CHEMISTRY
OF PROTEINS
Proteins: Main Agents of
Biological Function
• Catalysis:
–enolase (in the glycolytic pathway)
–DNA polymerase (in DNA replication)
• Transport:
–hemoglobin (transports O2 in the blood)
–lactose permease (transports lactose across the cell membrane)
• Structure:
–collagen (connective tissue)
–keratin (hair, nails, feathers, horns)
• Motion:
–myosin (muscle tissue)
–actin (muscle tissue, cell motility)
Amino Acids
• Building Blocks of Protein
• neurotransmitter transport
• Biosynthesis of porphyrins, purines, pyrimidines, and
urea
Amino Acids
•
•
•
•
•
About 500 amino acids are known
Twenty amino acids are commonly found in proteins
First discovered amino acid …asparagine (1806)
Last of the 20 was threonine (1938)
Named after the sources they were discovered from and
common characteristics
• Like glycine (glykos=sweet)
• Glutamate discovered in wheat gluten; asparagine from
asparagus.
Amino Acids
• Twenty different amino acids are commonly
found in proteins. They are all α–amino acids,
amino acids in which the amino group is
attached to the -carbon (the carbon atom next
to the carboxylate group)
• The α-carbon has two additional substituents, a
hydrogen atom and an additional chemical
group called a side chain (-R). The side chain
is different for each amino acid.
Structure of Amino Acid
• Amine group acts like a base, tends to be positive.
• Carboxyl group acts like an acid, tends to be negative.
• “R” group is variable, from 1 atom to 20.
• Two amino acids join together to form a dipeptide.
• Adjacent carboxyl and amino groups bond together.
Structure of Amino Acid
• All 20 of the common aa are alpha amino acids i.e., they
have carboxyl and amino group bonded to the same carbon
atom (α-carbon)
Structure of Amino Acid
• They differ from each other in their side chain or R groups,
which vary in structure, size and electric charge.
• it affects the solubility of aa in water and give its unique
biochemical properties.
Structure of Amino Acid
• They differ from each other in their side chain or R groups,
which vary in structure, size and electric charge.
• It affects the solubility of aa in water.
• In addition to common 20 aa amino acids there are many
less common ones as well. They are usually modified after aa
synthesis.
Amino Acids: Building Blocks of
Protein
• Proteins are heteropolymers of -amino acids
• Amino acids have properties that are well suited to
carry out a variety of biological functions:
–
–
–
–
Capacity to polymerize
Useful acid-base properties
Varied physical properties
Varied chemical functionality
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, and so on.
This nomenclature can also be
applied to the hydrogen atoms
attached to the carbons. A
hydrogen attached to an alpha
carbon is called an alphahydrogen (α-hydrogen), a
hydrogen on the beta-carbon is
a beta-hydrogen, and so on.
Glycine-the simplest amino acid
H
O
+
Glycine
H3N
–
C
C
O
(Gly or G)
H
• Glycine is the simplest amino acid. It is the
only one in the table that is achiral.
• In all of the other amino acids in the table
the a carbon is a stereogenic center.
General Amino Acid Structure
At pH 7.4
H
+H3N
α
C
COO-
R
Each of the amino acids used for protein synthesis has the same
general structure
H
O
+
H3N
–
C
CH3
Alanine
(Ala or A)
C
O
H
O
+
H3N
–
C
C
CH(CH3)2
Valine
(Val or V)
O
H
O
+
H3N
–
C
C
CH2CH(CH3)2
Leucine
(Leu or L)
O
Peptide bond formation
A peptide bond (amide bond) is a covalent chemical bond formed between two amino acid
molecules
Peptide bond formation
The condensation of two amino acids to form a
peptide bond (red) with expulsion of water
(blue).
When two amino acids form a dipeptide through
a peptide bond it is called condensation. In
condensation, two amino acids approach each
other, with the acid moiety of one coming near
the amino moiety of the other. One loses a
hydrogen and oxygen from its carboxyl group
(COOH) and the other loses a hydrogen from its
amino group (NH2). This reaction produces a
molecule of water (H2O) and two amino acids
joined by a peptide bond (-CO-NH-).
The two joined amino acids are called a
dipeptide.
Peptide bond formation:
- Each polypeptide chain starts on the left side by free amino group of the first amino acid enter
in chain formation . It is termed (N- terminus).
- Each polypeptide chain ends on the right side by free COOH group of the last amino acid and
termed (C-terminus).
Formation of a Dipeptide
Dehydration synthesis
Amino Acid + Amino Acid --> Dipeptide
Amino Acid + Dipeptide --> Tripeptide
A.A. + A.A. + …..+ Tripeptide --> Polypeptide
N-terminus & C-terminus
The N-terminus (also known as the amino-terminus, NH2-terminus,
N-terminal end or amine-terminus) refers to the start of a protein or
polypeptide terminated by an amino acid with a free amine group (NH2).
The C-terminus (also known as the carboxyl-terminus, carboxyterminus, C-terminal tail, C-terminal end, or COOH-terminus) is
the end of an amino acid chain (protein or polypeptide), terminated by
a free carboxyl group (-COOH).
When the protein is translated from messenger RNA, it is created from
N-terminus to C-terminus. The convention for writing peptide
sequences is to put the C-terminal end on the right and write the
sequence from N- to C-terminus.
Peptide Chain
Structure of Proteins
• Made up of chains of amino acids; classified by number of amino acids in a
chain
– Peptides: fewer than 50 amino acids
• Dipeptides: 2 amino acids
• Tripeptides: 3 amino acids
• Polypeptides: more than 10 amino acids
– Proteins: more than 50 amino acids
• Typically 100 to 10,000 amino acids linked together
• Chains are synthesizes based on specific bodily DNA
• Amino acids are composed of carbon, hydrogen, oxygen, and nitrogen
Peptides
• Peptides are compounds in which an amide bond
links the amino group of one a-amino acid and the
carboxyl group of another.
• An amide bond of this type is often referred to as a
peptide bond.
• A peptide bond (amide bond) is a covalent chemical
bond formed between two molecules when the
carboxyl group of one molecule reacts with the amino
group of the other molecule, causing the release of a
molecule of water (H2O), hence the process is a
dehydration synthesis reaction (also known as a
condensation reaction).
Examples on Peptides:
1- Dipeptide ( two amino acids joined by one peptide bond):
Example: Aspartame which acts as sweetening agent being used in
replacement of cane sugar. It is composed of aspartic acid and
phenyl alanine.
2- Tripeptides ( 3 amino acids linked by two peptide bonds).
Example: GSH which is formed from 3 amino acids: glutamic acid,
cysteine and glycine. It helps in absorption of amino acids, protects
against hemolysis of RBC by breaking H2O2 which causes cell
damage.
3- octapeptides: (8 amino acids)
Examples: Two hormones; oxytocine and vasopressin (ADH).
4- polypeptides: 10- 50 amino acids: e.g. Insulin hormone
Alanine and Glycine
H
H
O
+
H3N
+
–
C
CH3
C
O
O
H3N
–
C
H
C
O
Alanylglycine
H
H
O
O
+
H3N
–
C
CH3
C
N
C
H
H
C
O
• Two a-amino acids are joined by a peptide
bond in alanylglycine. It is a dipeptide.
Alanylglycine
H
H
O
O
+
H3N
–
C
CH3
C
N
C
H
H
C
O
C-terminus
N-terminus
Ala—Gly
AG
Essential, Nonessential, and
Conditional
• Essential – must be consumed in the diet
• Nonessential – can be synthesized in the body
• Conditionally essential – cannot be
synthesized due to illness or lack of necessary
precursors
– Premature infants lack sufficient enzymes needed
to create arginine
Protein Quality
• Complete proteins
– Contain all nine essential amino acids
– Usually animal source are complete proteins
meat, fish, milk, eggs
– Are considered higher quality
• Incomplete proteins
– Low in one or more essential amino acid
– Usually plant sources are incomplete
Rare Amino Acids
• 4-Hydroxyproline, 5-hydroxylysine found
in collagen.
• D-Glutamic acid in cell walls of bacteria
• D-Serine in earthworms
• -Aminobutyric acid, a neurotransmitter
• -Alanine, constituent of the vitamin
pantothenic acid.
• Modified amino acids. In addition to the
amino acids encoded by DNA that form the
primary structure of proteins, many proteins
contain specific amino acids that have been
modified by phosphorylation, oxidation,
carboxylation, or other reactions. When these
reactions are enzyme-catalyzed, they are
referred to as post-translational
modifications.
AMINO ACIDS: CLASSIFICATION
BASED UPON AMINO ACID SIDE
CHAINS
Common amino acids can be placed in five basic
groups depending on their R substituents:
• Nonpolar, aliphatic (7)
• Aromatic (3)
• Polar, uncharged (5)
• Positively charged (3)
• Negatively charged (2)
Nonpolar, Aliphatic Amino Acids
• Glycine is the simplest amino acid, and it
really does not fit well into any classification
because its side chain is only a hydrogen atom.
• Aliphatic: In aliphatic compounds, carbon
atoms can be joined together in straight chains,
branched chains, or non-aromatic rings.
• Nonpolar:
II- Classification according to polarity of side chain (R):
A- Polar amino acids: in which R contains polar hydrophilic group so
can forms hydrogen bond with H2O. In those amino acids, R may
contain:
1- OH group : as in serine, threonine and tyrosine
2- SH group : as in cysteine
3- amide group: as in glutamine and aspargine
4- NH2 group or nitrogen act as a base (basic amino acids ): as lysine,
arginine and histidine
5- COOH group ( acidic amino acids): as aspartic and glutamic .
B- Non polar amino acids:
R is alkyl hydrophobic group which can’t enter in hydrogen bonf
formation. 9 amino acids are non polar ( glycine, alanine, valine, leucine,
isoleucine, phenyl alanine, tryptophan, proline and methionine)
Isoelectric Point
• pH at which amino acids exist as the
zwitterion (neutral).
• Depends on structure of the side chain.
• Acidic amino acids, isoelectric pH ~3.
• Basic amino acids, isoelectric pH ~9.
• Neutral amino acids, isoelectric pH is
slightly acidic, 5-6.
=>
G.N. Ramachandran
• Used computer models of small polypeptides to
systematically vary φ and ψ with the objective of finding
stable conformations
• For each conformation, the structure was examined for
close contacts between atoms
• Atoms were treated as hard spheres with dimensions
corresponding to their van der Waals radii
• Therefore, φ and ψ angles which cause spheres to
collide correspond to sterically disallowed conformations
of the polypeptide backbone
Sequence Similarity
• Sequence similarity implies structural,
functional, and evolutionary commonality
• Low sequence similarity implies little
structural similarity
• Small mutations generally well-tolerated by
native structure – with exceptions!
Sequence Similarity Exception
• Sickle-cell anemia resulting from one
residue change in hemoglobin protein
• Replace highly polar (hydrophilic)
glutamate with nonpolar (hydrophobic)
valine
Sickle-cell mutation in
hemoglobin sequence
Normal Trait
• Hemoglobin molecules exist as single,
isolated units in RBC, whether oxygen
bound or not
• Cells maintain basic disc shape, whether
transporting oxygen or not
Sickle-cell Trait
• Oxy-hemoglobin is isolated, but deoxyhemoglobin sticks together in
polymers, distorting RBC
• Some cells take on “sickle” shape
Sickle-cell
RBC Distortion
• Hydrophobic valine replaces hydrophilic glutamate
• Causes hemoglobin molecules to repel water and be
attracted to one another
• Leads to the formation of long hemoglobin filaments
• Filaments distort the shape of red blood cells
(analogy: icicle in a water balloon)
• Rigid structure of sickle cells blocks capillaries and
prevents red blood cells from delivering oxygen
Hemoglobin Polymerization
Normal
Mutant
Capillary Blockage
Zwitter ion
At physiological PH (7.4), -COOH gp is
dissociated forming a negatively charged
carboxylate ion (COO-) and amino gp is
protonated forming positively charged ion
(NH3+) forming Zwitter ion.
The molecule attains both +ve and –ve charges
with NO NET charge
Zwitterions
• An acid -COOH and
an amine -NH2 group
cannot coexist
• The H+ migrates to the
-NH2 group
• COO- and NH3+ are
actually present, called
a “Zwitterion”
General Amino Acid Structure
At pH 7.4
H
+H3N
α
C
COO-
R
Each of the amino acids used for protein synthesis has the same
general structure
Zwitterions
pH = 1-5
pH = 10-14
more basic
more acidic
excess
H+
H
R
C
COOH
NH 3 +
at pI
(isoelectric
point)
charge = 0
H
R
C
COO-
excess OHH
R
C
COO-
NH 2
NH 3 +
Ionization states of aminoacids depends on pH
AA’s
pI
• The pI is the “isoelectric point”
• The pI is the pH where
NO charge is on the AA:
at pI
charge = 0
(Not necessarily
at a neutral pH)
H
R
C
COO-
NH 3 +
Classification of amino acids based
on the polarity of their side groups
•
•
•
•
Non-polar amino acids
Polar amino acids with no charge
Polar amino acids with positive charge
Polar amino acids with negative charge
Non Polar Amino Acids
Non Polar Amino Acids have equal number of
amino and carboxyl groups and are neutral.
These amino acids are hydrophobic and have
no charge on the 'R' group. The amino acids in
this group are alanine, valine, leucine,
isoleucine, phenyl alanine, glycine,
tryptophan, methionine and proline.
Polar Amino Acids with no charge
These amino acids do not have any charge on the 'R'
group. These amino acids participate in hydrogen
bonding of protein structure. The amino acids in this
group are serine, threonine, tyrosine, cysteine,
glutamine and aspargine.
Polar Amino Acids with Positive
Charge
• Polar amino acids with positive charge have
more amino groups as compared to carboxyl
groups making it basic. The amino acids,
which have positive charge on the 'R' group
are placed in this category. They are lysine,
arginine and histidine.
Polar Amino Acids with Negative
Charge
• Polar amino acids with negative charge have
more carboxyl groups than amino groups
making them acidic. The amino acids, which
have negative charge on the 'R' group are
placed in this category. They are called as
dicarboxylic mono-amino acids. They are
aspartic acid and glutamic acid.
Polar Amino Acids with Negative Charge
• Since their side chains are all nonpolar and
therefore hydrophobic, these amino acids are
referred to as hydrophobic amino acids. This is
true in spite of the fact that the carboxylic acid
and amine groups make the individual amino
acid molecules polar rather than nonpolar.
Metabolic Fate of Amino Acids
Figure 6.7