Unit 1 : Molecules and their interaction relevant to Biology

Molecules and their interaction relevant to Biology

CSIR means Council of Scientific Industry and Research.  NET means National Entrance Test. UGC means University grant commission.

This unit part has the study material on Basic chemistry, Biomolecules, Metabolic studies, Enzymology and Protein conformation. 

Unit 1 Syllabus
  • Structure of atoms, molecules, and chemical bonds.
  • Composition, structure, and function of biomolecules (carbohydrates, lipids, proteins, nucleic acids, and vitamins).
  • Stabilizing interactions (Van der Waals, electrostatic, hydrogen bonding, hydrophobic interaction, etc.).
  • Principles of biophysical chemistry (pH, buffer, reaction kinetics, thermodynamics, colligative properties).
  • Bioenergetics, Glycolysis, oxidative phosphorylation, coupled reaction, group transfer, biological energy transducers.
  • Principles of catalysis, enzymes and enzyme kinetics, enzyme regulation, mechanism of enzyme catalysis, isozymes.
  • The conformation of proteins (Ramachandran plot, secondary, tertiary and quaternary structure; domains; motif and folds).
  • Conformation of nucleic acids (A-, B-, Z-,DNA), t-RNA, micro-RNA.
  • Stability of protein and nucleic acid structures.
  • Metabolism of carbohydrates, lipids metabolism, amino acids, nucleotides and vitamins.

This is the complete topic wise study material on Unit 1: MOLECULES AND THEIR INTERACTION RELEVANT TO BIOLOGY.

Interconversion of the Nucleotides

During the catabolism of nucleic acids, nucleoside mono- and diphosphates are released. The nucleosides do not accumulate to any significant degree, owing to the action of nucleoside kinases. These include both nucleoside monophosphate (NMP) kinases and nucleoside diphosphate (NDP) kinases. The NMP kinases catalyze ATP-dependent reactions of the type: (d)NMP + ATP <——> (d)NDP + […]

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CSIR UGC NET Life sciences Practice Tests

Biomolecules Practice Test 1

A biomolecule is any molecule that is present in living organisms, including large macromolecules such as proteins, polysaccharides, lipids, and nucleic acids, as well as small molecules such as primary metabolites, secondary metabolites, and natural products. Check this Part I (Part A) section Practice Papers: CSIR UGC NET Compulsory – Model Paper 1 CSIR UGC […]

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basics of bioenergetics - Free energy transformation

Bioenergetics : Study of Free Energy Transformation and its changes

Thermodynamics is the branch of physical chemistry that deals with the energy changes and Biochemical thermodynamics (or biochemical energetics or bioenergetics asit is also called) is the field of biochemistry concerned with the energy transformation and use of energy by living cells (Energy transformation). The chemical reactions occurring in living beings (or biochemical reactions) are […]

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Vitamins - LifeScience

VITAMINS: What are Vitamins and its sources (Basic Guide)

In developed countries, vitamin deficiencies result mainly from poverty, food fads, drugs, or alcoholism. Vitamin toxicity (hypervitaminosis) usually results from taking mega doses of Vitamin A, D, B6, or niacin. Vitamins may be fat soluble (vitamins A, D, E, and K) and water-soluble (B and C Vitamins). The B vitamins include biotin, folate, niacin, pantothenic […]

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chemical bonding

What is Chemical Bonding? Basic Mechanism of Bonding

During the nineteenth century, chemists arranged the then-known elements according to chemical bonding, recognizing that one group (the furthermost right column on the Periodic Table, referred to as the Inert Gases or Noble Gases) tended to occur in elemental form (in other words, not in a molecule with other elements). It was later determined that […]

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Clinical Significances of Purine Metabolism

Clinical problems associated with nucleotide metabolism in humans are predominantly the result of abnormal catabolism of the purines. The clinical consequences of abnormal purine metabolism range from mild to severe and even fatal disorders. Clinical manifestations of abnormal purine catabolism arise from the insolubility of the degradation byproduct, uric acid. Gout is a condition that […]

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What is Enzyme Catalysis ?

What is Enzyme Catalysis ?

What is enzyme ? Enzymes are organic molecules, pretentious in nature that re specialized to catalyze biological reactions. Here these can be termed as “Biological Catalysts” (or) “Biocatalysts” (or) “Middle man of the Nature”. What is Enzyme ? What is the meaning? The name ‘enzyme‘ (enG=in; zymeG=Yeast) literal means “in yeast“. This was referred to […]

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What are Lipids ? How to Classify?

Lipids are involved mainly with long-term energy storage. They are generally insoluble in polar substances such as water. Secondary functions of lipids include structural components (as in the case of phospholipids that are the major building block in cell membranes) and “messengers” (hormones) that play roles in communications within and between cells. Lipids are composed […]

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Catabolism and Salvage of Pyrimidine Nucleotides

Catabolism of the pyrimidine nucleotides leads ultimately to β-alanine (when CMP and UMP are degraded) or β-aminoisobutyrate (when dTMP is degraded) and NH3 and CO2. The β-alanine and β-aminoisobutyrate serve as -NH2 donors in transamination of α-ketoglutarate to glutamate. A subsequent reaction converts the products to malonyl-CoA (which can be diverted to fatty acid synthesis) […]

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Carbohydrate Metabolism - Basic Overview

Carbohydrate Metabolism – Basic Overview

Since all digestible forms of carbohydrates are eventually transformed into glucose, it is important to consider how glucose is able to provide energy in the form of Adenosine triphosphate (ATP) to various cells and tissues. Glucose is metabolized in three stages in carbohydrate metabolism. They are… Glycolysis the Krebs Cycle Oxidative phosphorylation Carbohydrate Metabolism Basic […]

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Transfer RNA (tRNA)

Transfer RNA (abbreviated tRNA) is a small RNA (usually about 74-95 nucleotides) that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. It has a 3′ terminal site for amino acid attachment. This covalent linkage is catalyzed by an aminoacyl tRNA synthetase. It also contains […]

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Nucleic Acids : Basics and Types

Nucleic acids are polymers composed of monomer units known as nucleotides. There are a very few different types of nucleotides. The main functions of nucleotides are information storage (DNA), protein synthesis (RNA), and energy transfers (ATP and NAD). Nucleotides, shown in Figure 1, consist of a sugar, a nitrogenous base, and a phosphate. The sugars […]

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Isoenzymes are Special Proteins with Catalytic activity. Why?

Isoenzymes are Special Proteins with Catalytic activity. Why? (MCQ)

Isoenzymes are proteins with different structure which catalyze the same reaction. Frequently they are oligomers made with different polypeptide chains, so they usually differ in regulatory mechanisms and in kinetic characteristics. From the physiological point of view, isozymes allow the existence of similar enzymes with different characteristics, “customized” to specific tissue requirements or metabolic conditions. […]

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Metabolism of Lipids in Humans

Metabolism of Lipids in Humans (Short Guide)

The major aspects of the metabolism of lipids are involved with Fatty Acid Oxidation to produce energy or the synthesis of lipids which is called Lipogenesis. Lipid metabolism is closely connected to the metabolism of carbohydrates which may be converted to fats. This can be seen in the diagram on the left. The metabolism of […]

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Allosteric Enzymes are Special Modulators. Why?

Allosteric Enzymes are Special Modulators. Why?

A Modulator is a metabolite which, when bound to the allosteric site of an enzyme, alter its kinetic characteristics. The modulators for allosteric enzymes may be either stimulatory or inhibitory. Many enzymes do not demonstrate hyperbolic saturation kinetics, or typical Michaelis-Menten kinetics. Graphs of initial velocity vs. substrate demonstrate sigmoidal dependency of v on S, […]

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Coupling Reactions in Biological Systems

Coupling Reactions in Biological Systems and its Importance

Every day your body carries out many non-spontaneous reactions. As discussed earlier, if a non-spontaneous reaction is coupling reactions to a spontaneous reaction, as long as the sum of the free energies for the two reactions is negative, the coupling  reaction will occur spontaneously. What is a coupled reaction What is its importance in biological […]

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Carbohydrates : Classification and its Basics

Carbohydrates have the general formula [CH2O]n where n is a number between 3 and 6. Note the different CH2O units in Figure 1. Carbohydrates function in short-term energy storage (such as sugar); as intermediate-term energy storage (starch for plants and glycogen for animals); and as structural components in cells (cellulose in the cell walls of […]

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Enzyme Kinetics : Kinetic Study of Enzymatic Reactions

Enzyme Kinetics : Kinetic Study of Enzymatic Reactions

Enzyme kinetics is the study of the chemical reactions that are catalysed by enzymes. In enzyme kinetics, the reaction rate is measured and the effects of varying the conditions of the reaction are investigated. Studying an enzyme’s kinetics in this way can reveal the catalytic mechanism of this enzyme, its role in metabolism, how its […]

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Formation of Deoxyribonucleotides

The typical cell contains 5 to10 times as much RNA (mRNAs, rRNAs and tRNAs) as DNA. Therefore, the majority of nucleotide biosynthesis has as its purpose the production of rNTPs. However, because proliferating cells need to replicate their genomes, the production of dNTPs is also necessary. This process begins with the reduction of rNDPs, followed […]

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Structure of Atoms and Molecules

Most of the Universe consists of matter and energy. Energy is the capacity to do work. Matter has mass and occupies space. All matter is composed of basic elements that cannot be broken down to substances with different chemical or physical properties. Elements are substances consisting of one type of atom, for example Carbon atoms […]

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AMINO ACIDS

Proteins : Basic and Structural organization

Proteins are very important in biological systems as control and structural elements. Control functions of proteins are carried out by enzymes and proteinaceous hormones. Enzymes are chemicals that act as organic catalysts (a catalyst is a chemical that promotes but is not changed by a chemical reaction). Proteins Basic Units: The building block of any […]

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What is Thermodynamics ? Explain the Thermodynamic Laws?

What is Thermodynamics ? Explain the Thermodynamic Laws?

Energy exists in many forms, such as heat, light, chemical energy, and electrical energy. Energy is the ability to bring about change or to do work. Thermodynamics is the study of energy. First Law of Thermodynamics: Energy can be changed from one form to another, but it cannot be created or destroyed. The total amount […]

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Nucleic Acid Stability : Stabilization in biological systems

Nucleic Acid Stability : Stabilization in biological systems

Nucleic acid structures are stabilized by non-covalent intramolecular interactions between the bases. All biological processes involving DNA and RNA require these structures to be in the stable and in the appropriate conformation. It is important to know how nucleic acids form their biologically active states and how these active states are stabilized. Importance of Nucleic […]

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Nucleic Acids Structures

Nucleic Acid Structures: Basic structures of Nucleosides, Nucleotides

In Nucleic acid structures, there are two types of nucleic acid. They are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are polymers of nucleotides linked in a chain through phosphodiester bonds. In biological systems, they serve as information-carrying molecules or, in the case of some RNA molecules, catalysts. This brief review will focus on aspects of the […]

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Clinical Relevance of Tetrahydrofolate

Tetrahydrofolate (THF) is regenerated from the dihydrofolate (DHF) product of the thymidylate synthase reaction by the action of dihydrofolate reductase (DHFR), an enzyme that requires NADPH. Cells that are unable to regenerate THF suffer defective DNA synthesis and eventual death. For this reason, as well as the fact that dTTP is utilized only in DNA, […]

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why water is an universal solvent ?

Why Water is an Universal Solvent?

It can be quite correctly argued that life exists on Earth because of the abundant liquid water. Other planets have water, but they either have it as a gas (Venus) or ice (Mars). This relationship is shown in Figure 1. Recent studies of Mars reveal the presence sometime in the past of running fluid, possibly […]

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pH concpet

pH Concept: What are the Basics and Importance of pH concept

The nature of the solution (acidic, alkaline (or) neutral) can be represented in terms of either hydrogen ion concentration (or) hydroxyl ion concentration. This nature explains the pH concept. In 1909, Sorenson used a logarithmic scale for expressing the H+ concentration. This scale was called “pH”, Where “P” stands for ‘Power’ and ‘H’ for hydrogen […]

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Protein domians and its classification

Protein Domains and Protein Domain Classification

When discussing protein fold we first need to identify the folding unit. Such unit is called a protein domain. This means that when we talk about fold classification we actually mean PROTEIN DOMAIN CLASSIFICATION. Protein domains are the basic building blocks of a protein, Structural Organization of Proteins and they are also the basic evolutionary […]

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biochemical mechanism and properties of ATP

Biochemical Properties and Mechanism of ATP

ATP contains two phosphoanhydride bonds (connecting the 3 phosphates together) and one phosphoester bond (connecting a phosphate to the ribose ring). The pKa’s for the reactions H+ ATP3- —> ATP4- + H+ and HADP2- —> ADP3- + H+ are about 7.0, so the overall charges of ATP and ADP at physiological pH are -3.5 and […]

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Ramachandran plot

Ramachandran Plot : Polypeptide chain conformation

Ramachandran plot is a plot of the torsional angles – phi (φ)and psi (ψ) – of the residues (amino acids) contained in a peptide. In sequence order, φ is the N(i-1),C(i),Ca(i),N(i) torsion angle and ψ is the C(i),Ca(i),N(i),C(i+1) torsion angle. The plot was developed in 1963 by G. N. Ramachandran,  by plotting the φ values […]

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