Lecture 3 & 4 ppts: Bacterial Metabolism Flashcards
Give an example of a solute
Sodium chloride
Define halophile and osmotolerance
Halophile: loves salts
Osmotolerance: has a salt limit
Define acidophile, neutrophil, and alkaliphile
Acidophile: Likes acidic environments
Neutrophil: Likes neutral environments
Alkaliphile: Likes basic environments
Define psychrophile, mesophile, thermophile
Psychrophile: Likes extreme cold
Mesophile: Likes moderate temperatures
Thermophile: Likes extreme heat
Define piezophile (barophile)
Likes high-pressure environments
Define obligate aerobe, obligate anaerobe, and microaerophile
Obligate aerobe: Needs lots of air/ oxygen
Obligate anaerobe: Needs no air/ oxygen
Microaerophile: Likes a little air/ oxygen, but not a lot
Define metabolism
The total of all chemical reactions occurring in the cell
Define anabolism and catabolism
Anabolism: the biosynthesis of new organic molecules from smaller organic and inorganic compounds
Catabolism: breaking down of molecules into smaller units while releasing energy, ‘fueling reactions’
Microbes are big producers of what two elements?
Oxygen and nitrogen
Define and give examples of the 3 types of cellular work
1) Chemical: synthesis of complex biological molecules
2) Transport: taking up nutrients, eliminating wastes, and maintaining ion balances
3) Mechanical: movement of structures that are part of the cell (motility, rotation of flagella, partitioning of chromosomes)
Define chemoorganotroph, chemolithotroph, and phototroph
Chemoorganotroph: energy source is organic molecules
Chemolithotroph: energy source is inorganic molecules
Phototroph: energy source is light
Define autotroph and heterotroph
Autotroph: Carbon source is CO2
Heterotroph: Carbon source is organic molecules
Define organotroph and lithotroph
Organotroph: electron source is organic molecules
Lithotroph: electron source is inorganic molecules
The most commonly used practical form of energy is?
ATP
Give 3 examples of altered ATP, and briefly describe how altering ATP works
-Guanosine, cytidine, uridine
-Enzymes hydrolyze bonds and alter original triphosphate molecule of ATP to make different energy sources
Name the basic purposes of GTP, CTP, and UTP (guanosine, cytidine, uridine)
GTP: protein synthesis
CTP: lipid synthesis
UTP: peptidoglycan, and polysaccharide synthesis
Give 5 examples of cellular processes that are exergonic reactions.
Aerobic respiration
Anaerobic respiration
Fermentation
Phototrophy
Chemolithotrophy
Give 3 examples of cellular processes that are endergonic reactions
Chemical work
Transport work
Mechanical work
Give 4 examples of carbon sources
CO2, sugars, amino acids, and fatty acids
Define substrate level phosphorylation
The generation of ATP (or GTP/UTP, etc)) from ADP (or GDP/ UPT, etc) by chemical reaction
Define oxidative phosphorylation
An alternative way to create ATP generated by a proton gradient
Define oxidation-reduction (redox) reactions
Electrons move from an electron donor to an electron acceptor
The ETC (electron transport chain) of bacteria is very similar to that of what?
Mitochondria
Describe the chemiosmotic hypothesis and how it relates to the ETC
As electrons move through the chain, energy is generated; this energy allows protons to be pumped across the membrane to create electrochemical gradient. This gradient (charge separation) is the energized state called Proton Motive Force
Give a quick 5 bullet-point synopsis of what happens during the ETC
1) NADH is an electron donor
2) A series of redox reactions that pump protons through the membrane
3) The electrochemical gradient is established
4) Oxygen is the final electron acceptor
5) ATP synthase accepts protons to generate ATP
What are the three pathways of glucose catabolism, and which is the most common?
1) Embden-Meyerhof pathway: most common
2) Entner-Doudoroff pathway: only in prokaryotes
3) Pentose Phosphate Pathway
Describe the Embden-Meyerhof pathway of glucose catabolism
-It’s an amphibolic pathway, which means it’s both anabolic and catabolic
-Starts with glucose, 2 ATP are used to generate 3 Glyceraldehyde 3-phosphate
-Fructose 1,6 biphosphate; glucose are involved
-Nicotinamide adenine dinucleotide
-Generates NADH, which is an electron donor
-Redox active coenzyme
-The end product of this pathway is pyruvate
Describe the Entner-Doudoroff pathway of glucose catabolism
-Only found in prokaryotes
-NADPH is generated in this pathway, which is also an electron donor
-The production of KDPG
-Part 1 end products are pyruvate and glyceraldehyde 3-phosphate
-Part 2 end product is pyruvate
-Creates 2 pyruvates, doesn’t create 2 extra ATPs like the embden-meyerhof pathway (but does still generate ATP)
Describe the Pentose Phosphate Pathway of glucose catabolism
-Starts with 3 glucose-6
-Changing the chemistry of sugar, ultimately ending up with pyruvate
-Know that the glyceraldehyde-3-p and 6-phosphogluconate are a part of the pathway
-Ancient origin; may be older than the other pathways. It’s carried out by enzymes in the cells, but can be done without them.
Describe the TCA Cycle (Aka Krebs Cycle, Aka Citric Acid Cycle)
-NADH is made right when it enters the cycle
-Acetyl-coenzyme A plays a large role
-GDP is broken down into GTP, which are the high-energy molecules
-FAD and FADH2 are and NAD and NADH are electron donors; there are 5 electron donors in the cycle
-The process oxides pyruvate into 3 carbon dioxides
-Generates GTP
Describe what happens to the ETC if we grow bacteria with low aeration in the stationary phase
Then there’s only a certain amount of oxygen to help the ETC run, so they generate less hydrogen and have to conserve
What is proton motive force driven by?
The proton gradient and active transport
What is the ATP yield from aerobic respiration, and what kind of phosphorylation do these ATP come from?
-Yields 32 ATP
-Primarily from oxidative phosphorylation, but also uses some substrate-level phosphorylation.
Define chemorganotropy
Anaerobic glucose metabolism
What is anaerobic glucose metabolism called?
Chemorganotrophy
Describe the diversity of electron acceptors and why it’s important
-There’s a huge diversity of electron acceptors, which is important for the diversity of microbes in general.
-Diversity is impacted by nitrate waste that leaks from farms, factories, etc into the environment; nitrate occurs in oxygen depleted sediments and soils.
What type of reaction is chemorganotrophy
A dissimilatory nitrate reduction (denitrification)
What does chemorganotrophy break down, and what does three things does it break down into?
Nitrate > nitrite > nitric oxide > nitrogen gas
Nitrites oxidate iron atoms in hemoglobin, which means _____ nitrite consumption can lead to poor oxygen
high
What are the four unifying themes of fermentation?
1) NADH is oxidized to NAD+
2) Oxygen is not needed
3) Electron acceptor is pyruvate
4) ETC cannot operate, which leads to reduced ATP production
What happens to pyruvate during fermentation, and why do people find this valuable?
Pyruvate is converted to lactate and/or X (which is then turned into Y); X & Y can be used in weapons production
True or false: A lot of fermenters can be explosive, so they’re often used to manufacture weapons
True
List 4 types of fermentation
1) Lactic acid fermentation (has two types)
2) Alcohol (ethanol) fermentation
3) Complex fermentation
4) Other fermentation substrates: variety of sugars, amino acids, and organic acids
List and describe the two different types of lactic acid fementers
1) Homolactic fermenters: use the Embden-Meyerhof pathway to reduce pyruvate to lactate (lactate dehydrogenase). (tldr: only make lactate)
2) Heterolactic fermenters: also produce ethanol and CO2
Briefly describe reactants and products of alcohol (ethanol) fermentation
Sugars > ethanol + CO2 (enzyme: alcohol dehydrogenase)
Briefly describe the components of complex fermentation
Mixed acid (#1, 5, 6, 8, 9)
Butanediol (#1, 4, 5, 6, 9)
Give examples of monosaccharides and disaccharides, and describe what monosaccharides do
Monosaccharides such as: lactose, mannose, fructose are modified by enzymes to make the sugar the enzyme wants to carry down the pathway
Disaccharides such as: maltose, sucrose, lactose, cellobiose
List 4 other types of catabolism not otherwise talked about
Lipid catabolism, protein catabolism, fatty acid beta oxidation, and transamination
Describe what happens in lipid catabolism and protein catabolism
1) Lipids: Tricylglycerols and other lipids are broken down with lipases into fatty acids
2) Proteins: Polypeptides are broken down by proteases into amino acids
Describe what happens in fatty acid beta oxidation and transamination
1) Fatty Acid Beta Oxidation: 2 carbons are broken down for every fatty acid broken down because they’re good sources of electron donors, as well as acetyl-Coa.
-The fatty acid carbon sources can be extremely beneficial to the cell.
2) Transamination: If the cell is starving and needs pyruvate, they can take an amino acid and a-Ketoglutarate to for pyruvate and glutamate
-Intermediates of the krebs cycle are produced
What are the energy and carbon sources in phototrophy?
Light is a source of energy; the pigments in the cell (chlorophyll b and bacteriochlorophyll a) trap light energy
Carbon source is often CO2
Describe how pigments are important to phototrophy
-Alternating/ conjugated double bonds of the pigments allow for the generation of electron resonance (meaning they bounce from double bond to double bond)
-The types of chlorophyll have a great versatility in wavelength absorption
In what types of organisms does oxygenic photosynthesis occur, and briefly describe its two stages
1) Occurs in plants, eukaryotic algae, and cyanobacteria
2) Photons initiate the transfer of electrons, then:
-Photosystem 1 traps light at longer wavelengths
-Photosystem 2 traps light at shorter wavelengths
Photosystem 1 traps light at _____ wavelengths, and photosystem 2 traps light at ______ wavelengths
longer; shorter
Describe what happens during the light reactions of oxygenic photosynthesis
-Generates O2 and NADPH; needs H2O to initiate photolysis
-Initiate the two photosystems
-Electrons flow from H2O to NADP with aid of energy from photosystems; ATP is synthesized by noncyclic photophosphorylation
-ATP and NADPH are then used to generate CO2 in the dark reactions
What are the reactants and products of oxygenic photosynthesis?
ATP and NADPH are used to generate CO2 in the dark reactions
What is cyclic photophosphorylation? What does it produce, and what organisms use it?
-Cyclic photophosphorylation is used to generate ATP by organisms who have only developed one photosystem
-Produces no oxygen and no NADPH is made
-Used by all phototrophic bacteria, but plants can shift to this when their ATP runs low
____________ are the type of bacteria that evolved the second photosystem
Cyanobacteria
Cyanobacteria are Gram-____________
negative
Describe the ecological and evolutionary contributions of cyanobacteria
-Organisms that evolve photosystem II
-They’ve had a large impact on how we’ve estimated how long life has been around (4.5 billion years/ as old as the universe)
-Big impacts in the astrobiology field (Richard Hoover claims he found cyanobacteria inside a meteorite
Name the 3 structures unique to cyanobacteria
1) Gas vesicles
2) Phycobilisomes
2) Thylakoid
Describe phycobilisomes
Found only in cyanobacteria, they’re antenna on the thylakoids that are loaded with photopigments to take in light; >95% energy efficiency. Are recycled when the cell is starving.
Describe the morphology diversity, colony formation, and motility of cyanobacteria
-Very diverse shapes (rod-structures, spiral strands, balls of cells, etc)
-Usually form a colony with a gelatinous sheath around it
-No flagella, but can move together as a colony
What does bacterial photosynthesis resemble, what does it have for efficiency, and what is the most important thing they produce?
-Resembles plant system
-Has an on/ off switch for efficiency
-Produce oxygen (among other things) and are used in the generation of ‘clean and green energy’
Describe the problem of algal blooms
-The organisms can excrete toxins during algal blooms when there are to too many bacteria in one area
-Implicated in causing ALS
Describe anoxygenic (or anaerobic) phototrophy; what is it, what type of bacteria use it, and how fast is it compared to oxygenic phototrophy
-Defined as photosynthesis without the use of oxygen
-There’s a cyclic electron flow during anoxygenic phototrophy due to only having 1 photosystem
-Carried out by purple sulfur bacteria and nonsulfur bacteria
-Much slower than oxygenic phototrophy and generates less ATP
>Green sulfur bacteria have chlorosomes (store chlorophyll) and a baseplate to make up for only having 1 photosystem
What is unique about green sulfur bacteria?
They have chlorosomes that store chlorophyll and a baseplate to make up for only having 1 photosystem
Name two light-processing structures
Phycobilisomes and chlorosomes
Name the 3 types of phototrophy
1) Anoxygenic phototrophy
2) Oxygenic phototrophy
3) Rhodopsin-based phototrophy
Describe rhodopsin-based phototrophy
A light-driven proton pump; conformation changes translocate protons to the periplasm and generates a pH gradient for chemiosmosis (No ETC!)
What are the 3 major groups of chemolithotrophs?
Hydrogen-oxidizing
Nitrifying
Sulfur-oxidizing
Define and describe chemolithotrophy; what is its definition, and what is its major disadvantage?
-Defined as the breaking down of inorganic substances for energy
-These substrates have a much higher reduction potential than organic substrates; so if less energy is obtained, the bacteria need to eat more to grow
What can be directly oxidized to provide electrons for ETC and PMF, and what is this called?
Sulfite; sulfite oxidation
Describe the two methods of sulfur oxidation
-Sulfite can be directly oxidized to provide electrons for ETC and PMF
-Can also be oxidized and converted to APS; this process yields electrons + ATP (substrate level phosphorylation)
Describe the unusual electron flow in the ETC of Nitrobacter
-Nitrate can go with forward electron flow to make ATP and PMF, or reverse electron flow to make NADH for biosynthesis
-Can’t generate a ton of ATP
-When nitrites are converted to nitrates, nitrates are readily absorbed by the plants
Define anabolism; what type of bacteria do it, and when does it go backwards?
-Heterotrophs degrade their carbon sources into one or more intermediates of the central metabolic pathway
-Only goes backwards if the cell is eating itself
List the 6 principles governing biosynthesis
1) Large molecules are made from small molecules
2) Many enzymes are bifunctional
3) Some enzymes function in one direction only
4) Anabolic pathways are irreversible
5) Catabolism and anabolism are physically separated
6) Catabolism and anabolism use different cofactors
What are the 3 phases of the Calvin cycle?
1) Carboxylation
2) Reduction
3) Regeneration
In what two places does the Calvin Cycle occur?
Occurs in:
1) The stroma of chloroplasts
2) The carboxysomes of bacteria
Describe the Calvin cycle (what is it, what is its goal, where does it occur, and what are its 3 phases?)
-Defined as the reductive pentose phosphate pathway; aka carbon fixation.
-Its goal is to convert carbon dioxide and water into organic compounds to be used by the cell
-Its 3 phases are carboxylation, reduction, and regeneration
-Occurs in stroma of chloroplasts and in carboxysomes of bacteria
-There is also a reductive TCA cycle
Describe the difference between enzymes and ribozymes
Proteins called enzymes
RNA called ribozymes
What do enzymes do?
Speed up chemical reactions (catalysts)
Describe the concept of feedback inhibition in cellular chemical reactions
-A method of matching supply with demand
-Each pathway branch is independently controlled
-This is because enzymes have a pH and temperature optima
Define chemolithotropy and what organisms do it
-Energy source is inorganic molecules
-Exclusive to microbes
Describe the scientific method in the context of microbiology
-Most microbiological studies can fulfill the requirements of testing
-However, evolutionary studies cannot provide any frame of reference because these studies are very difficult to do.
What are the 3 main pieces of evidence that support the current history of life on earth?
1) Macro and microfossils
2) Carbon dating (of rocks and life)
3) Physicochemical environment of earth
Who wrote The Origin of Life? What does it describe?
-Oparin in the 1920s
-Describes a ‘primeval soup’ of organic molecules that could be created in an oxygenless atmosphere because of sunlight
What did Haldane say about the origins of life in the 1920s?
Said oceans were a ‘hot dilute soup’ from which the organic compounds formed
Describe the Primordial Soup Theory from 1952 (who did it, what 4 things did they combine, and what were their results?)
-Miller and Urey
-They combined H2O, H2, CH4, NH4 in a glass chamber and applied electrical shocks
-1 week later, 15% of carbon was organic molecules (i.e. amino acids)
What does the theory of thermal proteinoids say, and who wrote it?
-Says heating amino acid mixtures leads to polymer formation and catalysis
-Sidney Fox
Define abiogenesis
The study of how organic biological life can naturally arise from inorganic matter
What did the 1986 World Hypothesis argue?
That RNA is the original, most primitive molecule (i.e. it came first) because it:
-Has a capacity for storing, copying, and replicated genetic information
-Can have enzymatic properties (regulate gene expression and synthesize proteins)
-Is linked to protein, DNA, and cellular energy
What are the 3 pieces of evidence that support RNA as the original, most primitive molecule?
-Has a capacity for storing, copying, and replicated genetic information
-Can have enzymatic properties (regulate gene expression and synthesize proteins)
-Is linked to protein, DNA, and cellular energy
Describe the conditions of prebiotic earth
Low oxygen, high UV, temperature extremes
Analyzing stromatolites (rock layers) told us what about the history of life?
The appearance of cyanobacteria signifies the introduction of oxygen into the atmosphere
In what year was the first direct evidence for primitive cellular life found? How old was the evidence?
-In 1977 the first direct evidence of primitive cellular life was 3.5 billion year old fossils from Australia.
-Have since found Stromatolites in Greenland from 3.7bya
What is the first step of cellular organization? Who demonstrated this?
Oparin described ‘coacervates’, which are microspheres of phospholipids.
It showed the self-organizing capacity of polymeric molecules, which is the first step toward cellular organization
The ______ (the primitive version of a prokaryotic cell) evolved into Archaea and Bacteria
pogenote
Describe the extremophiles of archaea
-Lithotrophic, anaerobic
-Chemically distinct membranes
-Tolerate high temps, high salinity, and high acidity
Define endosymbiosis
The interaction between two organisms in which one organisms lives within the other
Describe the endosymbiotic hypothesis (who wrote it, what does it mean, and what 3 things is it the origin of?)
-Lynn Margulis, 1980
-Endosymbiosis: The interaction between two organisms in which one organisms lives within the other
-Generally accepted as the origin of 3 eukaryotic organelles: mitochondria, chloroplasts, and hydrogenosomes
True or false: In endosymbiosis, the bacteria eventually lose the ability to live independently
True
List the 3 pieces of evidence for the Endosymbiotic Hypothesis
1) Mitochondria and chloroplasts have bacteria-like DNA and ribosomes; mitochondria also performs binary fission
2) Rickettsia species (obligate intracellular bacteria) has a genome that is mores similar to mitochondria than any other bacteria
3) Cyanobacterial genus lives inside marine invertebrates; it’s thought to be an ancestry of chloroplasts and plants and algae
Describe the Hydrogen Hypothesis
Anaerobic bacterium produce H2 and CO2 as end products of metabolism, which leads to either:
1) The endosymbiont developing the ability to perform aerobic respiration (mitochondria)
2) The endosymbiont saying the same (hydrogenosome: small organelles in organic protists)
It was about ___________ years ago when cyanobacteria began to synthesize oxygen on the surface; before that, oxygen was absorbed in the water and land for ______________ until it accumulated in the environment
2.4 billion; 1.3 billion years
Describe The Great Oxygenation Event
-About 2.4 billion years ago when cyanobacteria began to synthesize oxygen on the surface
-Oxidized methane into carbon dioxide
-Potentially a ‘snowball earth’ episode that threw a bunch of water on earth and drastically increased oxygen levels
Define the Gaia Hypothesis
A self-regulating Earth is controlled by the community of living organisms
Define panspermia and give an alternative name for it
-The theory that life exists throughout the universe and is distributed by meteoroids, asteroids, and SSSBs (small solar system bodies)
-Also called exogenesis
