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Winter 2023 - Biology > Cycle 4: Primary Metabolism > Flashcards

Cycle 4: Primary Metabolism Flashcards

1
Q

What is carbon fixation?

A

turning CO2 gas into sugar (carbon)

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2
Q

Why is there no chlorophyll in hot, tropical waters?

A

less nutrients in warm water at high temperature (ex. no iron) – unlike tap

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3
Q

what type of free energy/entropy reaction is photosynthesis?

A

high entropy to low entropy so low free energy to high free energy = endergonic (+∆G) and energy input

CO2 oxidized with light creating reduced glucose (free energy increases)

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4
Q

what is a redox reaction?

A

oxidation-reduction reaction

one reactant must reduce and one reactants must oxidize

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5
Q

what is bacteriorhodopsin?

A

light driven proton pump found o inner membrane of archaea

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6
Q

How does bacteriorhodopsin work?

A
  1. sunlight enters bacteriorhodopsin
  2. protons pumped across membrane outside of cell and into plasma membrane
  3. ATP synthase takes ADP and phosphate group and makes ATP and pumps H+ back into cytoplasm
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7
Q

how is channelrhodopsin related to bacteriorhodopsin?

A

homologous – common ancestor

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8
Q

Why is bacteriorhodopsin not photosynthesis?

A

no CO2 reduction, it is only a light dependent reaction

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9
Q

how is bacteriorhodopsin like an autotroph and heterotroph?

A

autotroph because light energy use
heterotroph because still brings in carbon which reduces to ratty acid

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10
Q

What is photosynthesis?

A

conversion of light energy to chemical energy (sugar/organic molecules = carbohydrates)

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11
Q

What are autotrophs?

A

organisms that produce their own food

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12
Q

What are chemoautotrophs?

A

uses H2S and Fe2+ as energy source but is rare, which is why oxygenic photosynthesis is better because water is abundant

–> these are some bacteria and archaean

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13
Q

When did photosynthesis evolve?

A

2.5 bya in bacteria (which don’t have chloroplasts)
–> this included photosystems and Calvin cycle

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14
Q

is chloroplasts needed for photosynthesis?

A

some bacteria are photosynthetic but don’t have chloroplasts so no!

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15
Q

Where does the Calvin cycle occur?

A

stroma of chloroplast

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16
Q

Where does the light reactions/photosystems occur?

A

thylakoid membrane

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17
Q

What are the two phases of photosynthesis?

A

light reactions and Calvin cycle

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18
Q

What do the light reactions do?

A

input light energy captured by pigment molecules on photosystem

takes in ADP + Pi and NADP+ from Calvin cycle

synthesize NADPH and ATP

H2O oxidized to release O2 and use electrons to reduce NADP+ to NADPH

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19
Q

What does the Calvin cycle do?

A

input CO2 and NADPH + ATP from light reactions

produce glucose

this is carbon fixation

produces NADP+ and ADP + Pi

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20
Q

How does a photosystem work in light reactions?

A
  1. light energy absorbed by antenna complex which has pigment molecules
  2. photon migrates through pigment molecuels
  3. reaction centre chlorophyll is oxidized and removed electron is excited and goes to primary electron acceptor
  4. high energy electron moves through transport chain and reduces NADP+ to NADPH
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21
Q

What is the difference between PSI and PSII?

A

PSI = P700 because PEA optimally absorbs light at 700nm

PSII = P680 because PEA optimally absorbs light at 680nm

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22
Q

What does the photon of light do for redox potential?

A

increases redox potential = negative redox potential = easy to oxidize/take electron away

23
Q

What are P680, P680+, and P680*?

A

P680 - group state PEA

photon absorbed

P680* - excited PEA

electron removed

P680+ - oxidized PEA

electron continues in ETC

electron from oxidized water added

P680+ reduces to P680

24
Q

What is the nature of p680+?

A

highly reactive - why we need water to provide electron

25
Q

What is the result of p680+ taking D1 protein’s electron?

A

D1 protein is bound to P680 PEA in complex
PSII is damaged frequently because p680 is highly reactive and takes electron from anywhere

26
Q

How is damaged PSII fixed?

A

high light exposure = damaged D1 removed, PSII is inactive, new D1 inserted through chloroplast protein synthesis

active PSII

**unless lincomysin blocks chloroplast translation

27
Q

how is the Calvin cycle, a cycle?

A

part of reaction regenerates substrate (RuBP)

28
Q

What is ATP’s purpose in the Calvin cycle?

A

provides phosphate and drives endergonic non-spontaneous reactions because carbon has more energy than CO2

29
Q

What are the steps of the Calvin cycle?

A
  1. fixation: RuBP is fixed with CO2 creating phosphoglycerate though enzyme Rubisco
  2. reduction: Phosphoglycerate (PGA) with ATP
    - PGA reduced by NADPH creating G3P which makes glucose
  3. regeneration: ATP and other G3P makes RuBP
30
Q

Why is respiration exergonic?

A

high free energy to low free energy (spontaneous, no energy input) low entropy to high entropy

31
Q

What is the role of mitochondria in Chlamy cells?

A

pyruvate oxidation, citric acid cycle

32
Q

What is the difference between catabolism and anabolic?

A

catabolic: taking energy rich molecules and turning them to energy poor molecules (ex. respiration)

use catabolic to make ATP

anabolic: precursor molecules to cell macromolecules

**intermediate steps don’t need to be the same

33
Q

How does catabolic vs anabolic relate to ∆G?

A

catabolism - exergonic (ADP to ATP)

anabolism - endergonic (ATP to ADP)

34
Q

What are the ratios of ATP and NADH?

A

ADP to ATP (issue with ATP to ADP means ADP more than ATP)

and

NAD+ to NADH

35
Q

What is energy coupling?

A

using ATP to drive a non-spontaneous reaction

**endergonic reactions don’t actually occur in the cell, adding ATP makes the process exergonic

36
Q

Why is it important that FADH2 comes after complex I?

A

easier to reduce that complex 1 (easier to add electron)

37
Q

Where does oxidative phosphorylation occur?

A

inner mitochondrial membrane

38
Q

What are the two sections of oxidative phosphorylation?

A

electron transport:
1. NADH oxidized and e- passes through complexes on inner mito membrane
2. FADH2 oxidized and e- passes through complexes
3. electron used to reduce H and O2 back to H2O
4. H+ pumped across membrane through out with complexes by H2O oxidation

chemiosmosis:
1. ADP + Pi turns to ATP when H+ is pumped into mitochondrial matrix

39
Q

Why chemiosmosis is built of proton gradients….(why not other molecules)?

A

creation of electrochemical gradient of abundant molecule

40
Q

Importance of redox-active cofactors in electron transport?

A

requirement of Fe iron

41
Q

why do electrons move spontaneously down the chain?

A

redox potential increase –> more and more easy to add electron in cofactor because each cofactor has greater affinity for electron that the one before until oxygen – terminal e- acceptor

spontaneous! exergonic high to low free energy

42
Q

What is uncoupling?

A

uncoupler between electron transport chain and ATP synthase in OxPhos which takes H+ before it reaches ATP synthase and given route to pump proton back to mitochondrial matrix

– free energy is not conserved bc no ATP being made

43
Q

Why chemical uncouplers (dinitrophenol) are toxic…..how does it alter metabolism?

A

decreases ATP production bc ATP synthase can’t function wo pumping H+

44
Q

How metabolism shifts in response to low oxygen?

A

high oxygen: aerobic respiration: pyruvate from glycolysis enters citric acid cycle and OxPhos

low oxygen: fermentation: pyruvate stays in cytosol: lactate/ethanol

45
Q

How is metabolism controlled when low oxygen?

A

pyruvate dehydrogenase complex: gatekeeping inside mitochondrial membrane that tells pyruvate if it can enter the mito or not

gene that gets induced to make PYRUVATE DEHYDROGENASE KINASE inhibits PYRUVATE DEHYDROGENASE COMPLEX so pyruvate can’t enter mito

46
Q

How cancer cells remodel normal respiration…role of glucose transporter, hexokinase, and PK

A

upregulaton of glucose transport
up regulation of hexokinase (enzymes of glycolysis)
pyruvate dehydrogenase kinase ALWAYS inhibits pyruvate complex not matter [O2]

47
Q

What is the Warburg Effect?

A

cancer cells, even under aerobic conditions (high O2 conc) rely only on glycolysis for ATP not OxPhos

48
Q

How is cancer detected based on metabolism using radioactive forms of glucose?

A

see cancer cells rapid uptake of glucose (to transport)

49
Q

What are the three stages of cellular respiration?

A

glycolysis

pyruvate oxidation

oxidative phosphorylation

50
Q

Where does glycolysis occur? What is input? What is output?

A

occurs in cytosol

input glucose and NAD+

output: G3P + ATP makes pyruvate

NAD+ reduced to NADH (e- taken from G3P)

51
Q

What is substrate level phosphorylation?

A

transfer of phosphate group from a high energy substate molecule to ADP to make ATP

52
Q

Where does the citric acid cycle occur? What are the inputs? Outputs?

A

mitochondrial matrix

pyruvate enters through transport protein from cytosol

acetyl-CoA group oxidized to CO2

Input: NAD+, CoA, ADP, and FAD

Output: CO2, NADH, ATP, and FADH2

53
Q

What are the relative free energies of glucose, pyruvate, and CO2?

A

glucose > pyruvate > CO2

Winter 2023 - Biology (11 decks)

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