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

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

1Small molecules¶

• 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

2Large molecules¶

2.1Acids and bases¶

• 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)

2.2Isomerism¶

• 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)

2.3Components of a cell¶

• 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

2.4Sugars¶

• 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)

2.5Nucleic acids¶

• 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

2.6Lipids¶

• 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

2.7Proteins¶

• 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

3Cellular membranes¶

3.1Membrane structure¶

• 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

3.2Tissue formation¶

• 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

3.3Selective permeability¶

• 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

4Organisation of the cell¶

• 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

4.1Prokaryotic cells¶

• 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

4.2Eukaryotic cells¶

• Up to ten times larger than prokaryotes
• 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

4.3The cytoskeleton¶

• 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
• 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

5Energy, enzymes, and metabolism¶

• 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

5.1Enzymes¶

• 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

6Pathways that release energy¶

• 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

6.1Glucose oxidation¶

• Glucose: C6H12O6 + 6O2 &rarr; 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 &rarr; methanol &rarr; methanal &rarr; methanoic acid &rarr; 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
• 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

6.2Aerobic pathways¶

• 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)

6.3Formation of ATP¶

• 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

6.4Fermentation¶

• 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
• 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)
• 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)

6.5Metabolic pathways¶

• 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

7Photosynthesis¶

• Responsible for oxygen in the atmosphere, biomass, food etc
• Carbon dioxide and water &rarr; 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