Please enable JavaScript.

Coggle requires JavaScript to display documents.

An Introduction toMetabolism (Forms of energy (Energy, capacity to cause…

- - - - Begins with a specific molecule
      - Then altered in a series of defined steps
      - Results in a certain product
      - Each step is catalyzed by a specific enzyme
        (Starting molecule) A-enzyme 1/reaction 1->B-enzyme 2/reaction 2->C-enzyme 3/reaction 3->D (Product)
      - Some metabolic pathways release energy by breaking down complex molecules to simpler compounds
    - - Breakdown pathways
      - Cellular respiration is a major pathway of catabolism
        
        Sugar glucose and other organic fuels are broken down in the presence of oxygen to carbon dioxide and water
        
        Pathways can have more than one starting molecule and/or product
      - Energy that was stored in the organic molecules becomes available to do the work of the cell
    - - Consume energy to build complicated molecules from simpler ones
      - Sometimes called biosynthetic pathways
      - Examples; synthesis of an amino acid from simpler molecules and the synthesis of a protein from amino acids
- - - - Enable cells to release chemical energy from food molecules and use the energy to power life processes.
- - - - Energy can be transferred and transformed, but it cannot be created or destroyed
      - Also known as the principle of conservation of energy
    - - Entropy, a measure of molecular disorder or randomness
        
        Physical disintegration of a system’s organized structure is a good analogy for an increase in entropy
        
        Helps understand why certain processes are energetically favorable and occur on their own
        
        Spontaneous process
        
        By itself leads to an increase in entropy that process can proceed without requiring an input of energy
        
        Spontaneous reaction, keeps going
        
        Spontaneous does not imply a process would occur quickly, it is energetically favorable
      - Every energy transfer or transformation increases the entropy of the universe
- - - - The system gives up enthalpy and H decreases
      - Or T(delta)S must be positive
        
        The system gives up order and S increases
        
        Every spontaneous process decreases the systems free energy and processes that have a positive zero (delta)G are never spontaneous
        
        (Delta)G can be negative only when
      - (Delta)H and T(delta)S are tallied, (delta)G is negative
  - - - As a reaction moves to equilibrium, free energy of reactants and products decrease
  - - - Proceeds with a net release of free energy
        
        Chemical mixture loses free energy (G decreases) (delta)G is negative for an exergonic reaction
      - Energy outward
      - Occur spontaneously
    - - Absorbs free energy from its surroundings
      - (G increases) (delta)G is positive
      - Non spontaneous
      - Magnitude of (delta)G is the quantity of energy required to drive the reaction
      - Uphill
- - - - Pushing of endergonic reactions that do not occur spontaneously
        
        Synthesis of polymers from monomers
    - - Pumping of substances across membranes against the direction of spontaneous movement
    - - Beating of cilia
        
        Contraction of muscle cells
        
        Movement of chromosomes during cellular reproduction
    - - Use of exergonic process to drive an endergonic one
      - ATP is responsible for mediating energy coupling in cells
        
        Also acts as the immediate source of energy that powers cellular work
  - - - Bonds between the phosphate group can be broken by hydrolysis
        
        When the terminal phosphate bond breaks by additional water molecules, a molecule of inorganic phosphate(HOPO3^2-) leaves ATP
        
        It then becomes ADP, adenosine diphosphate
        
        The reaction is exergonic
        
        Releases 7.3 kcal of energy per mole of ATP hydrolyzed
  - - - Shuts inorganic phosphate and energy is called ATP cycle
        
        Couples the cells energy yielding (exergonic) processes to the energy consuming (endergonic)
- - - - Catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction
    - - Free energy of activation
      - Initial investment of energy for starting a reaction, the energy required to contort the reactant molecules so the bonds can break
      - Abbreviation; E
      - Amount of energy needed to push the reactants to the top of an energy barrier, or uphill
      - Often supplied by heat in the form of thermal energy that reactant molecules absorb from its surroundings
        
        Thermal energy accelerates the reactant molecules
        
        Agitates the atoms within the molecules
        
        Makes the breakage of bonds more likely
        
        When molecules absorbed enough energy to break, reactants are unstable (transition state)
  - - - Heat speeds up all reactions
        
        Catalysis, catalyst selectively speeds up a reaction without itself being consumed
        
        Enzymes catalyzes a reaction by lowering the barrier E
        
        Enables the reactant molecules to absorb enough energy to reach transition state even at moderate temperatures
        
        An enzyme can not change (delta)G for a reaction; it cannot make an endergonic reaction exergonic
        
        Enzymes can only hasten reactions that would eventually occur
        
        1 more item...
- - - - Reactant an enzyme acts on is referred to as the enzymes substrate
      - Enzyme binds to its substrate when there are two or more reactants
      - Forms enzyme substrate complex
        
        Enzyme and sun rates join, the catalytic action of the enzyme converts the substrate to the product of the reaction
        
        Most enzyme names end in ase
    - - Restricted region of the enzyme molecule actually binds to the substrate
      - Typically a pocket or groove on the surface of the enzyme where catalysis occurs
      - Usually formed by only a few of the enzymes amino acids, with the rest of the protein molecule providing a framework
        
        Determines the shape
        
        Specificity of an enzyme is attributed to a complementary fit between the shape of its active site and the shape of the substrate
        
        An enzyme is not stiff structure locked into a given shape
        
        Induced fit
        
        Clasping handshake
        
        Tightening of the binding after initial contact
        
        Brings chemical groups of the activation site into positions that enhance their ability to catalyze the chemical reaction
  - - - The active site provides a template on which the substrates can come together in the proper orientation for a reactant to occur between them
    - - The enzyme may stretch the substrate molecules toward their transition state forms
        
        Stressing and bending critical chemical bonds to be broken during the reaction
    - - The solution would be without an enzyme
    - - Sometimes this process involves brief covalent bonding between the substrate and the side chain of an amino acid of the enzyme
- - - - Optimal conditions favor the most active shape for the enzyme
        
        The rate of an enzymatic reaction increases with increasing temperature
        
        Substrates collide with active sites more frequently when the molecules move rapidly
        
        Thermal agitation of the enzyme molecule disrupts the hydrogen bonds, ionic bonds, and other weak interactions that stabilize the active shape of the enzyme
        
        Protein molecule eventually denatures
        
        Without denaturing the enzyme optimal temperature allows greater numbers of molecular collisions
        
        Also allows fastest conversion of the reactants to product molecules
      - Human enzyme optimal temperature is 35-40C
      - Optimal pH values for most enzymes are in the range of pH 6-8
  - - - If the cofactor is an organic molecule
  - - - At times the inhibitor attaches to the enzyme by covalent bonds, the inhibitor is then usually irreversible
    - - Reduce the productivity of enzymes by blocking substrates from entering active sites
      - Can be overcome by increasing the concentration of substrate so the active sites become available
    - - Do not directly compete with the substrate to bind to the enzyme at the active site
      - They impede enzymatic reactions by binding to another part of the enzyme
        
        This causes the enzyme molecule to change shape in a way that active site becomes less effective at catalyzing the conversion substrate to product
- - - - Each is composed of a polypeptide chain with its own active site
        
        The entire complex oscillated between 2 different shapes
        
        1 catalyticaly active and the other inactive
        
        Simplest allosteric regulation, and activating or inhibiting regulatory molecule binds to a regulatory site
        
        Can also be called allosteric site
        
        Often located where subunits join
    - - Substrate molecule binding to one active site in a multisubunit enzyme triggers a shape change in all subunits, increases catalytic activity at other active sites
      - Amplifies the response of enzymes to substrates
        
        One substrate molecule primes an enzyme to act on additional substrate molecules more readily
      - Is also considered allosteric regulation
        
        It’s binding affects catalysis in another active site
- - - - glycolysis can accept a wide range of carbohydrates for catabolism
        
        the digestion of disaccharides including sucrose, provides glucose and other monosaccharides as fuel for respiration
        
        proteins can also be used for fuel but must be digested to their constituent amino acids
        
        catabolism can also harvest energy stored in fats obtained either from food or from fat cells in the body
        
        after fats are digested to glycerol and fatty acids the glycerol is converted to glyceraldehyde 3 phosphate (intermediate of glycolysis)
        
        beta oxidation breaks the fatty acid down to 2 carbon fragments
        
        1 more item...
  - - - organic monomers obtained from digestion can be used directly
        
        compounds formed as intermediates of glycolysis and the citric acid cycle can be diverted into anabolic pathways as precursors from the cell can synthesize the molecules it requires
        
        glucose can be made from pyruvate and fatty acids can be synthesized from acetyl CoA
        
        anabolic or biosynthetic pathways do not generate ATP they consume it
        
        glycolysis and the citric acid cycle function as metabolic interchanges that enable our cells to convert some kinds of molecules to others
        
        metabolism is versatile and adaptable
  - - - feedback inhibition the end product of the anabolic pathway inhibits the enzyme that catalyzes an early step of the pathway
        
        prevents the needless diversion of key metabolic intermediates from uses that are more urgent
        
        cell controls its catabolism
        
        when the cell works hard and its ATP concentration begins to drop respiration speeds up
        
        when there is plenty of ATP to meet demand respiration slows down
        
        sparing organic molecules for other functions
        
        1 more item...
- - - - Light reactions capture solar energy and use it to make ATP and transfer electrons from water to NADP+ forming NADPH
        
        Calvin cycle uses the ATP and NADPH to produce sugar from carbon dioxide
        
        Energy enters the chloroplasts as sunlight becomes stored as chemical energy in organic compounds
- - - - Some energy taken out of chemical storage can be used to do work, the rest dissipates as heat
    - - Fermentation
        
        Partial degradation of sugars or other organic fuel that occurs without oxygen
      - Aerobic respiration
        
        Oxygen is consumed as a reactant along with organic fuel that occurs without oxygen
        
        Cells of most eukaryotic and many prokaryotic organisms can carry out aerobic respiration
        
        Anaerobic respiration
        
        Prokaryotes use substances other than oxygen as reactants that harvests chemical energy without oxygen
    - - Includes both aerobic and anaerobic processes
      - It’s often referred to as aerobic process
      - Formula: C6H12O6+6O2—>6CO2+6H2O+energy(ATP+heat)
  - - - Electron transfers are called oxidation reduction reactions
        
        the electron donor is the reducing agent
        
        energy must added o pull an electron away from an atom
        
        the more electronegative the atom the more energy is required
        
        the electron acceptor is oxidizing agent
    - - Loss of electrons from one substance
    - - Addition of electrons to another substance
      - Adding electrons
      - Adding negatively charged electrons to an atom reduces the amount of positive charge of that atom
  - - - glucose is not oxidized in a single step it is broken down
        
        each glucose is catalyzed by an enzyme
        
        electrons are stripped from the glucose
        
        hydrogen atoms are not transferred directly to oxygen, they are passed to an electron carrier
        
        this coenzyme is called nicotinamide adenine dinucleotide
        
        NAD+ is oxidzied and the reduced form is NADH
        
        1 more item...
  - - - occurs in the cytosol
        
        begins the degradation process by breaking glucose into two molecules of a compound called pyruvate
        
        pyruvate enters the mitochondrion and s oxidized to a compound called acetyl CoA
    - - Acetyl CoA enters the citric acid cycle
        
        the breakdown of glucose to carbon dioxide is completed
        
        carbon dioxide produced by respiration represents fragments of oxidized organic molecules
    - - energy released at each step of the chain is stored in a form the mitochondrion can make ATP from ADP
        
        ATP synthesis is called oxidative phosphorylation
        
        it is powered by the redox reactions of the electron transport chain
      - substrate level phosphorylation
        
        smaller amount of ATP formed directly in few reactions of glycolysis and the citric acid cycle
        
        occurs when an enzyme transfers a phosphate group from a substrate molecule to ADP
- - - - pyruvate is first converted to a compound called acetyl coenzyme A, or Acetyl CoA
        
        links glycolysis and the citric acid cycl
        
        carried out by a multienzyme complex that catalyzes 3 reactions
        
        pyruvates carboxyl group, somewhat oxidized and carries little chemical energy
        
        2 carbon fragment is oxidized and the electrons transferred to NAD+, stores energy in NADH
        
        coenzyme A (CoA) sulfur containing compound derived from a B vitamin attaches its sulfur atom to 2 carbon intermediate forming acetyl CoA
        
        is high in potential energy and is exergonic
  - - - Acetyle CoA adds its 2 carbon acetyl group to oxaloacetate producing citrate
        
        citrate is converted to its isomer, isocitrate by removing 1 water moleucle and adding another
        
        isocitrate is oxidized reducing NAD+ to NADH resulting compound loses a CO2 molecule
        
        another CO2 is lost and resulting compound is oxidized reducing NAD+ to NADH remaining molecule is attached to coenzyme A by an unstable bond
        
        CoA is displaced by phosphate group which is transferred to GDP form GTP which can also be used to generate ATP
        
        2 hydrogens are transferred to FAD forming FADH2 and oxidizing succinate
        
        1 more item...
- - - - folding of inner membrane to form cristae increases its surface area
        
        provides space for thousands of copies of each component of the electron transport chain in a mitochondrion
    - - remaining electron carriers between ubiquinone and oxygen are proteins
  - - - ATP synthase
        
        populating inner membrane of the mitochondrion or prokaryotic plasma membrane are many copies of a protein complex
        
        enzyme that makes ATP from ADP and inorganic phosphate
      - chemiosmosis
        
        energy stored in the form of a hydrogen ion gradient across a membrane is usd to drive cellular work such as synthesis of ATP
        
        chemiosmosis is an energy coupling mechanism that uses energy stored in the form of an H+ gradient across a membrane to drive cellular work
      - proton motive force
        
        emphasizing the capacity of the gradient to perform work
  - - - phosphorylation and the redox reactions are not directly coupled to each other
        
        ATP yield varies slightly depending on the type of shuttle used to transport electrons from the cytosol into the mitchondrion
        
        use of the proton motive force generated by the redox reactions of respiration to drive other kinds of work
- - - - alcohol fermentation
        
        pyruvate is converted to ethanol
        
        releases carbon dioxide from the pyruvate
        
        acetaldehyde is reduced by NADH to ethanol
        
        regenerates the supply of NAD+ needed for the continuation of glycolysis
        
        converts to the 2 carbon compound acetaldehyde
        
        lactic acid fermentation
        
        pyruvate is reduced directly by NADH to form lactate as an end product
        
        regenerating NAD+ with no release of CO2
  - - - all 3 use glycolysis to oxidize glucose and other organic fuels to purivate
        
        net production of 2 ATP by substrate level phosphorylation
    - - carry out only fermentation or anaerobic respiration
    - - organisms including yeasts and many bacteria can make enough ATP to survive using fermentation or respiration
- - - - Found mainly in the cells of the mesophyll
        
        Tissue in the interior of the leaf
        
        Carbon dioxide enters the leaf and oxygen exits by way of microscopic pores called stomata
        
        Chloroplast has two membranes surrounding a dense fluid called the stroma
        
        Suspended within the stroma is a third membrane system made of sacs called thylakoids
        
        Segregates the stroma from the thylakoid space inside the sacs
        
        1 more item...
  - - - Convert solar energy to chemical energy
        
        Light absorbed by chlorophyll drives a transfer of the electrons and hydrogen ions from water to an acceptor NADP+
        
        Light reactions use solar energy to reduce NADP+ to NAPH by adding electrons with an H+
        
        Light reactions also generate ATP using chemiosmosis to power the addition of a phosphate group to ADP called photo phosphorylation
    - - Named for Melvin Calvin and James Bashar and Andrew benson
        
        The cycle begins by incorporating CO2 from the air into organic molecules already present in the chloroplast
        
        Incorporation of carbon into organic compounds is known as carbon fixation
        
        Reduces the fixed carbon to carbohydrates by the addition of electrons
        
        Reducing power is provided by NADPH which acquired its cargo of electrons in the light reactions
        
        Convert CO2 to carbohydrates also requires chemical energy in the form of ATP which is also generated by the light reactions
- - - - Electromagnetic waves are disturbances of electric and magnetic fields rather than disturbances of a material medium such as water
        
        Distance between the crests of electromagnetic waves is called wavelength
        
        Electromagnetic spectrum, narrow band from 380 no to 750 no in wavelength
        
        Visible light can be detected as various colors by the human eye
        
        Photons, fixed quantity of energy
  - - - Spectrometer, ability of a pigment to absorb various wavelengths of light can be measured
        
        Absorption, graph plotting a pigments light absorption versus wavelength
        
        Absorption spectra of 3 types of pigments in chloroplasts
        
        Chlorophyll a
        
        Key light capturing pigment that participates directly in the light reactions
        
        Chlorophyll b
        
        Separate group of accessory pigments called carotenoids
        
        Action spectrum
        
        Profiles the relative effectiveness of different wavelengths of radiation in driving the process
        
        Carotenoids
        
        Hydrocarbons that are various shades of yellow and orange because they absorb violet and blue green light
  - - - Reaction center complex is an organized association of proteins holding a special pair of chlorophyll a molecules and a primary electron acceptor
        
        Light harvesting complex consists of various pigment molecules bound to proteins
        
        Primary electron acceptor, molecule capable of accepting electrons and becoming reduced
        
        Thylakoid membrane is populated by 2 photosystems
        
        Photosystem II (PS II)
        
        P680 Pigment is best at absorbing light having a wavelength of 680 nm
        
        Photosystem I (PS I)
        
        P700 pigment absorbs light of wavelength of 700nm
    - - Occurs during the light reactions of photosynthesis
        
        Photon of light strikes one of the pigment molecules in a light harvesting complex of PS II, boosting one of its electrons to a higher energy level
        
        Electron is transferred from the excited P680 to the primary electron acceptor
        
        Enzyme catalyzes the splitting of a water molecule into 2 electrons, 2 hydrogen ions and an oxygen atom
        
        Each photoexcited electron passes from the primary electron acceptor of PS II to PS I
        
        Potential energy stored in the proton gradient is used to make ATP in a process called chemiosmosis
        
        1 more item...
- - - - C3 plants
        
        First organic product of carbon fixation is a 3 carbon compound, 3-phosphoglycerate
      - C4 plants
        
        Preface Calvin cycle with an alternate mode of carbon fixation that forms a 4 carbon compound as its product
        
        2 types of photosynthetic cells
        
        Bundle sheath cells
        
        Arranged into tightly packed sheaths around the veins of the leaf
        
        Mesophyll cells
        
        Between the bundle sheath and the leaf surface are the more loosely arranged cells
    - - Adds CO2 to phosphoenolpyruvate forming a 4 carbon product oxaloacetate
        
        CO2 is fixed in the mesophyll cells the 4 carbon products are exported to bundle sheath cells through plasmodesmata
        
        Within bundle sheath cells the 4 carbon compounds release CO2 which is refined into organic material by rubisco and the Calvin cycle
  - - - CAM plants store organic acids they make during the night in their vacuoles until morning when the stomata closes
- - - - 50% of the organic material made by photosynthesis is consumed as fuel for cellular respiration in plant cell mitochondrion
        
        In most plants carbohydrateis transported out of the leaves to the rest of the plant in the form of sucrose a disaccharide
        
        After arriving at nonphotosynthetic cells, the sucrose provides raw material for cellular respiration and a multitude of anabolic pathways that synthesize proteins, lipids, and other products
  - - - Stockpile extra sugar by synthesizing starch and storing some in the chloroplasts themselves and some in storage cells roots, tubers, seeds, and fruits
        
        Photosynthesis is the process responsible for the presence of oxygen in our atmosphere
        
        Photosynthesis makes an estimated 150 billion metric tons of carbohydrates per year
- - - - Glyceraldehyde 3 phosphate (G3P)
        
        Carbohydrate produced directly from the Calvin cycle is not glucose it is 3 carbon sugar
        
        Phase 1: carbon fixation
        
        Incorporates each CO2 molecule, one at a time by attaching it to a five carbon sugar named fibulae bisphosphate
        
        Enzyme that catalyzes this first step is RuBP carboxylase oxygenate or rubisco
        
        Phase 2 reduction
        
        Each molecule of 3 phosphoglycerate receives an additional phosphate group from ATP becomes 1 3-bisphosphoglycerate
        
        Pair of electrons is donated from NADPH reduces 1 3-bisphosphoglycerate also loses a phosphate group in the process becomes glyceraldehyde 3-phosphate
        
        Phase 3 regeneration of the CO2 acceptor (RuBP)
        
        Carbon skeletons of five molecules of G3P are rearranged by the last steps of the Calvin cycle into 3 molecules of RuBP