Cell Structure, Energy, and Metabolism: Study Notes for College Biology

Cell Structure and Transport

Nuclear Transport and the Nucleus

The nucleus is the defining organelle of eukaryotic cells, responsible for storing and protecting genetic material. It coordinates gene expression and ribosome production.

• DNA Organization: Prokaryotes have a single circular chromosome; eukaryotes have multiple linear chromosomes.

• Functions: DNA is transcribed into mRNA; ribosome production begins in the nucleus.

• Nucleolus: Produces rRNA and assembles ribosomal subunits (rRNA + proteins).

• Nuclear Envelope: Double membrane (inner and outer), continuous with the rough ER.

• Nuclear Pore Complexes: Composed of ~30 proteins, highly selective, thousands per nucleus, transport hundreds of molecules per second.

• Transport:

  • Into nucleus: Proteins (e.g., DNA replication and transcription enzymes), nucleotides.

  • Out of nucleus: mRNA, ribosomal subunits.

• Nuclear Localization Signal (NLS): ~17 amino acids, rich in lysine and arginine, directs proteins into the nucleus via recognition by transport proteins.

Endomembrane System

The endomembrane system is a network of membranes involved in protein synthesis, modification, sorting, and transport.

• Secretory Pathway: DNA → mRNA → ribosome → rough ER → vesicle → Golgi → destination (plasma membrane, lysosome, secretion).

• Step-by-Step Flow:

  1. Transcription in nucleus produces mRNA.

  2. mRNA exits via nuclear pores.

  3. Translation begins in cytosol; signal sequence directs ribosome to rough ER.

  4. Protein enters ER lumen, folds, and is modified (glycosylation begins).

  5. Vesicle buds off, travels to Golgi apparatus.

  6. Golgi modifies, sorts, and tags proteins for their final destination.

• Signal Hypothesis: ER signal sequence (~20 amino acids) is recognized by SRP (signal recognition particle), which pauses translation and directs the ribosome to the ER. The protein enters via the translocon channel, the signal sequence is removed, and translation resumes into the ER lumen.

• Rough ER: Site of protein folding (with chaperones), disulfide bond formation, and glycosylation (addition of carbohydrates to form glycoproteins).

• Golgi Apparatus: Has cis (receiving), medial (modification), and trans (sorting/shipping) faces. Mannose-6-phosphate tags direct proteins to lysosomes.

• Vesicle Transport: Vesicles have specific protein markers to ensure correct targeting (like address labels).

Lysosome

Lysosomes are acidic organelles (pH ~5) containing hydrolytic enzymes for macromolecule degradation.

• Pathways to Lysosome:

  • Receptor-mediated endocytosis: Endosome → lysosome.

  • Phagocytosis: Phagosome → lysosome.

  • Autophagy: Autophagosome → lysosome.

Cytoskeleton

The cytoskeleton is a dynamic network of protein fibers that maintains cell shape, organizes internal structure, and enables movement.

• Actin Filaments (Microfilaments): Smallest, made of actin, involved in cell movement, muscle contraction, and cell division (cleavage furrow).

• Intermediate Filaments: Made of keratin and lamins, provide tensile strength, anchor the nucleus.

• Microtubules: Largest, made of tubulin dimers, form hollow tubes, resist compression, move chromosomes (mitotic spindle), transport vesicles, and form cilia/flagella.

• Motor Proteins: Kinesin (moves toward + end), dynein (toward − end), use ATP for movement.

• Cilia and Flagella: 9 + 2 microtubule arrangement; dynein causes sliding and bending. Eukaryotic flagella move with a whip motion; prokaryotic flagella rotate.

Energy and Enzymes

Metabolism and Energy Concepts

Metabolism encompasses all chemical reactions in a cell, organized into pathways. Energy transformations are central to metabolism.

• Potential Energy: Stored in chemical bonds, depends on electron arrangement.

• Enthalpy (ΔH): Heat content of a system.

  • Exothermic: Releases heat ($\Delta H < 0$)

  • Endothermic: Absorbs heat ($\Delta H > 0$)

• Entropy (ΔS): Measure of disorder; second law of thermodynamics states entropy increases.

• Gibbs Free Energy (ΔG): Determines spontaneity of reactions.

  • $\Delta G = \Delta H - T\Delta S$

  • $\Delta G < 0$: Spontaneous (exergonic)

  • $\Delta G > 0$: Nonspontaneous (endergonic)

  • $\Delta G = 0$: Equilibrium

Reaction Rates and Energy Coupling

• Reaction Rates: Increased by higher concentration, higher temperature, and proper orientation of reactants.

• Energy Coupling: Exergonic reactions power endergonic reactions, often via electron or phosphate transfer (e.g., ATP).

Redox Reactions

• Oxidation: Loss of electrons

• Reduction: Gain of electrons

• Electron Carriers: NAD+ → NADH, FAD → FADH2

ATP: The Energy Currency

• ATP Hydrolysis: $\mathrm{ATP} \rightarrow \mathrm{ADP} + \mathrm{P_i}$ releases ~7.3 kcal/mol

• Phosphorylation: Addition of phosphate increases energy of target molecule.

Enzymes: Biological Catalysts

• Function: Lower activation energy, do not change ΔG.

• Active Site: Specific to substrate, binds via weak interactions (hydrogen bonds, ionic interactions).

• Induced Fit: Enzyme changes shape upon substrate binding.

• Catalysis Steps:

  1. Substrate binding

  2. Transition state stabilization

  3. Product release

• How Enzymes Lower Activation Energy: Proper orientation, strain on bonds, stabilization of transition state.

• Enzyme Kinetics: Low substrate = linear increase; intermediate = slows; high = plateau (saturation).

• Cofactors: Inorganic (Zn2+, Mg2+, Fe2+); Coenzymes: Organic (vitamins, NADH, FADH2); Prosthetic groups: Permanently attached.

Enzyme Regulation

• Environmental Effects: Temperature and pH affect enzyme activity and structure.

• Inhibition:

  • Competitive: Competes for active site

  • Allosteric: Binds elsewhere, changes enzyme shape

• Covalent Modification: Phosphorylation (most common), can activate or deactivate enzymes.

• Feedback Inhibition: Final product inhibits an earlier enzyme in the pathway.

Metabolic Pathways

• Catabolic: Break down molecules, release energy.

• Anabolic: Build molecules, require energy.

• Evolutionary Ideas: Horowitz hypothesis, retro-evolution, patchwork evolution (propose how metabolic pathways evolved).

Cellular Respiration

Overview and Connections

• Photosynthesis: $\mathrm{CO_2} + \mathrm{H_2O} \rightarrow \text{glucose} + \mathrm{O_2}$

• Cellular Respiration: $\text{glucose} + \mathrm{O_2} \rightarrow \mathrm{CO_2} + \mathrm{H_2O} + \text{ATP}$

• Fermentation: Occurs without oxygen, regenerates NAD+

• Energy Sources (Ranked): 1) Carbohydrates, 2) Fats, 3) Proteins

Stages of Cellular Respiration

1. Glycolysis (cytosol): 10 steps, energy investment (uses 2 ATP), energy payoff (produces ATP and NADH). Net yield: 2 ATP, 2 NADH, 2 pyruvate.

2. Pyruvate Processing (mitochondrial matrix): Pyruvate → acetyl CoA, produces CO2 and NADH. Enzyme: pyruvate dehydrogenase. Regulated by ATP, NADH, acetyl CoA (inhibit); ADP, NAD+ (activate).

3. Citric Acid Cycle (matrix): Acetyl CoA + oxaloacetate → citrate. Per glucose (2 turns): 6 CO2, 6 NADH, 2 FADH2, 2 ATP. Regulated by ATP and NADH levels.

4. Electron Transport Chain (ETC) & Oxidative Phosphorylation (inner membrane):

   • Complex I: NADH dehydrogenase

   • Complex II: Succinate dehydrogenase

   • Complex III: Cytochrome c reductase

   • Complex IV: Cytochrome c oxidase

   • Electron carriers: Ubiquinone (Q), cytochrome c

   • Electrons move through complexes, energy pumps H+ into intermembrane space, creating a proton gradient.

   • Oxygen is the final electron acceptor, forming water.

5. Chemiosmosis & ATP Synthase: Proton gradient (proton motive force) drives ATP synthase (F0: proton channel; F1: ATP production). Rotation mechanism forms ATP. ~29 ATP per glucose.

Fermentation

• Occurs without oxygen; regenerates NAD+ when NADH builds up.

• Lactic Acid Fermentation: Pyruvate → lactate

• Alcohol Fermentation: Pyruvate → ethanol + CO2

• Only 2 ATP produced; serves as a backup system.

Photosynthesis

Overview of Photosynthesis

Photosynthesis is the process by which autotrophs use sunlight to synthesize carbohydrates from CO2 and water, releasing O2 as a by-product.

• Autotrophs: "Self-feeders" that make their own food.

• Heterotrophs: Must consume other organisms for food.

• Converts light energy to chemical energy (glucose).

• Requires sunlight, CO2, and H2O; produces glucose and O2.

Chloroplast Structure

• Double membrane (outer and inner).

• Thylakoids: Flattened membrane sacs containing pigments.

• Grana: Stacks of thylakoids.

• Thylakoid lumen: Space inside thylakoid.

• Stroma: Fluid outside thylakoids, site of Calvin cycle.

Light and Electromagnetic Radiation

• Light is electromagnetic radiation, with properties of both waves (wavelength) and particles (photons).

• Visible light is the range humans can see.

• Shorter wavelength = more energy; longer wavelength = less energy.

Pigments and Light Absorption

• Pigments: Molecules that absorb specific wavelengths; color is the wavelength not absorbed.

• Main Pigments:

  • Chlorophyll a: Primary pigment, absorbs blue and red, reflects green.

  • Chlorophyll b: Accessory pigment, expands absorption range.

  • Carotenoids (and xanthophylls): Absorb blue/green, reflect yellow/orange/red, protect from damage, transfer energy to chlorophyll.

• Spectra: Absorption spectrum (which wavelengths are absorbed); action spectrum (which wavelengths drive photosynthesis; most effective: blue and red).

• Structure of Chlorophyll: Head (ring with Mg2+, absorbs light); tail (hydrophobic, anchors in thylakoid membrane).

Gas Exchange (CO2 Intake)

• Leaves have a waxy cuticle to prevent water loss but also block gas exchange.

• Stomata: Openings controlled by guard cells; allow CO2 in, O2 out.

• CO2 moves by diffusion; Calvin cycle keeps CO2 concentration low, pulling more in.

Carbon Fixation and Calvin Cycle

• Carbon fixation: Incorporation of CO2 into organic molecules; most important reaction on Earth.

• Key Molecule: RuBP (ribulose bisphosphate), 5-carbon starting molecule.

• Key Enzyme: Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase), most abundant enzyme, slow and inefficient, can bind CO2 or O2 (photorespiration).

• Calvin Cycle (in stroma):

  1. Fixation: CO2 + RuBP → unstable 6C → 2 × 3-PGA

  2. Reduction: 3-PGA + ATP + NADPH → G3P (glyceraldehyde-3-phosphate)

  3. Regeneration: Some G3P regenerates RuBP (uses ATP)

• Key Output: G3P, used to make glucose, fructose, sucrose (transport sugar), and starch (storage).

• Location Differences: Starch stored in chloroplast; sucrose in cytosol.

• Almost all organic carbon originates from photosynthesis.

Regulation of Photosynthesis

• Light availability turns on photosynthesis proteins.

• High sugar levels inhibit photosynthesis and activate storage pathways.

• Rubisco is active in light, inhibited when CO2 is low (photorespiration favored).

Big Picture Connection

• Light reactions (thylakoid): Make ATP and NADPH.

• Calvin cycle (stroma): Uses ATP and NADPH to make sugar.

• Photosynthesis stores energy in glucose; glucose is later used in cellular respiration to make ATP.

• Energy flow: Sunlight → glucose → ATP → cellular work.