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MBB266 > bacterial bioenergetics - kelly > Flashcards

bacterial bioenergetics - kelly Flashcards

1
Q

name 4 properties of the bacterial resp chain that is different from the mitochondrial respiration chain

A

modular - mix and match components
complexity - number of enzymes/e- acceptors that allow bacteria to grow in many envs
branching - branched chains
gene regulation - composition of chain changes in response to growth conditions

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2
Q

in order to couple e- transfer to proton translocation, does ΔE (redox potential change) have to be bigger or smaller than Δp?
give an equation to describe this relationship

A

ΔE > Δp if e- transport is coupled to proton movement

the efficiency of this is expressed by H+/e- = ΔE/Δp

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3
Q

give 4 reasons for oxygen being a good electron acceptor

A

high abundance
diffusible across membranes
reasonable water solubility
high midpoint redox potential of H2O/O2 make it an excellent e- acceptor

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4
Q

give 2 reasons for oxygen being a bad electron acceptor

A

incomplete reduction = ROS

Cells must produce enzymes to destroy ROSs

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5
Q

name 3 important anaerobic resp processes

A

methanogens
sulphur bac
nitrate reducers and denitrifiers

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6
Q

name 4 reductases and the cofactor they use

A
  • Nitrate reductase – Molybdenum co-factor
  • Nitrite reductase – C-type haem (Fe)
  • Nitrous oxide reductase – Cu cofactor
  • Fumarate reductase – FAD cofactor
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7
Q

why is menaquinone used instead of ubiquinone in e. coli anaerobic resp chains?

A

has lower redox potential - easier to find a suitable e- acceptor

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8
Q

name the 3 principles of fermentation

A
  • The conversion of glucose to pyruvate by, for example glycolysis conserves energy by substrate level phosphorylation but is an incomplete catabolic pathway
  • NADH generated during the process needs to be re-oxidised (redox balance)
  • In the absence of an electron acceptor the microbe must re-oxidise NADH by the formation of fermentation products that are more reduced that the starting substrate
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9
Q

what is the impact on [ATP] [Biomass] in fermentation?

A

a large concentration of fermentation products means that there are low atp and biomass yields, thereby increasing flux to fermentation products

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10
Q

name 6 types of fermentation and what each pathway produces

A 
alcoholic - ethanol
homolactic - lactate 
heterolactic - lactate and ethanol
mixed acid -  formate acetate, ethanol
acetone butanol - acetate, acetone, isopropanol, butyrate, butanol, ethanol
malolactic - lactate from malate
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11
Q

describe alcoholic fermentation, state how ATP and NAD+ are generated and give key enzymes

A

• Occurs commonly in yeasts but also a few bacteria
• Glycolysis produces (2)pyruvate and ATP by SLP (substrate level P)
• (2)Pyruvate decarboxylated to acetylaldehyde by pyruvate decarboxylase (+2CO2)
• (2) Acetaldehyde reduced to ethanol by alcohol dehydrogenase enzyme, using (2)NADH as an e- donor, thus regenerating (2)NAD+
• Ethanol is sole fermentation end product
• At 12-15% ethanol yeast is killed
OVERALL: 2ATP/mol glucose

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12
Q

describe the difference between simple diffusion and carrier-mediated facilitated diffusion

A

• Simple diffusion
o Non-saturable – rate increases linearly with [solute]
o Not inhibited by energy coupling inhibitors
• Carrier-mediated
o Saturation kinetics – due to binding site for the solute within the carrier
o Active transport – requires cellular energy to accumulate the solute against its concentration gradient
o Inhibited by energy coupling inhibitors

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13
Q

define accumulation ratio

A

AR=[solute inside cell]/[solute outside cell]

diffusion AR = 1

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14
Q

what is the difference between primary active transport and secondary active transport?

A

primary:
- depends on direct hydrolysis of chemical bonds to release free energy for transport
secondary:
- using a pre-existing ion concentration gradient to transport substances across a membrane (commonly pmf)

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15
Q

name 4 primary active transporters

A

PEP driven (phosphotransferase systems)
ATP driven (ABC systems)
ATP driven solute-ATPases
decarboxylation driven

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16
Q

name 4 secondary active transporters

A

uniports
symports
antiports
TRAP transporters (bac only)

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17
Q

give a named example of a symport and its substrates

A

LacY permease

- lactose and H+

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18
Q

give 2 examples of an antiport and their substrates

A

DcuA (coupled with Frd) - succinate and fumarate

OxlA - oxalate(2-) and formate(1-)

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19
Q

name a TRAP transporter and its substrate

A

dctPQM
transports C4 dicarboxylates (malate, fumarate, succinate)
uses H+ (pmf)

20
Q

give an example of a ABC transporter and its substrate

A

BtuCDF

transports b12

21
Q

name the substrate of a decarboxylation driven transporter

A

oxaloacetate –> pyruvate + CO2

uses 2Na+ ions

22
Q

name 2 p-type solute translocating ATPases and name their substrates

A

kdp K+ uptake system
K+ using ATP hydrolysis

E. coli Cu exporter
Cu+ using ATP hydrolysis

23
Q

state the starting and end compound(s) of homolactic fermentation, key enzymes and where NADH/NAD+/ATP are evolved. which bacteria use this fermentation?

A

Glucose –> 2 pyruvate –> 2 lactate
pyruvate –> lactate by lactate dehydrogenase (regen of 2NAD+)
aldolase
2NADH used GAP–>1,3BP
lactic acid bacteria gram +ve aerotolerant
OVERALL: 2 ATP made

24
Q

state the starting and end compound(s) of heterolactic fermentation, key enzymes and where NADH/NAD+/ATP are evolved. which bacteria use this fermentation?

A

glucose –> 2pyruvate –> lactate + ethanol
pyruvate—>lactate = LDH enz
phosphoketolase does SLP
lactate formation arm = 2ATP regen, NADH use and NAD+ regen
ethanol formation arm = 2NAD+ regen
2NADH used in main pathway (before branchpoint)
lactic acid bacteria
OVERALL: 1ATP/mol glucose

25
Q

state the starting and end compound(s) of mixed acid fermentation, key enzymes and where NADH/NAD+/ATP are evolved. which bacteria use this fermentation?

A 
glucose ---> 2 pyruvate ---> 2 formate + ethanol + acetate
enzymes: phosphotransacetylase (PTA)
Acetate kinase - ACK
Formate hydrogen lyase (FHL)
Pyruvate formate lyase (PFL)
ADH
2NADH used
2NAD+ regen
3ATP formed
2SLP (by Pta and Ack)
E. coli
OVERALL: 3ATP/1 mol glucose
26
Q

state the starting and end compound(s) of ABE fermentation, the key enzymes and where NADH/NAD+/ATP are evolved. which bacteria use this fermentation?

A 
glucose ---> 2pyruvate ---> 1ethanol + 3acetone + 6butanol (biofuel) (+3 others)
anaerobic clostridia bacteria
5 NAD+ regen
2 NADP+ regen
4 ATP made
ADH and BDH used
27
Q

state the starting and end compound(s) of malolactic fermentation, key enzymes and where NADH/NAD+/ATP are evolved. which bacteria use this fermentation?

A 
malate ---> lactate
lactic acid bacteria
MleA catalyses
no redox balancing/ATP gen
uses antiport malate2-/lactate1-
28
Q

name the 2 systems for protein translocation across the inner membrane, state simply how they work

A

SEC - protein threaded through then folds in periplasm

TAT - protein folded in cytoplasm, passes through TAT folded

29
Q

describe the SEC mechanism of protein translocation across IM

A
  • Chaperone protein SecB binds nascent protein – prevents folding
  • Signal sequence directs protein to SecYE – forms pore that protein is threaded through
  • SecA = ATPase, drives transport process (with help from Δψ)
  • After export, N-terminal signal sequence is removed by periplasmic signal peptidase
  • Requires accessory protein SecG
30
Q

name and explain the 3 regions of the sec signal sequence

A

o N-terminus: Positively charged (K/R) - Stop signal
o Hydrophobic α-helical region (18-21 a/a) - This inserts into membrane (is cleaved off)
o C terminus: signal peptidase cleavage site (AXA)

31
Q

state how proteins with cofactors are transported across IM

A

• Many electron transport proteins are located in the cytoplasm
• A simple threading mechanism would mean the cofactor was lost
• Cytochromes c:
o Cytochrome c protein enters periplasm via Sec system
o Haem (cofactor) exported separately
o Ligase enzyme binds haem to cytochrome c (at CXXCH motif) after translocation
• All other redox proteins with cofactors are exported via a totally different system, as fully folded proteins

32
Q

describe when the TAT (twin arginine translocase) system is used and in which kingdoms it is found

A

• Found in bacteria, archaea, and plant chloroplasts
• Often used for proteins that contain complex cofactors
o Cofactor inserted in protein as it folds in cytoplasm
• Proteins that are exported via TAT have 2 Arg residues next to each other in the signal sequence

33
Q

describe the TAT mechanism

A

• Signal peptide of TAT substrate recognised and bound by TatBC complex
• TatA polymerises to create a pore (variable diameter to suit that of translocated protein)
o Protein goes through TatA
o Driven by pmf (no ATP)
o Pore size modified by addition/loss of subunits
• After translocation signal sequence cleaved
• TatA and TatBC complexes dissociate
• Tat system mainly used for e- transport proteins, allows proteins to function in periplasm

34
Q

name and explain the 3 regions of the TAT signal sequence

A 
n-terminal region:
contains RR motif
Hydrophobic region
doesnt really do much, may help tatA and tatBC bind
c-region
AXA cleavage region
35
Q

why do bacteria need to secrete proteins beyond the periplasm?

A

extracellular enzymes for digestion

virulence factors

36
Q

which secretion systems transport across the OM only and which transport across the OM and into another cell?

A 
•	Secretion across the OM only
TSS5
TSS2
TSS1
•	Secretion across the OM and into another cell
TSS3
TSS4
TSS6
37
Q

describe the TSS1 system

A

• Used to secrete HlyA (haemolysin) only
o Bacteria use HlyA to release haem for Fe collection
• 3 components:
o ABC-transporter (HlyB) which is connected to (in IM),
o HlyD – multidomain protein which interacts with (in IM),
o TolC – an outer membrane porin-like protein (in OM)
• C-term of HlyA is recognised by HlyB
o HlyA is transported as un unfolded protein (driven by ATP hydrolysis)
• Entire protein is translocated (no signal sequence)

38
Q

describe the TSS2 system

A

• General transporter
• Secretory protein loaded onto platform in periplasm
o Platform pushed out of cell by polymerisation
o Imagine syringe plunging – similar to this
o Requires ATP
• Protein delivered to periplasm by TAT/SEC

39
Q

describe the TSS5 system

A

• Autotransporter – transports itself
• 1 protein
C-terminal part of the secreted protein forms a β-barrel (porin like) in OM
Rest of protein transported through itself (passenger domain)
• Passenger domain is cleaved off and translocator domain (β-barrel) is left then degraded
• Initial transfer to the periplasm is via Sec system
• Used for some bacterial virulence factors
• Structure of protein domains:
N-terminus: signal sequence
Middle: Passenger domain (exported protein)
C terminus: translocator domain (β-barrel)

40
Q

describe the TSS3 system

A

• Acts like needle
Tip injects proteins into eukaryotic cells
• Goes through IM, OM and into another cell
• Structure resembles flagella
Evolutionary link
Found that some flagella export proteins
• ATP driven
• Effector proteins (proteins that disrupt the host cell functioning in some way) and toxins secreted

41
Q

describe the TSS4 system

A

• ATP hydrolysis in cytoplasmic domain
• Transports protein/DNA
Involved in conjugation
Found in some pathogens for protein secretion into host cells
- Eg Agrobacterium tumefaciens (vir plasmid) and Helicobacter pylori (cag protein – disrupts cytoskeleton)
• Genes for this protein encoded on ‘pathogenicity island’
• Related to pilus proteins

42
Q

describe the TSS6 system

A

• Recently discovered in various gram -ve cells
• Syringe-like system related to phage injection apparatus
Maybe phage derived system
• ATP driven
• One example ‘’scratches’’ OM of another bacteria and delivers enzymes that dissolve peptidoglycan
Doesn’t have to target OM of another bacteria

43
Q

which transport systems transport proteins folded

A

TAT
TSS3
TSS4
TSS6

44
Q

which transport systems transport proteins unfolded

A

SEC
TSS1
TSS2 (can do folded via TAT)
TSS5 (can do folded via TAT)

45
Q

which protein transport systems use ATP as an energy source?

A 
SEC (uses pmf too)
TSS1
TSS2
TSS3
TSS4
TSS5
TSS6
46
Q

which protein transport systems use pmf as an energy source?

A

SEC (uses ATP too)

TAT

47
Q

give an example of a (specific) molecule that is transported via each protein translocation system

A 
sec - periplasmic
tat - cofactor proteins
TSS1 - haemolysin
TSS2 - extracellular enzymes
TSS5 - IgA protease
TSS3 - Toxins/effectors
TSS4 - effectors/DNA
TSS6 - effectors/lytic enzymes

MBB266 (6 decks)

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