NEET MDS Lessons
Biochemistry
Ampholytes, Polyampholytes, pI and Zwitterion
Many substances in nature contain both acidic and basic groups as well as many different types of these groups in the same molecule. (e.g. proteins). These are called ampholytes (one acidic and one basic group) or polyampholytes (many acidic and basic groups). Proteins contains many different amino acids some of which contain ionizable side groups, both acidic and basic. Therefore, a useful term for dealing with the titration of ampholytes and polyampholytes (e.g. proteins) is the isoelectric point, pI. This is described as the pH at which the effective net charge on a molecule is zero.
For the case of a simple ampholyte like the amino acid glycine the pI, when calculated from the Henderson-Hasselbalch equation, is shown to be the average of the pK for the a-COOH group and the pK for the a-NH2 group:
pI = [pKa-(COOH) + pKa-(NH3+)]/2
For more complex molecules such as polyampholytes the pI is the average of the pKa values that represent the boundaries of the zwitterionic form of the molecule. The pI value, like that of pK, is very informative as to the nature of different molecules. A molecule with a low pI would contain a predominance of acidic groups, whereas a high pI indicates predominance of basic groups.
Nomenclature for stereoisomers: D and L designations are based on the configuration about the single asymmetric carbon in glyceraldehydes
For sugars with more than one chiral center, the D or L designation refers to the asymmetric carbon farthest from the aldehyde or keto group.
Most naturally occurring sugars are D isomers.
D & L sugars are mirror images of one another. They have the same name. For example, D-glucose and L-glucose
Other stereoisomers have unique names, e.g., glucose, mannose, galactose, etc. The number of stereoisomers is 2 n, where n is the number of asymmetric centers. The six-carbon aldoses have 4 asymmetric centers, and thus 16 stereoisomers (8 D-sugars and 8 L-sugars
An aldehyde can react with an alcohol to form a hemiacetal
Similarly a ketone can react with an alcohol to form a hemiketal
Pentoses and hexoses can cyclize, as the aldehyde or keto group reacts with a hydroxyl on one of the distal carbons
E.g., glucose forms an intra-molecular hemiacetal by reaction of the aldehyde on C1 with the hydroxyl on C5, forming a six-member pyranose ring, named after the compound pyran
The representations of the cyclic sugars below are called Haworth projections.
Fructose can form either:
- a six-member pyranose ring, by reaction of the C2 keto group with the hydroxyl on C6
- a 5-member furanose ring, by reaction of the C2 keto group with the hydroxyl on C5.
Cyclization of glucose produces a new asymmetric center at C1, with the two stereoisomers called anomers, α & β
Haworth projections represent the cyclic sugars as having essentially planar rings, with the OH at the anomeric C1 extending either:
- below the ring (α)
- above the ring (β).
Because of the tetrahedral nature of carbon bonds, the cyclic form of pyranose sugars actually assume a "chair" or "boat" configuration, depending on the sugar
IONIZATION OF WATER, WEAK ACIDS AND WEAK BASES
The ionization of water can be described by an equilibrium constant. When weak acids or weak bases are dissolved in water, they can contribute H+ by ionizing (if acids) or consume H+ by being protonated (if bases). These processes are also governed by equilibrium constants
Water molecules have a slight tendency to undergo reversible ionization to yield a hydrogen ion and a hydroxide ion :
H2O = H+ + OH−
The position of equilibrium of any chemical reaction is given by its equilibrium constant. For the general reaction,
A+B = C + D
SELENIUM
normal serum level is 50-100 mg/day
Selenium dependent enzymes include glutathione Peroxidase and 5-de-iodinase. Selenium concentration in testis is the highest in adult. It is very necessary for normal development and maturation of sperm.
Biotin
Biotin helps release energy from carbohydrates and aids in the metabolism of fats, proteins and carbohydrates from food.
RDA The Adequate Intake (AI) for Biotin is 30 mcg/day for adult males and females
Biotin Deficiency Biotin deficiency is uncommon under normal circumstances, but symptoms include fatigue, loss of appetite, nausea, vomiting, depression, muscle pains, heart abnormalities and anemia.
Applications of the Henderson-Hasselbalch equation
• Calculate the ratio of CB to WA, if pH is given
• Calculate the pH, if ratio of CB to WA is known
• Calculate the pH of a weak acid solution of known concentration
• Determine the pKa of a WA-CB pair
• Calculate change in pH when strong base is added to a solution of weak acid. This is represented in a titration curve
• Calculate the pI
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.