Amino Acids and Peptides

Amino Acids and Peptides

• Amino acids contain carboxyl and amino organic groups.
• Amino acids are building blocks for proteins.
• There are 20 amino acids to build up a protein.
• Proteins are the most abundant macromolecules in living cells.
• Amino acids link together by peptide bonds.
• At physiological pH (~7.4), amino acids are zwitterions with positive and negative charges on the same molecule.
• An amino acid has a central carbon atom, the α-carbon, attached to four different groups including: Carboxyl group, Amino group, Hydrogen, R group (side carbon chain)
• Amino acids consist of a sulphur atom including: Cysteine (Cys) and Methionine (Met)

Function of Amino Acids

• Amino acids act as enzymes/catalysts.
• They are metabolic intermediates.
• They carry energy and waste products.
• Act as hormones.

Properties of Amino Acids

• All standard amino acids (except Glycine) have an asymmetric α-carbon atom called a chiral center.
• All amino acids exists in two stereoisomeric forms, L-stereoisomers & D-stereoisomers (Enantiomers).
• With the exception of glycine, the amino acids present in protein molecules are L-stereoisomer.
• A compound with two or more chiral carbons will have 2n possible stereoisomers.
• L-amino acids rotate plane-polarized light to the left, and are predominantly found in proteins.
• They are actively involved in enzyme activity and protein synthesis, recognized by most enzymes, and synthesized by living organisms.
• L-amino acids are generally less stable than D-amino acids.
• Examples of L-amino acids include L-Glutamate and L-Alanine, which are common in proteins.
• D-amino acids rotate plane-polarized light to the right, and are rare in nature but can be found in the bacterial cell walls and antibiotics.
• They have a limited role in specialized functions like bacterial peptidoglycan, are not commonly recognized by enzymes, are produced synthetically or found in microorganisms, and are more stable.
• Examples of D-amino acids are D-Alanine and D-Glutamate, which are present in bacterial cell walls.
• L and D isomers are mirror images.
• L isomers are found in proteins and D amino acids are found in rare bacteria cell walls.
• An α-carboxyl group, -COOH, is part of all amino acids and participates in peptide bond formation.
• The Alpha carbon is the first one adjacent to the functional group.

Amino Acids as Zwitterions

• In water solution, amino acids ionize and form dipolar ions (zwitterions).
• Zwitterions contain both positively charged (cation) and negatively charged (anion) groups.
• The carboxyl group will deprotonate (lose proton) while the amino group will protonate (gain proton).
• Amino acids are soluble in polar solvents like water and insoluble in nonpolar organic solvents like hydrocarbon, this is due to the presence of zwitterions.

Amino Acids as Acids and Bases

• Amino acids in aqueous solution are ionized and can act as acids and bases.

Isoelectric Point (pI)

• It is the pH at which an amino acid carries no net electrical charge
• For amino acids, this occurs when the molecule exists predominantly in its zwitterionic form.
• In an electric field, amino acids in acidic media will move to the cathode.
• In basic media, amino acids will move to the anode.
• A titration curve is a plot of the pH versus equivalents of base added during titration of an acid.
• Glycine, a nonpolar amino acid, has one α-carboxyl group and one α-amino group, and its titration curve consists of two stages.

Physical Properties of Amino Acids

• Most amino acids are water soluble and insoluble in organic solvents.
• Has a melting point in higher temperature at >200°C.
• Sweet tasting amino acids: Glycine, Alanine, & Valine
• Bitter tasting amino acids: Arginine & Isoleucine
• Amino acids act as drugs, for example, D-penicillamine for Wilson's disease. N-acetylcysteine for cystic fibrosis, as an antioxidant. Gabapentin as an anticonvulsant.

Protein Denaturation

• It is the disruption of secondary, tertiary and quaternary structure by cleavage of non covalent bonds which causes denaturation of proteins.
• Agents for denaturation include: Physical actions like heat, UV, and ultrasound; & Chemical actions like acids, alkalines, heavy metals, salts, urea, and detergents

Types of Denaturation

• Precipitation: Denatured proteins become insoluble and separate from the solution. Caused by extreme pH changes, heavy metals, or high salt concentrations. Eg: adding acid to milk causes casein coagulation.
• Coagulation: Irreversible denaturation of protein by heat. Eg: egg coagulation by heat.
• Flocculation: Precipitation of proteins at the isoelectric point. Eg: milk casein precipitation.

Peptide Bond

• It is a specific type of amide bond formed between the -COOH group of one amino acid and the amine group of another.
• Formed through a condensation reaction (dehydration process)
• Peptides are always written in the N to C direction (head to tail).
• Each peptide ONLY has one free -COOH group & one free -NH₂ group
• Amino acids are connected head to tail using Carbodiimide with dehydration.

Formation of Peptide Bonds

• The combination of two amino acids results in a dipeptide.
• A combination of three amino acids is a tripeptide.
• Four amino acids make a tetrapeptide.
• Combining 5-10 amino acids creates an oligopeptide.

Classifications of 'R' & their Chemical Properties

• Nonpolar (Hydrophobic) includes: Aliphatic and Aromatic
• Polar (Hydrophilic) includes: Neutral (uncharged), Acidic, and Basic
• Aliphatic hydrocarbons are nonpolar and hydrophobic, with examples like -CH3 or CH(CH3)2 and commonly found in the core proteins..
• Aromatic hydrocarbons contain an aromatic ring, are partially hydrophobic, absorb UV light and become fluorescent, such as Tryptophan, Tyrosine and Phenylalanine.
• Neutral and uncharged side chains are polar but do not carry charge at physiological pH and are involved in H-bonding, and example being –OH (hydroxyl) or -CONH₂. Examples of this include Serine, Cysteine ,& Asparagine.
• Acidic side chains carry a negative charge, and act as proton donors at physiological pH (~7.4), playing roles in enzyme active sites, for example,  -COOH (carboxyl). Aspartic acid/Aspartate, Glutamic acid/Glutamate
• Basic side chains are carry a positive charge and are proton acceptors at physiological pH (~7.4) and are crucial for negatively charged DNA interactions. Examples include Lysine, Arginine and Histidine

Applications of Amino Acids

• Tryptophan is a biosynthetic precursor of serotonin that regulates sleep, mood, and appetite.
• MSG-monosodium glutamate is the sodium salt of glutamic acid used as a flavor enhancer that may influence the nervous system with symptoms of headaches, nausea, and rapid heart rate.

Peptide Bond - Protein Synthesis

• Protein synthesis involves the formation of peptide bonds
• Condensation reactions occurs and removes water molecules.
• The location is ribosomes in cells
• Peptide bond formation occurs during translation of mRNA.
• Ribosomes facilitate the condensation reaction between amino acids brought by tRNA

Peptide Bond - Protein Digestion

• Protein digestion involves the breakdown of peptide bonds
• Hydrolysis reaction occur which adds water molecule
• Processes regenerating the original amino acids.
• The location is the Digestive system in the stomach and small intestine
• Pepsin acts in the stomach at acidic pH to break peptide bonds.
• Trypsin and Chymotrypsin are pancreatic enzymes.

Metabolism Process Includes

• Peptide bond formation (condensation) and breakdown (hydrolysis) occurring continuously in metabolic pathways.
• Protein synthesis builds new enzymes, hormones, and structural proteins.
• Protein degradation recycles of amino acids for energy production or biosynthesis of new proteins

Peptide Examples Include

• Glutathione: tripeptide of glutamic acid + cysteine + glycine, present in RBC and other tissues and has functions that regulate oxidation and reduction reactions, maintain RBC membrane structure, prevent haemoglobin oxidation, facilitates amino acid absorption, helps detoxification of xenobiotics, destroys destructive free radicals, and keeps iron in ferrous state in haemoglobin by preventing methaemoglobin formation.

• Thyrotropin Releasing Hormone (TRH): is a tripeptide made of glutamic acid, histidine, and proline and is secreted by the hypothalamus to causes anterior pituitary glands release thyrotropic hormone to regulate thyroid hormones, prolactin secretion, and central nervous system.

• Enkephalin & Endorphins: pentapeptides act as Methionine - enkephalin (Tyr - Gly - Gly - Phe - Met) and Leucine - enkephalin (Tyr - Gly - Gly - Phe - Leu) that start with tyrosine binding too opioid receptors. They are found in the brain and nervous system and function to inhibits sense of pain, and control emotional state.

• Antidiuretic hormone (ADH) Vasopressin: is a nonapeptide (9 amino acids) secreted by the posterior pituitary glands that regulate water balance acting on the kidneys and increase blood pressure by narrowing blood vessels.

• Bradykinin: is a nonapeptide (9 amino acids) produced from plasma proteins by snake venom enzymes and allows it to interact with different receptors & enzymes, with consisting of two primary receptors including receptors induced during tissue injury/inflammation and one expressed in most tissues that stimulates the pain receptor. It is responsible for visceral pain and blood pressure regulation and is a potent vasodilator, reducing blood pressure.

• Oxytocin: is a nonapeptide secreted by the hypothalamus, and released from the posterior pituitary gland which functions in labour and delivery, in triggering uterine contractions; in lactation as bonding (love hormone), stress reduction; social recognition behaving as sexual behaviour; mood regulation, cardiovascular effect helps lower blood pressure.

• Angiotensin: Types of amino acids include the following that affect blood pressure and cognitive function, with issues in tissue repair:

  • Angiotensin I: a decapeptide.
  • Angiotensin II is an octapeptide.

• Angiotensin III is a heptapeptide that stimulate aldosterone release.

• Angiotensin IV is a hexapeptide involving cognition and tissue.

• Aspartame: A dipeptide is 200 times sweeter than sucrose and has low calories as sweetener:

  • Made of Aspartic acid + Phenylalanine
  • If the amino acids are in D configuration: This peptide bitter

• Insulin: made of two peptide chain that are linked together with disulfide bonds (~51 amino acids):

  • A-chain has about 21 amino acids.
  • B-chain has about 30 amino acids

• Insulin helps regulate: Blood sugar, regulate fat, protein, ketogenesis, facilitative ion transport, hormones; but malfunctions can indicate Hyperglycemia , Diabetes, or Ketoacidosis

Biological Activities of Polypeptides

• Enzymatic activity - polypeptides from enzymes which catalyze reactions.
  • Speed up reactions by lowering activation energy.
  • Ex: Amylase: breaks down starch into sugar during digestion.
  • Ex: Protease: degrades proteins into amino acids.
  • Ex: DNA polymerase: catalyzes DNA replication.
  • Ex: Lipase: breaks down fats into fatty acids and glycerol.

Hormonal Function

• Regulate various physiological processes.
• Ex: Insulin regulates blood glucose.
• Ex: Glucagon counteracts insulin by raising blood glucose.
• Ex: Oxytocin is involved in childbirth & bonding behaviors. -Ex: Adrenocorticotropic Hormone (ACTH) stimulates cortisol release from adrenal glands.

Structure Roles

• Polypeptides provide structural support and form components of cells/tissues. -Ex: Collagen: fibrous polypeptide in skin, tendons and bones. Provides tensile strength. -Ex: Keratin: present in hair and nails offering protection. -Ex: Elastin: elasticity in tissues like blood vessels & skin.

Transport & Storage

• Some polypeptides are specialized for transport and storage of particles.
  • Ex: Hemoglobin: transports oxygen in red blood cells.
  • Ex: Myoglobin: stores oxygen in muscles for energy.
  • Ex: Ferritin: stores iron in cells.
  • Ex: Transferrin: transports iron through the blood.

Immunological Role -

• Polypeptides play vital role in the immune system for pathogens.
  • Ex: Immunoglobulins identify and neutralize pathogens.
  • Ex: Cytokines act as signalling molecules to the immune responses.
  • Ex: Defensins act as antimicrobial proteins.

Signalling and Regulation

• Polypeptides function as signaling molecules to regulate communication, cell growth and calcium levels. -Ex: Neuropeptide: regulating pain
  • Ex: Growth factors for cell growth.
  • Calcitonin controls calcium homeostasis of the body.

Receptor and Channel Functions

• Transports, uptake and channels of substances for substance flow. Ex: Insulin which binds and triggers glucose levels and uptakes. -Ex: Ion channels, maintaining ions and membranes.
  • Ex: G-protein key cellular transduction.

Movement Functions

• Polypeptides are essential for movement for organisms. -Ex: Actin and myosin help in contractions for muscle movement. -Ex: Tubulin, which transfers intracellular material

Antimicrobial and Support

• Support that helps organisms combat infections. -Ex: Bacteriocins- growth of competing bacteria.
  • Ex: Cathelicidins and helps by disrupting membranes.
  • Ex: Defensins form material

Storage of Energy and Gene Regulation

• Energy Storage: -Pollypeptides help with fasting purposes and help with material.
• Regulation of Gene Expression: -Transcript, for gene activity -Ex: Chaperores, for protein folding