5.2 Energy for biological processes Flashcards
why organisms require energy
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
how much energy released in hydrolysis of ATP
30.5 kJ mol^-1
hydrolysis of ATP
requires ATPases and water
ATP -> ADP + Pi
releases energy for cell to use
condensation of ATP
ADP + Pi -> ATP + H2O
requires energy generated from respiration
anabolic reaction definition
large molecules synthesised from smaller molecules
catabolic reaction definition
hydrolysis of larger molecules into smaller ones
ATP role
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
ATP structure
phosphorylated nucleotide
made up of adenine, ribose sugar, 3 phosphate groups
phosphodiester bond between ribose and phosphate group
phosphoanhydride bond between phosphate groups
why ATP is universal energy source
occurs in all living cells
source of energy that can be used in small amounts
energy definition
ability to do work
importance of hydrolysis of ATP and respiration releasing heat
keeps living organisms “warm”
helps maintain internal temperature for enzyme-controlled reactions
glycolysis summary
first stage in respiration
pyruvate is produced from glucose
occurs in cytoplasm
glycolysis stages
phosphorylation (1) (energy investment)
lysis
phosphorylation (2)
dehydrogenation and formation of ATP (energy generation)
phosphorylation (1)
energy investment phase
2 phosphate groups (released from 2 ATP molecules required)
attach to glucose molecule
forms hexose biphosphate
lysis in respiration
destabilises molecule
causes hexose biphosphate to split into x2 triose phosphate molecules
phosphorylation (2)
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
dehydrogenation and formation of ATP in glycolysis
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
substrate level phosphorylation definition
formation of ATP without involvement of electron transport chain
alternate name for pyruvate
pyruvic acid
NAD stands for
nicotinamide adenine dinucleotide
NADH means
reduced NAD
what happens to pyruvate after glycolysis
actively transported into mitochondria for link reaction (aerobic conditions)
converted into lactate (anaerobic in animals)
converted into ethanol (anaerobic in plants and prokaryotes)
function of matrix in mitochondria
contains enzymes for Krebs cycle, link reaction, mitochondrial DNA
function of intermembrane space in mitochondria
proteins pumped in here by electron transport chain
conc. builds up quickly as space is small
function of outer mitochondrial membrane in mitochondria
separates contents of mitochondrion from rest of cell (compartmentalisation)
maintains ideal conditions for aerobic respiration
structures in inner mitochondrial membrane in mitochondria
contains electron transport chains and ATP synthase
function of cristae in mitochondria
projections of inner membrane increases surface area
faster rate of oxidative phosphorylation
why oxidative decarboxylation is called the link reaction
links anaerobic glycolysis to aerobic steps of respiration in mitochondria
link reaction steps
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
acetyl CoA in full
acetylcoenzyme A
link reaction as an equation
2pyruvate + 2NAD + 2CoA -> 2CO2 + 2NADH + 2 acetyl CoA
coenzyme A function
accepts acetyl group
forms acetyl CoA
carries acetyl group to Krebs cycle
Krebs cycle facts
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
Krebs cycle method
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
number of carbon on acetyl
2 carbons
number of carbons on oxaloacetate
4 carbons
number of carbons on citrate
6 carbons
how oxaloacetate is regenerated
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
chemiosmosis definition
flow of protons down their concentration gradient across a membrane through a channel associated with ATP synthase
electron transport chain structure
chain of carrier transfer proteins containing Fe3+ ions
electron transport chain mechanism
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
how proton gradient is generated
protons accumulate in intermembrane space
proton gradient forms across membrane, generates chemiosmotic potential
what is chemiosmotic potential
also known as proton motive force (pmf)
source of potential energy
chemiosmosis mechanism
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
purpose of oxygen in oxidative phosphorylation
combined with electrons coming off electron transport chain and with protons diffusing down ATP synthase channel
forms water
4H+ + 4e- + O2 -> 2H2O
how many protons pumped by complex I
4
how many protons pumped by complex II
none
how many protons pumped by complex III
4
how many protons pumped by complex IV
2
products of glycolysis
2 pyruvate
4 ATP (net = 2)
2 NADH
products of link reaction
2 acetyl CoA
2 CO2
2 NADH
produce of Krebs cycle (per molecule of glucose)
4 CO2
6 NADH
2 ATP
2 FADH2
ATP synthase enzyme
large and protrude from inner membrane
associated with proton channel (basepiece)
headpiece (rotates) attached to base piece by stalk/axle
number of ATP molecules produced by NADH and FADH2
25 ATP molecules per 10 NADH molecules
3 ATP molecules for 2 FADH2 molecules
maximum theoretical yield per molecule of glucose during aerobic respiration
glycolysis = 2 link reaction = 0 Krebs cycle = 2 oxidative phosphorylation = 28 total = 32
why theoretical yield is rarely achieved in respiration
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
why aerobic respiration cannot occur without oxygen
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
why anaerobic respiration is required
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
ethanol/alcoholic fermentation pathway
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
enzymes and coenzymes in ethanol fermentation
pyruvate decarboxylase with thiamine diphosphate
ethanol dehydrogenase
lactate fermentation pathway
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
fate of lactate
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
why lactate is carried away from muscle tissue
pH would be lowered in muscle tissue
inhibit action of many enzymes involved in glycolysis and muscle contraction
ATP yield of anaerobic respiration
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
how to use haemocytometre
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
haemocytometre structure
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
substrate used in respiration by brain and red blood cells
glucose only
how carbohydrates are stored in organisms
animals, some bacteria = glycogen
plants = starch
all respiratory substrates
carbohydrates
lipids
proteins
chief respiratory substance
glucose monosaccharides (e.g. fructose, galactose) converted to glucose by isomerase enzymes disaccharides hydrolysed to monosaccharides for respiration
how lipids are used for energy
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
beta oxidation method
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
how proteins used as substrate in aerobic respiration
keto acid produced from deamination
enters respiratory pathway as pyruvate, acetyl CoA or oxaloacetic acid
respiratory substrates during starvation or prolonged exercise
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
mean energy value of lipids
39.4 kJ g^-1
mean energy value of proteins
17.0 kJ g^-1
mean energy value of carbohydrates
15.8 kJ g^-1
how much energy is released by molecules in aerobic respiration
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
respiratory quotient formula
RQ = CO2 produced / O2 consumed
ratio so no units
RQ value meaning
RQ > 1 indicates some anaerobic respiration takes place
as more CO2 is produced than O2 consumed
factors affecting rate of respiration
temperature
substrate concentration
type of respiratory substrate
availability of oxygen
why photosynthesis came first
aerobic respiration requires oxygen
oxygen is by-product of photosynthesis
until photosynthesis evolved, no free oxygen in atmosphere
so photosynthesis had to come first
evolution of chloroplast
endosymbiotic theory photosynthetic bacteria acquired by eukaryotic cells by endocytosis to produce first algal/plant cells passed on to next generation
size and shape of chloroplast
varies
usually between 2-10 micrometers
usually disc-shaped
chloroplast structure
inner membrane folded into lamellae / thylakoids
thylakoids stack in piles (grana)
intergranal lamellae link different stacks of grana
grana contain up to 100+ thylakoids
grana function in photosynthesis
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
stroma function in photosynthesis
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
chloroplast features
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
membranes structure function in photosynthesis
made up of double membrane (envelope)
outer membrane highly permeable
inner membrane selectively permeable, has transport proteins embedded in it
photosynthetic pigments
absorbs certain wavelengths of light
reflects other wavelengths (colours we see)
arranged in photosystems in thylakoid membranes
chlorophyll 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
2 forms of chlorophyll a
P680 in photosystem 2 (6-8 = -2)
P700 in photosystem 1
accessory pigments
chlorophyll b
carotenoids
xanthophylls
chlorophyll b
absorbs light at wavelengths between 400-500 and 640nm
appears yellow-green
carotenoids
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
xanthophylls
absorbs blue and green light (375-550nm)
reflects yellow light
photosystem
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
products of photosynthesis
nucleic acids
amino acids
lipids
carbohydrates
ATP in light-dependent reaction
ADP + Pi + energy -> ATP
light is used as energy source to phosphorylate ADP (photophosphorylation)
ATP in light-independent reaction
ATP is hydrolysed
ATP -[water]-> ADP + Pi + energy
NADP name
nicotinamide adenine dinucleotide phosphate
NADP
coenzyme
accepts electrons and protons to becomes reduced
store of energy as “reducing power” which drives bio synthetic reactions in LIS
reduced NADP
NADPH2
NADPH
reduced NADP
NADPH + H+
pigment arrangement in photosystems
funnel-shaped light-harvesting cluster held in place in thylakoid membrane by proteins
action spectrum definition
graph that shows wavelengths of light that are actually used in photosynthesis
absorbance spectra and action spectra
closely matched together
suggests wavelengths of light used in photosynthesis
photolysis definition and equation
splitting of water in the presence of light
2H2O -> 4H^+ + 4e^- + O2
role of water during photosynthesis
source of protons used in photophosphorylation
donates electrons to chlorophyll to replace those lost when light strikes chlorophyll
source of oxygen (for aerobic respiration)
non-cyclic photophosphorylation
involves PSI and PSII
produces ATP, O2 and NADPH2
cyclic photophosphorylation
involves only PSI produces ATP (less than non-cyclic)
non-cyclic photophosphorylation method
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
non-cyclic photophosphorylation alternate name
Z-scheme
electron carrier for electrons excited from PSI
ferredoxin
protein-iron-sulfur complex
how NADP is reduced in non-cyclic photophosphorylation
protons that pass down ATP synthase enzymes are accepted, along with electrons, by NADP
catalysed by NADP reductase
cyclic photophosphorylation method
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
cyclic photophosphorylation example
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
where photolysis occurs
in photosystem II
importance of carbon dioxide with life
source of carbon for production of all organic molecules in all carbon-based life forms
Calvin cycle method
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
factors affecting rate of photosynthesis
light intensity
temperature
carbon dioxide concentration
how light intensity and CO2 concentration affects rate of photosynthesis (graph)
increases then plateaus
effect of low light intensity on Calvin cycle
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
effects of low [CO2] on Calvin cycle
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
effect of temperature on Calvin cycle
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
temperature at which photorespiration occurs
30°C
why lactate fermentation pathway is reversible
pyruvate is converted to lactic acid
with no other products formed (that can be lost)
lactate dehydrogenase is able to reverse the reaction
why ethanol fermentation pathway is irreversible
pyruvate is converted into ethanol and CO2
irreversible as CO2 is lost
decarboxylase enzymes unable to reverse the reaction
