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Metabolism (Terms (metabolic pathways (A>enzyme 1>B>enzyme 2>C…

- - - - A is starting molecule
      - each enzyme creates a different reaction that transforms molecule
      - C is end product
  - - - work: moving matter against opposing forces like gravity and friction
    - - motion of objects
      - thermal energy
        
        random movement of atoms or molecules
        
        heat: thermal energy in transfer from one object to another
      - light energy can be harnessed to perform work
        
        like powering photosynthesis in plants
    - - energy that an object has because of its position or shape
      - not kinetic (not moving)
      - chemical energy
        
        potential energy available for release in a chemical reaction
        
        glucose is high in chemical energy
    - - 1) woman climbing a diving board is converting kinetic energy to potential energy
      - 2) when she jumps, she converts potential into kinetic; heat from friction is transferred to the water
- - - - as temp. rises, substrates are more likely to bump into active sites bc they move around quicker
  - - - the reactant an enzyme acts on
    - - when enzyme and substrate are joined
    - - a restricted region of the enzyme where the substrate binds
    - - tightening of binding of substrate to enzyme is like a clasping handshake
  - - - nonprotein catalytic helpers that bind to enzymes permanently or loosely with substrates
      - these are usually minerals, and why we need minerals in our diet
      - coenzyme
        
        if the cofactor is an organic molecule like vitamins
    - - competitive inhibitors
        
        mimics the substrate and blocks the active site so real substrate can't attach
      - noncompetitive inhibitor
        
        binds to the enzyme (not on the active site) and alters its shape
        
        substrate might still be able to bind to active site but enzyme no longer functions effectively
      - sarin gas and DDT (banned) inhibited nervous system enzymes and caused death
  - - - protein's function is affected when a regulatory molecule binds to it
      - allosteric activation
        
        stabilizes an enzyme complex (multiple enzymes attached to each other) so that they all stay in active working form
      - allosteric inhibition
        
        stablizes the inactive form of enzyme complex so none of the enzymes will work
        
        this controls enzyme so it doesn't make more molecules than are necessary and resources aren't wasted
      - cooperativity
        
        a substrate attaches to an active site of one enzyme, which triggers other enzymes in enzyme complex to lock in active form
    - - when an end product attaches to the initial enzyme in a metabolic pathway, this stops the enzyme from making more of this product
- - - - G is the free energy of a system
      - is equal to (final state of G) - (initial state of G)
    - - H is the system's enthalpy (total energy/order of a system)
      - T is temp. in Kelvin
      - S is entropy (disorder of a system)
  - - - spontaneous reaction
        
        spontaneous can perform work only when it is moving towards equilibrium
      - exergonic because energy is released
      - ATP turns into ADP
      - ex. cellular respiration
      - products end up with less energy than reactants
      - final energy state is least likely to change and is more stable
    - - nonspontaneous: energy is constantly added
      - endergonic bc energy is absorbed
      - ADP turns into ATP
      - ex. photosynthesis
      - products end up with more energy than reactants
      - unstable bc ends up with potential energy
    - - :small_red_triangle:G=0
      - cannot do work
      - max stability
  - - - this would mean that a cell can no longer do work and it is dead
- - - - endergonic and anabolic bc building up potential energy in glucose
      - increasing enthalpy (total order of universe)
  - - - mesophyll cell has about 30-40 chloroplasts
        
        chloroplast has 2 membranes surrounding a dense fluid (stroma)
        
        inside stroma is another 2-membrane system with thylakoids stacked into grana
        
        chlorophyll is green pigment that resides in thylakoid membranes
    - - H2O absorbed by roots is delivered to leaves through veins
      - leaves also use veins to send sugar to roots and other nonphotosynthetic parts of the plant
    - - 6CO2 + 6H2O +light energy :arrow_right: C6H12O6 + 6O2
        
        6H2O are expelled by photosynthesis while 12H2O are taken in, we use a net of 6H2O instead
    - - O2 given off by plants is from H2O and not CO2
        
        H2O is split into O2, H+, and e- (for energy)
        
        O2 is not necessary for plants, so it's expelled as a waste product
      - CO2 is used to make glucose and provides the oxygen in the 6H2O given off
      - H+ are used to make glucose and the 6H2O given off
    - - 6CO2 becomes reduced (gains e-) to become glucose
      - 6H2O becomes oxidized (loses e-) to become 6O2
      - e- increase in potential energy= endergonic
    - - 1) light reactions (photo part)
        
        convert solar energy to chemical energy
        
        water is split (catabolic/exergonic & increases entropy)
        
        light is absorbed so that NADP+ can accept e- and H+
        
        NADP+ is nicotinamide adenine dinucleotide phosphate
        
        NADP+ is reduced to NADPH (endergonic/anabolic/increases enthalpy)
        
        ATP is also made using chemiosmosis to phosphorylate ADP
        
        called photophosphorylation bc light reactions power this step
        
        endergonic/anabolic/increasing enthalpy
        
        occurs in the chloroplast
      - 2) Calvin Cycle (synthesis part)
        
        CO2 is incorporated into organic molecules already present in chloroplast
        
        called carbon fixation
        
        Calvin Cycle reduces fixed carbon into carbohydrates using NADPH (transfers e-) and energy from ATP
        
        exergonic/catabolic/increases entropy when breaking ATP and NADPH to release energy
        
        anabolic/endergonic/increase enthalpy to make glucose
        
        occurs in the stroma
  - - - light travels in electromagnetic waves
      - wavelength
        
        distance between the crests of electromagnetic waves
      - electromagnetic spectrum
        
        entire range of radiation
      - visible light is detected as numerous colors by the eye
      - photons are energy wavelengths from the sun
    - - pigments are light receptors that absorb visible light
        
        spectrophotometer measures how many wavelengths of light can be absorbed by a pigment
        
        absorption spectrum is a graph of the pigment's light absorption vs. wavelength
        
        pigments in chloroplasts
        
        chlorophyll a participates directly in light reactions
        
        chlorophyll b
        
        carotenoids
      - colors are visible bc their wavelengths bounce off the object
        
        white reflects all colors
        
        black absorbs all colors and has more heat from the sun's wavelengths
    - - organic molecules and proteins organized in thylakoid membrane
      - reaction center complex holds cholorphyll a and a primary e- acceptor
      - light-harvesting complex consists of various pigments bound to proteins
      - photosystem II occurs 1st in process while photosystem I occurs after
    - - flow of e- through photosystems to release energy to power synthesis of ATP and NADPH synthesis
    - - e- transport chain between PSII and PSI allow e- to travel to each other
        
        NADP+ reductionase takes in 2e-, H+ (from the stroma), and NADP+ to reduce to NADPH
        
        e- increase in potential energy as the pass through e- transport chain, so NADPH has highest e- potential energy
      - chemiosmosis allows H+ ions to move out of the thylakoid through ATP synthase (down their gradient)
        
        this helps physphorylate ADP
      - cytochrome complex allows cotransport of e- flow from protein to protein and pumps in H+
      - light energy is converted to chemical energy in ATP and NADPH
  - - - Phase 1: Carbon Fixation
        
        3 CO2s come in (one at a time, each cycle only takes in one CO2) and rubisco attaches it to RuBP
        
        this creates PGA
      - Phase 2: Reduction
        
        ATP phosphorylates PGA, and creates intermediates
        
        intermediates are phosphorylated with NADPH and become G3P (a sugar, half of glucose)
        
        one G3P exits cycle, and the other 5 are recycled
      - Phase 3: Regeneration of RuBP (CO2 acceptor)
        
        3 ATP are used to turn G3P back into RuBP, and cycle begins again by RuBP accepting another CO2
      - net reactants: 9 ATP and 6 NADPH
        
        net products: one G3P which joins up with another G3P to make glucose
  - - - C3 plants are most plants, produce PGA (3 carbon molecule) in their Calvin Cycle
        
        on hot days, their stomata partially close, CO2 intake decreases, which leads to O2 being used in Calvin Cycle instead
        
        this is called photorespiration bc no glucose is made, instead CO2 is produced and expelled; this is bad for plants
    - - C4 plants
        
        produce a 4-carbon molecule (oxaloacetate or malate) at beginning of Calvin Cycle (not PGA)
        
        sugarcane and corn
        
        have bundle-sheath cells and mesophyll cells
        
        bundle-sheath cells are arranged as tightly-packed sheaths around veins of leaf
        
        Calvin Cycle is done here
        
        mesophyll cells are loosely-packed around the bundle-sheath cells
        
        CO2 is taken in here and extra step happens before Calvin Cycle
        
        process
        
        1) in mesophyll cell: CO2 and PEP are joined by PEP carboxylase to make oxaloacetate or malate
        
        2) 4-carbon molecule moves into bundle-sheath cell through plasmodesmata
        
        3) 4-carbon molecule releases CO2 and pyruvate
        
        CO2 is entered into Calvin Cycle, and eventually sugar is produced
        
        pyruvate trvels back to mesophyll cell and is made into PEP with help of ATP
        
        are considered more efficient than C3 plants bc they can operate at higher temps. and use less water and resources
      - CAM plants
        
        succulent (water-storing plants)
        
        open their stomata at night and close during the day (opposite of C3 plants)
        
        water and CO2 can't enter leaves during the day
        
        take in CO2 at night and incorporate it into a variety of organic acids (crassulacean acid metabolism CAM)
        
        organic acids are stored until daytime when light reactions provide ATP and NADPH for Calvin Cycle where CO2 is released from these organic acids to make glucose for the plant
    - - scientists have been trying to convert rice into a C4 plant in order for it to be more efficient
- - - - entropy increases whenever the arrangement of matter is more disordered
    - - process that can continue occurring without requiring constant energy
      - only needs one little spark
      - like an explosion or a car rusting over time
  - - - like cold water inside a thermos
      - energy and matter can't be transferred from system to surroundings
    - - energy and matter can be transferred between system and its surroundings
      - organisms are open systems
- - - - pushes endergonic reactions bc they don't happen spontaneously
      - ATP triggers enzymes to conduct chemical reactions
      - monomers build polymers
    - - pumps substances across membranes against direction of spontaneous movement
      - like carrier proteins and Na-K pump
    - - moving of cilia and flagella, contraction of muscle cells, and movement of chromosomes during mitosis
      - like motor proteins moving vesicles along microtubules
    - - the use of an exergonic process to drive an endergonic one
      - ATP powers this most of the time
  - - - made up of ribose, adenine, and 3 phosphate chain
    - - RNA nucleotides have ribose, nitrogenous base and one phosphate group
    - - turns into ADP
      - release of energy
  - - - this is what happens when you shiver
    - - the molecule that has received a phosphate group (forms a covalent bond)
  - - - happens really fast bc body needs a lot of ATP constantly
- - - - partial degradation of sugars that occurs without oxygen
    - - most efficient; oxygen and organic fuels are consumed
      - cellular respiration
        
        consuming oxygen and glucose, produce CO2 and water
        
        C6H12O6+6O2:arrow_right:6CO2+6H2O+energy(ATP+heat)
        
        breakdown of starch into glucose is exergonic and spontaneous (no input of energy)
        
        Goal: harvest energy in glucose to produce ATP for cells to do work
        
        energy flow and conversion from glucose to ATP
        
        glucose to NADH to e- transport chain to proton-motive force to ATP
        
        exergonic and catabolic bc breaking down of glucose releases energy, and endergonic and anabolic bc takes that energy to make ATP
        
        increases entropy (disorder of the system and universe)
        
        3(or 4) stages
        
        1) glycolysis
        
        occurs in cytosol, glucose is broken down into 2 pyruvate molecules
        
        catabolic/exergonic/increases entropy
        
        2) pyruvate oxidation and the citric acid cycle
        
        pyruvate enters mitochondria and is oxidized into acetyl CoA
        
        acetyl CoA enters citric acid cycle; breakdown of glucose to CO2 is complete
        
        CO2 represents oxidized glucose
        
        catabolic/exergonic/increases entropy
        
        oxidative phosphorylation: e- transport and chemiosmosis
        
        phosphorylates ADP to make ATP from energy released as e- move down e- transport chain
        
        in mitochondria; 90% of ATP made here
        
        substrate-level phosphorylation
        
        when ATP is made in the first 2 stages of cell. resp.
        
        10% of ATP is made here
        
        anabolic/endergonic/increases enthalpy
        
        34% of energy in glucose is converted to ATP; the rest is given off as heat (used to regulate body temp. or given off through sweat)
    - - in chemical reactions, electrons transfer from one reactant to another (oxidation-reduction)
      - oxidation
        
        the loss of electrons from one substance
      - reduction
        
        the addition of electrons to another substance, which reduces its positive charge
      - Xe- + Y :arrow_right: X + Ye-
        
        X becomes oxidized by losing an electron, and Y becomes reduced by gaining that electron
        
        reducing agent: electron donor (Xe-)
        
        oxidizing agent: electron acceptor (Y)
      - glucose loses an e- and CO2 becomes oxidized, oxygen gains an e- (bc more electroneg.) and H2O becomes reduced
    - - derivative of the vitamin niacin
      - an electron carrier, a coenzyme
      - NAD+ is the oxidized form
        
        glucose (substrate) attaches to dehydrogenase (enzyme)
        
        then NAD+ (coenzyme) attaches to dehydrogenase and accepts 2e- and 1 proton from 2 hydrogen atoms
      - NADH is its reduced form, bc it has accepted 2e- and 1proton (from hydrogen)
        
        now represents stored energy that is used to make ATP
    - - proteins inside inner membrane of mitochondria
      - e- are carried by NADH to the top of e- transport chain, e- travel to the bottom
        
        e- lose energy as they travel down toward the oxygen end (O2 is more electroneg.)
        
        e- that have reached O2 end meet up with H+, forming water
  - - - "sugar splitting" glucose is split into 2, making 2 pyruvate molecules
        
        oxidation of glucose releases 4e- and 4H+
        
        2 NADH are made by giving each NAD+ 2e- and 1H+
        
        occurs in cytoplasm w/ or w/out oxygen
        
        2 ATP are used (exergonic/catabolic)
      - 4 ATP formed from substrate-level phosphorylation (endergonic/anabolic)
      - net results
        
        2 pyruvate and 2 H2O
        
        2 ATP
        
        2 NADH and 2H+
    - - Pyruvate Oxidation
        
        when oxygen is present, the 2 pyruvate molecules travel inside the mitochondrion to be oxidized
        
        the oxidation of glucose is then completed
        
        each pyruvate molecule contains 3 carbons
        
        when pyruvate is oxidized, it releases one carbon, which creates a CO2 when the carbon meets up with a O2
        
        2 carbons left over are oxidized to form one NADH (endergonic, anabolic) and one acetyl CoA
        
        acetyl CoA contains high potential energy and is made from coenzyme A attaching itself to the 2-carbon molecule
        
        net results
        
        two CO2
        
        2 NADH
        
        2 acetyl CoA
      - Citric Acid Cycle
        
        Krebs cycle
        
        catabolic bc oxidizes acetyl CoA and gives its e- to make NADH, ATP, and FADH2
        
        occurs in matrix of mitochondria
        
        steps
        
        1) one acetyl CoA enters cycle and joins with oxaloacetate to make citrate
        
        2) decomposition of citrate back to oxaloacetate produces energy-rich molecules
        
        3) cycle happens again with the next acetyl CoA
        
        one glucose=2 pyruvate= 2 acetyl coA
        
        net results
        
        4 CO2 relased as waste products
        
        2 ATP
        
        6 NADH
        
        2 FADH2
        
        GTP (guanosine triphosphate) is similar to ATP and made from GDP
        
        once GTP is made, it phosphorylates ADP to make ATP, then turns back into GDP
    - - overview: NADH and FADH2 (e- carriers) carry e- to the top of e- transport chain
        
        e- move down the chain as they are attracted to more electronegative atoms until they meet oxygen at the end (most electroneg.)
        
        as e- move down the chain, ATP is produced, and at the end, 1/2O2, 2e-, and 2H+ join to form H2O
      - pathway of e- transport
        
        e- transport chain is a collection of proteins with e- carriers embedded in inner membrane of mitochondria (cristae)
        
        contains multiprotein complexes (I-IV) that pass e- to their more electroneg. neighbors
        
        cytochromes
        
        e- carriers between ubiquinone and oxygen; have prosthetic group (heme group) with an iron atom that accepts and donates e-
        
        prosthetic groups are nonprotein components (like cofactors and coenzymes) that are essential for the catalytic functions of some enzymes
      - chemiosmosis: energy-coupling mechanism
        
        ATP synthase (enzyme that makes ATP) reside in inner membrane of mitochondria
        
        ATP is made whenever H+ ions travel down their gradient inside the matrix of mitochondria through ATP synthase in the mitochondria's inner membrane
        
        chemiosmosis
        
        the flow of H+ across a membrane that releases energy to drive cellular work
        
        exergonic release of H+ energy to produce ATP (endergonic)
        
        endergonic/anabolic
        
        proton-motive force
        
        a force is created whenever H+ ions are pumped out of the matrix through e- transport chain proteins
        
        this force allows H+ to move back into the matrix through ATP synthase proteins in the inner membrane
        
        powered by e- transport chain operations
      - e- transport chain drives oxidative phosphorylation
  - - - some prokaryotes use another electroneg. atom instead of oxygen at the end of e- transport chain
      - glycolysis occurs whether oxygen is present or not
        
        fermentation consists of glycolysis occurring again and again
        
        ATP is made only from substrate-level fermentation in glycolysis
        
        less ATP (about 2) is made in fermentation and anaerobic respiration than aerobic respiration (30-32)
        
        since fermentation doesn't have an e- transport chain, NADH transfer their e- to pyruvate
    - - alcohol fermentation
        
        pyruvate is converted to ethanol, producing CO2 in the middle of the process
        
        conducted by bacteria and yeast
      - lactic acid fermentation
        
        pyruvate is reduced directly into lactate, with no production of CO2 or alcohol
        
        performed by some fungi and bacteria for dairy (cheese and yogurt)
        
        human muscle cells produce ATP with lactic acid fermentation whenever oxygen is scarce (during extreme exercise)
        
        excess of lactate doesn't cause muscle pain, it is caused by trauma to muscle fibers which lead to inflammation
    - - facultative anaerobes can do this or aerobic respiration
        
        human muscle cells are facultative anaerobes
  - - - we obtain most of our calories from carbs such as sucrose and starch that have to broken down into glucose 1st
      - extra glucose gets converted into glycogen to be stored (can broken down later when needed)
      - proteins can be broken down into amino acids and used to build more proteins
        
        deamination: amino groups are removed from amino acids before they are passed through glycolysis and citric acid cycle
        
        ammonia is created bc of this and excreted as urine
      - lipids are broken down into glycerol and fatty acids
        
        glycerol is broken down into G3P (glyceraldehyde 3-phosphate)
        
        most energy in fats is stored in fatty acids, which are broken down into fragments containing 2-carbons each (beta oxidation)
        
        a gram of fat produces more than twice as much ATP as a gram of carb
    - - food provides energy and carbon
        
        amino acids from digested proteins can be used to make other proteins
        
        cells synthesize molecules for the body from sub-units taken from food
        
        this requires ATP
        
        if we eat excess food, fat is made from extra food sub-units and stored
    - - cell doesn't waste energy to make more of a substance it doesn't need
        
        feedback inhibition
        
        the end product inhibits enzyme that catalyzes an early step of the pathway
        
        cell controls its catabolism
        
        when there's not enough ATP, cell. resp. speeds up and vice versa
        
        speeds up or inhibits enzymes based on what cell needs