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Bio Test 4 Study Set

QuestionAnswer
What are the main elements of cell signaling? (4) 1) Signal (from outside the cell) 2) Receptor (at the cell) 3) Signal transduction (in the cell) 4) Response (of the cell)
T or F: Chemical signals (messages) can only come from neaby (a local level). False, chemical signals (messages) can come from near (at a local level) or far (from a distance)
What are target cells vs non-target cells? Target cells have a receptor for the ligand, whereas non-target cells will not have a receptor that can respond to the ligand
What does a receptor have that is specific to a certain ligand? It has a specific binding site for a ligand
T or F: Only one signaling molecule can act at a time on one cell. False, many different signaling molecules can act at the same time on one cell
What determines how the cell will respond to the received signal? The different combination of signaling molecules bound to its receptors
What type of macromolecule are receptors? Proteins
Where are receptors located in the cell? At the cell surface (at the membrane as a transmembrane protein), inside the cytoplasm, or in organelle membranes
What is a ligand? A signal molecule
What do receptors interact with? Ligands (signal molecules)
How do receptors function? The ligand will bind to the receptor, causing the receptor to undergo a conformation (shape) change, which can initiate the signaling process inside the cell
Does the ligand typically change its shape? No
Describe the propagation that occurs in the receptor when a ligan binds to it. The receptor's shape change begins where the ligand binds and is then propagated throughout the entire protein, as all the bonds and interactions in the protein are dependent on one another so a change at one site effects the overall protein shape
Does a ligand binding to a recpetor only change the shape of the receptor at the binding site? No, the shape change is proagated throughout the whole protein
What is the shape/structure of the receptor for the epinephrine pathway? It is a receptor with 7 transmembrane helices
What term describes the strength of binding between two molecules? Affinity
What quantifies the affinity of a receptor for its ligand? The dissociation constant (KD)
What is KD defined as? The concentration of free ligand at which half of the protein receptor sites are bound by the ligand
What are the units of KD? Concentration units
The smaller the KD, the stronger or weaker the binding? The stronger the binding
The greater the KD, the stronger or weaker the binding? The weaker the binding
Will increasing the concentration of the ligand change the KD? No
What factors could change the KD of a receptor for its ligand? Changing the pH or changing the temperature
T or F: KD must be determined experimentally. True
Is receptor-ligand binding reversible or irreversible? Reversible
What type of bonds/interactions will occur between ligands and receptors and why? Non-covalent bonds/interactions because covalent bonds are too strong and will likely not allow for the binding to be reversible
T or F: Receptor-Ligand specificity is absolute. False, chemically similar ligands may be able to form bonds with the same receptors
What is an agonist? An agonist is a compound that binds the receptor and produces a similar effect to the natural ligand by causing a similar allosteric change in the receptor
What is an antagonist? A molecule that bonds the receptor, but blocks the normal response because the shape change that occurs is not exactly the same
T or F: Different receptors may be able to bind the same ligand. True
Give an example of a ligand that can bind to two different receptors. Acetylcholine
If a ligand can bind two different receptors, what determines the cellular response and will they be different? The receptor and the changes the receptor causes inside the cell determines the cellular response and this could be different (acetylcholine excites in one pathway and inhibits in another)
What are the 2 ways of turning off a signal and identify which one is slower and which one is faster? 1) Slower: The signal diffuses away, gradually lowering the signal by reducing concentration 2) Faster: Enzymes degrade the signal
What are 2 types of transmembrane receptors? Ligand-gated ion channels and G-protein coupled receptors
What do ligand-gated ion channels do? the receptor is an ion channel that opens when bound to a ligand, allowing ions to flow based on concentration and charge gradient
T or F: Some receptors are ion channels, but all ion channels are receptors for chemical signals. False, some receptors are ion channels, but not all ion channels are receptors for chamical signals
What does epinephrine signaling cause? Liver cells to break down gylcogen into glucose, sending the glucose into the blood stream. This glucose will then be taken up by muscle cells and metabolized to produce ATP
What are the components of the epinephrine signaling pathway? (5) 1) G-protein couple receptor 2) G-protein 3) Effector proteins (adenylyl cyclase) 4) Secondary messangers (cAMP) 5) Protein Kinases (Protein Kinase A and others)
How many phosphate groups does GDP have? 2 (Guanosine diphosphate)
How many phosphate groups does GTP have? 3 (Guanosine triphosphate)
What type of receptor is the epinephrine receptor? A G-protein coupled receptor
What happens when epinephrine binds to the G-protein coupled receptor? It results in a conformational change in the receptor
Where is the G-protein located? At the inner leaflet of the plasma membrane
How does the G-protein coupled receptor activate the G-protein? Once epinephrine is bound to the receptor and changes its shape, the receptor's shape change allows it to bind to and activate the G-protein
What does the G-protein act as an intermediary between? Between the receptor and an effector protein
What does it mean for the G-protein to become activated, and what occurs as a result of this? When the G-protein becomes activated, it has undergone a shape change. The result of this is it will exchange GDP for GTP
What is nucleotide exchange? Nucleotide exchange is when the G-protein loses affinity for GDP due to its shape change, and it gains affinity for GTP
Where does the GTP come from during nucleotide exchange? There is always a pool of GTP available in the cytoplasm (no chemical bonds or phosphorylation are occuring to create GTP)
Once a G-protein is activated, how is it inactivated? Through hydrolysis which allows the protein to lose its GTP and return to having GDP
How does the removal of the signal (the ligand) affect the shape of the protein receptor? It will return to its original shape that it had been prior to the binding of the ligand
How does the activated G-protein activate the effector protein? A GTP-bound subunit of the G-protein (the alpha subunit) diffuses through the inner leaflet of the plasma membrane and makes contact with an inactive effector protein
What happenes when the GTP bound subunit makes contact with the effector protein? It activates the effector protein, through allosteric change
What is the effector protein in the epinephrine pathway? adenylyl cyclase
What has a direct effect on the behavior of the target cells? Effector proteins
What does adenyly cyclase catalyze the formation of? Catalyzes the formation of cAMP (3'-5'-cyclic AMP)
What is the second messenger in the epinephrine pathway? cAMP
When it is active does adenylyl cyclase create one or many cAMP molecules? Many!
How is effector protein --> second messenger a form of amplification within the pathway? Because while it is active, just one adenylyl cyclase can make many cAMP molecules
What do second messengers do? Amplify and distribute the signal within the cell
Generally, what characterizes second messengers? (4) -small molecules -rapidly produced inside the cell in response to signaling -serve to amplify the signal by binding to downstream proteins in the signaling cascade -allow the cell to respond to receptor binding with multiple events within the cell
Generally, activation of one epinephrine receptor produces about how many molecules of cAMP, and what does this illustrate in the pathway? Produces about 20 molecules of cAMP, illustrating amplification in the pathway
What do the second messengers do after being catalyzed? They bind to regulatory subunits, changing their shape, so they can no longer bind the catalytic subunits, releasing them
What is the reaction in which adenylyl cyclase acts as the enzyme? ATP --> cAMP + 2Pi
When cAMP is not present, what do the regulatory subunits do? They bind the catalytic subunits and prevent the catalytic activity
Once the catalytic subunits are released, what do they become? Active protein kinases
What are protein kinases? Enzymes that catalyze the covalent addition of a phosphate group onto a protein
How does the kinase get the phosphate to add to a target protein? The kinase removes a phosphate from an NTP (nucleotide triphosphate) and attaches it to a target protein, using the NTP pool available in the cytoplasm
Does phosphorylation activate or inactivate the target protein? It can do either one depending on the particular protein, location of phosphate group, etc.
What does protein phosphatase do? De-phosphorylates a protein (removes phosphate)
What does the phosphorylation of a protein cause? A conformational change to that protein that either activates or inhibits it
What is the kinase in the epinephrine pathway? Protein Kinase A
What 2 target proteins does active Protein Kinase A phosphorylate? 1) Phosphorylase kinase 2) gylogen synthase
What happens when active Protein Kinase A phosphorylates phosphorylase kinase? It activates it leading to a kinase cascade that promotes glycogen breakdown
What happens when active Protein Kinase A phosphoyrlates glycogen synthase? It inhibits it preventing any further glycogen synthesis
What is a kinase cascade? A common module in signaling transduction pathways, in which there is a series of sequential phosphorylation events involving multiple kinases in the signaling pathway
Since each kinase can phosphorylate more than one copy of its target protein, what does the cascade allow for? Signal amplification
What protein does phosphorylase kinase phosphorylate in the cascade and what does this do? glycogen phosphorylase, which activates it
What protein does gylcogen phosphorylase phosphorylate and what does this do? Gylcogen, which breaks off a phosphorylated glucose monomer
What happens to the phsophorylated glucose monomer that is broken off from glycogen in the pathway? Phosphatase removes the phosphate from glucose, allowing it to exit through the GLUT2 transporter
Where do Kinases use their phosphate from vs. where do phosphorylases use their phosphates from? Kinases use phosphate from NTP, while Phosphorylases use a cellular pool of phosphate in the cytoplasm
In all, one epinephrine led to about how many glucose molecules being released from the liver cell into the blood stream? About 10,000 glucose molecules
What is thermodynamics? The study of energy transformations
What does thermodynamics allow us to determine? Whether a reaction will occur spontaneously
What is Gibbs free energy (G)? The energy available to do work
In order for a chemical reaction to procced spontaneously, does there have to be more energy associated with the reactants or the products? There has to be more energy associated with the reactants
What is the eqaution for change in free energy? Delta G = Gfinal - Ginitial
Is delta G greater than or less than 0 for spontaneous reactions and is energy released or required? Delta G is less than 0 and energy is released
Is delta G greater than or less than 0 for nonspontaneous reactions and is energy released or required? Delta G is greater than 0 and energy is required
Are atoms created or destroyed in chemical reactions? Atoms are neither created nor destroyed in chemical reactions
For nonspontaneous reactions to occur, what must happen? They must be energetically coupled to spontaneous reactions
When a nonspontaneous reaction is energetically coupled with a spontaneous reaction, what will the overall Delta G be (positive or negative)? Negative delta G, for the spontaneous reaction has to have more energy to drive the nonspontaneous reaction
T or F: All chemical reactions proceed toward equilibrium. True
What is chemical equilibrium? A state during the progression of a reversible chemical reaction in which the forward rate of reaction is equivalent to the reverse rate
When equilibrium is reached, do reactants and products present at relative concentrations have any further tendency to change with time? No, their concentrations will no longer be changing
What is a dynamic state? A characteristic of chemical equilibrium in which all of the reactants and products are still being synthesizes, however, since it is equilibrium and this is occurring at equal rates, there concentrations do not change
What is a reactions equilibrium state? The specific set of conditions for the reaction in which the rate of the forward reaction equals the rate of the reverse reaction
What is the equilibrium constant Keq? The ratio of the concentration of products to the concentration of reactants at equilibrium
What is the formula for Keq? Keq = [products] / [reactants]
What value(s) of Keq shows you have more reactants than products? 0 < Keq < 1
What value(s) of Keq shows you have an equal amount of products and reactants? Keq = 1
What value(s) of Keq shows you have more products than reactants? Keq > 1
What are the units of Keq? concentration units
At chemical equilibrium, are individual reactant molecules still being converted to products and individual product molecules still being converted to reactants? Yes!
What does Le Chatelier's Principle state? That moving toward equilibrium is a spontaneous process (thermodynamically favorable), whereas moving away from equilibrium is nonspontaneous
Would moving away from equlibrium require or release energy? Require energy (nonspontaneous process)
Would moving toward equilibrium (restoring equilibrium) require or release energy? Release energy (spontaneous process)
What is the Reaction Quotient, Qr? It describes a reaction at any point, including equilibrium.
T or F: Keq is a special case of Qr. Yes
What is the eqaution for the Reaction Quotient? Qr = [Products] / [Reactants]
When Qr < Keq, which reaction is favored? The forward reaction is favored and spontaneous (-Delta G)... the reverse reaction would be +Delta G
When Qr > Keq, which reaction is favored? The reverse reaction is favored and spontanous (-Delta G)... the forward reaction would be +Delta G
Does chemical equilibrium mean that [products] = [reactants]? No, just that the rate of the forward and the rate of the reverse reactions are equal
T or F: Enzymes can change the thermodynamic properties of chemical reactions. In other words, enzymes can affect delta G. False, they can only increase their rates (they have no affect on the delta G of the reaction)
What role do enzymes have in chemical reactions? Enzymes act as catalysts to increase the rate of a chemical reaction
How do enzymes increase the rate of a chemical reaction? By lowering the activation energy required to start a chemical reaction
What is activation energy? The energy the reactants must possess to undergo a chemical reaction
How do enzymes lower the activation energy of a chemical reaction? By helping substrates (reactants) interact (not by providing any input of energy)
In what ways can an enzyme help substrates (reactants) to interact? (3) -By orienting them next to each other so they could interact -Placing the substrate under physical strain, weakening its covalent bonds -Temporarily transfer an electrical charge to the substrate, promoting a reaction
What macromolecule are most enzymes? Proteins
What is the region in which the enzyme binds substrates? The active site
T or F: The shape of an enzyme's active site allows specific bonds for specific molecules. True
What happens to the enzyme after the reaction is complete and the product is released? Its shape will remain unchanged from what it had been originally and it can then bind another substrate molecule
What is the induced fit model of binding? Most enzymes change shape upon binding their substrates...this induced fit then allows the reaction to proceed
Do enzymes catalyze chemical reactions in the forward or the reverse direction? Both the forward and the reverse!
Can enzymes speed up reactions in a thermodynamically unfavorable direction? No, despite being able to catalyze both forward and reverse reactions, enzymes only speed up reactions in the thermodynamically favorable direction
Can an enzyme force a thermodynamically unfavorable reaction? No!
T or F: The degree to which an enzyme increases the reaction rate varies by enzyme True
What is kinetics? How the rates of an enzyme catalyzed reaction change over time as substrate is added
How is reaction rate or velocity determined? Experimentally
What is Vmax in kinetics? The maximum rate at which the reaction can proceed
When can you tell that Vmax has been reached? When the graph reaches a plateau
What is Km and what does it equal? Km (aka Michaelis constant) is the affinity of an enzyme for its substrate and is equal to the substrate concentration at which the reaction reaches 50% of its maximum velocity (or 1/2 Vmax)
Does a lower Km reflect a higher or lower affinity? A higher affinity
What factors could change Km? Km depends on the shape of the active site, so changes that affect the shape of a protein can change Km
What factors could change the rate (V) of the reaction? Changing the Km
What is the result of adding more enzyme concentration in terms of Vmax and Km? Vmax will increase, but Km will stay the same (1/2 Vmax occurs at the same substrate concentration)
What does it mean when an enzyme can be regulated? Meaning they can become more active (catalyze the reaction faster) or inhibited (catalyze the reaction more slowly)
What is allosteric regulation? When a molecule binds away from the active site of an enzyme, changing the shape of the enzyme to either increase or decrease the affinity of the enzyme for its substrate
Is allosteric regulation reversible or irreversible? Reversible
What is allosteric inhibition? When a molecule binds away from an enzymes active site, changing its shape in a away that decreases its affinity for its substrate
What is allosteric activation? When a molecule binds away from an enzymes active site to change its shape in a way that increases its affinity for its substrate
What bonds likely form between allosteric regulators and the enzymes and why? non-covalent bonds because they are weak enough to be broken and allosteric regulation is a reversible process
What is a competitive inhibitor? A molecule that binds to the active site of an enzyme, blocking the substrate from binding
What is metabolism? The broad term to describe all the chemical reactions needed to sustain life
What is catabolism? The break down of larger molecules into smaller components
What is anabolism? Buidling larger molecules from smaller components
What is a metabolic pathway? A series of linked chemical reactions catalyzed by enzymes
What is cellular respiration? The process by which glucose is broken down to CO2 and H2O, releasing ATP
What do energy carrier molecules do? They store energy, and through energetic coupling can power unfavorable reactions
What are the energy carrier molecules in cellular respiration? ATP, NADH, and FADH2
What is an example of energetic coupling allowing the driving of energetically unfavorable reactions with ATP? ATP hydrolysis releases energy (favorable) and can be coupled with a process that requires energy (unfavorable) to allow it to run (sum of delta G must be below 0)
How does ATP carry its energy? In its bonds
How does ATP release its stored energy? Through ATP hydrolysis
Why is ATP a good energy carrier? (3) -ATP readily transfers a phosphate in catalyzed reactions -Simplification: it is a common "fuel" for most energy-requiring reactions -Limited availability: Concentrations can be regulated
How do NADH and FADH2 store their energy? In 2 electrons
How do NADH and FADH2 release their energy? Through catalyzed redox reactions (where they give up their 2 electrons)
Why is glucose broken down in a series of stages/steps rather than in one reaction coupling? Because it allows for much more ATP to be formed (at least 30), rather than just forming only 1 ATP if it weren't broken into stages
What are the 4 stages of breaking down glucose into ATP and where do each occur in the cell? 1) Gycolysis--> in the cytoplasm 2) Pyruvate oxidation --> in the mitochondrial matrix 3) Citric acid cycle --> in the mitochondrial matrix 4) Oxidative phosphorylation --> in the inner mitochondrial membrane/mitochondrial matrix
What is substrate-level phosphorylation vs. oxidative phosphorylation? In s.l. phosphorylation, energy to power the reaction and the phosphate group comes from the substrate, whereas in ox. phosphorylation, energy to power the addition of the inorganic phosphate comes from the H+ gradient
What 2 molecules can begin glycolysis, and based on each what is the difference in what energy will be invested? 1) glucose --> must invest 2 ATP 2) glucose-1-phosphate --> must invest 1 ATP
What are the net results of glycolysis for each possible starting molecule? Include the number of carbons on relevant outcome molecules. -Glucose will net: 2 ATP, 2 NADH, and 2 pyruvate (3 C's on each) -Glucose-1-phosphate will net: 3 ATP, 2 NADH, and 2 pyruvate (3 C's on each)
Why does glucose need to invest 1 more ATP than glucose-1-phosphate? Because it must be phosphorylated to become glucose-6 phosphate, whereas glucose-1-phosphate already has the phosphate group, so it can frelly undergo an isomerization reaction to become G-6-P
Where does glucose/glucose-1-phophate come from? (3) From the diet and transported into cells or broken down from glycogen stored in liver cells (and transported through the blood to other cells) or in liver and muscle cells and used directly in those cells (G-1-P only)
What energetic coupling occurs in glycolysis with glucose? ATP hydrolysis is coupled with converting glucose into glucose-6-phosphate
What is the cleavage phase of glycolysis? The 6 carbon sugar is cleaved into two 3 carbon sugars
How can reactions that are unfavorable in standard conditions proceed in cellular conditions? In metabolic pathways, a fav. rxn in the pathway moves in the fwd direction, thus the reactant of that rxn, acting as the product of a previously linked rxn, will have a lower concentration and thus lower Qr allowing the prev. rxn to go in the fwd dir.
What are oxidation-reduction (redox) reactions? Chemical reactions in which electrons are transferred from one reactant to another
When a molecule is losing electrons is it oxidized or reduced and will it typically gain or lose an H? It is oxidized and typically loses an H (lower energy state)
When a molecule is gaining electrons is it oxidized or reduced and will it typically gain or lose an H? It is reduced and typically gains an H (higher energy state)
How many electrons does NADH carry and what molecule does it become? NADH carries 2 electrons and become NAD+ after losing the 2 electrons
T or F: Energy carriers can be created through redox reactions. True
How is ATP produced during The Gycolysis energy harvest phase? ATP is produced by substrate-level phosphorylation, in which the phophate comes from a substrate molecule and is added onto ADP to produce ATP
How does feedback regulation of metabolism occur? Through allosteric regulation of critical enzymes by the eventual products of the pathway (remember allosteric inhibition and allosteric activation of enzymes)
What is negative feedback? The product of a process inhibits an earlier step to limit its own production
What is positive feedback? The product of a process promotes an earlier step to increase its own production
What acts as the allosteric regulator of many metabolic enzymes? ATP
What enzyme is the primary point of feedback control in glycolysis? Phosphofructokinase (PFK)
Describe how ATP demonstrate a type of feedback regulation in cellular respiration. ATP demonstates neg. feedback as when its conc. is low it will not bind to the regulatory site of PFK and continue to be produced When its conc. is high it will bind to the regulatory site of PFK, resulting in an allosteric change that inhibits prod. ATP
Does ATP act as a substrate or regulator of PFK enzymatic activity? Both!
Does the regulatory site of PFK have high or low affinity for ATP and what does this mean? Low affinity for ATP, meaning ATP will only act as a regulator when it is at high conc. (and no longer needs to be produced)
Does the active site of PFK have high or low affinity for ATP? High affinity for ATP
What is the starting molecule of pyruvate oxidation and in what quantity? 2 Pyruvates
Where does pyruvate oxidation occur? mitochondrial matrix
What are the products of pyruvate oxidation and their quantities? 2 NADH, 2 Acetyl CoA, and 2 CO2 waste
What is the starting molecule of the citric acid cycle and in what quantity? 2 Acetyl CoA
What does it mean for the citric acid cycle to be both a pathway and a cycle? It is a pathway because it is a series of linked chemical reactions catalyzed by enzymes. It is a cycle because the original reactant is also a product of a later step of the pathway
Where does the citric acid cycle occur? Mitochondrial matrix
What is the main goal of the citric acid cycle? To produce energy carriers via redox reactions
What are the products of the citric acid cycle? 6 NADH, 2 FADH2, 2 GTP, and 4 CO2 waste
What happens to the GTP produced in the citric acid cycle? It can be converted to ATP by a phosphorylation reaction
Does allosteric regulation occur only in glycolysis? No, key enzymes throughout the entire metabolic pathway undergo allosteric regulation
Where does oxidative phosphorylation occur? In the mitochondrial matrix and intermembrane space (proteins span inner mitochondrial membrane)
What is the electron transport chain? A series of proteins and other molecules embedded in the inner mitochondrial membrane
What happens at protein complex I in the ETC? NADH donates 2e-
What happens at protein complex II in the ETC? FADH2 donates 2e-
How do the electrons move through the chain in the ETC? Through a series of redox reactions
Which protein complexes in the ETC are proton pumps? Complexes I, III, and IV are proton pumps
What do the protein complexes that act as pumps do in the ETC? Complexes I, III, and IV act as proton pumps and when they gain energy from donated e-'s they move H+ against its gradient to create a proton gradient
What is the final electron acceptor in the ETC and what does it do? Oxygen, which accepts 2e- and 2 H+ to form water
What happens if oxygen is not present in the ETC process? The last protein complex will be unable to donate its electron because there is nothing there to accept it, so it will back up the whole process and stop it from proceeding
Does the beginning of the ETC or the end of the ETC have more free energy associated with it? The beginning of the ETC has more free energy associated with it because it needs to power rest of the chain after it
Where does the free energy released from the redox reactions go? To the proton gradient
What is ATP Synthase and what does it do? ATP synthase is an enzyme embedded in the inner mitochondrial membrane that allows H+ to flow down its gradient through it, in turn allowing ATP synthase to harness this energy into catalyzing the formation of ATP
Through what process does ATP Synthase catalyze ATP? Through oxidative phosphorylation
What gradients are present during the Oxidative phosphorylation process? Both charge and concentration gradients
What must go into oxidative phosphorylation? NADH, FADH2, and O2
What is the product of oxidative phosphorylation? 26+ ATP and H2O
Created by: ndimarco31
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