Introduction to Proteins and Amino Acids

• Amino acids are the building blocks of proteins
• Amino acids have a carboxyl group (-COOH), an amino group (-NH2), a hydrogen atom (-H), and a unique side chain (R group)
• Alpha-amino acids have their amino and carboxyl groups attached to the same alpha-carbon atom
• More than 300 amino acids exist in nature
• Only 20 amino acids are essential for making proteins in the body
• Some amino acids have their amino and carboxyl groups on different carbons

Classification of Amino Acids

• Amino acids are classified based on chemical structure, nutritional or biological function, and metabolic fate

Classification by Chemical Structure

• Amino acid classification based on the amino acid side chain
• Nonpolar, Aliphatic amino acids include Glycine, Alanine, Valine, Leucine, and Isoleucine
• Aromatic amino acids include Phenylalanine, Tryptophan (essential), and Tyrosine (non-essential)
• Sulfur-containing amino acids include Methionine and Cysteine
• Methionine is an essential amino acid
• Hydroxyl-containing amino acids include Serine and Threonine
• Threonine is an essential amino acid
• Acidic amino acids are negatively charged, and include Aspartate and Glutamate
• Aspartate and Glutamate are non-essential
• Amidic amino acids include Asparagine and Glutamine
• Asparagine and Glutamine are non-essential
• Basic amino acids are positively charged, and include Arginine, Lysine, and Histidine
• Arginine, Lysine, and Histidine are charged and essential
• Proline is an imino acid and non-essential

Classification by Nutritional or Biological Function

• Essential amino acids cannot be synthesized by the body and must be obtained from the diet
• Essential amino acids include Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Arginine (semiessential), Lysine, and Leucine,
• Non-essential amino acids can be synthesized by the body and are not essential in the diet
• Non-essential amino acids include Glycine, Cysteine, Alanine, Tyrosine, Serine, Glutamine, Asparagine, Aspartate, and Glutamate
• Semi-Essential amino acid is essential during periods of growth, stress, or illness, example is Arginine

Classification by Metabolic Fate

• Ketogenic amino acids can be converted into ketone bodies, examples include Leucine and Lysine
• Glucogenic amino acids can be converted into glucose
• All amino acids except Leucine and Lysine are glucogenic
• Mixed amino acids can be converted into both glucose and ketone bodies and include Phenylalanine, Isoleucine, Tyrosine, and Tryptophan

Uncommon Amino Acids

• Uncommon amino acids are not part of the 20 fundamental amino acids
• Uncommon amino acids are derived from post-translational modifications or unique synthesis processes
• Uncommon amino acids play critical roles in protein function, structure, and biochemical pathways
• 4-Hydroxyproline stabilizes collagen structure and is found in collagen
• 5-Hydroxylysine involved in collagen cross-linking and found in collagen
• 6-N-Methyllysine is a component of contractile proteins and is found in myosin
• Gamma-Carboxyglutamate binds calcium in blood clotting proteins and is found in prothrombin (clotting factor)

Selenocysteine

• Selenocysteine that contains selenium instead of sulfur (derived from serine)
• Selenocysteine introduced during protein synthesis (not a post-translational modification)
• Found in active sites of oxidation-reduction enzymes
• Example of where its found: Glutathione peroxidase

Ornithine and Citrulline

• Ornithine and Citrulline are intermediates in the urea cycle
• The urea cycle plays a key role in nitrogen metabolism

Properties of Amino Acids

• All amino acids are alpha amino acids
• The amino group is attached to the alpha carbon
• Glycine is the only amino acid without an asymmetric alpha carbon

Optical Activity

• Alpha Carbon is asymmetric except for glycine
• L-Amino Acids are found in proteins
• D-Amino Acids are found in some bacterial products
• Glycine is not optically active

Amphoteric Nature

• Amino acids have both acidic (COOH) and basic (NH2) groups
• Amino acids can act as both acids and bases depending on the pH
• At the isoelectric point (pI), an amino acid has no net charge
• The COOH group is negatively charged, and the NH2 group is positively charged
• A zwitterion is a molecule with both positive and negative charges

Effects of pH on Amino Acid Behavior

• At low pH (acidic), high hydrogen ion (H+) concentration resulting in both amino and carboxyl groups are protonated
• The NH2 becomes NH3+
• The COOH remains COOH
• Overall charge is positive
• At neutral pH (around pI), the amino acid exists as a zwitterion with NH3+ (positively charged) and COO- (negatively charged) and net charge is neutral
• At high pH (basic), a low hydrogen ion (H+) concentration where both amino and carboxyl groups lose protons
• The NH3+ becomes NH2
• The COOH becomes COO-
• Overall charge is negative

Beyond Proteins: Amino Acid Functions

• In addition to their role as building blocks of proteins and peptides, amino acids serve a variety of functions
• Glycine aids in detoxification and synthesizes heme
• Methionine serves as a methyl donor in metabolism
• Tyrosine synthesizes thyroid hormones (T3, T4), epinephrine, norepinephrine, and melanin
• Tryptophan synthesizes niacin (Vitamin B3) and serotonin
• Histidine synthesizes histamine
• Aspartate and Glutamine are involved in pyrimidine synthesis
• Glycine, Aspartic Acid, Glutamine are involved in purine synthesis

Proteins and Biologically Active Peptides

• Proteins (polypeptides) are polymers of amino acids linked by peptide bonds
• Their structure and function are dictated by the sequence of amino acids
• Proteins play crucial roles in various biological processes
• Proteins range in size from two to many thousands of amino acids
• Biological activities are not always related to size or molecular weight

Small Peptides

• Small peptides can have significant biological effects
• An example is Aspartame (dipeptide L-aspartyl-L-phenylalanine methyl ester), a low-calorie artificial sweetener

Examples of Small Peptides

• Oxytocin stimulates uterine contractions during childbirth, plays a crucial role in labor, and milk ejection; 9 amino acids
• Bradykinin inhibits inflammation and mediates pain, reducing tissue inflammation; 9 amino acids
• Thyrotropin-Releasing Factor stimulates the release of thyroid-stimulating hormone (TSH) from the pituitary, helping regulate thyroid function; 3 amino acids
• Glutathione is an antioxidant, protecting cells from oxidative stress, crucial for cellular detoxification; 3 amino acids
• Amanitin (toxic peptide) inhibits RNA polymerase in cells, leading to cell death, responsible for the toxicity of certain mushrooms; 8 amino acids
• Gramicidin A (antibiotic) disrupts bacterial cell membranes, leading to bacterial cell death, and acts as antibiotic; variable amino acids

Slightly Larger Peptides and Oligopeptides

• Insulin regulates glucose metabolism by promoting glucose uptake in cells, regulates and controls blood sugar levels; 51 amino acids
• Glucagon raises blood glucose levels by stimulating glycogen breakdown, opposes insulin to increase blood glucose levels during fasting; 29 amino acids
• Corticotropin stimulates the adrenal cortex to release cortisol in response to stress regulates the body's stress response and immune function; 39 amino acids

Proteins

• Proteins are long chains of amino acids with specific sequences.
• Their structure is directly influenced by the gene sequence.
• Even a single amino acid change can alter function (e.g., sickle cell anemia).

Classifications of Proteins

• Proteins can be classified based on Function, Shape, and Composition.

Classification Based on Shape

• Globular Protein: Spherical, compact, water-soluble, less stable, biologically active and examples include Insulin, Myoglobin, Antibodies and Enzymes
• Fibrous protein: Linear, structural, insoluble in water, and more stable examples include Keratin, Collagen, Elastin and Myosin

Classification Based on Function

• Transport Function: Proteins that transport molecules across the body e.g. Hemoglobin, Transferrin
• Catalytic Function: Enzymes speed up biochemical reactions e.g. Lactase, Pyruvate kinase.
• Storage function: Store vital molecules for later use e.g Myoglobin, Ferritin.
• Defense Function: Proteins involved in immune defense. e.g. Immunoglobulins

More Functions of Proteins

• Structural Function: Provides structure, strength, and elasticity. e.g. Collagen, and Keratin
• Nutrient Function: Provides nutrients for biological systems. e.g. Casein, and Albumin.
• Infective Agents: Prions act as infective proteins causing disease e.g Prions
• Buffering Function: Plasma proteins act as buffers to maintain pH balance e.g. Albumin, and Haptoglobin.
• Gene Expression: Involved in gene regulation and packaging e.g Histones, and Nucleoproteins.
• Regulatory Function: Controls physiological processes through protein hormones e.g Insulin, and Hormone receptors.

Classification Based on Composition

• Simple proteins : Proteins composed only of amino acids. E.g. Albumins and Globulins
• Derived proteins :Proteins derived from simple or complex proteins after hydrolysis or denaturation. E.g. Casein and Peptones
• Complex Proteins:Proteins made from amino acids combined with non-protein parts (lipids, carbohydrates, nucleic acids, metals). E.g. Glycoproteins and Metalloproteins

Conformation of Proteins

• Proteins have unique three-dimensional structures, known as their conformation.
• Their function is determined by this structure.
• Proteins have four structural levels: Primary, Secondary, Tertiary, and Quaternary.

Primary Structure

• Primary structure describes the sequence of amino acids in a polypeptide chain.
• These amino acids are held together by peptide bonds.
• Primary structure determines the protein's final structure and function.
• The protein sequence is read from left to right and starts with the N-terminal amino acid.
• It ends with the C-terminal amino acid, remainder are called amino acid residue

Secondary Structure

• Secondary structure characterizes the local folding of the polypeptide chain into structures:
• Alpha helix: Right-handed spiral, stabilized by hydrogen bonds.
• Beta sheet: Extended structure with hydrogen bonds between chains.

Secondary Structure: α-helix

• The a-helix is a spiral structure with peptide bonds coiled tightly inside and side chains sticking out.
• It is a right-handed helix (coils turn clockwise), more stable than the left-handed version.
• There are 3.6 amino acids per turn of the helix.
• a-helices are usually found inside the protein structure and are stabilized by hydrogen bonds within the chain (intra-chain).
• These bonds are weak individually, but together, they help keep the helix stable

Secondary Structure: β-pleated sheet

• ẞ-pleated sheet: More extended structure than the a-helix.
• The structure is pleated because the C-C bonds are tetrahedral and can't be straight.
• Stabilized by hydrogen bonds between NH and C=O of adjacent peptide segments.
• The segments may run in the same direction or in opposite directions.
• Beta bends are stabilized by disulfide bridges.
• In an antiparallel ẞ-sheet : Chains are oriented in opposite directions, and the amino acid side chains alternate above and below the plane of the sheet.
• Hydrogen bonding occurs between different chains

Tertiary Structure

• Tertiary Structure describes the overall 3D folding of a protein
• The protein's tertiary structure is influenced by covalent bonds (such as disulfide bridges) and noncovalent bonds (including hydrophobic forces, ionic bonds, and hydrogen bonds).
• Hydrophobic side chains are located in the interior, and hydrophilic side chains are on the exterior.

Quaternary Structure

• Quaternary structure refers to the arrangement of multiple polypeptide chains in a protein.
• Not all proteins have a quaternary structure.
• Each polypeptide chain is called a subunit, and it has its own primary, secondary, and tertiary structure.
• The polypeptide chains are held together by the same forces that stabilize tertiary structure. -Monomer: 1 subunit -Dimer: 2 subunits -Tetramer: 4 subunits
• Insulin is made up of two subunits, linked by two disulfide bridges.

Insulin

• A homopolymer is made up of identical subunits.
• A heteropolymer is made up of different subunits.
• Insulin is a heteropolymer

Haemoglobin

• Haemoglobin is a tetramer made up of two identical dimers, (αβ)₁ and (αβ)2,where the numbers refer to dimer 1 and dimer 2. Within each dimer, the two polypeptide chains are tightly held together, primarily by hydrophobic interactions.

Summary

• Proteins are classified based on Function, Shape, and Composition. -Proteins have structures as Primary, Secondary, Tertiary, and Quaternary, -Classification of proteins helps understand their diverse biological roles and functionality.

Explore the roles and classifications of proteins and amino acids. Learn about insulin's function, amino acid types, and factors influencing protein structure. Understand ketogenic and glucogenic amino acids.