GPAT Organic Chemistry Syllabus

Why are 19 of the 20 standard amino acids optically active, and what configuration do they have?

Their alpha carbon is a chiral center (four different groups), making them optically active. Naturally occurring amino acids have the L-configuration. Glycine is the exception (achiral, R = H).

Classify amino acids by side-chain polarity into the four main groups.

(1) Nonpolar/hydrophobic, (2) polar uncharged, (3) acidic (negatively charged, e.g., Asp, Glu), and (4) basic (positively charged, e.g., Lys, Arg, His).

What is a peptide bond and which functional groups form it?

A peptide bond is an amide linkage formed between the carboxyl group of one amino acid and the amino group of another, with loss of a water molecule (condensation).

Define the primary structure of a protein.

The primary structure is the linear sequence of amino acids in the polypeptide chain, held together by covalent peptide bonds.

What are the two main types of secondary structure in proteins and what stabilizes them?

Alpha-helix and beta-pleated sheet. Both are stabilized by hydrogen bonds between backbone carbonyl (C=O) and amide (N-H) groups.

Define the tertiary structure of a protein and list the bonds that stabilize it.

Tertiary structure is the overall 3D folding of a single polypeptide. Stabilized by hydrophobic interactions, hydrogen bonds, ionic (salt) bridges, and covalent disulfide bonds.

What is the quaternary structure of a protein? Give an example.

The arrangement of two or more polypeptide subunits into a functional multi-subunit protein. Example: hemoglobin (two alpha and two beta subunits).

What is protein denaturation and which structural level is preserved?

Denaturation is the loss of secondary, tertiary, and quaternary structure (and function) due to heat, pH, or chemicals, without breaking peptide bonds. The primary structure remains intact.

Which disulfide bond forms between two cysteine residues, and what role does it play?

A covalent S-S (disulfide) bond forms by oxidation of two cysteine -SH groups. It cross-links and stabilizes tertiary/quaternary protein structure.

Name the colorimetric test used to detect peptide bonds in proteins and its positive result.

The biuret test; a positive result gives a violet/purple color in the presence of two or more peptide bonds with Cu2+ in alkaline solution.

What does the ninhydrin test detect and what color is produced?

Ninhydrin detects free alpha-amino acids (and amines); it produces a purple/blue (Ruhemann's purple) color; proline gives a yellow color.

Which amino acids are aromatic, and which one absorbs UV light at ~280 nm most strongly?

Aromatic amino acids: phenylalanine, tyrosine, and tryptophan. Tryptophan absorbs most strongly near 280 nm, used to estimate protein concentration.

Which amino acid is technically an imino acid and why is it conformationally restrictive?

Proline; its side chain forms a ring with the alpha-amino nitrogen (secondary amine/imino), restricting rotation and disrupting alpha-helices (helix breaker).

What is the Henderson-Hasselbalch relationship used for with amino acids?

pH = pKa + log([conjugate base]/[acid]); used to determine the ratio of protonated/deprotonated forms of ionizable groups and to calculate buffering and pI.

What are polycyclic aromatic hydrocarbons (PAHs)?

PAHs are organic compounds composed of two or more fused aromatic (benzene) rings containing only carbon and hydrogen, with delocalized pi-electron systems.

What is the simplest polycyclic aromatic hydrocarbon and its molecular formula?

Naphthalene, C10H8 - two fused benzene rings sharing a common edge.

Compare the structures of anthracene and phenanthrene.

Both are C14H10 with three fused rings. Anthracene has the three rings fused in a linear (straight) arrangement; phenanthrene has them in an angular (bent) arrangement.

How are the carbon positions of naphthalene labeled, and which is more reactive in electrophilic substitution?

The positions are alpha (1,4,5,8) and beta (2,3,6,7). The alpha (1-) position is generally more reactive in electrophilic aromatic substitution because the intermediate is more stabilized.

What product forms when naphthalene undergoes nitration, and at which position?

Naphthalene undergoes nitration mainly at the alpha (1-) position to give 1-nitronaphthalene.

How does sulfonation of naphthalene illustrate kinetic vs thermodynamic control?

At low temperature (~80degC) the kinetic product 1-naphthalenesulfonic acid (alpha) dominates; at high temperature (~160degC) the thermodynamic product 2-naphthalenesulfonic acid (beta) dominates.

What are the major products of catalytic/oxidative reactions of naphthalene: hydrogenation and oxidation?

Partial hydrogenation gives tetralin (1,2,3,4-tetrahydronaphthalene) and full gives decalin (decahydronaphthalene). Vigorous oxidation (e.g., V2O5) gives phthalic anhydride.

Why are some PAHs of toxicological concern, and give a notable carcinogenic example.

Many PAHs are mutagenic/carcinogenic because they are metabolized to reactive epoxide/diol-epoxide intermediates that bind DNA. Benzo[a]pyrene is a well-known potent carcinogen.

What is Huckel's rule for aromaticity?

A planar, cyclic, fully conjugated molecule is aromatic if it contains (4n+2) pi electrons, where n is a non-negative integer (0,1,2,...).

How many pi electrons does naphthalene have, and does it obey Huckel's rule?

Naphthalene has 10 pi electrons (4n+2 with n=2), so it satisfies Huckel's rule for the fused system and is aromatic.

What is the Haworth synthesis used to prepare?

The Haworth synthesis is a multistep route to prepare naphthalene (and substituted naphthalenes) starting from benzene and succinic anhydride via Friedel-Crafts acylation, reduction, cyclization, and aromatization.

Why is the resonance/delocalization energy per ring of naphthalene less than that of benzene?

Naphthalene's pi electrons are shared across the fused system unevenly, so its total resonance energy (~61 kcal/mol) is less than twice benzene's (~36 kcal/mol each), making naphthalene more reactive than benzene.

What is the difference between aliphatic and aromatic compounds?

Aliphatic compounds are open-chain or non-aromatic ring hydrocarbons (and derivatives) with localized bonds. Aromatic compounds contain a cyclic, planar, conjugated (4n+2) pi-electron system giving special stability.

What is a homologous series? Give one characteristic property.

A homologous series is a family of organic compounds with the same general formula and functional group, differing by a -CH2- unit. Members show a gradual gradation in physical properties (e.g., boiling point) with increasing molecular mass.

What is tautomerism, and name a common example relevant to organic functional classes.

Tautomerism is a type of isomerism where isomers interconvert by migration of a proton and shifting of a double bond. The classic example is keto-enol tautomerism (ketone/aldehyde <-> enol).

What is the difference between a peptide, polypeptide, and protein?

A peptide is a short chain of amino acids (typically <~50 residues); a polypeptide is a longer single chain; a protein is one or more polypeptides folded into a functional 3D structure.