We have spent much of thesemester interweaving the idea of how important structu

Question

We have spent much of thesemester interweaving the idea of how important structure is to function at the molecular level. Discuss this idea in depth by following the outline below,gradually developing your discussion from simple and small structures to larger and more complex ones.

1. Basic Chemistry—atoms,valence shells (electrons), types of bonds, polar vs.nonpolar molecules

2. Functional Groups—what functional groups result from the interactions and structures discussed in #1?
Give examples with some general properties of the functional groups you choose to use. Discuss the importance of hydrogen bonding.

3. Implications/Effects of #1 and #2 in the following

a. Water b. Carbon (why so important to life c. pH d. membranes e. enzymes f. other proteins (non-­enzyme) g. nucleic acids (base pairing in various processes) h. cell cycle i. gene expression (especially the initiation of transcription)

Explanation / Answer

The most common atoms found in biological molecules are

Carbon

Oxygen

Hydrogen

Nitrogen

Phosphorous

Sulfur

2,4, and 6

Functional groups:

Hydroxyl group

R

Polar

Occur in alcohols, and participate in ester and ether linkages

R – CO - R

Polar

Occur in aldehydes and ketones

Carboxyl group

R - COOH

Acidic, they can release H+ ions into solutions

Occur in acids, and form ester linkages with alcoholic group

Methyl group

R – CH3

Non-polar

Amino group

R – NH2

Accepts H+ ions and hence, are considered basic

Amino acids

Phosphate group

R – 0 – H2PO3

Acidic, they can release H+ ions into solutions

Nucleotides, as NTP, NdP, and NMP, organic and inorganic phosphate, energy rich compounds like creatine phosphate

Sulhydryl group

R - SH

Polar

Amino acids

Hydrogen bonding: It is an electrostatic attraction between polar groups with Hydrogen attached to a highly electronegative atom. Hydrogen bonds occur in either intramolecular or intermolecular. Hydrogen bonds are weaker than covalent bonds, but molecules generally establish a large number of hydrogen bonds, the cumulative effect of the total number of hydrogen bonds holds the bonding molecules stronger.

The properties of hydrogen bonding are due to unequal sharing of electrons between Hydrogen and a highly electronegative atom like oxygen or nitrogen. Hydrogen bond is directional (it has polarity) and is strong, it produces interatomic distances shorter than that of van der Waals. Most of the properties of water are due to the hydrogen bonding between oxygen and hydrogen atoms in it.

Properties of water:

A water molecule is composed of two hydrogen atoms and one oxygen atom. Each of the two hydrogen atoms share a pair of electrons with oxygen atom. The sharing of electrons is through overlap of the 1s orbitals of the hydrogen atoms with two hybridized sp3 orbitals of the oxygen atom.

The bond angle of H – O – H is 104.5o . The average hydrogen – oxygen interatomic distance is 0.0965 am. Due to this arrangement of water molecules, water molecule is asymmetric. The diameter of water molecule is about 2.75 Ao and is smaller than most other common atmospheric molecules like O2, N2, CO2. The density of water vapor is 62% of the density of dry air. The molecular mass of water is 18.015 g/mol.

Oxygen atom is highly electronegative and tends to attract the single electrons from hydrogen atoms, leaving the hydrogen atoms bare. Due to this, each of the two hydrogen atoms has partial positive charges, and oxygen atom has a partial local negative charge, located in the zone of the unshared orbitals. Thus, water has an electric dipole, though the net charge is zero.

Due to this electric dipole, two water molecules that are close together tend to attract each other. The attraction is between the partially negative charged oxygen and partial positive charge on hydrogen atom of adjacent water molecule. This leads to further redistribution of the electronic charges, which strengthens the interaction.

Due to tetrahedral arrangement of the electrons (bond angle 109.47o about the oxygen tom, each water molecule can form bonds with four neighboring water molecules. The high reactivity of water is due to this extensive hydrogen bond forming ability.

Carbon: Carbon can form covalen bonds with four different atoms. It can form covalent bonds with carbon also. Carbon can form double or triple bonds also with another carbon. The four groups attached to carbon are in different geometrical arrangement, which makes a molecule with different shape an different properties. It can form isomers.

Carbon

Oxygen

Hydrogen

Nitrogen

Phosphorous

Sulfur

2,4, and 6

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