Intermediary Metabolism (Basic Notes)

One of the major reasons for studying Biochemistry is to understand how living organisms utilize the chemical energy in their environment to carry out their biochemical activities. It is Intermediary Metabolism.

This requires an understanding of the simpler principles of physical chemistry and thermodynamics as they apply to living organisms.

Also required is an appreciation of the so-called “energy-rich compounds’ that permit the living organism to trap and subsequentially utilize the chemical energy contained in the food materials it consumes.

intermediary metabolism

What is Metabolism?

The sun is the ultimate source of energy for all life on the planet earth. That energy, like sunlight, is trapped by photosynthetic organisms and used to convert CO2 into the organisms’ cellular material composed mainly of proteins, carbohydrates, and lipids but also smaller amounts of nucleic acids, Vitamins, coenzymes, and other compounds.

Some of those products of photosynthesis (carbohydrates and lipids) are in turn, utilize by the nonphotosynthetic organisms, mainly animals as a source of energy for growth, development, and reproduction.

Types of Metabolic Reactions

There are THREE types of reactions are present in Metabolism. They are

Exothermic Reactions

The reactions release energy and that, therefore, has negative enthalpy changes. On reaction energy diagrams, the products of exothermic reactions have energy levels lower than those of starring materials.

Endothermic reactions

The reactions absorb energy and that, therefore, have positive enthalpy changes. In reactions energy diagrammed, the products of endothermic reactions have higher energy levels than the starting materials.

Isothermic reaction

This type of reaction has not released any energy.

Bonds Cleavage and its types

In Intermediary Metabolism, a covalent bond (σ-bond) is formed by the help of two atoms by the sharing of a pair of electrons. When the two atoms are separated from each other, bond fusion (or cleavage) is said to have taken place.

The cleavage process can occur in two ways: a) Homolytic cleavage and   b) Heterolytic cleavage

a) Homolytic cleavage

When one electron of the bonding pair goes with each of the departing atoms of the fission is symmetrical (0r) homogenous and is called “Homolytic cleavage” (or) “Homolysis”.

A-B (or) A:B    –>  A. + .B

  • The two fragments are produced as a result of hemolytic fission carry an odd electron each and are called “Free Radicals”.
  • These are transitory and at once react with other radicals (or) molecules by going one more electron to restore the stable bonding pair.

b) Heterolytic Cleavage

When a covalent bond breaks in a fashion that both the bonding electrons are appropriated by one of the two departing fragments (atoms or groups), it is said to have undergoes “Heterolytic cleavage” (or) “Heterolysis“.

A-B (or) A:B –> A: + B+

  • The heterolytic cleavage yields one positive & one negative ion.
  • These reactions take place more readily in polar solvents like water and are catalyzed by the presence of ionic catalysts (e.g.: acidic (or) basic)

Bond Length

Intermediary Metabolism

Atoms involved in the formation of a bond can not come close together to each other than a certain distance where the potential energy is minimum.

The average distance between the nuclei of two atoms bonded to each other is used under the name of bond length or bond distance.

Thus bond length may be defined as the average distance between the centers of nuclei of the two bonded atoms. It is expresses in angstrom (A0) units (1A0 =10-8 cm).

Points to remember:

  • Multiple bonds (double or triple bond between two atoms) is always shorter than the corresponding single bond.
  • Bond length decrease with the increase in ‘s’ character since an s-orbital is smaller than a p-orbital. thus
  1. sp3 C-H = 1.093 Ao (in alkanes)
  2. sp2C-H = 1.087 Ao (in Alkenes)
  3. sp C-H = 1.057 Ao (in Alkynes)
  • Since bond distance is the sum of the ionic or covalent (atomic) radii of the two concerned atoms, the factors, and trends observed in the ionic or atomic radii will apply on the bond distance.

Bond Angle

The molecules made up of three or more atoms, the average angle between the bonded orbital is known as a bond angle, Ф. Fundamentally, the value of the bond angle largely depends on the nature of the bonds concerned. The bond angle in the water molecule formed by the overlapping of two s-orbitals of hydrogen atoms with one 2p orbital of oxygen atom should be of 900. The actual H-O-H bond angle is 1040 31’. Bong angles are important to analyze the behavior of molecules in intermediary metabolism.

Points to remember

  • Repulsion between atoms or groups attached to the central atoms: the positive charge, developed due to high electronegativity of oxygen, on the two hydrogen atoms in water causes repulsion among themselves which increases the bond angle, H-O-H from 900 to 1050.
  • Hybridization of bonding orbital: Hybridization of bonding orbital also plays a very important role in determining the values of bond angles.
Bond typesp3sp2sp
Bond angle 1090 28’ 1200 1800
  • Repulsion due to non-bonded electrons: the deviation of the normal tetrahedral bond angle of 1090 28’ in H2O (1050), NH3 (1070), etc. Although their central atoms are in an sp3 hybridized state.

Classification of Metabolic Reagents

Now let us discuss about the metabolic reagents in intermediary metabolism.  The presence of a charge on the reactant although certainly helps the attack of the reagent on the reactant, it is far from being essential.

Indeed the requisite unsymmetrical charge distribution may be induced by the mutual polarization of the reagent and reactant on their close approach as when bromine adds to ethylene.

Thus on the basis of the above principle, most of the reagents can be classified into the following two types.

1.Electrophilic reagents (Electrophiles)

The name implies electrophilic (electro=electron, phile=love) reagents are electron seeking (or) loving and thus attack the substrate at the point of maximum electron density. Thus an Electrophile is a species having electron-deficiency atom (or) center.

The electrophilic reagent may be positively charged species or neutral molecules with the electron-deficient center. Some of the important electrophiles are given below:

E.g.: H+, Br+, NH4+, SO3, R-N+≡N,

It is interesting to note that since the electrophiles are capable of accepting electrons pair, they are Lewis acids.

The reactions involving the attack of electrophiles are known as an electrophilic reaction.

2. Nucleophilic reagents (Nucleophiles)

The reagent possessing at least one lone pair of electrons is known as nucleophilic reagents (or) nucleophiles (nucleo=nucleus; phile=love).

Since they possess higher electron density, they attack the substance at the point of minimum electron density. The nucleophilic reagent may be a negatively charged species or neutral molecule with free electron pair (s).

Some of the important nucleophiles are given below:

E.g.: OH, Br, CN, C00, R.C≡C, CH3COCH2, H-O-H, R-O-R, R-O-H, R-S-H, R-NH2, R2-NH2, :NH3, LiAlH4.

It is interesting to note that since the nucleophiles are capable of donating electrons pair, they are Lewis bases.

The reaction involving the attack of nucleophiles is referred to as nucleophilic reactions.

Intermediary Metabolism

Metabolic Phases

Thousands of chemical reactions are taking place inside a cell in an organized, well co-organized, and purposeful manner; all these are collectively called Intermediary Metabolism. The term Metabolism came from the Greek language (metaboleG = Change; balleinG= to throw).

In living organisms, there are three different phases of metabolic phases done. These are :

  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.
Intermediary metabolism

Intermediary metabolism serves the following purposes

Metabolism is the overall process through which living systems acquire and utilize the free energy they need to carry out their functions. The term Catabolism and Anabolism were coined by the physiologist Gasket in 1886.

  • Chemical energy is obtained from the degradation of energy-rich nutrients.
  • Food materials are converted into the building block precursors of cellular macromolecules. These building blocks are later made into macromolecules, such as proteins, nucleic acids, polysaccharides, etc.
  • Biomolecules required for specialized functions of the cell are synthesized. Specialized functions of the cell are synthesized.
  • Metabolic pathways are taking place with the help of sequential enzyme systems. These pathways are regulated at three levels:
  1. Regulation through the action of allosteric enzymes: Which increases or decreases in the activity under the influence of effector molecules.
  2. Hormonal regulation: Hormones are chemical messengers secreted by different endocrine glands.
  3. Regulation at the DNA level: The concentration of the enzyme is changed by regulation at the level of synthesis of the enzyme.
  • Metabolism is broadly divided into TWO types: a) Catabolism and b) Anabolism

a) Catabolism

It is a degradation process. A degradative process in which complex molecules are broken down into simpler ones; includes processes such as Cellular Respiration and Digestion. The meaning of the Catabolism came from Greek (kataboleG = Throwing down; balleinG= to throw). It is also spelled as katabolism. The energy released during this process is trapped chemical energy, usually as ATP. Eg: Cellular Respiration

b) Anabolism

It is a biosynthesis process. A constructive process in which complex molecules are synthesized from simpler ones; consumes rather than produce cellular energy; includes processes such as Photosynthesis and assimilation; opposite of catabolism. The meaning of the Anabolism came from Greek (AnaboleG = Throwing up; balleinG= to throw). This needs energy. Eg: Photosynthesis

Metabolic Pathways

An array of enzyme-catalyzed chemical reactions that bring about transformations of certain organic compounds vital to the organism, constitute “Metabolic pathways” (or) “Metabolic routes”.

Three Principle characteristics of metabolic pathways, there are Irreversible pathways, Typical irreversible metabolic pathways, and Branched metabolic pathways.

1. Irreversible pathways

These are highly exergonic reactions. If two metabolites are metabolically inter-convertible, the pathway from the first to the second must differ from the pathway from the second back to the first. Example of irreversible pathways is Carbohydrate Oxidation, Fatty acid Oxidation, and Heme Biosynthesis.

2. Typical irreversible metabolic pathways

To obtain the product, a metabolic sequence should be essentially irreversible. Examples fro typical metabolic pathways are Glycolysis, Synthesis and Degradation of liver glycogen from (or) to Glucose.

3. Branched metabolic pathways

Some metabolic sequences may have a common path for many steps and then branch into two (or) more separate paths. Examples to the Branched metabolic pathways are, in carbohydrates metabolism, “Glucose-6-Phosphate” act as starting precursor molecule for the following pathways. Glycogen synthesis, EMP pathway (or) Glycolysis, HMP shunt.

Intermediary Metabolism

Metabolism is the term used to describe the interconversion of chemical compounds in the body, the pathways taken by individual molecules, their interrelationships and the mechanisms that regulate the flow of metabolites through the pathways.

All the metabolic activities take place in the Liver. Metabolic pathways fall into THREE categories:

  1. Anabolic pathways-These are involved in the synthesis of larger molecules from smaller molecules. E.g.: Proteins from amino acids; Polysaccharides from monosaccharide.
  2. Catabolic pathways: These are involved in the breakdown of larger molecules into smaller molecules E.g.: Amino acids from Proteins and Monosaccharide from Polysaccharides.
  3. Amphibolic pathways: which occur at the “crossroads” of metabolism, acting as links between the anabolic and catabolic pathways. E.g.: Citric acid cycle.

Pathways that process the Major Products of Digestion

The nature of the diet sets the basic pattern of metabolism. There is a need to process the products of digestion of dietary carbohydrates, lipids, and protein.

These are mainly glucose, fatty acids and glycerol, and amino acids, respectively. All the products o digestion are metabolized to a common product, acetyl~coA, which is then oxidized by the citric acid cycle.

Metabolism can be considered in different types based on the Biomolecule:

  1. Carbohydrate Metabolism
  2. Amino acid Metabolism
  3. Lipids Metabolism
  4. Nucleotide Metabolism
  5. Porphyrin Metabolism
  6. Vitamin Metabolism
  7. Mineral Metabolism

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