NEET MDS Lessons
Biochemistry
General structure of amino acids
- All organisms use same 20 amino acids.
- Variation in order of amino acids in polypeptides allow limitless variation.
- All amino acids made up of a chiral carbon attached to 4 different groups
- hydrogen
- amino group
- carboxyl
- R group: varies between different amino acids
- Two stereoisomers (mirror images of one another) can exist for each amino acid. Such stereoisomers are called enantiomers. All amino acids found in proteins are in the L configuration.
- Amino acids are zwitterions at physiological pH 7.4. ( i.e. dipolar ions). Some side chains can also be ionized
Structures of the 20 common amino acids
- Side chains of the 20 amino acids vary. Properties of side chains greatly influence overall conformation of protein. E.g. hydrophobic side chains in water-soluble proteins fold into interior of protein
- Some side chains are nonpolar (hydrophobic), others are polar or ionizable at physiological pH (hydrophilic).
- Side chains fall into several chemical classes: aliphatic, aromatic, sulfur-containing, alcohols, bases, acids, and amides. Also catagorized as to hydrophobic vs hydrophilic.
- Must know 3-letter code for each amino acid.
Aliphatic R Groups
- Glycine: least complex structure. Not chiral. Side chain small enough to fit into niches too small for other amino acids.
- Alanine, Valine, Leucine, Isoleucine
- no reactive functional groups
- highly hydrophobic: play important role in maintaining 3-D structures of proteins because of their tendency to cluster away from water
- Proline has cyclic side chain called a pyrolidine ring. Restricts geometry of polypeptides, sometimes introducing abrupt changes in direction of polypeptide chain.
Aromatic R Groups
- Phenylalanine, Tyrosine, Tryptophan
- Phe has benzene ring therefore hydrophobic.
- Tyr and Trp have side chains with polar groups, therefore less hydrophobic than Phe.
- Absorb UV 280 nm. Therefore used to estimate concentration of proteins.
Sulfur-containing R Groups
- Methionine and Cysteine)
- Met is hydrophobic. Sulfur atom is nucleophilic.
- Cys somewhat hydrophobic. Highly reactive. Form disulfide bridges and may stabilize 3-D structure of proteins by cross-linking Cys residues in peptide chains.
Side Chains with Alcohol Groups
- Serine and Threonine
- have uncharged polar side chains. Alcohol groups give hydrophilic character.
- weakly ionizable.
Basic R Groups
- Histidine, Lysine, and Arginine.
- have hydrophilic side chains that are nitrogenous bases and positively charged at physiological pH.
- Arg is most basic a.a., and contribute positive charges to proteins.
Acidic R Groups and their Amide derivatives
- Aspartate, Glutamate
- are dicarboxylic acids, ionizable at physiological pH. Confer a negative charge on proteins.
- Asparagine, Glutamine
- amides of Asp and Glu rspectively
- highly polar and often found on surface of proteins
- polar amide groups can form H-bonds with atoms in other amino acids with polar side chains.
Keq, Kw and pH
As H2O is the medium of biological systems one must consider the role of this molecule in the dissociation of ions from biological molecules. Water is essentially a neutral molecule but will ionize to a small degree. This can be described by a simple equilibrium equation:
H2O <-------> H+ + OH-
This equilibrium can be calculated as for any reaction:
Keq = [H+][OH-]/[H2O]
Since the concentration of H2O is very high (55.5M) relative to that of the [H+] and [OH-], consideration of it is generally removed from the equation by multiplying both sides by 55.5 yielding a new term, Kw:
Kw = [H+][OH-]
This term is referred to as the ion product. In pure water, to which no acids or bases have been added:
Kw = 1 x 10-14 M2
As Kw is constant, if one considers the case of pure water to which no acids or bases have been added:
[H+] = [OH-] = 1 x 10-7 M
This term can be reduced to reflect the hydrogen ion concentration of any solution. This is termed the pH, where:
pH = -log[H+]
Riboflavin: Vitamin B2
Riboflavin, or vitamin B2, helps to release energy from foods, promotes good vision, and healthy skin. It also helps to convert the amino acid tryptophan (which makes up protein) into niacin.
RDA Males: 1.3 mg/day; Females: 1.1 mg/day
Deficiency : Symptoms of deficiency include cracks at the corners of the mouth, dermatitis on nose and lips, light sensitivity, cataracts, and a sore, red tongue.
The Effects of Enzyme Inhibitors
Enzymes can be inhibited
- competitively, when the substrate and inhibitor compete for binding to the same active site or
- noncompetitively, when the inhibitor binds somewhere else on the enzyme molecule reducing its efficiency.
The distinction can be determined by plotting enzyme activity with and without the inhibitor present.
Competitive Inhibition
In the presence of a competitive inhibitor, it takes a higher substrate concentration to achieve the same velocities that were reached in its absence. So while Vmax can still be reached if sufficient substrate is available, one-half Vmax requires a higher [S] than before and thus Km is larger.
Noncompetitive Inhibition
With noncompetitive inhibition, enzyme molecules that have been bound by the inhibitor are taken out
- enzyme rate (velocity) is reduced for all values of [S], including
- Vmax and one-half Vmax but
- Km remains unchanged because the active site of those enzyme molecules that have not been inhibited is unchanged.
- There are two important phospholipids, Phosphatidylcholine and Phosphatidylserine found the cell membrane without which cell cannot function normally.
- Phospholipids are also important for optimal brain health as they found the cell membrane of brain cells also which help them to communicate and influence the receptors function. That is the reason food stuff which is rich in phospholipids like soy, eggs and the brain tissue of animals are good for healthy and smart brain.
- Phospholipids are the main component of cell membrane or plasma membrane. The bilayer of phospholipid molecules determine the transition of minerals, nutrients, and drugs in and out of the cell and affect various functions of them.
- As phospholipids are main component of all cell membrane, they influence a number of organs and tissues, such as the heart, blood cells and the immune system. As we grown up the amount of phospholipids decreases and reaches to decline.
- Phospholipids present in cell membrane provide cell permeability and flexibility with various substances as well its ability to move fluently. The arrangement of phospholipid molecules in lipid bilayer prevent amino acids, carbohydrates, nucleic acids, and proteins from moving across the membrane by diffusion. The lipid bi-layer is usually help to prevent adjacent molecules from sticking to each other.
- The selectivity of cell membrane form certain substances are due to the presence of hydrophobic and hydrophilic part molecules and their arrangement in bilayer. This bilayer is also maintained the normal pH of cell to keeps it functioning properly.
- Phospholipids are also useful in the treatment of memory problem associated with chronic substances as they improve the ability of organism to adapt the chronic stress.
Role of Coenzymes
The functional role of coenzymes is to act as transporters of chemical groups from one reactant to another.
Ex. The hydride ion (H+ + 2e-) carried by NAD or the mole of hydrogen carried by FAD;
The amine (-NH2) carried by pyridoxal phosphate
Glycogenolysis
Breakdown of glycogen to glucose is called glycogenolysis. The Breakdown of glycogen takes place in liver and muscle. In Liver , the end product of glycodgen breakdown is glucose where as in muscles the end product is Lactic acid Under the combined action of Phosphorylase (breaks only –α-(1,4) linkage )and Debranching enzymes (breaks only α-(1,6) linkage )glycogen is broken down to glucose.