Fundamental Knowledge: Cell Biology & Metabolism
Part 1: Cell Structure & Function
Eukaryotes vs. Prokaryotes vs. Viruses
| FEATURE | EUKARYOTES | PROKARYOTES | VIRUSES |
|---|---|---|---|
| Nucleus 🧠 | Present, membrane-bound | Absent, has nucleoid region | Absent, is acellular |
| Organelles 🏭 | Present, membrane-bound | Absent | Absent, not a cell |
| Ribosomes ⚫ | 80S (60S + 40S) | 70S (50S + 30S) | Uses host's ribosomes |
| Genetic Material 🧬 | Linear DNA with histones | Circular DNA, no histones | DNA or RNA |
| Cell Wall 🧱 | Plants (cellulose), Fungi (chitin) | Peptidoglycan | Protein capsid instead |
| Size 📏 | 10–100 µm | 0.1–5.0 µm | 20–300 nm |
| Reproduction 🔄 | Mitosis, Meiosis | Binary Fission | Hijacks host cell machinery |

Prokaryotic vs. Eukaryotic Cells

Basic Structure of a Virus
🔬 Relative Biological Sizes
| Object | Approximate Size |
|---|---|
| Amino Acid | ~1 nm |
| Antibody (Protein) | ~10 nm |
| Virus | ~100 nm |
| Mitochondrion | ~2 µm |
| Bacterium (E. coli) | ~3 µm |
| Red Blood Cell | ~7 µm |
| Animal Cell (generic) | ~10-30 µm |
| Plant Cell | ~10-100 µm |
💧 Osmosis in Animal & Plant Cells
| Solution | Animal Cell 🦓 | Plant Cell 🌳 |
|---|---|---|
| Hypotonic Solution | Lysed (bursts) | Turgid (normal) |
| Isotonic Solution | Normal | Flaccid |
| Hypertonic Solution | Shriveled | Plasmolyzed |

Osmosis in Animal Cells

Osmosis in Plant Cells
Key Cellular Organelles and Structures 🏭
| Organelle | Key Function(s) |
|---|---|
| Nucleus | Contains DNA, controls cell activities |
| Ribosome | Synthesizes proteins |
| Rough ER | Protein synthesis/modification for secreted/membrane proteins |
| Smooth ER | Lipid synthesis, detoxification, calcium storage |
| Golgi Apparatus | Modifies, sorts, and packages proteins and lipids |
| Lysosome | Digestion of macromolecules, recycling cellular components |
| Peroxisome | Metabolizes fatty acids; neutralizes toxic compounds (H₂O₂) |
| Mitochondrion | Cellular respiration, ATP production |
| Chloroplast | Photosynthesis (in plants and algae) |
| Vacuole | Storage (water, nutrients, waste), turgor pressure (plants) |
| Centrosome | Microtubule organizing center, forms spindle fibers in mitosis (animal cells) |

Diagram of an Animal Cell

Diagram of a Plant Cell

Nucleus & Endoplasmic Reticulum

Structure of a Ribosome

Golgi Apparatus & Endomembrane System
Structure of a Peroxisome
Hierarchical Structure of Proteins 💪
| Level | Description | Stabilizing Bonds |
|---|---|---|
| 1° Primary | Linear sequence of amino acids | Peptide bonds |
| 2° Secondary | α-helices and β-sheets | Hydrogen bonds (backbone) |
| 3° Tertiary | Overall 3D shape of one polypeptide | R-group interactions (hydrophobic, ionic, disulfide) |
| 4° Quaternary | Assembly of multiple polypeptides | Same as tertiary |
Cytoskeleton 🏗️
| Component | Functions |
|---|---|
| Microfilaments (Actin) | Cell shape/motility, muscle contraction, cytokinesis |
| Intermediate Filaments | Mechanical strength, nuclear lamina, anchoring |
| Microtubules (Tubulin) | Intracellular transport (rails), cilia/flagella, mitotic spindle |
Microfilaments, Intermediate Filaments, Microtubules
Major Motor Proteins 🚚
| Protein | Track & Role |
|---|---|
| Kinesin | Microtubules (Moves toward (+) end (cell periphery)) |
| Dynein | Microtubules (Moves toward (-) end (cell center), cilia/flagella motion) |
| Myosin | Actin filaments (Muscle contraction, cytokinesis) |

Kinesin and Dynein on Microtubule
Substance Transport Across the Membrane 🚪
| Transport Type | Energy? ⚡ | Examples |
|---|---|---|
| Simple Diffusion | No | O₂, CO₂, lipids |
| Facilitated Diffusion | No | Glucose, ions (via channels) |
| Osmosis | No | Movement of water across a semipermeable membrane |
| Active Transport | Yes (ATP) | Na⁺/K⁺ pump |
| Bulk Transport | Yes (ATP) | Endocytosis, Exocytosis |

Fluid Mosaic Model

Sodium-Potassium Pump

Endocytosis and Exocytosis
Cell Adhesion & Junctions 🤝
| Junction Type | Function | Key Proteins |
|---|---|---|
| Tight Junctions | Seals cells, prevents leakage | Occludins, Claudins |
| Adherens Junctions | Connects actin filaments | Cadherins |
| Desmosomes | Anchors cells (mechanical strength) | Cadherins |
| Hemidesmosomes | Anchors cells to basement membrane | Integrins |
| Gap Junctions | Allows communication | Connexins |

Tight Junction, Desmosome, Gap Junction
Part 2: Metabolism & Enzymes
Cellular Respiration & Fermentation ⚡
| Process | Location | Key Outputs |
|---|---|---|
| Glycolysis | Cytoplasm | 2 Pyruvate, 2 ATP (net), 2 NADH |
| Pyruvate Oxidation | Mitochondrial Matrix | 2 Acetyl-CoA, 2 CO₂, 2 NADH |
| Citric Acid Cycle | Mitochondrial Matrix | 4 CO₂, 2 ATP, 6 NADH, 2 FADH₂ |
| Oxidative Phosphorylation | Inner Mitochondrial Membrane | ~28 ATP, H₂O |
| Fermentation | Cytoplasm | Lactate or Ethanol, NAD⁺ |

Structure of a Mitochondrion
Photosynthesis ☀️🌿
| Process | Location | Key I/O |
|---|---|---|
| Light-Dependent Reactions | Thylakoid Membrane | IN: Light, H₂O → OUT: O₂, ATP, NADPH |
| Calvin Cycle | Stroma | IN: CO₂, ATP, NADPH → OUT: G3P (sugar) |

Structure of a Chloroplast
Part 3: Genetics & Molecular Biology
Core Genetic Processes (Central Dogma) 📜
| Process | Template → Product | Key Enzyme/Machinery |
|---|---|---|
| Replication | DNA → DNA | DNA Polymerase |
| Transcription | DNA → RNA | RNA Polymerase |
| Translation | mRNA → Protein | Ribosome |
Mitosis vs. Meiosis
| Feature | Mitosis (👯♀️ Identical) | Meiosis (🎲 Diverse) |
|---|---|---|
| Purpose | Growth, repair | Gamete production |
| Daughter Cells | 2, diploid (2n), identical | 4, haploid (n), diverse |
| Key Event | Separation of sister chromatids | Crossing over & separation of homologs |
Gene Regulation 🧬 On/Off
| Feature | Prokaryotes (🦠 Simple) | Eukaryotes (🦓 Complex) |
|---|---|---|
| Primary Control | Transcription (Operons) | Multiple levels (Chromatin, Transcription, Post-transcriptional) |
| RNA Processing | Minimal | Extensive (splicing, 5' cap, poly-A tail) |
PCR Steps 🧪
| Step | Process |
|---|---|
| 1. Denaturation (~95°C) | Separate DNA strands |
| 2. Annealing (~55°C) | Primers bind to template |
| 3. Extension (~72°C) | Taq polymerase synthesizes new DNA |
Recombinant DNA Tools 🛠️
| Tool | Function |
|---|---|
| Restriction Enzymes | Cut DNA at specific sequences |
| DNA Ligase | Join DNA fragments |
| Plasmids | Vectors to carry foreign DNA into cells |
🎲 Patterns of Inheritance
| Pattern | Description |
|---|---|
| Monohybrid Cross | Tracks one trait (e.g., Rr x Rr → 3:1 phenotype). |
| Dihybrid Cross | Tracks two traits (e.g., RrYy x RrYy → 9:3:3:1 phenotype). |
| Incomplete Dominance | Heterozygote has an intermediate phenotype (e.g., red + white = pink). |
| Codominance | Both alleles are fully expressed in the heterozygote (e.g., AB blood type). |
| Sex-Linked Inheritance | Inheritance of a trait on a sex chromosome (X or Y). |
| Lethal Allele | An allele that causes death when homozygous. |
| Genetic Linkage | Genes on the same chromosome tend to be inherited together. |
| Test Cross | Crossing an unknown dominant with a homozygous recessive to find its genotype. |
💥 Types of Mutations
| Category | Type | Description |
|---|---|---|
| Gene Mutations | Point Mutation | Changes a single base. Can be silent, missense, or nonsense. |
| Gene Mutations | Frameshift | Insertion or deletion of bases not in a multiple of three. Highly disruptive. |
| Chromosomal Mutations | Structural | Deletion, duplication, inversion, translocation. |
| Chromosomal Mutations | Numerical | Abnormal number of chromosomes (e.g., Trisomy). |
Part 4: Advanced Topics
The Cell Cycle: Phases & Checkpoints
| Phase | Key Events |
|---|---|
| G1 Phase | Cell growth, protein synthesis, organelle duplication. Ends at G1 checkpoint. |
| S Phase | DNA replication (synthesis) occurs. Chromosomes are duplicated. |
| G2 Phase | Further growth and preparation for mitosis. Ends at G2 checkpoint. |
| M Phase | Mitosis (nuclear division) and Cytokinesis (cytoplasmic division). |
| Checkpoint | Checks For | Key Proteins |
|---|---|---|
| G1 Checkpoint | Cell size, nutrients, DNA damage | p53, Rb |
| G2 Checkpoint | DNA replication complete, DNA damage | MPF (Cdk1/Cyclin B) |
| M (Spindle) Checkpoint | Chromosome attachment to spindle | APC/C |
💀 Cell Death: Apoptosis vs. Necrosis
| Feature | Apoptosis | Necrosis |
|---|---|---|
| Apoptosis | Cell shrinks, forms apoptotic bodies | No inflammation, clean removal |
| Necrosis | Cell swells and bursts (lysis) | Causes inflammation |
📡 Signal Transduction Pathways
| Pathway | Basic Steps |
|---|---|
| GPCR Pathway | Ligand → GPCR → G-protein → Enzyme → 2nd Messenger (cAMP) |
| RTK Pathway | Ligand → RTK dimerization → Autophosphorylation → Relay proteins activated |
🌱 Stem Cells
| Type | Potency | Source |
|---|---|---|
| Embryonic (ES) Cells | Pluripotent | Inner cell mass of blastocyst |
| Adult Stem Cells | Multipotent | Various tissues (e.g., bone marrow) |
| iPS Cells | Pluripotent | Reprogrammed adult cells |
Theme 1: Eukaryotic and Prokaryotic Cells
#1
Theme 2: Structure of the Cell Membrane
#2
Theme 3: Protein Structure
#3
Theme 4: Active and Passive Transport
#4
Theme 5: Enzyme Reaction Rate and Temperature
#5
Theme 6: Enzyme Reaction Rate and Substrate Concentration
#6
Theme 7: Competitive Inhibition
#7
Theme 8: Electron Transport Chain
#8
Theme 9: Calvin-Benson Cycle
#9
Theme 10: C₄ Plants
#10
Theme 11: CAM Plants
#11
Theme 12: Differences in Photosynthetic Mechanisms
#12
Theme 13: The Cell Cycle
#13
Theme 14: Apoptosis
#14
Theme 15: DNA Replication
#15
Theme 16: Transcription and Translation
#16
Theme 17: Regulation of Gene Expression
#17
Theme 18: The Cytoskeleton
#18
Theme 19: Signal Transduction
#19
Theme 20: Cancer
#20
Theme 21: Protein Sorting and Vesicular Transport
#21
Theme 22: Cell Adhesion and the Extracellular Matrix
#22
Theme 23: Meiosis and Genetic Diversity
#23
Theme 24: Cellular Respiration: Glycolysis and Citric Acid Cycle
#24
Theme 25: Stem Cells and Cell Differentiation
#25
Theme 26: DNA and RNA Structure
#26
Theme 27: Properties of the Genetic Code
#27
Theme 28: Mendel's Laws: The Law of Segregation
#28
Theme 29: Mendel's Laws: The Law of Independent Assortment
#29
Theme 30: Gene Mutation Types and Effects
#30
Theme 31: Chromosomal Abnormalities
#31
Theme 32: Epigenetics
#32
