Macromolecules of the Cell: Structure, Function, and Analysis

Macromolecules of the Cell

Introduction to Macromolecules

Macromolecules are large, complex molecules essential for cellular structure and function. They include proteins, nucleic acids, polysaccharides, and lipids, each playing distinct roles in the cell.

• Definition: Macromolecules are polymers made up of smaller subunits called monomers.

• Types: Proteins (amino acids), nucleic acids (nucleotides), polysaccharides (sugars), and lipids (fatty acids and glycerol).

• Polymerization: Formation of macromolecules by joining monomers through condensation reactions.

• Importance: Structural support, catalysis, information storage, and energy storage.

• Example: DNA is a nucleic acid polymer storing genetic information.

Water, Hydrophobicity, and Hydrogen Bonds

Water is a polar molecule, crucial for biological systems due to its ability to form hydrogen bonds and influence hydrophobic interactions.

• Polarity: Water's polarity allows it to dissolve many substances and participate in hydrogen bonding.

• Hydrophobicity: Nonpolar molecules tend to aggregate in water, driving membrane formation and protein folding.

• Hydrogen Bonds: Weak interactions important for stabilizing macromolecular structures.

• Equation: $\delta^+$ and $\delta^-$ indicate partial charges in water molecules.

Proteins

Protein Functions

Proteins are versatile macromolecules with diverse functions in the cell.

• Enzymes: Catalyze biochemical reactions, increasing reaction rates.

• Structural Proteins: Provide physical support and shape (e.g., collagen).

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

• Regulatory Proteins: Control cellular processes (e.g., transcription factors).

• Transport Proteins: Move substances across membranes (e.g., hemoglobin).

• Hormonal Proteins: Facilitate communication between cells (e.g., insulin).

• Receptor Proteins: Allow cells to respond to chemical signals.

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

• Storage Proteins: Store amino acids (e.g., ferritin).

Protein Structure

Proteins have hierarchical structures that determine their function.

• Primary Structure: Linear sequence of amino acids.

• Secondary Structure: Local folding patterns (α-helix, β-sheet) stabilized by hydrogen bonds.

• Tertiary Structure: Overall 3D shape formed by interactions among side chains.

• Quaternary Structure: Association of multiple polypeptide chains.

Peptide Bond Formation

Peptide bonds link amino acids in proteins through condensation reactions.

• Equation: $\text{Amino acid}_1 + \text{Amino acid}_2 \rightarrow \text{Dipeptide} + H_2O$

• Example: Formation of a peptide bond between glycine and alanine.

Protein Folding and Health

Proper folding is essential for protein function; misfolding can lead to diseases such as prion disorders.

• Chaperones: Assist in correct protein folding.

• Prions: Misfolded proteins that can cause neurodegenerative diseases.

Amino Acids

Amino acids are the building blocks of proteins, each with unique side chains affecting protein structure and function.

• Structure: Central carbon, amino group, carboxyl group, side chain (R group).

• Classification: Nonpolar, polar, acidic, and basic amino acids.

• Table: Abbreviations for Amino Acids

  Name	3-letter code	1-letter code
  Alanine	Ala	A
  Arginine	Arg	R
  Asparagine	Asn	N
  Aspartic acid	Asp	D
  Cysteine	Cys	C
  Glutamine	Gln	Q
  Glutamic acid	Glu	E
  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

Nucleic Acids

Structure and Function

Nucleic acids store, transmit, and express genetic information. The two main types are DNA and RNA.

• Monomers: Nucleotides, each consisting of a phosphate group, a sugar (ribose or deoxyribose), and a nitrogenous base.

• DNA: Double-stranded helix, stores genetic information.

• RNA: Single-stranded, involved in protein synthesis and regulation.

• Equation: $\text{Nucleotide}_n + \text{Nucleotide}_{n+1} \rightarrow \text{Dinucleotide} + H_2O$

Double Helix Structure of DNA

DNA's double helix is stabilized by hydrogen bonds between complementary bases (A-T, G-C).

• Base Pairing: Adenine pairs with thymine, guanine pairs with cytosine.

• Antiparallel Strands: Strands run in opposite directions (5' to 3' and 3' to 5').

Polysaccharides

Structure and Function

Polysaccharides are polymers of sugars, serving as energy storage and structural components.

• Monosaccharides: Simple sugars (e.g., glucose).

• Disaccharides: Two monosaccharides linked by glycosidic bonds.

• Polysaccharides: Long chains of monosaccharides (e.g., starch, cellulose, glycogen).

• Equation: $\text{Glucose}_n \rightarrow \text{Polysaccharide}$

Lipids

Structure and Function

Lipids are hydrophobic molecules important for membrane structure, energy storage, and signaling.

• Types: Fatty acids, triglycerides, phospholipids, steroids.

• Functions: Membrane formation, energy storage, insulation, signaling.

• Example: Phospholipids form the bilayer of cell membranes.

Techniques in Cell Biology

SDS-PAGE: Separating Proteins by Size

SDS-PAGE is a technique used to separate proteins based on their molecular weight.

• Principle: Proteins are denatured and coated with SDS, giving them a uniform negative charge.

• Separation: Proteins migrate through a polyacrylamide gel; smaller proteins move faster.

• Application: Used to analyze protein purity and estimate molecular weight.

Immunoblotting (Western Blot)

Western blotting detects specific proteins using antibodies after separation by SDS-PAGE.

• Steps: Transfer proteins to a membrane, incubate with primary and secondary antibodies, visualize bands.

• Application: Used to confirm protein identity and quantify expression levels.

Gene Manipulation and Editing

Modern cell biology uses genetic techniques to study and modify gene expression.

• Blocking Gene Expression: Downregulation or knockout of specific genes.

• RNA Interference: Use of small RNAs to silence gene expression.

• CRISPR Genome Editing: Precise modification of DNA sequences using guide RNAs and Cas9 enzyme.

Small RNA Molecules

Small RNAs regulate gene expression by binding to target mRNAs and inhibiting translation or promoting degradation.

• Types: siRNA, miRNA.

• Function: Post-transcriptional regulation of gene expression.

Bioinformatics and 'Omics'

Bioinformatics integrates computational tools to analyze large-scale biological data, such as genomics and proteomics.

• Genomics: Study of entire genomes.

• Proteomics: Study of all proteins in a cell or organism.

• Application: Identifying gene functions, disease markers, and evolutionary relationships.

Summary Table: Macromolecules and Their Functions

Macromolecule	Monomer	Main Functions
Protein	Amino acid	Catalysis, structure, transport, regulation
Nucleic acid	Nucleotide	Genetic information storage and transfer
Polysaccharide	Monosaccharide	Energy storage, structure
Lipid	Fatty acid, glycerol	Membrane structure, energy storage, signaling

Additional info: Some slides contained humorous or non-academic content, which was omitted from these notes. All major topics were expanded with academic context for completeness.