Final Flashcards
How are hydrolytic exo-enzymes used?
- secreted extracellularly
- breaking down large substrates into components via addition of H2O
What are the 4 major classes of proteases
-Metalloproteases
- Serine proteases
- Cysteine proteases
- Aspartate proteases
What proteases serve as virulence factors?
- Elastaste
- Hyaluronidase
- Collagenase
How can proteases be a drug target
- 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
Is energy needed for amino acid uptake?
Yes, ATP
- amino acids can be assimilates or catabolized
What are the 2 families of ABC systems amino acid uptake
- Polar amino acid transport family (Histidine premeases)
- Hydrophobic amino acid transport family
How does amino acid deamination work?
- Yields a- keto acids
* can feed into central metabolism where they are oxidized for energy (ATP) by NADH producing dehydrogenases
What are the 3 phases of anaerobic digestion?
- 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
What are the 3 principle microbial groups?
- Fermentative microbes (acidogens)
- Hydrogen- producing, acetate- forming microbes (acetogens)
- Methanogenic archaea (methanogens = archea)
What happens during hydrolysis and fermentative acidogenesis?
Hydrolytic enzymes of microbial heterotrophs hydrolyze polymer substrates into smaller products, primarily monomeric units then consumed
Key enzymes: Lipases, proteases, cellulases, amylases, pectinases
What happens during acetogenesis?
Reverse acetyl co A pathway
What happens during methanogenesis?
2 main routes:
1. Hydrogenotrophic
hydrogen: CO2+ 4H2 –> CH4+ 2H2O
2. Acetoclastic (majority of biomethane 66%)
acetate: Ch3Cooh –> CH4+CO2
What are the enzymes that allow aerobes to survive in o2 rich environments
Super oxide dismutase (SOD) + catalase
What is the saccharification process?
Amylase endohydrolase hydrolyzes the alpha glycosidic bonds of starch while glucoamylases break dextrin oligomers into glucose and maltose
What does cellulase do?
Catalyze hydrolysis of beta 1,4 glycosidic linkages of cellulose polymer
Microbes can grow in aerobic and anaerobic conditions using what process?
substrate level phosphorylation
What is fermentation?
Catabolic process where organic molecules serve as electron donors and acceptors
- regeneration NAD electron carrier
What is the purpose of pyruvate in fermentation?
Starting point of many fermentations
What is the simplest fermentation?
homolactic fermentation using lactate dehydrogenase
What is alcoholic/ ethanol fermentation?
- 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
What are the 2 fermentations that allow for renewable biofuel energy (ABE fermentation)?
- acidogenesis: acetate and butyrate are formed
- solventogenesis: ethanol, butanol and acetone formed
How are biogeochemical elements cycled?
depends on size, reservoir location, chemical recalcitrance, and chemical reactivity (N2 vs. O2)
- smaller reservoir size= faster cycling and disruption
What theory did Joseph Fourier propose?
The Greenhouse Effect theory
What are the repercussions of carbon cycle destabilization?
- fossil fuel consumption increased the amount of CO2 in the environment
- resulting in ocean acidification
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
What is the name of the acterium isolated by Chaim Weizmann?
Clostridium acetobutylicum
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
What happens during solventogenesis?
Clostridium converts acetate and butyrate acid to butanol and acetone
What happens when pH drops due to acidogenesis?
expression of solventogenic genes
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
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
What is a chemolithoautotroph?
an organism that oxidizes inorganic chemicals for electrons needed to autotrophically fix CO2
What are the 4 carbon fixation pathways autotrophs use to fix CO2 and support ecosystems?
- reverse TCA cycle- Chlorobium
- Reductive Acetyl-CoA pathway- clostridium
- 3 hydroxy- propionate- chloroflexus
- Calvin cycle- algae
Autotroph definition
organism that anabolically builds complex organic chemicals from inorganic carbon
Mixotroph definition
organism that can grow using autotrophy and heterotrophy
heterotroph definition
organism that catabolizes complex organic chemicals for energy as well as carbon skeletons
What do methanotrophic bacteria use for energy?
CH4
What compound does carboxydotrophic bacteria use?
carbon monoxide
- use calvin cycle
- hallmark is aerobic CODH-ACS synthase enzyme
What are the 2 different CODH/ACS?
Mo-Fe-Flavin containing enzymes found in aerobic bacteria
Fe-Ni containing enzymes found in anaerobic bacteria
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
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
What happens during the reductive acetyl CoA pathways
CO2 used to form acetyl CoA
- most efficient of all carbon assimilation pathways
What happens during the 3-hyrdoxypropionate cycle?
Co2 used to produce ATP and NADPH
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
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
What is a thioautotrophic bacteria
obtain energy for biosynthesis through sulfide oxidation
requiring sulfur and oxygen
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
What are the 2 types of bioelectrochemical systems?
- Microbial fuel cells- using exo-electrogenic bacteria to breakdown chemicals and donate useful electrons through a circuit
- for electricity - Microbial electrosynthesis cells- electrotrophic bacteria on the cathode accept electrons to store input electrical energy as chemical fuel bonds
- for biofuel
What are the 2 electron transfer mechanisms?
- direct electron transfer- geobacter
- soluble mediators- shewanella
What is the point of a photopigment- absorbed light
- used to build PMF while NADP+ is the interim electron acceptor
What happens during non- cyclic photophosphorylation?
- electrons travel in a unidirectional path from the initial e- donor (H2O) to the e- acceptor
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
What is the energetic link between light and dark reactions in photosynthesis?
ATP and NADPH
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
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
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
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
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
What happens during the regeneration phase of the calvin benson cycle?
- consuming 3 ATP and yielding new RuBP substrate
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
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
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
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
What are the 2 classes of autoinducers?
- acyl homoserine lactone based (gram-negative)
- Oligopeptide-based (gram-positive)
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
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
What method was discovered by Tomasz and Nealson?
Quorom sensing
GO OVER LUX R STEPS IN QUOROM SENSING LECTURE
What are the 4 steps V. fischerii uses to perform quorum sensing?
- basal level of constitutive AHL signal expression
- local AHL signal accumulation due to increased cell density
- intracellular signal recognition
- autoinduction plus positive feedback activation of gene targets
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`
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
What is exogenous metabolism?
- starved cells catabolize to reserve intracellular components to ensure survival
- occurs during extreme nutrient limitation conditions
What components help reserve storage materials?
- glycogen
- lipids: PHa, wax esters, TAGS
- proteins
- polyphosphate
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
How is glycogen used in catabolism?
- used early during starvation
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
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
What lipids are used for energy storage?
PHA (polyhydroxyalkanoates)
TAG (triacylglycerides)
Wax esters
What bacteria are TAGs used by?
used mainly by high GC gram positive actinomycetes
What is the purpose of phosphates?
polyphosphate-accumulating organisms
- transferring p from the excess ATP
- useful for enhancing biological phosphorus removal
What is the purpose of peptides?
- cyanobacteria also use proteins
- microbes using proteins
How does cyanophycin use polypeptides?
- pigment in antenna complex
- non ribosomal synthesis
- CO2 and NH3 released, blue green cells turn yellow
- active in heterocysts
