Microbial metabolism

Question 1

What does the nitrogen cycle maintain?

Answer 1

pool of biologically available nitrogen

Question 2

What do Nitrosomonas do?

Answer 2

NH4+ → NO2-

Question 3

What do Nitrobacter do?

Answer 3

NO2- → NO3-

Question 4

Why does ammonia stay in soil more regularly than nitrate?

Answer 4

Nitrate is readily assimilated by plants, but is water soluble and is easily leached from the soil. However, positively charged ammonia is adsorbed to negatively charged clay soils

Question 5

What kind of process is denitrification?

Answer 5

Anaerobic

reduction

Question 6

What is ammadox?

Answer 6

Ammonia is oxidised to dinitrogen anaerobically using nitrite as an electron acceptor process is called anammox
performed by bacteria called
Planctomycetes

Question 7

What special organelle does planctomycetes have that stops hydrazine diffucing across the membrane?

Answer 7

Ladderane

fused cyclobutane rings of ladderanes pack tightly together to form a dense barrier

Question 8

Is the reducion of nitrogen to ammonia exergonic?

Answer 8

Yes

with high energy barrier

Question 9

How is activation enegry of nitrogen fixation overcome in biological fixation?

Answer 9

Binding and hydrolysis of ATP

Question 10

What is Nitrogen fixation catalysed by?

Answer 10

Dinitrogenase reductase and dinitrogenase

Question 11

Describe the structure of Dinitrogenase Reductase?

Answer 11

MW= 60kDa
is a dimer (identical subunits)
4Fe-4S cluster at the interface and a binding site for ATP/ADP on each subunit

Question 12

Describe the structure of Dinitrogenase?

Answer 12

Two types of cofactor

i) two p clusters consisting of bridged pairs of 4Fe-4S clusters
ii) Two iron molybdenum cofactors containing sulphur and homocitrate

Question 13

How are electrons transfered from pyruvate to dinitrogenase?

Answer 13

Via ferredoxin( or flavodoxin) and dinitrogenase reductase

Question 14

What does Dinitrogenase reductase do?

Answer 14

reduces dinitrogenase one electron at a time with at least 6 electrons required to fix one molecules of N2

Question 15

Why are there 8 electrons per N2 molecule in nitrogen fixation?

Answer 15

6 electrons to fix one N2

2 electrons to reduce H+ to H2

Question 16

explain e- flow in nitrgenase reductase?

Answer 16

Only reduced nitrogenase reductase with 4Fe-4S in oxidation stae +1 with two MgATP molecules can associate with nitrogenase.
During this MgATP are hydrolysed to MgADP
single electron tranfered from Fe protein (4Fe-4S) cluster into the MoFe protein.
Fe protein then regenerated

Question 17

in Nitrogenase complex what is the site of substrate binding and reduction? evidence?

Answer 17

FeMo cofactor
Certain mutant strains that are deficient in FeMo cofactor biosynthesis are inactive, but can be activated by the addition of an isolated FeMo cofactor
In a CO-inhibited MoFe protein, electron-nuclear double resonance (ENDOR) spectroscopy shows that the CO binds to the FeMo cofactor, not to the P cluster

Question 18

What does the p cluster do?

Answer 18

mediates electron transfer between the Fe protein and the substrate reduction site of the feMo cofactor because
X-ray crystal structures place the P cluster between the Fe protein [4Fe-4S] cluster and the FeMo cofactor

Amino acid substitutions between the P cluster and the FeMo cofactor perturb the intramolecular transfer of electrons from the P cluster to the FeMo cofactor

Question 19

How do Leguminous plants remove o2

Answer 19

leghaemoglobin

Question 20

Why is No toxic to bacteria

Answer 20

diffuse across bacterial membrane
cause respiratory inhibition and cell death
No can react with superoxide (made by NADPH oxidase) to form peroxynitrite this can nitrate protein tyrosine residues

Question 21

How do Bacteria encounter No during infection

Answer 21

dietary nitrite with stomach acids produce NO
Reduction of nitrate and nitrite by gut bacteria
Production via iNOS and eNOS

Question 22

How does the immune system respond to bacterial antigens?

Answer 22

Gram negative pathogens have LPS moieties
Two glucosamine residues are bound to six fatty acids, and a complex oligosaccharide
o specific chain determines serotype of the bacterium

In response to bacterial lipopolysaccharide (LPS), a signalling mechanism triggers the production of nitric oxide (NO) by iNOS in macrophages and neutrophils.

Question 23

Describe iNOS

Answer 23

N terminal
Oxygenase domain initial binding for substrate uses a haem prosthetic and BH4
C terminal domain Reductase (FMN and FAD)
Calmodulin binding group between iNOS isoform calcium sensitibe

Question 24

Mechanism for NOS?

Answer 24

Some isoforms of NOS are activated by Ca2+/calmodulin (e.g. endothelial eNOS)
NO stimulates guanylate cyclase which increases cGMP levels: this inhibits calcium entry into the cell resulting in diminished eNOS-dependent NO production
iNOS is calcium insensitive binds CAM permenantly

Question 25

How do Ecoli combat CO toxicity?

Answer 25

No is converted to nitrate or nitrous oxide by flavohaemoglobin Hmp under aerobic or anaerobic conditions respectively NO is converted to nitrous oxide via the Flavorubredoxin/Flavorubredoxin Reductase system NorVW under anaerobic conditions. NO is reduced by the periplasmic cytochrome c nitrite reductase NrfA. The diiron protein YtfE repairs iron-sulphur clusters damaged by nitrosative stress. An NO-tolerant respiratory oxidase is induced, Cytochrome bd-I (or CydAB), which facilitates aerobic respiration under microaerobic conditions.

Question 26

How does Cytochrome bd confer resistance to No mediated respiratory inhibition in E coli?

Answer 26

facilitates growth of bacteria in the presence of NO

Question 27

How does flavohaemoglobin Hmp of E coli detoxify NO?

Answer 27

NO is detoxified to nitrate or nitrous oxide under aerobic or anaerobic conditions, respectively:

Question 28

How is Hmp regulated?

Answer 28

Transcriptional regulator NsrR represses hmp transcription in the absence of NO upon NO exposure iron sulphur clused nitrosylated causing loss of DNA binding hmp expression is then induced. regulated at transciptional lebel by homocysteine.

Question 29

Hmp regulation anaerboic conditions?

Answer 29

NO reacts with the iron sulphur cluster of FNR | alleviates repression of hmp gene

Question 30

How can NO cause antibiotic resistance?

Answer 30

bNOS

Question 31

What does Hydroxamate do?

Answer 31

import iron

Question 32

What are iron binding agents called?

Answer 32

siderophores

Question 33

What are Enterobactins?

Answer 33

produced by bacteria Chelate extracellular iron. siderophores bind iron extremely tightly

Question 34

What kind of pathogens utilise haem as an Fe source?

Answer 34

Gram negative pthogens

Question 35

Explain regulation of iron uptake genes by Fur

Answer 35

Fur is a transcriptional repressor under condiitions of low iron apo-fur dissociates from the promoter regions of iron-responsve genes allowing transcription to take place.

Question 36

What are Lf and CP produced by?

Answer 36

Neutrophils

Question 37

What does the host do in resoinse erythrocyte lysis?

Answer 37

hemopexin sequesters liberated haem. | haptoglobin sequester haemoglobin

Question 38

How does S aureus compete for iron with the host?

Answer 38

Expression of S aureus iron acquisition systems. Alleviation of FUr mediated transcriptional respression. Produces sideophores to scavenge iron from serum.# Isd catalyses extraction of haem through cell wall

Question 39

Explain Isd system?

Answer 39

isdC transports haemto the isdDEF membranetransport system.

Question 40

How do metals help s.aureus combat host defences?

Answer 40

iron deals with NO and peroxide Manganese superoxide

Question 41

When are secondary metabolites formed?

Answer 41

End of exponential growth or during stationary phase its not needed for growth and repoduction highly dependent on growth conditions.

Question 42

What are the most well known auto inducers?

Answer 42

gama butyrolactones of the actinomysetes (Gram+) AHL of Gram- Oligopeptides of Gram+ (bacteriocins)

Question 43

example of Gama butrolactones?

Answer 43

A factor

Question 44

What can A factor do?

Answer 44

induce Antibiotic production becuase stimulates the formation of more than 10 mRNA transcripts

Question 45

A factor mechanism?

Answer 45

A factor binds to ArpA repressor is emoved from DNA binding site allowing expression of target genes

Question 46

What is a modified Bacteriocins called?

Answer 46

lantibiotics

Question 47

How is bacteriocin production regulated?

Answer 47

Quorum sensing

Question 48

What has the smallest genome?

Answer 48

Endosymbionts and parasites | archaeon nanoarchaeum equitans 490kbp