192 terms

APBio Test Review Energetics (CH 8, 9, 10)

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Catabolic Pathway
degradative process that generates energy as an end product
Anabolic Pathway
energy consuming process that builds more complex molecules from simpler ones
What is energy?
the capacity to do work, and capacity to cause change.
Kinetic Energy
energy associated with movement (includes thermal energy)
Potential energy
stored energy that can potentially be converted to another form of energy and do work
Chemical Energy
may be stored as form of potential in a molecule
Thermodynamics
Study of the energy transformations within a defined system vs. surroundings
First Law of Thermodynamics
Energy can be transferred or transformed but neither created nor destroyed (Conservation of Energy)
Second of Thermodynamics
every energy transfer or transformation increases the disorder of the universe
The stability of matter is greatest
At the lowest energy state
Spontaneous (Gibbs)
the process will run without an outside input of energy (Delta G is negative)
Gibbs free energy of a system
delta G= G (final)-G(initial)
In a spontaneous change
the system becomes more stable, the released free energy can be harnessed to do work
ATP (Adenosine Tri-phosphate)
produced by cellular respiration (breaking down of glucose leads to energy release that drive ATP synthesis which is endergonic)
Hydrolysis of ATP
Exergonic reaction
How does ATP power cellular work
Energy coupling mechanism (the use of an exergonic process to drive an endergonic one) Hydrolysis of ATP releases energy that can drive endergonic reactions (breaking of high energy bond between phosphates in ATP releases energy)
What type of things do cell use energy for?
Mechanical work, Transport work, and chemical work
Catalyst
a chemical agent that speeds up a reaction without being consumed by the reaction
Enzyme
(biological catalysts) speed up metabolic reactions by lowering energy barrier, enzymes are not consumed by the reaction itself, very selective in the reactions that they catalyze, can ONLY lower the activation energy barrier they CANNOT change the delta G for a reaction nor it cannot make an endergonic reaction exergonic. Mostly proteins, each enzyme has an optimal temperature and pH that favor the most active conformation of the protein molecules, many require non-protein helper that binds to the enzyme for catalytic activity
Activation Energy Barrier
chemical reaction involves bond breaking and bond forming. A major factor in determining the rate of a particular reaction
Substrate
the molecule that an enzyme acts on.
Coenzyme
organic such as vitamins
Cofactors
inorganic such as metals
Enzyme inhibitors
molecules taht selectively interfere with the action of specific enzymes
reversible inhibition
inhibitor bound loosely by weaker bonds
Irreversible inhibition
inhibitor bound by covalent bonds (toxins and poisons are often irreversible enzyme inhibitors)
Enzyme Inhibition is necessary to...
regulate proper level of substrates being produced
competitive inhibitor
mimics the substrate competing for the active site
Noncompetitve inhibitor
binds to the enzyme away from the active site altering the conformation of the enzyme so that its active site no longer functions
ALLOSTERIC ENZYMES AND REGULATORS
a complex form of an enzyme, multi subunits (each have an active site but also regulatory site where regulator binds) unstable without regulator binding. Multiple subunits (polypeptides) each subunit has active and regulatory site. Require additional molecules (activator or inhibitor=regulator) both activator or inhibitor can bind. if activator bind it binds to the regulatory site and it locks the enzyme in its active form. Inhibitory binds to enyme it stabalizes the enzyme in inactive form. without regulators it is a flaky enzyme. regulators are reversible and noncompetitive.
Cooperativity
each subunit can bind to a substrate, binding of one subunits activates the remaining and it takes less time for them to bind bcs they cooperate. (hemoglobin- oxygen binding to hemoglobin)
What is the relationship between anabolic and catabolic pathways?
Anbolic pathways synthesize more complex organic molecules using the energy derived from catabolic pathways
What does not represent an enerygy transformation
The coupling of ATP hydrolysis to the production of a proton gradient across a membrane by a proton pump
Organisms are described as thermodynamically open systems
Organisms aquire energy from, and lose energy to, their surroundings.
Consider the growth of a farmer's crop over a season, what correctly states a limitation imposed by the first or second law of thermodynamics
To obey the first law, crops must represent an open system
What is the relevence of the first law of thermodynamics to biology?
Energy can be freely transformed among different forms as long as the total energy is conserved
Which is the most abundant form of energy in a cell?
chemical energy
Example of the second law of thermodynamics as it applies to biological reactions
The aerobic respiration of one molecule of glucose produces six molecules each of carbon dioxide and water
What is true according the second law of thermodynamics
the decrease in entropy associated with life must be compensated for by increasing entropy in the environment in which life exists
If the entropy of a living organism is decreasing what is occuring simultaneously?
Energy input into the organism must be occuring to drive the decrease in entropy
When one molecule is broken down into 6 component molecules what is true?
delta S is positive
An exergonic reaction is a chemical reaction that...
Releases energy when proceeding in the forward direction
What is an example of an endergonic reaction?
glucose+fructose=sucrose
What determines the sign of delta G for a reaction?
the free energy of the reactants and the free energy of the products
Metabolic pathways in cells are typically far from equilibrium. What process tends to keep these pathways away from equilibrium?
Pathways can be displaced from equilibrium either by adding free energy or by removal of the products of the pathway or by other reactions
What is an example of the cellular work accomplished with the free energy derived from the hydrolysis of ATP, involved in the production of electrochemical gradients?
proton movement against a gradient of protons
In general, the hydrolysis of ATP drives cellular work by...
releasing free energy that can be coupled to other reactions
What describes some aspect of ATP hydrolysis being used to drive the active transport of an ion into the cell against the ion's concentration gradient?
This is an example of energy coupling
Much of the suitability of ATP as an energy intermediary is related to the instability of the bonds between the phosphate groups. These bonds are unstable because _____.
The negatively charged phosphate groups viforously repel one another and the terminal phosphate group is more stable in waterthan it is in ATP
When 1 mole of ATP is hydrolyzed in a test tube without an enzyme, about twice as much heat is given off as when 1 mole of ATP is hydrolyzed in a cell. What explains these observations?
in the cell, the hydrolysis of ATP is coupled to other endergonic reactions
What best characterizes the role of ATP in cellular metabolism?
The free energy released by ATP hydrolysis may be coupled to an endergonic process via the formation of a phosphorylated intermediate.
The formation of glucose-6-phosphate from glucose is an endergonic reaction and is coupled to what reaction or pathway?
the hydrolysis of ATP
A chemical reaction is designated as exergonic rather than endergonic when _____.
the potential energy of the products is less than the potential energy of the reactants
What is changed by the presence of an enzyme in a reaction?
the activation energy
What do the sign and magnitude of the ΔG of a reaction tell us about the speed of the reaction?
Neither the sign nor the magnitude of ΔG have anything to do with the speed of a reaction.
How do enzymes lower activation energy?
by locally concentrating the reactants
Above a certain substrate concentration, the rate of an enzyme-catalyzed reaction drops as the enzymes become saturated. What would lead to a faster conversion of substrate into product under these saturated conditions?
Either increasing the enzyme concentration or slightly increasing the temperature will increase the rate of product formation.
Enzyme activity is affected by pH because _____.
high or low pH may disrupt hydrogen bonding or ionic interactions and thus change the shape of the active site
Succinylcholine is structurally almost identical to acetylcholine. If succinylcholine is added to a mixture that contains acetylcholine and the enzyme that hydrolyzes acetylcholine (but not succinylcholine), the rate of acetylcholine hydrolysis is decreased. Subsequent addition of more acetylcholine restores the original rate of acetylcholine hydrolysis. What correctly explains this observation?
Succinylcholine must be a competitive inhibitor with acetylcholine.
The process of stabilizing the structure of an enzyme in its active form by the binding of a molecule is an example of _____.
allosteric regulation
The binding of an allosteric inhibitor to an enzyme causes the rate of product formation by the enzyme to decrease. Why does this decrease occur?
The allosteric inhibitor causes a structural change in the enzyme that prevents the substrate from binding at the active site.
Under most conditions, the supply of energy by catabolic pathways is regulated by the demand for energy by anabolic pathways. Considering the role of ATP formation and hydrolysis in energy coupling of anabolic and catabolic pathways, what is most likely to be true?
High levels of ADP act as an allosteric activator of catabolic pathways
Which term most precisely describes the cellular process of breaking down large molecules into smaller ones?
Catabolism
Which of the following is (are) true for anabolic pathways?
They consume energy to build up polymers from monomers.
Which of the following is an example of potential rather than kinetic energy?
a molecule of glucose
Which of the following is true of metabolism in its entirety in all organisms?
Metabolism consists of all the energy transformation reactions in an organism.
Which of the following is true for all exergonic reactions?
The reaction proceeds with a net release of free energy.
Which of the following is most similar in structure to ATP?
an RNA nucleotide
When chemical, transport, or mechanical work is done by an organism, what happens to the heat generated?
It is lost to the environment.
Reactants capable of interacting to form products in a chemical reaction must first overcome a thermodynamic barrier known as the reaction's
activation energy
During a laboratory experiment, you discover that an enzyme-catalyzed reaction has a G of -20 kcal/mol. If you double the amount of enzyme in the reaction, what will be the G for the new reaction?
-20 kcal/mol
The active site of an enzyme is the region that
is involved in the catalytic reaction of the enzyme.
Zinc, an essential trace element for most organisms, is present in the active site of the enzyme carboxypeptidase. The zinc most likely functions as a
cofactor necessary for enzyme activity.
When you have a severe fever, what grave consequence may occur if the fever is not controlled?
change in the tertiary structure of your enzymes
How does a noncompetitive inhibitor decrease the rate of an enzyme reaction?
by changing the shape of the enzyme's active site
How might an amino acid change at a site distant from the active site of the enzyme alter the enzyme's substrate specificity?
by changing the shape of the protein
The mechanism in which the end product of a metabolic pathway inhibits an earlier step in the pathway is most precisely described as
feedback inhibition.
If an enzyme in solution is saturated with substrate, the most effective way to obtain a faster yield of products is to
add more of the enzyme.
How does an enzyme increase the rate of the chemical reaction it catalyzes?
An enzyme reduces the free energy of activation (EA) of the reaction it catalyzes. (An enzyme catalyzes a reaction by lowering EA, enabling the reactant molecules to absorb enough energy to reach the transition state even at moderate temperatures.)
fermentation
anaerobic process that produces little ATP, includes glycolysis, and restores NAD+
aerobic respiration
catabolic pathway which requires oxygen and occurs in cytoplasm and mitochondria
anaerobic respiration
catabolic pathway which does not require oxygen and occurs only in cytoplasm
oxidation
loss of electrons from atoms of a substance
reduction
addition of electrons to atoms of a substance
reducing agent
electron donor in a redox reaction
oxidizing agent
electron acceptor in a redox reaction
NAD+
electron carrier used in cellular respiration to transfer electrons from Kreb's cycle to ETC
electron transport chain (ETC)
(1) transfer of electrons from glucose via NADH/FADH2 to transmembrane proteins and subsequently using their high energy to pump protons to intermembrane space in mitochondria or thylakoid space in chloroplasts
citric acid (Kreb's) cycle
(B) 2nd step of cellular respiration that breaks down AcetylCoA to 2 carbon dioxide, 1 ATP, 3NADH, and 1 FADH2 molecules in mitochondrial matrix (aerobic)
glycolysis
(A) 1st step of cellular respiration that splits glucose into 2 molecules of pyruvic acid and 2 ATPs (anaerobic, catabolic/exergonic)
Pi (not π)
inorganic phosphate
oxidative phosphorylation
(3) synthesis of ATP from ADP and Pi at ATP synthase using energy from glucose electrons which are ultimately transferred to oxygen (final electron acceptor) using ETC in mitochondrial cristae (aerobic)
substrate level phosphorylation
synthesis of ATP by transferring a phosphate group directly to ADP using an enzyme
chemiosmosis
(3) movement of protons down their concentration gradient coupled to ATP synthesis
proton motive force
potential energy stored in form of an electrochemical gradient generated by pumping hydrogen ions across membranes during ETC
alcohol fermentation
conversion of pyruvate to carbon dioxide and 2-carbon compound in absence of oxygen to regenerate NAD+ needed for glycolysis (in yeast)
lactic acid fermentation
conversion of pyruvate to 3-carbon compound in absence of oxygen to regenerate NAD+ needed for glycolysis (in our muscles)
obligate anaerobes
organisms that can only survive WITHOUT oxygen
beta oxidation
metabolic pathway that breaks down fatty acids into two-carbon fragments which enter Krebs cycle as acetyl CoA
redox
electron transfer reactions that occur together and in which one chemical is oxidized and the other reduced
formation of acetyl CoA
metabolic link between glycolysis and aerobic respiration
cellular respiration
exergonic process that includes 3 steps and releases energy (ATP) by breaking down glucose and other molecules in presence of oxygen
cytochromes
iron-containing proteins that play key role in electron transport chains in mitochondria, chloroplasts, and cell membranes of prokaryotes
ATP synthase
enzyme in mitochondrial cristae and chloroplast thylakoids that uses energy of proton gradient to add a phosphate group to ADP and so form ATP
facultative anaerobes
organisms that can survive with OR without oxygen
dehydrogenases
enzymes that transfer hydrogen atoms
isomerases/mutases
enzymes that move atoms within a molecule
kinases/phosphatases
enzymes that transfer phosphate groups
adolases
enzymes that cut molecules
enolases
enzymes that add double bonds to molecules
photosynthesis (definition)
process of harnessing light energy to build carbohydrates in autotrophs (ex. plants, cyanobacteria)
photosynthesis (equation)
6 CO2 + 6 H2O + light energy --> C6H12O6 + 6 O2
autotroph
organism that CAN capture energy from sunlight or chemicals and use it to produce its own food (producer)
heterotroph
organism that CANNOT produce its own food and therefore obtains it by consuming other living things (consumer)
light-dependent reactions
1st step of photosynthesis during which light energy is captured and used to synthesize ATP and NADPH
light-independent reactions (aka Calvin cycle)
2nd step of photosynthesis during which CO2 is incorporated into a sugar molecule using ATP and NADPH produced during the light dep. rx.
thylakoid membranes of chloroplasts
location of light-dependent reactions
stroma of chloroplasts
location of light-independent reactions
inverse
What is the relationship between wavelength and energy?
pigments
substances that can absorb particular wavelengths of light energy
absorption spectrum
graph of a pigment's ability to absorb various wavelengths of light
action spectrum
graph of a plant's photosynthesis rate at different wavelengths of light
violet, blue and red
Which wavelengths of the visible light spectrum do chlorophylls ABSORB?
green and yellow
Which wavelengths of the visible light spectrum do chlorophylls REFLECT?
carotenoids
accessory pigments in chloroplasts that broaden the spectrum of colors used in photosynthesis (absorb green/blue but reflect red/yellow/orange)
mesophyll
(C) ground tissue of a leaf, sandwiched between upper and lower epidermis that specializes in photosynthesis
chlorophyll b
pigment, green/olive, in chloroplast
chlorophyll a
pigment, blue/green, in chloroplast
excited state
when absorbed photon energy causes electron to move away from nucleus
photosystems
located in the thylakoid membrane and trap light energy and use it to excite electrons
parts of photosystems
accessory (aka antenna) pigments, reaction center chlorophyll a, primary electron acceptor
reaction-center complex
(4) centrally located proteins associated with a special pair of chlorophyll a molecules and a primary electron acceptor
light harvesting complex
(3) proteins associated with pigment molecules that capture light energy and transfers it to center of a photosystem
photosystem II (PS II)
1st of two light harvesting units in thylakoid membrane that passes excited electrons to reaction-center chlorophyll
primary electron acceptor
(2) electrons from the reaction-center in thylakoid membranes are transferred to this molecule
water
splitting this molecule replaces electrons which are excited and passed to primary electron acceptor in PSII
O2
released as a byproduct of splitting water
photosystem I (PS I)
2nd of two light-capturing units in thylakoid membranes that replaces its electrons by those from the 1st complex and results in production of NADPH
proton-motive force
created by pumping hydrogen ions from stroma to thylakoid space during electron transport chain between PS II and PS I
ATP synthase
enzyme that synthesies ATP by utilizing a proton-motive force
Calvin cycle, dark reactions, and carbon fixation
other names for light independent reactions
3 steps of light independent reaction
1. carbon fixation
2. reduction
3. regeneration of RuBP
reduction
step in Calvin cycle that produces sugar G3P
carbon dioxide
molecule reduced in Calvin cycle to produce sugar
thylakoids
(C) flattened membranous sacs inside chloroplasts that contain systems which convert light energy to chemical energy
absorbed
energy is ____________ in photosynthesis
released
energy is _____________ in cellular respiration
glucose and oxygen
reactants of cellular respiration
carbon dioxide and water
reactants of photosynthesis
glucose
source of electrons used in ETC of cellular respiration
intermembrane space
site of proton gradient built up in cellular respiration
thylakoid space
site of proton gradient built up in photosynthesis
NAD+ and FAD
high energy electron carrier(s) before reduction in cellular respiration (after they drop off electrons at ETC)
NADH and FADH2
high energy electron carrier(s) after reduction in cellular respiration (after they pick up electrons from Kreb's cycle)
NADP+
high energy electron carrier(s ) before reduction in photosynthesis (after they drop off electrons for Calvin cycle)
NADPH
high energy electron carrier(s ) after reduction in photosynthesis (after they pick up electrons from ETC)
ATP
energy product(s) from ETC in cellular respiration
ATP and NADPH
energy product(s) from ETC in photosynthesis
H2O
reactant(s) oxidized in photosynthesis (source of electrons)
cyclic electron flow
light dependent reactions using only photosystem I to pump protons and generate excess ATP (not NADPH)
linear electron flow
light dependent reactions involving both photosystems; electrons from H2O are used to reduce NADP to NADPH
rubisco
enzyme with affinity for both CO2 and O2 that catalyzes first step of Calvin cycle by adding CO2 to ribulose bisphosphate (RuBP)
PEP carboxylase
enzyme with great affinity for CO2 (gas) adds it to phosphoenolpyruvate (PEP) to form oxaloacetate (4-carbon solid) prior to photosynthesis
stomata
pore-like openings on underside of leaves that allow gases (CO2 and O2) and water to diffuse in and out
bundle-sheath cells
tightly packed around the veins of a leaf (site of Calvin cycle in C4 plants)
photorespiration
occurs on hot, dry days when stomata close, O2 accumulates and Rubisco fixes O2 rather than CO2, using up ATP, O2 and sugars
C3 plants
do not separately fix CO2 and use Rubisco in Calvin Cycle
C4 plants
spatially separate carbon fixation (mesophyll cells) from Calvin Cycle (bundle-sheath cells); use PEP carboxylase instead of Rubisco to fix CO2
CAM plants
temporally separate carbon fixation (day) and Calvin Cycle (night); use PEP carboxylase instead of Rubisco to fix CO2
autotroph
organism capable of synthesizing its own food from CO₂ and other inorganic raw materials. The producers.
heterotroph
an organism that depends on other's complex organic substances for nutrition.
photoautotroph
plants that use energy from sunlight to convert carbon dioxide and water to carbon compounds.
chlorophyll
the green pigment located within chloroplasts. It absorbs light energy to drive the synthesis of food molecules in the chloroplast.
mesophyll
the tissue in the interior of the leaf, contains 30-40 chloroplasts
stroma
thick fluid contained in the inner membrane of a chloroplast, surrounding thylakoids membranes.
photosynthesis
process by which plants and some other organisms use light energy to convert water and carbon dioxide into oxygen and high-energy carbohydrates such as sugars and starches
6CO₂ + 12H₂O + Light Energy → C₆H₁₂O₆ + 6O₂ + 6H₂O
splitting of water
photolysis
photophosphorylation
The process of generating ATP from ADP and phosphate by means of a proton-motive force generated by the thylakoid membrane of the chloroplast during the light reactions of photosynthesis.
carbon fixation
incorporating CO₂ from the atmosphere into organic molecules from the chloroplast
rubisco
Ribulose biphosphate carboxylase, an enzyme that fixes CO₂ together with RuBP.
RuBP
ribulose biphosphate
electromagnetic spectrum
the entire range of radiation
spectrometer
a machine that measures the ability of a pigment to absorb various wavelengths of light
reaction center
where the first light-driven chemical reaction of photosynthesis occurs, e⁻ goes in, gets excited and jumps up, grabbed by PEA
primary electron acceptor
grabs the e⁻ when it gets excited and dumps it into ETC
photosystem II
first photosystem, center is p680, takes in H₂O, splits and leaves out 1/2 O₂ and takes 2 e⁻, excites electrons and sends to primary acceptor
photosystem I
takes e⁻ from ETC and excites them (uses light), gives them to primary acceptor in noncyclic, go down ETC again
noncyclic electron flow
A route of electron flow during the light reactions of photosynthesis that involves both photosystems and produces ATP, NADPH, and oxygen. The net electron flow is from water to NADP+.
G3P
glyceraldehyde-3-phosphate, the threecarbon sugar formed in the Calvin cycle
mesophyll cell
more loosely arranged between bundle-sheath and leaf surface. takes in CO₂, fixed by PEP carboxylase
PEP carboxylase
adds CO₂ to PEP, higher affinity to CO₂ than rubisco
CAM plants
(crassulacean acid metabolism) temporal adaptation, open stomata during the night, closed during day. store organic acids made during night in vacuoles

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