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[start]
[q] UNIT 3
[a] Cellular Energetics
[q] What are enzymes?
[a]
1. Proteins that catalyze (speed up) reactions.
2. The enzyme is not used up in the reaction, they can be used again and again.
The names of enzymes usually end in “ase”
ex: lactase, amylase, sucrase, ATP synthase
[q] How do an enzymes work?
[a]
1. Enzymes have a sort of mouth called the active site where a substrate goes.
2. The substrate is something that is reacting. The substrate IS used up in the reaction.
3. Each enzyme is designed for a specific substrate, the substrate fits into the specific enzymes active site.
[q] Sucrase example on back of card
[a]
[q] What is induced fit?
[a] The enzyme gives the substrate a hug. I.e. the enzyme changes its shape a little so the substrate fits
[q] What is competitive inhibition?
[a] if something has a similar shape to the substrate, it might fit into the active site and block substrates from getting in, making the enzyme not function anymore.
[q] What is noncompetitive inhibition?
[a] A noncompetitive inhibitor will bind to the enzyme’s allosteric site and the active site will change shape, so the enzyme will not function anymore
[q] What is a cofactor/coenzyme?
[a] Something that goes into the active site to help the substrate fit
[q] How do enzymes catalyze reactions?
[a]
Enzymes lower activation energy
remember that phrase for the AP
[q] What factors can affect enzyme function?
[a]
1. Temperature: to high or to low of a temperature can denature the enzyme
2. PH: To high or to low PH can also denature the enzyme.
recall that denatured proteins go back to primary folding structure.
3. Amount of substrate: if there is a lot of substrate, there won’t be enough enzymes to break all of it down.
ex: lactose intolerant people often still have some lactase, just not enough to break down all the lactose.
4. inhibitors
[q] What happens when a cell is using more energy than it makes?
[a] it dies.
[q] What is a metabolic pathway?
[a] A series of reactions that form a final product. The product of one reaction goes on to be a reactant in another reaction and so on until the final product is made.
[q] Equation for photosynthesis
[a]
6 water and 6 carbon dioxide make a glucose and 6 dioxygens
6CO2 + 6H2O ——> C6H12O6 + 6O2
the 6O2s are “breathed” out
[q] What is the goal of photosynthesis?
[a] capture energy from the sun to make sugars (glucose)
[q] Where did photosynthesis first evolve?
[a] Cyanobacteria
[q] First phase of photosynthesis:
[a] Light dependent reactions (electron transport chain)
[q] First step of electron transport chain:
[a] 1. Photosystem 2 is energized by light, which splits an H2O
2. water splitting provides an electron (e-) and pumps an H+ ion through the transport protein
[q] Second step of electron transport chain:
[a] The highly energized e- goes to the next transport protein, supplying the energy to pump another H+ ion through
[q] Third step of electron transport chain:
[a]
1. The electron moves to Photosystem 1 and is energized by light again
2. Another H+ is pumped through a transport protein.
[q] Fourth step of electron transport chain:
[a] The electron can’t just float around after this wreaking havoc, so NADP+ accepts the e-, turning it into NADPH
[q] Fifth and final step of electron transport chain:
[a]
1. Because there is now a bunch of H+s at the top, they want to flow down via diffusion because of the concentration gradient.
2. The 3 H+s flow through the enzyme ATP synthase, which adds a phosphate to ADP (adenosine diphosphate) to make ATP (adenosine triphosphate).
ATP synthase is both an enzyme and a transport protein. Remember ions need to diffuse through proteins, and things that end in “ase” are enzymes.
[q] Second phase of photosynthesis:
[a] Light independent reactions (Calvin cycle)
[q] What happens in the Calvin cycle?
[a]
1. 3 CO2 molecules are taken in
2. 6 ATP and 6 NADPH are spent (came from e- transport chain. ATP turns to ADP and NADPH turns to NADP+)
3. the oxygen and 3 carbons from 3 CO2 and the 6 Hydrogens from 6NADPH come together to make half of a glucose
4. The Calvin cycle goes around again providing more oxygen, 3 more carbons and 6 more hydrogens to make the other half of glucose (C6 H12 O6)
Glucose is the final product
[q] Chemical equation for cellular respiration
[a] glucose and 6 dioxygens make 6 water and 6 carbon dioxide and a bunch of ATP
C6H12O6 + 6O2 –> 6CO2 + 6H2O + ATP
Opposite of photosynthesis equation
[q] Step 1 of cellular respiration (CR):
[a]
Glycolysis (occurs in cytoplasm):
1. 2 ATP is used to split 1 glucose (C6H12O6) into 2 C-C-C-P
(the phosphorus comes from the ATP)
2. To get rid of the phosphorus, 2 ATP is made for each, turning them into C-C-C (Pyruvate).
3. NAD+ accepts the electrons created from this turning it into NADH
Produced in this step:
2 ATP spent, 4 ATP made
2 NADH made
2 Pyruvate made
Net produced: 2 ATP, 2 NADH
[q] Step 2 of CR:
[a]
Pyruvate oxidation (occurs in mitochondria):
Two CO2 molecules are made from each of the pyruvate, turning them from C-C-C into C-C (acetyl-coA). NAD+ accepts electrons again making more NADH.
Produced this step:
2 CO2 made (gets breathed out)
2 NADH made
Net produced: 2 ATP, 4 NADH
[q] Step 3 of CR:
[a]
Krebs cycle/citric acid cycle (in mitochondria):
1. the acetyl-coA (C-C) go through the Krebs cycle. Details aren’t important, but know what this makes
2. makes 3 NADH, 1 ATP, FADH2, and 2CO2 (breathed out)
3. this happens twice to use both the acetyl-coA
Produced this step:
2 ATP made
6 NADH made
2 FADH2 made
Net produced: 4 ATP, 10 NADH, 2 FADH2
[q] Step 4 of CR
[a] Electron transport chain/oxidative phosphorylation (in mitochondria):
1. NADH gets made back into NAD+, supplying 2 electrons (the whole purpose of them was to carry the e-s to this step.) This pumps an H+ ion through a transport protein.
2. FADH2 splits into FAD, supplying 2 more e-s, pumping more H+ through
3. electrons pump more H+ through another protein.
4. Because e-s can’t just float around, the e-s combine with 1/2 O2 and 2H to make water.
5. Because of the concentration gradient, all the H+s (there is a lot, varies by organism) flow through ATP synthase to make ADP into ATP
[q] TOTAL CREATED:
[a]
Electron transport chain:
About 30 ATP from the NADH electrons
About 4 ATP from the FADH2 electrons
First three steps:
4 ATP
TOTAL: about 38 ATP! (varies per organism, can be as low as 30)
This all was made from one glucose
[q] Why is it better for different chloroplasts in different cells to be different colors/different shades of green?
[a] They will be able to absorb different wavelengths of light, which means more energy, the plants will be more fit.
[q] Metabolism
[a] the totality of an organisms chemical reactions that result from interactions between molecules within the cell
[q] metabolic pathway
[a] a sequence of chemical reactions undergone by a compound in a living organism, start with substrate end with product
[q] catabolic
[a] breaking a complex molecule down into its simpler parts, releasing energy. ie. cellular respiration
[q] anabolic
[a] using energy to build complex molecules from simpler molecules. ie. protein synthesis
[q] Bioenergetics
[a] the study of how organisms manage their energy resources
[q] energy
[a] capacity to cause change, do work
[q] heat(thermal energy)
[a] kinetic energy associated with random movement of molecules
[q] chemical energy
[a] potential energy available for release in a chemical reaction, energy within bonds
[q] exergonic reaction
[a] a reaction with a net release of free energy, negative free energy, spontaneous
[q] endergonic reaction
[a] a reaction that absorbs free energy from its surroundings, non-spontaneous, positive free energy
[q] catalyst
[a] a chemical agent that speeds up chemical reactions without being consumed by the reaction
[q] enzymes
[a] a catalytic protein, speeds up metabolic reactions by lowering activation energy, very specific, reusable, unchanged by reaction
[q] activation energy
[a] initial energy needed to start a chemical reaction, free energy for activating reaction, given off by heat
[q] induced fit
[a] brings the chemical groups of the active site into positions that enhance their ability to catalyze the reaction, makes the enzyme more effective
[q] cooperativity
[a] another type of allosteric activation, binds to one active site but locks ALL active sites open, allowing products to be constantly produced
[q] Substrate
[a] the REACTANT that an enzyme acts on
[q] Enzyme-Substrate Complex
[a] enzyme and substrate
[q] Active Site
[a] region on the enzyme where substrate binds
[q] Hydrogen and Ionic Bonds
[a] substrate held in active site by WEAK interactions
[q] Lock and Key
[a] active site on enzyme fits substrate exactly
[q] hydrolysis
[a] The addition of water to a polymer or dimer to split it into monomers.
[q] cofactors
[a] non-protein enzyme helpers ex. zinc, iron, copper
[q] coenzymes
[a] organic enzyme helpers ex. vitamins
[q] Denature
[a] above a certain temp activity declines, protein unwinds
[q] Renature
[a] coils it back to normal after temp gets too high and the activity decreased
[q] Feedback inhibition
[a] end product of a pathway that continues to produce product (positive) and then turns off (negative)
[q] Allosteric Regulation
[a] can accelerate or inhibit production and enzyme activity by attaching to another part of the protein. this changes the shape of the active site which inhibits substrates from bonding and producing more products
[q] Activator
[a] one of the allosteric regulators, stabilizes and keeps active site open for production, wedges open
[q] Inhibitor
[a] a substance that interferes with the action of a catalyst
[q] Competitive Inhibitor
[a] inhibitor that mimics original substrate by blocking the original substrate
[q] Noncompetetitive Inhibitor
[a] bind to another part of enzyme to change shape and block substrate from producing
[q] Factors that affect enzymatic rate of reaction
[a] environment, pH, temp, salinity, chemicals that infuse enzyme, substrate concentration, enzyme concentration
[q] V-max
[a] Maximum rate of reaction
[q] free energy
[a] energy available to do work
[q] bioenergetics
[a] (1) The overall flow and transformation of energy in an organism.
(2) The study of how energy flows through organisms.
[q] enzymes
[a] Proteins that act as biological catalysts/Increases the rate of a reaction by lowering the reaction’s activation energy/remain unaffected by the reaction/doesn’t change the reaction/doesn’t make reactions occur that would otherwise not occur at all
[q] organic catalysts
[a] Speed up the rate of a reaction without altering the reaction itself/Catalyze the reactions without being changed in the reaction themselves
[q] exergonic reactions
[a] Reactions in which the products have less energy than the reactants/Energy is given off during the reaction
[q] endergonic reactions
[a] Reactions that require an input of energy/products have more energy than the reactants
[q] activation energy
[a] energy needed to get a reaction started
[q] enzyme specificity
[a] Term used to say that enzymes only catalyze one kind of reaction
[q] substrates
[a] the reactants of enzyme-catalyzed reactions
[q] enzyme-substrate complex
[a] substrate A + substrate B + enzyme -> ______ -> enzyme + product
[q] induced fit
[a] Enzyme has to change its shape slightly to accommodate the shape of substrates
[q] coenzymes
[a] Organic factors, such as vitamins, that help enzymes in catalyzing a reaction/they accept electrons and pass them along to another substrate/two examples are NAD+ and NADP+
[q] cofactors
[a] Inorganic elements, usually metal ions, that help catalyze reactions
[q] allosteric sites
[a] a region of the enzyme other than the active site to which a substrate can bind
[q] allosteric regulators
[a] substances that can either inhibit or activate enzymes
[q] allosteric inhibitor
[a] Binds to an allosteric site and keep the enzyme in its inactive form
[q] allosteric activator
[a] Binds to an enzyme and induce its active form
[q] feedback inhibition
[a] Allosteric enzymes are subject to ______ in which the formation of an end product inhibits an earlier reaction in the sequence
[q] competitive inhibition
[a] A substrate has a shape that fits the active site of an enzyme and can take the place of the substrate and inactive the enzyme
[q] noncompetitive inhibition
[a] Inhibitor binds with the enzyme at a site other than the active site and inactivates the enyzme by altering its shape, preventing the enzyme from binding with the substrate at the active site
[q] first law of thermodynamics
[a] Energy cannot be created or destroyed. In other words, the sum of energy in the universe is constant.
[q] second law of thermodynamics
[a] Energy transfer leads to less organization/ the universe tends toward disorder (or entropy)
[q] entropy
[a] a thermodynamic quantity representing the amount of energy in a system that is no longer available for doing mechanical work
[q] photosynthesis
[a] Involves the transformation of solar energy into chemical energy/ 6CO2 + 6H20 + sunlight -> C6H12O6 + 6O2
[q] cellular respiration
[a] C6H12O6 + 6O2 -> 6CO2 + 6H2O + ATP
[q] aerobic respiration
[a] Cellular respiration that uses oxygen, Glycolysis -> Formation of acetyl CoA -> The Krebs Cycle -> Oxidative phosphorylation
[q] anaerobic respiration
[a] Cellular respiratioin without oxygen
[q] glycolysis
[a] Splitting of glucose into two three-carbon molecules called pyruvic acid, occurs in the cytoplasm, net of 2 ATPs produced, 2 pyruvic acids formed, 2 NADS produced
[q] pyruvic acid
[a] the three-carbon compound that is produced during glycolysis and needed for both the aerobic and anaerobic pathways of cellular respiration that follow glycolysis
[q] acetyl coenzyme A
[a] Formation of this is the second step in aerobic respiration, each pyruvic acid converts to this and CO2 is released and 2NADH is produced
[q] Krebs cycle (or citric acid cycle)
[a] third step in aerobic respiration, occurs in the matrix of the mitochondria, produces 1 ATP, 2 NADH, and 1 FADH2, loses two carbons released as CO2
[q] oxaloacetate
[a] a four carbon molecule that combines with acetl CoA to form a seix-carbon molecule, citric acid
[q] citric acid
[a] six-carbon molecule formed after acetyl CoA combines with oxaloacetate
[q] cytochromes
[a] Proteins in the electron transport chain which contain heme groups, which have iron atoms that accept and donate electrons
[q] pH gradient (or proton gradient)
[a] Created by the pumping of hydrogen ions into the intermembrane space, the potential energy established in this gradient is responsible for the production of ATP
[q] ATP synthase
[a] large protein that uses energy from H+ ions to bind ADP and a phosphate group together to produce ATP on the matrix side of the channel
[q] oxidative phosphorylation
[a] The production of ATP using energy derived from the redox reactions of an electron transport chain.
[q] fermentation
[a] Under anaerobic conditions, pyruvic acid is converted to either lactic acid or ethyl alcohol (or ethanol)
[q] lactic acid
[a] One end product of fermentation, pyruvic acid is converted to 2______ + 2NAD+
[q] ethanol (or ethyl alcohol)
[a] One end product of fermentation, pyruvic acid is converted to 2 _____ +CO2+2NAD+
[q] electron transport chain
[a] Done in the cristae, uses the 2 NADH molecules from glycolysis, 2 NADH molecules from the production of acetyl CoA, 6 NADH molecules from the Krebs cycle, and 2 FADH2 from the Krebs Cycle, The electron carriers (NADH and FADH2) “shuttle” electrons to the electron transport chain, and the hydrogen atomas are split into 2H+ and 2e-, then the high-energy electrons from NADH and FADH2 are passed down the ______, which is a series of protein carrier molecules that are embedded in the cristae
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