Study Notes: The Macromolecules of the Cell (Chapter 3, Becker's World of the Cell)

The Macromolecules of the Cell

Introduction

Cells are composed of four major families of macromolecules, which are large molecules made up of thousands of covalently connected atoms. These macromolecules are essential for the structure, function, and regulation of the cell's activities.

• Proteins (amino acids)

• Nucleic acids (nucleotides)

• Polysaccharides (sugars)

• Lipids (fatty acids)

Macromolecule Synthesis

• Each major biological macromolecule—proteins, nucleic acids, and polysaccharides—is composed of a relatively small number (1–20) of repeating monomeric units.

• Polymers are synthesized by condensation reactions, where activated monomers are linked together by the removal of water.

• Once synthesized, polymer molecules fold into stable, energy-efficient three-dimensional shapes.

• Most biological macromolecules in cells are synthesized from about 30 common small molecules.

Proteins

Importance and Functions

• Proteins are crucial macromolecules, accounting for more than 50% of the dry mass of most cells.

• They are involved in essential cellular processes such as photosynthesis, cell-to-cell communication, and gene regulation.

• Proteins are classified into nine major classes based on their functions.

Classes of Proteins

1. Enzymes: Catalysts that increase the rates of chemical reactions (e.g., sucrase).

2. Structural proteins: Provide physical support and shape (e.g., keratin, collagen).

3. Motility proteins: Responsible for contraction and movement (e.g., actin, myosin).

4. Regulatory proteins: Control and coordinate cell function (e.g., transcription factors).

5. Transport proteins: Move substances into and out of cells (e.g., Na+/K+ ATPase pump).

6. Signaling proteins: Facilitate communication between cells (e.g., insulin).

7. Receptor proteins: Enable cells to respond to chemical stimuli from the environment (e.g., growth factor receptor).

8. Defensive proteins: Protect against disease (e.g., antibodies).

9. Storage proteins: Reservoirs of amino acids and metal ions for later use (e.g., ovalbumin in egg whites).

The Monomers: Amino Acids

• Proteins are linear polymers of amino acids.

• Over 60 different amino acids are present in a cell, but only 20 are used in protein synthesis.

• Each amino acid has a carboxyl group, amino group, hydrogen atom, and a unique R group attached to a central α carbon.

• No two different proteins have the same amino acid sequence.

Common Small Molecules in Cells

Kind of Molecule	Number Present	Names of Molecules	Role in Cell
Amino acids	20	See list in Table 3-2	Monomeric units of all proteins
Aromatic bases	5	Adenine, Cytosine, Guanine, Thymine, Uracil	Components of nucleic acids
Sugars	Varies	Glucose, Ribose, Deoxyribose	Energy metabolism; component of starch, glycogen, RNA, DNA
Lipids	Varies	Fatty acids, Cholesterol	Energy metabolism; components of phospholipids and membranes

Amino Acid Structure and Properties

• All amino acids (except glycine) exist in two stereoisomeric forms: D- and L-amino acids. Only L-amino acids are present in proteins.

• The specific properties of amino acids depend on the nature of their R groups.

Classes of R Groups

• Nine amino acids have nonpolar, hydrophobic R groups.

• Eleven amino acids are hydrophilic, with R groups that are either polar or charged at cellular pH.

• Acidic amino acids are negatively charged; basic amino acids are positively charged.

• Polar amino acids tend to be found on the surfaces of proteins.

Categories of Amino Acids

• Nonpolar

• Polar

• Acidic

• Basic

Abbreviations for Amino Acids

Amino Acid	Three-Letter Abbreviation	One-Letter Abbreviation
Alanine	Ala	A
Arginine	Arg	R
Asparagine	Asn	N
Aspartic acid	Asp	D
Cysteine	Cys	C
Glutamine	Gln	Q
Glycine	Gly	G
Histidine	His	H
Isoleucine	Ile	I
Leucine	Leu	L
Lysine	Lys	K
Methionine	Met	M
Phenylalanine	Phe	F
Proline	Pro	P
Serine	Ser	S
Threonine	Thr	T
Tryptophan	Trp	W
Tyrosine	Tyr	Y
Valine	Val	V

Polypeptides and Proteins

Polymerization and Peptide Bonds

• Amino acids are linked together stepwise into a linear polymer by dehydration (condensation) reactions.

• As the three atoms comprising H2O are removed, a covalent C—N bond (peptide bond) is formed.

Directionality of Polypeptides

• Polypeptides have directionality due to the formation of peptide bonds.

• The end with the amino group is called the N-terminus.

• The end with the carboxyl group is called the C-terminus.

Protein Synthesis and Structure

• The process of elongating a chain of amino acids is called protein synthesis.

• The immediate product of amino acid polymerization is a polypeptide.

• A polypeptide becomes a protein only after assuming a unique, stable, three-dimensional shape (conformation) and becoming biologically active.

• Proteins can be represented by ribbon model, space-filling model, wire, and backbone models.

Monomeric and Multimeric Proteins

• Proteins with a single polypeptide are monomeric proteins.

• Proteins with two or more polypeptides are multimeric proteins (e.g., dimers, trimers).

• Hemoglobin is a tetramer, consisting of two α subunits and two β subunits.

Protein Folding and Stability

Bonds and Interactions

• Both covalent bonds and noncovalent interactions are needed for a protein to adopt its proper shape (conformation).

• Interactions involve carboxyl, amino, and R groups of amino acids (amino acid residues).

Types of Bonds and Interactions

1. Disulfide bonds (covalent)

2. Hydrogen bonds

3. Ionic bonds

4. Van der Waals forces

5. Hydrophobic interactions

Disulfide Bonds

• Covalent disulfide bonds form between the sulfur atoms of two cysteine residues.

• Formed by removal of two hydrogen ions (oxidation); broken by addition of two hydrogens (reduction).

• Disulfide bonds confer considerable stability to protein conformation.

Categories of Disulfide Bonds

• Intramolecular disulfide bonds: Between cysteines in the same polypeptide.

• Intermolecular disulfide bonds: Between cysteines in different polypeptides (e.g., insulin).

Noncovalent Bonds and Interactions

• Include hydrogen bonds, ionic bonds, van der Waals interactions, and hydrophobic interactions.

• Individually weaker than covalent bonds, but collectively strongly influence protein structure and stability.

Hydrogen Bonds

• Form in water and between amino acids in a polypeptide chain via their R groups.

• Bond strength: 5 kcal/mol.

• Donors: Hydroxyl or amino groups with hydrogen atoms covalently linked to electronegative atoms.

• Acceptors: Carbonyl or sulfhydryl groups with electronegative atoms that attract donor hydrogen.

Example

• Enzyme catalysis: Sucrase accelerates the breakdown of sucrose into glucose and fructose.

• Structural support: Keratin forms hair and nails; collagen provides strength to connective tissues.

• Transport: Na+/K+ ATPase pump regulates ion movement across membranes.

• Defense: Antibodies recognize and neutralize pathogens.

Additional info: These notes cover the first half of Chapter 3, focusing on proteins and their structure, function, and the chemical basis of their diversity. Further sections would include nucleic acids, polysaccharides, and lipids as macromolecules of the cell.