Chapter 5: Macromolecules – Proteins and Nucleic Acids

Macromolecules

Introduction to Macromolecules

Macromolecules are large, complex molecules essential for life, including proteins, nucleic acids, carbohydrates, and lipids. This chapter focuses on proteins and nucleic acids, their structure, function, and importance in biological systems.

Proteins: Structure and Function

Overview of Proteins

Proteins are polymers made from 20 different amino acids. Their diverse structures result in a wide variety of functions within living organisms.

• Polypeptide vs. Protein: A polypeptide is a single linear chain of amino acids, while a protein is one or more polypeptides folded into a functional shape.

• Amino Acids: The building blocks of proteins, each with a central (α) carbon, an amino group, a carboxyl group, a hydrogen atom, and a unique side chain (R group).

Structure of Amino Acids

Each amino acid has a common structure but differs in its side chain (R group), which determines its properties.

• Central (α) Carbon: The central atom to which all groups are attached.

• Amino Group: $\ce{-NH_2}$

• Carboxyl Group: $\ce{-COOH}$

• R Group: Variable side chain that determines the amino acid's characteristics.

Classification of Amino Acids

Amino acids are classified based on the properties of their side chains:

• Nonpolar Side Chains (Hydrophobic): Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline

• Polar Side Chains (Hydrophilic): Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine

• Electrically Charged Side Chains (Hydrophilic):

  • Acidic (Negatively Charged): Aspartic acid, Glutamic acid

  • Basic (Positively Charged): Lysine, Arginine, Histidine

Group	Amino Acids	Properties
Nonpolar	Gly, Ala, Val, Leu, Ile, Met, Phe, Trp, Pro	Hydrophobic
Polar	Ser, Thr, Cys, Tyr, Asn, Gln	Hydrophilic
Acidic	Asp, Glu	Negatively charged, hydrophilic
Basic	Lys, Arg, His	Positively charged, hydrophilic

Peptide Bonds and Polypeptide Formation

Amino acids are linked by peptide bonds to form polypeptides. The peptide bond forms between the carboxyl group of one amino acid and the amino group of another, releasing water (a dehydration reaction).

• Polypeptide Backbone: Repeating sequence of atoms along the chain, with side chains (R groups) extending from it.

• N-terminus: The end of the polypeptide with a free amino group.

• C-terminus: The end with a free carboxyl group.

Levels of Protein Structure

Proteins have up to four levels of structure, each contributing to their function:

• Primary Structure: The unique sequence of amino acids in a polypeptide.

• Secondary Structure: Local folding patterns stabilized by hydrogen bonds, such as α-helix and β-pleated sheet.

• Tertiary Structure: The overall 3D shape formed by interactions between R groups, including hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges.

• Quaternary Structure: Association of multiple polypeptide chains into a functional protein (e.g., hemoglobin).

Protein Function

The function of a protein depends on its structure. Proteins perform a wide range of functions in cells:

• Enzymatic Proteins: Catalyze biochemical reactions (e.g., amylase).

• Defensive Proteins: Protect against disease (e.g., antibodies).

• Storage Proteins: Store amino acids (e.g., ovalbumin in egg white).

• Transport Proteins: Move substances (e.g., hemoglobin transports oxygen).

• Hormonal Proteins: Coordinate organismal activities (e.g., insulin regulates blood sugar).

• Receptor Proteins: Respond to chemical stimuli (e.g., nerve cell receptors).

• Contractile and Motor Proteins: Enable movement (e.g., actin and myosin in muscles).

• Structural Proteins: Provide support (e.g., collagen, keratin).

Factors Affecting Protein Structure

Protein structure can be affected by environmental conditions such as pH, salt concentration, and temperature. Denaturation occurs when a protein loses its native structure and function due to these changes.

Nucleic Acids: Storage and Transmission of Hereditary Information

Overview of Nucleic Acids

Nucleic acids are polymers that store, transmit, and express hereditary information. The two main types are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

Structure of Nucleotides

Nucleic acids are made of monomers called nucleotides, each consisting of three parts:

• Phosphate Group

• Pentose Sugar: Ribose (RNA) or deoxyribose (DNA)

• Nitrogenous Base: Purines (adenine, guanine) or pyrimidines (cytosine, thymine, uracil)

Type	Bases	Sugar
DNA	Adenine, Guanine, Cytosine, Thymine	Deoxyribose
RNA	Adenine, Guanine, Cytosine, Uracil	Ribose

Nucleotide Linkage and Directionality

Nucleotides are joined by phosphodiester bonds between the 5' phosphate group of one nucleotide and the 3' hydroxyl group of the next, creating a sugar-phosphate backbone with directionality (5' to 3').

DNA Structure

DNA consists of two antiparallel strands forming a double helix. The strands are held together by hydrogen bonds between complementary bases (A-T, G-C).

• Antiparallel: The two strands run in opposite directions (5' to 3' and 3' to 5').

• Base Pairing: Specific pairing: Adenine with Thymine, Guanine with Cytosine.

Central Dogma of Molecular Biology

The central dogma describes the flow of genetic information: DNA is transcribed into RNA, which is translated into protein.

• Replication: DNA makes a copy of itself.

• Transcription: DNA is used as a template to synthesize RNA.

• Translation: RNA directs the synthesis of proteins.

Equation for Peptide Bond Formation:

$\ce{Amino ext{-}acid_1} + \ce{Amino ext{-}acid_2} \rightarrow \ce{Dipeptide} + \ce{H_2O}$

Equation for Phosphodiester Bond Formation:

$\ce{Nucleotide_1} + \ce{Nucleotide_2} \rightarrow \ce{Dinucleotide} + \ce{H_2O}$

Additional info: The notes have been expanded to include definitions, examples, and context for each topic, as well as tables for amino acid classification and nucleic acid comparison.