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BIOL 112 (Winter 2011) notes for Part I: The cell (Professor Vogel's section). From January 5, 2011 to February 11, 2011.

The below is mostly review of basic chemistry
Atomic structure: protons, neutrons, electrons
Mass of proton = standard unit of measure called the dalton OR amu (1 amu is roughly 1.7 x 10^-24 g)
Matter: anything that occupies space, and has mass (which is a quantity of matter, circular definitions ftw)
Inertia: resistance to change of state of motion
Classification of matter:
- Separable by physical means = mixture
  - Homogeneous (uniform throughout, e.g. salt solution) or heterogeneous (not, e.g. milk - fat in a water-based medium)
- Not separable by physical means = substance
  - Compound (decomposable by chemical process) or element (not)
Atomic mass = mass of neutrons, protons and electrons in amu (atomic mass units)
- Neutrons and protons have mass 1, electrons have a mass of something like 0.0005
- Note that atomic mass is different from atomic weight - atomic weight is the weighted average of the atomic mass of the isotopes of an element
- Relative atomic mass is a synonym for atomic weight, and this is rarely a whole number
- Also note that neutrons and protons don't have exactly the same mass; we approximate
- Furthermore, due to binding energy ...
- But in any case the lesson here is that atomic mass and weight are rarely whole numbers for several reasons
- The explanation in the lecture itself is a bit misleading, and doesn't really account for the difference between atomic mass and weight
The periodic table, classifies elements in groups and families, primarily
Isotopes: different number of neutrons, but identical chemical properties (determined by protons and neutrons)
- However, due to the number of neutrons, can be unstable (i.e. radioactive - emit alpha, beta or gamma radiation from the nucleus)
Chemical bonding: Aufbau principle, electrons fill up s orbitals before p orbitals
- Atoms can form bonds until their outermost shell is filled
- Covalent bonds - sharing of electrons (to some degree), strong, predictable lengths and angles, can be double or TRIPLE
  - Polar covalent bonds - when electrons are more attracted to one nucleus than the other, e.g. with water
  - This results in a dipole
  - On the other hand, in a C-C bond, for instance, the electrons are shared quite equally
- Ionic bonds - attraction of opposite charges (basically covalent but electronegativity difference is greater, usually >1.8 - not in scope of course)
- You'll learn, if you haven't already, that a lot of explanations in basic chem/bio courses are simplifications (i.e. lies)
- van der Waal's forces: interactions of electrons of nonpolar substances
- Hydrophobic interactions: nonpolar substances in the presence of polar substances
- Bond energy: energy needed to separate two "bonded" atoms under physiological conditions (?)
Electronegativity: tendency of an atom to attract electrons (when it occurs as part of a compound)
- Increases as atomic radius decreases and nuclear charge increases; ionization energy is similar, but slightly different

Acids donate hydronium ions (H+, simplified as hydronium ions)
Strong acids vs. weak acids - strong = release many H+ ions (simplified as, they release all their ions), weak = only some
Depends on pKa value; like covalent/ionic bonding, there is a continuum, but just pretend that what is said in this class is true
Bases accept H+, release OH-
Ex, NaOH is a strong base
Amino group (NH₂): important part of many biological compounds (principal component of protein), weak base
Water: weak base AND acid, pH of pure water is 7, but almost all water is acidic due to dissolved ions, gases (e.g. CO₂) etc
pH is concentration of hydrogen, measured in logarithms - pH of 7 ==> 10^-7 mol / L
Buffers: make the solution resistant to pH change (reacts with added bases and acids)
- Can be composed of a weak acid and its conjugate base. The actual reactions are probably out of the scope of this course
- Buffers can have different ranges over which they act
- But once that range has been overshot, they no longer act as buffers
The relation of functional groups to acid/base theory:
- Proteins are all amino acids - they have an amine group so they can accept, carboxyl group so they can donate
- Others: ketones (O in the middle), aldehydes, etc
- Side chains - ex, phosphates can add charges, sulfhydryl groups can combine, etc
- Phosphate groups can store energy, release it; that's why they're part of the energy currency (ATP)

Isomers: same chemical formula, different geometric structure
- Structural: different structural formula; a functional group is attached to a different carbon atom
- Stereoisomers: same chemical formula, different arrangement of atoms in space
  - Optical isomers (enantiomers), chiral compounds, mirror images of each other
  - Geometric isomers, ex cis & trans isomers (different sides of a double bond, which cannot rotate)

IN A CELL, WE HAVE:
- Lipids: good at forming barriers and compartments, as they resist the flow of aqueous solutions
- Nucleic acids and proteins
- Carbohydrates: energy storage, surface properties, rigid structure
We are 70% water - most of the rest is biological polymers etc
WE ARE ALL MADE OF THE SAME FUNCTIONAL UNITS
Condensation reactions - one way to make a polymer
- Monomers, H + OH --> H₂O, then we get polymers
Hydrolysis: breaking a polymer, consumes a molecule of water for every bond broken

Carbohydrates: energy storage, building blocks for other molecules (nucleic acids)
Serve as structural components - insect exoskeletons are made of chitin, which is just modified sugar
- Attached to most membrane proteins, and through this give identity to cells by uniquely identifying their surface
- For example, blood types determined by the type of sugar
Ex: monosaccharides, disaccharides (2), oligosaccharides (3-20), polysaccharides (100+) (somehow 21-99 neglected)
General formula for a carbohydrate: CH₂O
- Glucose: C₆H₁₂O₆
- In polymers, of course, the formula is slightly different due to the loss of water
When sugar dissolves - alpha and beta forms of ring structures, convert between them
- There is "handedness" in these systems, which is how you get flow in such systems
Glyceraldehydes - 3 carbon sugars, important
Five-carbon sugars: ribose, deoxyribose, important in DNA
Six-carbon sugars: hexoses, the ones we consume and metabolise (alpha-manose, alpha-galactose, fructose which is not a true hexose)
Two glucose molecules can form 11 possible linkages
- However, enyzmes drive the formation of particular reactions, to ensure that only certain stable linkages are formed
- Glycosidic linkage: formation of disaccharides through condensation reaction, ex sucrose from fructose and glucose
- Maltose, cellobiose are structural isomers
Plant cell walls: cellulose
Starch and glycogen (in food, e.g. potatoes; easily broken down)
Macromolecular structures:
- Linear (cellulose) - long, branched, stable - gives strength to plant walls
- Curved, moderately branched (amylopectin) - also in plants
- Curved and highly branched (glycogen, a polysaccharide) - gives strength, shape to cells
Chitin: modified glucose, has an acetyl group attached to it (COCH₃)

One of the four classes of macromolecules found exclusively in living organisms
Are polymers made of monomeric units (nucleotides)
Encode genes, specialised for the storage, transmission and use of genetic information
Can replicate to transmit the information to the next generation
Transcribed into RNA, which is translated into proteins
Central dogma of molecular biology:
- DNA can reproduce itself (replication)
- And DNA can copy its information into RNA (transcription)
- (which can then specify a sequence of amino acids in a polypeptide - translation(
- Generally speaking, unidirectional - can't go from proteins to DNA usually (some viruses, RNA to DNA)
- Life is just a long uninterrupted sequence of DNA replication
Nucleotides also have roles in ATP and GTP - energy transducer and sources (as phosphate backbones are energy rich) in reactions
- Also in transmission of nervous signals
Nucleotide: one or more phosphate groups, sugar, base
- Sugar: pentose, two flavours
  - Either a hydroxyl group on one position (ribose, in RNA)
  - Or not such hydroxyl group (deoxyribose, in DNA)
  - This difference changes the backbone, etc
- Phosphate group: can be mono, di, or tri
  - Bindings are very energy rich, when bindings are opened, lots of energy available
- Base nitrogen-containing single or double ring compounds
  - Pyrimidines: CT/U, smaller (single)
  - Purines: AG, larger (double)
  - Of course, hydrogen bonds between A-T (two bonds), C-G (three bonds, a little more stable)
  - Always one purine and one pyrimidine, so both bondings are the same size
Double-helical structure of DNA proposed by Watson and Crick; based on Rosalind Franklin's x-ray diffraction pattern (crystallography)
- Base inside, phosphate outside
- Sugar molecule has 3 carbons; 5th has a phosphate group; always reacts with the 3rd carbon atom of the next one
- So a 5' 3' connection, alternating
- Polar molecule, etc
- Cells can only synthesise DNA (polymerisation) in the 5' 3' direction, because of the direction of adding carbon?
- Backbone: phosphate, sugar, alternating
- The DNA backbone is negatively charged; bases are planar
RNA: single stranded, uracil instead of thymine, single-stranded
- Bases still want to pair, however, so you get little loops etc, making for elaborate structures
- RNA structures also have enzymatic capabilities

Nonpolar hydrocarbons, insoluble in water (due to nonpolar covalent bonds in carbon chain), like to clump together
Roles:
- Energy storage - most common (fats and oils)
- Cell membranes (phospholipids)
- Capture of light energy (carotenoids)
- Also hormones and vitamins (steroids, modified fatty acids), thermal insulation, and electrical insulation of nerves
Fats and oils: simple lipids (triglycerides), composed of glycerol (alcohol with 3 OH groups) plus 3 fatty acids, with ester linkage
- Condensation reaction: one fatty acid per OH group on the glycerol, they combine to form triglycerides
- Saturated fatty acids: no double bonds, very straight and neatly packed, solid at room temp, mostly in animals (who need energy more)
- Unsaturated: double bonds cause kinks (as carbon atoms aren't saturated by H), prevent tight packing, so liquid at room temp
- Trans-fatty acids (geometric isomer, as opposed to cis)
Phospholipids: similar structure to above, but phosphate group replaces one fatty acid
- Head has a positive charge, neck is negative, so hydrophilic head, hydrophobic tail
- So both hydrophilic and hydrophobic ... forms a bilayer
- The hydrophobic tails line up, and the heads face outward (on both sides), so a natural membrane - bilayer
- Helps protect stuff from the outside world, naturally (no enzymes or anything needed)
- Note that it's not a bond - just an aggregation, so things can travel through this membrane
Carotenoids: light-absorbing pigments
- E.g. beta-carotene; symmetric molecule, when the body cuts it in half we get two vitamin A molecules
- This is something that the body cannot synthesise itself, but important for vision, embryonic development etc

You can use the backbone of a protein to idealise the minimum volume a protein can occupy etc
The types of amino acids present are related to the 3-dimensional shapes of proteins
Views: backbone, sticks (electron orbitals), spheres (molecules), surface (nooks and crannies)
Every membrane in your body has some protein component
Professor Vogel's favourite amino acid (serine 360)
- Adding this amino acid to a protein changes the structure completely, changes the way cells divide
- Because of a few additional charges added - electrostatic forces propagate through entire molecule
Proteins: polymers of amino acids
- A few amino acids (called peptides, e.g. pheromones) to thousands of them (titin: 33,000 amino acids)
- Folding is crucial to function of protein, largely (but not entirely) dictated by sequence of amino acids
- Means we can make a prediction of the shape of protein based on its sequence of amino acids (which have different properties etc)
- Can have many shapes, e.g. porin, lets things in and out, looks like a pretzel
  - Whether or not something can go in doesn't depend only on shape - also on charge etc
20 amino acids: at the cytoplasmic pH (acidic), have lost hydrogen on carboxyl group, goes to other end
- amino group + carbon + side chain + carboxyl group, links to another one that does not have an extra H+
  - The two form a peptide linkage - N terminal (NH3+ one) and C terminal (other one), for a protein - like poles
  - The side chain is the only specific part of an amino acid; the rest is the same
  - Determines how amino acids next to each other will behave (based on its charge)
- Results in a peptide backbone, repeating units: N-Cstuff-C-N-Cstuff-C.
- The precise sequence of amino acids: primary structure
- You can tell, from a protein's structure. what function it has; many categories
Arginine, histidine, lysine - positively charged hydrophilic side chains
Aspartic acid, glutamic acid - negatively charged hydrophilic side chains
Serine, threonine, asparagine, gultamine, tyrosine: polar but uncharged hydrophilic side chains
- Tyrosine, threonine can be modified off hydroxyl group
- Tyrosine has pi bonds, forms a 6-carbon aromatic side chain, affects neighbours by constraining them (stearic effects)
Glycine: smallest amino acid, most flexibility, can adopt many different shapes (results in disordered parts of proteins)
Cysteine: sulfhydrl group can form disulfide bond, constrains the kind of shape protein can adopt
Proline: weird side chain, breaks things up
Alanine, Isoleucine, leucine, methionine, phenylalanine, tryptophan, valine: nonpolar hydrophobic side chains
Secondary structure: certain types of patterns will produce a different function, so proteins performing similar functions will have some similar regions
- Shape determined primarily by hydrogen bonds between the backbone of amino acids
- Three most common ones: alpha helix, beta pleated sheet, and loops (can mess around here, to change shapes and enhance functionality)
  - Alpha-helix: forms a straight rod, hydrogen bonds within rod formed by backbone, parallel to axis of helix
  - Side groups project outward from helix (even if internal)
  - Alpha helices can only go through plasma membranes if they have only hydrophobic amino acid side chains
  - Proteins can also form antiparallel coils - long, flexible, strong, can exert torquel so motor proteins usually have coils
  - Coiled coils arise when two alpha-helices have hydrophobic amino acids at every 4 positions (1 turn every 3.6 amino acids)
  - Beta pleated sheet: flat plates, ribbons ?
  - Strands can be parallel or antiparallel, can come from different polypeptides
Basic unit of proteins: polypeptides (amino acid chains) linked together
- Condensation reactions - carbon and nitrogens together, forms peptidyl bond (covalent)
Polypeptide: chain of amino acid monomers, from N terminus until C terminus
Hydrogen bonding between amino acids: major driver in formation of higher-order structure from polypeptides
Easy to predict helices - characteristic set of amino acids and their position relative to each other
- Sheets, not as predictable (they're strong though)
- Still, we can determine protein structure using crystallography, NMR etc
Loops: usually between highly ordered structures (e.g. helices - common motif in organisms)
- Proline - fits neither in a helix nor a sheet because it makes a kink in the peptide
- Due to its side chain, sort of makes a closed loop; N carries no H for hydrogen bonding
- So I guess it results in a loop
3D structure of proteins determined by:
- Location of covalent disulfide bridges
  - Example: two cysteines can work together to make a covalent bond, forming a stable loop in the chain
  - Often loops move around a lot, but are fixed in relation to each other, due to covalent bonds
- Location of secondary structures
  - E.g. parallel beta sheets buried, antiparallel usually on surface
- Ionic interactions between positive and negative charged side chains (form salt bridges)
- Hydrophobic R groups aggregate, away from water (surface)
- Forces between R groups (van der Waals for hydrophobic R, electrostatic for charged)
Protein structure: made piece by piece
- First piece: always a methionine (basically the start amino acid, N-terminus)
- Last piece (C-terminus): variable (can be anything), usually disordered
- Shape of proteins - critical in how they communicate and link to each other
Experimental evidence that primary structure specifies 3D structure:
- Ribonuclease, stable enzyme, added chemicals that disrupt hydrogen and ionic bonds (urea) and disulfide bridges
- Also subject to temperature, low (?) pH, to completely denature the protein
- Then, slowly remove the chemical agents ... the original 3D structure is restored, omg!!!
- Note that this experiment depends on complete denaturation
- Partial denaturation can be irreversible (e.g. boiling)
  - For example, flipping hydrophobic regions to the surface and hydrophillic to the interior
  - Not all the bonds will be disrupted, so it can't regain its 3D structure after
  - Happens when you start cooking eggs - egg whites are partially denatured, yolk, not yet
Polypeptide: polymer of amino acids, linked by peptidyl bonds; in many cases, is the entire protein
- Many proteins composed of more than one polypeptide - e.g. hemoglobin
- Protein domains: parts of a polypeptide with distinct functions
- Kinase: enzyme, speeds up the process of transferring a phosphate to a hydroxyl group (so phosphylester?), negative charge
- Activate themselves - phosphorylate (?), autoactivation = regulatory event, to change activity of a protein
Electrostatic steering: how proteins join together, due to shape and surface chemistry (charges etc)
Chaperones: specialised proteins, keep temporarily exposed hydrophobic regions of other proteins from interacting inappropriately
- They sequester newly synthesised proteins, give them time to fold away from disruptive forces
- Think of proteins as really attractive strippers trying to put their clothes on in a room full of people trying to take them off
- Chaperones are essentially dressing rooms where strippers can put their clothes on
- I don't know, similar to the in-class analogy
- Structure of chaperone: protective cavity, nice physiological environment inside which proteins can fold
- Example: HSP60 (heat shock protein 60, ubiquitous) - protect against thermal stress
- Proteins can bind and enter (through electrostatic steering), fold, are released

Structure, due to phospholid bilayers: fluid mosaic model
Phospolipids form a sort of lake, fluid (no covalent bonds), proteins floating around
Four types of movement of phospholipids:
- Lateral diffusion: basically drifting sideways
- Flexion: move left and right (individual I think)
- Rotation
- Flip-flop: upper and lower molecules switch places, rare because hydrophillic goes through hydrophobic interior
Energetically favourable for bilayers to form an enclosed/sealed space
- So a sheet, yes, but with the edges all touching (natural configuration)
- Offers an interesting glimpse into how cells evolved ... makes sense
  Membranes may vary in lipid composition
Phospholipid chain length, degree of saturation, phosphate groups etc
Can even change seasonally, for example in hibernating animals, degree of saturation
Membranes can also contain cholesterol
- Cholesterol: steroid, also lipid (no hydrophillic head, only hydrophobic tail)
- Very rigid, embedded in fatty acid to make the membrane more solid
- Can counteract the effects of unsaturated fatty acids (the kinky ones)
Can also contain proteins - the number and kind vary with cell function
- Peripheral membrane proteins: no hydrophobic regions, interact with hydrophilic heads or exposed parts of integral membrane proteins
- Integral membrane proteins: partially or fully embedded, have both hydrophilic and hydrophobic domains
- Again, no covalent bond here, just hydrophilic/hydrophobic interactions
- Transmembrane proteins: anchored membrane proteins (polar proteins covalently attached to lipid), also has non-polar parts, can have loops
Some membrane proteins can move freely within bilayer; others anchored to specific region
- Experiment: show that proteins embedded in membrane can diffuse freely within that membrane
- One mouse cell, one human cell, both covered with membrane proteins
- After a few hours, they sort of mix, resulting in one half-green, half red cell
Membranes also have carbohydrates on outer surface - recognition sites for other cells and molecules
- Glycolipids: carbohydrate + lipid
- Glycoproteins: carbohydrate + protein
- Different combinations of these give cells an identity, like bar codes sort of; so other cells can recognise similar cells

Related to the above - similar cells recognise each other, come together
Example with sponges: pressed through filter, to separate into single cells
After a few hours, the same sponge is formed again - apparently the cells were able to come back together
Homotypic: most common, how tissues are formed; cells with the same molecule sticking out bind
Heterotypic: two cells with different proteins bind; example, sperm and ovum
Cell-cell junctions: specialised structures that hold cells together
- Tight junctions (occluding)
- Cell-cell anchoring junctions - example, desmosomes
- Channel forming junctions (gap junctions)
- Example: epithelial cells, have all these junctions
- Compartmentalised - have apical region for one task, basolateral region for another task
- Tight junctions, in this case, seal the intercellular space, and separate apical from basolateral region
- Desmosomes act like spot welds, like a plug, connecting cytoskeletons of neighbouring cells (e.g. cadherins - linked to cancer, as cells leave where they're supposed to be); keratin fibres
- Gap junctions: allow communication, e.g. hydrophobic on outside, but polar on inside, so polar molecules can pass through, between cells (like an ethernet cable)
Cell-matrix junctions: link cells to the extracellular matrix (keep them in place), done by integrins
- On the inside of cells, attached to actin filaments inside cell, extracellcular matrix outside
- For cancer to metastasize, it would have to get rid of this connection

So membranes can control what passes through
Passive transport (diffusion - random movement toward equilibrium), no metabolic energy required
- Of course, at equilibrium, particles continue to move, but there is no net change in distribution (dynamic equilibrium)
- Due to Brownian motion of individual molcules due to thermal motion, collisions
- Diffusion rate depends on size of molecules, temperature of solution, and concentration gradient (difference between concentration in areas)
Permeability - water and lipid-soluble molecules can diffuse easily
- Electrically charged and polar molecules, not so much
- Hydrophobic move through the most easily
- Small uncharged polar molecules, not as easily (water can, of course)
- Large uncharged polar molecules, probably not
- Ions - no way, need active transport
- Osmosis: diffusion of water through membranes, passive, depends mostly on the number of solute particles present, not on type
- Hypertonic: higher solute concentration in solution than cell, water will leave the cell and cell will shrink
- Isotonic: same solute concentration as rest of cell (e.g. blood cells)
- Hypotonic: lower solute concentration compared to cell; water will enter the cell, which will grow until it explodes
- Animal cells placed in hypotonic solutions may burst; plant cells have rigid cell walls, build up turgor pressure, stop more water from entering
- Why you would die when drinking 200g of NaCl but not 200g of glucose ... because glucose weighs more, so fewer particles, meh
- Facilitated diffusion: for large polar and charged substances that aren't readily diffused
  - Depends on channel proteins and carrier proteins
  - Channel proteins: hydrophilic pore, hydrophobic outside, polar things can go through; e.g. ligand gate ion channels (signal tells them to open) or voltage gate (when a certain voltage is reached)
  - Carrier proteins transport polar molecules across membranes in both directions, e.g. glucose, binds to carrier, comes through
  - Kind of like elevators I guess? Can be saturated, the number of carrier proteins limits the rate of diffusion
Active transport - pumped in or out, but energy needed; against concentration gradient
- Unidirectional: proteins involved, either uniporters, or sympoters, or antiporters
- Unipoter: takes only one type of thing, sends it through
- Sympoter: takes two things, moves them in same direction
- Antiporter: two things, opposite directions (from opposite sites)
- Primary active transport: (requires direct hydrolysis of ATP, on the spot, for that reaction)
- Secondary active transport: energy comes from an ion concentration gradient, established by primary active transport
- Example - sodium-potassium pump, oh god not this again
  - Eventually you get lots of sodium outside, lots of potassium inside
  - When pumping out 3 sodiums and 2 potassium, uses the energy of ATP and builds up a positive charge outside
  - The pump controls the net movement of ions - one out
  - And so generates a membrane potential (electrical charge), omg nerve impulses
  - Also builds up a concentration gradient that allows other processes to occur

Robert Hooke, first person to see a cell using a microscope (cork)
Cell theory:
- Cells are the fundamental units of life
- All organisms are composed of cells (or maybe just one lol)
- All cells come from pre-existing cells
Implications of cell theory:
- Functions of cells are similar
- Life is continuous
- Origin of life = origin of cells
Cells are usually small; exceptions:
- Bird eggs (each is one cell, and no, the nucleus is not the yolk; it's somewhere in the egg white)
- Some neurons
- Some algae
- Bacteria cells
But typically cells are small for a high surface area to volume ratio
- Volume determines the amount of chemical activity in the cell per unit time
- Surface area determines the amount of substances that can pass the cell boundary
- So reaction rate inside a cell is limited more by the surface area
- As you need a lot of surface area in order to get all the shit you need to pass into the cell

No nucleus obviously, although they have DNA; eubacteria and archaea
Cells very small; individuals are unicellular, but often found in chains or clusters (colonies etc)
Very successful - adapt to extreme conditions etc
Enclosed by plasma membrane
Thread of DNA, usually circular, contained in nucleoid
Cytoplasm: watery solution (cytosol), suspended particles
Ribosomes - site of protein synthesis (smaller than eukaryotic ribosomes)
Gram staining - thick peptidoglycan cell wall leads to gram positive, thin leads to negative
- Some antibiotics, such as penicillin, target the peptidoglycan cell wall specifically (so best against gram positive bacteria obviously)
Some have capsule: gelatinous outer layer, prevents from drying out (and also protects from white blood cells sometimes)
Some special features developed by some bacteria:
- Photosynthetic bacteria have internal membrane system, contains the necessary molecules (e.g. cyanobacteria)
- Others have internal membrane folds attached to plasma membrane - can function in cell division or energy-releasing reactions
- Some have flagella, made of protein flagellin
- Some have pili - hairlike structures projecting from surface, let bacteria stick to others (helpful for conjugation - sexual rep)
- Some rod-shaped (bacilli) have cytoskeleton made of an actin-like protein

Up to ten times larger than prokaryotes
Major advancement: compartmentalisation
Distinct nuclei enclosed in membrane, have membrane-bound organelles (like a little organ for the cell)
Endomembrane system: derived from outer membrane, has invaginated, complex structure
- This internal membrane system works efficiently, communicates etc
- Lipid bilayers - vesicles can bud off, or fuse (like bubbles forming, unforming etc)
- Also keeps cytosol protected from contents of vesicle or vice versa
- Endoplasmic reticulum: network of interconnected membranes, connected to nuclear envelope; large surface area
  - Rough ER: ribosomes attached, closer to nucleus; newly made proteins enter this lumen; modified, folded, transported to other regions via vesicles; most membrane-bound proteins synthesised here
  - Smooth ER: more tubular, no ribosomes (further from nucleus); stuff comes here to degrade; vesicles dock here and release drugs etc (oxidised here with a hydroxyl group, more soluble for excretion)
  - Smooth ERs are usually larger in drug users
  - They also synthesise lipids and steroids, degrade glycogen
- Golgi apparatus: stacks of flat membrane sacs (cisternae), midway between ER and membrane
  - Distribution apparatus, like a post office (or airport, I LIKE THIS BETTER)
  - Vesicles coming in, fuse with cis region (close to ER)
  - Go inside lumen, so things are modified (e.g. glycoproteins), then released as vesicles on the trans side, transported to outside of cell
  - Two main roles: receives proteins from ER to further modify them (especially adding oligosaccharides to membrane lipids)
  - And concentrate, package, and sort proteins before sending them to their destination through the trans-region
- Lysosomes: vesicles containing digestive enzymes that come in part from the Golgi; usually quite acidic
  - Think of them as the wandering stomachs of the cell; sites for breakdown of food and foreign material brought in by phagocytosis
  - They can also digest cell materials themselves (autophagy), ex: anorexics, cells don't have enough food, need to eat themselves
  - Also, when cell components are damaged and need to be removed and replaced by new ones
  - First, primary lysosome, fuses to form secondary lysosomes, which actually digest
  - Food is then secreted into the cytoplasm; unwanted stuff is ejected from cell
- Endomembrane system also includes plasma membrane and nuclear envelope
- All these membranes communicate with each other via vesicles; are very collaborative
Other things in animal cells:
- Centrioles (which make mitotic spindles for cell division)
- Nucleus usually the largest organelle, holds DNA; replication and transcription happen here, as does assembly of ribosomes (in nucleolus)
  - Nucleoplasm: chromatins ? Can't really hear what she's saying
  - Nuclear pores: control what goes in and out (DNA can't leave of course)
  - Nuclear localisation signal: binds to pore, signal for things being taken into the nucleus
  - In an interphase nucleus, chromatins are long, spread out, milky thing
  - When it is ready to divide, chromatin condenses, forms chromosomes
- Ribosomes: sites of protein synthesis (receive messenger RNA)
  - Are in both prokaryotic and eukaryotic cells, similar structure in both
  - Consist of ribosomal RNA (rRNA), more than 50 different protein molecules
  - Can be found floating in cytoplasm, in the ER, in chloroplasts, in nucleus etc
- Mitochondria: power plants (make energy)
  - Take the energy of fuel molecules (glucose), transform their energy into the bonds of energy-rich ATP (which cells can readily use)
  - The process of cellular respiration
  - Cells that require a lot of energy (e.g. muscle cells) have more mitochondria
  - Two membranes: outer membrane surrounds it
  - Inner membrane folds inward, to form cristae; large surface area for proteins involved in cellular respiration reactions
  - Space between membranes (matrix): contains ribosomes and mitochonrdrial DNA (different from nuclear DNA)
Some things specific to plant cells:
- Rigid cell wall, usually made of cellulose
- Also plastids, only in plants and some pigments; e.g. chloroplasts, contain the pigment chlorophyll, double membrane, DNA, ribosomes
  - Chloroplasts are stacked together like pitas - granum = stack of thylakoids
  - Other plastids: chromoplasts, contain red, orange, yellow pigments for flowers
  - Leucoplasts: storage, starch and fats (e.g. in potatoes)
- Vacuoles, in plant and protist cells: huge, store waste products and toxic compounds (dumpsters)
  - Provide structure for plant cells - water enters by osmosis (due to high solute concentration), results in turgor pressure
Having all these organells has allowed diversification of functions, and eventual specialisation into tissues
How did eukaryotic cells evolve? Two main theories:
- Endomembrane system originated from invagination of plasma membrane (some bacteria have the beginnings of this)
  - This would result in more compartmentalise, more surface area, etc
- Endosymbiosis theory: mitochondria and plastids arose when one cell engulfed another
  - So mitochondria would have existed separately, until one day a bacterium swallowed one up
  - Same with cyanobacteria - engulfed, eventually reduced to a chloroplast
  - Evidence for this: mitochondria and cyanobacteria have their own DNA, which differ from eukaryotic DNA
  - Japan: discovery of a single-cell eukaryote, Hatena, ingested a green alga
  - The green alga lost most of its function, became reduced
  - Curiously, when the cell divides, one daughter cell is green, the other not
  - The other not-green one will go on to ingest another green alga, presumably out of jealousy

Supports and maintains cell shape - but also dynamic (allows cells to change shape)
Holds organelles in position
Also imparts polarity to cells, so organelles can be moved from one point to another
Involved in cytoplasmic streaming
Interacts with extracellular structures to hold cell in place
Cells can flatten up on certain surfaces, become round on others; due to communication from outside
- When cells lose the ability to do this, they tend to become cancerous, oh no
- This is because they lose contact adhesion
Also present in prokaryotic cells
Have three components: (all formed of polymers; subunits are globular, dynamic proteins that harvest energy, usually ATP)
- Microfilaments: monomer (actin) forms trimer, which polymerises (triple string of pearls etc)
  - Have a plus end and a minus end; grows more at plus end
  - So stuff can be moved around by placing it at the plus end, lol
  - Microfilaments usually at periphery of cell, near plasma membrane
  - Actin = ancient proteins, almost the same in plant and animal cells (?); actin and myosin in muscle cells result in contraction
  - Microfilaments also involved in formation of pseudopods (lol amoebae), when actin starts to grow out as a bundle, depolymerise and contract, pulling the cell forward as it does so
  - Cells move around by actin and myosin binding (reversible), energy cycle
  - This bind and release linked to action of a molecular lever at head (how cells move forward)
  - In some cells, microfilaments form meshwork just inside plasma membrane
  - Example: microvilli in human intestine, to increase surface area for absorption (not dynamic)
- Intermediate filaments: thicker than microfilaments, not as thick as microtubules (many polymers)
  - Don't grow and shrink so much - stable network in cells
  - Animal cells have these; plants, yeast don't
  - Many different kinds - tough, ropelike protein assemblages, not dynamic, resist tension, anchor cell structures in place (esp. nucleus)
- Microtubules: separate chromosomes during cell division
  - Long, hollow tubes, composed of the protein tubulin (dimer), plus and minus end
  - Also form a rigid internal skeleton in some cells, but dynamic (can form, unform, whatever)
  - Have + and - ends
  - Can change length rapidly by adding or loser dimers
  - Act as a framework for motor proteins, along with microfilaments
- They all work together to produce a dynamic system, allows cells to change shape, stay rigid, divide, etc
Cilia and eukaryotic flagella, present on every cell
- Made up of microtubules in "9+2" array
- They have the same arrangement; only difference is length (cilia shorter, usually many more)
- Flagella are longer, usually one or two, movement is snakelike
- Microtubules can be formed in basal bodies, which promote their organisation and assembly based on a template etc
  - In the basal body, triplet organisation (9 triplets)
Centrioles: identical to basal bodies, except in a different place (near nucleus, not membrane) - formation of mitotic spindle
Motor proteins: undergo reversible shape changes, powered by ATP hydrolysis
- Dynein, binds to microtubule doublets, also moves chromosomes away from each other (for the mitotic spindle)
- Nexin: can cross-link doublets, prevent them from sliding; cilium bends
- Kinesin: binds to vesicle, helps move it along (cargo domain); usually kinesins work together, move up microtubule; long walks
Experiments to determine the function of cellular components:
- Inhibition: drug that inhibits structure or process; does the function still occur?
- Mutation: examine a cell that lacks the gene for the structure or process

Potential (chemical, concentration gradients, charge imbalances etc) vs. kinetic energy
Metabolism: sum total of all chemical reactions in an organism
- Anabolic: complex molecules made from simple; energy input required
- Catabolic reactions: complex molecules broken down to simple; energy released
It takes energy to impose order on a system; a lot of order in biological systems, comes at cost of lots of energy
- Total energy (enthalphy - H) = Gibbs free energy (G) + entropy (S) * temperature (T)
$\Delta G$ between products and reactions - if negative, free energy released; if positive, energy consumed
If free energy is not available, no reaction occurs
Magnitude of G depends on delta H (total energy added or released) and change in entropy
Example: breaking apart ATP molecule to produce ADP; the high-energy bond is full of energy
- When you break protein into amino acids through hydrolysis, increase in entropy and thus -delta G scales with delta S
First law: energy never destroyed etc
Second law: entropy increases through energy transformations so living organisms need constant supply of energy to maintain order
Exergonic reactions: release free energy (-deltaG): catabolism, complexity decreases (generates disorder)
- So products have less free energy than reactants (think of ball rolling down hill)
Endergonic reactions: consume free energy (+deltaG), anabolism; complexity increases
- Think of pushing ball up a hill (products have more energy, so you need a certain amount of energy to initiate)
In principle, chemical reaction can run in both directions
- So both the forward and reverse reaction are balanced, with deltaG = 0 at the equilibrium point
- The value of deltaG gives you the point of equilibrium - near-zero values of deltaG relate to easily reversible reactions
- If deltaG is very negative, will produce more product than reactant
- If deltaG is very positive, will produce more reactant than product
- Just think of it in terms of balls rolling down hills etc (ball will tend towards the bottom of the hill)
Example: 100% glucose 1-phosphate initially, at equilibrium you have 95% glucose 6-phosphate (as 1 to 6 is exergonic)
So nothing ever really goes to completion (except asymptotically)
ATP: nucleotide adenosine triphosphate, captures and releases free energy (energy currency of cell)
- When hydrolysed (phosphorylester ? bond broken), releases much energy
- Can phosphorylate, or donate phosphate groups, to other molecules
- ATP, when it releases energy, is clearly very exergonic
- Formation of ATP from ADP is endergonic; formation and breakdown reactions coupled
- Remember the tertiary phosphate group, at the end

Catalysts: speed up the rate of reaction; not themselves altered by reaction
- Do not make impossible reactions possible; just lower activation energy by providing an alternate reaction pathway
Enzyme (protein): framework in which unfavoured reactions can take place, special kind of catalyst ?
Cells find ways to lower activation energy to make reactions proceed
- Transition states - unstable forms, higher free energy
- Activation energy can come from heating a system (more kinetic energy)
- Enzymes and ribozymes lower the energy barrier, bring reactants together, or stabilise things in states
Biological catalysts (enzymes, ribozymes) highly specific - specific substrates (reactants) they use
- Substrate molecules bind to the active site of the enzyme
- The 3D shape of the enzyme determines its specificity
- Enyzme-substrate complex held together by electrical attraction etc, dynamic
- Enzymes don't change final equilibrium or deltaG; just ensure that the reaction can start
Mechanisms for catalysing reactions:
- Reducing dimensionality (orienting substrate molecules, bringing together atoms that will bond)
- Physical strain (can stretch bonds in substrate molecules, making them unstable)
- Chemical charge (can temporarily add chemical groups to substrates)
Shape of enzyme active sites allows a specific substrate to fit (lock and key)
- Binding depends on hydrogen bonds, electrostatic attraction, hydrophobic interactions
- Many enzymes change shape when they bind to the substrate - induced fit
Some enzymes require partners:
- Prosthetic groups: non-amino acid groups, e.g. lipids bound to enzymes to stabilise
- Cofactors: inorganic ions
- Coenzymes: small carbon-containing molecules, not bound permanently to enzymes; e.g. ligands
The rate of a catalysed reaction depends on substrate concentration
- Concentration of enzyme usually lower than concentration of substrate
- At saturation, all enzymes are bound to substrate - maximum rate
- Used to calculate enzyme efficiency - turnover (molecules of substrate converted per unit of enzyme)
Reactions organised in metabolic pathways, interconnected both in space and in time
Inhibitors: regulate enzymes by binding to them and slowing reaction rates
- Naturally-occurring inhibitors regulate metabolism
- For example, you're a bacterium, feasting on sugar, so you start metabolising
- But then you run out of sugar ... so you need to stop metabolising otherwise you end up losing energy
- Bacteria have a (negative?) feedback loop that can inhibit metabolism (raise activation energy somehow)
- Irreversible inhibition: covalently bond to side chains in active site - permanently inactivates enzyme
  - Example, nerve gas - once it goes in it never comes out
- Reversible inhibition: bonds noncovalently, prevents substrate from bonding temporarily
  - For example, enzyme modified by another enzyme so that it can no longer catalyse reactions, geometrically
- Competitive inhibitors: compete with substrate, bind at the same active site
- Noncompetitive inhibitors: same as above, but bind to the enzyme at a different site (change shape of enzyme, alters active site, prevent binding) - allostery
  - Example: hemoglobin, quaternary structure, cooperative
  - Allosteric enzymes more sensitive to changes in concentration of substrate (graph: like acid-base titration or S versus log graph for nonallosteric)
Every enzyme is most active at a particular pH
- It influences the ionisation of functional groups
- e.g. at low pH, COO- reacts with H+ to form COOH which is no longer charged; affects protein folding and thus enzyme function
- Compartmentalisation is a way of safeguarding reactions etc, keeping them confined to a certain area (e.g. in the cell)
Same thing with optimal temperature
- Active form: enzyme can bind to shit
- Inactive form: enzyme cannot bind to shit

Being alive costs energy ... where does this energy come from etc (animals: food; plants: light)
Food/light is broken down (food) or built up (light) into fuel molecules
- This is GLUCOSE

Glucose: C₆H₁₂O₆ + 6O2 → 6COs + 6H2O + free energy (deltaG is -686 kcal/mol)
Must be broken down in many progressive substeps (to prevent it from exploding I guess)
Each reaction is catalysed by a specific enzyme
In eukaryotes, metabolic pathways are compartmentalised in organelles (part of the reason for their efficiency)
Each pathway regulated by key enzymes
Metabolic pathways similar in all organisms
- Glycolysis: glucose is converted into pyruvate (only 3 carbon atoms) - 1:2
- Cellular respiration (aerobic; needs oxygen present), converts pyruvate into H2O and CO2
  - Complete oxidation, gives you 32 ATPs per glucose molecule; more efficient
  - Pathways: pyruvate oxidation and the citric acid cycle (Krebs cycle)
  - Pyruvate oxidation: broken down into 3 carbon dioxides; releases energy, either as ATP or electron carriers
  - Third pathway (respiration chain), the electron carriers from above are recycled (oxidation phosphorylation), generating ATPs
  - Energy transfer due to redox reactions (oil rig); oxidising agent makes the other one oxidised (so is reduced)
  - In glucose combustion, glucose is the reducing agent, O2 the oxidising agent
- OR fermentation (anerobic): converts pyruvate into CO2, and lactic acid or ethanol
  - Incomplete oxidation, gives you two ATP per glucose
  - A lot of energy still trapped in the waste products (lactic acid and ethanol)
How is free energy harvested? Let's look at methane, the simplest carbohydrate
- Most reduced state corresponds with the highest free energy (most electrons)
- Carbon more electronegative than hydrogen, so the electrons are closer to the carbon
- But if you add oxygen (exchange a H), the carbon is oxidised and sort of loses an electron
- The more oxidised, the less free energy
- Scale: methane → methanol → methanal → methanoic acid → carbon dioxide
- Carbon dioxide - most oxidised state, virtually no energy left (the C-H bond is very energy-rich however)
- So in each oxidation step, free energy is released
Ways of harvesting this free energy:
- Use to convert immediately from ADP to ATP (12 kcal/mol); less common
- More efficiently: electron carriers are made to accept these electrons (50 kcal/mol of energy produced)
  - Coenzyme NAD+ - key electron carrier in redox reactions
  - Add one H+ and 2 electrons, this reduces it into NADH
  - This reduced form (NADH) is then used in the respiratory chain (oxidised then, releasing energy) to produce ATP
Remember that at pretty much every step in cellular respiration, some ATP is produced; but only significantly so at the end
- Protongradient: drives oxidative phosphorylation, energy from oxidation of NAD and FAD (to produce ATP)
These pathways all occur in different parts of the cell in eukaryotes
- Glycolysis and fermentation: outside mitochondria
- Everything else, inside (respiratory chain in inner membrane, krebs and pyruvate oxidation in matrix)
- In prokaryotes: cytoplasm has glycolysis, fermentation, krebs cycle; repiratory chain and pyruvate oxidation on plasma membrane

More on glycolysis: glucose broken down into 2 pyruvates
- First, you need to input energy to overcome activation energy of reaction - requires 2 ADP
- Takes place in the cytosol
- Generates no CO2, produces a small amount of energy
- Net change: glucose becomes 2 molecules of pyruvate, and yu get 2 molecules of ATP and 2 NADH
Pyruvate oxidation: links glycolysis and krebs cycle; occurs in mitochondrial matrix
- Pyruvate (3 carbons) oxidised to acetate (2 carbons) and carbon dioxide
- NAD+ reduced to NADH, capturing some of the energy from the above oxidation
- The remaining energy is stored by combining acetate and coenzyme A to form a huge complex (acetyl-coA)
- Catalysed by pyruvate dehydrogenase (60 proteins, 5 co-enzymes) - this is incidentally what arsenic inhibits
Acetyl CoA is the starting point of the citric acid cycle
- Inputs: water, acetyl CoA, water and electron carriers (NAD+, FAD, GDP)
- Most of the electron carrier stuff etc done here (most of the energy transferred this way)
- Outputs: CO2, reduced electron carriers, GTP (which converts ADP to ATP)
- The acetyl CoA is hooked to a 4-carbon atom (oxaloacetate), forming citrate (citric acid), becomes isocitrate
  - Loses first one carbon as carbon dioxide, then another
- Then regenerates to become oxaloacetate eventually (many intermediate steps, ATP etc produced)
- Citric acid cycle is in steady state - concentration of intermediates don't change
- Cycle continues when starting materials are available (reoxidised electron carriers and acetyl CoA)
- Total yield: 6 carbon dioxide, 10 NADH, 2 FADH2, 4 ATP
- Electron carriers need to be reoxidised so that they can take part in the cycle again, and to free the energy to make ATP
  - Occurs either in oxidative phosphorylation (if O2 present) or fermentation (if anaerobic)

Oxidative phosphorylation: ATP synthesised using energy released by reoxidation of electron carriers
Extremely exergonic reaction - too much energy is produced, doesn't happen in cells
Instead, happens in little steps: electron transport and chemiosmosis
Electron transport:
- Happens in inner mitochondrial membrane
- Electrons from NADH and FADH2 are passed through respiratory chain of membrane; energy set free at each step
- This energy released is used to build up a proton gradient, protons pumped into inner membrane space
  - Creates both a concentration gradient and a charge difference (potential energy - proton-motive force)
  - This force is converted into the production of ATP
- This series of membrane-associated protein complexes: large, protein complex (1-4), enzymes, etc
Chemiosmosis
- Protons diffuse back into the mitochondrial matrix through the channel protein ATP synthase (can't pass through membrane)
- When protons pass through it, the channel deforms, catalysing production of ATP
- Results in ATP synthesis through diffusion ?
- ATP leaves the mitochondria once made, which keeps the concentration low (drives the forward reaction - synthesis over hydrolysis)
- Proton gradient is of course constantly maintained by electron transport and proton pumping
- ATP synthesis can be uncoupled - if a different H+ diffusion channel is inserted into the mitochondrial membrane, energy set free lost as heat
  - Useful for hibernating animals etc; H+ released as heat instead of coupled to ATP synthesis
  - Uncoupling protein: thermogenin
Experiment proving that an H+ gradient drives ATP synthesis
- Using pH of 9 in the inner membrane, pH of 7 on the outside
- Resulted in the production of ATP

Glycolysis is the same for aerobic and anaerobic pathways
But if you don't have oxygen, you might as well keep doing glycolysis to get a bit of ATP
However, you end up using all your NAD+ this way ... so fermentation is a way of regenerating NAD+ (which accepts electrons)
Fermentation occurs in the cytosol
NADH+ goes to NAD+ + H+ + 2e- (oxidation of NADH)
- Thus regenerating NAD+
- More than one way of doing this - many fermentation pathways
- Two major pathways: lactic acid fermentation and ethanol fermentation
- Lactic acid fermentation:
  - Pyruvate is reduced by the enzyme lactate dehydrogenase to produce lactate (going backwards in a way)
  - Which produces more NAD+
  - The end product is lactic acid (lactate), high-energy molecule but it stops there
  - This results in sore muscles (so when you use your muscles a lot, eventually supply of O2 dwindles, so muscles do this)
- Alcoholic fermentation:
  - Occurs in yeast, some plant cells
  - Requires two reactions
  - First, decarboxylation reaction (results in aldehyde ethanal)
  - Ethanal is then reduced into ethanol
  - End result: just like 2 ATP, lol (incomplete combustion)
  - So obviously less efficient than cellular respiration, more of a short-term solution (long-term for yeast I guess)

Glucose isn't the only thing involved in metabolic reactions
Other products enter metabolic pathways, all interrelated
Catabolic products enter the pathways at different steps
Intermediate products leave at some steps to be involved in other reactions
Lots of hustle and bustle
Catabolic interconversions:
- Polysacchardies are hydrolysed to glucose
- Lipids broken down to glycerol and fatty acids (eventually acetyl CoA)
- Proteins hydrolysed to amino acids, feed into glycolysis or krebs cycle
- Most are reversible
Anabolic interconversions:
- Gluconeogenesis: glucose formed from citric acid cycle and glycolysis intermediates, for storage (undo previous reactions?)
- Acetyl CoA can be used to make fatty acids
Glycolysis, krebs cycle, respiratory chain subject to allosteric regulation (effector molecule binds to site other than active site)
- Regulation by conformational change (not competitive binding)
- Changed so that it can either bind or not bind, depending on step and purpose I guess
- Negative feedback loop: if you have too much ATP, need to stop the cycle somehow; ATP can inhibit further production of itself
- By blocking various enzymes at various points (potent inhibitor)
- Low levels of ATP and high ATP: activator, to activate enzymes
- Enough citrate can inhibit glycolysis, or activate fatty acid synthesis (too much acetyl CoA, get rid of it ... you get fat)
- ^ Example of a positive feedback loop

Responsible for oxygen in the atmosphere, biomass, food etc
Carbon dioxide and water → glucose, water and oxygen
- Light is required to split carbon dioxide molecules
- Water is the source of the oxygen released (experiment done with radioactive tracers)
Two pathways:
- Light reactions (light energy converted to chemical energy as ATP and NADPH)
- Then carbon-fixation reactions (light independent), ATP from NADPH from above, plus carbon dioxide, produces carbohydrates
Everything happens in the chloroplast
Photons are absorbed by molecules in this case
Molecules that absorb specific wavelengths in the visible range: pigments
- Example, chlorophyll absorbs red and blue light, and so leaves are green
- Accessory pigments: cover the parts of spectrum that chlorophyll doesn't
- Carotenoids and phycobilins; transfer the energy to chlorophylls
- These pigments are found in chloroplasts, in thylakoids
- When a pigment molecule absorbs a photon, the energy is usually transferred to another molecule
  - Although it can be released as heat or light - fluorescence (lower wavelength)
  - Or it can use it to drive a chemical reaction, which also happens but not interesting in this context
- Target molecule must be near, with the right orientation and the right structure
- Resonance energy transfer: electrons are excited from one molecule to the next (no electrons are transferred)
- Chlorophyll becomes a reducing agent
- The electron donated passed through chain of electron carriers onto NADP, which becomes NADPH and H+; ATP is made
Electron transport:
- Noncyclic, produces NADPH and ATP, requires two photosystems
  - Photosystem II results in water being split, due to a positive charge (?)
  - Light energy oxidises water, makes ATP
  - Photosystem I, different wavelength (more IR)
  - Positively charged pigment does not split water, accepts electron
  - The photosystems result in Z scheme
- Cyclic: ATP only
- Calvin cycle: same as carbon fixation, water and carbon dioxide converted into organic compounds
- Whatever

Notes for Part I: The Cell (Vogel's Section)

1Small molecules¶

2Large molecules¶

2.1Acids and bases¶

2.2Isomerism¶

2.3Components of a cell¶

2.4Sugars¶

2.5Nucleic acids¶

2.6Lipids¶

2.7Proteins¶

3Cellular membranes¶

3.1Membrane structure¶

3.2Tissue formation¶

3.3Selective permeability¶

4Organisation of the cell¶

4.1Prokaryotic cells¶

4.2Eukaryotic cells¶

4.3The cytoskeleton¶

5Energy, enzymes, and metabolism¶

5.1Enzymes¶

6Pathways that release energy¶

6.1Glucose oxidation¶

6.2Aerobic pathways¶

6.3Formation of ATP¶

6.4Fermentation¶

6.5Metabolic pathways¶

7Photosynthesis¶