quiz 3 Flashcards
What is thermodynamics
the study of energy and its transformations
what is the system and what is it called for things outside the system
system is the object under study and everything else is its surroundings
what are the three type of systems and describe them
isolated: system and surroundings does not exchange matter or energy
closed: only exchanges energy
open: exchanges energy and matter
name an example of an open system
Humans, organisms
What is the first law of thermodynamics
energy can be transformed from one form to another but it can’t be created nor destroyed
what is the second law of thermodynamics (2)
1) the total disorder (entropy) of a system and its surroundings always increase but the total energy of the universe does not change
2) Entropy of universe always increase
what is energy
the capacity to do work
what are the two states of energy and what is the difference
kinetic (energy of motion) and potential (stored energy)
name some forms of energy
chemical, thermal, electrical, radiant, mechanical
How (or to where) is energy transformed/transferred
energy is transferred between reactants and products, and between reactants or products and their surroundings.
What is the energy of reaction/ energy of formation
energy released or absorbed during chemical reaction
What is a spontaneous reaction
a chemical or physical reaction that will occur without an input of energy
what are two factors that determine whether a reaction is spontaneous or not
1) the change in energy content of a system
2) its change in entropy
Do reactions tend to be spontaneous when products have less potential energy than reactants or more PE?
reactions tend to be spontaneous when products have less potential energy than reactants
what is enthalpy and what is the variable assigned to it
Enthalpy is the potential energy in a system, (H)
When is a reaction exothermic
Reactions that release energy or when the products have less PE than reactants (Delta H is negative)
When is a reaction endothermic
Reactions that absorb energy or when products have more PE than reactants (Delta H is positive)
Reactions tend to be spontaneous if products are (more or less) ordered than the reactants
less ordered
Reactions tend to be spontaneous if products have (greater or lesser) entropy than the reactants
greater
What is gibbs free energy
the portion of a system’s energy that is available to do work
what is the equation of gibbs free energy
Delta G= Delta H - T(delta S) Delta G is change in free energy Delta H is change in enthalpy T is temp in kelvin Delta S is change in entropy
For a reaction to be spontaneous, Delta G must be (positive or negative)
Delta G must be negative
Name an example where a negative Delta H dominates making the reaction spontatneous
Combustion of methane (large loss of potential energy meaning negative enthalpy
Name an example where delta S dominates making the reaction spontaneous
Melting of ice at room temp, decrease in order dominates
Fix this statement.
In many spontaneous biological reaction, reactants fully convert to products since the reaction has a negative delta G
In many spontaneous biological reaction, reactants may not fully convert to products even though the reactions have a negative delta G
What is the equilibrium point in a reaction
a state of balance between the opposing factors pushing the reaction in either directions
As a system moves toward equilibrium, what happens to free energy and delta G
free energy progressively lowers to its lowest point when system achieves equilibrium (delta G= 0)
Why is moving away from equilibrium not spontaneous
it requires free energy
When delta G is near 0, is the reaction reversible
yes
in a chemical equation, how are reversible reactions showed
double arrow
why do many reaction in living organism never reach equlibrium
because living systems are open and the supply of reactants is constant and products don’t accumulate
why is delta g of life always negative
organisms constantly take in energy rich molecules and use them to do work
when do organisms reach equilibrium (delta G = 0)
only when they die
What is an exergonic reaction (3)
Reaction that releases free energy
Delta G is negative because the products contain less free energy than reactants
spontaneous reaction
what is an endergonic reaction (3)
reactants must gain free energy from surroundings to form products
Delta G is positive because products contain more free energy than the reactants
non spontaneous reaction
Define metabolic pathway
a series of reactions in which the products of one reaction are used immediately as reactants in the next reaction
Name the 2 different metabolic pathways
Catabolic pathway (or a single catabolic reaction) and anabolic pathway (anabolic reaction or biosynthetic reaction). Catabolic pathway is breakdown of complex molecules to simpler compounds (delta G is negative) Anabolic pathway is build of complicated molecules from simpler ones (delta G is positive)
What is the chief energy currency of the cell
ATP (adenosine triphosphate)
What is ATP composed of
ribose, adenine, and 3 phosphate group
where is the energy stored in ATP
in the high energy bonds between the phosphates
What is the purpose of ATP( other than being the primary energy currency)
ATP is used to drive endergonic reactions
What is made after hydrolysis reaction with ATP
ADP and a inorganic phosphate (Pi)
What is the delta G of ATP hydrolysis
-7.3 kcal/mol
ADP can be hydrolyzed into what
AMP
what is energy coupling
ATP hydrolyzed where the terminal phosphate group is transferred to a reactant molecule involved in endergonic reaction
What is phosphorylation
addition of a phosphate group to a molecule
What is a requirement for phosphorylation
An enzyme is needed with a specific site that binds both ATP and the reactant molecule to bring the two together
Is ATP synthesis an endergonic or exergonic reaction
Endergonic reaction
Where do we find the energy for ATP synthesis
energy from exergonic breakdown of carbohydrates, proteins, and fats (food)
Approximately how many ATP molecule are hydrolyzed and resynthesized each second in a typical cell
10 million
What is the ATP/ADP cycle
continual hydrolysis and resynthesis of ATP
What are redox reactions
Where oxidation and reduction occurs in a reaction
Electrons pass from one atom to another carry energy with them
what is oxidation and what is reduction
Oxidation is when an atom or molecule loses an electron
Reduction occurs when an atom or molecule gains an electron
T/F
A spontaneous reaction has a activation energy of 0
false
What is the variable assigned to activation energy
Ea
What is activation energy
The amount of energy needed to make bonds unstable (destabilize chemical bonds) and ready to be broken (the transition state)
What is a catalyst
substance that lowers the activation energy thereby accelerating the rate of reaction
What are enzymes
catalyst that cannot violate the law of thermodynamic
Do enzymes alter delta G of the reaction
no
How does an enzyme work in enzymatic reactions
enzymes combines briefly with reacting molecules and is unchanged when the reaction is complete
what is the reactant that an enzyme acts on called?
substrate
what is enzyme specificity
Each type of enzyme catalyzes the reaction of a single type of substrate or group of closely related molecules
What is an active site
a small pocket or groove in the enzyme that the substrate interacts with
what is induced fit
when the substrate binds at the active site, both enzyme and substrate molecules are distorted, making the chemical bonds in substrate ready for reaction (as opposed to lock and key model)
Once an enzyme substrate complex is formed, catalysis occurs- the substrate is converted into (how many products?)
one or more
which macromolecule do enzymes belong in
protein
Are enzymes consumed in a reaction
no, they are not consumed and can be reused so only a small amount is needed
What allows enzyme to stabilize a temporary association between substrates
unique 3d shape of enzyme (active site)
Cells have (how many) enzymes (inside, outside, or both) the cell
thousands, inside and outside
how do we know if something is an enzyme by its name and how do we know its respective substrate
the enzyme will end in -ase and refer to its substrate or type of reaction (maltase, amylase, proteinase, ribonuclease in ainfensens experiment, etc)
What is a cofactor
a nonprotein group that binds to the enzyme for catalytic activity. Some are metallic ions (iron, copper, magneisum, zinc, manganese)
what is a coenzyme
a cofactor that is a small organic molecule, which are often derived from vitamins
what is an example of a coenzyme
NAD/NADP
Name 3 major mechanisms that are part of enzymes that stabilize the transition state
1) bringing the reacting molecules together
2) exposing the reactant molecules to altered charge environment that promote catalysis
3) changing the shape of the substrate molecules
name 4 factors affecting enzyme activity
1) Concentration of substrate and other molecules that bind to enzymes
2) control mechanisms that modify enzyme activity (inhibitors)
3) temperature
4) pH- ionic interactions hold enzymes together
when enzyme concentration is kept constant, what happens to the rate of reaction as we increase substrate concentration
the rate of reaction will increase until it flattens out, this means the enzymes are saturated and the rate is solely dependent on the amount of enzyme molecules and how fast they work, no longer increase of substrate will increase rate
what are enzyme inhibitors
nonsubstrate molecules that bind to an enzyme and decrease its activity
what are competitive inhibitors
a inhibitor that competes with the substrate for the same active site
what are noncompetitive inhibitors
a inhibitor that binds at a site other than active site, causing the enzymes shape to change so that substrates can’t bind to the active site
what is allosteric regulation and allosteric site
reversible binding of a regulatory molecule to the allosteric site (location on enzyme other than active site). Enzymes will have 2 alternate conformations: high affinity state (active) and low affinity state (inactive)
what is allosteric activation
an allosteric activator binds to an enzyme on the allosteric site and the enzyme goes from low affinity state to high affinity state
what is allosteric inhibiton
allosteric inhibitor goes into allosteric site and enzyme goes from high affinity state to low affinity state
what is negative feedback (feedback inhibition) and how is it related to allosteric inhibition
the product inhibits the process. The product is the allosteric inhibitor
What is regulation by chemical modification of an enzyme
chemical linkages to ions, functional groups, or other molecules that induce changes in enzyme that increase or decrease its activity
name an example of regulation by chemical modification of an enzyme
phosphorylation by protein kinases may activate or deactivate a protein
what do kinases do
transfer phosphate group from ATP to another molecule (kinase like kinetic energy??)
Typically, as temperature rises, how does the rate of reaction respond
rate of reaction typically increases
why can too high a temperature lower rate of reaction for an enzymatic reaction
kinetic motion increases and eventually hydrogen bonds break and the enzymes denature
What is optimum temperature
the ideal temperature for an enzyme where enzymatic activity is at its peak
what is the optimal pH of most enzymes
neutral, 7
what is the optimal pH of stomach enzymes (like pepsin)
acidic, 2
what is the RNA world
earliest forms of life might have inhabited RNA world, with no DNA or proteins to play critical roles.
This is because ribozymes were informational molecules and had enzymatic function (could accelerate rate of certain biological reactions)
Name some functions of ribozymes (2)
cutting and splicing reactions that remove surplus segments from RNA molecules
Catalyze linkage of amino acids in protein synthesis
What are autotrophs
Organisms that harvest sunlight and convert radiant energy into chemical energy
what are heterotrophs
organisms that live off the energy produced by autotrophs
extract energy from food via digestion and catabolism
what is cellular respiration
collection of metabolic reactions that breaks down food molecules to produce energy in the form of ATP (think mitochondria)
what is aerobic respiration and what organisms is it found in
form of cellular respiration in eukaryotes and many prokaryotes, oxygen is reactant in ATP producing process
what is anaerobic respiration and what organisms is it found in
form of cellular respiration found in some prokaryotes, molecule other than oxygen (sulfate or nitrate) is used in ATP producing process
what is the end goal of respiration
to produce ATP
is cellular respiration one redox reaction or many
many redox reactions
energy is released from oxidation in the form of what?
electrons
electrons are shuttled by electron carriers, name a electron carrier and where does it deliver to
NAD+ to an electron transport chain
at the electron transport chain, what happens
electron energy is converted to ATP
what is the final electron acceptor in aerobic respiration, anaerobic, and fermentation
oxygen for aerobic
inorganic molecule for anaerobic
organic molecule for fermentation
how do we obtain free energy for cellular work such as ATP synthesis in redox reactions
electrons release some of their energy as they pass from a donor molecule to an acceptor molecule
in redox reactions, do molecules only accept electrons? name an example or counter example
no they don’t only accept electrons, they accept protons too. Oxygen accepts protons to make water
what is the standard chemical equation for making ATP from glucose. Is this aerobic or anaerobic? What is the delta G
C6H12O6 + 6O2 + 32ADP + 32Pi –> 6H2O + 6CO2 + 32ATP
Aerobic
-686kcal/mol
in aerobic respiration, can the large amount of energy be released at the same time?
no, it must be released in small steps
Are the electron carriers soluble or insoluble? Are they membrane bounded or not?
soluble and membrane bound
Are all carriers easily oxidized and reduced
yes
what do electron carriers carry
electrons, some can carry electrons and protons
what is the function of dehydrogenase enzyme
facilitate transfer of electrons from a fuel molecule to a molecule that acts as an electron carrier
what is the most common electron carrier
coenzyme nicotinamide adenine dinucleotide (NAD+)
in cellular respiration, what does the Dehydrogenase do to the NAD+
dehydrogenase transfers 2 electrons and 1 proton to NAD+ (oxidized form) to result into complete reduction to NADH (reduced form)
what does NAD+ and NADH have in common in structure? how are they different?
Both have adenine, 2 ribose and 2 phosphate groups, and nicotinamide. NAD+ has just 1 hydrogen bonded to the top carbon while NADH has 2 hydrogens connected to the top carbon
name the polymers of glucose that we need to know
glycogen, cellulose, and starch (and chitin if you want)
what are the 4 stages of oxidation of glucose in order and where in the cell does each occur
glycolysis (cytosol), pyruvate oxidation (mitochondrial matrix), krebs cycle (mitochondrial matrix), electron transport chain and Chemiosmosis (ATP production)(inner mitochondrial membrane)
in glycolysis enzymes break a (how many) carbon molecule of (what carbohydrate) into (what and how many)
enzymes break a 6 carbon glucose molecule into 2 3-carbon pyruvate molecules
what is substrate level phosphorylation
enzyme catalyzed reaction that transfers phosphate group from substrate to ADP
in pyruvate oxidation, enzymes convert what into what for the citric acid cycle
3-carbon pyruvate into a 2 carbon acetyl group
in the electron transport chain, electrons are delivered to what molecule and what is chemiosmosis established and what is it used for
electrons are delivered to oxygen by a sequence of electron carriers in the ETC
free energy released by electron flow generates an H+ gradient by chemiosmosis and ATP synthase uses the H+ gradient as the energy source to make ATP
whats the equation for Calories in terms of proteins fats and carbs?
9(fat)+4(carbs)+4(proteins) all in grams
What is the difference between substrate level phosphorylation and oxidative phosphorylation
substrate level phosphorylation is transferring a phosphate group from the molecule directly to ADP
oxidative phosphorylation is ATP synthase using energy from proton gradient
What is the chemical equation for glycolysis
Glucose + 2ADP + 2Pi + 2NAD+ + 4e- + 4H+ –> 2 pyruvate + 2ATP + 2 NADH + 2H+ + 2H2O
How much TOTAL ATP is made in glycolysis? How about NET ATP? How much NADH is made?
4 total, 2 net, 2NADH
what kind of transport moves pyruvate into the mitochondrial matrix
secondary active transport
pyruvate oxidation occurs where in eukaryotes and where in prokaryotes
mitochondria in eukaryotes and cytosol in prokaryotes
what is the equation for pyruvate oxidation for 1 glucose molecule (so start with 2 pyruvates)
2 pyruvate + 2CoA + 2NAD+ —> 2acetyl-CoA + 2NADH + 2H+ +2CO2
what are other names of the citric acid cycle (2)
Krebs cycle, tricarboxylic acid cycle
what are the products of Krebs cycle for 1 glucose molecule
6NADH, 4CO2, 2FADH2, 2ATP, 6H+, 2CoA
what is needed for the first step of Krebs cycle
oxaloacetate, acetyl CoA and citrate synthase
What has glucose been oxidized to up till the end of Krebs cycle
6CO2, 4ATP, 10NADH, 2FADH2
What are some allosteric inhibitors for phosphofructokinase? (3), What activates it?
Excess ATP, Citrate, and NADH inhibit it. AMP activates it
What inhibits pyruvate kinase? (2), what activates it?
high levels of ATP and Acetyl CoA inhibits it. high levels of Fructose 1,6- bisphosphate activates it
What inhibits pyruvate dehrdrogenase
high levels of NADH
what inhibits citrate synthase (2)
high levels of ATP and citrate
what inhibits hexokinase
glucose 6 phosphate
what does ETC and ETS stand for
electron transport chain and electron transfer system
ETC is where?
embedded in the inner mitochondrial membrane
Which protein complex do electrons from NADH enter into? How about FADH2?
complex 1 for NADH and complex 2 to FADH2
where is the higher concentration and where is the lower concentration of protons
high H+ in intermembrane compartment and low H+ in matrix
what are the two small mobile electron carriers in the etc
cytochrome c and ubiquinone (coenzyme Q)
what are cytochromes
proteins with a heme prosthetic group that contains an iron atom to accept and donate electrons
are electron carriers organized from high to low free energy or low to high free energy
high to low free energy
what is the last terminal electron acceptor and what is it reduced to
O2 accepts 4 protons to turn into 2H2O
which protein complexes actively move protons
complexes 1 3 and 4
what kind of gradient is the proton gradient
electrical and chemical gradient
What is chemiosmosis/chemiosmotic hypothesis
that the proton gradient powers ATP synthesis by ATP synthase
Is the basal unit towards the intermembrane compartment or the matrix
towards the compartment, where protons can enter
What connects headpiece and basal unit
the stalk, a peripheral stator bridges the basal unit and headpiece
which part rotates in ATP synthase and in which direction
the basal unit rotates counterclockwise
What is the theoretical energy yield for bacteria and eukaryotes
38 ATP for bacteria and 36 ATP for eukaryotes
what is the theoretical yield of energy per NADH and FADH2
3 ATP for NADH and 2 ATP for FADH2
why does FADH2 make less ATP than NADH
FADH2 starts in complex 2
why does eukaryotes produce 2 less ATP than bacteria
Eukarya use 2 ATP to move the NADH in glycolysis in the cytosol to the matrix while prokaryotes everything happens in the cytosol
what is the actual yield of energy in bacteria and eukaryotes
32 ATP for prokaryotes and 30 ATP for eukaryotes per glucose
What is the actual yield of NADH and FADH2
2.5 ATP’s for NADH and 1.5 ATP for FADH2
what causes the reduce yield of actual energy yield vs theoretical yield (2)
Leaky inner membrane where Protons move through other channels other than the ATP synthase
use of proton gradient for other purposes other than ATP synthesis
Describe Racker and Stoeckenius experiment
they made a synthetic phospholipid membrane vesicles with a portion made of bacteriorhodopsin, a light activated proton pump, and ATP synthase. The ATP synthase was oriented so the headpiece was on the outside of the vesicle and added ADP and Pi to the medium.
Results show that the light made a proton gradient and that gradient drove ATP synthase to make ATP.
how many protons and electrons are removed in a molecule when making NADH from NAD+
2 electrons and 2 protons
what did srikanth talk about siamese cats
near the nose and ears and paws , the enzyme that makes the dark pigment has optimal activity at lower temperatures, hence the different colors
what is phosphatase
enzyme that dephosphorylates
name an example of a reversible compeitive inhibitor
aspirin
aspiring inhibits what enzyme
cyclo-oxygenase
name an example of a irreversible compeitive inhibitor
pencillin
name an example of non compeitive inhibitor
cyanide
is dna negatively charged, why or why not
yes because of the phosphate group
name an example of a cell that is in g0
neurons
what is another name for anabolic pathway
biosynthetic reaction
do catalyst and enzymes increase rate of rxn
yes
