Stuff I Don't Know

Unit 3: 

Lecture 19: 

• Major body-plan functions: Gas exchange, Feeding, Transport, Sensory/Nervous systems, Locomotion.

• Across lineages: Bacteria → Protists → Plants → Fungi → Basal animals → Protostomes → Deuterostomes.

• Big Steps in Origin of Life:

  1. Information replication systems.

  2. Metabolism → organic molecules and polymers.

  3. Bioenergetics → energy transformation.

  4. Lipid membranes → define cell boundaries but create permeability challenges.

Scaling Limits in Insects

• Larger body → O₂ depletion in tubes unless tracheal density increases.

• Empirical limit: beetles ~ 16 cm max size (> 90% leg volume = tracheae).

Cephalochordates

• Gas exchange across body surface.

• Ciliary feeding via “gill slits.”

• Closed circulation but no true heart or respiratory pigments.

Lecture 21: 

• Organisms evolved two pumps to:

  1. Minimize diffusion distance (Δx) across exchange membranes.

  2. Maximize partial pressure gradients (ΔP) for O₂ and CO₂.
     → Both are true and essential for efficient metabolism.

• V. Alternative Aquatic Respiratory Strategies

  1. External gills: e.g., aquatic salamanders; high SA exposed to water.

     Cutaneous respiration: skin gas exchange (frogs, larval fishes).

  2. Air gulping and accessory organs:

     • Gulping air in O₂-poor waters.

     • Esophageal or pharyngeal outgrowths → primitive lungs / swim bladders.

A. Fishes & Amphibians – Positive Pressure Ventilation

• Use buccal (pumping) muscles to push air into lungs.

• Exhalation mostly passive.

• Example: Gar, Lungfish, Amphibians.

• Lungs with faveoli (honeycomb septa) → ↑ surface area.

B. Amniotes – Negative Pressure Breathing

• Air drawn in via thoracic expansion.

• Lepidosaurs: rib muscles expand body wall; faveoli present.

• Mammals: diaphragm + intercostal muscles expand thorax.

  • Lungs not attached to ribs.

  • Millions of alveoli (~3×10⁸ in humans) with dense capillaries.

  • Gas exchange by diffusion only across thin membranes.

VIII. Evolutionary Summary

• Transition: aquatic gills → lungs → alveoli / parabronchi.

Pneumothorax (Collapsed Lung)

Air enters pleural cavity → surface tension lost → lung collapses.

Perfluorocarbons: liquids with high O₂ solubility.

Axes of Diversity in Gas Exchange

1. Phylogeny – independent evolution of respiratory organs.

2. Size – scaling impacts surface area-to-volume ratio.

3. Metabolic Rate – higher metabolism → greater O₂ demand.

4. Medium – air vs. water strongly alters efficiency.

Lecture 23:

Core Components

Pumps

1. Unlocalized mechanisms:

   • Ciliary beating, peristalsis, muscle contractions.

2. Localized mechanisms:

   • Hearts (animals), leaves (plants).

   • Operate as pressure or suction pumps.

Osmotic Flow

• Water moves into regions with higher solute concentration (osmosis).

B. Pressure Flow

• Water moves toward lower pressure (tension) regions.

Gradient

• ψ highest in soil → lowest in leaves/air → drives upward flow.

Push” from Below (Root Pressure)

• Active transport of ions into xylem → osmotic influx of water.

• Creates positive pressure (root pressure).

Lecture 25:

Warm water ≠ good for O₂!

• Gas solubility ↓ with temperature.

Henrys Law: 

If C < Cₑq → gas dissolves.
If C > Cₑq → gas bubbles out

Hemoglobin:

When there is a lower pH, hemoglobin releases more oxygen. 

Single Circulation (Fish)

• Blood passes through gill capillaries → pressure drop → body.

• Low residual pressure limits tissue perfusion.

• Adaptations: large gills, counter-current exchange to maximize O₂ uptake.

XII. 🐡 Lungfish: Transitional Design

• Mix of gill and lung circulation.

• Ductus arteriosus connects pulmonary and systemic flows.

• Laminar flow minimizes mixing of oxygenated and deoxygenated blood.

Double Circulation – Single Ventricle (Amphibians)

3-chambered heart (2 atria, 1 ventricle):

• Some mixing of blood.

• Advantage: separation of pressures → higher systemic flow.

Partial Septum – Intermediate Form

• Reptiles: 3 chambers + partial septum.

• Improves separation between systemic and pulmonary flows.

• Precursor to fully divided circulation.

XV. 🐶 Divided Circulation (Mammals and Birds)

A. Anatomy

• Right side: pulmonary circuit (low pressure).

• Left side: systemic circuit (high pressure).

• No mixing between circuits (no arterial shunt)

XVII. 👶 Fetal Circulation (Mammals)

• Placenta: O₂ source → lungs bypassed.

• Two shunts:

  1. Foramen ovale: R→L atrium mixing (if fails to close → cyanosis).

  2. Ductus arteriosus: connects pulmonary to systemic arteries (if fails → heart failure).

• Both must close at birth for normal adult circulation.

Invertebrate Convergence

• Cephalopods: three hearts (one systemic + two branchial).

• Independent evolution of double circulation.

• Allows boost in pressure after gas exchange → efficient tissue perfusion.

Resistance is dynamic: vessels constrict/dilate to redirect flow.

Lecture 27:

Electrochemical Gradients 

Functions unified by this physics:

• Stomatal opening (plants)

• Sucrose transport

• Kidney filtration

• Neuronal signaling

• Nutrient absorption

• H⁺ cotransport → plants/fungi (e.g., H⁺/sucrose symporter).

• Na⁺ cotransport → animals (e.g., Na⁺/glucose symporter).

• Cnidarians: first extracellular digestion (hydrolytic enzymes in gut).

• Bilaterians: complete digestive tracts with regional specialization:

  • Mechanical breakdown

  • Storage

  • Enzyme secretion

  • Absorption

  • Elimination

Nutrient Assimilation: 

1. Prey capture/ingestion – strategy varies by lineage.

2. Mechanical reduction – teeth, gizzards, mandibles.

3. Storage – crop/stomach; intermittent feeding; HCl sterilization.

4. Chemical digestion – enzymatic hydrolysis of polymers.

5. Absorption – small-molecule transport across membranes.

6. Elimination – undigested waste removal.

Ruminants

• Four-chambered stomach: rumen → reticulum → omasum → abomasum.

• Symbiotic microbes digest cellulose; cud re-chewed.

• Efficient at extracting energy/vitamins from poor diets.

Small Intestine – Primary Site

• Receives enzymes from:

  • Pancreas:

    • NaHCO₃ neutralizes acid.

    • Amylases → sugars.

    • Proteases → peptides → amino acids.

    • Lipases → fats → monoglycerides + fatty acids.

Large Intestine (Colon)

• Reabsorbs water and minerals from food waste.

• Houses microbiota aiding final digestion (vitamin K, biotin production).

Ficks Law For Diffusion Optimimzation: 

Optimizes Fick’s Law variables:

• Large A (surface area)

• Large ΔP (pressure or concentration difference)

• Small Δx (distance).

Stomach

• HCl denatures proteins + sterilizes food.

• Pepsin begins protein digestion.

• Muscular contractions mix chyme.

Mouth / Teeth

• Mechanical breakdown → increases surface area for enzymes.

Lecture 29: 

• Hydroregulation – regulate organismal water content
  Osmoregulation (or ionoregulation)– regulate organismal solute content

• Osmosis - universal principle of passive water flow across a semi-
  permeable membrane down water’s concentration gradient

• Diversity:
  Wall-less cells – osmotic maintenance
  Walled cells - turgor maintenance

• Many bacterial and eukaryotic membranes have water channel
  proteins called aquaporins that mediate passive osmotic flow.

• Hypertonic solution - higher solute concentration in the solution relative to the
  vesicle
  •Hypotonic solution - lower solute concentration in the solution relative to the vesicle
  •Isotonic solution - same solute concentration in the solution and the vesicle

• Turgid Cell: Hypotonic Solution 

• Flaccid Cell: Isotonic Solution

• Plasmolyzed: Hypertonic Solution 

• Walled cells of aquatic organisms maintain higher solute conc. than the surrounding
  fresh or salt water environment

- Osmolarity: 

• Sum of all the dissolved materials in the body fluid

Ionoconformers – same ionic and therefore, the same osmotic composition as the
environment
• Osmoconformers – same total osmolarity as the environment but different solute
composition
• Osmoregulators – different osmolarity and solute compositions

What Animals Need To Accomplish: 

Appropriate ionic composition
• Appropriate osmotic concentration (osmolarity) – moles of
solute/liter of solution
• Often fixed relative to the environment = osmotic maintenance
• Removal of solute waste = excretion
Especially nitrogenous wastes

Life in Seawater - Most invertebrates
• Some marine invertebrates – ionoconformers (Jellyfish and Flatworm)
[internal ions] = [seawater ions]
No ionic or osmotic gradients - no net exchange

• Most marine invertebrates - osmoconformers (Lobster?)
Total internal osmolarity = seawater osmolarity
No osmotic gradient - no net H2O exchange
Ion differences between seawater and cells
Ion differences maintained via active transport

Sea Birds: 

-Urine is not high in salt 

-They excrete salt through nasal glands. 

• Fish in Saltwater

• But opposite gradients than
  SW fish
  • Ions - active uptake in
  chloride cells at gills or skin
  • High cellular osmolarity - gain
  water
  • Excretion - easy (as before),
  but
  Dilute urine
  Copious amounts
  Passive diffusion of salts

Unit 2: 

Lecture 10: 

• Electron carrier - any molecule capable of a redox reaction

• Electron transport chain (ETC) - a sequence of electron carriers
  that perform coupled redox reactions

• ATP synthase: Converts H+ gradient into ATP

• Oxidative phosphorylation:
  Inputs: electrons from NADH and FADH2 and oxygen
  Outputs: H+ gradient, reduced oxygen (H2O), oxidized NAD+

• ✅ Markdown Table

  Group / Metabolism	Initial Electron Donor	Final Electron Acceptor (X)	Product From Donor	Product From Accepting Electrons (Y)
  Organotrophs	Glucose	O₂	CO₂	H₂O
  Sulfate reducers	H₂ or organics	SO₄²⁻	H₂O or CO	H₂S
  Methanogens (hydrogen oxidizers)	H₂	CO₂	H₂O	CH₄
  Methanogens (acetoclasts)	CH₃COOH (disproportionation)	CO₂	CO2	CH₄
  Iron reducers	Organics	Fe³⁺	CO₂	Fe²⁺
  Methanotrophs	CH₄	O₂	CO₂	H₂O
  Nitrifiers	NH₃	O₂	NO₂⁻	H₂O

  • For aerobic respiration, the ETC uses high energy electron carriers as
    the electron donor and O2 as the electron acceptor
    Many organisms use different donors and acceptors in ETC

Phototrophy in halophilic archaea: 
• Create H+ gradient across membrane with bacteriorhodopsin, a
light-driven proton pump
• No ETC required to run ATP synthase
• No O2 produced
• Autotrophic, but carbon fixed differently than
cyanobacteria or chloroplasts

Simple photosynthetic ETC - purple S bacteria

Part I: Non-cyclic electron flow
1) Cyt c shuttle oxidizes H2S to form
2H+ and S and carries e- to the
photosystem
2) Photosystem absorbs light -
boosts e- from cytochrome c
shuttle to high energy state
3) e- reduces NAD+ to form NADH

Part II: Cyclic electron transport
1) Photosystem absorbs light -boosts e- from cytochrome c shuttle to high energy state
2) Quinone shuttle moves e- to cytochrome complex and H+ across the membrane.
3) ATP synthase uses H+ electro-chemical gradient for ATP synthesis

Very different processes
• aerobic respiration – NADH oxidation and O2
reduction
• anaerobic respiration - different initial e- donors
and terminal e- acceptors (e.g., NO3- reduction)
• photosynthesis – O2 oxidation and NADPH
reduction
• Homologous carriers -> common evolutionary origin
• Different complexes, carriers, and/or donors/acceptors for
specialized functions
• Same end product - H+ gradient for ATP synthesis

• Flux is number of molecules moving
  through a given area per unit time

• Flow = movement of molecules
  • Force causes flow
  • Flow is resisted

• Lecture 11
  
  Shared eukaryotic features:

  • Membrane-bound nucleus

  • Mitochondria (ATP synthesis)

  • Cytoskeleton with microtubules & actin

  • Complex internal membranes

  • Linear chromosomes

  • Mitosis & meiosis

Origin of Mitochondria

• Two hypotheses:

  1. Hydrogen hypothesis: Archaeal host + α-proteobacterium mutualism → mitochondria

  2. Symbiotic origin before full eukaryotic complexity

• Excavata evidence:

  • Some lack classical mitochondria → secondary loss or modified organelles (e.g., hydrogenosomes)

Eukaryotic Lineages: 

Amoebozoans:

• Unicellular though with multicellar stages

• Amoeba like with pseudopods

• No photosynthetic lineages 

• Heterotrophic: Loboseans, Plasmodial and, cellular slime molds
  Feature: Can make fruiting bodies which release spores

• Loboseans: engulf prey via phagocytosis.

Plants:

- Unicellular and Multicellular

-Photosynthetic Lineages:  Red and green algae; land plants including bryophytes,
pteridophytes, gymnosperms and angiosperms

-Primary Endosymbiosis

-No heterotrophic lineages 

-First to colonize land, Chlamydomonas example of origin
of sex

Excavates:

-Unicellular

-Have flagella

-Photosynthetic: Euglenid

-Secondary Endosymbiosis

-Heterotrophic: Parabasalids, Diplomonads (parasites) 

• Many have lost mitochondria; most are parasites or symbionts
  

Rhizarians: 

-Unicellular 

-Many produce shells

-Photosynthetic; Some cercozoa 
-Secondary endosymbiosis

-Heterotrophic: Foraminifera, Radiolarians, Rest of cercozoa

-CaCO3 shells make limestone; Photosynthetic cercozoans retained nucleomorph

-Radiolarians 

Stramenophiles: 

• Uni & multi cellular

• Two unequal flagella 

• Diatoms (no flagella), brown algae (two types pigment)

• Secondary endosymbiosis

• Heterotrophic; Oomycetes (aquatic saprobes)

• Diatomes deposit silica in cell walls- make diatomaceous earth. Brown
  algae make kelp forest

• Alveolates: 

• Unicellular 

• Alveoli

• Dinoflagellates 

• Ciliates and apicomplexans (parasites)

• Paramecium have sex without reproduction 
  

Asexual

• Offspring are clones (genome unchanged)

• n = haploid, 2n = diploid

Sexual

• Meiosis: diploid → 4 haploid cells

• Fertilization (syngamy): fusion of 2 haploids → zygote (2n)

• Mitochondria: from α-proteobacteria → aerobic ATP production.

• Chloroplasts: from cyanobacteria 
  

Two Hypotheses

1. Late Origin: Excavates diverged before mitochondria evolved.

2. Early Origin + Loss: Mitochondria arose first, but were lost secondarily in Excavates.

   • Evidence favors Early Origin: mitochondrial-derived genes remain in nuclear DNA, and hydrogenosomes retain remnants of mitochondrial pathways.

   • ⇒ Single origin of mitochondria at base of eukaryotes.

Chlamydomonas

• Unicellular green alga with isogametes (+/–).

• Mating-type (mt) locus determines gamete identity:

  • gsp (+) → produces + transcription factor.

  • gsm (–) → produces – transcription factor.

• Low nitrogen → gamete formation.

• After fusion (+ and –), a zygote forms.

  • gsp + gsm proteins form a heterodimer transcription factor.

  • Activates zygote-specific genes → meiosis → haploid spores.

Gamete types:

• Isogamy: equal-sized gametes.

• Anisogamy: different sizes.

• Oogamy: non-motile egg + motile sperm.

Lecture 12:

Eras:

Cambrian < Devonian < Carboniferous < Permian < Mesozoic < Cenozoic < Present 

Five Core Requirements Multicellularity 

1. Extracellular environment – structural framework for cell adhesion and signaling.

2. Division of labor – specialized cell types.

3. Resource allocation – coordinated nutrient and energy distribution.

4. Proliferation inhibition – controls over unregulated growth.

5. Programmed cell death (apoptosis) – removes damaged or redundant cells.

Challenges to Multicellularity 

• Cheating/Cancer: cells acting selfishly within a multicellular collective → seen across life forms.

• Who reproduces? Conflict between somatic and germ cells.

• How to reproduce? Need coordination between mitosis and meiosis.

• Closest relatives to land plants = charophytes (aquatic green algae)  (especially Charales).

Lecture 13:

Four major radiations:

1. Bryophytes (non-vascular)

• Include mosses, liverworts, hornworts.

• Dominant gametophyte (haploid) stage.

• Require water for fertilization (motile sperm).

• Abundant in moist habitats.

• Zygote develops into a diploid embryo (young sporophyte retained on gametophyte).

1. Pteridophytes (seedless vascular)

Evolution of xylem (water/mineral transport) and phloem (sugar transport).

• Sporophyte dominant, gametophyte small and free-living.

• Examples: ferns, horsetails, lycophytes.

• Sporangia found on large sporophytes (e.g., fern fronds).

1. Gymnosperms (seeded, non-flowering)

1. Angiosperms (seeded, flowering)

All major domesticated crops are angiosperms.

Gymnosperm vs. Angiosperm Seed Comparison

Why Move to Land?

• More light for photosynthesis.

• Less competition for CO₂ and nutrients.

• New habitats with fewer predators.

Challenges of Terrestrial Life

1. Desiccation (water loss).

2. Gravity (need for structural support).

3. Gas exchange (CO₂/O₂ regulation).

4. Reproduction without water.

5. Efficient nutrient/water transport.

• Choanoflagellates are the closest living unicellular relatives of animals. Choanocytes (collar cells) in sponges closely resemble choanoflagellates, suggesting shared ancestry.

• Multicellularity may have evolved as a response to environmental/food cues.

Fungal Evolution

• Fungi evolved from aquatic, flagellated ancestors (similar to chytrids).

• 5 major clades; colonized land after acquiring complex multicellular structures.

• Hyphae = threadlike filaments, form mycelia (body of fungus).

  • Septate hyphae: divided by cross-walls (septa) with pores.

  • Coenocytic hyphae: multinucleate without complete cell separation.

B. Mechanism of Growth

• Hyphal networks enable large surface area for absorption.

• Fungal evolution parallels plants/animals—land colonization occurred after complexity evolved.

• Filamentous: division along one axis.

• Parenchymatous: division along multiple axes → true tissues.

Benefits of Multicellularity

1. Improved diffusion & nutrient transport.

2. Cell adhesion creates stable colonies.

3. Division of labor – specialized cells for different functions.

4. Increased surface area (e.g., villi in intestines, leaf structures).

5. Cooperation and efficiency enhance survival.

Lecture 15:

Fungal Nutrition

A. Nutritional Mode

• Chemoheterotrophs – obtain carbon and energy from organic compounds.

• Extracellular digestion + absorption: secrete enzymes to break down complex substrates, then absorb nutrients.

Fungi Feeding Strategies

Mycorrhizae and Lichens – “Fungus + Root” Mutualism

• Symbiosis between fungi and plant roots found in ≈ 90% of terrestrial plants.

• Great agricultural and evolutionary importance:

  • Fungi enhance nutrient and water uptake (P, N minerals).

  • Plants provide carbohydrates to the fungus.

• Thought to have been co-symbionts of early land plants, helping them colonize terrestrial environments.

• Lichens are fungus + alga or cyanobacterium, they pretty much do the same thing with roots. 

Ecosystem Importance of Fungi

• Decomposers: recycle organic + inorganic nutrients → critical for soil fertility.

• Symbionts: essential to plant nutrient acquisition and ecosystem productivity.

• Pathogens: regulate populations → ecological balance.

• Indicators: lichen sensitivity → air quality monitoring.

Lecture 16:

What Is an Animal?

• Multicellular, heterotrophic, lack cell walls.

• Possess extracellular matrix (ECM) with collagen and cell-adhesion genes.

• Hox genes → specify body plan & axis formation.

• Behavioral hallmarks: movement, feeding, interaction.

• Metazoans – all multicellular animals.

• Eumetazoans – true tissues, symmetry, nerves.

• Bilaterians – bilateral symmetry, triploblasty, cephalization.

“Basal” Animals (Non-bilaterians)

A. Porifera (Sponges)

Body Plan

• No symmetry 

• Few cell types – choanocytes, amoebocytes, porocytes.

• Monoblastic 

Reproduction – asexual (budding) or sexual (sperm + egg).

-No gas exchnage system 

Cnidaria (Jellyfish, Corals, Anemones)

Body Plan

• Radial symmetry

• Diploblastic

• Two forms – polyp (sessile) & medusa (free-swimming).

• GV Cavity

Ctenophores: 

• Radial diploblasts with ctenes (ciliary “combs” for motion).

• Possess flow-through gut (mouth → anal pore).

• Capture prey with colloblasts (sticky cells, not stinging).

• Simple nerve net; locomotion via cilia.

-Triploblasty – adds mesoderm → true muscle & organ systems. 

• Protosomes: Mouth first 

• Arrow worms are bilateral and triploblastic 

Deuterosomes: Anus first

Chordata

A. Defining Traits (All Chordates Have)

1. Pharyngeal slits (behind mouth)

2. Notochord (flexible, rod-shaped support structure)

3. Dorsal hollow nerve cord (from ectoderm)

4. Segmented muscles (somites)

5. Post-anal tail (used for propulsion)

Lampreys

• First vertebrates: internal skeleton, skull, brain, gills, circulatory system.

• Form & Function:

  • Gas Exchange: gills; muscular pharynx pumps water.

  • Feeding: use muscular pharynx to bore into other fish.

  • Transport: true heart + blood pigments.

  • Sensory: specialized eyes, ears, nose.

  • Support: cartilage vertebrae assist notochord

Gnathostomes (Jawed Vertebrates)

• Evolutionary milestone: jaws from pharyngeal skeleton.

• Examples: Sharks, rays (Chondrichthyes).

• Features:

  • Gas Exchange: gills.

  • Feeding: hinged jaws, mineralized teeth.

  • Transport: closed system.

  • Sensory: enhanced vision + smell.

  • Locomotion: paired fins for control.

Bony Fishes (Osteichthyes)

• Ray-finned fishes (Actinopterygii)

• Lobed-finned fishes (Sarcopterygii) – key for land transition.

• Form & Function:

  • Gills for O₂ capture.

  • Jaws for feeding.

  • Circulation: single-loop heart → gills → body → heart.

  • Highly developed sensory systems.

  • Muscles on skeleton enable efficient swimming.

Tiktaalik – The “Fishapod”

• Transitional fossil between fish and amphibians.

Amniotes (Reptiles, Birds, Mammals)

A. Adaptations for Land

• Amniotic egg with protective membranes.

• Dry, scaly skin reduces water loss.

• Reproduction independent of water.

Birds (Aves) & Mammals (Mammalia)

A. Convergent/Independent Features

• Homeothermy (endothermy) → constant body temperature.

• Insulation: feathers (birds), hair (mammals).

• High metabolic rates.

Unit 1:

Lecture 3:

Foundational Concepts

• Energy types

  • Kinetic energy = energy of motion (includes heat/thermal energy = random motion of atoms/molecules)

  • Potential energy = due to location/structure

  • Chemical energy = potential energy stored in bonds, released in chemical reactions

• Energy conversions

  • Energy can change forms but is not created/destroyed (1st Law)

  • Example: Diver on platform → diving (PE → KE) → climbing (KE of muscles → PE)

• Open and closed systems: Earth
  • Matter is recycled within an organism or between organisms

• For matter, Earth is a closed system – no mass in or out

• Energy arrives on earth, is transformed by life, and then flows out again
  - For energy, Earth is an open system

• Earth radiates energy based on its temperature

• If Earth had no atmosphere, it’s temperature would be 254K

The First and Second Laws of Thermodynamics: 

• 1st law: Energy is conserved
  • 2nd law: Entropy of the universe is
  increasing

Amount of Energy Needed to Drive Reactions

• Lightning Bolt: 5 × 10^-29

• Chemical Energy in ATP: 4.9 ATP

• Energy in a Photon of Sunlight: 0.6 Photons

• Thermal Collision: 49 Collisions

• Light is highly usable energy. Heat is not very useful for metabolic work. Energy flows in a biological system from usable to unusable forms

• Metabolite – any molecule transformed in a metabolic reaction
  • Calvin Cycle: 6 low-energy CO2 converted to 1 high-energy glucose with reduced C bonds

Physical Work To Move Ions Across Cell Membrane: 

• Phosphorylate ion pump protein changing its shape and moving ions 

• 1st law of thermodynamics - bioenergetics
  • Energy is conserved
  Enthalpy H = 0 (in the universe)
  • Total energy in the universe is neither created nor destroyed in any process. But it can be transformed or converted from one form to another

• Kinetic energy is energy associated with motion. 

• Heat (thermal energy) is kinetic energy associated with random movement of atoms or molecules

• Potential energy is energy that matter posseses becaue of its location or structure 

• Chemical energy is potential energy available for release in a chemical reaction 

• Energy can be converted from one to another (but not created/destroyed)

• 2nd Law of Thermodynamics:

• Reactants have more energy than products 

• For a closed system, a spontaneous reaction will obey DELTA G < 0

• Spontaneous reactions (i.e. requiring no additional energy) proceed in the direction that reduces free energy, G (i.e. the useful energy available to do chemical work)
  OR In biological systems, spontaneous bioenergetic and metabolic reactions tend to proceed in the
  direction that releases unusable heat into the environment.

• For a spontaneous process, the universe is getting more disordered over time

• For a physical system, where there is no chemical reaction, the entropy of the universe is increasing

• -Organisms create local order by increasing disorder in surroundings
  -Although many reactions are exergonic, they don’t all happen spontaneously or quickly

Entropy Driven Order:

• Membranes (phospholipid bilayers)

  • Amphipathic molecules (hydrophilic heads, hydrophobic tails)

  • Spontaneous bilayer formation: reduces water ordering, increases entropy

  • First membranes separated life from non-life

• Hydrophobic interactions

  • Non-polar molecules cluster due to polar water pushing them together

• Protein folding

  • Hydrophobic amino acids buried inside protein, water molecules released (entropy ↑)

  • Folding produces functional proteins

  • Chaperonins aid folding of complex proteins

• Organisms are open systems that:

  1. Use thermodynamically favored processes to convert energy & matter

  2. Harness high-quality free energy (ΔG) for life processes

  3. Release low-quality energy (heat)

  4. Maintain order by exporting disorder into surroundings

Lecture 5:

Using Molecular Data for Phylogeny

• DNA as traits:

  • Mutates slowly and steadily → useful molecular clock.

  • Differences build phylogenies.

• Choice of sequences matters:

  • Fast-changing: good for close relatives (e.g., mtDNA, 3rd codon positions, introns).

  • Slow-changing: good for distant relatives (e.g., rRNA, histones, highly conserved genes).

• Strong selection constraints:

  • Exons (1st & 2nd codon positions), histones, rRNA, tRNA evolve very slowly.

• Rates of sequence change:

  • mtDNA > nuclear DNA.

  • Introns > coding DNA.

  • 3rd codon > 1st & 2nd codons.

4. Matching Data to Divergence Times

• Humans vs. chimps (6 My) → mtDNA.

• Primates vs. rodents (100 My) → nuclear amino acids.

• Mammals vs. flies (1000 My) → rRNA.

• Key principle: Sequence evolution rate must match the divergence scale.

5. Carl Woese & the Three Domains

• Woese’s contributions (1977, 1987):

  • Used rRNA → universal molecular marker.

  • Discovered Archaea as distinct from Bacteria and Eukarya.

• Why rRNA?

  • Universal (all organisms have it).

  • Essential to translation (not transferred laterally).

  • Strong selection → slow mutation rate (ideal molecular clock).

6. Limits of Molecular Data

• Molecular data show similarities but not always temporal order (who came first).

• Need fossils or gene duplication events to root trees.

• Example: Jawless fish as outgroup to tetrapods and bony fish.

• Prokaryotes → fossil record sparse → rooting more difficult.

7. Rooting the Tree of Life

• Old gene duplication method:

  • Universal gene duplicated before divergence.

  • Two copies (A & B) exist in all three domains.

  • Tree of A roots tree of B, and vice versa.

  • Example: Elongation factors, ATPase subunits.

• Iwabe et al. 1989: Used duplicated genes to root tree → supported three-domain model.

8. Complications in the Tree of Life

• Horizontal/Lateral gene transfer (LGT):

  • Exchange of DNA between unrelated organisms.

  • Especially common in prokaryotes.

  • Example: Thermophiles with nearly identical thermotolerance genes despite large rRNA differences.

• Vertical gene transfer (VGT): Parent to offspring transmission.

• Result: Some genes reflect species history, others reflect gene transfer history.

9. Competing Models of the Universal Tree

• rRNA-based tree: Assumes mostly vertical inheritance → supports LUCA (Last Universal Common Ancestor).

• Whole-genome tree:

  • Suggests an early Last Universal Common Ancestral Community (LUCAC) with extensive lateral gene transfer.

  • Distinct lineages emerged post-LUCAC.

10. Origin of Eukaryotes

• “Ring of Life” model:

  • Eukaryotes = fusion of bacteria (mitochondrial ancestor: α-proteobacteria) and archaea.

• Archaean ancestor:

  • Likely from Asgard archaea lineage.

  • 2017 & 2020 studies point to Heimdallarchaeota as closest archaeal relative.

• Two-domain hypothesis:

  • Eukaryotes nested within archaea → perhaps only Bacteria + Archaea, with Eukarya emerging from within archaea.

Tree of Life concepts:

• No “main” vs “side” branches → all lineages equally valid.

• Morphological similarity ≠ relatedness (can be convergence).

• Example: Trees based on molecular sequences revealed convergence.

• Cousins ≠ ancestors → extant lineages are not ancestral forms.

Lecture 6:

• Key requirements for life:

  1. Metabolism (chemical reactions to build/use molecules).

  2. Information storage (inheritance, replication).

  3. Organization (cell-like compartments).

  4. Replication (ability to make copies of self).

Wächtershäuser’s Iron-Sulfur World Hypothesis (1980s–2000):

• Life began in hydrothermal vents (high temp & pressure).

• Mineral clusters catalyzed complex organic molecules: pyruvate, nucleotides, peptides.

• Citric acid cycle steps can occur in lab (but need CO input).

Information First

• Argument: Life cannot evolve without inheritance.

  • Consistency required; otherwise random change dominates.

• Organisms need information to:

  1. Code for enzymes (survival).

  2. Pass information to next generation.

  3. Use a genetic code to produce enzymes.

• Central dogma: DNA → RNA → Protein.

• Universal genetic code arose before divergence of Bacteria, Archaea, and Eukarya.

• Caveats:

  • Genetic code varies slightly in some organisms.

  • Some viruses (RNA viruses) deviate from central dogma.

Key Properties of Information Systems

• Stability: information constancy.

• Fidelity: accuracy in readout.

• Redundancy: multiple copies.

• Entropy: degradation over time.

• Trade-offs: Stability vs. mutations, fidelity vs. reading errors.

DNA vs. RNA

• DNA:

  • More stable (double-stranded).

  • Fewer errors, redundancy, but not catalytic.

• RNA:

  • Less stable (single-stranded, reactive ribose, no redundancy).

  • Higher error rate.

  • Autocatalytic (ribozymes).

  • Can act as enzyme

Early Earth: 

• Oparin–Haldane (1920s): early Earth atmosphere (H₂, N₂, CO₂, CH₄, NH₃).

• Reactions produced amino acids, nucleotides, sugars.

• Miller–Urey experiment: simulated early atmosphere → amino acids formed.

• Extraterrestrial input: Murchison meteorite (1969) contained amino acids, lipids.

• Hydrothermal vents as alternative source.

Explaining Similarities & Differences in Life

• Shared features across domains:

  • Central dogma, genetic code, ATP synthase.

• Differences:

  • Cell walls:

    • Bacteria: peptidoglycan.

    • Archaea: glycoprotein S-layer.

    • Eukarya: variable.

  • Membranes:

    • Bacteria: unbranched lipids, ester linkages.

    • Archaea: branched lipids, ether linkages, monolayer.

    • Eukarya: unbranched lipids, ester linkages.

-Thermophilic archaea and bacteria are closest to the root of tree of life

Lecture 7

Operons: clusters of genes (polycistronic RNA) encoding proteins with related functions.

• Components: regulator, promoter, operator, structural genes.

• Example: lac operon (lactose metabolism).

• Shapes: coccus, bacillus, spirillum.

• Structural diversity examples: cyanobacteria (Nostoc, Merismopedia), myxobacteria, stalked bacteria (Caulobacter).

• Bacteria: no nucleus, circular chromosome with single origin, peptidoglycan walls, ester-linked membranes, no histones.

• Archaea: no nucleus, circular chromosome with 1–3 origins, diverse walls (no peptidoglycan), ether-linked branched lipids, histones present.

• Eukarya: nucleus, multiple linear chromosomes, organelles, ester-linked membranes, histones, 80S ribosomes.

-Gram-positive: thick peptidoglycan, mostly chemoheterotrophs.

Gram-negative: thinner, complex wall; huge metabolic diversity.

Pathogens

• Only bacteria (not archaea) are pathogenic.

• Spread via lateral gene transfer (LGT).

• Pathogenicity islands (PI): gene clusters enabling virulence.

• Type III secretion system (T3SS): injects toxins into host cells.

• Extremophiles: hyperthermophiles, methanogens, halophiles.

Lecture 8:

• Energy metabolism = redox.

  • Reduction = gain e⁻.

  • Oxidation = lose e⁻.

• Electron carriers: NAD⁺/NADH, FAD/FADH₂, quinones, cytochromes.

Lecture 10: 

• Photoautotrophs: light + CO₂ (cyanobacteria, plants, algae).

• Photoheterotrophs: light + organic carbon (halophilic archaea).

• Chemoorganoautotrophs: organic compounds + CO₂ (methanotrophic bacteria).

• Chemoorganoheterotrophs: organic compounds for both energy & carbon (most prokaryotes, saprobes, parasites, pathogens).

• Chemolithoautotrophs: inorganic compounds + CO₂ (methanogenic archaea, sulfur/nitrogen/iron oxidizers).

• Chemolithoheterotrophs: inorganic compounds + organic carbon (various bacteria).

Factors Affecting Flux

• Gradient (ΔC): greater concentration difference → faster diffusion.

• Distance (Δx): thinner membranes → faster diffusion.

• Surface area (A): larger area → greater total diffusion.

• Diffusion coefficient (D):

Unit 4: