Biochem Topic #7 (Lectures 20-23)

Components in TCS (two component regulatory systems)

Histidine Kinase and response regulator

Response Regulator Structure

N Term receiver domain

C term DNA binding domain

PhoP-PhoQ TCS

Found in Salmonella

Activated in host cell conditions (Low Mg2+, low pH, antimicrobial peptide presence)

Function of TCS

Ligand induced binding triggers autophosphorylation

Phosphorylation of response regulator which binds directly to DNA for gene expression

Mechanisms the PhoP-PhoQ activates

mgtA expression-Blocked by high concs of Mg2+

rstA-increases Fe2+ uptake

Chromophore

Molecule absorbing light

Light Reactions location

thylakoid membrane (chloroplast)

Carbon assimilation location

stroma (chloroplast)

Phycobilins

pigments used by cyanobacteria and red algae to absorb light

Chl a and Chl b

Pigments to absorb light. a found in all plants b only in green algae and land plants

Carotenoids

Accessory pigments absorb light at other wavelengths and protect from ROs

Photochemical reaction center

special pair of chlorophyll molecules (Chl)2 that convert light energy to chemical

Antenna molecules

pigments around the photochemical reaction center

ETC and charge separation

Flow of electrons through ETC causes proton to be pumped across thylakoid membrane used to produce ATP 

Cyclical electron flow

produces only ATP

Noncyclical electron flow

ATP+NADPH

PS1 vs PS2 Abs range

PS1-Far red (700nm)

PS2-Red (680nm)

Z scheme Explained

PS2 light gives initial boost to higher energy state

Descend through cytochrome b6f producing ATP

PS1 photon boosts up again reach summit giving energy to NADP+ forming NADPH 

PSII function

Splits water, release O2, supplies electrons and adds protons to lumen

PSI function

Excites electrons again reduces NADP+ to NADPH 

stoichiometry of light dependent reactions

2 photons-transfers one electron from H2O to NADP+

8 photons-release one O2

Calvin Cycle 3 Stages

Fixation of CO2

Reduction of 3-phosphoglycerate to a triose

Regeneration of ribulose 1,5 biphosphate (RuBP) (5/6 of triose molecules used to do this)

Location of the 13 enzymes in Calvin cycle

stroma

Rubisco Function

Fixes CO2 to RuBP to create two 3-phosphoglycertae (first stable product for c3 plants)

Rubisco form 1

Found in most plants

Rubisco form 2 

Found only in certain photosynthetic bacteria 

Rubisco Structure

8 large subunits (encoded in chloroplast genome)

8 small subunits (encoded in nuclear genome)

Rubisco Cofactors

Carbomoylated Lys and Mg2+

Carbon Assimilation summary

Rubisco fixes CO2 to RuBP to create two 3-phosphoglycertae

ATP and NADPH reduce 3-PGA to G3P (glyceradahyde 3 phosphate) 

Some G3P recycled to created more RuBP

Carbon Assimilation Stoichiometry

6 NADPH and 9 ATP Per G3P

Pi-Triose antiporter

imports Pi for photophosporylation and exports G3P for sucrose construction 

Photorespiration

Occurs because of high O2 presence rubisco can also accept O2 instead of CO2

Creates only one G3P and one wasteful G2P

Oxidative photosynthetic carbon cycle

Chloroplast, peroxisome and mitochondria

converts G2P into serine and eventually G3P

C4 Pathway

Concentrates CO2 around rubisco limiting photorespiration

PEP carboxylase and Rubisco Locations in C4 plants

Pep Carboxylase-mesophyll

Rubisco-Bundle sheath

C4 plant first stable intermediate 

Oxaloacetate

C4 Plants stoichiometry

5 ATP to assimilate one CO2

3 ATP- C3 Plants

Nitrification 

Oxidation of NH4+ to (NO2-) and then to NO3-

Denitrification

Reduction of NO3- and NO2- to N2 (Only anaerobic bacteria)

annamox bacteria

Anaerobic conversion of NH3 and NO2- to N2

NH4+ harm

can dissipate pH gradients

Steps of NO3- assimilation

Nitrate Reductase reduces NO3-(nitrate) to NO2- (Nirtrite)

Nitrite reductase reduces NO2- to NH4+ (ammonium)

Nitrogen Fixation

N2 to usable forms of nitrogen like NH4+ or NO3-

Catalyzed by nitrogenase

Anaerobic N-fixing bacteria location

Within plant cells called heterocysts (No PSII=no oxygen production)

Glutamine synthase

Catalyzes the conversion of ammonium into amino acids (1st step)

End product is glutamine

GOGAT (aka glutamate synthase)

NADH GOGAT-non photosynthetic tissue

Fd GOGAT-cholorplasts

end product is 2 glutamates

Aminotransferase

Form other amino acids from taking amino group from Glu and putting on a-keto acid

Sulfur Assimilation in plants

Taken up as sulfate (SO4 2-) by H+-SO42- symporter

Needs to be activated first to form APS and PPi 

ATP Sulfurylase

Catalyzes the activation of sulfate

Sulfur assimilation Stoichiometry

Requires 10 e- to be converted to Cys