Chapter-6

Amino acids and proteins

Outline
• Introduction
• Structural features of Amino acids
• Physical and chemical Properties
• Classification of Amino Acids
• Peptide bond formation
• Oxygen-Binding Proteins

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• Introduction
• AA are biomolecules containing an amino
group, a carboxylic group, and a side
chain that is specific to each amino acid.
• The nature of the side chain determine the
type if the AA.

• AA are the basic structural building units of

protein.
• The name ―amino acid‖ comes from the word
amine (amino) and the carboxylic acid
(carboxyl group).

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Structural features of Amino acids

• Elemental components: C, H, O, N and S atoms

• All AA have an amino group (-NH3+), a carboxylate (-
COO-) group and a hydrogen bonded to the same
carbon atom (the α-carbon)

• They differ from each other in their side

chain called R group.
• R groups vary in structure, size and
electric charges and influence the
solubility of amino acids in water.

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Structural features of Amino acids . . .
• The natural configuration of the -carbon is L.
• D-Amino acids are found in the cell walls of bacteria and
certain peptide of antibiotics
• The D-amino acids are not genetically encoded, but derived
from the epimerization of L-isomers
• L-amino acids are those with -amino group on the left and
D-amino acids are those with -amino group on the right

• Except glycine, all amino acids have chiral center. i.e. all
the four groups attached to the α-carbon are different

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 Physical and chemical Properties
• Physical Properties
• Amino acids are colorless, crystalline solid.
• All have high melting points greater than 200oc
• They are soluble in water, slightly soluble in alcohol
• R-group of amino acids and pH of the solvent play important role in
solubility.
• On heating to high temperatures, they decompose.
• All amino acids (except glycine) are optically active,
• that is, they rotate plane-polarized light

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 Chemical Properties
• Zwitterionic property
• A zwitterion is a molecule with functional groups of
which at least one has a positive and one has a
negative electrical charge.
• The net charge of the entire molecule is zero.

• A zwitterion can act as either an acid (proton donor):

• or a base (proton acceptor):

• Amphoteric property
• They act as both as acids and base due to the
presence of amine and carboxylic group. 6
Classification of Amino Acids

• Classified in to five basic groups depending on

their R substituents
• Nonpolar, aliphatic (7): The R groups are nonpolar
and hydrophobic

• Aromatic (3): participate in hydrophobic interactions.

• Polar, uncharged (5): The R groups of these amino
acids are more soluble in water, or more hydrophilic

• Positively charged (3): the R-group are basic or

positively charged.

• Negatively charged (2): the R-group are acidic or

negatively charged.
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 Classification of Amino Acids . . .

• The R groups in
this class of
amino acids are
nonpolar and
hydrophobic

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 Classification of Amino Acids . . .

• Their aromatic side

chains, are relatively
nonpolar (hydrophobic).
• All can participate in
hydrophobic
interactions.

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Classification of Amino Acids . . .

• The R groups of these amino

acids are more soluble in
water, or more hydrophilic,
than those of the nonpolar
amino acids, because they
contain functional groups
that form hydrogen bonds
with water.

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Classification of Amino Acids . . .

• Amino acids in
which R-group is
basic or positively
charged.

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Classification of Amino Acids . . .

• Amino acids in
which R-group is
acidic or negatively
charged.

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Classification of Amino Acids . . .
Based on nutrition

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 Structure and nomenclature of peptides,
Peptide bond formation
• The α-carboxyl group (C) of one amino acid can
react with the α-amino group (N) of another amino
acid to form an amide bond and release water.

• The bond between the C

and N atoms of each
amide group is called
a peptide bond, and the
resulting molecules are
called peptide.

• Peptide molecules are

composed of two or
more AAs joined through
amide formation.
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Peptide bond formation

• di-peptides – two aa,

• tri-peptides – three aa, and so forth.

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 Protein structure
• Based on their complexity,
structures of proteins are
classified as
• Primary,
• Secondary,
• Tertiary And
• Quaternary

• What levels of structure involve

hydrogen bonding?
• What types of structure is the
result of interactions between
amino acids that are far apart in
the primary structure?
• What levels of structure are
affected by denaturation?

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Primary structure

• Refers to the linear sequence of AA

structural units.
• also refers to the number and
sequence of AA, the constituent
units of the polypeptide chain.
• reported starting from the amino-
terminal (N) end to the carboxyl-
terminal (C) end.

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Secondary structure
• Refers to the spatial arrangement of a
polypeptide’s backbone atoms.
• The 2dary structure involves α-helices, β-
sheets.

 Stabilized by
hydrogen bonds
between N-H and
C=O groups.

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Secondary structure . . .

• Due to the regular formation of hydrogen bonds

parallel to the axis of the helix, alpha Helix structure
is more stable than Beta pleated Sheet structure.

• alpha Helix – H-bond is within strands (intra-strand).

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Secondary structure . . .

• ß-sheet can be either parallel or anti-parallel

depending on whether the strand directions (N-
terminus to C-terminus) are the same or opposite.
• The anti-parallel ß-sheet is more stable due to
the more well-aligned hydrogen bonds.

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Tertiary structure
• describes the folding of its secondary structural
elements.
• It refers to the three-dimensional structure of an
entire polypeptide.
• Results from interactions between side chains, or
between side chains and the polypeptide
backbone.

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 Tertiary Structure . . .

• Stabilize by:
 hydrophobic interactions,
 electrostatic interactions
 hydrogen bonds
 Covalent disulfides

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Quaternary structure
• Refers to the interaction of one or more subunits to form a
functional protein, using the same forces that stabilize the
tertiary.
• Individual chains may be identical, somewhat similar, or
totally different.
• Multiple proteins held together to function as one, held
together by variety of attractive forces (same as tertiary)

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26
Classification . . .
 Based on the chemical nature and solubility,
proteins are classified as:

• Simple proteins:
• Composed of only amino acid residue.
• On hydrolysis these proteins yield amino acids.
• It is further divided into:
• Fibrous protein: Keratin, Elastin, Collagen
• Globular protein: Albumin, Globulin, Glutelin,
Histones

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Classification . . .

• Conjugated proteins:
• Combined with non-protein moiety.
• Eg. Nucleoprotein, Phosphoprotein, Lipoprotein,
Metalloprotein etc.

• Derived proteins:
• Derivatives or degraded products of simple and
conjugated proteins.
• They may be :
• Primary derived protein: Proteans, Metaproteins,
Coagulated proteins
• Secondary derived proteins: Proteosesn or
albunoses, peptones, peptides

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 Oxygen-Binding Proteins

 Myoglobin and hemoglobin may be the most-studied and best-

understood proteins.
 They were the first proteins for which three-dimensional
structures were determined.

 Oxygen can be bound to a Heme prosthetic group

 a prosthetic group is a compound permanently associated with a

protein that contributes to the protein’s function.

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 Oxygen-Binding Proteins…

 Heme (or haem) consists of a complex organic ring structure,

protoporphyrin, to which is bound a single iron atom in its
ferrous (Fe2+) state.
 The iron atom has six coordination bonds
 4 Nitrogen of protoporphyrin ring
 Globin chain ( N of Proximal Histdine)
 Molecular oxygen

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 Oxygen-Binding Proteins…

 The coordinated nitrogen atoms (which have an electron

donating character) help prevent conversion of the heme iron
to the ferric (Fe 3+) state.
 Iron in the Fe 2+ state binds oxygen reversibly; in the Fe 3+ state
it does not bind oxygen.
 Heme is found in a number of oxygen-transporting proteins, as
well as in some proteins, such as the cytochromes, that
participate in oxidation-reduction(electron-transfer) reactions

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 Oxygen-Binding Proteins…

 When oxygen binds, the electronic properties of heme iron change

 change in color from the dark purple of oxygen-depleted venous
blood to the bright red of oxygen-rich arterial blood.

 Some small molecules, such as carbon monoxide (CO) and nitric

oxide (NO), coordinate to heme iron with greater affinity than does
O2.
 When a molecule of CO is bound to heme, O2 is excluded, which is
why CO is highly toxic to aerobic organisms

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 Myoglobin Has a Single Binding Site for Oxygen

 Myoglobin (Mr 16,700; abbreviated Mb) is a relatively simple

oxygen-binding protein found in almost all mammals, primarily in
muscle tissue
 As a transport protein, it facilitates oxygen diffusion in muscle.
Myoglobin is a single polypeptide of 153 amino acid residues with
one molecule of heme.
 It is typical of the family of proteins called globins, all of which
have similar primary and tertiary structures.
 The polypeptide is made up of eight alpha-helical segments
connected by bends
 About 78% of the amino acid residues in the protein are found in
these alpha-helices. 35
36
• The structure of myoglobin. (PDB ID 1MBO) The eight alpha-helical
segments (shown here as cylinders) are labeled A through H.
• Nonhelical residues in the bends that connect them are labeled AB, CD,
EF, and so forth, indicating the segments they interconnect.
• A few bends, including BC and DE, are abrupt and do not contain any
residues; these are not normally labeled. (The short segment visible
between D and E is an artifact of the computer representation.)
• The heme is bound in a pocket made up largely of the E and F helices,
although amino acid residues from other segments of the protein also
participate. 37
 Myoglobin…

Myoglobin, with its hyperbolic binding curve for oxygen is

relatively insensitive to small changes in the concentration of
dissolved oxygen and so functions well as an oxygen-storage
protein.

A curve describing the binding of oxygen to myoglobin.

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 Oxygen Is Transported in Blood by Hemoglobin

Nearly all the oxygen carried by whole blood in animals is

bound and transported by hemoglobin in erythrocytes (red
blood cells).
 Normal human erythrocytes are small (6 to 9 µm in diameter),
biconcave disks.
 They are formed from precursor stem cells called
hemocytoblasts in response to erythropoietin.
 Up on maturation they lose their intracellular organelles—
nucleus, mitochondria, and endoplasmic reticulum 39
 Hemoglobin…

to survive for only about 120 days

Their main function is to carry hemoglobin
In arterial blood, hemoglobin is about 96% saturated with oxygen.
In the venous blood, hemoglobin is only about 64% saturated.
Hemoglobin, with its multiple subunits and O2-binding sites, is
better suited to oxygen transport than myoglobin.

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 Hemoglobin…
 Hemoglobin Subunits Are Structurally Similar to Myoglobin

 Hemoglobin (Mr 64,500; abbreviated Hb) is roughly

spherical, with a diameter of nearly 5.5 nm.
 It is a tetrameric protein containing four heme prosthetic
groups, one associated with each polypeptide chain.
 Adult hemoglobin contains two types of globin, two -chains
(141 residues each) and two β-chains (146 residues each).
 Each subunit contains:
• 1 Globin Chain and 1 Heme group with a central Fe2+ ion
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(Ferrous ion)
42
 Hemoglobin…

1 Heme binds with 1 Oxygen molecule

• 4 Heme binds with 4 Oxygen molecule
• 1 OxyHb = 4 Globin+4Heme+4Oxygen

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 Hemoglobin…

 Hemoglobin Undergoes a Structural Change on Binding

Oxygen

 Two major conformations of hemoglobin: the R state and the T

state. T ―tense‖ and R ―relaxed‖
 Oxygen has a significantly higher affinity for hemoglobin in the R
state.
 Oxygen binding stabilizes the R state.
 The T state is most stable when oxygen is not bound
(deoxyhaemoglobin).
 Oxygen binding promotes transition to the R state.

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 Hemoglobin…
 Hemoglobin undergoes a transition from a low-affinity state (the
T state) to a high-affinity state (the R state) as more O2
molecules are bound.
 As a result, hemoglobin has a hybrid S-shaped, or sigmoid,
binding curve for oxygen
 The T R transition occurs more as more O2 molecules
interact with a second and subsequent subunits of Hb.
 The last (fourth) O2 molecule binds to a heme in a subunit that is
already in the R state, and hence it binds with much higher
affinity than the first molecule. 45
46
 A sigmoid (cooperative) binding curve.
 A sigmoid binding curve can be viewed as a hybrid
curve reflecting a transition from a low-affinity to a
high-affinity state.
 Cooperative binding, as manifested by a sigmoid binding
curve, renders hemoglobin more sensitive to the small
differences in O2 concentration between the tissues and
the lungs, allowing hemoglobin to bind oxygen in the
lungs (where pO2 is high) and release it in the tissues
(where pO2 is low).
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 Hemoglobin…
 Oxygen binding to hemoglobin is both allosteric & cooperative.
 An allosteric protein is one in which the binding of a ligand (a
molecule bound reversibly to a protein) to one site affects the
binding properties of another site on the same protein.
 As O2 binds to one binding site, the hemoglobin undergoes
conformational changes that affect the other binding sites—an
example of allosteric behavior.
 Conformational changes between the T and R states, mediated
by subunit-subunit interactions, result in cooperative binding,
making it easier for additional molecules of O2 to bind.
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Thank You!

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