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.
Polar (Uncharged)
| Amino Acid | Key Feature |
|---|---|
| Serine (S) | Hydroxyl group |
| Threonine (T) | Hydroxyl group |
| Asparagine (N) | Amide group |
| Glutamine (Q) | Amide group |
| Tyrosine (Y) | Phenol group |
| Cysteine (C) | Thiol group |
Mnemonic: "Santa’s Team Never Quit Trying Cookies" (S, T, N, Q, T, C)
Non-Polar (Hydrophobic)
| Amino Acid | Key Feature |
|---|---|
| Glycine (G) | Smallest side chain |
| Alanine (A) | Methyl group |
| Valine (V) | Branched chain |
| Leucine (L) | Branched chain |
| Isoleucine (I) | Branched chain |
| Methionine (M) | Sulfur-containing |
| Proline (P) | Cyclic structure |
| Phenylalanine (F) | Aromatic ring |
| Tryptophan (W) | Indole ring |
Mnemonic: "Grandma Always Visits London In May For Perfect Weather" (G, A, V, L, I, M, F, P, W)
Sphingosine is an amino alcohol present in sphingomyelins (sphingophospholipids). They do not contain glycerol at all.
Sphingosine is attached by an amide linkage to a fatty acid to produce ceramide. The alcohol group of sphingosine is bound to phosphorylcholine in sphingomyelin structure. .
Sphingomyelins are important constituents of myelin and are found in good quantity in brain and nervous tissues.
CALCIUM
Total calcium in the human body is 1 to 1.5kg, out of which 99% is seen in bone and 1% in extracellular fluid. The main source of calcium is milk.
The daily requirement of calcium for child is 1200mg/day and for adult it is 500mg/day. During pregnancy /lactation the calcium requirement is 1500mg/day.
The absorption of calcium takes place in 1st and 2nd part of deuodenum. Calcium absorption requires carrier protein, helped by Ca2+ - dependent ATpase.
Factors responsible for increase in calcium absorption include Vitamin D, Parathyroid hormone, acidity and amino acids. Factors such as phytic acid,oxalates, malabsorption syndromes and Phosphates decreases calcium absorption. The normal calcium level in blood is 9-11mg/dl.
Weak Acids and pKa
• The strength of an acid can be determined by its dissociation constant, Ka.
• Acids that do not dissociate significantly in water are weak acids.
• The dissociation of an acid is expressed by the following reaction: HA = H+ + A- and the dissociation constant Ka = [H+ ][A- ] / [HA]
• When Ka < 1, [HA] > [H+ ][A- ] and HA is not significantly dissociated. Thus, HA is a weak acid when ka < 1.
• The lesser the value of Ka, the weaker the acid.
• Similar to pH, the value of Ka can also be represented as pKa.
• pKa = -log Ka.
• The larger the pKa, the weaker the acid.
• pKa is a constant for each conjugate acid and its conjugate base pair.
• Most biological compounds are weak acids or weak bases.
These can be synthesized by the body from other compounds.
| Non-Essential Amino Acids | Key Functions |
|---|---|
| Alanine | Energy production, glucose metabolism |
| Asparagine | Nervous system development |
| Aspartic acid | DNA synthesis, neurotransmission |
| Glutamic acid | Brain function, neurotransmitter |
| Serine | Cell membranes, metabolism |
The body makes these from carbohydrates and other amino acids.
CHOLESTEROL AND ITS IMPORTANCE
Cholesterol is an important lipid found in the cell membrane. It is a sterol, which means that cholesterol is a combination of a steroid and an alcohol .
It is an important component of cell membranes and is also the basis for the synthesis of other steroids, including the sex hormones estradiol and testosterone, as well as other steroids such as cortisone and vitamin D.
In the cell membrane, the steroid ring structure of cholesterol provides a rigid hydrophobic structure that helps boost the rigidity of the cell membrane.
Without cholesterol the cell membrane would be too fluid. In the human body, cholesterol is synthesized in the liver.
Cholesterol is insoluble in the blood, so when it is released into the blood stream it forms complexes with lipoproteins.
Cholesterol can bind to two types of lipoprotein, called high-density lipoprotein (HDL) and low-density lipoprotein (LDL).
A lipoprotein is a spherical molecule with water soluble proteins on the exterior. Therefore, when cholesterol is bound to a lipoprotein, it becomes blood soluble and can be transported throughout the body.
HDL cholesterol is transported back to the liver. If HDL levels are low, then the blood level of cholesterol will increase.
High levels of blood cholesterol are associated with plaque formation in the arteries, which can lead to heart disease and stroke.