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BIOL 107 > Quiz #5 > Flashcards

Quiz #5 Flashcards

1
Q

What is ATP?

A

Adenosine triphosphate

Most energy coupling in cells is mediated by ATP, the energy “currency” of the cell

Made in cellular respiration, used in most cell reactions

Stores potential energy due to bond position and composition

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2
Q

What structures make up ATP?

A

Phosphate groups
Phosphoanhydride bonds
Adenine
Ribose

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3
Q

How does the hydrolysis of ATP perform work?

A

In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction

Overall, the couples reactions are exergonic

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4
Q

What is a catalyst?

A

Chemical agent that speeds up a reaction without being consumed, an enzyme is a catalyst is a molecule (usually a protein)

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5
Q

How do enzymes catalyze reactions?

A

Every chemical reaction between molecules involves bond breaking and bond forming

Initial energy needed to start a chemical reaction is called free energy of activation or activation energy

Both endergonic and exogenic reactions have activation energy

The reactants must absorb enough energy from the surroundings to reach an unstable transition state, where bonds can break

Enzymes catalyze reactions by lowering the activation energy barrier

Enzymes do not affect change in free energy

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6
Q

What are the steps of catalysis?

A
  1. Substances enter active site, enzyme changes shape to enfold the substances (induced fit)
  2. Substances held in active site by weak interactions (hydrogen bonds and ionic bonds)
  3. Active site can lower energy of activation and speed up reaction
  4. Substances are converted to products
  5. Products are released
  6. Active site is available for two new substrate molecules
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7
Q

How do enzymes lower the activation energy?

A
  1. Bringing reactants together (if there are two or more)
  2. Physically stressing the substrate bonds, induced fit shifts shape of enzyme-substrate complex, bending of bonds makes them easier to break
  3. Providing favourable micro environment for reaction, cluster of acidic side chains in the enzyme active site
  4. Direct participation in the chemical reactions, temporary bonds between active site and substrate, and subsequent regeneration of the active amino acid side chain after reactants leave active site
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8
Q

What are some factors that can affect enzyme function?

A
  1. Temperature
  2. pH
  3. Cofactors
  4. Enzyme inhibitors
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9
Q

How does temperature affect enzyme function?

A

In general, enzymes work better as temperature increases (but only to a point)

Increased movement of reactants increases chance of contact with enzyme

Above a certain temperature, their activity rapidly declines

Too much thermal activity causes the enzyme to lose its shape (denaturation)

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10
Q

How does pH affect enzyme function?

A

Most enzymes work best at a specific range of pH, typically 6-8

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11
Q

How do cofactors affect enzyme function?

A

Many enzymes require an additional component bound to them in oreler to function properly

Inorganic molecules or coenzymes

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12
Q

How do enzyme inhibitors affect enzyme function?

A

Certain chemicals selectively inhibit the actions of specific enzymes

Competitive and non-competitive inhibitors

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13
Q

What are competitive enzyme inhibitors?

A

Have a similar shape to the normal substrate and can bind to the active site of the enzyme

They do not participate in any reason

Compete with the real substrate for access to enzyme

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14
Q

What are non-competitive enzyme inhibitors?

A

Inhibit the function of enzyme by binding to a different location that isn’t the active site

Inhibitor binding can affect: the shape of the active site, and the function of the active site, without interfering with substrate docking

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15
Q

What is Allosteric Regulation?

A

A protein’s function at one site is affected by the binding of a molecule to another site

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16
Q

What is Feedback Inhibition?

A

Feeds back and inhibited enzyme function

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17
Q

What are Autotrophs?

A

Survive without anything derived from other organisms

Use inorganic C as carbon source to produce inorganic molecules

Almost all plants are photo autotrophs, they use light energy to “fix” carbon

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18
Q

What are heterotrophs?

A

Consumers

Consume plants (direct) or other animals (indirect)

Use inorganic C as their carbon source

Most heterotrophs including humans, depend on photo autotrophs for food and O2

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19
Q

What are structures in the leaves in a plant?

A

Leaves are the major locations of photosynthesis

CO2 enters and O2 exits through the stomata

Chloroplasts are found mainly in mesophyll tissue, the interior tissue of the leaf

Chlorophyll (green pigment) is in thylakoid membranes

Stoma is the dense interior fluid

Thylakoids may be stacked in many grana

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20
Q

What is photosynthesis?

A

6CO2 + 6H2O + light —> C6H12O6 + 6O2

Divided into two main reaction sets: light reactions and Calvin cycle

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21
Q

What are light reactions?

A

In thylakoid

Convert light energy into chemical energy (ATP and NADPH)

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22
Q

What is the Calvin Cycle?

A

Occurs in stroma

Energy stored in ATP and NADPH drives fixation of carbon into carbohydrates

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23
Q

How is photosynthesis a redox reaction?

A

H2O is oxidized

CO2 is reduced

24
Q

What is a redox reaction?

A

Various reactions in which electrons are transferred from one molecule to another

Reduction: the gain of one or more electrons
Oxidation: the lose of one or more electrons

The reactant that becomes reduced is said to be the oxidizing agent

The reactant that becomes oxidized is said to be the reducing agent

Energy is transferred

25
Q

How is NADP formed?

A
  1. NAD+ reduced by 2 H atoms (taken from a donor molecule), supplies 2 electrons and one H+ to reduce NAD+, achieved by a dehydrogenase enzyme
  2. Electrons in the reduced form (NADH + H+) can be transferred to other molecules
  3. If another phosphate is attached to the bottom sugar, this gives the related molecule “NADP”
26
Q

How is light harvested and used?

A
  1. Light: a form of electromagnetic energy, travels in waves
  2. Pigments: are substances that absorb visible light, different pigments absorb different wavelength
  3. Structures involved in photosynthetic electron transfer: are in the thylakoid membrane
27
Q

What is a spectrophotometer?

A

Can determine how much light gets absorbed by a substance (and which wavelength are best absorbed)

28
Q

What light works best for photosynthesis?

A

Violet-blue and red light

29
Q

What is Chlorophyll A?

A

Is the main photosynthetic pigment

30
Q

What are accessory pigments?

A

Chlorophyll B: broadens spectrum for photosynthesis

Carotenoids: absorb excessive light that can damage chlorophyll

31
Q

What are the photo systems?

A

A photosystem consists of a reaction-centre complex surrounded by light harvesting complexes

Photosystem II functions first in the pathway

32
Q

What is a reaction centre?

A

Energy from absorption of photons in all other pigment molecules in a photosystem is transferred to a pair of “chlorophyll a” molecules in a reaction centre

A special pair of “chlorophyll a” molecules in the reaction centre absorb a characteristic wavelength of light (P680)

33
Q

What are the steps of Linear Electron Flow in Photosynthesis?

A
  1. Proton strikes a pigment molecule in PSII
  2. Electron is transferred to primary e- acceptor (pheophytin), P680+ is a very strong oxidizing agent, the loss of it’s electron leaves a hole that must be filled
  3. H2O is split and it’s electrons are transferred one at a time, to P680+ (reducing it to P680), the two protons are released into the thylakoid space
  4. photo-excited electrons from PSII move to PSI via an electron transport chain (Pi, cytosome, b6f, Pc), pheophytin is the primary e- acceptor for PSII
  5. “Fall” to a lower energy level (exergonic), proton pumping driven by electrons moving through cytochrome b6f complex
  6. Light harvesting PSI pigments independently cause P700 to lose electrons (and become photooxidated to P700+)
  7. P700+ accepts electrons that arrive via the e- transport chain of PSII
  8. NADP+ reductase catalyze the transfer of electrons from Ferraro in (Fd) to NADP+, two e- and 1H+ (from stroma) are required to make NADPH
34
Q

What are is the dark pathway of photosynthesis called?

A

Linear (non-cyclic) electron flow pathway of photosynthesis

35
Q

What is the formation of ATP by the electron flow pathway called?

A

non-cyclic photophosphorylation

36
Q

What is the source of electrons in the electron flow pathway of photosynthesis?

A

H2O is the source of electrons for this pathway as they continually replace those lost from “chlorophyll a” reaction center molecules
potential energy of electrons decreases with each transfer down the electron transport chain

37
Q

What is chemiosmatic coupling?

A

first proposed by Peter Mitchell (1961) to explain how ATP can be made from a protein concentration gradient across a membrane
make a gradient, then funnel these protons through structures to do work, get energy from protein gradient

38
Q

What is the ATP Synthase?

A

energy stored in H+ gradient is harnessed to make ATP
this is an example of chemiosmosis, the use of the energy in a proton (H+) gradient to drive cellular work
the gradient has potential energy, called the “proton motive force”

39
Q

What are the structures of the ATP synthase?

A 
stator
rotor
catalytic knob
enzyme contains a pore that allows H+ to slow back from the thylakoid space to stroma
3-4 protons required per ATP
40
Q

How can the cell produce enough ATP without making excess NADPH?

A

plants “sense” levels of NADPH, depending on the balance of ATP:NADPH, they can engage the cyclic electron flow pathway

if excess NADPH accumulated, there would be fewer NAD+ molecules, so the linear electron flow reaction would stall (the electrons would have no where to go), high energy electrons can be dangerous, so instead, they cycle back to Pq and safely dissipate their energy by pumping protons via the electron transport chain

41
Q

What is cyclic electron flow?

A

photoexcited electrons can take an alternative path

cyclic electron flow uses photosystem I, but not photosystem II

no production of NADPH

no release of oxygen

but it can make ATP from protons (2 H+ transferred from stroma into thylakoid space per electron)

cyclic flow is likely an ancient mechanism (some photosynthetic bacteria only use this pathway)

plants that have a defective cyclic pathway can grow only in low light levels, perhaps the cyclic pathway protects plants from the high light intensity

42
Q

What is a summary of cyclic electron flow?

A
  1. Electrons circle back to fill “holes” in photosystem I reaction center
  2. The transfer of electrons is from ferredoxin to plastoquinone, instead of to NADP+
  3. Proton pumping at b6f complex from stroma to thylakoid space contributes to the H+ gradient, H+ gradient used by ATP synthase to create ATP, from ADP + P
  4. In this manner, ATP is produced via: cyclic photophosphorylation
43
Q

How is chemical energy in ATP and NADPH used to fix CO2 in carbohydrates?

A

occur via the calvin cycle

in the stroma of the chloroplast

44
Q

What is the Calvin Cycle?

A

Rubisco adds CO2 to a 5-carbon sugar called ribulose 1,5-bisphosphate (RuBP) already present in the stroma

CO2 + RuBP (5-carbon) –> 6-carbon molecule (unstable intermediate) –> 2 molecules of 3-phosphoglyceric acid (3 carbons each)

CO2 is fixed in first step of cycle, don’t need ATP or NADPH for this step, they are required to regenerate RuBP

45
Q

What is Phase 1 of the Calvin Cycle (Carbon Fixation)?

A
  1. Rubisco catalyzes the reaction of bringing carbon dioxide into the organic molecule or ribulose bisphosphate, adds another carbon to a five carbon molecule
  2. 6-carbon molecule is unstable and breaks apart into 3-carbon molecules
  3. 3 phosphoglycerate get phosphorylated ATP is involved, ATP is hydrolyzed, in the process another phosphate is added to both of these structures, two ATP molecules are required
46
Q

What is Phase 2 of the Calvin Cycle (Reduction)?

A

NADPH is involved

both 1,3-biphosphoglycerate molecules are reduced by NADPH electrons are transferred from NADPH to the molecules

transfer of electrons causes a release of inorganic phosphate, so now we have two glyceralehyde 3-phosphate (G3P)

47
Q

What is Phase 3 of the Calvin Cycle (Regeneration of RuBP)?

A

2 G3P molecules are used to generate RuBP

we need another ATP molecule, phosphate from ATP is added to the molecule

after this reaction we don’t have anymore G3P but we are left with one extra carbon

if the Calvin Cycle is done three times, you will generate 3 carbons

the cycle has to regenerate three times in order to generate a useful G3P (made from the three carbons)

48
Q

What are G3P molecules used for?

A

every 3 turns gives one “extra” G3P molecules

used to synthesize 6-carbon glucose and more complex molecules

glucose often converted to starch for storage

serves as energy sources when broken down

serves as a carbon source for building other molecules needed by plant

49
Q

The generation of one “useable” molecules of G3P consumes how many ATP and NADPH?

A

9 ATP (used for endergonic reactions of the cycle)

6 NADPH (used to reduce fixed carbon)

50
Q

What happens if rubisco combines with O2 instead of CO2?

A

RuBP + O2 –> 3 carbon molecule (stays in Calvin Cycle) + 2 carbon molecule called glycolate (leaves Calvin Cycle)

2 carbon molecule furthers metabolism, requires O2 consumption, CO2 is released (the opposite of what happens in photosynthesis)

51
Q

What happens when CO2/O2 concentration is relatively high?

A

photosynthesis is favored

carboxylase action

52
Q

What happens when CO2/O2 concentration is relatively low?

A

photorespiration is favored

oxygenase action

53
Q

Why would a low CO2/O2 ratio ever occur?

A

it can develop within the plant on very bright hot days

plants photosynthesize at high rates, CO2 consumed, O2 produced

pores on leaves (stomata) close to prevent loss of H2O, internal O2 concentration goes up, internal CO2 concentration goes down

54
Q

How do you solve the rubisco problem?

A

fix carbon at night, when its cooler and stomata can open

fix carbon in a different cell and send the organic molecule to the Calvin Cycle

55
Q

How have some species of plants developed elaborate mechanisms to avoid photorespiration?

A

PEP carboxylase: fixes the carbon out of the atmosphere, and is not inhibited by high O2

C4 photosynthesis: carbon fixation and the Calvin Cycle occur in different types of cells

CAM photosynthesis: carbon fixation and the Calvin Cycle occur in the same cells at different times

BIOL 107 (11 decks)

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