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A-Level Biology > 5.2 Energy for biological processes > Flashcards

5.2 Energy for biological processes Flashcards

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1
Q

why organisms require energy

A

active transport (e.g. endocytosis, sodium/potassium pump)
synthesis of large molecules e.g. protein
movement (brought about by cilia, flagella)
DNA replication
cell division
activation of molecules

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2
Q

how much energy released in hydrolysis of ATP

A

30.5 kJ mol^-1

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3
Q

hydrolysis of ATP

A

requires ATPases and water
ATP -> ADP + Pi
releases energy for cell to use

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4
Q

condensation of ATP

A

ADP + Pi -> ATP + H2O

requires energy generated from respiration

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5
Q

anabolic reaction definition

A

large molecules synthesised from smaller molecules

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6
Q

catabolic reaction definition

A

hydrolysis of larger molecules into smaller ones

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7
Q

ATP role

A

standard intermediary between energy-releasing and energy-consuming metabolic reactions
main storage of energy as releases energy in small amounts
hydrolysis is immediate and one step reaction so is quick

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8
Q

ATP structure

A

phosphorylated nucleotide
made up of adenine, ribose sugar, 3 phosphate groups
phosphodiester bond between ribose and phosphate group
phosphoanhydride bond between phosphate groups

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9
Q

why ATP is universal energy source

A

occurs in all living cells

source of energy that can be used in small amounts

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10
Q

energy definition

A

ability to do work

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11
Q

importance of hydrolysis of ATP and respiration releasing heat

A

keeps living organisms “warm”

helps maintain internal temperature for enzyme-controlled reactions

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12
Q

glycolysis summary

A

first stage in respiration
pyruvate is produced from glucose
occurs in cytoplasm

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13
Q

glycolysis stages

A

phosphorylation (1) (energy investment)
lysis
phosphorylation (2)
dehydrogenation and formation of ATP (energy generation)

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14
Q

phosphorylation (1)

A

energy investment phase
2 phosphate groups (released from 2 ATP molecules required)
attach to glucose molecule
forms hexose biphosphate

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15
Q

lysis in respiration

A

destabilises molecule

causes hexose biphosphate to split into x2 triose phosphate molecules

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16
Q

phosphorylation (2)

A

another phosphate group added to each triose phosphate
forms 2 triose biphosphate molecules
doesn’t require ATP as
phosphate groups come from free inorganic phosphate ions in cytoplasm

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17
Q

dehydrogenation and formation of ATP in glycolysis

A

two triose biphosphate molecules oxidised by dehydrogenase enzymes removing 1 hydrogen ATOM in each molecule(dehydrogenated)
forms 2 pyruvate molecules
NAD coenzymes accept removed hydrogen atoms (reduced), forms 2 NADH
4 ATP molecules formed from phosphate groups from triose biphosphate molecules

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18
Q

substrate level phosphorylation definition

A

formation of ATP without involvement of electron transport chain

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19
Q

alternate name for pyruvate

A

pyruvic acid

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20
Q

NAD stands for

A

nicotinamide adenine dinucleotide

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21
Q

NADH means

A

reduced NAD

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22
Q

what happens to pyruvate after glycolysis

A

actively transported into mitochondria for link reaction (aerobic conditions)
converted into lactate (anaerobic in animals)
converted into ethanol (anaerobic in plants and prokaryotes)

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23
Q

function of matrix in mitochondria

A

contains enzymes for Krebs cycle, link reaction, mitochondrial DNA

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24
Q

function of intermembrane space in mitochondria

A

proteins pumped in here by electron transport chain

conc. builds up quickly as space is small

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25
Q

function of outer mitochondrial membrane in mitochondria

A

separates contents of mitochondrion from rest of cell (compartmentalisation)
maintains ideal conditions for aerobic respiration

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26
Q

structures in inner mitochondrial membrane in mitochondria

A

contains electron transport chains and ATP synthase

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27
Q

function of cristae in mitochondria

A

projections of inner membrane increases surface area

faster rate of oxidative phosphorylation

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28
Q

why oxidative decarboxylation is called the link reaction

A

links anaerobic glycolysis to aerobic steps of respiration in mitochondria

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29
Q

link reaction steps

A

pyruvate enters mitochondrial matrix (actively transported by carrier protein pyruvate proton symplast)
pyruvate is decarboxylated (CO2 removed) and dehydrogenated (hydrogen atom removed)
NAD accepts hydrogen atoms (reduced to form NADH)
forms acetate (has acetyl group C=O)
acetyl groups bound by coenzyme A to form acetyl CoA

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30
Q

acetyl CoA in full

A

acetylcoenzyme A

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31
Q

link reaction as an equation

A

2pyruvate + 2NAD + 2CoA -> 2CO2 + 2NADH + 2 acetyl CoA

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32
Q

coenzyme A function

A

accepts acetyl group
forms acetyl CoA
carries acetyl group to Krebs cycle

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33
Q

Krebs cycle facts

A 
occurs in mitochondria
occurs twice per molecule of glucose
forms 4 CO2 molecules (per molecule of glucose)
forms 2 ATP 
forms 2 FADH2
forms 6 NADH
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34
Q

Krebs cycle method

A

acetyl group (delivered by acetyl CoA) combined with oxaloacetate to form citrate
citrate is decarboxylated and dehydrogenated, forms one NADH, one CO2 and 5 carbon compound
5 carbon compound decarboxylated and dehydrogenated further, eventually regenerating oxaloacetate

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35
Q

number of carbon on acetyl

A

2 carbons

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36
Q

number of carbons on oxaloacetate

A

4 carbons

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37
Q

number of carbons on citrate

A

6 carbons

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38
Q

how oxaloacetate is regenerated

A

5 carbon compound decarboxylated and dehydrogenated, forming one NADH, one CO2 and 4 carbon compound
4 carbon compound temporarily combines and released by CoA
substrate level phosphorylation occurs, 1 ATP made
4 carbon compound dehydrogenated, forming 1 FADH2 and different 4 carbon compound
atoms rearranged in 4 carbon molecule, catalysed by isomerase enzyme
dehydrogenated again (forms NADH), regenerates oxaloacetate

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39
Q

chemiosmosis definition

A

flow of protons down their concentration gradient across a membrane through a channel associated with ATP synthase

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40
Q

electron transport chain structure

A

chain of carrier transfer proteins containing Fe3+ ions

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41
Q

electron transport chain mechanism

A

NADH and FADH2 binds to complex I and reoxidised in matrix (releases hydrogen atoms as protons and electrons) to electron transport chain
hydrogen ions/protons enter solution in matrix
electrons pass along chain of electron carriers (complex 1 to 2 to 3 to 4) (Fe ions reduced (into 2+) and reoxidised (back to 3+))
energy created by electrons passing along chain used to pump protons across intermembrane space

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42
Q

how proton gradient is generated

A

protons accumulate in intermembrane space

proton gradient forms across membrane, generates chemiosmotic potential

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43
Q

what is chemiosmotic potential

A

also known as proton motive force (pmf)

source of potential energy

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44
Q

chemiosmosis mechanism

A

protons cannot diffuse through lipid bilayer (impermeable to protons as they are charged)
protons diffuse through proton channel associated with ATP synthase enzymes (in inner membrane) down proton concentration gradient
flow of protons cause conformational change in ATP synthase
causes ADP + Pi to combine to form ATP

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45
Q

purpose of oxygen in oxidative phosphorylation

A

combined with electrons coming off electron transport chain and with protons diffusing down ATP synthase channel
forms water
4H+ + 4e- + O2 -> 2H2O

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46
Q

how many protons pumped by complex I

A

4

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47
Q

how many protons pumped by complex II

A

none

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48
Q

how many protons pumped by complex III

A

4

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49
Q

how many protons pumped by complex IV

A

2

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50
Q

products of glycolysis

A

2 pyruvate
4 ATP (net = 2)
2 NADH

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51
Q

products of link reaction

A

2 acetyl CoA
2 CO2
2 NADH

52
Q

produce of Krebs cycle (per molecule of glucose)

A

4 CO2
6 NADH
2 ATP
2 FADH2

53
Q

ATP synthase enzyme

A

large and protrude from inner membrane
associated with proton channel (basepiece)
headpiece (rotates) attached to base piece by stalk/axle

54
Q

number of ATP molecules produced by NADH and FADH2

A

25 ATP molecules per 10 NADH molecules

3 ATP molecules for 2 FADH2 molecules

55
Q

maximum theoretical yield per molecule of glucose during aerobic respiration

A 
glycolysis = 2
link reaction = 0
Krebs cycle = 2
oxidative phosphorylation = 28
total = 32
56
Q

why theoretical yield is rarely achieved in respiration

A

some ATP used to actively transport pyruvate into mitochondria
some ATP used in shuttle system to transport some NADH (made during glycolysis) into mitochondria
some protons may leak out through outer mitochondrial membrane

57
Q

why aerobic respiration cannot occur without oxygen

A

oxygen cannot act as final electron acceptor at end of oxidative phosphorylation
protons diffusing through channels associated with ATP synthase cannot combine with electrons and oxygen to form water
proton gradient reduces as conc. of protons in matrix increases
oxidative phosphorylation ceases
NADH and FADH2 cannot be reoxidised
Krebs cycle and link reaction stop

58
Q

why anaerobic respiration is required

A

glycolysis can still take place
NADH generated needs to be reoxidised for glycolysis to continue
cannot be reduced with oxidative phosphorylation due to absence of oxygen

59
Q

ethanol/alcoholic fermentation pathway

A

occurs in fungi and plants
one molecule of pyruvate decarboxylated into ethanal (catalysed by pyruvate decarboxylase with coenzyme thiamine diphosphate)
ethanal accepts 2 hydrogen atoms from NADH (reduced to ethanol, catalysed by ethanol dehydrogenase)
NADH is reoxidised in NAD in this process, allows glycosis to continue

60
Q

enzymes and coenzymes in ethanol fermentation

A

pyruvate decarboxylase with thiamine diphosphate

ethanol dehydrogenase

61
Q

lactate fermentation pathway

A 
occurs in mammals
pyruvate accepts 2 hydrogen atoms from NADH (catalysed by lactate dehydrogenase)
pyruvate reduced to lactate
NADH reoxidised to NAD
glycolysis can continue
62
Q

fate of lactate

A

lactate in muscle tissue carried away to liver via blood
when there is more oxygen, it may be:
converted to pyruvate
recycled to glucose and glycogen

63
Q

why lactate is carried away from muscle tissue

A

pH would be lowered in muscle tissue

inhibit action of many enzymes involved in glycolysis and muscle contraction

64
Q

ATP yield of anaerobic respiration

A

fermentation doesn’t produce ATP
allows glycolysis to continue so net gain of 2 ATP per glucose molecule
glucose only partly broken down so many more molecules can undergo glycolysis
yield of ATP via anaerobic respiration

65
Q

how to use haemocytometre

A

breathe onto underside of coverslip to moisten it
slide coverslip horizontally onto slide, carefully press down with index while pushing with thumbs
when coverslip correctly in position, 6 rainbow patterns visible
depth of central chamber = 0.1 mm now
place pipette tip at entrance of groove and allow liquid to fill chamber
leave for 5 minutes
place haemocytometre slide on microscope stage with one of grids over stage aperture
Focus with x40, then x100
central portion of grid is FOV
count cells in central and 4 corner squares

66
Q

haemocytometre structure

A

special thick slide with sloped edges and grooves

if grooves form H-shape, two etched grids present so 2 counts can be made from same sample

67
Q

substrate used in respiration by brain and red blood cells

A

glucose only

68
Q

how carbohydrates are stored in organisms

A

animals, some bacteria = glycogen

plants = starch

69
Q

all respiratory substrates

A

carbohydrates
lipids
proteins

70
Q

chief respiratory substance

A 
glucose
monosaccharides (e.g. fructose, galactose) converted to glucose by isomerase enzymes
disaccharides hydrolysed to monosaccharides for respiration
71
Q

how lipids are used for energy

A

triglycerides hydrolysed by lipase to glycerol and fatty acids
glycerol converted to triose phosphate (joins in the middle of glycolysis)
fatty acids undergo beta oxidation

72
Q

beta oxidation method

A

fatty acids combine with CoA (requires ATP)
fatty acid-CoA enter mitochondrial matrix from cytoplasm
broken down into acetyl CoA (each producing 1NADH and 1FADH)
CoA released and acetyl group enters Krebs cycle

73
Q

how proteins used as substrate in aerobic respiration

A

keto acid produced from deamination

enters respiratory pathway as pyruvate, acetyl CoA or oxaloacetic acid

74
Q

respiratory substrates during starvation or prolonged exercise

A

insufficient glucose or lipid available
protein from muscle hydrolysed to amino acids (lose muscle mass) for aerobic respiration
can be converted to pyruvate or acetate and enter Krebs cycle

75
Q

mean energy value of lipids

A

39.4 kJ g^-1

76
Q

mean energy value of proteins

A

17.0 kJ g^-1

77
Q

mean energy value of carbohydrates

A

15.8 kJ g^-1

78
Q

how much energy is released by molecules in aerobic respiration

A

more hydrogen atoms in a molecule proportionally, more NADH+FADH, more protons donated to oxidative phosphorylation, more ATP produced
also more oxygen needed for more hydrogen atoms

79
Q

respiratory quotient formula

A

RQ = CO2 produced / O2 consumed

ratio so no units

80
Q

RQ value meaning

A

RQ > 1 indicates some anaerobic respiration takes place

as more CO2 is produced than O2 consumed

81
Q

factors affecting rate of respiration

A

temperature
substrate concentration
type of respiratory substrate
availability of oxygen

82
Q

why photosynthesis came first

A

aerobic respiration requires oxygen
oxygen is by-product of photosynthesis
until photosynthesis evolved, no free oxygen in atmosphere
so photosynthesis had to come first

83
Q

evolution of chloroplast

A 
endosymbiotic theory 
photosynthetic bacteria acquired by eukaryotic cells
by endocytosis 
to produce first algal/plant cells
passed on to next generation
84
Q

size and shape of chloroplast

A

varies
usually between 2-10 micrometers
usually disc-shaped

85
Q

chloroplast structure

A

inner membrane folded into lamellae / thylakoids
thylakoids stack in piles (grana)
intergranal lamellae link different stacks of grana
grana contain up to 100+ thylakoids

86
Q

grana function in photosynthesis

A

grana where first stage of photosynthesis takes place (light-dependent stage)

highly-folded so creates huge surface area for:
distribution of photosystems (contains photosynthetic pigments to trap sunlight)
electron carriers + ATP synthase enzymes to convert light energy into ATP

proteins embedded in thylakoid membrane hold photosystems in place

87
Q

stroma function in photosynthesis

A

fluid-filled matrix
contains enzymes needed for second stage of photosynthesis (light-independent stage)
contains starch grains (biggest structure in chloroplast), oil droplets, ribosomes (70S), a loop of DNA

88
Q

chloroplast features

A

inner membrane with transport proteins: controls molecules travelling between cell’s cytoplasm and stroma
many grana (with up to 100+ thylakoids): increases SA for more photosystems pigments, electron carriers, ATP synthase enzyme needed in light-dependent stage
photosynthetic pigments: arranged in photosystems, allows max. absorption of light
proteins embedded in grana: hold photosystems in place
fluid-filled stroma: contains enzymes needed for light-independent stage
grana surrounded by stroma: products made in LDS in grana can pass into stroma to be used in LIS
chloroplast DNA and ribosomes: can make some proteins needed for photosynthesis

89
Q

membranes structure function in photosynthesis

A

made up of double membrane (envelope)
outer membrane highly permeable
inner membrane selectively permeable, has transport proteins embedded in it

90
Q

photosynthetic pigments

A

absorbs certain wavelengths of light
reflects other wavelengths (colours we see)
arranged in photosystems in thylakoid membranes

91
Q

chlorophyll a

A

in “primary pigment reaction centre”
2 forms (P680 in photosystem 2, P700 in photosystem 1)
appears blue-green
absorbs red light (and some blue at 440nm)
contains Mg atom, when light hits it, pair of electrons get excited

92
Q

2 forms of chlorophyll a

A

P680 in photosystem 2 (6-8 = -2)

P700 in photosystem 1

93
Q

accessory pigments

A

chlorophyll b
carotenoids
xanthophylls

94
Q

chlorophyll b

A

absorbs light at wavelengths between 400-500 and 640nm

appears yellow-green

95
Q

carotenoids

A

absorb blue light of wavelengths 400-500nm
reflects yellow and orange light
they absorb light not normally absorbed by chlorophylls and pass energy on to chlorophyll a

96
Q

xanthophylls

A

absorbs blue and green light (375-550nm)

reflects yellow light

97
Q

photosystem

A

funnel-shaped light-harvesting cluster of photosynthetic pigments
accessory pigments absorb different wavelengths of light to maximise amount of sunlight utilised
accessory pigments funnel energy associated to different wavelengths to chlorophyll a

98
Q

products of photosynthesis

A

nucleic acids
amino acids
lipids
carbohydrates

99
Q

ATP in light-dependent reaction

A

ADP + Pi + energy -> ATP

light is used as energy source to phosphorylate ADP (photophosphorylation)

100
Q

ATP in light-independent reaction

A

ATP is hydrolysed

ATP -[water]-> ADP + Pi + energy

101
Q

NADP name

A

nicotinamide adenine dinucleotide phosphate

102
Q

NADP

A

coenzyme
accepts electrons and protons to becomes reduced
store of energy as “reducing power” which drives bio synthetic reactions in LIS

103
Q

reduced NADP

A

NADPH2
NADPH
reduced NADP
NADPH + H+

104
Q

pigment arrangement in photosystems

A

funnel-shaped light-harvesting cluster held in place in thylakoid membrane by proteins

105
Q

action spectrum definition

A

graph that shows wavelengths of light that are actually used in photosynthesis

106
Q

absorbance spectra and action spectra

A

closely matched together

suggests wavelengths of light used in photosynthesis

107
Q

photolysis definition and equation

A

splitting of water in the presence of light

2H2O -> 4H^+ + 4e^- + O2

108
Q

role of water during photosynthesis

A

source of protons used in photophosphorylation
donates electrons to chlorophyll to replace those lost when light strikes chlorophyll
source of oxygen (for aerobic respiration)

109
Q

non-cyclic photophosphorylation

A

involves PSI and PSII

produces ATP, O2 and NADPH2

110
Q

cyclic photophosphorylation

A 
involves only PSI
produces ATP (less than non-cyclic)
111
Q

non-cyclic photophosphorylation method

A

photon of light strikes PSII
light energy channeled to primary pigment reaction centre
excites pair of electrons inside chlorophyll
escapes chlorophyll molecule, captured by electron carrier (protein with iron at centre in thylakoid membrane)
electrons lost are replaced by electrons derived from photolysis
electrons passed along electron transport chain, releasing energy at each step
energy released is used to create ATP via chemiosmosis (same as in mitochondria)
eventually electrons are captrued by chlorophyll in PSI, replacing those lost from PSI
electrons energised from PSI captured by another electron carrier and passed along another electron transport chain, releasing more energy used to form more ATP
electrons and protons accepted by NADP in the stroma, which becomes reduced NADP

112
Q

non-cyclic photophosphorylation alternate name

A

Z-scheme

113
Q

electron carrier for electrons excited from PSI

A

ferredoxin

protein-iron-sulfur complex

114
Q

how NADP is reduced in non-cyclic photophosphorylation

A

protons that pass down ATP synthase enzymes are accepted, along with electrons, by NADP
catalysed by NADP reductase

115
Q

cyclic photophosphorylation method

A 
light strikes PSI
electron pair in chlorophyll becomes excited
escapes chlorophyll
passes through electron carrier system
small amount of ATP generated
electrons return back to PSI
116
Q

cyclic photophosphorylation example

A

guard cells only contain PSI
only produces ATP when actively transporting potassium ions into cell
lowers water potential so water follows by osmosis
causes guard cells to swell
open stoma

117
Q

where photolysis occurs

A

in photosystem II

118
Q

importance of carbon dioxide with life

A

source of carbon for production of all organic molecules in all carbon-based life forms

119
Q

Calvin cycle method

A

5-carbon (carbon dioxide acceptor) ribulose phosphate (RuBP) carboxylated by adding CO2
catalysed by RuBisCo, CO2 has been fixed
forms unstable 6-carbon intermediate, breaks down immediately
forms 2 molecules of 3-carbon compound glycerate-3-phosphate (GP)
2 x GP reduced by accepting hydrogen atoms from NADPH2, using 2 ATP
forms 2 x triose phosphate (TP)
2TP is converted to RuBP, requiring ATP
RuBP is regenerated and cycle repeats 6 more times

10 out of 12 total TP molecules used to regenerate RuBP
2 remaining TP molecules is product

120
Q

factors affecting rate of photosynthesis

A

light intensity
temperature
carbon dioxide concentration

121
Q

how light intensity and CO2 concentration affects rate of photosynthesis (graph)

A

increases then plateaus

122
Q

effect of low light intensity on Calvin cycle

A

less ATP and NADPH2 formed as light-dependent stage occurs slower
less GP is reduced to TP and reformed to RuBP
GP levels increase (GP accumulates)
TP and RuBP levels drop

123
Q

effects of low [CO2] on Calvin cycle

A

RuBP can accept less CO2 to be converted to GP
less GP and TP can be made
RuBP levels increase (RuBP accumulates)
GP and TP levels decrease

124
Q

effect of temperature on Calvin cycle

A

low to 30°C: rate increases with temperature if CO2, water, light not limiting
30°C: competition from photorespiration (O2 acts as competitive inhibitor of CO2 for Rubisco), reduces production of TP and other products
45°C: enzymes denatured, further reducing TP concentrations

125
Q

temperature at which photorespiration occurs

A

30°C

126
Q

why lactate fermentation pathway is reversible

A

pyruvate is converted to lactic acid
with no other products formed (that can be lost)
lactate dehydrogenase is able to reverse the reaction

127
Q

why ethanol fermentation pathway is irreversible

A

pyruvate is converted into ethanol and CO2
irreversible as CO2 is lost
decarboxylase enzymes unable to reverse the reaction

A-Level Biology (24 decks)

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