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Definition
| is the harnessing of photoexcited electrons to power cell growth, it is the ultimeate source of electrons driving metabolism. |
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| An ancient form of photoptrophy based on a single-protien light driven proton pump, used by many halophilic (salt loving) archaea and marine bacteriea like Halobacterium salinarum |
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| proteobacteria that contian homologs of the protein bacteriorhodopsin... found in 13% of marine bacteria. |
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| Bacteriorhodopsin structure and function |
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Definition
Contains 7 hydrophobic alpha helices surrounding a molecule of retinal, which is attached to the nitrogen end of a lysine residue. As the double bonds in retinal absorb light, photoexcitation occurs and one of there electrons gets excited.
As it falls back to ground state, retinal shifts position, causing the entire protein to shift, and making it pick up a proton, as retinal shifts again, the proton gets released on the other side of the pump, thus pumping one H+ across the membrane.
This proton gradient drives ATP synthesis by a typical F1F0 ATP synthase |
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Definition
halobacterium salinarum archaea pack their cell membranes with bacteriorhodopsin so it can catch more light rays since it is spread over a large surface area.
The protein forms trimers that pack in hexagonal arrays and forme the "purple membrane" |
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| ETS-based photosynthesis overview |
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Definition
| photoexcitation of a light absorbing pigment (like chlorophyll)leads to the separation of an electron from a donor molecule such as H2O or H2S. Each electron is then transferred to an ETS, which generates a proton potential and the reduced cofactor NADPH. Proton potential again drives ATP synthesis thru F1F0 ATP synthase. |
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Definition
these are the main light absorbing pigments, they each contain a chomophore which is a light-absorbing electron carrier.
In cyanobacteria chlorophylls a and b absorb red light and blue light, respectively, which is why they reflect green. Chlorophylls in anaerobic phototrophs are often purple because they absorb the most in the far red spectrum. |
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The chromopore contains a htereoaromatic ring that surrounds a magnesium ion. This absorbs a photon and allows the chlorophyll to switch between excited and relaxed states
There are slight differences in their substituents around the ring which causes the chlorophylls to alter their absorption spectra |
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many molecs of chlorophyll are grouped in a circle to what is called an antenna complex
These complexes are arranged like a satellite dish and cluster around accessory proteins. These clusters then form a ring around the reaction center. |
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| the protein complex in which chlorophyll photoexcitation connects to the ETS. When one of the chlorophylls absorb a photon it gets transferred from chlorophore to chlorophore until it reaches the reaction center for electron transfer to the ETS. |
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purple bacteria are anaerobic bacteria that absorb light at a different spectrum then aerobic bacteria. They usually absorb more red and green (from cartenoids) which causes them to look purple or brown. They light they absorb isn't strong enough to break down H2O so they only use H2S. Found in the bottom of the ocean where other aerobic bacteria are not around.
They also absorb light more efficiently by folding their chloroplasts into oval pockets called thylakoids. The interior fold of the thylakoid is the lumen and the interior space is called the stroma |
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Term
| common design for photolysis |
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Definition
1. Atenna system- a complex of chlorophylls and accessory pigments in the membrane that collects photon and transfers the energy to the reaction center.
2. Reaction center complex- the energy from the chlorophyll photoexcitation is used to separate the electron from a small molecule such as H2S (PS 1) or from bacteriochlorophyll (PS 2)
2. Electron Tranport System (ETS)- each photo excited electron enters the ETS. In PS 1 the electron is separated and added to NADP+ to form NADPH. In PS 2 the oxygenic Z pathway electrons flow from PS 2 to PS 1 and release and O2 from H2O forming an H+ potential
4. Energy Carriers- In PS 1 electrons are used to make NADPH, and in PS 2 electron transfer provides energy to pump protons and drive synthesis of ATP |
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Term
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Definition
| very similar to PS 1 in the oxygenic Z pathway, it sepearates electrons assoicated with hydrogens from H2S or an organic electron donor. This electron is used to reduce NADP to NADPH, which provides reductrive energy for CO2 fixation. They can also produce a net proton gradient by consuming H+ inside the cell and generating it outside the cell, making a proton potential to drive ATP synthesis |
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also similar to PS II in the oxygenic Z pathway, it separates an electron from bacteriochlorophyll (because the photon energy absorbed is insufficient to split hydrogenated substrtaes), and the electron is then transferred to the ETS where as it is transferred from quinone to cytochrome 2 protons are exchanged forming a proton potential that drives ATP synthesis, ultimately the electron returned to the bacteriochlorophyll. This is called cyclic photophosphorylation.
No direct way to make NADH or NADPH for biosynthesis |
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Term
| Oxygenic photolysis (the Z pathway) |
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Definition
Found in cyanobacteria and chloroplasts, combines key features of PS 1 and 2. The chlorophylls they use can absorb shorter wavelengths which provide higher energy and are able to split water and yield a greater overall energy. Splitting of water yields 2 protons and electrons per molecule. For every 2 electrons that quinone takes it requires another 2 protons, plus an additional 2 protons from cytochrome bf, causes and overall potential of 6H+.
Proton gradient is approximately 3 ATP per O2
They also have energy to yield NADH of NADPH from PS 1. |
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Term
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Definition
also known as anabolism, is the building of complex biomolecules.
Requirements:
Essential elements like C, H, O, N, and others
Reduction- by a reducing agent such as NADPH
Energy- by coupilng reactions to ATP hydrolysis, NADPH oxidation, or ion flow down a transmembrane concentration gradient
Many substrates for this arise from glycolysis and the TCA cycle
Genomic and energetic costs of biosynthesis led to microbes to evolve cost-saving strategies such as regulation, genome degeneration, and secondary products |
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Definition
elements required for biosynthesis as mentioned before.
Carbon is obtained either through CO2 fixation (autotroph) or thru acquisition of organic molecules made by otehr organisms
Autotrophs form carbon into acetyl-CoA that serve as substrates or building blocks
Heterotrophs break down molecs like sugars and peptides to form acetyl-CoA and other substrates. |
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Definition
many cellular structures require reduction of the substrate.
Cell componenets like lipids and amino acids are more reduced than the substrates available so their biosynthesis must include reduction by a reducing agent such as NADPH |
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Definition
energy is required to build complex structures.
Biosynthetic enzymes spend energy by coupling their reactions to the hydrolysis of ATP, oxidation of NADPH, or the flux of ions down a transmembrane ion gradient |
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Term
| Substrates for biosynthesis |
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Definition
Most substrates come from glycolysis and the TCA cycle.
The TCA cycle provide pyruvate for the back bone of some amino acids, and also gives many amino acids their carbon skeleton from the oxaloacetate intermediate
Oxaloacetate is replaced by combining pyruvate with CO2 and an energy source.
This is an anapleuortic pathway used to replace a necessary intermediate
Glycolysis also provides glycines, and glycerol 3-phosphate which is used as the glyceride backbone of lipids. |
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Definition
a metabolic pathway that both synthesizes (anabolic) and degrades (catabolic) metabolites
EXAMPLE: The TCA Cycle |
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Regulation occurs so that the metabolism avoid making more than what they need and have constant amounts of metablic intermediates like ATP NADH2 and NADPH2.
Allosteric enzymes are used at key points of the pathway to control the metabolism and can bee either activated or inhibited |
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Definition
Each turn of the cycle uses one molecule of CO2 and condenses it with 1,5 biphosphate. For every 3 turns of the cycle one molecule of G3P is used in biosynthesis, 2 molecs of G3P can be condensed to form glucose
It can also enter biosynthesis of amino acids, vitamins, and other essential components of the cell
G3P is the fundamental unit of carbon assimilation into biomass
Discovered by Melvin Calvin, it play a major role in removing atmospheric CO2 or the fixation of carbon dioxide
Performed by Oxygenic phototrophic bacteria, Chloroplasts of algae and plants, facultatively anaerobic purple bacteria, and lithotrophic bacteria |
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| Overview of the Calvin cycle aka reductive phnetose phosphate cycle |
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Definition
3 main phases:
1. Carboxylation and splitting 6C -> 2[3C]
-Ribulose 1,5-biphosphate condenses with CO2 and H2O to form a 6C molecule, which immediately splits into two 3-phosphoglycerate (PGA) molecules
-Reactions are catalyzed by Rubisco
2. Reduction of PGA to G3P
-the carboxy group of PGA is phosphorylated by ATP, and then hydrolyzed and reduced by NADPH
-this generates glyceraldehyde 3-phosphate
3. Regeneration of ribulose 1,5-biphosphate
-one of every six G3P is converted to glucose
-the other five molecules enter a series of reactions that regenerate 3 molecules of ribulose 1,5-biphosphate |
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Term
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Definition
short for 1,5-biphosphate carbon dioxide reductase/oxidase, consists of small (S) and large (L) subunits.
-catalyzes the condensation of CO2 to ribulose 1,5-biphosphate, and the splitting of the unstable 6C intermediate into two 3C PGA molecules |
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Definition
many organisms have Rubisco complex within polyhedral structures called carboxysomes
These carboxysomes take up bicarbonates (HCO3-) which is then immediately converted to CO2 by carbonic anhydrase
CO2 is then fixed by rubisco |
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| Carbon-concentrating mechanism |
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Definition
CO2 can readily diffuse through phospholipid membranes, making it hard to concentrate the levels of CO2 high enough for Rubisco to function
So CO2 is converted in to bicarbonate (HCO3) which can be trapped in by the cytoplasm.
Inside the cell HCO3 is taken up by carboxysomes which fixes CO2 from HCO3.
Rubisco in the carboxysomes then converts the CO2 directly to G3P |
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Term
| The reductive or reverse TCA cycle |
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Definition
Most portions of the TCA cycle are reversible, which allows some CO2 to be used to regenerate acetyl-CoA and build sugars.
All organisms can fix small amounts of CO2 that regenerate TCA cycle intermediates
Some bacteria and archaea can use the entire TCA cycle in reverse to regerneate acetyl-CoA and build sugars
It uses 4 to 5 ATP's to fix four molecules of CO2 and generate one oxaloacetate
Reduction is performed by NADPH or NADH and reduced by ferredoxin (FDH2). |
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| Reductive acetyl-CoA pathway |
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Definition
used by anaerobic soil bacteria, autotrophic sulfate reducers, and methanogens
0two CO2 molecules are condensed through converging pathways to form the acetyl group of acetyl-CoA.
-carbon monoxide is an intermediate
-the reducing agent is H2 instead of NADPH |
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| Fatty Acid Synthase Complex |
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Definition
| contiains all the enzymes and componenet binding proteins bound together in promiximity, so that all steps occur in one place |
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| Biosynthesis of Fatty Acids |
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Definition
Molecules of acetyl-CoA are carboxylated to malonyl-CoA
The coenzyme A is replaced by acyl carrier protein (ACP) making malonyl-ACP
-Malonyl-ACP condenses with the growing chain
-the growing chain now contains a ketone, which is reduced to CH2 by 2 NADPH
Successive addition can continue many times to build a saturated fatty acid of indefinite length |
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Term
| Unsaturation of Fatty Acids |
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Definition
Unsaturation or formation of a double bond in the fatty acid chain can occur during elongation
A special dehydratase enzyme forms the double bond between the third and fourth carbons |
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| Regulatoin of Fatty Acid Synthesis |
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Definition
Fatty acid synthesis uses large amounts of reducing energy and must be regulated closely.
3 ways of regulation
-Acetyl-CoA carboxylase regulates its own transcription
-Starvation blocks fatty acid synthesis through the "stringent response"
-Low temperature favors unsaturated fatty acids by inducing expression of the dehydratase enzyme |
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Definition
many bacteria synthesize polyesters such as polyhydroxybutyrate
These polyester chain are made in the same way as fatty acids, using a cycle to form a long chain by repeated esterfication of the carboxylic acid group of the chain with is hydroxyl group of another unit
Often stored in inclusion bodies, they are used as energy storage, and are not soluble in water.
They are depolymerized when energy is needed |
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Term
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Definition
Polyketides are a diverse group of metabolites taht inclue the antibiotic erthromycin
They are synthesized by an enormous enzyme complex called a modular enzyme, which consists of multiple modules, which add similar but nonidentical units to a growing chain
- Like fatty acids, they are built by successive condensation of malonyl-ACP units, butch each malonyl group carries a unique extension or R group
In erythromycin they are methyl groups |
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Definition
-N2 is ultimate source and sink of biospheric, several oxidized and reduced forms also occur
In some species of bacteria and archaea N2 gas is fixed into ammonium ion (NH4+)
-Aquatic cyanobacteria develop special cells called heterocysts to fix N2
-Photosynthesis is turned off to maintain anaerobic conditions |
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| Mechanism of Nitrogen Fixation |
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Definition
-nitrogen fixatnio is an enomously energy-intensive process
-The same mechanism is used in most species:
N2 + 8H + 8e + 16 ATP -> 2 NH3 + H2 + 16 ADP + 16 Pi
-about 10 ATPs are consumed per N2 fixed
-Nitrogen fixation is catalyzed by the enzyme nitrogenase |
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Term
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Definition
includes two kinds of subunits:
-a protein with an iron-sulfure core (Fe protein)
-a protein containing a complex of molybdenum, iron, and sulfur protein (FeMo protein)
Electrons acquired by Fe protein (with energy from ATP) are transferred to FeMo proteinto reduce nitrogen |
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Term
| 4 reduction cycles through nitrogenase |
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Definition
1. Fe protein acquires 2 e- from an electron transport protein such as ferredoxin, and then transfers them to the FeMo center.
2. The FeMo center binds 2H+, which is reduced to H2 gas
3. N2 can now bind to the active site by displacing the H2
4. Successive pairs of H+ and e- reduce: N2 -> HN=NH -> H2N-NH2 -> 2NH3 |
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Term
| Regulation of Nitrogen fixation |
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Definition
- Oxygen an dNH4+ availability regulate expression of the nif genes, which encode nitrogenase and otehr nitrogen-fixation proteins
-Regulation of nif is mediated by several molecular regulators including:
- a nitrogen starvatino sigma factor (sigma 54)
-NtrB-NtrC two-component signal transduction system
When NH4 conc. is low then NtrC is phosphorylated by NtrB and this binds DNA to promote nitrogenase expression |
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Definition
oxidized sulfur molecules serve as aelectron acceptors for bacteria that synthesize the appropriate reductases
SO4 + 2e -> SO3 + 6e (sulfur reductase) -> H2S |
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Term
| biosynthesis of amino acids |
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Definition
carbon skeletons of AA's come from the diverse intermediates of the metabolism
-certain AA's arise directly from key metabolic intermidiates, ex. Glutamate from 2-oxoglutarate
-Other amino acids are synthesized from preformed AA's, ex. Glutamine and arginine from glutamate
-Others are made from more than one source, ex. leucine nad isoleucine can be made from succinate as well as pyruvate. |
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Term
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Definition
most bacteria assimilate NH4 by condensing it:
with 2-oxoglutarate to form glutamate
or with glutamate to form glutamine
-glutamate and glutamine contribute an amine and their C skeletons to the synthesis of other AA's
Transamination is the transfer of ammonia between two metabolites
ex. Glutamate transfers NH3 to oxaloacetate, makine aspartate and 2-oxoglutarate.
The reaction is reversible |
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Term
| Synthesis of complex amino acids |
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Definition
Some amino acids require long patheays involving numerous enzymes
ex. Arginine synthesis generally invovles a doezen different enzymes distributed among 4-8 operons
-Aromatic AA;s are build form a common pathway that branches out
-synthesis is tightly regulated during both transcription and translation |
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Term
| Purine and pyrimidine synthesis |
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Definition
They aren't built as isolated units, but are built onto a ribose 5-phosphate substrate to form a nucleotide.
Before synthesis of the nucleotide begins Ribose 5-phosphate is converted into 5-phosphoribosyl-1-PP (PRPP) |
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Term
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Definition
The hydrolysis of PRPP releases the pryophosphate, spending 2 high energy bonds, this drives the reaction forward to make purine.
The pyrophosphate is replaced by an amine from glutamine
The purine ring is built out of successive additions of amines plus a formyl group.
The first purine formed is inosine, which can then be converted into AMP (adenosine monophosphate) and GMP (guanosine monophosphate) |
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Term
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Definition
It is built slightly differently
-the six-membered pyrimidine ring forms from aspartate plus carbamoyl phosphate.
-the pyrimidine ring then displaces the pyrophosphate of PRPP, attaching by a nitrogen to the ribosyl carbon 1
The first pyrimidine made is uracil, which can then be converted to CMP (cytosine) or TMP (thymine) |
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Term
| Biosynthesis of tetrapyrrholes |
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Definition
Tetrapyrroles are conjugated ring systems that include chlorophylls, hemes, hemoglobin, and coenzyme B12
The individual pyrrhole rings are generated by either the glutamate pathway or the glycine-succinate pathway.
Once pyrroles are formed, an enzyme condenses four of them in a chain then cyclizes to form the corrin ring system
-the final step of cyclization includes reersal of the D-ring linkage to yield uroporphyrinogen III
-enters various pathways to form the different tetrapyrrole derivatives. |
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