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MBB266 > bacterial bioenergetics - kelly > Flashcards

bacterial bioenergetics - kelly Flashcards

(47 cards)

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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

Study These Flashcards
A

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

20
Q

give an example of a ABC transporter and its substrate

Study These Flashcards
A

BtuCDF

transports b12

21
Q

name the substrate of a decarboxylation driven transporter

Study These Flashcards
A

oxaloacetate –> pyruvate + CO2

uses 2Na+ ions

22
Q

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

Study These Flashcards
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?

Study These Flashcards
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?

Study These Flashcards
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
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?
``` 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
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?
``` 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
state the starting and end compound(s) of malolactic fermentation, key enzymes and where NADH/NAD+/ATP are evolved. which bacteria use this fermentation?
``` malate ---> lactate lactic acid bacteria MleA catalyses no redox balancing/ATP gen uses antiport malate2-/lactate1- ```
28
name the 2 systems for protein translocation across the inner membrane, state simply how they work
SEC - protein threaded through then folds in periplasm | TAT - protein folded in cytoplasm, passes through TAT folded
29
describe the SEC mechanism of protein translocation across IM
* 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
name and explain the 3 regions of the sec signal sequence
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
state how proteins with cofactors are transported across IM
• 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
describe when the TAT (twin arginine translocase) system is used and in which kingdoms it is found
• 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
describe the TAT mechanism
• 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
name and explain the 3 regions of the TAT signal sequence
``` n-terminal region: contains RR motif Hydrophobic region doesnt really do much, may help tatA and tatBC bind c-region AXA cleavage region ```
35
why do bacteria need to secrete proteins beyond the periplasm?
extracellular enzymes for digestion | virulence factors
36
which secretion systems transport across the OM only and which transport across the OM and into another cell?
``` • Secretion across the OM only TSS5 TSS2 TSS1 • Secretion across the OM and into another cell TSS3 TSS4 TSS6 ```
37
describe the TSS1 system
• 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
describe the TSS2 system
• 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
describe the TSS5 system
• 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
describe the TSS3 system
• 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
describe the TSS4 system
• 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
describe the TSS6 system
• 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
which transport systems transport proteins folded
TAT TSS3 TSS4 TSS6
44
which transport systems transport proteins unfolded
SEC TSS1 TSS2 (can do folded via TAT) TSS5 (can do folded via TAT)
45
which protein transport systems use ATP as an energy source?
``` SEC (uses pmf too) TSS1 TSS2 TSS3 TSS4 TSS5 TSS6 ```
46
which protein transport systems use pmf as an energy source?
SEC (uses ATP too) | TAT
47
give an example of a (specific) molecule that is transported via each protein translocation system
``` 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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