Structural Biology Notes – 10BT43

Structural Biology Notes Unit 1-Introduction

Unit 2-Structure of Proteins Notes

Unit 4-Notes

Unit 5-Biophysical Techniques-Notes

Unit 6-Spectroscopic Techniques-Notes

Unit 7 and 8-Notes

Unit 3–Notes

Unit 1 Sample Notes

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Levels of Molecular Organization
Animal and plant cells contain approximately 10000 different kinds of molecules referred to as biomolecules. One of these, water, may constitute 50-95% of a cell’s content by weight, while ions such as sodium, potassium and calcium may account for another 1%. Almost all other kinds of molecules are organic which are principally composed of six elements: C,H2,O2,N2,P and S.  [Refer PDF FIle to view in a proper format]

The properties of one element carbon are responsible for the almost infinite variety of organic molecules. Carbon atoms can form 4 strong covalent bonds either to other carbon atoms or to atoms of other elements. Of central importance in organic chemistry are the hydrogen and carbon containing compounds called hydrocarbons. Although hydrocarbons are relatively unimportant in living organisms, but several aspects of their chemistry are relevant to the biochemistry.

The number of compounds that contain carbon are many times greater than the number of compounds that do not contain carbon. Organic molecules containing thousands of atoms the arrangement of atoms in molecules can be very complicated hence to determine the structure of compounds. The answer to this question came to August Kekule. Carbon atoms can form long chains of thousands of atoms or rings of all sizes; the chains and rings have branches and crosslinks. Each different arrangement of atom corresponds to a different compound and each compound has its own characteristic set of chemical and physical properties. It is not surprising that more than 10 million compounds of carbon are known today and that this number is growing by half a million per year.
In 1990, the journal science selected diamond, one of the allotropic forms of carbon as the molecule of the year and a runner-up was another newly developed allotrope of arbon, C60 Buckminsterfullerene. In 1916, two kinds of chemical bonds were described: the ionic bond by Walther Kossel (in Germany) and the covalent bond by G.N.Lewis (University of California). The introduction of quantum mechanics in 1926 by Erwin Schrodinger (of university of Zurich) caused a tremendous change in ideas about how molecules are formed.
Atom has a positively charged nucleus surrounded by electrons arranged in concentric shells or energy levels called orbit. There is a maximum number of electrons that can be accommodated in each shell: 2 in 1st shell, 8 in 2nd shell, 8 or 18 in 3rd shell and so on using. The greatest stability is reached when the outer shell is full, as in noble gases. Both ionic and covalent bonds arise from the tendency of atoms to attain a stable configuration of electrons.
Structure of Water
Water (H2O) is composed of 2 atoms of hydrogen and 1 atom of oxygen. Each hydrogen atom is linked to 2 oxygen atom by single covalent bond . Since oxygen is more electronegative than hydrogen , there is a separation of charge within the molecule .i.e. asymmetrical and have a band geometry with a bond angle of 104.5 ° due to unbalanced distribution of charge, becomes dipolar. Since water has got opposite charges on two points and due to large difference in electronegativity of hydrogen and oxygen the hydrogen of water molecules are attracted to unshared pairs of electrons of another molecule. This non-covalent relationship is called hydrogen bond, which is due to strong electrostatic action rather than a true bond.
In addition to hydrogen bonds, the water interact with other molecules through three more types of non-covalent interactions. The electrostatic interaction causes hydration of ions and solvation of charged species in water. Van der waals forces are weak transient electrostatic interactions between permanent or induced dipoles. Hydrophobic interactions when water mixed with non-polar substances, they coalesce into droplets because water-water interactions are stronger than non-polar interactions. Water has a variety of unusual properties because of attractions between two polar regions. The slightly negative regions of one molecule are attracted to the slightly positive regions of nearby molecules, forming a hydrogen bond. Each water molecule can form hydrogen bonds with up to four neighbors.



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There are three major types of biological macromolecules in living systems.
• Carbohydrates
• Nucleic acids
• Proteins
Though treated separately in different segments, the principles governing the organization of three-dimensional structure are common to all of them.
• Each of these macromolecules are made up of monomer units:
• monosaccharide — for carbohydrate
• nucleotide — for nucleic acids
• amino acid — for proteins
Macromolecular interactions involving proteins:
• Quaternary structure refers to proteins formed by association of polypeptide subunits.
Individual globular polypeptide subunits may associate to form biologically active oligomers.
• The subunits may be identical or they may be different.
• Subunit interaction is entirely Noncovalent between complementary regions on the subunit surface and involve following interaction:
– Hydrophobic
– Hydrogen bonding
– Electrostatic (ionic)
• If covalent links exist (such as disulfide bridges) then the structure is not considered quaternary. In proteins with quaternary structure the disaggregated subunits alone are generally biologically inactive.
• Examples of quaternary structure, Hemoglobin.
• Hemoglobin is composed of four subunits of two types, alpha and beta, represented as

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• Triose phosphate isomerase is a dimer of identical subunits.
Quaternary structure in proteins is the most intricate degree of organization considered to be a single molecule.
Incorporation of nonprotein components into proteins
• The resulting species are called conjugated proteins.
Classification of proteins by composition divide proteins into two categories.
• Simple proteins consist of only polypeptide.
• Conjugated proteins also contain a nonprotein moiety which frequently plays a role in biological function.
– It may participate in function directly.
– It may influence the shape of the protein.
Many different kinds of compound /macromolecules are found in conjugation/interaction with proteins. A few examples are:
• Protein-Carbohydrate
• Protein-lipid
• Protein DNA
• Protein-protein
• Protein-Heme



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