Amino Acids, Peptides and Proteins

Amino Acids

• Amino acids are the building blocks of proteins, and there are 20 standard amino acids.
• Each amino acid has a central carbon called the alpha-carbon, which is attached to four different groups: an amino group, a carboxyl group, a hydrogen atom, and a distinctive side chain.
• Amino acids can be classified based on their polarity, with four main categories: non-polar, uncharged polar, positively charged, and negatively charged.
• Essential amino acids cannot be synthesized by the human body and must be obtained through the diet, while non-essential amino acids can be synthesized.
• Amino acids have a tetrahedral structure, with a side chain carboxyl group, amino group, and alpha-carbon.

Structure of Amino Acids

• The alpha-carbon is chiral, except for glycine.
• Amino acids have a zwitterionic structure, with a positive charge on the amino group and a negative charge on the carboxyl group.
• Amino acids can be classified into different types based on their polarity, including:
  • Non-polar (hydrophobic): Alanine, Glycine, Proline, Phenylalanine, Tryptophan, Methionine, Leucine, Valine
  • Uncharged polar: Serine, Threonine, Glutamine, Asparagine, Cysteine, Tyrosine
  • Positively charged (basic): Lysine, Arginine, Histidine
  • Negatively charged (acidic): Aspartic acid, Glutamic acid

Functions of Amino Acids

• Amino acids are the building blocks of proteins.
• They are precursors to a variety of nitrogen-containing molecules.
• They are a source of energy.
• They are components of certain types of proteins.
• They can act as chemical messengers, such as neurotransmitters.
• They can be part of hormone derivatives.

Classification of Amino Acids

• Amino acids can be classified based on their polarity, as mentioned earlier.
• They can also be classified as essential or non-essential, based on whether the human body can synthesize them.

Physical Properties of Amino Acids

• Amino acids are soluble in water.
• They have a melting point.
• They have a taste, with some being sweet and others being bitter.
• They have an optical property, with all standard amino acids having a chiral center.
• They have an ultraviolet absorption spectrum.

Isoelectric Point of Amino Acids

• The isoelectric point (pI) is the pH at which an amino acid has no net charge.
• The pI is influenced by the ionic states of the alpha-carboxyl and alpha-amino groups and any ionizable groups in the side chains.

Titration of Amino Acids

• Titration involves the gradual addition or removal of protons.
• It is used to predict the charge of an amino acid at a given pH.
• It is used to devise a procedure for separating amino acids based on their charges.

Peptides

• Peptides are amino acid polymers with a molecular weight of several thousand to millions of daltons.
• They are involved in the neuroendocrine system as hormones, hormone releasing factors, neuromodulators, or neurotransmitters.
• Examples of peptides include:
  • Glutathione
  • Oxytocin
  • Vasopressin
  • Metenkephalin
  • Leuenkephalin
  • Atrial natriuretic factor
  • Substance P
  • Bradykinin
  • Glucagon
  • Corticotrophin
  • L-aspartylphenylalanylmethyl ester (aspartame)

Proteins

• Proteins are complex, organic nitrogenous substances with high molecular weights.
• They are essential constituents of all organisms.
• They are derived from Greek word "proteios", meaning primary or holding first place.
• Functions of proteins include:
  • Enzymatic catalysis
  • Transport and storage
  • Coordinated motion
  • Mechanical support
  • Immune protection
  • Generation and transmission of nerve impulses
  • Control of growth and differentiation
  • Cell signalling
  • Hormones
  • Major components of biological membranes

Classifications of Proteins

• Based on composition, physical and chemical properties:
  • Simple proteins
  • Conjugated proteins
  • Derived proteins
• Based on the shape and physical characteristics of the protein:
  • Fibrous proteins
  • Globular proteins
• Based on biologic function:
  • Enzymes
  • Storage proteins
  • Regulatory proteins
  • Structural proteins
  • Protective proteins
  • Transport proteins
  • Contractile or motile proteins
  • Exotic functions of proteins (e.g. monellin, antifreeze protein, resilin)

Structure of Proteins

• Formation of the peptide bond:
  • Amide linkages between the alpha-carboxyl group of one amino acid and the alpha-amino group of another
  • Individual amino acids are called amino acid residues
  • The residue with a free amino group at the leftmost residue is called the amino terminus or N-terminal
  • The residue with a free carboxylate group at the right is called the carboxyl terminus or C-terminal
• Nomenclature:
  • Peptides are named from the sequence of constituent amino acids
  • Beginning at the left with the N-terminal residue towards the C-terminal residue at the right
  • Amino acid residues in polypeptides are named by dropping the suffix -ine or -ate in amino acid and replacing by -yl except for C-terminal amino acid
  • -ine ending indicates its alpha carboxyl group not involved in peptide bond formation
• Levels of structural organization:
  • Primary structure: the linear sequence of amino acid residues linked by peptide bonds
  • Secondary structure: due to the formation of hydrogen bonds between peptide bonds
  • Tertiary structure: the 3-dimensional structure of proteins
  • Quaternary structure: the arrangement of multiple polypeptide chains in a protein

Primary Structure

• The linear sequence of amino acid residues linked by peptide bonds
• Important because many genetic diseases result in proteins with abnormal amino acid sequences
• Deals with:
  • Quantitative amino acid composition
  • Sequence of amino acid
  • Number of peptide chains

Secondary Structure

• Due to the formation of hydrogen bonds between peptide bonds
• Two types:
  • Coils or helices: brought by intrachain hydrogen bonding
  • Sheets or pleats: brought by interchain hydrogen bonding

Tertiary Structure

• Refers to the 3-dimensional structure of proteins
• Indicates how secondary structural features assemble to form domains and how they relate to each other
• Types of proteins in tertiary structures:
  • Fibrous: has structural roles
  • Globular: contains several types of secondary structure in the same polypeptide chain### Protein Folding and Modification
• Peptidyl prolyl cis-trans isomerase accelerates protein folding.
• Protein disulfide isomerase occurs mainly in the endoplasmic reticulum.

Levels of Structural Organization of Proteins

• Quaternary structure is exhibited by proteins containing more than one polypeptide chain.
• The arrangement of polypeptide subunits or chains is held together by non-covalent interactions like hydrophobic interactions, electrostatic interactions, and hydrogen bonds.

Life Cycle of Proteins

• The life cycle of a protein begins with synthesis on a ribosome, whose primary structure is dictated by mRNA.
• As synthesis proceeds, the polypeptide chain folds into its native conformation.
• Folding may be accompanied by processing events like proteolytic cleavage or the formation of disulfide bonds.
• Subsequent covalent modifications may attach molecules like fatty acids for translocation to a membrane.
• Binding an allosteric effector may trigger the adoption of a catalytically active conformation.
• Over time, proteins get damaged by chemical attack, deamidation, or denaturation.
• Damaged proteins may be "labeled" by the covalent attachment of several ubiquitin molecules and subsequently degraded to their component amino acids.

Protein Misfolding

• Protein misfolding results in improperly folded molecules that are tagged and degraded within the cell.
• Amyloid disease is caused by a mutation in a particular gene that produces an altered protein, leading to the formation of long, fibrillar protein assemblies consisting of β-pleated sheets.
• Prion disease is a fatal neurodegenerative disease characterized by spongiform changes, astrocytic gliomas, and neuronal loss from the deposition of insoluble protein aggregates in neuronal cells.

Protein Analysis

• Protein analysis involves partial breakdown into manageable fragments followed by stepwise analysis from one end of the chain to the other.
• Steps involved in protein analysis include purification of protein, determining amino acid composition, determining N and C terminals, determining amino acid sequence, checking the number of polypeptides, and chromatography.

Protein Purification

• Characteristics of proteins that are used in separation procedures include solubility, charge, polarity, size, and binding capacity.
• Different chromatography techniques are used based on these characteristics, such as paper chromatography, thin layer chromatography, ion exchange chromatography, electrophoresis, hydrophobic interaction, gel filtration chromatography, ultracentrifugation, and affinity chromatography.