Organic Chemistry: Amines and Amino Acids - SS3 Chemistry Past Questions and Answers - page 3

Amino Acids: Structure, Classification, and Properties:

Structure:

Amino acids are organic compounds that serve as the building blocks of proteins. They consist of a central carbon (alpha carbon) bonded to four groups: an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom (H), and a variable side chain (R group). The R group differs among different amino acids, giving each amino acid its unique properties and characteristics.

Classification:

Amino acids can be classified based on the nature of their R groups:

1.    Nonpolar Amino Acids: These amino acids have hydrophobic R groups, usually composed of hydrocarbon chains, and are not easily soluble in water.

Example: Alanine (Ala), Valine (Val), Leucine (Leu)

2.    Polar Amino Acids: These amino acids have hydrophilic R groups, containing functional groups such as -OH or -NH2, and are generally soluble in water.

Example: Serine (Ser), Threonine (Thr), Asparagine (Asn)

3.    Charged Amino Acids: These amino acids have hydrophilic R groups with full or partial charges, making them highly soluble in water and involved in ionic interactions.

a.    Positively Charged (Basic) Amino Acids: R groups contain amino groups with a positive charge at physiological pH.

Example: Lysine (Lys), Arginine (Arg), Histidine (His)

b.    Negatively Charged (Acidic) Amino Acids: R groups contain carboxyl groups with a negative charge at physiological pH.

Example: Aspartic Acid (Asp), Glutamic Acid (Glu)

Properties:

1.    Amphoteric Nature: Amino acids act as both acids (due to the carboxyl group) and bases (due to the amino group), making them amphoteric substances.

2.    Zwitterions: In a neutral pH environment, amino acids exist as zwitterions, which are dipolar ions with both positive and negative charges on the same molecule.

3.    Isoelectric Point (pI): The pH at which an amino acid is electrically neutral (equal number of positive and negative charges) is known as the isoelectric point.

Significance in Protein Formation:

Amino acids are the fundamental units that link together through peptide bonds to form polypeptide chains, which then fold and interact to create proteins. The sequence and arrangement of amino acids in a polypeptide chain dictate the protein's structure and function, including enzymatic activity, structural support, and molecular recognition.

Examples of Amino Acids in Biological Systems:

1.    Glycine (Gly): Glycine is the simplest amino acid and is nonpolar. It plays a significant role in collagen, a fibrous protein that provides structural support to connective tissues.

2.    Serine (Ser): Serine is a polar amino acid that acts as a phosphorylation site in many signalling pathways, regulating protein function and cell signalling.

3.    Lysine (Lys): Lysine is a basic amino acid with a positive charge, crucial for histone proteins' role in DNA packaging and gene regulation.

4.    Glutamic Acid (Glu): Glutamic acid is an acidic amino acid involved in neurotransmission as a major excitatory neurotransmitter in the central nervous system.

In conclusion, amino acids are the building blocks of proteins and play diverse roles in biological systems. Their unique structure, classification based on side chains, and properties significantly influence protein formation and function. The variation in R groups among amino acids allows proteins to exhibit a wide range of structures and functions, making them essential for life's processes.

A peptide bond is a covalent bond that forms between the amino group of one amino acid and the carboxyl group of another amino acid during protein synthesis, resulting in the formation of a peptide chain.

The primary structure of a protein refers to the linear sequence of amino acids in the polypeptide chain, which is determined by the genetic code.

The secondary structure of a protein is formed by hydrogen bonding between the amino acid side chains, leading to the formation of alpha-helices and beta-sheets.

Chaperone proteins, also known as molecular chaperones, play a crucial role in assisting newly synthesised proteins to fold correctly and preventing the formation of non-functional protein aggregates.

Enzymes are a type of protein that act as biological catalysts, speeding up chemical reactions in cells without being consumed in the process. They lower the activation energy required for reactions to occur, thereby increasing the reaction rate.

The correct order of protein structure, from simplest to most complex, is primary structure, secondary structure, tertiary structure, and quaternary structure.

Peptides and Proteins: Structure, Classification, and Functions

Structure and Classification:

Peptides and proteins are composed of amino acids linked together through peptide bonds. A peptide is a short chain of amino acids, while a protein is a larger, more complex molecule consisting of one or more polypeptide chains. Peptides can be classified based on their length:

1.    Dipeptide: Two amino acids linked together.

2.    Tripeptide: Three amino acids linked together.

3.    Oligopeptide: A short chain of amino acids.

4.    Polypeptide: A long chain of amino acids, typically with 50 or more residues.

5.    Protein: A complex molecule consisting of one or more polypeptide chains.

Functions:

Proteins are involved in a wide range of biological functions, including:

1.    Enzymes: Proteins act as catalysts, speeding up biochemical reactions in cells.

2.    Structural Support: Proteins provide mechanical support and shape to cells and tissues.

3.    Transport: Certain proteins transport molecules and ions across cell membranes.

4.    Hormones: Proteins act as chemical messengers, regulating various physiological processes.

5.    Immunity: Antibodies are specialised proteins that recognize and neutralise foreign substances.

6.    Receptors: Proteins on cell surfaces detect and respond to external signals.

7.    Storage: Proteins can store essential nutrients and ions in cells.

8.    Contractile Proteins: Proteins enable muscle contraction.

9.    Gene Regulation: Some proteins regulate gene expression by controlling transcription and translation.

Protein Structure:

Proteins possess four levels of structure:

1.    Primary Structure: The linear sequence of amino acids in the polypeptide chain. This sequence is determined by the genetic code.

2.    Secondary Structure: Localised folding of the polypeptide chain into specific patterns, such as alpha helices and beta sheets, stabilised by hydrogen bonding between the backbone atoms.

3.    Tertiary Structure: The overall three-dimensional folding of the entire polypeptide chain, driven by various interactions like hydrophobic interactions, hydrogen bonds, disulfide bridges, and ionic interactions.

4.    Quaternary Structure: Present in proteins with multiple polypeptide chains, it refers to the arrangement of these subunits to form the final functional protein complex.

Importance of Protein Structure in Function:

The unique three-dimensional structure of a protein determines its function. Proper folding is essential for a protein to be functional. Misfolded or denatured proteins often lose their biological activity. The specificity of a protein's structure allows it to interact specifically with other molecules, such as substrates, ligands, or other proteins, to perform its designated function.

Examples of Protein Functions:

1.    Enzymes: DNA polymerase is a critical enzyme involved in DNA replication.

2.    Structural Support: Collagen provides structural support to skin, bones, and connective tissues.

3.    Transport: Haemoglobin transports oxygen in red blood cells.

4.    Hormones: Insulin regulates glucose metabolism.

5.    Immunity: Antibodies defend against pathogens and foreign substances.

6.    Receptors: Rhodopsin is a light-sensitive protein in the retina involved in vision.

7.    Contractile Proteins: Actin and myosin are essential for muscle contraction.

8.    Gene Regulation: Transcription factors control gene expression.

In conclusion, peptides and proteins play crucial roles in biological systems. Peptides are short chains of amino acids, while proteins are larger and more complex molecules. Proteins exhibit diverse functions due to their specific three-dimensional structures, allowing them to participate in various cellular processes. Understanding the structure, classification, and functions of peptides and proteins is vital in comprehending the molecular basis of life and the development of therapeutic interventions for diseases related to protein dysfunction.