Chemistry of Proteins – Biochemistry Slideshow – First Year – Block 1

• Chemistry of amino acids
  • Lippincott’s Biochemistry
• Structure of Proteins
  • Lippincott’s Biochemistry
• Classification of Proteins
  • Biochemistry by Mushtaq Ahmed Vol I
• Plasma Proteins
  • Medical Biochemistry by Chatter Jea
• Techniques to study proteins

• Proteins are the most abundant macromolecule in the living cells and constitute 50% or more of their dry weight.
• They are found in all cells and all parts of the cells.
• Proteins also occur in great variety, hundreds of different proteins may be present in a single cell.  
• Proteins have many different biological roles. 

Definition of Proteins

• Proteins are the nitrogenous compounds made of a variable numbers of amino acid residues joined to each other by a covalent bond called peptide linkage.

Proteins

• Amino acid polymers are often differentiated according
  to their molecular weight or the number of amino acid residues they contain.
• Molecules with molecular weight ranging from several
  thousand to several million daltos (D) are called polypeptides.
• Those with low molecular, typically consisting of fewer
  than 50 amino acids are called peptides.
• The term protein describe molecules with more than 50
  amino acids

Biomedical importance

• In addition to providing the monomer units from which polypeptide chains of proteins are synthesis, the L-α-amino acids and their derivatives participate in cellular functions as diverse as nerve transmission and the biosynthesis of porphyrins, purines, pyrimidines, and urea.

• Short polymers of amino acids called peptides perform prominent roles in the neuroendocrine system as hormones, hormone-releasing factors, neuromodulators, or neurotransmitters.

• Neither human nor any other higher animals can synthesize 10 of 20 common L-α-amino acids in amounts adequate to support.
• While proteins contain only L-α-amino acids, microorganisms elaborate peptides that contain both D- and L-α-amino acids.

Proteins are built from a repertoire of 20 amino acids

• Amino acids are the building blocks of proteins.
• An a– amino acid consists of a central carbon atom called the a carbon, linked to an amino group, a carboxylic group, ahydrogen atom, and a distinctive R group.
• The R group is often referred to as the side chain.
• With four different groups connected to the tetrahedral a- carbon atom,  a-amino acid are chiral; the two mirror-image forms are called the L-isomer and the D-isomer.

• Only L amino acid are constituents of proteins.
• Amino acids in solution a neutral pH exist predominantly as dipolar ions (also called zwitterions).
• In the dipolar form , the amino group is protonated ( -NH₃⁺ ) and the carboxyl group is deprotonated ( -COO^– ).

• The ionization state of an amino acid varies with pH.
• Amino acids are amphoteric molecules; that is , they can act as either an acid or a base.
• Such compounds are often called ampholytes.
• Molecule that contain an equal number of ionizable groups of opposite charge and that therefore bear no net charge are termed zwitterions.
• Amino acids in blood and most tissues thus should be represented as in this form:

At its Isoelectric pH (pI), an Amino Acid Bears No Net Charge

• The isoelectric species is  the form of a molecule that has an  equal number of positive and negative charges and thus is electrically neutral.
• The isoelectric pH, also called pI, is the pH midway between pKa values on the either side of the isoelectric species.    

Classification of amino acids

• The 20 L-α-amino acids, present in proteins are genetically coded for proteins synthesis. These amino acids are classified into different classes on the basis of :
• Structure of ‘R’ group.
• Polarity of ‘R’ group and
• Nutritional classification [need for growth and maintaining health]     

ACIDIC AND BASIC PROPERTIES OF AMINO ACIDS

• Amino acids in aqueous solution contain weakly acidic α-carboxyl groups and weakly basic α-amino groups.
• In addition, each of the acidic and basic amino acids contains an ionizable group in its side chain.  
• Thus, both free amino acids and some amino acids combined in peptide linkages can act as buffers.
• The quantitative relationship between the concentration of a weak acid (HA) and its conjugate base (A~) is described by the Henderson-Hasselbalch equation.

Amino acids and Neurotransmitters

• Two amino acids deserve some special notice because they are both key precursors to many hormones and neurotransmitters (substances involved in the transmission of nerve impulses).
• Two of the neurotransmitter classes are simple derivatives of the two amino acids tyrosine and tryptophan.
• Tryptophan → Serotonin.
• Phenylalanine → Epinephrine.   

The Genetic Code Specifies 20 L-a- Amino Acids

• Of the over 300 naturally occurring amino acids, 20 constitute the monomer units of proteins.
• This is true for proteins from all form of life on earth and reflects the universality of the genetic code.
• Specific proteins may, however, contain of these 20 amino acids that arise by a methylated, formylated, acetylated, carboxylated or other derivatives process known as Posttranslational modification.

Non-standard amino acids

• In addition to the 20 standard amino acids that are common in a proteins, other amino acids are have been  found as components of only certain types of proteins.
• 4-Hydroxyproline                Plant cell wall
• 5-Hydroxylysine                  Collagen
• N-Methylysine                      Myosin
• g-Carboxyglutamate             Blood clotting protein
• Desmosine                             Elastin
• Selenocysteine +

Essential Amino acids

• Human body can not synthesize the essential amino acids, so they must essentially be present in our diet.
• Plant proteins
• Animal proteins
• Some essential amino acids are absent in plant proteins.  

Arginine and Histidine are synthesized in children in less amount for growth hence are called semi essential amino acids.

Peptide Bonds

• Amino acids can be polymerized to form chains.
• Polymers composed of two, three, a few (3-10), and many amino acid units are known, respectively, as dipeptides, tripeptides, oligopeptides,and polypeptides.
• After they are incorporated into a peptide, the individual amino acids (monomeric units) are referred to as amino acid residues.   

Protein structure

• Primary
• Secondary
• Tertiary
• Quaternary  

Primary structure of a protein

• The number & sequence of amino acid residues along the peptide chain is called the primary structure.
• The primary structures of a large numbers of polypeptides have been elucidated
• Insulin (51)
• ribonuclease (124)
• α chain of hemoglobin (141)
• β chain of hemoglobin (146)
•  oxytocin (8)
• ACTH (38)
• calcitonin (32).

Amino acid sequence determines  Primary structure

Secondary structure

• a- Helix
• b-Pleated sheets

a-Helix

• The alpha Helix is a coiled Structure stabilized by intrachain hydrogen bonds.
•  It is a clockwise, rod like spiral and is formed by intarchain H bonding between the C = O group of each amino acid and the  –NH₂ group of the amino acid that is situated 4 residues ahead in the linear sequence.

Beta pleated sheets

• The β pleated sheet ( or, more simply , the β sheet) differ markedly from the rodlike α- helix.
• A polypeptide chain, called a β strand, in a β sheet is almost fully extended rather than being tightly coiled as in the α helix.  

A Parallel b-pleated sheet

• Adjacent β strands run in the same direction. Hydrogen bonds connect each amino acid on one strand with two different amino acids on the adjacent strands.

An antiparallel b-pleated sheet

• Adjacent β strands run in opposite direction. Hydrogen bonds between NH and CO groups connect each amino acids to a single amino acid on an adjacent strand, stabilizing the structure.   

Loops & Bends

• Roughly half of the residues in a “typical” globular protein reside in α-helices and β- sheets and half in loops, turns, bends and other extended configurations features.  

Supersecondary structure

• Many globular proteins contain combination of α-helix and β-pleated sheet secondary.
• These patterns are called supersecondary structure. 
• In the βαβ unit, two parallel β-pleated sheets are connected an α- helix segments.
• In the β-meander pattern, two antiparallel β-sheets are connected by polar amino acids and glycines to effect an abrupt change in direction of the polypeptide chain called reverse or β-turn.
• In αα-units, two successive α-helices separated by a loop or nonhelical  segment become enmeshed because of compatible side chains.
• Several β-barrel arrangements are formed when various b-sheet configurations fold back on themselves.
• When an antiparallel b-sheet doubles back on itself in a pattern that resemble a common Greek pottery design, the motif is called the Greek key.

Tertiary structure

• The overall three –dimensional structure of protein is the tertiary structure of protein.
• The shape of globular proteins involve interaction between amino acid residues that may be located at considerable distance from each other in the primary sequence of the polypeptide chain and includes a-helices and b-sheet.
• Noncovalent interactions between the side chains of amino acid residues are important in stabilizing the tertiary structure and include (i) hydrophobic (ii) electrostatic interaction as well as (iii) hydrogen bond.(iv) Disulphide bonds
• In addition, covalent linkages may occur involving disulfide bond formation between cysteine residues. 
• Proteins tend to fold so that the atoms are packed closely together.
• Therefore, van der Waals forces between the atoms play an important role in stabilizing the structure of proteins.
• Occur between nonpolar side chains.  

Tertiary Structure

• Strong bonds
• Peptide bond
• Disulfide bond
• Weak bonds
• Hydrophobic
• Electrostatic
• Hydrogen  

Domains

• A domain is a section of protein structure sufficient to perform a particular chemical or physical task such as binding of a substrate or other ligand.
• Other domains may anchor a protein to a membrane or interact with a regulatory molecule that modulates its functions.  

• Two-domain structure of the subunit of a homodimeric enzyme, a bacterial class II HMG-CoA reductase.
• As indicated by the numbered resides, the single polypeptide begins in the large domain, enters the small domain, and ends in the large domain.

Folding of protein

The three-dimensional structure of a protein, a linear polymer of amino acids, is dictated by its amino acid sequence.   

Quaternary Structure

• Quaternary structure is a property of proteins that consists of more than one polypeptide chain.
• Each chain is called a subunit.
• Quaternary structure is the three-dimensional structure of a protein composed of multiple subunits.
• Commonly occurring example are dimers, trimers, and tetramers, consisting of two, three, and four polypeptide chain 
• These subunits are held together by some types of non-covalent interactions involved in tertiary structure, that is, hydrophobic and electrostatic interactions and hydrogen bonds.