BIOCHEMISTRY!

PROTEINS

• Amino acids (molecular formula/structure)

• Classifications of AA
• Peptide bonds
 PROTEIN
• Is a naturally-occuring, unbranched polymer in
which the monomer units are amino acids.

• CHONS
 Amino Acids and Peptide Bonds

• An amino acid usually contains a carboxyl group, an

amino group and a side chain, all bonded to the
alpha carbon atom.
• Amino acids are usually on the L-conformation.
• At physiologic pH, amino acids carry a positive charge
on their amino groups and a negative charge on their
carboxyl groups.
 Amino Acids and Peptide Bonds
• The side chains of the amino acids contain
different chemical groups. Some side chains
carry a charge.
• Peptide bonds link adjacent amino acid
residues in a protein chain.
 CARBOXYL GROUP

The carboxyl group is an organic

functional group consisting of a carbon
atom double bonded to an oxygen atom
and single bonded to a hydroxyl group.

The carboxyl group is commonly written

as -C(=O)OH or -COOH.
 AMINO GROUP

• A functional group
that consists of a nitrogen atom attached
by single bonds to hydrogen atoms, alkyl
groups , aryl groups , or a combination of
these three.
• An organic compound that contains an
amino group is called an amine.
• Written as –NH2
 ALPHA CARBON

The alpha carbon in organic chemistry refers

to the first carbon that attaches to a
functional group (the carbon is attached at the
first, or alpha, position). By extension, the
second carbon is the beta carbon.
 L-form vs. D-form
• L stands for levorotatory.
• D stands for dextrorotatory.
Mirror images: Enantiomers (take
note)
Non-superimposable Mirror images

Enantiomers

Chiral Centers

Chiral molecules
• In nature, the vast majority of amino
acids take the L configuration as opposed
to the D configuration.
• The L and D configurations are
enantiomers of each other, in other
words, they have the same chemical
structure and order to their molecules,
but they are mirror images of each other.
• Molecules with enantiomers polarize light
that is shown through it, and assigned an L
or D based on which way the light bends
when shown through a solution.
• Most amino acids naturally only occur in the
L conformation, which make them
enantiomerically pure.
• Interestingly enough, most medications are
only active in one of the two conformations,
and the enantiomer actually causes the side
effects associated with that drug.
• However, it isn't cost effective to isolate
the active enantiomer and the side
effects generally aren't bad enough to
warrant a need for it (thalidomide is an
example that comes to mind; the
enantiomer of the safe drug is what
caused the birth defects).
• However, amino acids are naturally
isolated in their conformation so they are
sold as L-amino acid.
 AMINO ACIDS:

• About 20 Amino acids (standard amino acids)

are used for the synthesis of proteins by the
mRNA-directed process that occurs in
ribosomes.
• Other amino acids exist for which there is no
genetic code.
 STRUCTURE OF AMINO ACIDS

a. Most amino acids contain

carboxyl(+), an amino group (-), and a
side chain (R group), all attached to
the alpha carbon atom.
 Exceptions:
1. Glycine does not have a side chain. Its alpha
carbon contains two hydrogens.
2. In proline, the nitrogen is part of the ring

b. All of the 20 amino acids except glycine are

of the L-configuration. Because glycine does
not contain an asymmetric carbon atom, it is
not optically active and thus, it is neither D
nor L.
C. The classification of amino acids is based
on their side chains.
CLASSIFICATION OF AMINO ACIDS
BASED ON SIDE CHAIN
 HYDROPHOBIC AMINO ACIDS
Hydrophobic amino acids have side chains that
contain aliphatic groups that can form
hydrophobic interactions.

(Leucine, isoleucine, valine, glycine and alanine)

*ALIPHATIC and AROMATIC AMINO ACIDS (with

few exceptions)
 1. ALIPHATIC AMINO ACIDS
• nonpolar and hydrophobic.
• Hydrophobicity increases with increasing number of
C atoms in the hydrocarbon chain.
• Prefer to remain inside protein molecules with the
exception of alanine and glycine (ambivalent)
• GlyAl can be inside or outside the protein molecule.
• Glycine has such a small side chain that it does not
have much effect on the hydrophobic interactions.
 2. AROMATIC AMINO ACIDS

• nonpolar
• To different degrees, all aromatic amino acids
absorb ultraviolet light.
• (Tyrosine, Tryptophan, Phenylalanine)
• Tyrosine and tryptophan absorb more than
do phenylalanine
 2. AROMATIC AMINO ACIDS

• Exception: Tryptophan is a borderline

member of the nonpolar group because it can
weakly interact with water molecules through
hydrogen bonding with the NH ring location
on Tryptophan’s side chain ring structure.
 2. AROMATIC AMINO ACIDS

• Tryptophan is responsible for most of the

absorbance of ultraviolet light (ca. 280 nm) by
proteins.
• Tyrosine is the only one of the aromatic amino
acids with an ionizable side chain.
• Tyrosine is one of three hydroxyl containing
amino acids.
HYDROXYL, SULFHYDRYL, AND
DISULFIDE
 HYDROXYL GROUPS

• Hydroxyl groups found on serine,

tyrosine, and threonine can form
hydrogen bonds.
(OH-Oxygen is in covalent bonding with
hydrogen)
 SULFHYDRYL GROUPS
• Sulfur is found mainly in proteins in the form of
sulfhydryl groups (symbolized as –SH) or disulfide
group (symbolized as -S-S-).
• Sulfur is present in cysteine (-SH) and methionine (-
S-S)
• The sulfhydryl groups of two cysteines can form a
disulfide, producing cystine.
By convention, sulfur atoms are represented by
yellow spheres in molecular models.
IONIZABLE GROUP
• Ionizable groups are present on the side
chains of five amino acids.

• Aspartate, Glutamate, Histidine, Lysine, and

Arginine.

• They can carry a charge, depending on the

pH. When charged, they can form
electrostatic interactions.

(adding or removing one or more electrons

gives a net electric charge to an atom.)
AMIDES
• Amides are present on the side chains of
asparagines and glutamines.

• Amides are derived from carboxylic acids.

A carboxylic acid contains the -COOH
group, and in an amide the -OH part of
that group is replaced by an -NH2 group.

• So . . . amides contain the -CONH2 group.

AMIDES
• The side chain of proline forms a ring
with the nitrogen and is attached to the
alpha carbon.
• It is not an essential amino acid, which
means that the human body can
synthesize it. • It is unique among the 20
protein-forming amino
acids in that the amine
nitrogen is bound to not
one but two alkyl groups,
thus making it a
secondary amine.
 NONPOLAR, ALIPHATIC POLAR, UNCHARGED AROMATIC

GLYCINE CYSTEINE TRYPTOPHAN

ISOLEUCINE ASPARAGINE PHENYLALANINE
VALINE THREONINE TYROSINE
ALANINE GLUTAMINE
LEUCINE PROLINE
METHIONINE SERINE
 POSITIVELY CHARGED NEGATIVELY CHARGED

HISTIDINE GLUTAMATE
ARGININE ASPARTATE
LYSINE
 CLASSIFICATION OF AMINO ACIDS
BASED ON POLARITY AND CHARGES
(ACIDITY and BASICITY)
 NONPOLAR/HYDROPHOBIC AMINO
ACIDS
• Contains one amino group, one carboxyl
group, and a nonpolar side chain.
 NONPOLAR AMINO ACIDS
• VIMPP GALTry
VALINE GLYCINE
ISOLEUCINE ALANINE
METHIONINE TRYPTOPHAN
PROLINE
PHENYLALANINE
 POLAR/HYDROPHILIC AMINO ACIDS
• Contains one amino group, one carboxyl
group, and a polar side chain.

• Neutral, acidic, or basic (alkaline)

 POLAR, NEUTRAL (polar, uncharged)
• Contains one amino group, one carboxyl
group, and a polar but neutral side chain.

• Neither acid nor base at physiologic pH.

• Side chain can form hydrogen bond with water.
 POLAR, NEUTRAL AMINO ACIDS
• CAST GluTy
CYSTEINE
ASPARAGINE
SERINE
THREONINE
GLUTAMINE
TYROSINE
 POLAR, ACIDIC (polar, negatively
charged) AMINO ACIDS
• Contains one amino group, one carboxyl
group, and a second carboxyl group as the
side chain.

• Acidic at physiologic pH.

• Side chain -C(=O)OH bears a negative charge,
making it C(=O)O-
 POLAR, ACIDIC AMINO ACIDS
• ACID/ -ate
GLUTAMIC ACID/ GLUTAMATE
ASPARTIC ACID/ ASPARTATE
 POLAR, BASIC (polar, positively
charged) AMINO ACIDS
• Contains one amino group, one carboxyl
group, and a second amino group as the side
chain.

• Basic at physiologic pH.

• Side chain –NH2 bears a positive charge,
making it –NH3+
 POLAR, BASIC AMINO ACIDS
• HiLyAr
HISTIDINE
LYSINE
ARGININE
ESSENTIAL AMINO ACIDS
 Essential Amino Acids
• Standard amino acids that need to be
obtained from the diet because the human
body cannot synthesize it in adequate
amounts from another substances (lipids or
carbohydrates).
 ESSENTIAL AMINO ACIDS:
• PVT MAT HILL

PHENYLALANINE HISTIDINE
VALINE ISOLEUCINE
THREONINE LEUCINE
LYSINE
METHIONINE
ARGININE
TRYPTOPHAN
TABOO TOPIC
ACID-BASE PROPERTIES OF AMINO
ACIDS
ACID-BASE PROPERTIES OF AMINO ACIDS
• In pure form= white, crystalline solids with
relatively high decomposition points.
• Not very soluble in water.
• Amino acids are charged species.
AMINO ACID STRUCTURE
 IN NEUTRAL SOLUTION
• Carboxyl group loses proton

-COOH  -COO- + H+
• Amino group accepts proton

-NH2 + H+  -NH3+
 ZWITTERION
• O molecule that has a positive charge on one
atom and a negative charge on another atom,
but which has no net charge.
• In solution and solid states, amino acids exist
as zwitterion.
 IN ACIDIC AND ALKALINE SOLUTION

• Amino group accepts proton

FIN