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): A basic group attached to the alpha carbon.

• Carboxyl Group (–COOH): An acidic group also 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 Projection: A two-dimensional representation of a molecule showing the configuration of chiral centers.

• L and D Amino Acids: The L-form is the naturally occurring configuration in proteins. The position of the amino group on the left (L) or right (D) in the Fischer projection determines the designation.

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

• Enantiomers: Non-superimposable mirror images (L and D forms).

• Stereocenter/Chiral Carbon: A carbon atom bonded to four different groups.

Example: All standard amino acids except glycine are chiral.

Peptide Bond Formation

• Dipeptide Formation: Two amino acids join via a condensation reaction, forming a peptide bond (amide linkage) and releasing water.

Carbohydrates

Functional Groups in Carbohydrates

• Hydroxyl Groups (–OH): Present on most carbons.

• Aldehyde (–CHO) or Ketone (C=O): Monosaccharides are classified as aldoses or ketoses based on the presence of these groups.

Fischer Projections and Stereochemistry of Carbohydrates

• Fischer Projection: Used to represent the configuration of sugars.

• Chiral Carbons: Carbons bonded to four different groups; the number of chiral centers increases with sugar length.

• D and L Sugars: Determined by the position of the –OH group on the penultimate (second-to-last) carbon; right = D, left = L.

• Relationship Between Projections: Same compound, enantiomers, or diastereomers can be determined by comparing configurations at each chiral center.

Cyclic Monosaccharides and Anomers

• Cyclic Forms: Monosaccharides can cyclize to form rings (pyranose or furanose forms).

• D or L in Cyclic Form: Configuration is based on the original Fischer projection.

• α (Alpha) and β (Beta) Anomers: Differ in the position of the anomeric –OH group relative to the CH2OH group.

Example: In D-glucose, the β-anomer has the anomeric –OH group on the same side as the CH2OH group in the Haworth projection.

Disaccharide Formation and Glycosidic Linkages

• Disaccharide Formation: Two monosaccharides join via a condensation reaction, forming a glycosidic (acetal) linkage and releasing water.

• Glycosidic Linkage: The specific carbons involved (e.g., 1→4) and the α or β configuration must be identified.

Solution Chemistry

Electrolytes and Non-Electrolytes

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

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

Dissociation Equations for Ionic Compounds

• Dissociation: Ionic compounds separate into their constituent ions in water.

Example:

Molarity and Dilution Calculations

• Molarity (M): The number of moles of solute per liter of solution.

• Dilution: The process of reducing the concentration of a solution by adding more solvent.

Ionization of Acids and Bases in Water

• Acid Ionization: Acids donate protons (H+) to water, forming hydronium ions (H3O+).

• Base Ionization: Bases accept protons or release hydroxide ions (OH−).

Examples:

Acid/Base Strength and [H3O+]

• 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

• 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 of acetic acid with water:

• Acid: CH3COOH

• Conjugate Base: CH3COO−

• Base: H2O

• Conjugate Acid: H3O+

Summary Table: Key Concepts

Additional info: Academic context and examples have been added to expand on the brief points in the original study guide, ensuring the notes are self-contained and suitable for exam preparation.