Metabolic processes Flashcards
First law of thermodynamics
Eng cannot be created or destroyed, only transfered
Examples of energy transformation how
Climbing a slide & sliding down- Converting kinetic energy to potential energy back to kinetic energy
Relate first law of thermodynamics to cell resp and photosynth
All of our energy comes from the food we it,
or from the sun in plants
its an examples of energy transformation
open vs closed system relate to bio
open - when eng can be lost to surroundings (oven)
closed - when eng stays in system
biological orgs are open systems
chemical potential eng
chem pot eng - the amount of chem eng that could be released
the greater the energy the more unstable to bond is
the more stable it is the more eng it take to break
exergonic vs endergonic processes
ex, spontaneity
exergonic - release eng,
change in eng - neg
spontaneous
becomes more stable
ex. cell resp
uses hydrolysis
endergoinic - absorbs eng
increase in eng
not spontaneous
less stable
ex. photosynth
uses synthesis
What is energy transformation by coupling
Exergonic reactions drive endergonic reaction
the energy outputted in exergonic is used in endergonic reactions
coupling and atp hydrolysis
atp hydrolysis when phosphate breaks off
phosphate from atp bonds to another molecule, makes it more reactive.
high eng bond on ATP and why it is weak
High eng bond on third phosphate
each phosphate has negative charge, constantly pushing away from one another
makes region unstable, easy to break
What are the 3 types of cellular work
Transport
ex. pumping things across barrier
Mech
ex. contraction of muscle cells
Chem
ex. synthesis of polymers from monomers
substrate lvl phosphorylation vs oxidative phosphorylation
sub lvl phos - direct way
phosphate is transferred directly from “food” to ADP -> ATP
uses Enzyme, found in kreb, glycolysis (Pep + ADP - > pyruvate +
ATP)
oxidative phos - indirect method
uses a redox reaction to transfer electrons to NADH or FADH2
before using it in making ATP (etc)
Principle of Redox reactions (defs)
Oxidation - loses electrons, is oxidized, is reducing agent
Reducing - gains electrons, is reduced, is oxidizing agent
When the reaction is reversed the one that gains and loses swap
can be seen as loss or gain of H
What is NAD+
oxidizing agent in metabolism
often gets reduced to make NADH
a coenzyme
What is NADH
reducing agent in metabolism
can get oxidized to make NAD+
stores energy that can make ATP
worth 3 ATP
How can cell resp just be described as oxidation of glucose
what comes out of cell resp is H2O, CO2 and Eng
the glucose gets oxidized into CO2, it loses energy
the O2 gets reduced into H2O
C6H12O6+ 6O2 -> 6CO2+ 6H2O + Energy
Second law of thermodynamics
Energy transformation make the universe more disordered
entropy increases overtiem
it takes energy to have order
Heat and its relation to the second law of thermodynamics
organisms make give off heat
most random state of energy
increased entropy of the universe is caused mainly by heat
equilibrium meaning in chem reaction and life
means its at max stability
delta G = 0, equilibrium convert easily
reaction in closes system reach equilibrium and then do no work
if delta G = 0 in orgs they are dead (living things must not be equilibrium, disequilibrium causes work)
Diff sources of eng in human and uses
glycogen
- primary source of eng, only changes when it runs out
fats
- becomes main source when glucose is depleted
muscle tissue (protein)
- final resort, cells are breaking down (bad)
Equation of cellular respiration and goal
C6H12O6 + 6 O2 →6 CO2 + 6 H2O
to break glucose down and make 6 CO2
to collect eng in the form of atp
to move glucose electrons to O2, make 6 H2O
What are the 4 major stages of cell resp
glycolysis
oxidative decarboxylation(pyruvate oxidation)
krebs cycle
electron transport chain
what are the 7 enzymes used in cell resp
name, function, class
dehydrogenase - redox,1
kinase - phosphorylation, 2
lyase - cleavage, 4
decarboxylase - decarboxylation, 4
hydrase - hydration, 4
isomerase / mutase - isomerization, 5
synthase - synthesis, 6
What are the major steps of glycolysis
around 10
- atp-> adp
- isomeration
- atp->adp
- split into DHAP, G3P
- isomerization between G3P, DHAP
equilibrium - 2NaDH is made, dehydrogenase + phospho (p added)
- 2 Atp made, kinase, released
- isomerization
- water leaves (make PEP) lyase, released
- 2ATP made, kinase (puryvate)
energy investment phase vs energy payoff phase
energy investment phase - first 5
2 atp are put into glycolysis, invested
energy payoff phase - last 5
4 Atp are made from glycolysis, payoff
2 NADH
Why are all reaction in eng payoff phase doubled
the glucose breaks into 2 parts, the 2 parts each do the payoff phase
Which steps make or use energy in glycolysis
1.ATP - adp
3.ATP -> ADP
6.2 NADH is made
7.2 ATP is made
10.2 ATP is made
makes 4 atp
2 NADH
Purpose of fermentation
When there is no oxygen present, the cell can still make NAD+ for glycolysis to make ATP without O2
(ATP usually made in ETC)
method can be alcohol(yeasst) or lactic acid(humans)
Process of lactic acid fermentation
2pyruvate
takes 2NADH, turns it into 2NAD+
uses dehydrogenase
becomes 2lactate
NAD+ goes to glycolysis
Process of Alcoholic fermentation
2pyruvate
CO2 leaves
becomes 2 acetaldehyde
gets 2NADH into 2NAD+
becomes 2Ethenol
NAD+ goes to glycolysis
Lactic vs alcohol fermentation
alcohol fermentation not in humans, yeast, makes CO2, has middle step.
Ethanol will not be converted back to pyruvate ever
Lactate can be converted back
both regen 2NAD+
impact of lactic acid fermentation on the body
builds up in muscles, transported to liver
used to be thought to cause soreness actually just swelling
allows you to make eng without O2
gets tiring because less eng is made
Why does anaerobic respiration cause fatigue
no CO2 is released or H2O
The NADH made from glycolysis has to be used up. less energy is made
Energy molecules made at the end of anaerobic respiraiton
just 2 ATP
usually glycolysis makes 2 NADH also
Process of oxidative decarboxylation (steps, reaction type, enzyme )
Pyruvate
release CO2, decarboxylation, decarboxylase
NAD+ -> NADH, redox, dehydrogenase
add coenzyme A, synthesis, synthase
Makes acetyl coa
Major steps in kreb cycle
8, name enzymes
- Coa leaves, join c4 - c2 makes citrate, synthesis
- isomerization
- NADH made, CO2 release, redox,decarbox
- NADH made, CO2 release, COA added, redox, decarbox, synth
- ATP made, COA leaves, sub lvl phose(kinase), lyase
- FADH2 made, redox
- hydration, rearrange molec, makes malate
- NADH release, recreate molec to restart, redox, makes OAA
How much energy from Krebs and pyruvate oxidation (what step )
per 1 glucose
Py oX - 2 NADH (2)
Krebs - 6NADH (3.4.8), 2ATP(5), 2FADH(6)
Purpose of electron shuttle
bring NADH into mitochondria
indirect
needs to get to etc
Glycerol phosphate vs malate aspartate shuttle
gly phos - converts to FADH2, less efficient, molecs don’t go into matrix
malate aspartate - stays as NADH, uses glutamate and other things to change back, more molec involved
humans do both
What are the main steps in Malate aspartate shuttle
- dehydrogenase in cytoplasm, takes electrons from NADH to OAA, makes Malate
- Malate enters mitochondria
- Dehydrogenase in matrix removes electrons, adds to NAD+ makes NADH
- OAA becomes Aspartate with glutamate help
- Aspartate leaves
- Aspartate becomes OAA with aKG
WHat are the main steps in glycerol phosphate shuttle
DHAP takes H from NADH
becomes glycerol 3 phosphate
glycerol 3p goes into inner mito space
H attaches to FAD making FADH2
Glycerol becomes DHAP, leaves
What are the 2 methods of ATP synthesis
Substrate lvl phosphorylation - Direct, uses phosphate transfer, in glycolysis, krebs
oxidative phosphorylation - indirect ATP formation through redox reactions involving O2 as a final electron acceptor, driven by ETC, phos starts off free
combination of chemiosmosis and oxidation
Proteins in electron transport chain
also function
Complex 1 - takes 2e- from NADH, pumps protons out
Complex II only for FADH2, not a pump
ubiquinone (Q) - in bilayer, transfer e from Cl to CIII
CIII - pumps protons
cytochrome C - peripheral in IMM
CIV - pumps protons, leads electrons to O2, makes H2O
How can the type of electron shuttle change total ATP made?
Glycerol phosphate makes 1 FADH each round turns the 2NADH from glycolysis to 2 FADH
Malate aspertate keeps it the same
glyc phos shuttle would cause 36 atp total
malate aspertate cause 38 atp total
Where is citrate,OAA, pyr in cell resp, how much atp is made after them
pyr - 15, does not include glycolysis, elect shuttle
Citrate, Acetyl coa includes Kreb - 12
OAA, Malate is after kreb, just count electron shuttle?
Which way is the ATP synthase facing
cell resp - Bulb always in matrix of mitochondria
Photosynth - bulb in stroma
What is the driving force behind the energy transformation in ETC
Oxygen
How is each step in ETC a redox reaction
Movement of electrons
redox is transfer of electrons
each step electrons are transferred to another complex one thing gets oxidized and another gets reduced
describe Chemiosmosis
facilitated transport of protons
high conct of protons outside
passive transport
high to low cont, gradient is electrochemical
explain how NADH and FADH2 produce diff amt of ATP
NADH powers 3 pumps
FADH powrs 2 pumps
Define proton motive force
Movement of protons provides physical force causes conformational change in ATP synthase, makes ATP
What are the components of ATP synthase
rotar
Stator
Knob
Rod
What does the stator do in ATP synthase
anchored in the membrane holds rod stationary
What does the rotar do in ATP synthase
protein channel, transmembrane
rotate clockwise when protons pass down gradient
What does the knob do in ATP synthase
peripheral, catalytic site that phosphorylates ATP
has 2 types of subunits alpha, beta
beta has active site for ATP, 3 beta
Rotational catalysis
What does the rod do in ATP synthasee
spins, causes conformational change in Knob which creates ATP
What is rotational catlysis
when rod spins it causes conformational change in Knob.
interactions with rod dictates step in ATP synthesis
some int - loosly binds ATP
close int - strongly binds ATP
little int - ATP released
Give ex of energy transformation from kinetic to mech to chem pot eng
kinetic energy - > movement of H+/Protons through rotor
Mech - protons causes rotor and rod to spin
chem - mech eng causes conformational change in Knob, makes ATP
ATP has chem pot eng in phosphate bonds
photosynthesis vs cellular resp
cell resp - does not require light
photosynth - inorganic source of CO2
equation is reversed
What is the purpose of photosynth
use light eng to convert inorganic compounds into organic fuels that can store potential eng in carbon bonds
WHat aren’t cell resp and photosynth considered opposites
equation is reversed but the order of events and processes are not reversed
What is the overall equation for photosynth
light energy + CO2+ water - > glucose + O2
What is autotroph
orgs that get eng without eating others
uses inorganic resources
what - troph are plants
photoautotrophs
they can make eng without eating (light)
require input from inorganic substances from env
What troph are humans
chemoherterotroph
needs other orgs for eng
Name parts of leaf (7)
CEPSGSV
Cuticle - bottom and top layer
Epidermis - bottom and top under cuticle
Palisade mesophyll - longer cells on top
Spongy mesophyll - middle portion
Guard cells - gates at bottom
Stoma / stomata - space in between guard cells
Vascular bundle - lines
WHich part of leaf prevents water loss and gas exhcange
cuticle
WHat does do the guard cells do, location why
regulation gas exchange
found on the underside of the leaf so water cant evaporate out
what does the vascular bundle do
Transports water and nutrients
what does palisade mesophyll do and why shape
mainly photosynthesis, contains the most chloroplast
shaped as longer oval cells to more could fit in smaller area and get more sun
What are the parts of the chloroplast and function (6)
outer membrane
inner membrane
stroma - like mitochondrial matrix
thylakoid - disk thing
granum - stack of thylacoids
thylakoid space/ lumen
Stroma vs stoma
stroma - found in chloroplast, like mitochondrial matrix
stoma - part of leaf structure, in between guard cells, helps gas exchange
What type of light is used in photosynthesis
visible light
how to read absorbtion spectrum
Low parts are reflected light
colour on bottom is light being talked about
peaks are more absorbed (colour would not be seen)
How wavelengths correlate to colour
diff colors have diff wavelengths and energy
the shorter the wavelength the higher the eng
purple is high eng
red is low
WHat is a pigment
pigment - group of light absorbing molecs
ex chlorophyll, carotenoid
role of pigments in how we see colour
the colour of pigment is due to wavelength of light reflected back into eyes
pigments reflects certain wavelength
absorption vs reflection of light
you cannot see what it absorbs
the colour of the object is what it reflects
ex chlorophyll reflects green
Carotenoids colour vs chlorophyll colour
Carotenoid - reflect red orange, absorb blue green
chlorophyll - absorbs mainly red blue, reflects green
Main purpose of light reactions
takes in water and light
makes ATP NADH
O2 is byproduct
What are the 4 stages of light reaction
photoexcitation -light is absorbed and excites electrons
photolysis - energy from light is used to split water
electron transport - harnessing energy in elect to make gradient
photophosphorylation - atp synthesis due to electrochem grad and Proton mot force
What is photoexcitation
happens in chlorophyll in thylakoid
when atoms absorb eng from the sun and electrons get excited
excited electrons go to primary electron acceptor before it gets unexcited
What is a photosystem structure and function
cluster of hundreds pigments (chlorophyll, carotenoid)
embedded in transmembrane proteins of thylakoid membrane
(found in chloroplasts found in palisade mesophyll cell)
has reaction center chlorophyll and primary electron acceptor
How Photosystem captures eng
photon hits antennae pigment molecs
energy bounces around
eventually get to reaction centre chlorophyll
RC chlorophyll electron causes primary electron acceptor to trap electron and preserve eng
What is photosystem I and II
what is the P number
Diff types of photosystems
have diff optimal wavelengths to absorb
PI - has P700 reaction centre chlorophylll
PII - has P680, takes in electrons, is first
Parts of the light reaction ETC
Photosystem II
Plastoquinone (PQ)
Cytochrome complex (NOT Cyt C)
PC
PSI
FD
NADP+ reductase
What does the photosystem II do
First part in light ETC
Takes in light
takes in electrons
Excited eng in P680 gets captured by primary electron acceptor
P680 gets oxidized
does photolysis
What does PQ do
location, name
Plastoquinone
second step of light ETC
transfers electrons to cytochrome complex
found in thylakoid memb
also gets protons from stroma
lipid soluble
What does the cytochrome complex do
Third step
Part of light ETC
does not take in light
gets electrons from PQ
get protons from PQ pumps against gradient into lumen
Passes electrons to plastocyanin
What does plastocyanin do
location
Fourth step in light ETC
movable component on lumen side of thylakoid membrane
peripheral
transfers electrons to PI
What does Photosystem I do
step five in light ETC
electrons in P700 excited and captured by primary electron acceptor
P700 is oxidized
electrons from PC replace those lost
What does FD do
step six in light ETC
ferredoxin
mobile component on stromal side of thylakoid memb
transfers electrons from photosystem I to NADP+ reductase
IN CYCLIC ELECTRON FLOW
transfers electrons back to cytochrome complex
What does NADP+ reductase do
last step of light ETC
gets electrons from ferredoxin
attaches them to NADP+ final acceptor of electrons
NADP+ reduced to NADPH
What does NADPH do
provides eng for Calvin cycle
in reduction phase
Why must electrons be replaced in photosystem I
electrons lose energy by the time they get to PI.
electrons from photolysis in PII are used to replace them
What does ATP Synthase do in Light ETC
protons are pumped into lumen, makes high concentration
ATP synthase passive transports them out
ATP is produced in the stroma
What is photolysis
SOmething only photosystem II does
splits water into electron, H+ and 1/2(O2)
used to replace electrons lost in PI
How much eng does Light ETC make
1 ATP
1 NADPH
both go to calvin cycle
NADPH in reduction
ATP in regenertion
What is photophosphorylation
Making of ATP from ADP using the energy from light
done in ATP synthase in photosynth
Differences between light ETC and animal ETC (pump, names of Pumps, lipid sol, peri mob molec,source of elec, final acceptor, conc, ATP synth loc )
Proton pumps
2-3
Names of Pumps
Cytochrome comp - Complex 1,3,4
Lipid soluble mobile molecule
PQ - quinone
peri mobile molec
PQ,Plastocyanin, Ferredoxin - Cyt C
Source of elec
H2O, Photosystem II, I - NADH, FADH2
Final electron accepton
NADPH - O2 in H2O
high conct
in lumen - in inner mitochondrial space
where ATP synthase
thylakoid memb- IMM
What is cyclic ETC in photosynth, function and causes
when ferredoxin sends the electrons back to Cytochrome C
so that it can pump more protons
makes more ATP
No NADPH is made
ATP is used up faster than NADPH
WHen NADPH accumulates it triggers cyclic
Why is cyclic ETC needed in plants
linear ETC makes roughly same amt of ATP and NADPH
plant uses more ATP than NADH
cyclic increases ATP more efficiently
Rise in NADH will cause change to cyclic
Where does calvin cycle take place
3 diff plants
for C3/CAM plants - in chloroplast stroma
For C4 plants - in bundle sheath
What are the 3 phases of calvin cycle
Carbon fixation: takes in CO2
Reduction: uses eng to make organic comp
Renegeration: regenerates molec to go again
What happens in carbon fixation phase of calvin cycle
take in CO2 and starts with RuBP
uses Rubisco to join CO2 and RuBP to make 3x 6C
C3 plants - breaks into 2 groups of 3x3C
ends up as 6 x 3C
Synthesis, eng is absorbed
what is rubisco and its properties
synthase found in first step of calvin cycle in carbon fixation
very slow
most abundant protein on earth
leaves need a lot of it
What happens in the reduction phase of calvin cycle
- ATP sends P into each 3C molec (theres 6)
phosphorylation, kinase , absorbed - NADPH sends H to make G3P (uses 6 NADPH)
redox, dehydrogenase, absorbed - 1/6 of the G3P leave to become glucose (in similar way backwards glycolysis)
What happens in regeneration phase in calvin cycle
Other 5G3P continue on
1. G3P (3C) turns back into RuBP (3 x 5C) uses 3 ATP
synthesis, synthase, absorbed
What are C3 plants
first product of carbon fixation is 3C
more common than C4
not good in hot weather
limitations of C3 plants
not good in hot weather
close of stomata and cant do gas exchange
drop in CO2
increase in O2
no change to light reaction
no calvin cycle needs CO2 so no glucose made
Rubisco binds do O2 instead of CO2 causes problems
How can rubisco cause issues for C3 plants in hot weather
hot weather, close guard cell to protect water
No CO2
rubisco binds to O2 instead and makes PGA and PG instead of 2 PGA
PG is hard to use, too energy intensive to convert
What is photorespiration
when rubisco binds with O2 instead of CO2
makes no organic fuel (no calvin cycle)
no atp
wastes energy
makes H2O2 - bad
baggage from earlier time when much more CO2 and ability didnt matter
now its issue
What 2 other plant types have adapted to dry arid places
C4 plants
CAM plants
Describe C4 plants difference from C3
hardier
Corn, sugar cane
starts Calvin cycle witn a 4C instead of 3C
has bundle sheath cells
LIght and Calvin reaction happen at diff places
What are bundle sheath cells
found in C4 plants
surrounds vascular bundle with palisade mesophyll
What is the C4 adaptation
LIght reactions with O2 (in palisade) kept separate from Calvin cycle with CO2 (in bundle sheath)
Has PEP carboxylase to stop O2 from getting to bundle sheath
How do C4 plants bring CO2 to bundle sheath to avoid O2 interaction (6 steps)
- Palisade takes in CO2 and adds to PEP carboxylase
- Makes OAA
- turns into malate
- malate goes into bundle sheath
- malate releases CO2 and pyruvate
- CO2 is used, pyruvate goes back to palisade to become PEP carbox
describe CAM plants
crassulacean acid metabolism
succulents, cacti, pineapples
has Pep carboxylase
does light reaction in day calvin at night
How does the CAM plant overcome arid conditions
Works at night
CO2 Is stored at night to be used in the day
Day :Stomata closed, Conserve water, no CO2 uptake, Light reactions make ATP and NADPH and O2, Calvin cycle runs,
Night: takes in CO2, does PEP carboxylase, stores CO2 in malic acid vacuole
How does the CAM overcome the RUbisco problem
CO2 is stored at nightj
when calvin and light reactions take place in the day the stored CO2 are in high conct so RUbisco binds to them instead
factors that affect photosynth
Light intensity
Carbon dioxide concentration
Temperature
How to read light intensity graphs
measure of carbon fixation
in beginning light limits the production rate
graph increases until it plateaus, that is optimal
graph decreases because then the O2 concentration is too high causing photorespiration
What is light compensation point
minimum light intensity needed for plant to make carbon
point where the line crosses the x axis in light intensity graph
