode? To the
anode? Will remain in solution?
o Guidelines:
 when pH above pI = anionic
 when pH below pI = cationic
 when pH = pI = zwitterion form

o Answer:
 lys = (+)ly charged; will migrate to cathode
 glu = (-)ly charged; will migrate to the anode
 ala = pH is almost the same with pI = will
remain in solution.