Unit 3 Test Flashcards
Which organelle is key to cell signaling?
The plasma membrane
What directly connects the cytoplasm in adjacent cells?
Gap junctions in animal cells and plasmodesmata in animal cells
What are the types of Local and long distance cell signaling?
Local
- Junctions(cell to cell)
- Paracrine
- Synaptic
Long distance
1. Endocrine/hormone signaling
What is paracrine signaling?
A secreting cell acts on nearby target cells by discharging molecules of a local regulator into the extracellular fluid. This secreting cell has a vesicle bond to the membrane and conduct exocytosis
What is synaptic signaling? Where does this occur?
An electric signal causes a nerve cell to release neurotransmitter molecules into a synapse(gap between cells), stimulating a target cell. This occurs in the nervous system of animals
What is long distance signaling?
Specialized endocrine cells secret hormones into body fluids, often blood. Hormones reach virtually all body cells but are bound by only some cells
What are local regulators? Where do they come from?
Messenger molecules secreted by a signaling cell in the process of paracrine signaling
What are growth factors?
A class of local regulators that stimulate nearby target cells to grow and divide(paracrine signaling)
What 3 processes do cells that are receiving signals undergo?
- Reception: The target cell’s detection of a signaling molecule coming from outside the cell. A chemical signal is “detected” when the signaling molecule binds to the receptor protein located on or in the cell
- Transduction: A series of steps that converts the signal to a form that can bring about a specific cellular response
- Response: The transduced signal triggers a specific cellular response
What is a ligand?
The signal molecule binding to a receptor
What happens when a ligand bonds to a receptor cell?
The receptor usually changes shape and is activated by this shape change?
What are most signal receptors? their ligands?
Plasma membrane proteins, their ligands are generally water soluble and too large to pass freely through the plasma membrane
What are the two main types of membrane receptors?
- G protein-coupled receptors
2. Ligand-gated ion channels
What is a G protein?
A type of protein that bonds to the energy-rich molecule called GTP and a GPCR. When the GPCR is activated by a ligand, the G Protein(bound to the GTP too) goes and activates an inactive enzyme
What are G protein-coupled receptors?
plasma membrane receptors that are activated by G proteins bonding to a GTP molecule
What is a signal transduction pathway?
A sequence of changes in a series of different molecules during transduction
What are relay molecules?
The molecules(mostly proteins) in the signal transduction pathway
What is a ligand-gated ion channel? Where are these used a lot?
A receptor that acts as a “gate” for specific ions when it changes shape. It opens/closes when a signal molecule binds as a ligand. This may trigger and electric signal and is essential for the nervous system.
What is epinephrine?
A hormone that circulates through the blood, only reacting to certain cells. Initiates “fight or flight” response
What are intracellular receptors and how are they accessed?
Intracellular receptors are receptor proteins found in the cytosol or nucleus, and small or hydrophobic chemical messengers that can readily cross the membrane can activate the receptors
What are examples of intracellular receptors?
Steroid and thyroid hormones of animals and nitric oxide in plants and animals
Why are multistep pathways used in transduction?
They can amplify a signal, a few molecules can produce a large response. It provides more opportunities for coordination and regulation of cellular response than simpler systems do
What is the purpose of phosphorylation and dephosphorylation?
To regulate protein activity
What are protein kinases?
an enzyme that performs phosphorylation, they transfer phosphates from ATP to protein
What does adding phosphates to a protein do in phosphorylation?
Changes it from inactive to active
Why does phosphorylation “cascade” as it occurs?
It minimizes the amount of work necessary
What are first and second messengers?
First: The extracellular molecule(ligand) that binds to the receptor
Second: Small, nonprotein, water soluble molecules or ions that spread throughout a cell by diffusion
What is cyclic AMP?
(cAMP) A widely used secondary messenger that activates protein kinase A, which phosphorylates other proteins
What is adenylyl cyclase?
An enzyme in the plasma membrane that rapidly converts ATP to cAMP in response to a number of extracellular signals
Which part of the signal pathway is the phosphorylation cascade apart of?
Transduction
Where are intracellular receptors found?
The cytoplasm or nucleus
How can signal molecules reach intracellular proteins?
A signal cell passes through the membrane because they are hydrophobic enough to cross the hydrophobic interior of the membrane
What is a metabolic pathway?
A pathway that begins with a specific molecule and ends with a product, each step is catalyzed by enzymes
What is metabolism?
The totality of an organism’s chemical reactions
Where does metabolism come from?
Interactions between molecules within the cell
What are catabolic pathways?
Pathways that release energy by breaking down complex molecules into simpler compounds
What type of pathway is cellular respiration?
Catabolic pathway
What an anabolic pathway?
Pathways that consume energy to build complex molecules from simpler ones
What type of pathway is the synthesis of proteins?
Anabolic
What is the difference between thermal and heat energy?
Thermal energy: Kinetic energy associated with random movement of atoms or molecules
Heat: Thermal energy in transfer from one object to another
What is thermodynamics?
The study of energy transformations
What is the first law of thermodynamics?
This law states that energy in the universe is constant(cannot be created or destroyed). Also called the principle of conservation of energy
What is the second law of thermodynamics?
Every transfer or transformation of energy in the universe increases the entropy of the universe because some energy is lost as heat in every transfer/tranformation
What is entropy?
A measure of order/randomness
What is a spontaneous process? How does it affect entropy?
A spontaneous process occurs without energy input, increasing the entropy of the universe
How do catabolic and anabolic pathways work together?
Energy released from catabolic pathways are often stored and used to drive anabolic pathways
What is Gibbs free energy?
aka free energy, it is the portion of a system’s energy that can perform work when temp and pressure are uniform throughout a system
What is the change in free energy formula?
🔼G=🔼H-T🔼S
🔼H=System enthalpy
🔼S=Change in system entropy
T=Temp IN KELVIN
or
🔼G=G(final state)-G(initial state)
Why is 🔼G important?
We can use it to predict if i process is energetically favorable.
-🔼G=Can occur with no energy input(spontaneous) and vice versa
What does free energy measure?
A system’s instability, its tendency to change to a more stable state
What happens to free energy during a spontaneous change?
Free energy decreases, stability increases
What is the maximum state of stability in a rxn?
Equilibrium, forward and reverse rxns occur at the same rate. No work can be done and G is at its lowest possible value
What must a reaction be doing to be spontaneous?
Move towards equilibrium, decrease in G
What is an exergonic reaction?
A rxn with a net release of free energy, it is spontaneous and 🔼G is negative, G decreases
What is an endergonic rxn?
A rxn that absorbs free energy, is nonspontaneous, and 🔼G is positive, G increases
What does the magnitude of 🔼G represent in endergonic and exergonic rxns?
Exergonic: The maximum amount of work a rxn can perform
Endergonic: The quantity of energy required to drive the rxn
What is the key to maintaining lack of equilibrium in metabolism, a defining feature of life?
Products if reactions dont accumulate, they become reactants for the next step. Waste is expelled from the cell
What 3 kinds of work are performed by a cell?
- Chemical: Pushing of nonspontaneous/endergonic rxns, such as synthesis of polymers from monomers
- Transport: Pumping substances across membranes against the direction of spontaneous movement
- Mechanical: Contraction of muscle cells, beating of cilia, movement of chromosomes
What is energy coupling?
The use of an exergonic process to drive and endergonic one, usually mediated by ATP
What is ATP and its purpose?
ATP stands for Adenosine Triphosphate. It is composed of ribose(a sugar), adenine(a nitrogenous base) and 3 phosphate groups. It supplies energy, mediates energy coupling and is used to make RNA
How and why is ATP turned into ADP?
The bonds between the phosphate groups of ATP can be broken by hydrolysis. When the terminal phosphate bond is broken, a molecule of inorganic phosphate leaves the ATP, turning the triphosphate into diphosphate, or ADP. The rxn is exergonic and is used to drive endergonic rxns, making it exergonic overall
Where does the release of energy from hydrolyzing ATP come from?
The chemical change to a state of lower free energy, not the phosphate bond
What is a phosphorylated intermediate?
The recipient of the phosphate group(covalently bonded) that came from ATP hydrolysis
What is the key to coupling exergonic and endergonic reactions?
The formation of the phosphorylated intermediate, which is more reactive(less stable) than the unphosphorylated molecule
How does ATP Hydrolysis power transport and mechanical work?
It leads to a change in a protein’s shape and often its ability to bind to another molecule
How does ATP hydrolysis drive cell movement?
ATP is first bound noncovalently to a motor protein. Then it is hydrolyzed, releasing ADP and an inorganic phosphate group, then another ATP molecule can bind. At each stage, the motor protein changes its shape and ability to bind to the cytoskeleton, resulting in movement of the protein along the cytoskeletal track
How is ATP regenerated?
ATP is renewable and regenerated by the addition of a phosphate group to ADP. The energy to phosphorylate ADP comes from catabolic/exergonic rxns in the cell
Is the ATP regeneration process endergonic or exergonic? why?
Endergonic. Both directions of this reversible process are not spontaneous
What is activation energy? What is its most common form?
The initial energy needed to start a chemical reaction. It is often supplied as thermal energy that reactant molecules absorb
When enzymes catalyze a rxn, what do they change and what dont they change?
Enzyme catalyze by lowering the activation energy barrier by contorting the molecule into a high unstable state, but they dont effect 🔼G, or make an endergonic rxn exergonic, they just speed up reactions that would eventually happen anyway
What is a substrate?
The reactant an enzyme acts on
What is an enzyme-substrate complex?
An enzyme binding to its substrate
What is the active site?
The region on the enzyme, typically a pocket or groove, where a substrate binds. A complimentary fit between enzyme shape and substrate shape is present
How can an active site lower an activation energy barrier?
- orienting substrates correctly
- Straining substrate bonds toward their transition state form, reducing the amount of free energy needed
- Providing a favorable microenvironment
- Covalently bonding to the substrate or being apart of the reaction
What is the transition state?
A state when molecules have absorbed enough energy for the bonds to break
How can a rxn where activation energy must be overcome still result in net energy gain?
The formation of new bonds releases more energy than was invested in breaking the old bonds
Why can adding heat be bad to catalyze a reaction in some scenarios?
High temperatures denature proteins and kills cells and heat would speed up all reactions, not just necessary ones
What is an induced fit?
Induced fit brings chemical groups of the active site into positions that enhance their ability to catalyze a chemical reaction
What are cofactors?
Nonprotein enzyme helpers. Can be organic or inorganic
What are coenzymes?
An organic cofactor
What are competitive and noncompetitive inhibitors?
Competitive: Bind to the active site of an enzyme, competing with the substrate
Noncompetitive: Bind to another part of the enzyme, causing the enzyme to change shape and make the active site less effective
What is allosteric regulation?
Regulation that occurs when a regulatory molecule binds to a protein at one site and effects the protein’s function at another site. This can inhibit or stimulate the enzyme’s activity
How does a cell regulate metabolic pathways?
A cells switches on/off the genes that encode specific enzymes or by regulating enzyme activity
What forms does an enzyme have and how are these forms changed?
Active and inactive forms. An activator stabilizes the active form and an inhibitor stabilizes the inactive form
What is cooperativity?
A form of allosteric regulation that can amplify enzyme activity when one substrate molecule primes and enzyme to act on additional substrate molecules more readily
What is feedback inhibition?
A type of allosteric regulation where the end product of a metabolic pathway shuts down the pathway in order to prevent a cell from synthesizing more product than needed
How is a substrate held in an enzyme?
“weak” interactions such as H bonds and ionic bonds
In what forms does energy tend to enter and leave an ecosystem?
Enters as sunlight and leaves at heat
What is fermentation?
The partial degradation if sugars that occurs without O2
What is the difference between aerobic and anaerobic respiration?
Aerobic respiration(most efficient) consumes organic molecules and O2 and yields ATP
Anaerobic respiration is like aerobic respiration but consumes compounds other than O2
What releases energy stored in organic molecules in cellular respiration? What is this energy used for?
Transfer of electrons during chemical reactions, this energy is ultimately used to synthesize ATP
What are redox rxns?
Chemical reactions that transfer electrons between reactants
What occurs in oxidation and reduction?
Oxidation: Substances loses electrons(charge is increased)
Reduction: Substances gains electrons(charge is reduced)
What are oxidizing and reducing agents?
Reducing agent: Electron donor, is oxidized
Oxidizing agent: Electron acceptor, is reduced
What element do electrons move with in cellular respiration?
H
What are the three key pathways of respiration?
Glycolysis, the citric acid cycle, and oxidative phosphorylation
How do catabolic pathways yield energy?
By oxidizing organic fuels
What type of energy do organic molecules possess and why?
Potential energy, because of the arrangement of electrons in the bonds between their atoms
Generally, what are the reactants and products of cellular respiration?
Organic compounds+Oxygen➡️Carbon dioxide+Water+Energy
What happens in a redox reaction when there is NOT a complete transfer of electrons?
A change in the degree of electron sharing in covalent bonds occurs, based on how electronegative the elements are
What is oxidized and reduced in cellular respiration?
The fuel is oxidized and O2 is reduced
What makes for a good fuel in cellular respiration?
Organic molecules with an abundance of H
Where do the electrons from the organic compound usually first transferred to?
NAD+
What is NAD+?
A coenzyme the functions as the oxidizing agent during cellular respiration
What is NADH, where does it come from?
NADH is reduced from NAD+ in cellular respiration, it represents potential\stored energy that is tapped to synthesize ATP. It shuttles electrons that were removed from glucose to the “top” or higher energy part of the chain
What does NADH+ do in cellular respiration?
It passes electrons to the electron transport chain
What is the electron transport chain? What operates it and what is the result?
The electric transport chain is a number of proteins, mostly molecules, built into the inner membrane of the mitochondria of eukaryotic cells and plasma membrane of aerobically respiring prokaryotes conducting a series of controlled steps that yield energy used to regenerate ATP.
What is the general objective of each the 3 steps of harvesting energy from glucose?
- Glycolysis: breaks glucose into two molecules of pyruvate
- Citric acid cycle+Pyruvate oxidation: Completes breakdown of glucose
- Oxidative phosphorylation: Accounts for most of ATP syntheis
Why is NAD+ a good electron carrier?
It can cycle easily between NAD+ and NADH states
How does NAD+ trap electrons from glucose and other organic molecules?
Enzymes remove a pair of H atoms from the substrate(glucose), therefore oxidizing it. The enzyme delivers 2 electrons along with 1 proton and its coenzyme NAD+. The other proton is released as H+ into the surrounding solution
What happens at the “bottom”/lower energy part of the electron transport chain?
O2 captures the electrons that went down the electron transport chain with H+ to form water
How does the “cascade” down the electron transport chain work?
Electrons cascade down the chain from one carrier molecule to the next in a series of redox reactions, losing a small amount of energy until they reach oxygen. Each carrier is more electronegative than the carrier above it, allowing electrons to be pulled down the chain
What type of reaction is electron transfer from NADH to oxygen?
Exergonic
Which process generates the most ATP?
Oxidative phosphorylation because it is powered by redox reactions
How much ATP is made from glucose?
32 molecules of ATP per molecule of glucose degraded to CO2 and water by respiration
Where does glycolysis take place?
The cytosol
What type of pathways are glycolysis and the citric acid cycle?
Catabolic pathways
What does glycolysis do in cellular respiration?
Glucose is broken down into two molecules of pyruvate(how glycolysis harvests energy), then(in eukaryotes) the pyruvate enter the mitochondria where it is oxidized in Acetyl CoA, then enters the citric acid cycle
What happens in the citric acid cycle?
(Also called krebs cycle) The breakdown of glucose to carbon dioxide is completed
Where does the citric acid cycle take place?
Eukaryotes: mitochondria
Prokaryotes: Cytosol
What does oxidative phosphorylation do in cellular respiration?
The mode of ATP synthesis where energy released at each step of the electron transport chain is stored in a form the mitochondria can use to make ATP from ADP
Where do electron transport and chemiosmosis take place?
Eukaryotes: The inner membrane of the mitochondria
Prokaryotes: Plasma membrane
What 2 processes constitute oxidative phosphorylation?
electron transport and chemiosmosis
What is substrate level phosphorylation?
A mode of ATP synthesis that occurs during glycolysis and the citric acid cycle where an enzyme transfers a phosphate group from an organic molecule generated as an intermediate during the catabolism of glucose to ADP, instead of adding an inorganic phosphate to ADP as in oxidative phosphorylation
What are the 2 major phases of glycolysis?
- Energy investment phase
2. Energy payoff phase
What is the net yield fro glycolysis?
2 Puruvate+W H2O
2 ATP
2 NADH+2H+
How is NAD+ reduced to NADH in glycolysis?
The electrons/H+ released from oxidation of glucose are used to rredice NAD+ to NADH
What must be present for pyruvate to enter the mitochondria?
O2
What process links glycolysis and the citric acid cycle?
pyruvate is converted to acetyl coenzyme A (acetyl CoA)
What are the products of the citric acid cycle?
1 ATP, 3 NADH, and 1 FADH2 per turn
What are the steps of the citric acid cycle?
8 steps
- The acetyl group of CoA joins the cycle by combining with oxaloacetate, forming citrate
2-8. Decompose citrate back to oxaloacetate, making the process a cycle
Where is the oxidation of glucose completed?
Eukaryotic: Mitochondria
Prokaryotic: Cytosol
How is acetyl CoA made from pyruvate?
Pyruvate undergoes a series of enzymatic reactions that remove CO2 and oxidizes the remaining fragment, forming NADH from NAD+
What step is the only step that produces ATP in the citric acid cycle?
Step 5
What accounts for most of the energy extracted after the citric acid cycle and glycolysis?
NADH and FADH2
Where is the electron transport chain located?
The cristae of the mitochondrion
How do the carriers alternate states?
They are oxidized and reduced as they donate and accept electrons
What happens to the free energy of electrons as they go down the transport chain?
They drop in free energy
What is the purpose of the electron transport chain?
It breaks the large free energy drop going from food to O2 into smaller steps that release energy in manageable amounts
What is chemiosmosis?
The use of energy in an H+ gradient across a membrane to serve as power for ATP synthase
What happens to H+ during the transfer of electrons in the transport chain?
Electron transfer in the transport chain causes proteins to pump H+ from the mitochondrial matrix to the intermembrane space. H+ then moves back across the membrane, passing through the protein complex, ATP synthase
What is the role of ATP synthase in oxidative phosphorylation?
ATP synthase uses the exergonic flow of H+ to drive phosphorylation of ATP
What is a proton-motive force?
The H+ gradient that drives H+ back across the membrane through H+ channels via ATP synthase.
What does the proton-motive force do to the electron transport chain?
The energy stored in the proton motive force couples the redox reactions of the electron transport chain to ATP synthesis
What is the usual energy pathway in cellular respiration?
Glucose➡️NADH➡️ETC➡️Proton-motive force➡️ATP
What happens with cellular respiration when there is no O2?
The electron transport chain will cease to operate, and glycolysis couples with fermentation or anaerobic respiration to produce ATP
What are the electron transport chain steps in anaerobic respiration and fermentation?
Anaerobic: Uses ETC with a final electron acceptor that ISNT O2
Fermentation: Uses substrate level phosphorylation instead of ETC to generate ATP
What are the steps of fermentation(generally)?
Fermentation consists if glycolysis plus reactions that regenerate NAD+, which can be reused by glycolysis
What are the steps of alcoholic fermentation?
- Releases CO2 from pyruvate
2. Reduce acetylaldehyde to ethanol
What happens in lactic acid fermentation?
Pyruvate is reduced by NADH, forming lactate as an end product with no release of CO2.
What is similar and different in fermentation, anaerobic and aerobic respiration?
Similar
•All 3 use glycolysis with a net ATP of +2 to oxidize glucose and harvest chemical energy of food
•In all 3, NAD+ is the oxidizing agent that accepts electrons during glycolysis
Different
• The processes have different final electron acceptors(oxidizing NADH back to NAD+): fermentation has an organic molecule such as pyruvate or acetylaldehyde and O2 in cellular respiration
•Cellular respiration produces 32 ATP per glucose molecule; fermentation produces 2
What are obligate and facultative anaerobes?
Obligate: Carry out only fermentation and anaerobic respiration, cannot survive in the presence of O2
Facultative: (yeast and many bacteria) Can survive using fermentation or cellular respiration. Pyruvate is a fork in the metabolic road that leads to 2 alternate catabolic routes
How are various molecules prepared for cellular respiration? compare fats and carbs
- Proteins: must be digested to amino acids and amino groups must he removed before amino acids can feed glycolysis or the citric acid cycle
- Fats: digested to glycerol(used in glycolysis) and fatty acid
Fatty acids are broken down by beta oxidation and yield Acetyl CoA
An organized gram of fat produces more than twice the amount of ATP as carbs
How is ATP produced in glycolysis and the citric acid cycle?
substrate-level phosphorylation
How does oxidative phosphorylation use the electron transport chain?
It uses energy generated from the electron transport chain to power ATP synthesis
What are prosthetic groups?
Nonprotein components tightly bound to the ETC proteins that are essential for the catalytic functions of certain enzymes
What are cytochromes?
An iron-containing protein that is apart of the ETC’s
What is the difference between NADH and FADH2
FADH feed electrons into the second complex of the ETC, where as NADH feeds them at the beginning. FADH2 produces 1/3 less energy than NADH as a result, since less reactions occur
How does the mitochondria couple the ETC energy release with ATP synthesis?
Chemiosmosis
What is ATP synthase?
A protein complex with many copies residing in the inner membrane of the mitochondria(eukaryotes) or the plasma membrane(prokaryotes), the enzyme that actually makes ATP from ADP and inorganic phosphate.
How is ATP synthase powered?
Protons move one by one onto one of binding sites on the rotor causing it to spin in a way that catalyzes ATP production from ADP and inorganic phosphate
describe the process of H+ ions activating ATP Synthase
H+ ions flow down their gradient enter a half channel in he stator, which is anchored in the membrane. Then the H+ ions enter the rotor changing the shape of each subunit so that the rotor spins within the membrane. Each H+ ion makes one complete turn in the rotor then leaves for the second half of the stator channel into the mitochondrial matrix. The rotor spinning causes an attached rod to spin inside another knob it’s attached to, activating catalytic sites that make ATP form ADP and inorganic phosphate
How is an H+ gradient established?
The ETC uses the exergonic energy flow from the electrons from NADH and FADH2 to pump H+ into the membrane from the mitochondrial matrix into the intermembrane space. The H+ tends to flow back across the membrane, and the only way that can happen is via ATP synthase, coupling the redox reactions rxns of the ETC to ATP synthesis(chemiosmosis)
How is a proton motive force created?
The ETC causes H+ to be released into the surrounding solution. In eukaryotes, the electron carriers are spatially arranged in the inner mitochondrial membrane in such a way that H+ is accepted from the mitochondrial matrix and deposited into the intermembrane space
Where is chemiosmosis used other than oxidative phosphorylation?
Photosynthesis and plasma membranes and flagella in prokaryotes
How are anaerobic respiration and fermentation different?
Anaerobic respiration uses an electron transport chain, fermentation doesnt
How is glycolysis different in fermentation then anaerobic respiration?
Fermentation is an extensions of glycolysis that allows continuous generation of ATP via substrate level phosphorylation. NAD+ is recycled to NADH to repeat this process
What is the difference in what happens to pyruvate under aerobic and anaerobic conditions?
Aerobic: Pyruvate can be converted to acetyl CoA
Anaerobic: Lactic acid fermentation occurs
What is beta oxidation?
A metabolic sequence that break fatty-acids down into 2 carbon fragments, which enter the citric acid cycle as Acetyl CoA
