Unit 4 notes from textbook + slides Flashcards
what are the two ways organisms can harvest energy from their environment?
from the sun (phototrophs ie.plants)
from chemical compounds (chemotrophs ie. animals)
how else can organisms be classified?
can also be classified by where they get their carbon from
some convert CO2 into glucose (autotrophs ie.plants)
some obtain their carbon from organic molecules, eat other organisms (heterotrophs ie. animals)
classification of plants
photoautotrophs
what does metabolism mean?
the set of chemical reactions that convert molecules into other molecules and transfer energy in living organisms
classification of animals
chemoheterotrophs
chemical energy definition
form of potential energy held in the chemical bonds between pairs of atoms in a molecule
strong bonds do not contain much chemical energy (ie. do not require a lot of energy to remain intact)
weak covalent bonds require lots of chemical energy to stay intact which is why carbohydrates, lipids and proteins are rich sources of chemical energy
two branches of metabolism
catabolism: the set of chemical reactions that break down molecules into smaller units and in the process produces ATP
anabolism: the set of chemical reactions that build or synthesize molecules from smaller units and require an input of energy (ATP)
the more stable configuration is always the one with….
lower potential energy
structure of ATP
molecules of adenosine(adenine + 5 carbon sugar ribose) covalently linked to three phosphate groups with high potential energy
what is chemical equilibrium?
the rate of the forward reaction equals the rate of the reverse reaction and the concentrations of the reactants and products do not change
what is delta G?
the amount of energy available to do work
free energy of the products-free energy of the reactants
positive delta G-requires an input of energy
endergonic reaction definition
require an input of energy, positive delta G, not spontaneous
exergonic reaction definition
releases energy, neagtive delta G, spontaneous
ex. ATP hydrolysis
what is ATP broken down into?
ADP and Pi (inorganic phosphate)
what is the free energy difference influenced by?
concentration of reactants and products
the pH of the solution in which the reaction occurs
temperature
pressure
energetic coupling definition
process in which a spontaneous reaction (-deltaG) drives a nonspontaneous reaction (+deltaG)
cellular respiration process definition
a series of catabolic reactions that convert energy from food (ie. glucose) to ATP
how many molecules of ATP are produced from cellular respiration?
32
what are the two ways ATP is produced in cellular respiration?
1) substrate level phosphorylation: an organic molecule transfers a phosphate group directly to ADP to make ATP. produces a small amount of ATP.
2) oxidative phosphorylation: the chemical energy of organic molecules is transferred first to electron carriers. electron carriers transport electrons released during the catabolism of organic moloecules to the respiratory electron transport chain. They transfer electrons along a series of membrane associated proteins to a final electron acceptor (Oxygen) and in the process harness the energy released to produce ATP.
what are the four stages of cellular respiration?
stage 1: glucose is partially broken down to produce pyruvate and energy is transferred to ATP and reduced electron carriers, glycolysis
stage 2: pyruvate is oxidized to another molecule called acetyl-coenzyme A (acetyl-CoA), producing reduced electron carriers and releasing carbon dioxide
stage 3: citric acid cycle, in this series of chemical reactions the acetyl group is completely oxidized to carbon dioxide and energy is transferred to ATP and reduced electron carriers
stage 4: oxidative phosphorylation, reduced electron carriers generated in stages 1, 2, 3 donate electrons to the respiratory electron transport chain and a large amount of ATP is produced
purpose and products of glycolysis
glycolysis results in the oxidation of glucose and the synthesis of a relatively small amount of both ATP and reduced electron carriers
“splitting of glucose”
glycolysis begins with a molecule of glucose and produces pyruvate, 2 ATP, and 2 NADH
where do the steps of cellular respiration take place in eukaryotes and bacteria?
in euk: glycolysis takes place in the cytoplasm, while pyruvate oxidation, the citric acid cycle and oxidative phosphorylation take place in the mitochondria
in bacteria: glycolysis+pyruvate processing+citric acid cycle take place in cytoplasm, oxidative phosphorylation takes place in the cell membrane
three phases of glycolysis
1st phase: prepares glucose for the next two phases by the addition of two phosphate groups to glucose. destabilizes the molecule so it can be broken down in phase 2
Requires 2 molecules of ATP
2nd phase: cleavage phase, for each molecule of glucose entering glycolysis, two 3-carbon molecules enter phase 3
3rd phase: payoff phase, 4 ATP and two electron carrier NADH are produced. Net ATP production= 2
two molecules of pyruvate are produced
difference between what happens to pyruvate when oxygen is present and when it isn’t
when oxygen is present, pyruvate is converted to Acetyl-CoA, which then enters the citric acid cycle
when oxygen is not present, pyruvate is metabolized along a number of pathways (ex. fermentation)
fermentation definition
when oxygen is not present
fermentation is a process for extracting energy from fuel molecules that does not reply on oxygen or the electron transport chain but instead uses an organic molecule as en electron acceptor
NADH is converted to NAD+ when pyruvate is reduced
when there is no terminal electron acceptor ie oxygen
two major fermentation pathways
lactic acid fermentation: electrons from NADH are transferred to pyruvate to produce lactic acid and NAD+
ethanol fermentation: occurs in plants and fungi, pyruvate releases CO2 to form acetaldehyde and electrons from NADH are transferred to acetaldehyde to produce ethanol and NAD+
fermentation only produces 2 molecules of ATP
pyruvate oxidation purpose and products
in the presence of oxygen, pyruvate can be further oxidized to release more energy, first to Acetyl-CoA and then even further in the series of reactions in the citric cycle
the synthesis of acetyl-CoA from pyruvate results in 1 molecule of CO2, 1 molecule of NADH. However, a single molecule of glucose in glycolysis produces 2 pyruvate so…
2 CO2, 2 NADH and 2 acteyl-CoA are produced
mitochondria distinction of different spaces/membranes
rod shaped organelle surrounded by a double membrane
intermembrane space: the space between the inner and outer membrane
mitochondrial matrix: space enclosed by the inner membrane
details of pyruvate oxidation
pyruvate is transported into the mitochondrial matrix, where it is converted into acteyl-CoA
First, part of the pyruvate molecule is oxidized and splits off to form CO2
the electrons lost in the process are donated to NAD+, which is reduced to NADH
the remaining part of the pyruvate molecule, COCH3, still contains potential energy that is then transferred to coenzyme A (CoA)
this process forms the first substrate in the citric acid cycle, acteyl-CoA
where does the citric acid cycle take place?
in the mitochondrial matrix
result of the citric acid cycle
results in the complete oxidation of the acetyl group of acetyl Co-A, releases CO2 (source of CO2 that we exhale when we breathe)
produces 2 Acetyl-CoA molecules produced from a single molecule of glucose yield—2 ATP, 6 NADH, 2 FADH2
permeability of the inner mitochondrial membrane
selectively permeable
protons cannot passively diffuse across this membrane, use transporter/channel proteins
what results from the pumping of H+?
the result of pumping H+ into the intermembrane space is a proton gradient
two components of the proton gradient: a chemical gradient that results from the difference in concentration of protons and an electrical gradient that results from the difference in charge between the two sides of the membrane
oxidative phsophorylation result
the electron carriers NADH and FADH2 lead to the generation of a proton electrochemical gradient. this gradient is a source of potential energy used to synthesize ATP
chloroplasts structure
chloroplasts are bounded by two membranes
in the center of the chloroplast is a third, highly folded membrane that encloses a fluid filled space called the lumen. the photosynthetic electron transport chain is located in this membrane
the entire structure is called the thylakoid. the thylakoid is folded into grana, which resemble stacks of pancakes
the region between the inner membrane and the thylakoid membrane is called the stroma
Photosystem 1 and 2
Electrons flow from 2 to 1 along the photosynthetic electron transport chain. The energy captured by 2 allows electrons to be pulled from water; the energy captured by 1 allows electrons to be transferred to NADP+ to form NADPH
Z scheme
there is a large increase in energy as the electrons pass through each of the two photosystems. Overall decrease in energy occurs as electrons move between the two photosystems. This decrease in energy explains why electrons move in one “direction” through the photosynthetic electron transport chain. Running these reactions in the opposite direction would require an input of energy
photosynthetic electron transport chain products and purpose
produces NADPH and ATP, electrons flow from H2O to NADPH, electron flow is coupled to the pumping of protons, creating an electrochemical gradient used to synthesize ATP by ATP synthase
water donates electrons to one end of the photosynthetic electron transport chain, whereas NADP+ accepts electrons at the other end
what is responsible for the buildup of protons in the thylakoid lumen?
the oxidation of water releases protons and O2 in the lumen
bio element definition
elements found in cells and that are required for cellular function
what is the carbon source for humans typically?
glucose
electron sources: organic or inorganic compounds
organic= “Organo”
ex. glucose or glycerol
Inorganic= “Litho”
ex. water, nitrite, ammonia
if a molecule has the most oxygens bonded to a single carbon atom it is said to be the most…
oxidized
if a molecule has the most hydrogens bonded to a single carbon atom it is said to be the most…
reduced
in the cell, reduced carbon such as glucose is oxidized to CO2 to form products that are….
more strongly bonded
have less potential energy
more oxidized forms to carbon
purpose of cellular respiration
capture energy released, harnessed in the form of ATP
which steps of cellular respiration produce CO2?
pyruvate processing and oxidative phosphorylation
how is ATP synthesized in glycolysis?
via substrate level phosphorylation
cellular respiration overview
oxidation of glucose to CO2
the energy in the carbon bonds in glucose are broken down in steps
the energy is captured (harnessed) in the form of ATP and other high energy intermediates (NADH, FADH2)
what does CO2 production indicate in cellular respiration?
carbon atoms from glucose have been completely oxidized
substrate level phosphorylation vs oxidative phosphorylation
substrate level: substrate with phosphate then an enzyme removes phosphate from substrate to phosphorylate ADP then ATP is synthesized
Oxidative: involves membrane-bound enzymes and H+ gradient that drives ATP phosphorylation
what comes in and out in stage 1 og glycolysis?
IN:
2ATP
glucose
2NAD+
OUT:
2ADP
2 pyruvate
2NADH
in the absence of a terminal electron acceptor/cellular respiration a cell can still make ATP by substrate level phosphorylation in glycolysis if it…
oxidizes NADH to NAD+
to regenerate NAD+ for glycolysis
how is pyruvate converted to acteyl-CoA?
giving up 2electrons to NAD+ becomes NADH
oxidizing one carbon as CO2 (released as waste)
the acetly group left has lots of potential energy it is transferred to coenzyme A to become Acetyl CoA
citric acid inputs and outputs
IN:
Acetyl CoA
NAD+
FAD
ADP
OUT:
CO2
NADH
FADH2
ATP
CoA
why is the citric acid cycle called that?
it produces citrate
photosynthesis definition
conversion of light energy to chemical energy (stored in the bonds of carbohydrates)
photosythesis light dependant and independant reactions
phosphorylation- an electron transport chain
light dependant reaction: water is oxidized to produce O2
NADP is reduced to form NADPH
ATP is synthesized vis proton gradient driven by chemiosmosis
input photons and water output ATP, NADPH, O2
light independant reaction: then the calvin cycle uses these ATP and NADPH
CO2 is reduced to form carbohydrates (Carbon fixation)
light dependant reactions- “Photophos” in more depth
1) electrons are supplied by H2O
2) light energy is required for photosystem 2 to “strip” the electrons from the water
3) electrons move along the electron transport chain to provide energy to pump protons into the lumen
4) an electrochemical gradient is created in the thylakoid lumen
5) more light energy input at photosystem 1. This energizes the electrons to drive the reduction of NADP+
6) NADPH is synthesized in the stroma and will be used in the calvin cycle
7) ATP is synthesized in the stroma via chemiosmosis. H+ moves through the ATP synthase
what is oxygens role in cellular respiration?
oxygen accepts the electrons at the end of the chain-called terminal electron acceptor and is reduced to water
which direction are protons pumped?
matrix to intermembrane space
where does the energy to transport protons come from?
electron transport chain
the energy from the transfer of electrons is released in a series of redox reactions. the energy is used to pump protons.
the stroma in the chloroplast is analagous to_______in the mitochondria
Matrix
similar to cytoplasm
the thylakoid lumen in the chloroplast is analogous to______in the mitochondria
intermembrane space
ATP synthesis occurs in the chloroplast in the stroma and in the mitochondria it occurs in______
Matrix
In the light-dependant reactions of photosynthesis, light energy is used to oxidize _______to__________
H2O to O2
The electrons derived from H2O are used to reduce _______ to ________ in the light-dependant reactions
NADP+ to NADPH
oxygenic photophosphorylation
electrons from water reduce the photosystem 2 and realease O2
oxygenic meaning oxygen is a product of the reactions and released
why does phosphorylation not have a terminal electron acceptor?
the electrons end up on a molecule that is already present in the chloroplast i.e. NADP+
since it is already present in the cell it is NOT by definition a TERMINAL electron acceptor but a FINAL electron acceptor
endosymbiont theory
evidence that mitochondria and chloroplast evolved from ancient prokaryote
like bacterial cells they have:
-double membranes
-both have circular DNA
-both grow and multiply by binary fission
-both have their own ribosomes, synthesize proteins
location of calvin cycle in chloroplasts
stroma
carbon being fixed definition
converted from inorganic (ie. CO2) to organic form (has C-H bonds)(carboxylation reaction)
where does the ATP and NADPH for the calvin cycle in chloroplasts come from?
phosphorylation in the chloroplast thylakoids
the calvin cycle oxidizes the light-dependant reaction product_______to _________; and the electrons derived from this redox reaction are used to reduce ________to ________ in a light independant manner
NADPH to NADP+; CO2 to G3P
3 main phases of the clavin cycle
- carbon fixation: each CO2 (3CO2’s) reacts with RuBP producing two 3-phosphoglycerate molecules. The enzyme that catalyzes this reaction is called Rubisco. the attachment of CO2 to an organic compound is called carbon fixation
- reduction: the two 3-phosphoglycerate molecules are phosphorylated by ATP and reduced by NADPH to produce G3P
- regeneration: the remaing G3P is used in ATP dependant reactions that regenerate RuBP
how is the G3P related to cellular respiration?
after glucose splitting in glyoclysis the substrate produced is G3P, the G3P from the calvin cycle can enter glycolysis
fate of G3P in the chloroplast
these reduced forms of carbon can now be used in cellular respiration or be used to build other macromolecules
inputs and outputs of the calvin cycle
3CO2 in one G3P out
6ATP and 6NADPH in
6ADP and 6NADP out
rubisco is regenerated so it is not counted as an input/output
