Midterm 3 Study Guide: Carbohydrates and Proteins in Organic Chemistry

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Carbohydrates

Wedge-Dash Structure to Fischer Projection (and Vice Versa)

Organic chemists often use different structural representations to convey stereochemistry. Wedge-dash structures show three-dimensional orientation, while Fischer projections are a two-dimensional representation commonly used for carbohydrates.

Wedge-dash notation: Solid wedges indicate bonds coming out of the plane; dashed wedges indicate bonds going behind the plane.
Fischer projection: Vertical lines represent bonds going away from the viewer; horizontal lines represent bonds coming toward the viewer.
Conversion: To convert, orient the molecule so the main carbon chain is vertical, then assign groups according to their spatial arrangement.
Example: D-glucose can be drawn in both wedge-dash and Fischer projection forms.

Linear Form Carbohydrate to Haworth/Chair Form (and Vice Versa)

Carbohydrates exist in equilibrium between their linear (open-chain) and cyclic (ring) forms. The Haworth projection is used for cyclic forms, and the chair form is used for six-membered rings (pyranoses).

Linear form: Shows all carbons in a chain, with functional groups attached.
Haworth projection: Depicts the ring structure, with substituents above or below the plane.
Chair form: More accurate for six-membered rings, showing axial and equatorial positions.
Conversion: Cyclization occurs via nucleophilic attack of a hydroxyl group on the carbonyl carbon, forming a hemiacetal.
Example: D-glucose cyclizes to form α- and β-glucopyranose.

Carbohydrate Mechanisms: Hemiacetal-like and Epimerization-like Mechanisms

Carbohydrate reactions often involve hemiacetal formation and epimerization. Mechanisms are typically illustrated using Fischer projections.

Hemiacetal formation: The carbonyl group reacts with a hydroxyl group to form a ring.
Epimerization: Change in configuration at a single stereocenter, often via enolization.
Example: Glucose to mannose conversion involves epimerization at C-2.

Carbohydrate Oxidation/Reduction, Chain-Lengthening/Shortening

Carbohydrates can undergo oxidation (to form acids), reduction (to form alcohols), and chain-lengthening/shortening reactions. Equilibrium and acetal formation play important roles.

Oxidation: Aldoses can be oxidized to aldonic acids or aldaric acids.
Reduction: Aldoses can be reduced to alditols.
Chain-lengthening: Kiliani-Fischer synthesis adds a carbon to the chain.
Chain-shortening: Wohl degradation removes a carbon from the chain.
Equilibrium: Ring and chain forms interconvert; acetal formation stabilizes the ring.
Example: Glucose oxidation yields gluconic acid; reduction yields sorbitol.

Proteins and Amino Acids

Amino Acid Synthesis (Three Ways to Make Amino Acids)

Amino acids can be synthesized by several methods in organic chemistry. The three main methods are:

Strecker synthesis: Involves reaction of an aldehyde with ammonium and cyanide, followed by hydrolysis.
Gabriel synthesis: Uses phthalimide to generate primary amines, which can be converted to amino acids.
Reductive amination: Aldehydes or ketones react with ammonia and are reduced to form amino acids.
Example: Strecker synthesis of alanine from acetaldehyde.

Abbreviation to Structure (and Back) for Peptides

Peptides are composed of amino acids, which are often represented by three-letter abbreviations. Understanding how to convert between abbreviations and structures is essential.

Abbreviations: Ala (Alanine), Val (Valine), Gly (Glycine), etc.
Structure: Draw the peptide backbone, connect amino acid side chains according to sequence.
Example: Ala-Val is a dipeptide with alanine and valine linked by a peptide bond.

Peptide Synthesis

Peptide synthesis involves forming amide bonds between amino acids. Protecting groups are often used to prevent unwanted reactions.

Activation: Carboxyl group is activated (e.g., using DCC) to react with amino group.
Protecting groups: Fmoc, Boc, and others are used to protect amino or carboxyl groups.
Example: Synthesis of Ala-Val using DCC as a coupling agent.

Amino Acid Mechanisms

Mechanisms involving amino acids include acid-base reactions, nucleophilic substitution, and peptide bond formation. Mechanistic details are often illustrated in problem sets and lectures.

Acid-base: Amino acids can act as both acids and bases due to their amino and carboxyl groups.
Nucleophilic substitution: Amino group attacks activated carboxyl group to form peptide bond.
Example: Mechanism for peptide bond formation using DCC.

Key Equations and Mechanisms

Hemiacetal formation:
Strecker synthesis:
Peptide bond formation: