Medicinal Biochemistry: Proteins

• Medicinal Biochemistry aims to study molecular processes in the body under normal and pathological conditions.
• It seeks to provide a scientific foundation for understanding pathobiochemical mechanisms.
• Medical biochemistry contributes to the effective treatment of diseases.

Proteins

• Proteins are composed of amino acids linked by covalent peptide bonds.
• They differ in molecular weight.
• Proteins have roles in building and repairing body tissues.
• Proteins participate in immunity reactions.
• Proteins stimulate hormone production.
• Proteins function as enzymes.
• Some proteins are nucleoproteins.
• Some proteins are contractile proteins.
• Some proteins are blood proteins.
• Proteins have numerous specific functions in the body.
• Proteins provide fuel for the body's energy needs, yielding 4 kCal/gm.
• Proteins facilitate the digestion of foods and the absorption of nutrients.
• They participate in muscle contraction and movement.
• Proteins promote wound healing and regeneration of tissues.
• Proteins support the regulation and expression of DNA and RNA.
• Proteins help to store iron and copper.
• They help maintain acid-base balance.
• Proteins provide amino acids for fetal growth and lactation.
• Proteins enable the movement of molecules around the body.

Peptides, Polypeptides, and Proteins

• Peptides: Contain 2-10 amino acids linked by a peptide bond, such as aspartames and tulfsin.
• Polypeptides: Contain more than 10 amino acids and have up to 100 amino acids.
• Proteins: Contain more than 100 amino acids.

Glutathione

• It is a tripeptide that contains the amino acids glycine, cysteine, and glutamate.
• The reduced form of glutathione is GSH.
• Oxidized glutathione is GSSG.
• Glutathione reductase catalyses reversible reaction of converting reduced to oxidized glutathione.
• Cystine is a slightly water-soluble dipeptide in the skin and hair (10-14% of their mass)
• High levels of cystine can lead to cystinuria.

Insulin

• It is a polypeptide hormone composed of 51 amino acids.
• Insulin comprises two chains connected by disulfide bridges.
• Chain A contains 21 amino acids.
• Chain B contains 30 amino acids.
• It has a molecular mass of 5808 Da (g/mol).
• Insulin helps in the regulation of the metabolism of carbohydrates, lipids, and proteins.
• Insulin is best known for lowering blood glucose levels.
• Insulin is released from the β-cells of the pancreas.

Glucagon

• It increases blood glucose levels.
• Glucagon is secreted from the alpha cells of the pancreas.
• Glucagon is a straight-chain polypeptide hormone.
• Glucagon has a molecular weight of 3485 Da(g/mol).
• It is composed of 29 amino acid residues.

Heteroproteins

• Heteroproteins perform the same functions in different animal species and man.
• They differ in antigenic determinants.
• Human and bovine albumin are types of heteroproteins.

Isoproteins

• Isoproteins are the same protein found in different organs, tissues, or cellular compartments within a species.
• Muscle and liver lactate dehydrogenase are examples of isoproteins.

Alloproteins

• Alloproteins are only found in some individuals, e.g normal hemoglobins in different races and blood group antigens.
• They may have pathobiochemical roles, such as paraproteins like carcino-embryonic proteins and Ben-Jones protein.

Amino Acids

• Amino acids are structural blocks of proteins.
• Glycine is not a stereoisomer.
• Stereoisomers can occur in L-form (left-handed) and D-form (right-handed).
• L-isomers rotate polarized light to the left.
• D-isomers rotate polarized light to the right.
• The L-forms of amino acids make up human proteins.
• At physiological pH (around 7), the carboxyl (COO-) and amino group (NH3+) are charged.

Classification of Amino Acids by Radical Structure

• Aliphatic: glycine, alanine, valine, leucine, isoleucine.
• Hydroxy: serine, threonine.
• S-containing: cysteine, methionine.
• Aromatic: phenylalanine, tyrosine, tryptophan.
• Cyclic imino-acid: proline.
• Additional basic group: lysine, arginine, histidine.
• Additional carboxyl group and their amides: aspartate, glutamate, asparagine, glutamine.
• Val, lleu, Lys, Arg*, His*, Met, Trp, Thr, and Phe are semiessential.

Polarity and Hydrophobicity of Amino Acid Radicals

• Amino acids are divided into hydrophilic and hydrophobic based on the radicals at pH 7.0.
• Hydrophilic amino acids include Arg, His, Lys, Asp, Glu, Asn, Gln, Cys, Ser, Thr, and Gly.
• Polar uncharged amino acids can participate in hydrogen bonds.
• Polar charged amino acids include Arg, His, and Lys which are positively loaded.
• Asp and Glu are negatively charged.
• Hydrophobic amino acids include Ala, Val, Leu, Ile, Met, Pro, Phe, Tyr, and Trp.
• Radicals of hydrophobic amino acids can participate in hydrophobic interactions.

pKa

• pKa measures acidity or basicity.
• pKa is the negative logarithm of the acid dissociation constant (Ka).
• Isoelectric point (pl) is when the amino acid has no net charge.
• The amino acid is positively charged at a pH level that is lower than pl.
• Amino acid is negatively charged at pH level that is higher than pl.

Post-translational processing of Amino Acids

• In addition to the 20 common amino acids, there are some formed through specific biochemical processes:
• Hydroxyproline and hydroxylysine are produced post-translationally and are in collagen.
• Methyllysine is the methylation of lysine in histones.
• Desmosine is produced post-translationally and is found in elastin.
• Gamma-carboxyglutamate is formed and has a role in blood coagulation.
• Selenocysteine is formed from cysteine.
• Ornithine and citrulline are formed in the ornithine cycle during the disposal of ammonia.

Selenocysteine

• Selenocysteine has selenium
• Selenocysteine is unique among proteinogenic amino acids.
• tRNA synthesizes Selenium.
• eEF1A helps string together amino acids at the ribosome.
• eEFSec incorporates selenocysteine into proteins.

Levels of Protein Organization

• Primary structure, amino acid sequence.
• Secondary structure.
• Tertiary structure.
• Quaternary structure.

Primary Structure

• Primary structure is determined by the type, number, and sequence of amino acids.
• The number of polypeptide chains linked by a disulfide bridge also determines primary structure.
• The disulfide bridge helps create the tertiatry structure.
• It is made from covalent peptide bonds between the peptide groups of closely spaced amino acids by an amino acid condensation reaction.
• Primary structure determines higher levels of organization, such as secondary, tertiary and quaternary structure.
• Primary structure determines the spatial folding of the protein (conformation).

Primary structure of the insulin molecule

• Role of disulfide bridges: It connecting chains A and B
• Provides opportunity ti create tertiary structure
• allows distant regions to come together
• Also bends the A chain

Peptide Bond Formation

• The peptide bond (–CO–NH–) is involved in creation of primary and secondary structure.
• Covalent bonding exists betweeen peptide group in primary structure
• Hydrogen bonds exist in secondary structure

Primary Structure of Proteins

• Amino acids can be represented both with a three-letter code and with capital Latin letters.

Amino Acids and Molecular Masses

• Essential amino acids: Leu, Ile, Val, Lys, Met, Phe, Thr, Trp.
• Conditionally indispensable amino acids: His and Arg.

Proinsulin

• Proinsulin is a precursor to insulin: After hydrolytic separation of peptide C, chain A has 21 residues and chain B has 30 residues.
• Peptide C is integral to folding insulin and is removed and aids in the formation of disulfide binds.
• Measuring C-peptide in the blood is an accurate way to find out how much insulin your body is making
• Proinsulin has 86 amino acid residues

Secondary Structure

• Important in determination of peptide bond.

Secondary Structure Basic properties

• Peptide C-N bond is shorter and half-double.
• Hydrogen bonds form between closely spaced peptide groups.
• The four atoms C, O, N, H lie in one plane.
• Only free rotation around the simple bonds N-Cα (angle φ) and Cα-C (angle ψ) is allowed.
• Radicals attached to α-C atoms are in a preferred trans position.

Secondary Structures

• It is created by the interaction between hydrogen bonds.
• Alpha- and beta-helical regions can both be present in the same chain.

Parameters of Secondary Structures

• Ramachandran angles φ and ψ,
• Number of amino acid residues per one turn of the helix (n).
• Distance between α-C atoms of adjacent residues (d).
• Spiral stroke (p = n x d).
• Alpha-helix and the Beta-structure are themodynamically most stable

Alpha Helix and Beta Sheet

• Alpha helix contains hydrogen bonds only created only within one chain
• Beta Sheet has antiparallel course of strands of beta helix
• Beta Chain is the most stretched form of all forms of peptide chain

Characterization of the a-helix

• An average of 3.6 amino acid residues makes up each turn of helix.
• The distance between the two strokes is 0.54 nm.
• The C=O bond of one move participates in a hydrogen bond with the N-H of the next move.
• Alpha-helix conformation is stabilized by hydrogen bonding.
• Disturbance in structure is the resilt of steric hinderence by large amino acids

Beta Chain

• Chains form a slightly zigzag folded surface
• In Beta sheets: polypeptide chains and parallel or antiparallel

Closed Beta Sheets

• They form beta barrels
• Polar molecules can't membranes that are non polar
• Porins are integral to protein protein membranes and transfer molecules in the membrane of cell

Ordered and Disordered regions of polypeptide chain

• Loops should not be confused with the term "randomly folded chains
• Secondary structure - important for manifestation of biological activity in signal transduction
• α-helical and β-stranded regions together make up about 50% of the entire chain.

Super Secondary Structure

• Combinations of a-helices and β-structures are connected by loops
• Structures are characteristic of many porteins
• α-α (two alpha helices) connected by a single loop
• β-β (two beta helices) connected by a single loop
• β-α-β (a beta strand linked to an alpha strand which is also linked to a beta strand by loops)
• Complex forms like β-α-α-β Greek Key and β-barrel.

Domains

• Both secondary and supersecondary structures of proteins are organized like domains
• Domains are compact units connected by polypeptide backbone
• Domains help to perform specific functions
• The folding of one peptide in a given domain is not affected the folding in another domain.

Definition of Tertiary Structure

• This is an additional folding of the polypeptide chain in space, built from interconnected domains. Functions:
• Binding of small ligands
• Crossing the plasma membrane (transmembrane proteins)
• Containing the catalytic site (enzymes
• DNA-binding sites (in transcription factors)
• Providing a surface for specific binding to another protein;
• Tertiary is created by weak interaction forces

Chemical interactions involved in creating the creation of the tertiary structure.

• Inclusion of proline helps with maintaining tertiary structure and the formation of the chaijn ring
• Non/Covalent bonds can exist
• Protein can be split into globular/fibrill

Types of Chemical bonds

• Disulfide bonds (-S-S-
• Hydrophobic Interactions-
• Polar interactions- Ionic and Polar bonds

Globular proteins

• Idealized tertiary structures
• Water dipoles (hydration shell) are attracted to hydrophilic residues
• Have a spherical or elongated shape

Fibrillar proteins

• Proteins in which the axis is water
• Have bones/skin/tendons