11. Autotrophy Flashcards
What is the largest carbon reservoir on earth?
Mostly in rocks and sediment, although there is a lot of inorganic carbon under da seaaaaa
What is an autotroph? What types of autotroph are there?
Can fix CO2 into cell material.
Chemo- use inorganic compounds as energy source
Photo- use light as energy source
What are two types of chemoautotroph?
Obligate - metabolic pathways constitutively expressed
Facultative - may use organic matter/CO2 as carbon source -
What are the 6 ways of fixing carbon?
- Calvin-benson-bassham cycle
- Reverse tricarboxylic acid cycle (TCA, citric acid, krebs cycle)
- Reductive acetyl CoA pathway (used by acetogens/acidophiles){
- 3-hydroxypropionate pathway
- Decarboxylate/4-hydroxybutyrate pathway
- 3-hydroxypropionate/glyoxylate cycle
Describe some symbiotic relationships of chemoautotrophs (hint Under the seaaaaa)
Hydrothermal vents - symbiotic relationship between sulphide-oxidising chemoautotrophs and invertebrates. The CO2 produced by the calvin cycle provides organic carbon source for invertebrates.
What are most chemoautotrophs?
Aerobic living
In which type of -troph is the calvin cycle most common in?
Chemolithoautotrophs and oxygenic photoautotrophs
What is the most abundant enzyme on earth?
RuBisCO
What does RuBisCO catalyse? What is required for the reaction?
CO2 fixation
Energy and reducing power (ATP And NADH/NADPH)
What are the three steps in the calvin cycle?
Fixation: 5 carbon forms 6 carbon which splits into two 3 carbons
Reduction: 3C is phosphorylated and reduced to GA3P
Regeneration: 5C molecule reformed
Describe the steps in the calvin cycle including the exact molecules created/used
Fixation: Ribulose 1, 5 bisphosphate is carboxylated by RuBisCO (addition of CO2), 6C splits into two 3-phosphoglycerate molecules with the addition of H2O
Reduction: ATP phosphorylates 3-phosphoglycerate to 1,3-bisphosphoglycerate and NADH reduces it to glyceraldehyde-3-phosphate - this hexose sugar then undergoes glycolysis
Regeneration: Ribulose-5-phosphate is generated by glycolysis, this is phosphorylated by ATP to Ribulose 1,5 bisphosphate
What is the overall stoichiometry of the calvin cycle? Give it in equation form
6CO2 + 12NADPH + 18ATP –> C6H12O6(PO3H2) + 12NADP+ + 18ADP + 17Pi
Where are most of the enzyme of the calvin cycle found? Which one isn’t?
Most are found in the cytoplasm but RuBisCO is found in carboxysomes (polyhedral inclusion bodies)
What is the diameter of the carboxysomes?
120nm
How does the cell respond to varying CO2 and organic carbon conditions?
IF there is high CO2 levels then cells respond by synthesising lots of RuBisCO and packaging it into carboxysomes. If low then less RuBisCO.
If organic carbon is present (in facultative autotrophs), fixing of CO2 is not necessary, so RuBisCO is not produced
What may RuBisCO also produce which is harmful to glycolysis?
Phosphoglycolate (from oxygenation of Ribulose 1,5 bisphosphate) which can inhibit triode phosphate isomerase
Describe the four types of RuBisCO, where they are found, what subunits they are made up from
Type I: main type found in proteobacteria/cyanobacteria/algae/plants, L8 S8 configuration (8 large, 8 small subunits)
Type II: found in proteobacteria - L2
Type III: found in Archaea - L10
Type IV: RuBisCO like but involved in methionine salvage pathway - L2
What are the size of the subunits in RuBisCO?
Large: 50-55kDa
Small: 12-18kDa
Why does RuBisCO have such a low enzyme turnover when it’s bee around for so long?
O2 competes with CO2 for the active site - the enzyme was used when no oxygen was present so hasten yet got used to the fact that there is now oxygen (Rubisco also displays oxygenase activity)
What are the four types of Type I RuBisCO? What are they present in?
A: present in cyanobacteria, proteobacteria
B: cyanobacteria, green algae, plants
C: proteobacteria
D: non-green algae
Which is the most ancient type of RuBisCO?
TYPE II, also has the poorest CO2 affinity - operates exclusively under high CO2 and low O2 levels
What is the role of phosphoribulokinase?
Present in the regeneration step of the calvin cycle, responsible for regenerating ribulose 1,5 bisphosphate from ribulose 5 phosphate
What are the forms of PRK?
Occur as octamer in calvin cycle - unique but dimer in plants (subunits - 32-36kDa)
How is the activity of phosphoribulokinase regulated?
Tightly - by concentration of intracellular metabolites, phosphoenolpyruvate is an inhibitor of PRK.
PEP is a product of glycolysis, so the amount of this dictates the amount of carbon available (if more PEP then less PRK)
How may an organism switch from heterotrophic to autotrophic growth?
RuBisCO and PRK are induced (along with other enzymes in the calvin cycle)
What do the cbb genes encode?
Encode RuBisCO (and other enzymes in calvin cycle)
What are the four cbb genes? What do they code for? Where are they present on the chromosome?
cbbR - encodes transcriptional regulator
cbbL - encodes large subunit of RuBisCO
cbbS - encodes small subunit of RuBisCO
cbs - encodes carboxysome genes
cbbL, S and cbs are present as a single transcriptional unit found on chormosomes/plasmids OR EVEN BOTH WOWEE
Describe the structure and role of the cbbR protein?
Structure:
- Conserved N terminal DNA binding domain
- Central/C-terminal domains bind ligands and form multimer
- gene is constitutively transcribed
Function:
- Binds NADH and activates cbb operon
- must have repressor - maybe PEP (as don’t want Rubisco when organic matter around)
Why is type III RuBisCO present in archaea?
It has no need as halophiles with this RuBisCO can’t grow autotrophically using the calvin cycle - they use a modified acetyl coA pathway instead… Just because this enzyme is a homologue Type III RuBisCO doesn’t mean it does the same thing!
What is the rate limiting step of the calvin cycle?
The first step - fixation
