CH 3 - Study Guide: The Macromolecules of the Cell (Cell Biology)

Ch 3 - The Macromolecules of the Cell

Overview of Cellular Macromolecules

Cellular macromolecules are essential for structure, function, and information storage in all living organisms. The four major classes are proteins, nucleic acids, polysaccharides, and lipids. Each class is composed of specific monomers and assembled through distinct biochemical processes.

• Proteins: Polymers of amino acids, perform diverse cellular functions.

• Nucleic Acids: Polymers of nucleotides, store and transmit genetic information.

• Polysaccharides: Polymers of monosaccharides, serve structural and storage roles.

• Lipids: Diverse group, important for membranes, energy storage, and signaling.

Common Small Molecules in Cells

Cells utilize a limited set of small molecules as building blocks for macromolecules. These include amino acids, aromatic bases, sugars, and lipids, each with specific roles in cellular structure and metabolism.

Kind of Molecule	Number Present	Names of Molecules	Role in Cell
Amino acids	20	See Table 3-2	Monomeric units of all proteins
Aromatic bases	5	Adenine, Cytosine, Guanine, Thymine, Uracil	Components of nucleic acids
Sugars	Varies	Ribose, Deoxyribose, Glucose	Components of RNA, DNA, energy metabolism
Lipids	Varies	Fatty acids, Cholesterol	Membrane structure, energy storage

Polymerization: Formation of Macromolecules

Macromolecules are synthesized by condensation (dehydration) reactions, where monomers are joined and water is removed. This process is fundamental for the assembly of proteins, nucleic acids, and polysaccharides.

• Condensation Reaction: Joins monomers by removing a water molecule.

• Directionality: Polymers have distinct ends, such as N-terminus and C-terminus in proteins.

Proteins

Functions and Classes of Proteins

Proteins are the most versatile macromolecules, with nine major functional classes. Their roles range from catalysis to structural support and immune defense.

• Enzymes: Catalysts for biochemical reactions.

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

• Motility proteins: Enable movement (e.g., myosin).

• Regulatory proteins: Control cellular processes.

• Transport proteins: Move substances across membranes.

• Signaling proteins: Mediate communication between cells.

• Receptor proteins: Receive and transmit signals.

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

• Storage proteins: Store amino acids and other substances.

Amino Acids: The Monomers of Proteins

Proteins are polymers of 20 standard amino acids, each with a unique side chain (R group) that determines its properties. All amino acids share a common structure, except glycine, which is symmetric.

• Basic Structure: Central α carbon, amino group, carboxyl group, hydrogen, and R group.

• R Group: Defines the chemical nature (hydrophobic, hydrophilic, charged).

Classification and Abbreviations of Amino Acids

Amino acids are classified based on their side chains and are commonly referred to by three-letter and one-letter abbreviations.

Amino Acid	Three-Letter Abbreviation	One-Letter Abbreviation
Alanine	Ala	A
Arginine	Arg	R
Asparagine	Asn	N
Aspartate	Asp	D
Cysteine	Cys	C
Glutamate	Glu	E
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

Classes of Amino Acid R Groups

Amino acids are grouped based on the properties of their R groups: nonpolar (hydrophobic), polar (hydrophilic), and charged (acidic or basic).

• Nonpolar: Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline

• Polar, uncharged: Serine, Threonine, Cysteine, Asparagine, Glutamine

• Charged: Acidic (Aspartate, Glutamate), Basic (Lysine, Arginine, Histidine)

Peptide Bond Formation and Protein Directionality

Amino acids are linked by peptide bonds formed through condensation reactions. Polypeptides have directionality, with an N-terminus (amino end) and C-terminus (carboxyl end).

• Peptide Bond: Covalent bond between carboxyl group of one amino acid and amino group of another.

• Directionality: Sequence written from N-terminus to C-terminus.

Levels of Protein Structure

Protein structure is described in four hierarchical levels: primary, secondary, tertiary, and quaternary. Each level is essential for the protein's function and stability.

• Primary: Linear sequence of amino acids.

• Secondary: Local folding into α helices and β sheets, stabilized by hydrogen bonds.

• Tertiary: Three-dimensional conformation due to interactions among R groups.

• Quaternary: Assembly of multiple polypeptide subunits.

Quaternary Structure: Multimeric Proteins

Quaternary structure involves the interaction and assembly of multiple polypeptide subunits. Examples include hemoglobin (tetramer) and insulin (dimer).

• Monomeric: Single polypeptide chain.

• Multimeric: Two or more polypeptide chains (dimers, trimers, tetramers).

Protein Folding and Stability

Protein folding is stabilized by covalent and noncovalent interactions, including disulfide bonds, hydrogen bonds, ionic bonds, van der Waals forces, and hydrophobic interactions.

• Disulfide Bonds: Covalent bonds between cysteine residues.

• Hydrogen Bonds: Between backbone and side chains.

• Ionic Bonds: Between charged side chains.

• Van der Waals: Weak interactions between nonpolar groups.

• Hydrophobic Interactions: Nonpolar residues cluster away from water.

Secondary Structure: α Helix and β Sheet

Secondary structure arises from hydrogen bonding along the polypeptide backbone, forming α helices and β sheets. These structures are fundamental to protein architecture.

• α Helix: Spiral structure, stabilized by hydrogen bonds every 3.6 amino acids.

• β Sheet: Extended sheet-like structure, can be parallel or antiparallel.

Motifs and Domains

Motifs are combinations of secondary structures, while domains are discrete functional units of tertiary structure. Domains often retain function independently of the rest of the protein.

• Motifs: β–α–β, hairpin loop, helix-turn-helix.

• Domains: Regions with specific function, typically 50–350 amino acids.

Fibrous vs. Globular Proteins

Proteins are categorized as fibrous or globular based on their structure and function. Fibrous proteins provide mechanical support, while globular proteins are involved in dynamic cellular processes.

• Fibrous: Strand-like, water-insoluble, stable (e.g., keratin, collagen).

• Globular: Compact, spherical, water-soluble (e.g., enzymes, antibodies).

Nucleic Acids

Structure and Function of Nucleic Acids

Nucleic acids are linear polymers of nucleotides. DNA stores genetic information, while RNA is involved in its expression. Both are essential for heredity and cellular function.

• DNA: Repository of genetic information.

• RNA: Expression and regulation of genetic information.

Nucleotides and Nucleosides

Nucleotides consist of a five-carbon sugar, phosphate group, and nitrogenous base. Nucleosides lack the phosphate group.

• Pyrimidines: Cytosine, Thymine (DNA), Uracil (RNA).

• Purines: Adenine, Guanine.

Nucleic Acid Polymerization and Directionality

Nucleic acids are synthesized by linking nucleotides via 3ʹ,5ʹ phosphodiester bonds. The sequence is written from 5ʹ to 3ʹ direction.

• DNA: Double-stranded helix, antiparallel strands.

• RNA: Usually single-stranded, can form secondary structures.

Polysaccharides

Monosaccharides and Classification

Polysaccharides are polymers of monosaccharides, classified by the number of carbon atoms and functional groups (aldosugars, ketosugars).

• Trioses: 3 carbons

• Tetroses: 4 carbons

• Pentoses: 5 carbons

• Hexoses: 6 carbons (e.g., glucose)

• Heptoses: 7 carbons

Storage and Structural Polysaccharides

Storage polysaccharides include starch (plants) and glycogen (animals), both composed of α-D-glucose. Structural polysaccharides include cellulose (plants), chitin (fungi and animals), and bacterial cell wall components.

• Starch: Amylose (unbranched), amylopectin (branched).

• Glycogen: Highly branched, stored in liver and muscle.

• Cellulose: β-D-glucose, rigid structure, not digestible by most mammals.

• Chitin: N-acetylglucosamine, β(1→4) bonds.

Lipids

Classes and Functions of Lipids

Lipids are not true polymers but are considered macromolecules due to their high molecular weight. They are crucial for membrane structure, energy storage, and signaling.

• Fatty acids: Building blocks, amphipathic.

• Triacylglycerols: Energy storage, insulation, protection.

• Phospholipids: Membrane structure, amphipathic.

• Glycolipids: Membrane stability, cellular recognition.

• Steroids: Four-ring structure, hormones, cholesterol.

• Terpenes: Isoprene derivatives, vitamins, pigments.

Saturation of Fatty Acids

Fatty acids can be saturated (no double bonds) or unsaturated (one or more double bonds). Saturation affects physical properties and health implications.

• Saturated: Straight chains, solid at room temperature.

• Unsaturated: Bent chains, liquid at room temperature.

• Trans fats: Artificially produced, associated with health risks.

Phospholipids and Membrane Structure

Phospholipids are the main component of cellular membranes, forming bilayers due to their amphipathic nature. Sphingolipids and glycolipids contribute to membrane function and cell recognition.

• Phosphoglycerides: Glycerol backbone, two fatty acids, phosphate group.

• Sphingolipids: Sphingosine backbone, important in signaling.

• Glycolipids: Carbohydrate attached, cell recognition.

Steroids and Terpenes

Steroids are hydrophobic molecules with a four-ring structure, including cholesterol and steroid hormones. Terpenes are derived from isoprene and include vitamins and pigments.

• Cholesterol: Membrane component, precursor for steroid hormones.

• Steroid hormones: Estrogens, androgens, glucocorticoids, mineralocorticoids.

• Terpenes: Vitamin A, carotenoids, dolichol, ubiquinone.