Plants, Energy, and Carbon: Plant Biochemistry

Bio
121 LE2 | NAT BOHULANO

PLANTS, ENERGY, AND CARBON: PLANT

BIOCHEMISTRY

LIGHT AND PIGMENTS
MARCH 2, 2017
Photosynthetic Pigments: The Light Receptors
When light meets matter, it may be reflected, transmitted, or absorbed

Substances that absorb visible light are known as pigments

o Different pigmets absort light of different wavelengths
o When illuminated with white light, the color we see is the color most reflected or transmitted by the
pigment

Two classes of pigments:
Chlorophylls
Carotenoids
o Carotenes
o xanthophylls

CHLOROPHYLLS
Chlorophyll is the pigment primarily responsible for harvesting light for photosynthesis
o Molecule has 2 parts
Porphyrin ring
Composed of four nitrogenous pyrrole rings
Phytol tail
Derived from isoprene
Isoprene is a long chain of carbons
o When Mg2+ cofactor is inserted, the chlorophyll molecule is complete; if Mg2+ is lost, the molecule is called
pheophytin
Mg2+ is placed at the center of the porphyrin ring
Structure
Bio 121 LE2 | NAT BOHULANO

o Porphyrin ring: light absorbing "head"of molecule; there is a magnesium atom at the center
o Hydrocarbon tail: interacts with hydrophobic regions of proteins inside thylakoid membranes of chloroplasts
Forms
o There are four forms of chlorophyll, designated a, b, c, d
o Chlorophyll a is formed from protochlorophyll a by the action of NADPH: protochlorophyll oxidoreductase
o Chlorophyll b is synthesized from chlorophyll a
At normal conditions, a is usually greater than b
Ideal ratio: 3:1
o Chlorophyll c is found in diatoms, dinoflagellates, and brown algai

o Chlorophyll d occurs in red algae
Chlorophyll a
o Key light capturing pigment that participates directly in light reactions
o Blue green under visible light
Chlorophyll b
o Accessory pigment
o Olive green under visible light
Carotenoids accessory pigments also
Other pigments broaden the spectrum of colors that can be used for photosynthesis

CAROTENOIDS
The carotenoids are accessory pigments for photosynthesis
Various shades of yellow and orange because they absorb violet and blue-green light
o Are terpenoids found in thylakoids and in chromoplasts
o The two primary examples in plants are carotenes and xanthophylls
Carotenes are generally orange
Xanthophylls are yellow
o Beta-carotene absorbs blue light for photosynthesis
o All are antioxidants in humans and also in photosynthesis

Prevents chlorophyll a and b from photooxidation (oxidation brought about by excess energy)
o Common ay carbon-carbon double bonds; major differences lie in the rings
o Carotenes
B-carotene
*search structure*
Alpha-carotene
Lycopene

o Xanthophylls
Zeaxanthin
Lutein
Violaxanthin
An important function of carotenoids seems to be Photoprotection
Photoprotection
o The absorbance and dissipation of excess light energy that would otherwise damage chlorophyll or interact
with oxygen, forming reactive oxidative molecules that are dangerous to the cell

SPECTROPHOTOMETRY
A pigment's ability to absorb various wavelengths can be measured by a spectrophotometer
Machine send light through a solution of pigments and measures the fraction of light transmitted at each
wavelength
o White light is refracted and separated into different colors which corresponds to the wavelengths of visible
spectrum
o Slit in the maching pass light of selected wavelengt
o Light is made to pass through the extract
o Photoelectric tube reads the light transmitted
o Galvanometer reads the absorption
Ex. Chlorophyll absorbing green light:
High transmittance (low absorption) indicates chlorophyll does not absorb green light
Ex. Chlorophyll absorbing blue light
Low transmittance (high absorption) indicates chlorophyll absorbs blue light
A graph plotting a pigment's light absorption versus wavelength is called an absorption spectrum
o Absorption spectra for chlorophyll a, b, and caroteinoids (alpha and beta)
For chlorophyll a; violet-blue or red light work best for photosynthesis

Action spectrum
o This graph plots the rate of photosynthesis versus wavelength. The resulting action spectrum resembles the
absorptoin spectrum; deficiencies are due to the absorption of light by accessory pigments like carotenoids

o Refers to the profiles of the relative effectiveness of different wavelengths of radiation in driving a process
(ex. Photosynthesis)
o Measuring products ganern
o Was first demonstrated by Thomas Engelman in 1883
Exposed different segments of filamentous alga to different wavelengths by using a prism

He used aerobic bacteria, which concentrate near an oxygen source, to determine which segments of
alga were releasing the most O2 and thus photosynthesizing most
Bacteria congregated in greatest numbers around the parts of the alga illuminated with violet-blue or
red light

CHLOROPHYLL A
Is the main photosynthetic pigment
Accessory pigments light chlorophyll b broaden the spectrum used for photosynthesis
Accessory pigments called carotenoids absorb and dissipate excessive light that would otherwise damage
chlorophyll or interact with oxygen forming reactive oxidative molecules (free radicals) through photooxidation

o Photoprotection

RELATIONSHIP OF ABSORPTION SPECTRUM AND ACTION SPECTRUM
Halos nag mamatch
Discrepancy is seen in the part where carotenoids absorb because they are capable of absorption but do not drive
the photosynthetic process

EXCITATION OF CHLOROPHYLL BY LIGHT
When a pigment absorbs light, it goes from a ground state to an excited state
o Very unstable
When excited electrons fall back to the ground state, photons are given off, an after glow called fluorescence
When a molecule absorbs a photon of light, one of the molecule's electrons is elevated to an orbital where it has
more potential energy
When the electron is in its normal orbital, the pigment molecule is said to be in its ground state
Absorption of a photon boosts an electron to an orbital of higher energy, and the pigment molecule goes to an
excited state
The only photons absorbed are those whose energy is exactly equal to the energy difference between ground
state and excited state, and this energy difference varies from one kind of molecule to another
o Thus, a particular compound absorbs only photons corresponding to specific wavelengths; reason why each
pigment has a unique absorption spectrum
Excited state is only temporary; electron cannot stay for long; excited state is unstable
o When isolated pigment molecules absorb light, their excited electrons drop back down to the ground-state
orbital in a billionth of a second, releasing their excess energy as heat
o Afterglow made up of photons given off after electrons fall back to the ground state is called flourescence

PHOTOSYSTEM: A REACTION CENTER ASSOCIATED WITH LIGHT-HARVESTING COMPLEXES
Consists of a reaction center surrounded by light-harvesting complexes
Light-harvesting complexes funnel energy to reaction center
A primary electron acceptor in the reaction center accepts an excited electron from chlorophyll a
Chlorophyll molecules produce very different results in an intact chloroplasts as opposed to pigments in isolation
Chlorophyll molecules native environment: thylakoid membrane
A Photosystem is composed of a Reaction-center complex surrounded by several light-harvesting complexes
Reaction-center complex is an organized association of proteins holding a special pair of chlorophyll a molecules
Light-harvesting complex consists of various pigment molecules bound to proteins
o Number and variety of pigment enable photosystem to harvest light over a larger surface area and a larger
portion of the spectrum than single pigments alone
o Acts as an antenna for the reaction center complex
2D View of the light harvesting complex antenna complex
Antenna complex is a transmembrane pigment protein with 3 helical regions that cross the nonpolar
part of the membrane


Primary Electron Acceptor
o Found in the reaction-center complex contains a molecule that is capable of accepting electrons and
becoming reduced; this is called
Pair of chlorophyll a molecules in the reaction-center complex are special because their molecular environment
enables them to use the energy from light not only to boost one of their electrons to a higher energy level, but
also to transfer it to a different molecule-- the primary electron acceptor

Each photosystem functions in the chloroplast as a unit; primary converter of light energy to chemical energy

Carotenoids accept high energy wavelengths
Then chlorophyla b
Then chlorophyll a
Then reaction center (P680)
Transfer of excitation energy is just like a funnel
Diameter corresponds to energy level

Components of a Photosystem
Reaction system chlorophyll a
2 photosystems
Photosystem II functions first and is best at absorbing at 680 nm
Photosystem I is best at absorbing 700 nm
Works together to use light energy to generate ATP and NADPH


PHOTOSYNTHESIS

THE CHLOROPLAST

LIGHT DEPENDENT REACTIONS

MARCH 07, 2017
Recap:
Components of a photosystem
Light harvesting complexes
With pigment molecules like chlorophyll a and b and carotenoids that helps transfer energy
Reaction center
With special chlorophyll a molecules that is start of reaction gradeint
Primary electron acceptor
With electron gradient

The thylakoid membrane is populated by two types of photosystems that cooperate in the light reactions of
photosynthesis:
Two types of Photosystems
II and I (by order of discovery)
Differ in the max wavelength that they can absorb (wavelength maxima)
II -> best at wavelength of 680 nm
I -> best at wavelength 700 nm (far red area)
Work together to use light energy to generate ATP and NADPH
Two pigments are nearly identical chlorophyll a molecules, but association with different proteins in the thylakoid
membrane affects the electron distribution in the two pigments and accounts for the slight differences in their
light-absorbing properties

Proofs of two Photosystems
Quantum Yield of Photosynthesis
o

o No. of photochemical products/ total no. of quanta absorbed
o Indicates that far-red light alone is inefficient in driving photosynthesis
There is a drastic drop for far-red light of wavelengths greater than 680 nm
o Slight dip near 500 nm reflects somewhat lower efficiency of photosynthesis

Enhancement Effect
o The rate of photosynthesis when red and far-red lights are given together is greater than the sum of the
rates when they are given apart
o The enhancement effect provided essential evidence in favor of the concept that photosynthesis is carried
out by two photochemical systems working in tandem but with slightly different wavelength optima
o PS II (P680) is driven best by Red light and PS I (P700) is dreven best by Far Red light

Photochemical Reaction Pathway


First to function is PSII; between II and I is an electron transport chain

There is 2 electron transport chain in the chemical reaction
ATP and NADPH released in stroma where calvin cycle will occur
There is also the evolution of oxygen resulting from split of water from hydrogen and oxygen

2 Pathways for Electron flow
Cyclic and Non-cyclic (with 2 Photochemical systems; main purpose for the generation of ATP
(Photophosphorelation because it makes use of light)
Noncyclic
o with 2 Photochemical systems
o main purpose for the generation of ATP (Photophosphorelation because it makes use of light)
o Produces ATP and NADPH which is the reducing power
Steps

LINEAR ELECTRON FLOW
A flow of electrons through the photosystems and other molecular components built into the thylakoid membrane
Occurs during the light reactions of photosynthesis

In PS II
1. A photon of light strikes a pigment molecule in a LHC of PSII, boosting one of its electrons to have a
higher energy level
Excitation

As this electron falls back to ground state, a nearby electron is simultaneously raised to excited
state
This continues until energy is relayed to the pighment P680 pair in the PS II RCC and excites this
electron pair
2. Electron is transferred from the excited P680 to the primary electron acceptor; turns P680 to P680+
3. Enzyme catalyzes splitting of water
Photolysis of water
Splitting of water into H and O atoms
Supply of electrons one by one to P680, replacing an e- lost to the primary e- acceptor
O atom combins with another O atom forming O2
Electrons are supplied one by one to the P680+ pair, each electron replacing one transferred to
the primary electron acceptor
P680+ is the strongest biological oxidizing agent known; its electron hole must be filled
H+ released into the thylakoid space and O atoms form into O2
4. ETC
Passing of photoexcited e- from the primary e-acceptor of PSII to PSI via ETC
Components are similar to those of the electron transport chain that functions in cellular
respiration
ETC between PSII and PSI is made up of the electron carrier plastoquinone (Pq), a cytochrom
complex and a protein called Plastocyanin
5. Exergonic "fall" of electrons to a lower energy level provides energy for ATP synthesis
Proton gradients across the thylakoid membrane which is a form of membrane potential used to
produce ATP;
As electrons pass through the cytochrome complex, H+ are pumped into the thylakoid space,
contributing to the proton gradient that is subsequently used in chemiosmosis
IN PS I
6. nvolves Photosystem I
Transfer of light energy via LHC to PSI RCC excites eletron of the P700 pair of chlorophyll a
molecules located there
Captured photoexcited e- is then transferred to PSI's primary electron acceptor, creating a new
electron hole in the P700, turning it to P700+; which can now act as electron acceptor, accepting
an electron that reaches the bottom of the electron transport chain from PSII
7. 2nd ETC
Passing of photoexchited e-s from PSI's primary e'acceptor down to a second ETC through the
protein ferrodoxin (Fd)
Chain does not create proton gradient therefore does not produce ATP
8. Transfer of electrons from Fd to NADP+ and NADP+ reductase
Enzyme NADP+ reductase catalyzes the transfer of electrons from Fd to NADP+
2 electrons required for its reduction to NADPH; molecule is at a higher energy level than water,
so electrons are more readily available for the reactions of the calvin cycle
NADPH Reductase can only accept one proton (so may extra NADPH)

Oxygen-Evolving Complex
Only known biochemical system that carries out the photolysis of water leading to oxygen evolution
Hypothesis: Role of Mn, Cl, and Ca ions
Mn ions (4 clusters) undergo a series of oxidations known as S states (S1, S2, S3, S4) are linked to water oxidation
and oxygen generation
o PS II produces a strong oxidant
A cluster of four manganese ions associated with a small complex of proteins that are responsible for the splitting
(oxidation) of water and the consequent evolution of molecular oxygen.
Manganese absorbed and transported within the plant mainly as the divalent cation Mn2+

o Mn required as a cofactor of enzymes like decarboxylases and dehydrogenases
o Can be substituted for magnesium
o Photosynthetic Oxygen Evolution
o Manganoprotein
Part of an oxygen-evolving complex associated with photosystem II, where it accumulates charges
during the oxidation of water
OEC: Responsible for the splitting (oxidation) of water and consequent evolution of molecular oxygen
Located on the lumen side of the thylakoid membrain; bound to the D1 and D2 proteins of the PSII reaction center
and functions to stabilize the manganese cluster
Binds to Cl- which is necessary for the water splitting function
Cyclic Electron Flow: A second Phosphorylation Sequnce

Involved only PSII
Produces only ATP (No NADPH produced, no Oxygen is formed)
Cyclic electron flows generates surplus ATP, satisfying the higher demand in the Calvin cycle

oExcited electrons accepted by ferrodoxin is accepted again by Cytochrome complex

Controlled by the concentration of NADPH (feedback mechanism)
Cyclic Electron Flow
Uses photosystem I, but not photosystem II; Cyclic flow is a short circuit: the electrons cycle back from ferredoxin
(Fd) to the cytochrom complex

ATP SYNTHESIS MECHANISM

Thylakoid
o PSII and Photosystem I joined by ETC and another ETC connecting PSI to NADP+ Reductase
Proton gradiend due to high Proton concentration in the Thylakoid space
Protons pass through ATP synthase which then converts ADP to ATP (Photophosphorylation; addition of
Phosphate group to ADP to form ATP driven by light)
o Chemi-osmotic mechanism
o By proton gradient that drives diffusion

Functions of Light Reactions

The light reactions use solar power to generate ATP and NADPH
Proton Motive Force
o Created by a proton gradient
Photophosphorylation
Chemiosmotic mechanism
ATP required for carbon

Regulation between noncylcic and cyclic electron flow
The concentration of NADPH may help regulate which pathway, cyclic vs. noncyclic, electrons take through the
light reactions
If the chloroplast runs low on ATP for the Calvin cycle, NADPH will begin to accumulate
The rise in NADPH may stimulate a temporary shift from noncyclic to cyclic electron flow until ATP supply catches
up with demand

THE PHOTOSYNTHETIC CARBON REDUCTION CYCLE

March 14, 2017
CALVIN CYCLE
Light independent phase of photosynthesis
1. Carbon fixation (catalyzed by rubisco enzyme)

2. Reduction of intermediates

3. Regeneration of CO2 acceptor which is Ribulose BisPhosphate

The function of the pathway is to produce a single molecule of glucose
Also known as the Photosynthetic Carbon Reduction Cycle

1. Carbon Fixation
o Involves carboxylation: Co2 combines with RuBP to produce PGA
o RuBP carboxylase (rubisco) catalyzes the merging CO2 and RuBP (6 CO2 combine with 6 RuBP to produce 12
PGA)
o PGA is 3-Phosphoglycerate
o Intermediate: 2-Carboxy-3-ketoarabinitol-1,5-bisphosphate
A transient, unstable, enzyme bound intermediate
o Kaya c3 pathway because of 3-phosphoglycerate
o First reaction: Carboxylation
o Second reaction: Hydrolysis

2. Reduction
o ATP and NADPH are incorporated into PGAL or G3P, making it very energy-rich
o ADP, Pi, NADP+ are released and then reenergized in noncyclic photophosphorylatoin
o 12 ATP and 12 NADPH are used to convert 12 PGA to 12 PGAL or G3P
o G3P: Glyceraldehyde-3-phosphate
2. Regeneration
o Regenerating the 3 RuBP originally used to combine with 3 CO2
o Allows the cycle to repeat

o One G3P goes out and turns into glucose and other compound, the other 5 are used to be converted to 6
RuBP
6 ATP are used to convert 10 G3P to 6 RuBP
Overall:
9 ATP is used
6 NADPH is used

The Calvin cycle uses ATP and NADPH to convert CO2 to sugar
Carbon enters the cycle as CO2 and leaves as a sugar named G3P
The calvin cycle regenerates its material called RuBP
After 2 turns, G3P are created in Reduction step, but only 10 are used in Regeneration step; the two remaining
G3P are used to build glucose and other monosaccharides

Summary:

PHOTORESPIRATION

Alternative Mechanisms of Carbon Fixation have evolved in hot, arid climates
Dehydration is a problem for plants, sometimes requiring tradeoffs with other metabolic processes, especially
photosynthesis
On hot, dry days, plants close stomata, conserving water but also limiting photosynthesis
The closing of stomata reduces access to CO2 and causes O2 to build up
These conditions favor a seemingly wasteful process called photorespiration or photorespiratory oxygenation

Photosynthetic CO2 Fixation and Photorespiratory Oxygenation are Competing reactions
An imporant property of rubisco is its ability to catalyze both the carboxylation and the oxygenation of RuBP
o Oxygenation is the primary reaction in a process known as photorespiration
In photorespiration, rubisco adds O2 to the Calvin Cycle instead of CO2
Photorespiration consumes O2 and organic fuel and releases CO2

The flow of carbon in the leaf is determined by the balance between two mutually opposing cycles
The calvin cycle is capable of independent operation in the presence of adequate substrates generated by
photosyntetic electron transport
The C2 oxidative photcycle

Photorespiration: An Evolutionary Relic?
Photorespiration may be an evolutionary baggage -- a metabolic relic -- because rubisco first evolved at a time
when the atmosphere had far less O2 and more CO2

In many plants, photorespiration is a problem because on a hot dry day it can drain as much as 50% of the carbon
fixed by the calvin cycle
A two carbon compound (Phosphoglycolate) is formed in the chloroplast
Peroxisomes and mitochondria rearrange and split compound, releasing CO2

THE C4 DICARBOXYLIC ACID PATHWAY

C4 Plants
Special "add on" feature to C3 pathway
Plants minimize cost of photorespiration by incorporating CO2 into 4 carbon compounds in mesophyll cells -- prior
to calvin cycle
These four carbon compounds are exported to bundle sheath cells, where they release CO2 that is then used in
the Calvin Cycle
The CO2 concentration is maintained in the bundle sheath, favoring photosynthesis over photorespiration
C4 plants: sugarcane, corn, members of the grass family
C3 plants: rice, wheat, soybeans

Kranz Anatomy

PEP Carboxylase is the enzyme involved in C4

C4 derived from Oxaloacetate (4C)
o Also an intermediate in the citric acid cycle
o Converted into malate
o Malate (C4 acid) decarboxylated in bundle-sheathe cell where it is converted into pyruvate (C3 acid)

THE CRASSULACEAN ACID METABOLISM PATHWAY

CAM Plants
Another special add-on feature to C3 pathway
Members of crasssulaceae
"Crassulacean Acid Metabolism"
Open their stomata at night, incorporating CO2 into organic acids

Stomata close during the day, and CO2 is released from organic acids and used in the calvin cycle
Succulent plants, many cacti, pineapple
The physiology of this pathway is almost identical to C4 photosynthesis, with the following changes
o PEP Carboxylase still fixes CO2 to OAA, as in C4
o Malic acid (instead of Malate) is shuttled to the vacuole of the mesophyll cell, not moved out of the cell to
bundle sheath cells as in regular C4

o During the night, PEP carboxylase is active and malic acid accumulates in the cell's vacuole
o During the day, malic acid is shuttled out of the vacuole and converted back to OAA (oxaloacetate) in the
chloroplasts (Requiring 1 atp to adp) releasing CO2, which is then fixed by rubisco, continuing the calvin
cycle
Similarities of C4 and CAM pathways:
NEED
SPATIAL SEPARATION
TEMPORAL SEPARATION

Diurnal regulation of the Phosphoenolpyruvate (PEP) Carboxylase
Active night form is insensitive to malic acid
Phosphorylation of the serine residue (Ser-OP) yields a form of the enzyme which is active during the night and
relatively insensitive to malate
During the day, dephosphorylation of serine (Ser-H) gives a form of the enzyme

EXPORT AND STORAGE OF PHOTOSYNTHETIC PRODUCT

G3P
Not only used for synthesis of simple carbohydrates
Also used for synthesis of starch (storage form)
Amino acid production
Fatty acid production
Also for sucrose which is the exportable form of the carbohydrate

Carbohydrate synthesis
The synthesis of starch and sucrose are competing processes that occur in the chloroplast and the cytosol
respectively. When the cytosolic Pi concentration is high, chloroplast triose phosphate is exponed (?) to the
cytosol via the Pi in exchange for Pf and sucrose is synthesized. When the cytosolic P4 concentration is low, triose
phosphate is rezined (?) within the chloroplast, and starch is synthesized. The numbers facing the arows are
UDP Glucose used for sucrose
ADP Glucose used for starch

Next meeting: Translocation of the Products of Photosynthesis (Read daw in campbell)
Read in teiss and zeiger yung other parts nung kulang kanina
Campbell also

Translocation of product in photosynthesis

Phloem transports the products of photosynethesis and other organic nutrients
Translocation occurs through sieve-tube elements, or sieve-tube members
End walls are called sieve plats
Companoin cell
o Non conducting cell alongside each sieve tube element, and connected to it by its plasmodesmata
o Another term is transfer cell
Movement from sugar sources to sugar sinks
Phloem sap is an aquaeous solution that is mostly sucrose
It travels from a sugar source to a sugar sink
A sugar source is an organ that is a net producer of sugar, such as mature leaves
A sugar sink is an organ that is a net consumer or storer of sugar, such as a tuber or bulb, growing roots, shoot
tips, stems, fruits
First step
Sugar must be loaded into sieve-tube members being exposed to sinks (Phloem loading)
In many plant species, sugar moves by symplastic and apoplastic pathways

Loading of sucrose into phloem
Section of al leaf where you can see the mesophyll cells
Mesophyll cells are where sucrose comes from mostly
2 adjacent mesophyll cells unload into the bundle sheath cells to phloem parenchyma cell to companion or
transfer cell to seive tube element
2 pathways: symplastic and apoplastic
Sucrose from cell wall must move crossing a membrane as illustrated by (b)

o Requires ATP for proton pump
Apoplastic path favored more than symplastic
In many plants, phloem loading requires active transport
Prolton pumping and cotransport of sucrose and H+ enable the cells to accumulate sucrose

Pressure flow: The mechanism of sucrose translocation in angiosperms
In studying angiosperms, researchers have concluded that sap moves through a sieve tube by bulk flow driven by
positive pressure known as pressure flow

STEPS:
1. Loading of sugar into the sieve tube at the source reduces water potential inside the sieve tube elements

a. Causes tube to take up water by osmosis
b. Hypertonicity attracts water from adjacent xylem
2. Uptake of water generates a positive pressure (Pressure flow) that forces the sap to flow along the tube
3. Pressure releaved by unloading of sugar to the sink, lowering water potential, displacing h2o into nearby xylem
4. Water displaced recycled through the transpiration stream

What if there are more sinks than source?
Sinks vary in energy demands and capacity to unload sugars
In some plants, there are more sinks than can be supported by sources
Self-thinning; removing skins, plants may abort some flowers, young fruits, or seeds
o Results to larger but fewer fruits

Plant Cellular Respiration: How Plants Harvest Chemical Energy to Generate ATP

Photosynthesis
Process of incorporating energy from light
Respiration
Oppposite process
Extraction of the stored energy from glucose to form ATP (from ADP and Pi)
Generally considered to begin with glucose
A complicated process, basically the oxidation of glucose

Respiration: The Oxidation of Glucose
Oxidation of glucose basically involves
Splitting apart of G molecule until it becomes CO2
Removal of hydrogen atoms from carbon atoms
Combining of H+ with oxygen which is reduced
As the glucose molecule is oxidized, some of its energy is extracted in a series of small discrete steps and is stored
in the phosphoanhydride bonds of ATP
However, most of its energy is dissipated as heat energy

ATP
Thre phosphate groups attached to ribose attached to adenine

Bonds between phosphate group can by broken by hydrolysis
Hydrolysis of the end phosphate group forms adenosine diphosphate

March 21

Stages of Cell (Aerobic) Respiration (antok)


Stage 1: Glycolysis
Breakdown of the 6-C glucose molecule to two 3-C molecules of pyruvic acid or pyruvate
Direct burning would release an amount of energy many times larger than any carrier molecule could
capture
Stepwise oxidation using enzymes; cells degrade each glucose molecule step by step through coupled
reactions
Energy released from glucose breakdown is saved in high-energy bonds of ATP and other activated carriers
The controlled, stepwise oxidation of sugar in cells captures useful energy, unlike the simple burning of the
same fuel molecule
Direct burning has a higher activation energy compared to that needed by stepwise reactions

Stage 2: Krebs Cycle or Citric Acid Cycle
Further breakdown of the remnants of glucose molecule to CO2 and H2O, resulting to electrons
Substrate level phosphorylatoin
Stage 3: Electron Transport System/ Chain
Passage of resulting electorns from stage 2
Electron carriers:
NADH, FADH2
Stage 4: Oxidative Phosphorylation
The energy that is released as electrons move through the ETS and is used to form ATP from ADP and
phosphate

Pathatas of anareeobic respiration
Ethanil fermentation
Olants, fungi, ba
Lactic Fermentation

Glycolysis


Glycolysis
Central process in stage 2 catabolism
Oxidative breakdown of glucose
Produces ATP without involvement of oxygen
Occurs in cytosol
Evolved early in the history of life on earth
Glucose ---> pyruvate
Net gain: 2 mol ATP and 2 mol NADH per glucose mol broken down
Pathway: 10 steps
o Enzymes
Catalyze glycolysis ---> ase
Enzyme Type General Function Role in Glycolysis
Kinase Catalyzes the addition of A kinase transfers a phosphate group from ATP to
phosphate group to a substrate in steps 1 and 3; other kinases transfer
molecules a phosphate to ADP to form ATP in steps 7 and 10
ATP to Substrate
o 1: Hexokinase
o 3: Phosphofructokinase
Substrate to ADP for ATP
o 7: Phosphoglycerate kinase
o 10: Pyruvate Kinase
Isomerase Catalyzes the Isomerases in steps 2 and 5 prepare molecules for

rearrangement of bonds the chemical alterations to come
with in a single molecule 2: Phosphoglucose isomerase
5: Triose phosphate isomerase
Dehydrogenase Catalyzes the oxidation of The Step 6 enzyme glyceraldehyde-3-phosphate
a molecule by removing a dehydrogenase generates NADH
hydrogen atom plus an
electron (a hydride ion,
H-)
Mutase Catalyzes the shifting of a The movement of a phosphate by
chemical group from one phosphoglycerate mutase in Step 8 helps prepare
position to another the substrate to transfer this group to ADP to
within a molecule make ATP in Step 10


Energy released by breakdown of glucose is used to drive ATP synthesis from ADP and Pi
o Step 7 and 10
o Substrate-level phosphorylation
Transfer of phosphate group from substrate (sugar intermediate) to ADP
NADH

o Remainder of energy released during glycolysis stored in electrons in the NADH molecule produced in
step 6
o Produced through an oxidation reaction; where in electrons are removed from the sugar intermediate
glyceraldehyde-3-phosphate and transferred to NAD+
o 2 molecules formed per molecule of glucose
o In aerobic organisms:
NADH molecules donate their electrons to the electron-transport chain in the inner
mitochondrial membrane
Electron transfers release energy as the electrons fall from a state of higher energy to a lower
one
Electrons passed to O2, forming water
Giving up of electrons convert NADH to NAD+, making it available again for use in glycolysis
o In anaerobic organisms:
NAD+ can be regenerated by an alternate type of energy-yielding reaction called fermentation
Large amounts of ATP then generated in the mitrochondria through oxidative phosphorylation, which
requires oxygen consumption

FERMENTATION
In anaerobic conditions, pyruvate and NADH made by glycolysis remain in the cytosol
Pyruvate converted to excretory products:
o Lactate in muscle cells
o Ethanol and CO2 in yeast cells


NADH gives up electrons in cytosol and is converted back to NAD+ through energy-yielding pathways called
fermentation
Anaerobic respiration
o Alternate way of ATP production in bacteria and archae in the absence of oxygen
o Uses a molecule other than oxygen as the final electron acceptor
o Difference from fermentation:
Involves an electron-transport chain embedded in a membrane (plasma membrane of the microbe)

"Paddle Wheel"
Cells harvest energy from oxidation of organic molecule by coupling an energetically unfavorable reaction to
an energetically favorable one

Lactic Acid Fermentation
Pyruvate is reduced to lactate as an end product, without release of CO2
In fungi and bacteria: used to make cheese and yogurt
In human muscles: to generate ATP when O2 is Low

Ethanol Fermentation
Pyruvate is reduced to ethanol as an end product, with release of CO2
In yeast and some bacteria: used to make beers and wines

Beta Oxidation
Fatty acids can be converted to acetyl CoA in mitochondrial matrix

Protein Catabolism
Amino acids can be converted to pyruvate and other components of the TCA cycle

CITRIC ACID CYCLE
Also called tricarboxylic acid cycle or the Krebs cycle
Accounts for 2/3 of total oxidation of carbon compounds in most cells
Major product:

CO2, and high-energy electrons in the form of NADH
CO2: waste product
NADH: passed to the electron transport chain in the inner mitochondrial membrane
Electrons combine with O2 to produce H2O
Takes place in the mitochondrial matrix
Does not use O2, but requires O2 to proceed because the electron-transport chain (which uses O2 as its final
acceptor) that allows NADH to get rid of its electrons and thus regenerate NAD+ needed to keep the cycle going
Catalyzes the complete oxidation of the carbon atoms of the acetyl groups in acetyl CoA, converting them to CO2
Acetyl group not oxidized directly
Transferred from acetyl CoA to a larger four-carbon molecule, oxaloacetate, to form citric acid
Citric acid:
Six-carbon tricarboxylic acid
Citrate
Progressivelly oxidized, and the energy of this oxidation is harnessed to produce activated carriers (ATP and
NADH)
FADH2 (Reduced Flavin Adenine Dinucleotide)
1 produced per cycle from FAD and one molecule of the ribonucleoside triphosphate GTP (guanosine
triphosphate) from GDP


Oxidative Phosphorylation

On the inner mitochondrial membrane
Only step in the oxidative catabolism of foodstuffs that directly requires O2 from the atmosphere
Common misconcption
Atmospheric O2 is converted into CO2 that is released as a waste product
Oxygen atoms in CO2 in fact are supplied by water
O2 that we breathe is actually reduced to water
ANABOLIC PATHWAYS
Where intermediates formed in glycolysis and the citric acid cycle are siphoned off
Intermediates are converted by a series of enzyme-catalyzed reactions into
Amino acids
Nucleotides
Lipids
Small organic molecules
Ex.
Oxaloacetate ---> aspartate (AA)
Alpha-ketoglutarate ---> glutamate (AA)

THE COMPLETE CITRIC ACID CYCLE

Step 1
Enzyme removes a proton from the CH3 group on acetyl CoA
Negatively charged CH2 forms a bond to a carbonyl carbon of oxaloacetate
Loss by hydrolysis of the Coenzyme A (HS-CoA) drives the reaction slowly forward
Step 2
Isomerization reaction
Water is removed and then added back, which moves the hydroxyl group from one carbon atom to its
neighbor

Step 3
In the first of oxidation steps in the cycle, the carbon carrying the hydroxyl group is converted to a carbonyl
group
Immediate product is unstable, losing CO2 while still bound to the enzyme
Step 4
Alpha ketoglutarate dehydrogenase complex closely resembles the large enzyme complex that converts
pyruvate to acetyl CoA, the pyruvate dehydrogenase complex
Catalyzes an ocidation that produces NADH, CO2, and a high energy thioester bond to coenzyme A (CoA)
Step 5
Phosphate molecule from the solution displaces CoA;
Forms a high energy phosphate linkage to succinate
Phosphate passed to GDP to form GTP
In bacteria and plants, ATP is formed instead

Step 6
3rd oxidation reaction
FAD accepts two hydrogen atoms from Succinate
Step 7
Addition of water to fumarate places a hydroxyl group next to a carbonyl carbon
Creates malate
Step 8
4th oxidation step
Carbon carrying hydroxyl group is converted to a carbonyl group
Gives rise to oxaloacetate needed in step 1

How they discovered the citric acid cycle
Malonate: inhibits succinate dehydrogenase through competittive inhibition
Malonate added A, B, or C to malonate-poisoned tissue suspensions, E accumulated
E also accumulated when F, G, or G was added to malate-poisoned muscle


When muscle suspensions were incubated with pyruvate and oxaloacetate, citrate formed

OXIDATIVE PHOSPHORYLATION
Final stage in the oxidation of food molecules
Stage where chemical energy that is captured by activated carriers produced during glycolysis and citric acid cycle
it used to generate ATP
NADH and FADH2 transfer their high energy electrons to the electron transport chain
Electron-transport chain
A series of electron carriers embedded in the inner mitochondrial membrane in eukaryotic cells
Electrons pass through the series of electron acceptor and donor molecules that form the chain, which then
fall to successively lower energy states
Energy released is used to drive H+ (protons) across the inner membrane, from the mitochondrial matrix to
the inner membrane space
This generates a proton gradient across the inner membrane from the mitochondrial matrix to the
intermembrane space
Source of energy for many reactions such as phosphorylation of ADP to ATP
Excess O2 combine with protons to produce water
Occurs in both eukaryotic cells and aerobic bacteria

====

March 23, 2017

Recap
The conversion of pyruvate to acetylCoA and the Krebs cycle produce large quantities of electron carriers

The fall of electrons during respiration is stepwise, via an electron transport chain


In glycolysis and Krebs Cycle:
At key steps, hydrogen atoms are stripped from glucose and passed first to a coenzyme NAD+ as well as FAD

Topic: Key steps in glycolysis

CELL RESPIRATION
Harvest if useful energy from the chemical-bond energy locked in sugars as the sugar molecule is broken down
and oxidized
Activated carriers
ATP and NADH
Captures high energy released from sugar breakdown
Portable sources of chemical groups and electrons needed for biosynthesis
Metabolism
The totality of an organism's chemical reactions
Arises from orderly interactions between molecules

Metabolic Pathway
Begins with a specific molecule undergoing a series of defined steps each catalyzed by an enzyme and this process
leads to the creation of a product

Catabolic Pathways
Release energy by breaking down complex molecules to simpler molecules
Degradative processes
downhill
Cellular respiration:
Sugar glucose and other organic fuels are broken down in the presence of O2 to CO2 and H2O.
Energy becomes available for work

Anabolic Pathways
Consume energy to build complicated molecules from simpler ones
Biosynthetic pathways
Uphill

Bioenergetics
The study of how energy flows through living organisms

Energy
Capacity to cause change
Used to do work; movement of matter against opposing forces like gravity and friction

Kinetic Energy
Energy associated with the relative motion of objects
Moving objects may perform work by imparting motion to other matter

March 28

Accounting of ATP production by cellular respiration

Types of fermentation
Alcohol
Lactic acid

Alcohol fermentation pathway

Quiz on respiration

Oxidative Pentose Phosphate Pathway

Exam Coverage:

Up to lipid respiration in germinating seeds

Secondary metabolism covered in third exam nalang

April 02 Notes

Glycolysis and Krebs Cycle: Metabolic Hubs for Breakdown (catabolism) and synthesis (anabolism) of many different
types of molecules

The versatility of Catabolism
Catabolic pathways funnel electrons from many kinds of organic molecules into cellular respiration
Glycolysis accepts a wide range of carbohydrates
Proteins must be digested to amino acids; amino groups can feed glycolysis or the citric acid cycle
Fats are digested to glyceral (glycolysis) and fatty acids (generated by beta oxidation) (used in generating acetly
CoA for the citric acid cycle)
Mas maraming nagegenarate na chemical energy from fats compared to carbohydrates

Glucose-6-phosphate substrate for cellulose synthesis

Triose-phosphate formed during split of glucose (dihydroxyaceton phosphate, glyceraldehyde 3-phosphate)
which can be used for the synthesis of pyruvate
PEP usedfor synthesis of Shikimic acid through the shikimic acid pathway which is also used to form amino
acids for the production of secondary metabolites like auxin, proteins, and other amino acids
Oxaloacetate used very much in the synthesis of amino acids and alkaloids (another class of secondary
metabolites)
Alpha ketoglutarate important for protein synthesis and for the production of porphyrins (chlorophyll,
cytochrome, phytocrome)
Pyruvate important for synthesis of fatty acids, and isoprenoids (chlorophyll tail and caroteinoids) used in
production of giberellins and terpenes

Question: mauubusan ba ang intermediates?
There are mechanisms that replenish intermediates
"anaplerotic reactions"
Involves unique anaplerotic enzymes that replenish the intermediates
Anaplerotic Pathway for Oxaloacetate synthesis
Filling-up mechanisim for OAA replenisment
Carbon from glycoluysis delivered to Cac through 2 streams

Via PEP to oxaloacetate and malate
Via pyruvate and acetyl coa
Unique Features of Plant Citric Acid Cycle
Significant activity of Anaplerotic enzymes
Significant activity of NAD+ malic enzyme
Produces pyruvate
PEP carboxylase
To produce OAA from PEP
PEP Carboxylase and malate dehydrogenase
To produce malate from PEP
Pyruvate kinase and PEP carboxylase
Conversion of PEP 2-oxoglutarate, used in N assimilation
Unique in plants: step catalyzed by the succinyl-CoA synthetase produces ATP in plants (and GTP in animals)
Citrica Acid Cycle of Plants has unique features
Malate replenishing
Through oxaloacetate with malate dehydrogenase
Oxaloacetate replenishing through PEP carboxylase
Can also be through malate dehydrogenase
Pyruvate kinase from PEP replenishes pyruvate
Respiration of Lipids in Germinating Seeds
Triglyceride --> glycerol beta oxidation anabolism
----> fatty acids ---------------------------------> acetyl coa ---------------------->
Fadh2+NADH +H2 ---------------------->

Oil body: where lipids are broken down

Glyoxysome: oxidation of fatty acids through beta oxidation
citric acid cycle, but after formation of isocitrate, unique enzymes (Isocitrate lyase) in glyoxysome forms
glyoxylate and succinate
glyoxylate cycle
glyoxylate converted to malate through Malate synthase
intermediates like oxaloacetate and malate transported to the mitochondrion
succinate transferred to mitochondrion

Mitochondrion: where oxaloacetate malate succinate are involved in the citric acid cycle

Cytosol: Gluconeogenesis for the formation of sucrose

Enzymes:
Isocitrate lyase
Malate synthase

Quiz: from photosynthesis lesson last meeting (enzymes) and this meeting
Calvin cycle alternative

Plants, Energy, and Carbon: Plant Biochemistry

Hochgeladen von

Dokumentinformationen

Originaltitel

Copyright

Verfügbare Formate

Dieses Dokument teilen

Dokument teilen oder einbetten

Freigabeoptionen

Stufen Sie dieses Dokument als nützlich ein?

Sind diese Inhalte unangemessen?

Copyright:

Verfügbare Formate

Plants, Energy, and Carbon: Plant Biochemistry

Hochgeladen von

Copyright:

Verfügbare Formate

Bio

121 LE2 | NAT BOHULANO

PLANTS, ENERGY, AND CARBON: PLANT

o All are antioxidants in humans and also in photosynthesis

For chlorophyll a; violet-blue or red light work best for photosynthesis

Exposed different segments of filamentous alga to different wavelengths by using a prism

First to function is PSII; between II and I is an electron transport chain

Cyclic Electron Flow: A second Phosphorylation Sequnce

oExcited electrons accepted by ferrodoxin is accepted again by Cytochrome complex

1. Carbon fixation (catalyzed by rubisco enzyme)

PEP Carboxylase is the enzyme involved in C4

Isomerase Catalyzes the Isomerases in steps 2 and 5 prepare molecules for

o Ethanol and CO2 in yeast cells

E also accumulated when F, G, or G was added to malate-poisoned muscle

Glucose-6-phosphate substrate for cellulose synthesis

Das könnte Ihnen auch gefallen