PROTEINS

Proteins are the most abundant organic molecules in animals, playing important roles in all
aspects of cell structure and function. Proteins are biopolymers of acids, so named because the
amino group is bonded to the carbon atom, next to the carbonyl group. The physical and
chemical properties of a protein are determined by its constituent amino acids. The individual
amino acid subunits are joined by amide linkages called peptide bonds.

Structure of a general protein and its constituent amino acids. The amino acids are joined by
amide linkages called peptide bonds.

Proteins have an amazing range of structural and catalytic properties as a result of their varying
amino acid composition. Because of this versatility, proteins serve an astonishing variety of
functions in living organisms.

Structure and Stereochemistry of the Acids

Amino acids are the building blocks of proteins, and proteins are essential molecules that play
a wide range of critical roles in the body. The simplest acid is amino acid, called glycine. Other
common amino acids have side chains (symbolized by R) substituted on the carbon atom. For
example, alanine is the amino acid with a methyl side chain. Here's an overview of the structure
of amino acids and proteins:

1. Amino Group (NH2): Amino acids contain an amino group (NH2) at one end of the
molecule. This group is basic and can accept a proton (H+) to become positively
charged.

2. Carboxyl Group (COOH): At the other end of the amino acid is a carboxyl group
(COOH). This group is acidic and can lose a proton to become negatively charged.
 3. Central Carbon (α-Carbon): A central carbon atom (α-carbon) links the amino group,
carboxyl group, a hydrogen atom, and an R-group (side chain). The R-group varies
among different amino acids and determines the unique properties of each amino acid.

4. Hydrogen Atom (H): A single hydrogen atom is attached to the central carbon.

5. R-Group (Side Chain): The R-group is the variable part of the amino acid structure.
It distinguishes one amino acid from another. Different R-groups give amino acids their
unique properties, including size, charge, and hydrophobic or hydrophilic
characteristics.

Almost all the naturally occurring amino acids have the (S) configuration. They are called L-
amino acids because their stereochemistry resembles that of L-glyceraldehyde.

Amino acids combine many of the properties and reactions of both amines and carboxylic
acids. The combination of a basic amino group and an acidic carboxyl group in the same
molecule also results in some unique properties and reactions. The side chains of some amino
acids have additional functional groups that lend interesting properties and undergo reactions
of their own.

Amino acids are often denoted by abbreviations of three letters (in most cases the first three
letters of the name) or one letter. These are useful in writing out the long sequences of amino
acids that occur in peptides and proteins.

The standard amino acids are 20 common -amino acids that are found in nearly all proteins.
The standard amino acids differ from each other in the structure of the side chains bonded to
their carbon atoms. All the standard amino acids are L-amino acids.

Classification of amino acids

Amino acids are classified according to the side chain, R; the most useful way to do this is
according to their hydrophobicity, which determines their function in proteins. The most
hydrophobic are those with large apolar side chains, the most hydrophilic those with charged
side chains.

1. Nonpolar (Hydrophobic) Amino Acids:

 These amino acids have nonpolar R-groups that do not interact well with water.

 They are typically found in the interior of proteins.

 Examples include glycine, alanine, valine, leucine, isoleucine, proline,

methionine, and phenylalanine.

2. Polar (Hydrophilic) Amino Acids:

 These amino acids have polar R-groups that interact favorably with water.

 They are often found on the surface of proteins and can form hydrogen bonds
with water and other polar molecules.
  Examples include serine, threonine, tyrosine, asparagine, glutamine, and
cysteine.

3. Aromatic Amino Acids:

 Aromatic amino acids have a characteristic aromatic ring in their R-groups.

 They can participate in pi-pi stacking interactions and are involved in the
structural stability of proteins.

 The two aromatic amino acids are phenylalanine and tyrosine.

4. Acidic (Negatively Charged) Amino Acids:

 Acidic amino acids have carboxyl groups (COOH) in their R-groups.

 They can donate protons (H+) and carry a net negative charge at physiological
pH.

 Examples include aspartic acid (aspartate) and glutamic acid (glutamate).

5. Basic (Positively Charged) Amino Acids:

 Basic amino acids have amino groups (NH2) in their R-groups.

 They can accept protons (H+) and carry a net positive charge at physiological
pH.

 Examples include lysine, arginine, and histidine.

6. Sulfur-Containing Amino Acids:

 A subset of amino acids contains sulfur in their R-groups.

 Cysteine is notable for its thiol group (SH), which can form disulfide bonds with
other cysteine residues, contributing to protein structure and stability.

7. Amino Acids with Special Functions:

 Proline is unique due to its cyclic structure, which introduces rigidity into the
protein chain.

 Glycine is the smallest amino acid, and its R-group is a single hydrogen atom.
It imparts flexibility to protein structures.

8. Amino Acids Involved in Phosphorylation:

 Serine, threonine, and tyrosine are involved in protein phosphorylation, a

crucial post-translational modification that regulates protein function and
signaling pathways.
The classification of amino acids based on their properties is essential for understanding the
role of specific amino acids in protein structure and function. These properties influence how
amino acids interact with each other within a protein and with their surrounding environment,
ultimately determining the protein's behavior and function in biological processes.

Unusual Amino Acids

Most proteins contain only the 20 amino acids listed above, but a few contain unusual amino
acids such as 4-hydroxyproline and 3-hydroxylysine, which occur in collagen; Ɛ-
trimethyllysine, found in several Ca2+-binding proteins; y-carboxyglutamic acid, 3-methyl
histidine, pyroglutamic acid. They are formed by modification of the parent amino acid after
incorporation into protein.

IONIZATION OF AMINO ACIDS

Amino acids can exist in different ionization states depending on the pH of the environment.
This property is crucial for their function in biological systems.

1. Amino Group (NH2):

 The amino group of an amino acid can act as a weak base because it can accept
a proton (H+).

 In its ionized form, the amino group becomes NH3+ (ammonium ion) after
accepting a proton from water (H2O). The reaction is:

 NH2 + H2O ⇌ NH3+ + OH-

2. Carboxyl Group (COOH):

 The carboxyl group of an amino acid can act as a weak acid because it can
donate a proton (H+).

 In its ionized form, the carboxyl group becomes COO- (carboxylate ion) after
donating a proton to water. The reaction is:

 COOH ⇌ COO- + H+

3. Zwitterions (Ampholytes):

 Amino acids in their natural state exist as zwitterions, which are molecules that
have both a positively charged ammonium group and a negatively charged
carboxylate group.

 The zwitterion has an overall neutral charge and represents the predominant
form of amino acids at a specific pH known as the isoelectric point (pI).

4. pH Dependence:
  The ionization state of an amino acid is pH-dependent. The pKa values (acid
dissociation constants) of the amino and carboxyl groups determine the pH at
which an amino acid exists primarily in its ionized or non-ionized form.

 At a pH below its pI, an amino acid exists primarily in its cationic (positively
charged) form, with the ammonium group protonated.

 At a pH above its pI, an amino acid exists primarily in its anionic (negatively
charged) form, with the carboxyl group deprotonated.

 At the pI, the amino acid is in its zwitterionic form, with equal numbers of
positively and negatively charged groups.

5. Buffering Capacity:

 Amino acids can act as buffers, helping to maintain a stable pH in biological

systems. They can accept or donate protons as needed to resist significant
changes in pH.

Ionization States

pKa Values

 Each amino acid has specific pKa values:

o pKa1: Dissociation of the carboxyl group (typically around 2).

o pKa2: Dissociation of the amino group (typically around 9).

o pKa3: For amino acids with ionizable side chains, this represents the side
chain's dissociation (e.g., for aspartic acid, around 4.0).

Titration Curves

 The titration of an amino acid shows how the charge changes with pH.
 o Buffer Region: The pH range where the amino acid resists changes in pH due
to the presence of both protonated and deprotonated forms.

o Inflection Points: Correspond to pKa values, indicating where significant

changes in charge occur.

Importance of Ionization

1. Biological Activity:

o The charge state of amino acids affects protein folding, stability, and interaction
with other biomolecules.

2. Enzyme Function:

o Many enzymes rely on specific ionization states for their catalytic activity.

3. Separation Techniques:

o Ionization properties are utilized in techniques like electrophoresis and

chromatography.

The Isoelectric Point

Definition: The isoelectric point (pI) is the pH at which an amino acid has no net charge. At
this point, the positive and negative charges are balanced, and the molecule exists
predominantly in its zwitterionic form.

Key Concepts:

1. Zwitterion Formation:

o At physiological pH (around 7.4), amino acids typically exist as zwitterions,

where the amino group (-NH3⁺) is positively charged, and the carboxyl group
(-COO⁻) is negatively charged.

2. Calculating pI:

o For amino acids with two functional groups (like the standard amino acids):

o Where:

 pK₁ is the dissociation constant of the carboxyl group.

 pK₂ is the dissociation constant of the amino group.

 o For amino acids with ionizable side chains (like glutamic acid or lysine), the pI
calculation will involve the pKa values of the side chain as well.

3. Acidic and Basic Amino Acids:

o Acidic Amino Acids: (e.g., glutamic acid, aspartic acid)

 They have a side chain that can donate a proton, influencing the pI.

o Basic Amino Acids: (e.g., lysine, arginine)

 They have a side chain that can accept a proton, also affecting the pI.

4. pI and Solubility:

o At the pI, amino acids are less soluble in water, which is important for processes
like protein precipitation.

5. Applications:

o Understanding pI is crucial in protein purification techniques (like isoelectric

focusing) and can influence protein stability and function.

Example Calculation:

For an amino acid like glycine:

 pK₁ (carboxyl group) = 2.34

 pK₂ (amino group) = 9.60

Calculating pI:

pI=2.34+9.60/2=5.97

For an amino acid like aspartic acid (with an additional acidic side chain):

 pK₁ (carboxyl group) = 2.10

 pK₂ (side chain carboxyl group) = 3.86

 pK₃ (amino group) = 9.60

Calculating pI:

pI=3.86+9.60/2=6.73

Stereoisomers
All of the amino acids, except for glycine (Gly or G), have four different groups arranged
tetrahedrally around the central C. atom, and thus can exist in one of two stereoisomers. These
two stereoisomers (or enantiomers) are nonsuperimposable, mirror images and are termed the
D and L forms. Stereoisomers are physically and chemically indistinguishable by most
techniques, but can be distinguished on the basis of their different optical rotation of plane-
polarized light. Molecules are classified as dextrorotatory (D; Greek 'dextro' = right) or
levorotatory (L; Greek 'levo' = left depending on whether they rotate the plane of plane-
polarized light clockwise or anticlockwise. Only the L-amino acids are found in proteins. D-
Amino acids rarely occur in nature, but are found in bacterial cell walls and certain antibiotics.

PROTEINS

Proteins are complex macromolecules that play a wide range of essential roles in living
organisms. Their structure can be described at multiple levels, each level providing insight into
their function and properties. The primary, secondary, tertiary, and quaternary structures of
proteins are the key levels of protein structure:

1. Primary Structure:

 The primary structure of a protein refers to the linear sequence of amino acids
in the polypeptide chain.
  The sequence is determined by the genetic code and is unique to each protein.

 Alterations or mutations in the primary structure can profoundly affect a

protein's function.

2. Secondary Structure:

 Secondary structure refers to the local three-dimensional arrangements of amino

acids in a protein chain.

 The two most common secondary structures are alpha helices and beta sheets.

 Alpha helices are coiled structures held together by hydrogen bonds between
the amino and carboxyl groups of nearby amino acids.

 Beta sheets are extended, sheet-like structures stabilized by hydrogen bonds

between adjacent strands.

 Secondary structures are important for the overall folding of a protein.

3. Tertiary Structure:

 Tertiary structure describes the overall three-dimensional shape of a protein.

 It results from the interactions between amino acid side chains (R-groups) and
includes various types of bonds and forces:

 Hydrogen bonds: Stabilize the protein's folding.

 Disulfide bonds: Covalent bonds formed between cysteine residues.

 Hydrophobic interactions: Nonpolar R-groups cluster together to

minimize exposure to water.

 Ionic interactions: Attraction or repulsion between charged R-groups.

 Tertiary structure is essential for a protein's function and determines its active
sites and binding sites.

4. Quaternary Structure:

 Some proteins are composed of multiple polypeptide chains, or subunits, which

come together to form the complete, functional protein.

 The arrangement and interactions of these subunits in the quaternary structure

are critical for the protein's function.

 Hemoglobin, for example, is a tetrameric protein with four subunits.

 Not all proteins have quaternary structures; some exist as single polypeptide
chains.
Protein structure is fundamental to their function. The precise folding and arrangement of
amino acids enable proteins to carry out their specific roles in biological processes. The native,
functional conformation of a protein is typically maintained through a delicate balance of
noncovalent interactions, covalent bonds, and forces.

Any disruption in a protein's structure, such as denaturation (unfolding), can lead to a loss of
function. Understanding protein structure is crucial in fields like biochemistry and molecular
biology, as it allows scientists to comprehend the mechanisms of protein function, interactions,
and potential targets for drug development.