Cellular Respiration Flashcards
(131 cards)
1
Q
Metabolism
A
the sum of all chemical reactions in a cell or organism
2
Q
Energy
A
The ability to do work
work: moving an object against an opposing force
3
Q
Kinetic energy
A
the energy of motion, performs work by making objects move
4
Q
Potential energy
A
Energy that is stored within an object and dependent on
-chemical structure
-location
5
Q
To break a bond..
A
energy is absorbed since you need energy to pull reactants away
6
Q
To form a bond..
A
energy is released
7
Q
During a chemical reaction bonds ________ and bonds __________
A
Bonds break in reactant molecules and form in product molecules
8
Q
Bond energy
A
Energy required to break bonds
9
Q
Activation energy
A
The minimum amount of energy required to break bonds in reactants and start a reaction
10
Q
Transition state
A
The intermediate state where bonds are breaking in reactants and forming in products
11
Q
Exothermic
A
when there is a overall release of energy
-lower activation energy
-reactants have more energy than products
12
Q
Endothermic
A
when there is an overall absorption of energy
-products have more energy than reactants
-more activation energy required
13
Q
How do living organisms maintain their highly ordered structures?
A
Although the entropy of the universe is always increasing by expending energy, cells are able to maintain their highly ordered structures.
14
Q
ATP composition
A
three (-) charged phosphate groups which give it its energy, adenine, and a ribose sugar
Adenosine triphosphate
15
Q
What is ATP hydrolysis
A
water breaking apart atp molecules into adp and an inorganic phosphate and H+ ion
16
Q
ATP cycle
A
ATP turns into ADP and Pi by releasing free energy and using water -> exergonic
ADP and Pi turns into ATP by absorbing energy and releasing water -> endergonic
17
Q
Phosphorylation
A
the transfer of a phosphate group from ATP to another molecule to energize the reaction
18
Q
Enzymes
A
enzymes are biological catalysts proteins that speed up a chemical reaction by lowering its activation energy without being consumed or changing products
19
Q
Substrate
A
the molecule that binds onto the enzyme
20
Q
What is the active site
A
The site where substrates bind onto the enzyme
21
Q
How are enzymes usually named
A
-ase
22
Q
What is the lock and key model of the enzyme. Why is it not accurate?
A
The model that specific substrates are keys and enzymes are locks. It was not accurate because it could not explain why certain substrates could not bind to certain enzymes since enzymes are very specific and won’t just bind to every substrate
23
Q
Induced-fit hypothesis
A
The current model of the enzyme which shows that enzymes can undergo a conformational change where it changes shape so the active site can better fit the enzyme and then converts substrates into products
(still specific but after it binds it changes shape)
24
Q
4 factors affecting enzyme activity
A
- Enzymes and substrate concentration
- Enzyme inhibitors
- pH
- Temperature
25
Explain enzyme and substrate concentration effect on enzyme activity
The rate of reaction is proportional to the enzyme concentration.
Increasing the rate of substrates will speed up the reaction up to a certain point, until it plateaus due to to availability of enzymes
26
Why can enzymes be used so rapidly?
Because they are not used up in a reaction and are able to be reused, also why substrate concentration is more important affecting rate than enzyme conc.
27
Coenzymes
an organic molecule that acts as a cofactor of an enzyme
28
What is "saturation level"
when all enzymes are bound to a substrate and the point plateaus
29
How do enzyme inhibitors affect the enzyme activity
Enzyme inhibitors lower the rate which enzymes catalyze reactions or they could stop them completely
There are two types of enzyme inhibition:
1. competitve
2. non competitiive
-can be done on purpose, or a poison
30
Competitive Inhibtion
A molecule very similar to the substrates binds to the active site of an enzyme and blocks activity
-decreases the rate of reaction
31
Noncompetitive Inhibition
When an inhibitor molecule binds to allosteric or non-active site of the enzyme to block activity
-changes shape of the active site
32
What happens when the concentration of inhibitors are too high?
The reaction will stop completely
33
pH and temperature affect on enzyme activity
Enzymes have an optimal temperature and pH which they peak at
Temperature=increases rate of reaction (too high can denature the enzyme)
-40C
34
What is the optimal pH and temperature range of enzymes
Optimal pH = 6-8
Temperature = 40C
35
What is the allosteric site
Binding site for regulatory molecules (which is not on the active site)
36
What are regulatory molecules
Molecules that naturally regulate enzyme activity
37
Allosteric regulation
Molecules bind to allosteric site and cause conformational change which may allow or prevent the substrate from binding
38
Factors that affect enzymes activity
1. Enzymes and substrate concentration
2. Enzyme inhibitors
3. pH
4. Temperature
39
What happens when products accumulate in excess for enzymes?
Then the regulatory molecules (molecules at end of biochemical pathway) bind to the allosteric site of an enzyme and change the shape.
40
What does an allosteric activator/inhibitor do?
Activator: Stabilizes the enzyme to a shape that causes its active site to have a high affinity for substrate
Inhibitor: creates an inactive form of the enzyme
The inhibitor molecule changes the shape of an enzyme in such a way that the substrate is released from the active site
41
What are allosteric inhibitors a product of?
Biochemical pathways
42
What is feedback inhibtion in enzymes?
When a product is in excess, one of the product molecules part of the biochemical pathway will go back and inhibit the first enzyme of the pathway.
When a product is scarce, the inhibition is reduced and rate of reaction increases.
43
Why is feedback inhibition so important?
It ensures cellular resources are not being wasted
44
What do enzymes do to a reaction?
It decreases the activation energy required to start the reaction and forms products quicker
45
What must happen in a reaction before products form?
Bonds must break in the reactant molecules
46
Explain a rock on a hill with activation energy
A rock on a hill possesses a lot of potential energy but it cannot move down a hill spontaneously without a push which is the activation energy
47
Why is increasing temperature not the best way to speed up a chemical reaction?
Although it does speed up the reaction, there are two reasons:
-too high temperature damages the DNA and the proteins
-it speeds up every single reaction occuring in a cell and not just a specific one
-> certain chemical reactions in a cell must be regulated independently and know when to stop/start
48
Enzymes DO...
Enzymes DO NOT...
Do:
-lower the activation energy of a reaction and make them reach transition state faster
-increases the rate of a spontaneous (exergonic reaction)
Do not:
-supply free energy to a reaction
-make an endergonic reaction proceed spontaneously
-alter products
-get consumed
49
What are the ways enzymes lower activation energy/bring reactants to transition state with enzymes?
1. Bringing molecules together
-For reactions to occur, substrate molecules must collide with each other, when both bind to substrate its ideal for reaction to occur
2. Exposing reactants to a charged environment that promotes the reaction
-Active sites contain ionic groups that attract or repel some parts of the substrate - this helps position bonds in a favourable way
3. Changing shape of the substrate
-the active site can distort or strain the substrate to weaken bonds, this reduces amount of energy required to break the bonds
50
What is the rate of reaction dependent on?
Its proportional to the number of reactant molecules that can overcome the activation barrier to reach transition state
-when enzymes lower the activation barrier, it makes the reaction molecules overcome it more
51
What is controlled oxidation
Reactions that require small activation energies catalyzed by enzymes and smaller energy changes
-cellular respiration
52
Two types of redox reactions and explain what happens
Reduction (RIG)
-atom that gains electrons are "reduced"
Oxidation (OIL)
-atoms that lose electrons are "oxidized"
53
Reducing vs oxidizing agent
Reducing agents are substances that loses electrons (are oxidized)
Oxidizing agents are substances that gains an electron (are reduced)
54
Why is O2 an ideal electron acceptor in cellular respiration
Because of it's high electronegativity value
55
Aerobic cellular respiration
The process of extracting energy from food in the presence of oxygen
56
4 Stages of cellular respiration
1. Glycolysis
2. Pyruvate oxidation
3. Citric Acid cycle (kreb's cycle)
4. Electron transport chain and chemiosmosis
57
Substrate level vs oxidative phosphorylation
Both ways of generating ATP
Substrate-level phosphorylation
-> An enzyme transfers a phosphate molecule from a high energy substrate molecule to ADP to produce ATP
Oxidative Phosphorylation
-> ATP is formed indirectly through a series of redox reactions which releases free energy involving a final electron acceptor, usually O2 which create an electrochemical gradient across the inner mitochondrial membrane and makes ATP through ATP synthase
58
NAD+/NADH explain redox rxns
NAD+ is oxidizng agent
NADH is reducing agent
NAD+ -> NADH is reduction (1-3 c.r steps)
NADH -> NAD+ is oxidation (electron chain)
59
FAD/FADH2 reduced and oxidized form
FAD-> oxidized form, oxidizing agent
FADH2 -> the reduced form, reducing agent (gains 2 electrons and 2 protons)
60
What is the importance of energy carriers in redox reactions
61
Where do steps of cellular respiration occur in the cell, is oxygen required?
1. Glycolysis -> cytosol, no oxygen
2. Pyruvate oxidation -> matrix, oxygen
3. Citric acid cycle -> matrix, oxygen
4. Electron transport -> the inner mitochondrial membrane, oxygen
62
Explain the structure of mitochondria
-outer mitochondrial membrane
-intermembrane space
-matrix
-inner mitochondrial membrane
63
Anaerobic cellular respiration
A process that produces energy without oxygen, but an inorganic final oxidizing agent
64
Fermentation
A process that uses an organic compound as the final oxidizing agent to produce energy
-does not use electron transport
-organic compound final oxidizing agent
65
Glycolysis
what is it, where does it occur, what is involved
-The splitting of glucose
-Occurs in almost all organisms because it doesn't require oxygen
-Occurs in cytosol
-"energy investment" and "energy payoff" phase
-involves 10 enzyme-catalyzed reactions which oxidizes glucose and produces pyruvate
-is done by substrate-level phosphorylation
66
What molecules do mitochondria need to make ATP?
Pyruvate and oxygen (for electron transport chain)
67
What are the two phases of glycolysis? Explain all of them in detail.
The "energy investment phase"
-uses 2 ATP to break down glucose into two molecules of G3P
-the ATP is broken down into ADP molecules and the phosphate groups attach onto molecules in the cycle
The "energy payoff phase"
-produces 4 ATP from the 2 G3P molecules donating its phosphate to ADP and forming ATP
-also forms NADH and H+ from the reduction of NAD+ by 2e- and 2p+
68
State the overall equation for glycolysis
glucose + 2 ADP + 2 Pi + 2 NAD+ -> 2 pyruvate + 2 NADH + 2 ATP + 2 H+
69
How is energy lost during cellular respiration
Each subsequent step, energy tends to be lost and some is released as thermal energy. Some energy will be stored in molecules which will continue down the cycle.
70
Draw out the glycolysis steps and explain each step
-should include:
pi, ADP and ATP, should explain where the pi goes to and important molecules involved
-should inclue PFK enzyme
71
What are cristae
Folds in the inner membrane of the mitochondria which increase surface area
72
Pyruvate oxidation
-occurs in the matrix
-
73
How does pyruvate diffuse through the membranes?
The pyruvate molecule is synthesized in the cytosol therefore they must diffuse through both the inner and outer mitochondrial membrane.
The outer membrane pyruvate can diffuse through but a carrier is needed to cross the inner membrane
74
Explain the process of pyruvate oxidation
1. Diffuse through outer membrane and comes into inner membrane through a carrier protein
2. Decarboxylation reaction occurs, CO2 is removed from the pyruvate and forms CO2 as waste product
3. Dehydrogenation reaction occurs and removes the remaining two carbons and produces acetyl group which involves NAD+ being reduced into NADH by transferring 2e- and 1p+ releasing an H+ ion
4. The remaining acetyl group is bonded to coenzyme A (CoA) to form acetyl-CoA
75
Overall equation of pyruvate oxidation per one glucose molecule
2 pyruvate + 2 NAD+ + 2 CoA -> 2 NADH + 2 H + 2 Acetyl-CoA + 2CO2
76
Citric acid cycle general info:
-occurs in the matrix
-8 enzyme catalyzed reactions
-uses substrate level phosphorylation
-one acetyl-CoA per cycle
-all carbon atoms that were originally in glucose are converted into CO2
-once finished, CoA molecule is released again and participates in pyruvate oxidation
77
What is the purpose of the CoA enzyme
Its an enzyme that carries the acetyl group to the citric acid cycle and its released back to pyruvate oxidation after kreb's cycle.
78
Explain the citric acid cycle.
Refer to notes
79
How many carbons is the acetyl-CoA
2 carbons
80
Overall equation for citric acid cycle
1 Acetyl-Coa + 3 NAD+ + ADP + Pi + FAD -> CoA + ATP + 3 NADH + 3H+ + 2 CO2 + FADH2
81
NAD+ -> NADH
vs
NADH -> NAD+
NAD+ -> NADH is a reduction
NADH -> NAD+ is an oxidation
82
Why are NAD+ and FAD so important
These dehydrogenases at various points of cellular respiration take 2 protons and 2 electrons from substrate molecules and store them so at the end of the electron transport chain, the large amount of chemical potential energy is used to transfer electrons across and create ATP
-they carry the remaining hydrogen molecules from glucose
83
What happens to glucose during the cellular respiration cycle, explain the ending product before the electron transport chain occurs. What is left by the time the citric acid cycle is over?
-All the carbon present in glucose is oxidized and released as CO2
-Some ATP was produced by substrate level phosphorylation but most of the potential energy present in the glucose was captured by dehydrogenases NADH and FADH2
-all thats left of glucose molecule is hydrogens which are carried by NADH and FADH2 and the electrons associated with the protons carry a large amount of potential energy
84
What is the purpose of the electron transport chain
To extract all the chemical potential energy from the NADH and FADH2 molecules that was taken from glucose and transferring the electrons to the final electron acceptor, O2.
85
How does electronegativity change during the electron transport cycle
Each complex has increasing electronegativities (stronger pull on electrons)
86
How is water formed in the electron transport cycle
The final oxygen acceptor combines with 2 electrons from the chain and 2 protons from the matrix to form water
87
Overall steps of electron transport cycle:
Where does it occur, how does it work, what is the end product
Occurs in the inner mitochondrial membrane
1. NADH releases 2e- and causes protons to get pumped through complex I
2. Complex I passes e- into UQ and then FADH2 oxidizes into FAD and releases 2e- into the UQ shuttle
3. Complex III passes on 4e- to cytochrome c into complex IV
4. Electrons in complex IV are passed into the final e- acceptor O2 which takes 2 e- from the electron chain due to its high EN and 2p+ from the matrix and forms 2 water as a byproduct
88
What is oxygen's single vital task in cellular respiration, why is it a good final electron acceptor?
To pull electrons away from complex IV, it is good because it is so electronegative it pulls electrons from complex IV
89
For every O2 molecule we breathe in...
4 electrons are pulled through the chain and two water molecules are produced
this is because the final acceptor is 1/2 O2 which produces 1 molecule of water
90
Explain the process of chemiosmosis and how ATP is generated
-During electron transport, free energy from NADH, FADH2 interacting with O2, is released which drives the active transport of protons across the inner mitochondrial membrane into the intermembrane space
-UQ shuttle also brings protons across membrane
-H+ concentration of the intermembrane space becomes much higher than the H+ concentration of the matrix
-This causes an electrochemical gradient/proton motive force and is a form of potential energy
-The protons then go back to the matrix through ATP synthase (passive transport) and atp synthase forms ATP from ADP and Pi
91
What is the electrochemical gradient
The electrochemical gradient is a combination of the concentration gradient and the electrical potential charge (chemical gradient) which generates a proton motive force used to drive H+ protons across the inner mitochondrial membrane. This force is a form of chemical potential energy used to drive ATP synthesis.
92
What is the definition of chemiosmosis
The ability of cells to use proton-motive force which is a combination of the electrical potential charge gradient and concentration gradient in the membrane
-energy comes from energy-rich molecules like NADH
93
How much ATP is made per step in cellular respiration
Glycolysis - 2 ATP
CAA - 2 ATP
ETC - 34 ATP
94
In what form is the oxygen that is used during cellular respiration returned to the environment?
Water, the oxygen used in the electron transport chain makes water.
95
For every NADH.... ____ ATP is made
For every FADH2 .... ____ ATP is made
1 acetyl-CoA... ________ is made
NADH - 3 atp
FADH2 - 2 atp
Acetyl-CoA
96
Malate asparate shuttle
brings in NADH produced in glycolysis to mitochondria to participate in ETC
97
When does fermentation occur, what must the cell do thats important
When glucose is present but oxygen is not
-produces much less energy than aerobic respiration
-cells must have a way of regenerating NAD+ after NAD+ -> NADH because they have a limited supply
-produce less energy, but faster
98
Why do cells need to regenerate NAD+ in fermentation?
Because it is required for glycolysis to occur, fermentation uses the reduction of NAD+ instead of the ETC to produce lactate
99
When is lactic acid fermentation used by humans vs bacteria
It is used by bacteria or as a supplemental system in eukaryotes
-in humans it occurs during strenuous activity that causes a demand in ATP that exceeds the rate O2 can be brought in to electron transport chain
-when we are breathing deeply and heart is pumping, circulatory system can only provide a limited amount of oxygen gas per second
100
What is mitochondria limited by during cellular respiration
O2, not enough O2, it will slow down
101
Explain the lactic acid fermentation pathway
1. Glucose produces 2 molecules of ATP and pyruvate is converted into lactate
2. This pathway from pyruvate to lactate regenerates NAD+ which can be used to maintain high rate of glycolysis
3. If significant energy demands continue, lactate can accumulate in cells
102
What happens after exercise, when oxygen content of muscle cells return to normal levels?
The reaction reverses and regenerates pyruvate and NADH and follow to the CAA and ETC
103
Overall reaction for lactate fermentation
pyruvate, NADH + H+ -> NAD+ + lactate
104
Aerobic vs Anaerobic respiration
Reactants
Energy yield
Products
Location
Stages
Final acceptor
Anaerobic
-glucose
-2 atp
-lactic acid, yeast
-cytoplasm
-glycolysis, fermentation
Aerobic
-glucose, adp, oxygen
-38ATP
-CO2 and H2O
-cytoplasm and mitochondrion
-Kreb's cycle, ETC, glycolysis
105
What are photoautotrophs
Primary producers - they make their own food using sunlight energy
106
What are the two stages of photosynthesis?
-light dependent reactions (absorption of photons of light)
-light independent (calvin cycle, but are dependent on the products of light dependent reactions)
107
Where is the site of photosynthesis
In the chloroplast which are found inside photosynthetic cells
108
How are all organic molecules of plants assembled in?
All major organic molecules of plants are assembled directly or indirectly as products of photosynthesis.
109
Where are enzymes used to catalyze reactions of Calvin Cycle found?
In the stroma
110
How is light energy captured and converted into chemical potential energy?
-Absorption of a photon by a pigment molecule excites a single electron moving it from low energy/ground state to higher energy/excited state
-the difference between energy level of ground state and energy level of the excited state must be equivalent to the energy absorbed by the photon or else it can't be absorbed by pigment
111
Three possible outcomes of an electron after it reaches the excited state in pigment molecule:
1. Returns to ground state and releases as heat or fluorescence
2.Transfer its electron to a neighbouring pigment molecule and then return back to original ground state
3. Be transferred to a neighbouring molecule (primary electron acceptor)
-most important step/goal
112
3 types of pigments
-chlorophyll a (dominant pigment)
-> chlorophyll a becomes oxidized and donates it's electron the the final acceptor
-chlorophyll b and carotenoids are **accessory pigments** that transfer electrons after absorbing light
113
Antenna complex
A cluster of light absorbing pigments in the PHOTOSYSTEMS thylakoid membrane that captures then transfers energy to chlorophyll a
114
Reaction centre
The complex or proteins and pigments which contains the final electron acceptor and chlorophyll a passes it on
115
What happens to the wavelengths of light that are not absorbed?
They are transmitted (pass through) or reflected
-green and yellow light is reflected which is why leaves appear green
116
Why does chlorophyll a appear green?
Because green and yellow light is not absorbed, rather they are reflected since chlorophyll a doesn't absorb them, this is why in the fall time the colour turns into an orange-red colour because the chlorophyll pigments slowly lower in number.
The carotenoids in the leaf begin to show their colour since they reflect red and yellow light.
117
Chlorophyll - what is its role in photosynthesis and where is it found
Chlorophyll is a photosynthetic pigment molecule that is found in photosynthesis to absorb light and carry it to the final electron acceptor
-reflects green light, absorbs red and blue
-found in photosystems reaction centre and antenna complex
118
Where are pigment molecules bound to?
They are bound to photosystems in the pigment molecules inside of thylakoid membrane
119
Two kinds of photosystems
PSI and PSII
The reaction centre of photosystem I contains specialized P700 molecules which absorbs 700nm of light
The reaction centre of photosystem II contains P680 molecules which absorbs 680 nm of light
120
What contributes to high rates of oxidation-reduction reactions in the photosystems
High rates are achieved when the pigments in the photosystem absorb the light at a range of wavelengths and efficiently and how high energy electrons generated by photosystems can be used to drive ATP synthesis and assemble the high energy organic molecules that are used as food.
121
What is a proton gradient?
Which direction does it travel for ETC in photosynthesis and cellular respiration
The difference in H+ concentration across the cell membrane where the H+ in the intermembrane space is higher than the matrix
-form of potential energy
CR: matrix -> intermembrane space
PS: stroma -> thylakoid lumen
122
Explain the process of photosystem II absorbing light energy
1. Photon of light is absorbed and the **antenna complex** and transfers its energy to the P680 molecule
2. One of the electrons of P680 becomes excited from ground to state to excited state and turns into P680*
2. The excited electron is then transferred to a primary acceptor molecule which makes the acceptor (-) and the P680 (+)
3. P680+ is now extremely EN and can remove an electron from water which is assisted by the **water splitting complex** of PSII
4. The P680+ molecule and water splitting complex removes an electron (oxidizes) from water and then passes it onto P680+ to make it neutral again
5. The primary acceptor transfers electron to PQ and starts all over again
123
Explain the process of linear electron transport
1. PSII absorbs a photon of light and then the antenna complex excites the P680 into P680* and then makes the electron travel to primary acceptor making it A- and P680+, the P680+ along with water splitting complex interacts to remove electrons from water which turns P680 neutral and makes the primary acceptor transfer its electron to the PQ shuttle.
2. The electrons in PQ shuttle are transferred from PSII to cytochrome c and also releases gains H+ from stroma and pushes it into the lumen
3. Plastocyanin shuttles from cyt c to PSI
4. PSI absorbs photon of light, energizes electrons and then turns P700 into P700*->P700+ and then it gets neutralized by the e- from plastocyanin and then the primary acceptor transfers e- to ferredoxin
5. 2 electrons and proton are transferred from ferredoxin to NADP+ reductase and forms NADPH which consumes H+ from the stroma
124
What are the three ways H+ concentration is increased in the thylakoid lumen?
1. The water splitting complex releases 2 H+ for every water
2. PQ shuttles protons into the lumen
3. The reaction of ferredoxin releases 2e- also consumes H+ in the stroma which lowers the H+ concentration in stroma NADP+ -> NADP -> NADPH
125
How is ETC maintained in the linear electron transport cycle when it starts off with such a low energy molecule like water?
It is maintained by absorbing two photons of light in order to span the energy difference between H2O and NADPH and gives it enough potential energy to form a proton gradient and drive electron transport
126
Explain cyclic electron transport
Does not use PSII instead...
1. Absorbs photon of light from PSI and then energizes the P700* and then its turned neutral by plastocyanin
2. The electron is released by the primary acceptor and then goes to ferredoxin, instead of using electrons from ferredoxin to oxidize NADP+, it just transfers the electron back into PQ
4. This cycle continually reduces/oxidizes PQ and causes protons to move into the thylakoid lumen
5. The electrochemical gradient drives ATP synthesis
127
What is the benefit of cyclic electron transport?
-it doesn't use water so it conserves water
-it generates ATP faster since the Calvin cycle requires more ATP than NADPH
128
Calvin cycle
-where does it occur
-what does it use
It occurs in the stroma of the chloroplast
-uses ATP and NADPH to make molecules of G3P
129
Explain the whole Calvin cycle
Carbon fixation
-3 molecules of CO2 combines with 3 molecules of RuBP to form 6 PGA by a rubisco enzyme
Carbon reduction
-6 ATP are used to phosphorylate PGA and then immediately after 6 NADPH -> 6 NAD+ to reduce into 6 G3P
One G3P is released
Regeneration
-5 G3P is used to regenerate RuBP by using 3 ATP -> 3 ADP + 2 Pi which makes 3 RuBP
Cycle restarts
130
How many G3P molecules is released per calvin cycle
1 G3P is released and it requires 3 CO2, 9 ATP, and 6 NADPH
131
How many cycles is required in Calvin cycle to turn into one molecule of glucose?
You need 6 cycles, 6CO2
