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 = [pK_a-(COOH) + pK_a-(NH3⁺₎]/2

For more complex molecules such as polyampholytes the pI is the average of the pK_a 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.

Pentose Phosphate Pathway (Hexose Monophosphate Shunt)

The pentose phosphate pathway is primarily an anabolic pathway that utilizes the 6 carbons of glucose to generate 5 carbon sugars and reducing equivalents. However, this pathway does oxidize glucose and under certain conditions can completely oxidize glucose to CO₂ and water. The primary functions of this pathway are:

• To generate reducing equivalents, in the form of NADPH, for reductive biosynthesis reactions within cells.
• To provide the cell with ribose-5-phosphate (R5P) for the synthesis of the nucleotides and nucleic acids.
• Although not a significant function of the PPP, it can operate to metabolize dietary pentose sugars derived from the digestion of nucleic acids as well as to rearrange the carbon skeletons of dietary carbohydrates into glycolytic/gluconeogenic intermediates

Enzymes that function primarily in the reductive direction utilize the NADP⁺/NADPH cofactor pair as co-factors as opposed to oxidative enzymes that utilize the NAD⁺/NADH cofactor pair. The reactions of fatty acid biosynthesis and steroid biosynthesis utilize large amounts of NADPH. As a consequence, cells of the liver, adipose tissue, adrenal cortex, testis and lactating mammary gland have high levels of the PPP enzymes. In fact 30% of the oxidation of glucose in the liver occurs via the PPP. Additionally, erythrocytes utilize the reactions of the PPP to generate large amounts of NADPH used in the reduction of glutathione. The conversion of ribonucleotides to deoxyribonucleotides (through the action of ribonucleotide reductase) requires NADPH as the electron source, therefore, any rapidly proliferating cell needs large quantities of NADPH.

Regulation: Glucose-6-phosphate Dehydrogenase is the committed step of the Pentose Phosphate Pathway. This enzyme is regulated by availability of the substrate NADP⁺. As NADPH is utilized in reductive synthetic pathways, the increasing concentration of NADP⁺ stimulates the Pentose Phosphate Pathway, to replenish NADPH

Cori Cycle

The Cori Cycle operates during exercise, when aerobic metabolism in muscle cannot keep up with energy needs.

For a brief burst of ATP utilization, muscle cells utilize ~P stored as phosphocreatine. For more extended exercise, ATP is mainly provided by Glycolysis.

Lactate, produced from pyruvate, passes via the blood to the liver where it is converted to glucose. The glucose may travel back to the muscle to fuel Glycolysis.

The Cori Cycle costs 6 P in liver for every 2P made available in muscle. The net cost is 4 P Although costly in terms of "high energy" bonds, the Cori Cycle allows the organism to accommodate to large fluctuations in energy needs of skeletal muscle between rest and exercise.

The basic characteristics of enzymes includes

(i) Almost all the enzymes are proteins and they follow the physical and chemical reactions of proteins (ii) Enzymes are sensitive and labile to heat

(iii) Enzymes are water soluble

(iv) Enzymes could be precipitated by protein precipitating agents such as ammonium sulfate and trichloroacetic acid.

Monosaccharides: Aldoses (e.g., glucose) have an aldehyde at one end

They are classified acc to the number of carbon atoms present

Trioses, tetroses, pentose ( ribose, deoxyribose), hexoses  (glucose, galactose, fructose) Heptoses (sedoheptulose)

Glyceraldehyde simplest aldose

Ketoses (e.g., fructose) have a keto group, usually at C 2.

Dihydroxyacetone simplest Ketoses

The higher sugar exists in ring form rather than chain form

Furan  : 4 carbons and 1 oxygen

Pyrans : 5 carban and 1 oxygen

 These result from formation of hemiacital linkage b/w carbonyl and an alcohol group

3-D Structure of proteins

Proteins are the main players in the life of a cell. Each protein is a unique sequence of amino acid residues, each of which folds into a unique, stable, three dimentional structure that is biologically functional.

Conformation = spatial arrangement of atoms that depends on rotation of bonds. Can change without breaking covalent bonds.

• Since each residue has a number of possible conformations, and there are many residues in a protein, the number of possible conformations for a protein is enormous.

Native conformation = single, stable shape a protein assumes under physiological conditions.

• In native conformation, rotation around covalent bonds in polypeptide is constrained by a number of factors ( H-bonding, weak interactions, steric interference)
• Biological function of proteins depends completely on its conformation. In biology, shape is everything.
• Proteins can be classified as globular or fibrous.

There are 4 levels of protein structure

• Primary structure
  • linear sequence of amino acids
  • held by covalent forces
  • primary structure determines all oversall shape of folded polypeptides (i.e primary structure determines secondary , tertiary, and quaternary structures)
• Secondary structure
  • regions of regularly repeating conformations of the peptide chain (α helices, β sheets)
  • maintained by H-bonds between amide hydrogens and carbonyl oxygens of peptide backbone.
• Tertiary structure
  • completely folded and compacted polypeptide chain.
  • stabilized by interactions of sidechains of non-neighboring amino acid residues (fibrous proteins lack tertiary structure)
• Quaternary structure
  • association of two or more polypeptide chains into a multisubunit protein.