1
Q
How are hydrolytic exo-enzymes used?
A
- secreted extracellularly
- breaking down large substrates into components via addition of H2O
2
Q
What are the 4 major classes of proteases
A
-Metalloproteases
- Serine proteases
- Cysteine proteases
- Aspartate proteases
3
Q
What proteases serve as virulence factors?
A
- Elastaste
- Hyaluronidase
- Collagenase
4
Q
How can proteases be a drug target
A
- HIV is normally treated with protease inhibitors
- proteolytic cleavage of polypeptide precursors into mature enzymes and structural proteins is essential
- protease inhibitors mimic the viral protease’s actual substrates
5
Q
Is energy needed for amino acid uptake?
A
Yes, ATP
- amino acids can be assimilates or catabolized
6
Q
What are the 2 families of ABC systems amino acid uptake
A
- Polar amino acid transport family (Histidine premeases)
- Hydrophobic amino acid transport family
7
Q
How does amino acid deamination work?
A
- Yields a- keto acids
* can feed into central metabolism where they are oxidized for energy (ATP) by NADH producing dehydrogenases
8
Q
What are the 3 phases of anaerobic digestion?
A
- Hydrolysis and Fermentation: Organic waste is broken into VFAs, H2, and CO2
- Acetogenesis: Fermentation products consumed and Acetic Acid+ COs, H2
- Methanogenesis: Methanogens use H2 as energy source with CO2 as TEA to form methane
9
Q
What are the 3 principle microbial groups?
A
- Fermentative microbes (acidogens)
- Hydrogen- producing, acetate- forming microbes (acetogens)
- Methanogenic archaea (methanogens = archea)
10
Q
What happens during hydrolysis and fermentative acidogenesis?
A
Hydrolytic enzymes of microbial heterotrophs hydrolyze polymer substrates into smaller products, primarily monomeric units then consumed
Key enzymes: Lipases, proteases, cellulases, amylases, pectinases
11
Q
What happens during acetogenesis?
A
Reverse acetyl co A pathway
12
Q
What happens during methanogenesis?
A
2 main routes:
1. Hydrogenotrophic
hydrogen: CO2+ 4H2 –> CH4+ 2H2O
2. Acetoclastic (majority of biomethane 66%)
acetate: Ch3Cooh –> CH4+CO2
13
Q
What are the enzymes that allow aerobes to survive in o2 rich environments
A
Super oxide dismutase (SOD) + catalase
14
Q
What is the saccharification process?
A
Amylase endohydrolase hydrolyzes the alpha glycosidic bonds of starch while glucoamylases break dextrin oligomers into glucose and maltose
15
Q
What does cellulase do?
A
Catalyze hydrolysis of beta 1,4 glycosidic linkages of cellulose polymer
16
Q
Microbes can grow in aerobic and anaerobic conditions using what process?
A
substrate level phosphorylation
17
Q
What is fermentation?
A
Catabolic process where organic molecules serve as electron donors and acceptors
- regeneration NAD electron carrier
18
Q
What is the purpose of pyruvate in fermentation?
A
Starting point of many fermentations
19
Q
What is the simplest fermentation?
A
homolactic fermentation using lactate dehydrogenase
20
Q
What is alcoholic/ ethanol fermentation?
A
- Characteristic of yeast
- CO2 produced is the gas involved in the rising of yeast bread
- Carbon lost from pyruvate as its converted to ethanol
- Enzymes: pyruvate decarboxylase and alcohol dehydrogenase
21
Q
What are the 2 fermentations that allow for renewable biofuel energy (ABE fermentation)?
A
- acidogenesis: acetate and butyrate are formed
- solventogenesis: ethanol, butanol and acetone formed
22
Q
How are biogeochemical elements cycled?
A
depends on size, reservoir location, chemical recalcitrance, and chemical reactivity (N2 vs. O2)
- smaller reservoir size= faster cycling and disruption
23
Q
What theory did Joseph Fourier propose?
A
The Greenhouse Effect theory
24
Q
What are the repercussions of carbon cycle destabilization?
A
- fossil fuel consumption increased the amount of CO2 in the environment
- resulting in ocean acidification
25
Advantages of butanol
- powering existing motor vehicle engines directly
- produced by existing microbes without genetic modification or reliance on H2
- production relies on ABE fermentation
26
What is the name of the acterium isolated by Chaim Weizmann?
Clostridium acetobutylicum
27
What happens during acidogenesis?
-Clostridium uptakes and catabloizes glucose to pyruvate via EMP then decarboxylates to Acetyl-CoA
- Acetyl-CoA reduced to acetate (C2) or butyrate (C4)
- Acetic acid and butyric acid drop pH
28
What happens during solventogenesis?
Clostridium converts acetate and butyrate acid to butanol and acetone
29
What happens when pH drops due to acidogenesis?
expression of solventogenic genes
30
How are amino acids fermented?
oxidative deamination of one amino acid is coupled to the reduction of a second amino acid as the electron acceptor
- hydrogen gas formation possible
31
What is a stickland reaction?
- coupled oxidation of amino acids to organic acids
- NAD+ formed
- amino acids can be stickland acceptors or donors or both
- only histidine cannot be fermented by stickland reactions
32
What is a chemolithoautotroph?
an organism that oxidizes inorganic chemicals for electrons needed to autotrophically fix CO2
33
What are the 4 carbon fixation pathways autotrophs use to fix CO2 and support ecosystems?
1. reverse TCA cycle- Chlorobium
2. Reductive Acetyl-CoA pathway- clostridium
3. 3 hydroxy- propionate- chloroflexus
4. Calvin cycle- algae
34
Autotroph definition
organism that anabolically builds complex organic chemicals from inorganic carbon
35
Mixotroph definition
organism that can grow using autotrophy and heterotrophy
36
heterotroph definition
organism that catabolizes complex organic chemicals for energy as well as carbon skeletons
37
What do methanotrophic bacteria use for energy?
CH4
38
What compound does carboxydotrophic bacteria use?
carbon monoxide
- use calvin cycle
- hallmark is aerobic CODH-ACS synthase enzyme
39
What are the 2 different CODH/ACS?
Mo-Fe-Flavin containing enzymes found in aerobic bacteria
Fe-Ni containing enzymes found in anaerobic bacteria
40
What is used in the reverse TCA cycle as an electron donor?
- inorganic reduced compounds like H2 or sulfide
- providing energy to fix CO2 when organics absent
41
What happens during the reverse TCA cycle?
- incorporation of 2 CO2 and the input of 8 H and 2 ATP
- uses ATP citrate lyase to cleave citrate (KEY BRANCH POINT) into oxaloacetate and acetyl CoA
42
What happens during the reductive acetyl CoA pathways
CO2 used to form acetyl CoA
- most efficient of all carbon assimilation pathways
43
What happens during the 3-hyrdoxypropionate cycle?
Co2 used to produce ATP and NADPH
44
What is the difference between photosynthesis and chemosynthesis?
Photosynthesis uses CO2 and H2O to make carbs and oxygen
Chemosynthesis uses CO2+H2O+ hydrogen sulfide+ O2 to make carbs and sulphuric acid
45
What happens during tube worm sybiosis?
-Thioautotrophic sulfur bacteria reside symbiotically inside the various species of tubeworms
- worms absorb hydrogen sulfide which helps produce organic molecules for the tubeworm
46
What is a thioautotrophic bacteria
obtain energy for biosynthesis through sulfide oxidation
requiring sulfur and oxygen
47
What are bioelectrochemical systems?
- use microbes to convert chemical energy to electrical energy or vice versa
- use whole cells as biocatalysts to drive oxidation and reduction reactions at electrodes
48
What are the 2 types of bioelectrochemical systems?
1. Microbial fuel cells- using exo-electrogenic bacteria to breakdown chemicals and donate useful electrons through a circuit
- for electricity
2. Microbial electrosynthesis cells- electrotrophic bacteria on the cathode accept electrons to store input electrical energy as chemical fuel bonds
- for biofuel
49
What are the 2 electron transfer mechanisms?
1. direct electron transfer- geobacter
2. soluble mediators- shewanella
50
What is the point of a photopigment- absorbed light
- used to build PMF while NADP+ is the interim electron acceptor
51
What happens during non- cyclic photophosphorylation?
- electrons travel in a unidirectional path from the initial e- donor (H2O) to the e- acceptor
52
What happens during cyclic phosphorylation?
- production of ATP during light dependent stage of photosynthesis
- no photolysis of water and no NADP+ is reduced
- photosystem 1 is involved in 2 e- are released which are accepted by the ETC
- as electrons are transferred along the chain energy released pumps protons across the thylakoid membrane
53
What is the energetic link between light and dark reactions in photosynthesis?
ATP and NADPH
54
What happens during the calvin benson cycle?
- 3 CO2 molecules are consumed to form 1 3-carbon sugar
- 3 phases: carbon fixation, reduction, and regeneration of RuBP
- relies on light reactions to provide the AP and NADPH
55
What are the 2 main enzymes of the calvin benson cycle?
- phospho-rublokinase
makes ADP and ribulose 1,5-bisphosphate
- rubisco
carboxylates RuBP then rearranges and lyses to yield 2 3- carbon molecules
56
What are the substrates produced from the calvin benson cycle?
- for each glucose formed the calvin cycle uses 6 CO2 molecules and 9 ATP and 6 NADPH
- ATP and NADPH are regenerated during the light reactions
57
What happens during the first phase of the calvin benson cycle?
(CO2 fixation by rubisco)
- rubisco depends on the active site magnesium
- magnesium is essential in facilitating the conversion of the RuBP substrate to an enediolate that acts as a nucleophile toward a substrate CO2 molecule
58
What happens during the reduction phase of the calvin benson cycle?
- ATP donates a phosphate group to BPG via phophoglycerate kinase (phosphorylation)
- NADPH donates electron via glyceraldehyde 3-phosphate dehydrogenase (reduction)
- each step is completes 6 times in order to create 6 molecules of GAP
59
What happens during the regeneration phase of the calvin benson cycle?
- consuming 3 ATP and yielding new RuBP substrate
60
What is the rate-limiting step of the calvin benson cycle?
the formation of the enediolate
- first step in the mechanism of the completing oxygenase reaction
61
What is the challenge between rubisco and oxygen
- oxygen can bind easily to the site designed to bind to the CO2
- rubisco then attaches the oxygen to the sugar chain, forming a faulty oxygenated product
62
What are solutions to rubisco's inefficiency?
- protein overexpression
- multiple functional active sites
- transporters import bicarbonate and CO2 substrate into the cell
- carboxysome
- carbonic anhydrase
63
What does the carboxysome do?
- bicarbonate enters through pores in the proteinaceous shell
- mediates the conversation to CO2 for use by rubisco
- substrates enter the carboxysome as glyceraldehyde exits
64
What are the 2 classes of autoinducers?
1. acyl homoserine lactone based (gram-negative)
2. Oligopeptide-based (gram-positive)
65
Characteristics of gram-negative autoinducers
- linked to variable, species-specific R groups
- R group variability is a language that enables intra specific communication
- autoinducers exit the cell via diffusion or active trransport
66
Characteristics of gram positive autoinducers
- oligopeptides
- actively transported from the cell
- activate 2 component regulatory elements of neighbors via membrane receptor kinases and intracellular phosphorylation cascade to response regulator
67
What method was discovered by Tomasz and Nealson?
Quorom sensing
68
GO OVER LUX R STEPS IN QUOROM SENSING LECTURE
69
What are the 4 steps V. fischerii uses to perform quorum sensing?
1. basal level of constitutive AHL signal expression
2. local AHL signal accumulation due to increased cell density
3. intracellular signal recognition
4. autoinduction plus positive feedback activation of gene targets
70
What occurs during quorum sensing in gram-positive bacteria?
- constitutively expressed autoinducer peptides cannot diffuse across cell membranes
- export occurs through exporters involved in signal processing from larger precursors translated inside the cell
- export processing often integrates thiolactone rings or isoprenyl groups into the autoinducer peptides`
71
What is the purpose of apoptosis in bacteria?
- benefit members of their own species
- nutrients and essential growth factors are released during times of starvation
72
What is exogenous metabolism?
- starved cells catabolize to reserve intracellular components to ensure survival
- occurs during extreme nutrient limitation conditions
73
What components help reserve storage materials?
- glycogen
- lipids: PHa, wax esters, TAGS
- proteins
- polyphosphate
74
What compound is used to reserve carbohydrates in prokaryotes?
- glycogen (alpha 1,4 and 1,6 linked glucose)
- accumulated during the high-fed state
- glucose is produced through gluconeogenesis is accumulated in starch
75
How is glycogen used in catabolism?
- used early during starvation
76
What does glycogen phosphorylase do?
- cleaves glucose-1- phosphate from the terminal alpha-1,4-glycosidic bond
- de-branching enzyme targets alpha 1,6 branches
77
Tetrahalose
- alpha 1,1 linked glucose dimer
- normally not synthesized in bacteria but many can catabolize it via trehalase
- tetrahalose can also enable cells to survive severe deiccation
78
What lipids are used for energy storage?
PHA (polyhydroxyalkanoates)
TAG (triacylglycerides)
Wax esters
79
What bacteria are TAGs used by?
used mainly by high GC gram positive actinomycetes
80
What is the purpose of phosphates?
polyphosphate-accumulating organisms
- transferring p from the excess ATP
- useful for enhancing biological phosphorus removal
81
What is the purpose of peptides?
- cyanobacteria also use proteins
- microbes using proteins
82
How does cyanophycin use polypeptides?
- pigment in antenna complex
- non ribosomal synthesis
- CO2 and NH3 released, blue green cells turn yellow
- active in heterocysts
Microbial Physiology
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