Nitrogen Compounds Revision

Nitrogen Compounds revision PCl5, reflux then KCN (alc), heat

interactions that holds these structures in their native conformation

6.

β-pleated sheet

Carboxylic Acid/ Excess conc NH3 Sealed tube, ethanol, reflux

1.

HCl/H2SO4 (aq) reflux

NaOH (aq) reflux

Steps to transform: • Methylbenzene to 4-aminobenzoic acid

i. Conc HNO , conc H SO , 30’C ii.KMnO , acidified with H SO 3

4

2

4

2

4

iii. Reflux with Sn, followed bt NaOH

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CH3CH2CH2OH to CH3CH2CH(OH)COOH

i. K Cr O 2

2

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(aq), heat, immediate distillation

ii. HCN in small amount of KCN iii. HCl (aq), reflux 2.

Amines are weak bases

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Due to the availability of a lone pair of electrons on the nitrogen atom able to form a dative bond with a proton (H+)

• 3.

R-NH2 + H2O → R-NH3+ + OH•

Relative basicities

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Ammonia < 1° Amine < 2° Amine Increasing base strength, decreasing pKb →

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Electron-donating R groups increase the basicity by i. Increasing the electron density of the lone pair electrons on N, making it more available to accept a proton, and

7.

ii.Lowering

the positive charge on N in the conjugate and so stabilises it, therefore favouring the forward reaction to produce more OH-

4.

5.

• 8.

Acid-base properties of amino acids • Amino acids are less acidic than most carboxylic acids, and less basic than most amines

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Acidic part is the –NH3+ group, basic part is the –COO- group

• • •

Forms dipolar ions called zwitterions Amphoteric Pre-dominant form depends on the pH of the solution

Define:

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Peptide bond – When two amino acids join together Tripeptide – Three amino acids join together Primary structure – Sequence of amino acids in the polypeptide chain Secondary structure – Segments of the polypeptide backbone orientate into a regular pattern through hydrogen bonding Tertiary structure – Three-dimensional structure of the polypeptide Quaternary structure - Characteristic manner in which the individually folded polypeptide subunits are grouped

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Denaturation – Disruption in the secondary, tertiary and quaternary structures by the breaking of the non-covalent

α-helix • •

Stabilized by hydrogen-bonds between CO and NH groups in adjacent strands May be antiparallel or parallel Side chains on successive AA residues appear on opposite sides of the sheet

Right-hand screw NH group in each peptide link is hydrogen-bonded to the CO group of the fourth following peptide link 3.6 amino acids per turn

The tertiary structure of a protein refers to its three-dimensional structure of the polypeptide. • Hydrogen bonding i. Between polar side chains (-OH, -NH, =O, =NR groups) • van der Waals forces i. Electrostatic interactions among permanent or induced dipoles ii. Hydrophobic interactions – contributed by nonpolar side chains which cluster away from water to avoid destabilisation of side chains (a hydrophobic core is formed) • Ionic interactions i. Between two oppositely charged side chains (e.g. Asp and Lys) – usually groups that ionize in water • Disulphide bridges i. Between cysteine residues with the thiol (-SH) side chain

ii.R-SH + HS-R’ + [O] → R-S-S-R + H O 2

9.

The quaternary structure of protein refers to the spatial arrangements and association of the polypeptide subunits of proteins. • Haemoglobin as an example i. Formed from four polypeptide chains

10. Denaturation of proteins by •

Effect of Temperature i. Heating causes an increase in the thermal vibration of the molecule http://education.helixated.com An Open Source Education Project

2 | Page ii. Hydrogen bonding is disrupted

iii.Proteins denature and thus unfold •

Effect of pH i. If pH is lowered far below pI, the protein will only contain positive charges ii. Like charges repel each other and cause the denaturation of proteins iii. Likewise for high pH

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Effect of Heavy Metal Ions

i. Heavy

metal ions (Pb2+, Cd2+, etc) are positively charged ii. Compete with positively charged groups for attraction with negatively charged groups iii. Also bond with –SH groups (especially Hg2+) and disrupt disulphide bridges iv. Resident metal ions in certain proteins may also be displaced 11. Phenomena of denaturation: • In denaturation, solubility is drastically decreased, as occurs when egg white is cooked and the albumins unfold and coagulate to an insoluble white mass. • Milk is curdled by bacteria when it sours as the pH is changed