Outline
• Amino acids
Structure of amino-acids
Classification amino acids
Acid-base property of amino acids
Conversion of amino acids to specialized products
• Proteins
Function of protein
Classification of proteins
Denaturation of protein
Myoglobin & Hemoglobin
Amino Acids
Amino acids are the most
important “building blocks” of
proteins
There are over 300 naturally
occurring amino acids
Only 20 amino acids are commonly
found as constituent of mammalian
protein.
Amino Acids………
Because of the tetrahedral arrangement of the bonding orbital around
the - carbon atom, the amino acids have two possible stereoisomers
(D and L).
The amino acid residue in protein molecules are exclusively L-
stereoisomers
D- Amino acids have been found only in some bacterial cell wall and
certain peptide antibiotics like gramicidin
Standard Amino acids and their symbols
Only 20 amino acids that are coded by DNA, the genetic material in cell
They are the molecular instruments to express genetic information
Classification of Amino acids
1. According to side chain
Amino acids classified according to the properties of their side chain
(polarity, size and structural features)
1. Amino acids with non polar side chain (aliphatic)
Do not bind or give proton
Do not participate in hydrogen bond
They promote hydrophobic interaction
The imino group of proline is held in a rigid conformation that
reduces flexibility of polypeptide regions containing proline
2. Amino acids with uncharged polar side chain (R)
Can participate in hydrogen bond
-OH group of threonine & serine are
site for protein phosphorylation &
glycosylation that is important to
regulate a metabolic pathway
The R group is more soluble in
water (hydrophilic)
Cysteine is readily oxidized to form
a covalently linked dimeric amino
acid (disulfide bond) called cystine
3. Amino acids with aromatic R- group
All can participate in hydrophobic interaction
The hydroxyl group of tyrosine can form hydrogen bonds, and it is an
important functional group in some enzymes.
4. Positively charged (basic) R group
Have most hydrophilic R group
In many enzyme-catalyzed reactions Histidine residue facilitate the
reaction by serving as a proton donor/ acceptor since it has an
ionizable side chain with a pKa near neutrality (pKa= 6)
5. Negatively charged (acidic) R group
The amino acids aspartic and glutamic acids are proton donors
They are negatively charged at physiologic pH
They form ionic or electrostatic bond with positively charged
molecules
2. Classification of amino acids by synthesis
Based upon whether the amino acids can be synthesized in human
body or not, they can be:
Essential or Indispensable and
Non-essential or Dispensable amino acids
Essential AA cannot be synthesized in body & supplied in the diet
Non-essential AA can be synthesized in sufficient amount from the
intermediates of metabolism or as in the case of cysteine and
tyrosine from essential amino acids
Cysteine is synthesized from the essential amino acid methionine and
tyrosine is synthesized from phenylalanine
From non-essential amino acids, there is no diet dependency
1. Ketogenic AA: give intermediates convertible into acetyl-CoA or
acetoacetyl-CoA
2. Glucogenic AA: give intermediates of glycolysis or kreb’s cycle
(oxaloacetate, pyruvate, succinyl CoA, -KGA, fumarate) and thus can
be converted to carbohydrates.
Properties of amino acids
Amino acids can acts as bases and acids
AA has two ionizable groups: carboxyl & amino group capable of either
donating or accepting protons when the pH of the solution altered
AA in solution exist as dipolar ion, or Zwitterion that is no net charge
The pH at which an AA is electrically neutral is called isoelectric point
(pI) & the molecule has equal amount of positive and negative charges
Amino acids can acts as bases and acids…
Substances that have dual nature are called amphoteric
Optical Properties of the Amino Acids
Optical active compounds are chiral .
The one amino acid not exhibiting chirality is glycine since its '"R-
group" is a hydrogen atom.
All of the amino acids in proteins are all L-α-amino acids.
D-amino acids are never found in proteins, although they exist in
nature.
D-amino acids are often found in polypeptide antibiotics.
The aromatic R-groups in amino acids absorb ultraviolet light with an
absorbance maximum in the range of 280nm.
Formation of Peptide Bond
Peptide bond formation is a condensation reaction leading to the
polymerization of amino acids into peptides and proteins.
Peptides are small consisting of few amino acids.
A number of hormones and neurotransmitters, several antibiotics and
antitumor agents are peptides.
Condensation of the primary –COOH group of an AA & primary –NH2
group of another AA forms the peptide bond.
This requires energy and leaves a free amino group at one end (N-
terminus) and a free carboxylic acid group at the other end (C-
terminus) of the product dipeptide.
Proteins
Proteins are linear, unbranched
polymers of amino acids linked
head to tail, from carboxyl
group to amino group, through
covalent peptide bonds.
Polymers of subunits of the
polymerizable, genetically
coded 20 amino acids linked
together by peptide linkages
LEVELS OF PROTEIN STRUCTURE
1.Primary (1°) Protein Structure
linear sequence of amino acids.
2. Secondary (2°) Protein Structure
localized regional structures
3. Tertiary (3°) Protein Structure
overall shape of proteins
4. Quaternary (4°) Protein Structure
interactions between proteins.
Primary Structure
Primary structure of a protein describes identity and linear sequence
of amino acids that are interconnected by peptide bonds.
Conventionally, peptide sequence is written left to right.
The left side terminal AA is the peptide’s N-terminal and the final AA
towards the right end is the peptide’s C-terminal;
There is co-linearity between gene DNA, mRNA and the peptide
sequences : ‘Central Dogma’.
The mutational changes in DNA sequence are reflected on the
peptide sequence and final conformation and hence its function.
Relationship between the coding strand of DNA, the DNA
template strand, the mRNA transcript, and the protein produced
from the gene. The bases in mRNA are used in sets of three
(called codons) to specify the order of the amino acids inserted
into the growing polypeptide chain during the process of
translation.
Secondary Structure
Secondary structure of a protein is formed when a carbonyl group of one
peptide bond is intramolecularly H-bonded to amide group that are
located near each other of (C=O—H-N).
- helix : Most common secondary structure, about ¼ of all amino acid
residues in polypeptides are found in α-helices
β-pleated sheets :
Polypeptides (2-5 chains)
run inline with each other &
H bonding stabilizes the
structure.
polypeptide chains run in
parallel direction to each
other, called ‘parallel β-
pleated sheets’ (a)
run in opposite direction to
each other, called ‘anti-
parallel β-pleated sheets’ (b)
TERTIARY STRUCTURE
is special arrangement of various
regions/ domains .
formed by complicated folding&
super-folding of the peptide chain
into globular (fibrous) form of d/t
size.
Stabilized by interactions through
R-groups of composite amino acids
utilizing van der Waals, ionic,
hydrophobic, H and disulfide bonds.
Tertiary structure is dictated by
primary structure i.e. linear AA
sequence
QUATERNARY STRUCTURE
Specifies the nature of many polypeptides association in a defined geometric
positional configuration to make a functional protein.
The polypeptides in a quaternary protein could act in synergy, suppress or
stimulate the function(s) of each other
Many proteins contain 2, 3, 4 or more subunits : dimeric, trimeric, tetrameric
or oligomeric proteins
Oligomeric proteins are very common among enzymes e.g. carbonic
anhydrase is composed of 27 polypeptides
Polymeric proteins could be hetero-oligomers (i.e., several polypeptides each
with different sequence) or homo-oligomers (i.e., several polypeptides of the
same type
Quaternary structure stabilized by all types of secondary non-covalant bonds
and is the most sensitive to denaturation
CLASSIFICATION OF PROTEINS
I. Nutritional value: it depends upon their digestibility & amino acid
composition.
High biological value when they are digestible and contain all the
essential amino acids in well balanced proportions;
Low biological value when they are deficient in one or more amino acids
or contain them in a very low imbalanced amount or are indigestible.
Proteins of high biological value : all digestible proteins of animal origin (
dairy products like eggs, liver, fishes, red and white meats) and some proteins
of plant origin ( lentils and broad beans).
Proteins of low biological value : Most plant proteins and a few animal
proteins.
e.g. collagen deficient in trp and cys ; skin, hair and nail keratins are
indigestible.
CLASSIFICATION OF PROTEINS
II. Axial Ratio :, depending upon their molecular length, width indicated by
ultramicroscopic studies Proteins could be divided into globular or fibrous
Fibrous proteins : Proteins with an axial ratio of >10 are fairly resistant and
sturdy.
Majority have structural function e.g. keratins in hairs, wool, skin, nails
and cytoskeletons and myosin of the muscles
Globular proteins : The proteins with an axial ratio <10.
Less stable than fibrous proteins and more labile to denaturation.
Most globular proteins are metabolically active and function as enzymes,
hormones or transport proteins
e.g. Chymotrypsin, Igs, albumin, Hb and insulin
PROPERTIES OF PROTEINS
Denaturation:
Loss of native form with disruption of 2ndry , tertiary & quaternary structure
→ changes in physical and chemical characteristics & loss of biological activity.
No hydrolysis of peptide bonds, primary structure preserved
Factors disrupting weak secondary bonds responsible for maintaining protein
structure:
1. Physical manipulations : shaking, high T0 & ionizing radiations;
2. Chemical factors: organic solvents like acetone, strong alkalis and
acids; heavy metals, and formaldehyde, formamide, glyoxal, SDS ,
guanidine hydrochloride and isothiocyanate.
3. Some biological factors : e.g. insulinase that disrupts interchain disulfide
bond of insulin and inactivates it.
FUNCTIONS OF PROTEINS
Structural : Main structural component in bone, muscles, cytoskeleton and
cell membrane
Nutrition : Provide the body with essential amino acids
Catalytic : All metabolic enzymes are proteins in nature
Endocrine : Most hormones and all receptors are protein in nature
Defence : The antibodies (immunoglobulin) and complement system that
play an important role in the body’s defensive mechanisms are proteins in
nature
Osmotic Potential : Plasma proteins are responsible for most effective
osmotic pressure of the blood.
This osmotic pressure plays a central role in many processes, e.g.,
urine formation
FUNCTIONS OF PROTEINS…
Blood clotting factors are proteins
Transport : Proteins carry lipids in the blood forming lipoprotein complexes.
Proteins also carry, hormones, e.g., thyroid hormones and minerals, e.g.,
Ca, Cu & Fe.
Hemoglobin (a chromo-protein) carries O2 from the lung to tissues
Membrane transport : The proteins in the membranes act as channels or
transporters to allow selective molecules/ions to cross into or out of the cells
Gene Regulation : Control of cellular activities through control of gene
expression: Most factors required for DNA replication, transcription and
mRNA translation are protein in nature
Signal Transduction : Intercellular and intracellular signal transduction
carried out largely by proteins
