Amino Acids and Proteins

Functional Groups in Amino Acids

Amino acids are the building blocks of proteins and contain characteristic functional groups.

• Amino Group (–NH2): Basic group attached to the alpha carbon.

• Carboxyl Group (–COOH): Acidic group attached to the alpha carbon.

• R Group (Side Chain): Variable group that determines the identity and properties of the amino acid.

• Alpha Carbon (Cα): The central carbon atom bonded to the amino group, carboxyl group, hydrogen atom, and R group.

Example: Glycine has a hydrogen atom as its R group, while alanine has a methyl group (–CH3).

Fischer Projections and Stereochemistry of Amino Acids

Fischer projections are two-dimensional representations of three-dimensional molecules, commonly used for amino acids and carbohydrates.

• L- and D- Amino Acids: The configuration is determined by the position of the amino group on the Fischer projection. Most naturally occurring amino acids are L-isomers.

• Allowed Manipulations: Rotating the Fischer projection by 180° in the plane of the paper retains configuration; swapping two groups inverts configuration (forms enantiomer).

• Enantiomers: Non-superimposable mirror images; differ at all chiral centers.

• Chiral Center (Stereocenter): A carbon atom bonded to four different groups.

Example: L-alanine and D-alanine are enantiomers.

Peptide Bond Formation

Peptide bonds link amino acids together to form peptides and proteins.

• Peptide Bond: Formed by a condensation reaction between the carboxyl group of one amino acid and the amino group of another, releasing water.

Equation:

Carbohydrates

Functional Groups in Carbohydrates

Carbohydrates are polyhydroxy aldehydes or ketones.

• Aldehyde Group (–CHO): Present in aldoses (e.g., glucose).

• Ketone Group (C=O): Present in ketoses (e.g., fructose).

• Multiple Hydroxyl Groups (–OH): Attached to the carbon chain.

Fischer Projections and Stereochemistry of Carbohydrates

Fischer projections are used to represent the stereochemistry of carbohydrates.

• Chiral Carbons: Carbons bonded to four different groups; the number of chiral centers determines the number of possible stereoisomers.

• D- and L- Sugars: Determined by the configuration of the chiral carbon furthest from the carbonyl group. D-sugars have the –OH on the right; L-sugars have it on the left.

• Enantiomers: Mirror-image isomers (e.g., D-glucose and L-glucose).

• Diastereomers: Stereoisomers that are not mirror images.

Example: D-glucose and D-galactose are diastereomers.

Cyclic Forms and Anomers

Monosaccharides can cyclize to form ring structures, creating new stereoisomers called anomers.

• α (Alpha) Anomer: The –OH group on the anomeric carbon is trans (opposite side) to the CH2OH group.

• β (Beta) Anomer: The –OH group on the anomeric carbon is cis (same side) to the CH2OH group.

• D- or L- Cyclic Sugars: Determined by the configuration at the chiral center furthest from the anomeric carbon.

Disaccharide Formation and Glycosidic Linkages

Disaccharides are formed by the condensation of two monosaccharides, creating a glycosidic (acetal) linkage.

• Glycosidic Linkage: Covalent bond joining two monosaccharides via an oxygen atom.

• Acetal Formation: The linkage involves the anomeric carbon of one sugar and a hydroxyl group of another.

Example: Sucrose is formed from glucose and fructose via an α,β-1,2-glycosidic bond.

Solution Chemistry

Electrolytes and Non-Electrolytes

Compounds in aqueous solution can conduct electricity (electrolytes) or not (non-electrolytes).

• Electrolytes: Substances that dissociate into ions in water (e.g., NaCl, HCl).

• Non-Electrolytes: Substances that do not produce ions in solution (e.g., sugar, ethanol).

Dissociation Equations for Ionic Compounds

Ionic compounds dissociate into their constituent ions in water.

Example Equation:

Molarity and Dilution Calculations

Molarity (M) is a measure of concentration, defined as moles of solute per liter of solution.

• Formula for Molarity:

• Dilution Equation: Used to calculate the concentration or volume after dilution.

Ionization of Acids and Bases in Water

Acids and bases ionize in water to produce ions.

• Acid Ionization:

• Base Ionization:

Acid/Base Strength and [H3O+]

The strength of an acid or base is related to the concentration of hydronium ions in solution.

• Strong Acids/Bases: Completely ionize in water, producing high [H3O+] or [OH-].

• Weak Acids/Bases: Partially ionize, resulting in lower [H3O+] or [OH-].

Conjugate Acid-Base Pairs

In proton transfer reactions, acids and bases form conjugate pairs.

• Conjugate Acid: The species formed when a base gains a proton.

• Conjugate Base: The species formed when an acid loses a proton.

Example: In the reaction , NH3 is the base and NH4+ is its conjugate acid.

Additional info: This study guide covers foundational concepts in amino acid and carbohydrate chemistry, as well as essential solution chemistry calculations and acid-base theory, all of which are core topics in general chemistry and biochemistry.