Chapter 6: A Tour of the Cell

6.1: Biologists use microscopes and biochemistry to study cells

• Light Microscope (LM): Visible light passes through a specimen and glass lenses, which refract the light in a way that magnifies the image of the specimen

• Magnification: Image Size: Real Size ratio

  • Light microscopes magnify the image ~x1000

• Resolution: Measure of clarity of the image, inversely related to wavelength of light a microscope uses for imaging

• Organelles: Membrane enclosed compartments within cells

• Electron Microscope (EM): Beam of electrons is shone through specimen or onto its surface

• Scanning Electron Microscope (SEM): Electron beam scans surface of the sample which excites the surface elctrons. This is detected and translated into a 3D video

  • Useful for detailed study of topography of a specimen

• Transmission Electron Microscope (TEM): Electron beam aimed through very thin section of the specimen which has been stained with atoms of heavy metals, which attach to certain cellular structures and thus enhance electron density in some parts more than others. Pattern of density is translated into an image

  • Used to study internal cell structure

• Cell Fractionation: Take cells apart, seperate major organelles and other subcellular structures from each other using a centrifuge (differential centrifugation)

  • Differential Centrifugation: Spins test tubes holding mixtures of disrupted cells at a series of increasing speeds

• Cytology: Study of cell structure

• Biochemistry: Study of chemical processes of cells

6.2: Eukaryotic cells have internal membranes that compartmentalize their functions

• Prokaryotic Cells: Bacteria and archaea

  • DNA is in the nucleoid, which is not enclosed by a membrane

• Eukaryotic Cells: Fungi, animals, and plants

  • Most DNA is in the nucleus, bounded by a double membrane

• All cells…

  • Are bounded by a plasma/cell membrane

  • Have cytosol

    • Cytosol: Semifluid, jellylike substance where subcellular components are suspended

  • Have chromosomes with DNA

  • Have ribosomes

    • Ribosomes: Make proteins using gene instructions

• Cytoplasm: Interior of any type of cell

  • In eukaryotic cells, this is only the region beyween the nucleus and plasma membrane

  • In some prokaryotic cells, there are regions surrounded by proteins in which specific reactions happen

• Plasma Membrane: Selective barrier that allows passage of oxygen, nutrients, and wastes. A double layer of phospholipids and other lipids

6.3: The eukaryotic cell’s genetic instructions are house in the nucleus

• Nucleus: Contains most genes in the eukaryotic cell

• Nuclear Envelope: Encloses the nucleus and seperates its components from the cytoplasm

  • Double membrane, each a lipid bilayer with associated proteins

  • Envelope has lots of pores. At the lip of each, the inner and outer membranes of the nuclear envelope are continuous

  • Pore complex (intricate protein structure) lines each pore and regulates entry and exit of proteins, RNAs, and large complexes of macromolecules

  • Nuclear Lamina: Netlike array of protein filaments that maintains shape of nucleus by mechanically supporting the nuclear envelope, lines nuclear side of the envelope except at the pores

• Chromosomes: Discrete units that DNA is organized into, carry the genetic info

  • Chromatin: Complex of DNA and proteins making up chromosomes

• Nucleolus: Mass of densely stained granules and fibers adjoining part of the chromatin to synthesize RNA

  • Nucleus directs protein synthesis by synthesizing mRNA → mRNA transported to cytoplasm via nuclear pores → translated by ribosomes into primary structure of a specific polypeptide once it reaches the cytoplasm

• Ribosomes: Complexes made of ribosomal RNAs and proteins, carry out protein synthesis

  • Free Ribosomes: Ribosomes suspended in cytosol, which produce proteins that function within the cytosol

  • Bound Ribosomes: Outside the ER or nuclear envelope, produce proteins destined for insertion into membranes, packaging within organelles, or export from the cell (secretion)

6.4: The endomembrane system regulates protein traffic and performs metabolic functions

• Endomembrane System: Synthesizes proteins, transports proteins and organelles into membranes or out of the cell, metabolism, movement of lipids, and detoxification of poisons

  • System includes nuclear envelope, endoplasmic reticulum, golgi apparatus, lysosomes, vesicles and vacuoles, and plasma membrane

• Vesicles: Sacs made of membrane, transfer membrane sacs

• Endoplasmic Reticulum: Extensive network of membranes, accounts for 50%+ of the cell’s total membrane. Consists of cisternae, seperates lumen from cytosol, continuous with the nuclear envelope

  • Cisternae: Membranous tubules and sacs

  • ER Lumen/Cisternal Space: Internal compartment of ER, cavity

  • Smooth ER: Outer surface has no ribosomes

    • Synthesizes lipids, metabolism, detoxifies drugs and poisons, stores calcium ions

  • Rough ER: Studded with ribosomes on the outer surface of the membrane

    • As a protein is built, it goes through a pore in the ER’s membrane, entering the lumen to take proper shape. Then the ER membrane keeps them seperate, wrapped in membranes of vesicles, and are transported through transport vesicles

    • Glycoproteins: Most secretory proteins, proteins with carbohydrates covalently bonded to them

    • Rough ER grows in place by adding membrane proteins and phospholipids to its own membrane

• Golgi Apparatus: Modifies and stores products, then sends them to other destinations. Kind of like a warehouse that recieves, stores, ships, and even does some manufacturing

  • Group of associated flattened cisternae, looks like a stack of pita bread

  • Membranes of cisternae on opposite sides are different, cis and trans face

    • Cis face is near the ER, receives material from ER

    • Trans face gives rise to vesicles that pinch off and travel to other sites, transports material

    • Products are modified in transit between the two faces

  • Manufactures some macromolecules

    • ex. pectins and other noncellulose polysaccharides

• Lysosome: Membranous sac of hydrolytic enzymes that are used to digest (hydrolyze) macromolecules, work best in acidic encironments

  • Hydrolytic enzymes and lysosomal membrane are made by rough ER → golgi for processing

  • Phagocytosis: Engulfing smaller organisms or food particles, how amoebas and other unicellular protists eat

    • Food vacuole then fuses with the lysosome and enzymes digest the food

  • Autophagy: Process where lysosomes use their hydrolytic enzymes to recycle their own organic material. Damaged organelle or small amount of cytosol is surrounded by a double membrane and a lysosome fuses with the outer membrane of it. Inner membrane and material dismantled by lysosomal enzymes, resulting compounds are released to be reused by cytosol

• Vacuoles: Large vesicles derived from ER and golgi apparatus

  • Contractile Vacuoles: Pump excess water out of the cell

  • Central Vacuole: Large in mature plant cells, inside is cell sap (cell’s main repository of inorganic ions), plays major role in growth of plant cells which enlarge as it absorbs water

6.5: Mitochondria and chloroplasts change energy from one form to another

• Mitochondria: Sites of cellular respiration

  • Cellular Respiration: Metabolic process that uses oxygen to drive generation of ATP by extracting energy from sugars, fats, and other fuels

• Chloroplasts: Sites of photosynthesis in algae and plants

• Endosymbiont Theory: Nonphotosynthetic prokaryotes engulfed a photosynthetic bacteria, as they developed together in symbiosis, it turned into mitochondria/chloroplasts

  1. Double membranes in mitochondria, chloroplasts, and bacteria cells

  2. Replication method is similar

  3. Circular DNA

• Mitochondria has a phospholipid bilayer with a unique collection of embedded proteins. Outer membrane is smooth, inner membrane is convoluted with cristae

  • Cristae: Infoldings

  • Intermembrane Space: Region between membranes

  • Mitochondrial Matrix: Second compartment enclosed by inner membrane, has many different enzymes, mitochondrial DNA, and enzymes

• Thylakoids: Flattened, interconnected sacs in the chloroplast

  • Granum: Stack of thylakoids

  • Stroma: Fluid outside the thylakoid, has chloroplast DNA, ribosomes, and many enzymes

• Plastids: Family of closely related plant organelles

• Peroxisome: Spexialized metabolic compartment with a single membrane. Has enzymes that remove H atoms from substrates and transfer them to oxygen to produce hydrogen peroxide (H₂O₂)

  • Some use oxygen to break fatty acids down into smaller molecules

  • Ones in the liver detoxify alcohol and other harmful compounds

  • Has a enzyme that converts hydrogen peroxide to water

6.6: The cytoskeleton is a network of fibers that organizes structures and activities in the cell

• Cytoskeleton: Network of fibers extending throughout the cytoplasm. 3 main types of fiber

  • Microtubules: Thickest cytoskeleton fiber, hollow rods, made from tubulin proteins (dimers, molecule made of 2 subunits)

    • Tubulin dimer consists of a and B tubulin

    • Plus end releases dimers at a higher rate

  • Microfilaments/Actin: Thin solid rods build from two intertwined strands of the globular protein actin (twisted double chain)

    • Present in all cells

    • Can form structural networks when certain proteins bind along the side of a filament to make branches

  • Immediate Filaments: Intermediate diameter (between microtubules and microfilaments), specialized for bearing tension, diverse class of cytoskeletal elements, permanent even after cells die

• Centrosome: Region located near nucleus, where microtubules grow out of, the compression resisting girders of the cytoskeleton

  • Centrioles: Pair of them within the centrosome, each pair has 9 sets of triplet microtubules arranged in a ring

• Flagella & cilia sometimes in eukaryotic cells, cellular extensions that contain microtubules

  • Flagella have just a few in a cell and are longer than cilia. Beats in undulating motion like a fishtail

  • Motile cilia are in large numbers on the cell surface and have alternating power and recovery strokes like oars. May also be like a signal recieving antenna for the cell (these are nonmotile and there is only 1 per cell)

  • Both have 9+2 pattern, 9 doublets of microtubules in a ring with two single ones in its center

• Basal Body: Anchors cilia or flagellum microtubule assembly, structurally similar to a centriole

• Dyenins: Large motor proteins attached along each outer microtubule doublet in flagella and motile cilia. Has two feet that walk along the microtubule of the adjacent doublet

• Cortex: Outer cytoplasmic layer of a cell with a gel semisolid consistency

• Myosin: Protein that makes up actin filaments and thicker filaments to cause contraction of muscle cells

• Pseudopia: Cellular extensions that help a cell crawl along a surface

• Cytoplasmic Streaming: Circular flow of cytoplasm within cells

6.7: Extracellular components and connections between cells help coordinate cellular activities

• Cell Wall: Extracellular structure of plant cells, thicker than plasma membrane

  • Primary Cell Wall: Relatively thin and flexible wall secreted first by a young plant cell

  • Middle Lamella: Thin layer rich in sticky polysaccharides (pectins), between primary walls of adjacent cells, glues them together

• Some cells strengthen cell walls by secreting hardening substances into the primary wall

• Secondary Wall: Added between plasma membrane and primary wall with strong and durable matrix that affords the cell protection and support in cells that don’t secrete hardening substances into primary wall

• Extracellular Matrix (ECM): Elaborate animal cell structure like a cell wall

  • Collagen: Forms strong fibers outside the cells, most abundant glycoprotein in the ECM, ~40% total protein in the human body

    • Embedded in a network of proteoglycans

• Gibronectin: ECM glycoprotein, binds integrins to ECM

  • Integrins: Cell surface receptor proteins, span the membrane

• Plasmodesmata: Channels that connect cells, perforate plant cell walls

• Tight Junctions: Plasma membranes of neighboring cells are pressed very tightly against each other, bound by specific proteins

• Desmosomes: Fasten cells together into strong sheets, attach muscle cells to each other

• Gap Junctions: Provide cytoplasmic channels from one cell to an adjacent cell, create pores through which things may pass, necessary for communication between cells

6.8: A cell is greater than the sum of its parts

• Many components work together in a functioning cell

Chapter 7: Membrane Structure and Function

7.1: Cellular membranes are fluid mosaics of lipids and proteins

• Ampipathic: Has a hydrophillic and hydrophobic region

• Fluid Mosaic Model: Membrane is a mosaic of protein molecules bobbing in a fluid bilayer of phospholipids

• Integral Proteins: Penetrate hydrophobic interior of the lipid bilayer

  • Transmembrane Proteins: Span the membrane, majority of integral proteins

  • Others extend only partway into the interior

• Peripheral Proteins: Not embedded in bilayer, loosely bound to surface

• Glycolipids: Membrane carbohydrates covalently bonded to lipids

• Glycoproteins: Membrane carbohydrates covalently bonded to proteins

7.2: Membrane structure results in selective permeability

• Selective Permeability: Allows some substances to cross more easily than others

• Transport Proteins: Help hydrophillic substances pass through the membrane

• Aquaporins: Facilitates passage of water molecules through the membrane

7.3: Passive transport is diffusion of a substance across a membrane with no energy investment

• Diffusion: Movement of particles from high to low concentration

• Concentration Gradient: Region along which the density of a substance increases or decreases

• Passive Transport: Transport that requires no energy

• Osmosis: Diffusion of free water across a selectively permeable membrane

• Tonicity: Ability of a surrounding solution to cause a cell to gain or lose water

• Hypotonic: Solution has less solutes than in another

  • Water is hypotonic to everything.

  • Water enters cells.

  • Animal cell is Lysed 😢

  • Plant cell is Turgid 🙂

• Isotonic: Equal number of solutes in both solutions

  • Animal cell is Normal 🙂

  • Plant cell is Flaccid 😐

• Hypertonic: Solution has more solutes than another

• Water leaves cells.

  • Animal cell is Crenate 😢

  • Plant cell is Plasmolysed 😢

• Osmoregulation: Control of solute concentrations and water balance in organisms without rigid cell walls

• Facilitated Diffusion: Polar molecules and ions diffuse passively with the help of transport proteins

• Ion Channels: Channel proteins that transport ions

  • Gated channels: Open or close in response to a stimulus

7.4: Active transport uses energy to move solutes against their gradients

• Active Transport: Using ATP to transport a solute across a membrane

  • Enables internal concentrations to differ from external concentrations

  • ex. Sodium potassium pump

• Membrane Potential: Voltage across a membrane

  • Cytoplasmic side of a membrane is negative in charge relative to the extracellular side

  • Ranges from -50 to -200 mV

• Electrochemical Gradient: Combination of chemical force and an electrical force acing on an ion

• Electrogenic Pump: Transport protein that generates voltage across a membrane

  • Proton Pump: Actively transports protons out of the cell

• Cotransport: Using proton gradient to power something else

7.5: Bulk transport across the plasma membrane occurs by exocytosis

• Exocytosis: Secreting certain molecules by fusion of vesicles with the plasma membrane

• Endocytosis: Cell takes in molecules by forming new vesicles by pinching off part of the membrane.

  • Phagocytosis: Cell engulfs a particle by extending pseudopia around it and packaging it in a food vacuole

  • Pinocytosis: Cell continually “gulps” droplets of extracellular fluid into tiny vesicles

    • Receptor Mediated Endocutosis: Specialized type of pinocytosis, enables cell to aquire large quantitites of specific substances

Chapter 8: An Introduction to Metabolism

8.1: An organism’s metabolism transforms matter and energy

• Metabolism: Totality of an organism’s chemical reactions

• Metabolic Pathway: Specific molecule is altered in a series of defined steps, each catalyzed by a specific enzyme, resulting in a certain product

• Catabolic Pathways: Breakdown pathways, release energy

• Anabolic Pathways: Consume energy to build complex molecules from simpler ones

• Kinetic Energy: Energy associated with relative motion of objects

  • Thermal Energy: Kinetic energy associated with random movement of atoms or molecules

    • Heat: Thermal energy in transfer from one object to another

• Potential Energy: Energy that matter posesses because of its location or structure

• Chemical Energy: Potential energy available for release in a chemical reation

• Spontaneous Process: Process that can happen without input of energy, leads to an increease in entropy by itself

• Thermodynamics: Study of energy transformatios that occur in a collection of matter

  • First Law of Thermodynamics/Principle of Conservation of Energy: The energy of the universe is constant—Energy can be transferred and tranformed but not created or destroyed

  • Second Law of Thermodynamics: Every energy tranfer or transformation increases the entropy of the universe

    • Entropy: Measure of molecular disorder/randomness

8.2: The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously

• Free Energy: Portion of energy that can perform work when temperature and pressure are uniform

  • ΔG = ΔH - TΔS

    • ΔG is change in free energy

      • ΔG = G_{final state} - G_{initial state}

    • ΔH is change in system’s enthalpy (total energy)

    • ΔS is change in system’s entropy

    • T is absolute temperature in Kelvins

• Exergonic Reaction: Net release of free energy, negative ΔG

• Endergonic Reaction: Absorbs free energy from its surroundings, positive ΔG

8.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions

• Three main kinds of work that a cell does

  • Chemical Work: The pushing of endergonic reactions that would not occur spontaneously

    • ex. Synthesis of polymers from monomers

  • Transport Work: Pumping of substances across membranes against direction of spontaneous movement

  • Mechanical Work

    • ex. Beating of cilia contraction of muscle cells, movement of chromosomes during cellular reproduction

• Energy Coupling: The use of an exergonic process to drive an endergonic one, how cells manage energy resources to do work

• ATP (Adenosine Triphosphate): Sugar ribose + nitrogenous base adenine + chain of 3 phosphate groups (like a compressed spring)

  • Terminal phosphate bond can be broken by hydrolysis, when it is, splits into inorganic phosphate molecule (HOPO_3^2-or P_i) and ADP

    • ATP + H₂O —> ADP + P_i

    • ΔG = -7.3 kcal/mol (-30.5 kJ/mol)

• Phosphorylated Intermediate: Recipient molecule of phosphate group from ATP, which is made less stable

• ATP is renewable, and can be regenerated by the addition of phosphate to ADP

  • Free energy required to phosphorylate ATP comes from exergonic catabolism in the cell

  • Chemical potential energy stored in ATP drives most cellular work

1. It uses energy from catabolism to phosphorylate ADP and generate ATP

2. First one since second one involves the synthesis of ATP, which requires energy, so it is endergonic, which means free energy is positive

3. active

8.4: Enzymes speed up metabolic reactions by lowering energy barriers

• Enzyme: Macromolecule that acts as a catalyst

  • Catalyst: Chemical agent that speeds up a reaction without being consumed by it

• Activation Energy: Energy required to contort reactant molecules so bonds can break—amount of energy needed to push the reactants to the top of a barrier so the downhill part can begin

  • Lowered by enzymes

• Substrate: Reactant an enzyme acts on

  • Enzyme Substrate Complex: Enzyme binded with substrate

• Active Site: Restricted region of the enzyme that actually binds to the substrate

• Induced Fit: Tightening of binding after initial contact

• Cofactors: Nonprotein helpers for catalytic activitym either bound tightly to the enzyme or bound loosely and reversible along with the substrate

  • Coenzyme: Organic cofactor

• Competitive Inhibitors: Reversible inhibitors, resemble normal substrate molecule, compete for admission into the active site

• Noncompetitive Inhibitors: Bind to another part of the enzyme that changes the shape of the active site

8.5: Regulation of enzyme activty helps control metabolism

• Allosteric Regulation: Used to describe any case where protein’s function at one site is affected by binding of a regulatory molecule at another

  • Cooperativity: Substrate molecule binds to one active site in a multisubunit enzyme, triggers a shape change, increasing catalytic activity at other active sites, amplifies response of enzymes to substrates

    • One substrate primes an enzyme to act on other substrates more readily

• Feedback Inhibition: Metabolic pathway halted by inhibitory binding of its end product to an enzyme that acts early in the pathway

Chapter 9: Cellular Respiration and Fermentation

9.1: Catabolic pathways yield energy by ocidizing organic fuels

• Fermentation: Partial degredation of sugars or other organic fuels without ocygen

• Anabolic Respiration: Oxygen consumed as a reactant along with organic fuel

• Anaerobic Respiration: Oxygen is not the final oxidizing substance, used by some prokaryotes

• Cellular Respiration: Used to refer to aerobic process

  • C₆H₁₂O₆ + 6O₂ —> 6CO₂ + 6H₂O + Energy (ATP + heat)

• Glucose breakdown is exergonic, free energy change of ΔG = -686 kcal/mol

• Redox Reactions: Oxidation-Reduction reactions, electron transfers

  • Oxidation: Loss of Electrons

    • Oxidizing Agent: Electron donor

  • Reduction: Addition of Electrons

    • Reducing Agent: Electron acceptor

  • LEO the lion says GER!

    • Loss of Electrons Oxidation, Gain of Electrons Reduction

  • Redox reactions can also change the degree of electron sharing in covalent bonds

• Glucose is broken down in a series of steps catalyzed by enzymes

  • Electrons stripped from glucose at key steps

  • Each electron travels with a proton as a hydrogen atom

  • NAD is used as an electron carrier because it can easily cycle through NAD+ and NADH

• Electron Transport Chain: Mostly proteins built into the inner membrane of the mitochondria (this is in eukaryotes, in prokaryotes, it’s the plasma membrane), a ladder with higher and lower energy

• Three stages of cellular respiration: Glycolysis, Pyruvate Oxidation + Citric Acid Cycle, and Oxidative Phosphorylation

• Glycolysis: Breaks glucose into two molecules of pyruvate, which enters the mitochondrion and is oxidized into acetyle CoA, which goes into the citric acid cycle, occurs in the cytosol

• Citric Acid Cycle: Breakdown of glucose into carbon dioxide (in prokaryotes, this is in the cytosol)

• Oxidative Phosphorylation: Electrons combined with O₂ and H+, forming water. Energy released by each step helps turn ADP into ATP. Powdered by redox reactions of the ETC

  • Accounts for almost 90% of the ATP generated by respiration

• Substrate Level Phosphorylation: Enzyme transfers phosphate group from substrate to ADP

1. Aerobic respiration generates much more ATP since oxidative phosphorylation accounts for almost 90% of ATP produced by the cell

2. not sure

9.2: Glycolysis harvests chemical energy by oxidizing glucose to pyruvate

• 2 phases, energy investment and energy payoff

• Net energy yield is 2 ATP and 2 NADH per glucose

• Means “sugar splitting”, since glucose is split into 2 three carbon sugars, whihc are oxidized and rearranged to form pyruvate

9.3: After pyruvate is oxidized, the citric acid cycle completes the energy-yielding oxidation of organic molecules

• Acetyl Coenzyme (acetyl CoA): When entering mitochondria via active transport, pyruvate first converted into this

  1. Pyruvate’s carboxyl group is fully oxidized and given off as a molecule of CO₂

  2. Remaining two carbon fragment is oxidized, electrons transferred to NAD+ (now NADH)

  3. Coenzyme A (CoA) attached to two carbon intermediate, forming acetyl CoA

• Citric acid cycle has 8 steps, each catalyzed by a specific enzyme

  1. Acetyl CoA adds its acetyl group to oxaloacetate to make citrate

  2. Citrate converted to isocitrate, its isomer, by removing one water molecule and adding another

  3. Isocitrate is oxidized, reducing NAD+ to NADH. This compound loses a CO2

  4. Another CO₂ molecule is lost, and the compound is oxidized, reducing NAD+ to NADH

  5. CoA is displaced by a phosphate group, which is transferred to GDP, forming GTP (similar to ATP, can also be used to generate it)

  6. Two hydrogens transferred to FAD to form FADH₂, oxidizing the old compound

  7. Addition of water molecule rearranges bonds

  8. Substrate is oxidized, reducing NAD+ to NADH

• Oxaloacetate is made up of different carbon atoms each time around

• 3 NAD+ reduced each time

1. When NAD+ is reduced, it is exothermic

2. Citric Acid Cycle

3. Exothermic reations used to power endothermic ones

9.4: During oxidative phosphorylation, chemiosmosis couples electron transport to ATP synthesis

• In the inner mitochondrial membrane in eukaryotic cells (plasma membrane of prokaryote)

• Electrons acquired from glucose by NAD+ are transferred to first molecule of ETC in complex I

  • This is a flavoprotein, which returns to its oxidized form by passing electrons to an iron sulfur protein (Fe-S in complex I)

  • Then passed to ubiquinone, a small hyrophobic molecule that;s not a protein

  • Remaining carriers are cytochromes

• Cytochrome: Protein that accepts and donates electrons

  • Cyt₃ passes electrons to O₂ which is very electronegative, then picks up protons from the aqueous solution, forming water

    • FADH₂ also donates electrons to complex II, but there is 1/3 the amount of ATP produced

• Chemiosmosis: Process where energy stored in the hydrogen ion gradient across a membrane is used to drive cellular work (such as ATP synthesis)

  • Proton Motive Force: H+ gradient

• Most energy flows from glucose —> NADH —> ETC —> proton motive force —> ATP

• Around 30 to 32 ATP per glucose (2 glycolysis (substrate level phosphorylation), 2 ATP (substrate level phosphorylation), 26 or 28 (oxidative phosphorylation)

  • Ratio of NADH to ATP is not whole (phosphorylation and redox reactions not directly coupled to each other), around 4+ H+ reenter mitochondria via ATP synthase

    • Single NADH has enough proton motive force for 2.5 ATP

    • FADH₂ only enough for 1.5 ATP

Chapter 10: Photosynthesis

10.1: Photosynthesis feeds the biosphere

• Photosynthesis: Conversion turning energy of sun and light into chemical molecules

• Acquires organic compounds through autotrophic nutrition or heterotrophic nutrition

  • Autotrophs: “self feeders”, sustain selves without eating anything from other living beings

    • The producers, use CO₂ and inorganic raw materials

  • Heterotrophs: Live on compounds from other organisms

    • Decomposers: Eat remains of other organisms and feces

1. They consume autotrophs to sustain themselves

2. The algae can then produce more oxygen from the excess carbon dioxide

10.2: Photosynthesis converts light energy to the chemical energy of food

• Endosymbiont Theory: Chloroplast was from the cyanobacteria being engulfed by a eukaryotic cell, and they began to undergo symbiosis, same as mitochondria

• Chloroplast: Eukaryotic organelle that absirbs sunlight to drive synthesis of organic compounds

  • Found mainly in cells of mesophyll

    • Mesophyll: Tissue in interior of leaf, typically has 30-40 chloroplasts (each 2-4 µm by 4-7 µm)

• Stomata: Microscopic pores where CO₂ enters and O₂ exits

• Stroma: Dense fluid, surrounded by two membranes

  • Thylakoids: In stroma, segregates it from the thylakoid space

    • Grana: Columns of thylakoids

• Chlorophyll: Green pigment that gives leaves their color, in the membranes of thylakoids

• 6CO₂ + 12H₂O + Light Energy —> C₆H₁₂O₂ + 6H₂O + O₂

• Two parts of photosynthesis

  • Light Reactions (photo): Convert solar energy to chemical energy

    1. Water is split, providing a source of electrons and protons, and giving O as a byproduct

    2. Light absorbed by chlorophyll drives transfer of electrons and hydrogen ions from water to NADP+

    3. Solar energy used to reduce NADP+ to NADPH by adding a pair of electrons and H+

    4. Uses chemiosmosis to power addition of phosphate group to ADP

       • Photophosphorylation: Add phosphate group to ADP

    • Light energy converted to chemical energy as NADPH and ATP

      • NADPH as “reducing power” that can be passed along to electron acceptors

  • Calvin Cycle: Turns carbon dioxide into sugar

    1. Carbon Fixation: Incorporating CO₂ from air into organic molecules already present

    2. Reduces fixed carbon into carbohydrate by reducing it (using NADPH and ATP)

    • In the stroma

1. Idk lol

2. What? Too many big words

3. The Calvin cycle provides NADP+ and ADP, as well as produces glucose for energy.

10.3: The light reactions convert solar energy to chemical energy of ATP and NADPH

• Light is a form of electromagnetic energy

• Wavelength: Distance between crests

• Electromagnetic Spectrum: Range of radiation

  • Visible light: (purple) 380 nm — 740 nm (red) wavelength, colors

• Photons: Particles of light

• Pigments: Substances that absorb visible light

  • Spectrophotometer: Measures ability to absorb different wavelengths of light

• Chlorophyll a: Light capturing pigment that participates directly in light reactions

• Chlorophyll b: Accessory pigment

• Carotenoid: Hydrocarbons, may broaden spectrum of colors that drive photosynthesis, photoprotection

  • Photoprotection: To absorb and dissapate excessive light energy that would otherwise damage chlorophyll or form oxidadive molecules that are dangerous to the cell

• Action Spectrum: Profiles relative effectiveness of different wavelengths of radiation

• Absorption of a photon boosts an electron to a ring further than to the nucleus, meaning higher potential energy, and this is their excited state

  • Only photons absorbed are those with energy equal to energy diff between ground and excited state of electron, so only specific wavelengths

  • Can only stayfor a billionth of a second, releasing excess energy as photon and fluorenscence (afterglow) happens

• Photosystem: Composed of reaction center complex surrounded by light complexes

  • Reaction Center Complex: Organized association of proteins with a special pair of chlorophyll a molecules and a primary electron acceptor, purpose to convert light to energy

    • Primary Electron Accepter: Molecule capable of accepting electrons and being reduced

  • Light Harvesting Complex: Pigment molecules bound to proteins, traps light to transfer to the reaction center

• First step of light reaction, solar powered transfer of electron from the reaction center chlorophyll a pair to the primary electron acceptor

  • When chlorophyll electron excited, primary electron acceptor captures it in a redox reaction

• Two types of photosystems in the thylakoid membrane

  • Photosystem II (PSII): Reaction center chlorophyll a called P680, best at absorbing light with a wavelength of 680 nm (red).

    • P680 is the strongest biological oxidizing agent known, and its electron “hole” mmust be filled

  • Photosystem I (PSI): Reaction center chorophyll a called P700, best at absorbing light with a wavelength of 700 nm (far red)

• Linear Electron Flow: Flow of electrons through photosystems and other molecular components from the thylakoid membrane

  1. A photon of light strikes one of the pigment molecules, exciting one of its electrons.

  2. As it falls back down, an electron in a nearby pigment is excited, and this keeps going until it reaches the P680.

  3. An electron in the pair of cholophyll a is excited

  4. This electron is transferred from the excited P680 to the primary electron acceptor, and P680 is now P680+

  5. Enzyme splits water molecule into two electrons, two hydrogen ions, and an oxygen atom

  6. Electrons are supplied one by one to the P680+ pair, each electron replacing one transferred to the primary electron acceptor

  7. H+ released into thylakoid space

  8. Oxygen atom combines with another oxygen atom split from water, forming O₂

  9. Photoexcited electrons go from PSII to PSI using an electron transport chain (made of electron carrier plastoquinone and protein plastocyanin). Each component carries out redox reactions as electrons flow down

  10. This releases free energy used to pump H+ into thylakoid space and make a proton gradient

  11. Potential energy in proteon gradient is used to make ATP through chemiosmosis

  12. Light energy captured through light harvesting pigments to the PSI, exciting a P700 electron

  13. Photoexcited electron transferred to PSI’s primary electron acceptor, making it P700+, with a hole, so it accepts an electron from the bottom of the electron transport chain from PSII

  14. Photoexcited eectrons go to second electron transport chain (through protein ferredoxin)

  15. NADP+ reductae catalyzes fransfer of electrons to NADP+, which needs two electrons to be reduced into NADPH and also removes an H+ from the stroma

• Cyclic Electron Flow: Uses photosystem I but not photosystem II, alternate path. Electrons go from ferredoxin to cytochrome complex, them using plastocyanin to P700. Generates ATP but no production of NADPH or release of oxygen

1. Green, since all pigments absorb green the worst, and reflect/transmit it instead, hence the green appearance of the plant

2. H20, NADP+

3. No ATP is created

10.4: The Calvin Cycle uses the chemical energy of ATP and NADPH to reduce CO₂ to sugar

• In the stroma

• Similar to citric acid cycle, since the starting material is regenerated as some molecules enter and exit the cycle

• G3P (Glyceraldehyde 3 phosphate): Carbohydrate produced directly from Calvin cycle, cycle must take place 3 times to synthesize 1

• Carbon Fixation: Phase 1 of the Calvin cycle. Rubisco attaches CO₂ with ribulose biphosphate (RuBP), a five carbon sugar. It forms an unstable 6 carbon compound before splitting into 2 molecules of 3-Phosphoglycerate

  • Rubisco: Enzyme that joins RuBP and CO₂, the most abundant protein in chloroplasts & on earth

• Phase 2 is reduction. Each molecule gets a phosphate group from ATP (which becomes ADP) and a pair of electrons from NADPH (which becomes NADP+).

• In the last phase, regeneration, 1 G3P exits the cycle, while the other 5 regenerate into RuBP, which consumes 3 ATP in the process.

10.5: Alternative mechanisms of carbon fixation have evolved in hot, arid climates

• C₃ Plants: CO₂ combined with RuBP using rubisco

  • Rubisco can also bind O₂ instead of CO₂, producing CO₂ and using ATP instead of making it

  • Close stomatas on hot, dry days

• Photorespiration: Consumes O₂ (photo), produces CO₂ (respiration) using ATP and not producing sugar

  • Then uses the generated CO₂ for regular carbon fixation

• C₄ Plants: Alternate form of carbon fixation before Calvin cycle that produces a four carbon compound as first product

  • Evolved independently at least 45 seperate times. More efficient than C₃ since it uses less water and resources.

  • When weather is hot and dry, partially closes stomata

  • Photosynthesis starts in mesophyll cells but is completed in bundle sheat cells

    • Bundle Sheath Cells: Cells arranged into tightly packed sheaths around the veins of the leaf

  • PEP Carboxylase: Higher affinity for CO₂ than rubisco, no affinity for O₂

  1. PEP Carboxylase adds CO₂ to PEP, producing ocaloacetate, even when lower CO₂ concentration and relatively higher O₂ concentration

  2. Four carbon products exported to bundle sheath cells through plasmodesmata

  3. Within bundle sheath cells, an enzyme releases CO₂ and it is refixed by rubisco and the Calvin cycle

     1. This also regenerates pyruvate in the same wau, which is transported to the mesophyll cells (ATP converts pyruvate into PEP)

• Crassulacean acid metabolism (CAM): Carbon fixation mode, during night plants use CO₂ in orgaic acids (stored in mesophyll cells). During day stomatas closed, and CO₂ is released for use in Calvin Cycle

1. Turned into ATP through cellular respiration

Chapter 11: Cell Communication

11.1: External signals are converted to responses within the cell

• Earl W Sutherland investigated how animal hormone epinephrine leads to glycogen breakage

• Cellular communication has three stages in the signal transduction pathway

  1. Signal Reception: Cell’s detection of a signaling molecule coming from outside the cell, when the signaling molecule binds to a receptor protein at the cell’s surface

  2. Signal Transduction: Binding of signaling molecule changes the receptor protein and initiates transduction. Converts signal to a form that brings a specific cellular response

  3. Cellular Response: Transduced signal triggers a cellular response

  

11.2: Signal reception — A signaling molecule binds to areceptor, causing it to change shape

• Ligand: Molecule that specifically binds to another

  • Signaling molecule has a complementary shape to a site on the receptor and binds there, acting as a ligand

• G Protein Coupled Receptor: Cell surface transmembrane receptor that works with the help of a G Protein

  • G Protein: Protein that binds energy rich GTP

• Receptor Tyrosine Kinases (RTKs): Plasma membrane receptor with enzymatic activity, a protein kinase (enzyme that catalyzes transfer of phosphate groups from ATP to another protein)

• Ligand Gated Ion Channel: Membrane channel receptor with a region that acts as a “gate” and opens or closes when the receptor changes shape

11.3: Signal transduction — Cascades of molecular interactions transmit signals from receptors to relay molecules in the cell

• Protein Kinase: Enzyme that tranfers phosphate groups from ATP to a protein

• Phosphorylation Cascade: Series of different proteins in a pathway are phosphorylated and add a phosphate group to the next one in line

• Protein Phosphatases: Enzymes that can rapidly dephosphorylate (remove phosphate groups from) proteins

• Second Messengers: Small nonprotein water soluble molecules or ions which can easily spread through regions of the cell by fiddusion and particpate in participate in pathways initiated by G protein coupled receptors and receptor tyrosine kinases

  • Cyclic AMP (cAMP): Small molecule produced from ATP

    • Adenylyl Cyclase: Converts ATP to cAMP in response to an extracellular signal

  

  • Inositol Triphosphate (IP) and diacylglycerol (DAG) also lead to calcium release

11.4: Cellular response — Cell signaling leads to regulation of transcription or cytoplasmic activities

• Some pathways lead to a nuclear response—specific genes are turned on or off by activated transcription factors

  • In others the response involves cytoplasmic regulation

• Cellular repsonses are regulated at many steps

• Each protein in a signaling pathway amplifies the signal by activating mutliple copies of the next component

  • For long pathways the total amplification may be over a millionfold

• Scaffolding Proteins: Large relay proteins to which many other relay proteins are simultaneously attached to, permanently hold together networks of signaling proteins at synapses. Increase signaling efficiency

  • Pathway branching further helps the cell to coordinate signals and responses

11.5: Aptosis requires integration of multiple cell signaling pathways

• Aptosis: Controlled cell suicide, cellular agents chop up DNA and fragment organelles and other cytoplasmic components

Chapter 12: The Cell Cycle

12.1: Most cell division results in genetically identical daughter cells

• Cell Division: Reproduction of cells, distinguishes living things from nonliving

  • Helps with asexual reproduction, growth/development, and tissue renewal

• Genome: Cell’s DNA or genetic information

  • Human cell usually has about 2m of DNA, 250,000x the cell’s diameter

• Chromosomes: DNA are packaged into these structures

  • Chromatin: The DNA and proteins that is the building material of chromosomes

• Somatic Cells: All cells that aren’t the reproductive cells, contain 46 chromosomes (2 sets of 23)

• Reproductive Cells: Have half as many chromosomes as somatic cells (1 set of 23)

• Each duplicated chromosome has two sister chromatids with identical DNA molecules, attached along their lengths by cohesins

  • This is called sister chromatid cohesion

  • Centromere: Where the chromatid is most closely attached to the other one, the “waist”

• When the two sister chromatids seperate, they are now individual chromosomes

• Mitosis: Division of genetic material in the nucleus

  • Cytokinesis: Division of the cytoplasm, right after mitosis

  • Meiosis: Produce gametes(male sperm cell or female egg cell) through it, modified version of mitosis

1. In step 1, there is one. In step 2, there is one. In step 3, there are two.

2. 39, 39, 39

12.2: The mitotic phase alternates with interphase in the cell cycle

• Cell Cycle: Life of a cell from when it’s formed until division

• Mitotic (M) Phase: Mitosis + Cytokinesis, usually shortest part of cell cycle

  • 5 stages: prophase, prometaphase, metaphase, anaphase, and telophase

    • Prophase — pro, first, where nucleus is still there, chromosomes condensing

    • Metaphase — middle, where the chromosomes line up, nucleus gone

    • Anaphase — away, chromatids separated and moving away from middle (towards poles/centrioles)

    • Telophase — two, nuclei begin to form and chromosomes at complete opposite ends

• Interphase: ~90% of cell cycle, contains G₁ (1st gap) phase, S (synthesis) phase, and G₂ (2nd gap) phase

• Cell grows (G₁), keeps growing and copies it’s chromosomes (S), continues to grow as it finishes preparing for cell division (G₂), and divides (M).

• Mitotic Spindle: Forms in cytoplasm during prophase. Other microtubules partially disassemble to form it. They polymerize (elongate) by adding more subunits of tubulin, a protein, and shorten by losing them

  • Includes centrosomes, spindle microtubules, and asters

• Centrosome: Where spindle assembly starts, also organizes microtubules and provides structure

  • Pair of centrioles are at the center of the centrosome

  • During interphase in animal cells, it duplicates and forms two. They move apart during prophase and prometaphase (the two p’s) as spindle microtubules grow from them

    • By the end of prometaphase, they’re at opposite ends of the cell

• Aster: Radial array of short microtubules, comes from each centrosome

• Kinetochore: Structure of proteins, what the spindle attaches to. Each sister chromatid has one

• Metaphase Plate: Imaginary plate, where centromeres of duplicated chromosomes are at metaphase (middle)

• In animal cells, cytokinesis is through cleavage

  • Cleavage Furrow: Shallow groove in cell surface near old metaphase plate

• In plant cells, vesicles move along microtubules to middle of cell, where they coalesce (combine), making a cell plate

• Binary Fission: Reproduction where prokaryotic cell grows to double its size, then divides into two cells

• Origin of Replication: Where DNA of chromosome replicates, producing 2 origins

1. 6

2. In animals, there is a cleavage, in plants, there is only a cell plate

3. Prophase, prometaphase, metaphase

4. idk

5. It connects to the centromeres, pulling the centrioles apart.

6. idk

12.3: The eukaryotic cell cycle is regulated by a molecular control system

• Hypothetical evolution of mitosis is that it evolved from binary fission

  • This is because protists exhibit cell division between fission and meiosis

• Cell Cycle Control System: Molecules in cell that trigger and coordinate key events

• Checkpoint: Cell’s control point to see if everything is working

• Cyclin: Kinases (Enzymes that catalyze transfer of phosphate group) must attach to them to be active, a family of proteins

  • Cyclin Dependent Kinases (Cdks): The kinases attached to cyclins

  • Maturation/M-Phase Promoting Faction (MPF): First discovered cyclin-Cdk complex, triggers passage into M Phase

    • In anaphase, switches itself off by destroying its own cyclin

• 3 important checkpoints at G₁, G₂, and M

  • G₁checkpoint is usually considered most important, since it checks if the cell is fit for division. If doesn’t pass, it goes to G₀ phase, kind of like a limbo.

    • In G, the cell is not actively dividing and does its normal functions. It can be “called back” into G.

  • G₂ checkpoint makes sure all chromosomes have been replicated and replicated DNA is not damaged

    • If reparable, mitosis paused and it is fixed

    • If not, apoptosis (programmed cell suicide)

  • M checkpoint checks if sister chromatids are correctly attached to spindle, and is near the end of metaphase

    • When all chromosomes properly attached to spindle fibers, it proceeds into anaphase

• Growth Factor: Protein released by some cells to tell other cells to divide

• Density Dependent Inhibition: Crowded cells stop dividing

• Anchorage Dependence: To divide, it must be attached to something

• In cancer cells, they don’t stop dividing when growth factors are depleted

  • Benign Tumor: Abnormal cells remain at original site

  • Malignant Tumor: Spread to new tissues and impair functions of other tissues

  • Metastasis: Spread of cancer cells to distant locations from original site

1. It hasn’t passed through the S stage, synthesis

2. CDK and cyclin combine into MPF

3. idk