NEET MDS Lessons
Biochemistry
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
Enzymes are protein catalyst produced by a cell and responsible ‘for the high rate’ and specificity of one or more intracellular or extracellular biochemical reactions.
Enzymes are biological catalysts responsible for supporting almost all of the chemical reactions that maintain animal homeostasis. Enzyme reactions are always reversible.
The substance, upon which an enzyme acts, is called as substrate. Enzymes are involved in conversion of substrate into product.
Almost all enzymes are globular proteins consisting either of a single polypeptide or of two or more polypeptides held together (in quaternary structure) by non-covalent bonds. Enzymes do nothing but speed up the rates at which the equilibrium positions of reversible reactions are attained.
In terms of thermodynamics, enzymes reduce the activation energies of reactions, enabling them to occur much more readily at low temperatures - essential for biological systems.
Carbohydrates (glycans) have the basic composition
- Monosaccharides - simple sugars, with multiple hydroxyl groups. Based on the number of carbons (e.g., 3, 4, 5, or 6) a monosaccharide is a triose, tetrose, pentose, or hexose, etc.
- Disaccharides - two monosaccharides covalently linked
- Oligosaccharides - a few monosaccharides covalently linked.
- Polysaccharides - polymers consisting of chains of monosaccharide or disaccharide units
Acyl-CoA Synthases (Thiokinases), associated with endoplasmic reticulum membranes and the outer mitochondrial membrane, catalyze activation of long chain fatty acids, esterifying them to coenzyme A, as shown at right. This process is ATP-dependent, and occurs in 2 steps. There are different Acyl-CoA Synthases for fatty acids of different chain lengths.
Exergonic hydrolysis of PPi (P~P), catalyzed by Pyrophosphatase, makes the coupled reaction spontaneous. Overall, two ~P bonds of ATP are cleaved during fatty acid activation. The acyl-coenzyme A product includes one "high energy" thioester linkage.
Summary of fatty acid activation:
- fatty acid + ATP → acyl-adenylate + PPi
PPi → Pi - acyladenylate + HS-CoA → acyl-CoA + AMP
Overall: fatty acid + ATP + HS-CoA → acyl-CoA + AMP + 2 Pi
For most steps of the b-Oxidation Pathway, there are multiple enzymes specific for particular fatty acid chain lengths.
Fatty acid b-oxidation is considered to occur in the mitochondrial matrix. Fatty acids must enter the matrix to be oxidized. However enzymes of the pathway specific for very long chain fatty acids are associated with the inner mitochondrial membrane (facing the matrix).
Fatty acyl-CoA formed outside the mitochondria can pass through the outer mitochondrial membrane, which contains large VDAC channels, but cannot penetrate the mitochondrial inner membrane.
Transfer of the fatty acid moiety across the inner mitochondrial membrane involves carnitine.
Carnitine Palmitoyl Transferases catalyze transfer of a fatty acid between the thiol of Coenzyme A and the hydroxyl on carnitine.
Carnitine-mediated transfer of the fatty acyl moiety into the mitochondrial matrix is a 3-step process, as presented below.
- Carnitine Palmitoyl Transferase I, an enzyme associated with the cytosolic surface of the outer mitochondrial membrane, catalyzes transfer of a fatty acid from ester linkage with the thiol of coenzyme A to the hydroxyl on carnitine.
- Carnitine Acyltransferase, an antiporter in the inner mitochondrial membrane, mediates transmembrane exchange of fatty acyl-carnitine for carnitine.
- Within the mitochondrial matrix (or associated with the matrix surface of the inner mitochondrial membrane, Carnitine Palmitoyl Transferase II catalyzes transfer of the fatty acid from carnitine to coenzyme A. (Carnitine exits the matrix in step 2.) The fatty acid is now esterified to coenzyme A within the mitochondrial matrix
Control of fatty acid oxidation is exerted mainly at the step of fatty acid entry into mitochondria.
Malonyl-CoA inhibits Carnitine Palmitoyl Transferase I. (Malonyl-CoA is also a precursor for fatty acid synthesis). Malonyl-CoA is produced from acetyl-CoA by the enzyme Acetyl-CoA Carboxylase
AMP-Activated Kinase, a sensor of cellular energy levels, catalyzes phosphorylation of Acetyl-CoA Carboxylase under conditions of high AMP (when ATP is low). Phosphorylation inhibits Acetyl-CoA Carboxylase, thereby decreasing malonyl-CoA production.
The decrease in malonyl-CoA concentration releases Carnitine Palmitoyl Transferase I from inhibition. The resulting increase in fatty acid oxidation generates acetyl-CoA for entry into Krebs cycle, with associated production of ATP
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
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
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.