Introduction to Intermediary Metabolism

Introduction

Metabolism encompass all cellular processes which are essential to the survival of humans. These processes are generally divided into processes which generate energy from macromolecules (catabolism) and those which are used for building up biomolecules (anabolism). In summary, all cellular and indeed daily human functions require energy, generated in form of Adenosine Triphosphate (ATP) and metabolism serves as a reliable means for its generation and continual utilization.
The study of metabolism and metabolic processes is indeed important as it helps us understand the basis of certain disease conditions. For example, Type I Diabetes mellitus (DM) is as a result of insufficient production of insulin in an individual. Insulin is essential for the efficient uptake and utilization of glucose in cell. Therefore, Type I DM results in elevated blood concentrations of glucose. Also, certain drugs especially target specific pathways or enzymes. Understanding the relevance of the enzymes/pathways will help guide how we use certain drug/compounds. For example, folic acid is an important compound essential for the survival of most organisms. Parasites synthesize theirs de novo while humans can synthesize de novo and can absorb it from food. Drugs like sulphadoxine which inhibits dihydropteroate synthetase and pyrimethamine which inhibits dihydrofolate reductase are particularly effective because they target these enzymes can thus disrupt the normal cellular processes of the parasite.

Significance of Metabolism 

Metabolism is important for two major reasons:

1. Chemical energy is obtained from the degradation of energy rich nutrients (Catabolism)
2. Food materials are converted into the building block precursors of cellular macromolecules (Anabolism)

These processes of generation of energy involves a stepwise extracellular degradation of macromolecules such as starch and proteins. The units such as glucose are absorbed and subsequently broken down through a series of pathways for the generation of energy (ATP). The ATP generated in turn is used to fuel cellular processes including biosynthesis of biomolecules such as enzymes, including those necessary for the uptake of glucose, fatty acids, etc from the intestinal lumen. In short, all metabolic processes are linked and understanding the relevance of each process and how they relate to one another can help to further one’s understanding.

Phases of Metabolism 

Phases of Metabolism are:

1. Primary Metabolism
2. Secondary Metabolism
3. Tertiary Metabolism

1. Primary Metabolism: The primary metabolism includes Digestion.
2. Secondary Metabolism: The secondary Metabolism also called Intermediary Metabolism. It includes 
   • catabolism (breakdown process of biomolecules) and 
   • Anabolism (Synthesis process of the biomolecules).
3. Tertiary Metabolism: Biological oxidation and Oxidative phosphorylation are included in this type of metabolism

1. Primary Metabolism  

This phase comprises majorly of digestion. This is a process which is characterized by extracellular breakdown of large macromolecules such as protein and carbohydrate (e.g. Starch) into smaller macromolecules such as glucose which can readily absorbed in the intestinal lumen. Several organs are involved in this process, each playing an intrinsic but relevant role in the entire process as will be shown shortly.

• Stomach – The lining of the stomach produce hydrochloric acid which reduces the pH of the stomach to a range of 1-2. At this pH, most microbes contained in the food are killed off although some bacteria like Helicobacter pylori which causes ulcer can still thrive at this pH. In addition, the acidic pH assists in protein denaturation. This is because at this pH, the quaternary structure of most proteins are rendered unstable, resulting in its unfolding and subsequent exposure of the sites which can be acted upon by pepsin (a protease enzyme secreted by the mucosal cells), breaking them down into peptides that can be readily absorbed.
• Pancreas – production of digestive enzymes and of hormones, including amylase
  • proteases, peptidases
  • lipases
  • DNAse, RNAse
  • secretion of sodium bicarbonate to neutralize gastric acid as the stomach contents are washed down into the small intestine.
• Liver – The liver has a peculiar tissue structure that is optimized for rapid and efficient solute exchange between the percolating blood and the liver cells. It is organized into functional units called lobules. Blood from branches of the portal vein and of the liver artery percolates each lobule and flows towards its central vein, which drains it into the general circulation. Bile duct branches drain bile from each lobule to be stored in the gall bladder for subsequent secretion into the intestine.

Bile contains bile acids such as cholic acid, taurocholate and glycocholate, as well as sodium bicarbonate which contributes to the alkalinity of the small intestine. Other components includes cholesterol and bilirubin which excreted primarily via bile. Bile is important in solubilizing fat so as to render it accessible to enzymatic cleavage by pancreatic lipase and subsequently encourage its absorption. It is subsequently reabsorbed in the terminal ileum of the small intestine, from where it makes its way to the liver via the portal vein.

•  Small intestine – The small intestine provides the large surface area essential for the absorption of smaller macromolecules across the mucous cells by active transport. To this end, the surface of the small intestine is highly folded in order to maximize the surface available for substrate uptake. An example can be seen below with breakdown of macromolecules to small molecules and the subsequent uptake of the latter.

Starch —–> Maltose + Isomaltose 
——-> Glucose 

In the image above, starch is broken down to maltose and isomaltose, both of which are further broken down to yield glucose in the intestinal lumen. Glucose is then actively transported, against its concentration gradient, into the mucosal cells via the SGLT1 transporter, alongside two molecules of Na+. The glucose subsequently diffuses passively into the blood circulation via the GLUT2 transporter.

• Large intestine – The cumulative volume of the fluids secreted into the stomach and the small intestine exceeds four liters per day. It falls to the large intestine to recover most of that fluid. This inevitably slows down the transport of the gut contents, which in turn will cause them to be overgrown with bacteria.9 The bacterial flora is mostly harmless, though, and it even helps with breaking down undigested remnants in the gut content and thereby freeing up the water bound osmotically by them. They produce some vitamins, too, for example folic acid, but also some potentially toxic substances such as amines and ammonia. The latter are taken up and dealt with by the liver.

Role of Enzymes in Intermediary Metabolism 

From, glycolysis to the tricarboxylic acid cycle, all metabolic processes are mediated by enzymes. They may exist as a single unit or in a multimeric form but more important is the number of active site(s) on them. Enzymes can just have one active site; one active site per subunit for a multimeric enzyme; multiple active sites per subunit (fatty acid synthase).
Enzymes are protein-in-nature and as such, their activity is closely related to the precise arrangement and interaction of their amino acid residues and side chains. Think of the active site of an enzyme as key hole of a padlock. If a key does not fit, it would not enter. Even if it enters, it’s not a guarantee that it will open the padlock unless both padlock and key match. In the same way, enzymes adopt a conformational arrangement that improve its binding to a suitable substrate in order to effect its action.
The table below summarizes the function of each enzyme class:

Enzyme Class	Catalyzed Reactions
oxidoreductases	catalyze redox reactions, frequently involving one of the coenzymes NAD+, NADP+, or FAD
transferases	transfer functional groups between metabolites, e.g. a phosphate from ATP to a sugar hydroxyl group
hydrolases	catalyze hydrolysis reactions, such as those involved in the digestion of foodstuffs
lyases	perform elimination reactions that result in the formation of double bonds
isomerases	facilitate the interconversion of isomers
ligases	ligases form new covalent bonds at the expense of ATP hydrolysis

 

Regulation of Enzymes

1. Allosteric Induction/Inhibition: Allosteric activation/inhibition occurs when a different component (probably produced downstream a pathway) binds to an enzyme at a separate site from its substrate active site. This results in a conformational change in the enzyme which may alter the nature of amino acid interactions in the active site. In short, if binding of the component makes it easier for the enzyme to interact with its substrate via its active site, it is termed an activator whereas if the interaction results in a change that prevents the enzyme from interacting with its substrate, it is termed an inhibitor. An example can be seen where AMP serves as an allosteric activator of Phosphofructokinase which is essential for glycolysis and thus production of ATP. When ATP abounds, it displaces AMP and the same enzyme adopts a form that prevents further substrate binding and more production of ATP. 

1. Transcriptional induction/inhibition: This is usually employed by thyroid hormone, cortisol and steroids. This is the reason why those on steroidal medications are adviced to taper their doses. This is to ensure that the body does run short of these steroids which are essential for several bodily functions.
2. ubiquitin ligation, followed by proteolytic degradation: ubiquitin marks proteins for degradation by proteasomes.

Central Hub of Metabolism

All food taken in are eventually broken to down to their simple forms, including glucose, amino acids and fatty acids and utilized depending on the body requirements. For example, if an excess amount of glucose is present in the system, it is automatically converted into glycogen for storage. Glucose to be utilized is first broken down into pyruvate with a net gain of 2 molecules of ATP via glycolysis. Subsequently, pyruvate is converted to Acetyl-CoA which enters the mitochondria and is incorporated into the citric acid (TCA) cycle with the release of CO2, H2O and 1 molecule of ATP. Both processes are essential in the generation of ATP. In absence of glucose, amino acids can be mobilized and converted back to glucose in a process called gluconeogenesis. This can be used to supplement the shortage of glucose.
Please note the conversion from pyruvate to Acetyl-CoA is a one way streak and as such fatty acids which are converted directly into Acetyl-CoA cannot be converted back to glucose. This limits the pathways for energy generation to the TCA cycle. This is the reason why fatty acids cannot sustain the body for prolonged periods.

Glucose Metabolism 

Glucose is an essential component of metabolism and routinely required for the generation of ATP in cells. This occurs via glycolysis and the TCA cycle which yield a total of 3 molecules of ATP with the generation of CO2 and H2O. Elevated blood levels of glucose induce the production of insulin which bind to insulin receptors of cells. This mobilizes the GLUT transporters to the cell membrane where facilitate the entry of glucose into the cell. The glycolysis pathway as shown above takes effect from here resulting in the production of pyruvate with a net 2 molecules of` ATP.
The pyruvate is decarboxylated by pyruvate dehydrogenase in the mitochondria to yield Acetyl-CoA which is completely degraded in the citric acid cycle resulting in the production of one molecule of ATP.
The liver is involved in the direct regulation of blood glucose level via the actions of insulin. The enzyme first activates the enzyme hexokinase which phosphorylates glucose to glucose-6-phosphate thereby trapping it in the hepatocytes. Next it inhibits the enzyme glucose-6-phosphatase which would have hydrolyzed glucose-6-phosphate to release glucose in the hepatocytes and in addition increases the activity of glycogen synthase which would generate glycogen for storage in the liver and skeletal muscle.
Fat Metabolism 

Lipids occur in the body as triacylgylycerol, cholesterols, and polar lipids (phospholipids, glycolipids, etc). Triacylglycerol (TAGs) are concentrated mostly in adipose tissues and others mainly on membranes. TAGs provide the largest store of energy but it is confined to few pathways due to its inability to be turned back to glucose. This is because the conversion of pyruvate to Acetyl-CoA is a one-way streak. In the presence of excess glucose and glycogen sources, Acetyl-CoA is converted to fatty acids which eventually make their way to the adipose tissues. Glucose are also taken up by these adipocytes (facilitated by insulin via GLUT) and subsequently converted to glycerol, which together with the fatty acids already present are used for the synthesis of triacylglycerol (triglycerides) {see image below}. These triglycerides are stored in the adipose tissues due to the intracellular inhibition of lipase by insulin in the adipocytes.
TAGs can serve as fuel for the heart and skeletal muscles as free fatty acids. As ketone bodies they can supply energy to other organs including the brain for a short period because these are more soluble and thus are able to cross the Blood-Brain-Barrier.

Role of Amino Acids in Gluconeogenesis 

In the absence of glucose and glycogen, glucose can be synthesized de novo using amino  acids from a protein-rich diet or obtained from muscles. The exact point of entry is dependent on the particular amino acid in question. For example amino acids that yield TCA intermediates and pyruvate can be used in gluconeogenesis and thus are called glucogenic amino acids. Those amino acids that yield acetoacetone which is converted to Acetyl-CoA cannot be used to synthesize glucose for reasons already mentioned under “Fat metabolism”. These set of amino acids are called ketogenic amino acids and are primarily used for synthesis of fatty acids. 
Please note that only Leucine and Lysine are strictly Ketogenic whereas Phenylalanine, isoleucine, Threonine, Tryptophan and Tyrosine are both Ketogenic and Glucogenic.