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Microbiology > Lecture 3 & 4 ppts: Bacterial Metabolism > Flashcards

Lecture 3 & 4 ppts: Bacterial Metabolism Flashcards

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1
Q

Give an example of a solute

A

Sodium chloride

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2
Q

Define halophile and osmotolerance

A

Halophile: loves salts
Osmotolerance: has a salt limit

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3
Q

Define acidophile, neutrophil, and alkaliphile

A

Acidophile: Likes acidic environments
Neutrophil: Likes neutral environments
Alkaliphile: Likes basic environments

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4
Q

Define psychrophile, mesophile, thermophile

A

Psychrophile: Likes extreme cold
Mesophile: Likes moderate temperatures
Thermophile: Likes extreme heat

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5
Q

Define piezophile (barophile)

A

Likes high-pressure environments

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6
Q

Define obligate aerobe, obligate anaerobe, and microaerophile

A

Obligate aerobe: Needs lots of air/ oxygen
Obligate anaerobe: Needs no air/ oxygen
Microaerophile: Likes a little air/ oxygen, but not a lot

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7
Q

Define metabolism

A

The total of all chemical reactions occurring in the cell

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8
Q

Define anabolism and catabolism

A

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’

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9
Q

Microbes are big producers of what two elements?

A

Oxygen and nitrogen

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10
Q

Define and give examples of the 3 types of cellular work

A

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)

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11
Q

Define chemoorganotroph, chemolithotroph, and phototroph

A

Chemoorganotroph: energy source is organic molecules
Chemolithotroph: energy source is inorganic molecules
Phototroph: energy source is light

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12
Q

Define autotroph and heterotroph

A

Autotroph: Carbon source is CO2
Heterotroph: Carbon source is organic molecules

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13
Q

Define organotroph and lithotroph

A

Organotroph: electron source is organic molecules
Lithotroph: electron source is inorganic molecules

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14
Q

The most commonly used practical form of energy is?

A

ATP

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15
Q

Give 3 examples of altered ATP, and briefly describe how altering ATP works

A

-Guanosine, cytidine, uridine
-Enzymes hydrolyze bonds and alter original triphosphate molecule of ATP to make different energy sources

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16
Q

Name the basic purposes of GTP, CTP, and UTP (guanosine, cytidine, uridine)

A

GTP: protein synthesis
CTP: lipid synthesis
UTP: peptidoglycan, and polysaccharide synthesis

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17
Q

Give 5 examples of cellular processes that are exergonic reactions.

A

Aerobic respiration
Anaerobic respiration
Fermentation
Phototrophy
Chemolithotrophy

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18
Q

Give 3 examples of cellular processes that are endergonic reactions

A

Chemical work
Transport work
Mechanical work

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19
Q

Give 4 examples of carbon sources

A

CO2, sugars, amino acids, and fatty acids

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20
Q

Define substrate level phosphorylation

A

The generation of ATP (or GTP/UTP, etc)) from ADP (or GDP/ UPT, etc) by chemical reaction

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21
Q

Define oxidative phosphorylation

A

An alternative way to create ATP generated by a proton gradient

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22
Q

Define oxidation-reduction (redox) reactions

A

Electrons move from an electron donor to an electron acceptor

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23
Q

The ETC (electron transport chain) of bacteria is very similar to that of what?

A

Mitochondria

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24
Q

Describe the chemiosmotic hypothesis and how it relates to the ETC

A

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

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25
Q

Give a quick 5 bullet-point synopsis of what happens during the ETC

A

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

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26
Q

What are the three pathways of glucose catabolism, and which is the most common?

A

1) Embden-Meyerhof pathway: most common
2) Entner-Doudoroff pathway: only in prokaryotes
3) Pentose Phosphate Pathway

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27
Q

Describe the Embden-Meyerhof pathway of glucose catabolism

A

-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

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28
Q

Describe the Entner-Doudoroff pathway of glucose catabolism

A

-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)

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29
Q

Describe the Pentose Phosphate Pathway of glucose catabolism

A

-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.

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30
Q

Describe the TCA Cycle (Aka Krebs Cycle, Aka Citric Acid Cycle)

A

-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

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31
Q

Describe what happens to the ETC if we grow bacteria with low aeration in the stationary phase

A

Then there’s only a certain amount of oxygen to help the ETC run, so they generate less hydrogen and have to conserve

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32
Q

What is proton motive force driven by?

A

The proton gradient and active transport

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33
Q

What is the ATP yield from aerobic respiration, and what kind of phosphorylation do these ATP come from?

A

-Yields 32 ATP
-Primarily from oxidative phosphorylation, but also uses some substrate-level phosphorylation.

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34
Q

Define chemorganotropy

A

Anaerobic glucose metabolism

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35
Q

What is anaerobic glucose metabolism called?

A

Chemorganotrophy

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36
Q

Describe the diversity of electron acceptors and why it’s important

A

-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.

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37
Q

What type of reaction is chemorganotrophy

A

A dissimilatory nitrate reduction (denitrification)

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38
Q

What does chemorganotrophy break down, and what does three things does it break down into?

A

Nitrate > nitrite > nitric oxide > nitrogen gas

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39
Q

Nitrites oxidate iron atoms in hemoglobin, which means _____ nitrite consumption can lead to poor oxygen

A

high

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40
Q

What are the four unifying themes of fermentation?

A

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

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41
Q

What happens to pyruvate during fermentation, and why do people find this valuable?

A

Pyruvate is converted to lactate and/or X (which is then turned into Y); X & Y can be used in weapons production

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42
Q

True or false: A lot of fermenters can be explosive, so they’re often used to manufacture weapons

A

True

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43
Q

List 4 types of fermentation

A

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

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44
Q

List and describe the two different types of lactic acid fementers

A

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

45
Q

Briefly describe reactants and products of alcohol (ethanol) fermentation

A

Sugars > ethanol + CO2 (enzyme: alcohol dehydrogenase)

46
Q

Briefly describe the components of complex fermentation

A

Mixed acid (#1, 5, 6, 8, 9)
Butanediol (#1, 4, 5, 6, 9)

47
Q

Give examples of monosaccharides and disaccharides, and describe what monosaccharides do

A

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

48
Q

List 4 other types of catabolism not otherwise talked about

A

Lipid catabolism, protein catabolism, fatty acid beta oxidation, and transamination

49
Q

Describe what happens in lipid catabolism and protein catabolism

A

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

50
Q

Describe what happens in fatty acid beta oxidation and transamination

A

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

51
Q

What are the energy and carbon sources in phototrophy?

A

Light is a source of energy; the pigments in the cell (chlorophyll b and bacteriochlorophyll a) trap light energy
Carbon source is often CO2

52
Q

Describe how pigments are important to phototrophy

A

-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

53
Q

In what types of organisms does oxygenic photosynthesis occur, and briefly describe its two stages

A

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

54
Q

Photosystem 1 traps light at _____ wavelengths, and photosystem 2 traps light at ______ wavelengths

A

longer; shorter

55
Q

Describe what happens during the light reactions of oxygenic photosynthesis

A

-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

56
Q

What are the reactants and products of oxygenic photosynthesis?

A

ATP and NADPH are used to generate CO2 in the dark reactions

57
Q

What is cyclic photophosphorylation? What does it produce, and what organisms use it?

A

-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

58
Q

____________ are the type of bacteria that evolved the second photosystem

A

Cyanobacteria

59
Q

Cyanobacteria are Gram-____________

A

negative

60
Q

Describe the ecological and evolutionary contributions of cyanobacteria

A

-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

61
Q

Name the 3 structures unique to cyanobacteria

A

1) Gas vesicles
2) Phycobilisomes
2) Thylakoid

62
Q

Describe phycobilisomes

A

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.

63
Q

Describe the morphology diversity, colony formation, and motility of cyanobacteria

A

-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

64
Q

What does bacterial photosynthesis resemble, what does it have for efficiency, and what is the most important thing they produce?

A

-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’

65
Q

Describe the problem of algal blooms

A

-The organisms can excrete toxins during algal blooms when there are to too many bacteria in one area
-Implicated in causing ALS

66
Q

Describe anoxygenic (or anaerobic) phototrophy; what is it, what type of bacteria use it, and how fast is it compared to oxygenic phototrophy

A

-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

67
Q

What is unique about green sulfur bacteria?

A

They have chlorosomes that store chlorophyll and a baseplate to make up for only having 1 photosystem

68
Q

Name two light-processing structures

A

Phycobilisomes and chlorosomes

69
Q

Name the 3 types of phototrophy

A

1) Anoxygenic phototrophy
2) Oxygenic phototrophy
3) Rhodopsin-based phototrophy

70
Q

Describe rhodopsin-based phototrophy

A

A light-driven proton pump; conformation changes translocate protons to the periplasm and generates a pH gradient for chemiosmosis (No ETC!)

71
Q

What are the 3 major groups of chemolithotrophs?

A

Hydrogen-oxidizing
Nitrifying
Sulfur-oxidizing

72
Q

Define and describe chemolithotrophy; what is its definition, and what is its major disadvantage?

A

-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

73
Q

What can be directly oxidized to provide electrons for ETC and PMF, and what is this called?

A

Sulfite; sulfite oxidation

74
Q

Describe the two methods of sulfur oxidation

A

-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)

75
Q

Describe the unusual electron flow in the ETC of Nitrobacter

A

-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

76
Q

Define anabolism; what type of bacteria do it, and when does it go backwards?

A

-Heterotrophs degrade their carbon sources into one or more intermediates of the central metabolic pathway
-Only goes backwards if the cell is eating itself

77
Q

List the 6 principles governing biosynthesis

A

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

78
Q

What are the 3 phases of the Calvin cycle?

A

1) Carboxylation
2) Reduction
3) Regeneration

79
Q

In what two places does the Calvin Cycle occur?

A

Occurs in:
1) The stroma of chloroplasts
2) The carboxysomes of bacteria

80
Q

Describe the Calvin cycle (what is it, what is its goal, where does it occur, and what are its 3 phases?)

A

-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

81
Q

Describe the difference between enzymes and ribozymes

A

Proteins called enzymes
RNA called ribozymes

82
Q

What do enzymes do?

A

Speed up chemical reactions (catalysts)

83
Q

Describe the concept of feedback inhibition in cellular chemical reactions

A

-A method of matching supply with demand
-Each pathway branch is independently controlled
-This is because enzymes have a pH and temperature optima

84
Q

Define chemolithotropy and what organisms do it

A

-Energy source is inorganic molecules
-Exclusive to microbes

85
Q

Describe the scientific method in the context of microbiology

A

-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.

86
Q

What are the 3 main pieces of evidence that support the current history of life on earth?

A

1) Macro and microfossils
2) Carbon dating (of rocks and life)
3) Physicochemical environment of earth

87
Q

Who wrote The Origin of Life? What does it describe?

A

-Oparin in the 1920s
-Describes a ‘primeval soup’ of organic molecules that could be created in an oxygenless atmosphere because of sunlight

88
Q

What did Haldane say about the origins of life in the 1920s?

A

Said oceans were a ‘hot dilute soup’ from which the organic compounds formed

89
Q

Describe the Primordial Soup Theory from 1952 (who did it, what 4 things did they combine, and what were their results?)

A

-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)

90
Q

What does the theory of thermal proteinoids say, and who wrote it?

A

-Says heating amino acid mixtures leads to polymer formation and catalysis
-Sidney Fox

91
Q

Define abiogenesis

A

The study of how organic biological life can naturally arise from inorganic matter

92
Q

What did the 1986 World Hypothesis argue?

A

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

93
Q

What are the 3 pieces of evidence that support RNA as the original, most primitive molecule?

A

-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

94
Q

Describe the conditions of prebiotic earth

A

Low oxygen, high UV, temperature extremes

95
Q

Analyzing stromatolites (rock layers) told us what about the history of life?

A

The appearance of cyanobacteria signifies the introduction of oxygen into the atmosphere

96
Q

In what year was the first direct evidence for primitive cellular life found? How old was the evidence?

A

-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

97
Q

What is the first step of cellular organization? Who demonstrated this?

A

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

98
Q

The ______ (the primitive version of a prokaryotic cell) evolved into Archaea and Bacteria

A

pogenote

99
Q

Describe the extremophiles of archaea

A

-Lithotrophic, anaerobic
-Chemically distinct membranes
-Tolerate high temps, high salinity, and high acidity

100
Q

Define endosymbiosis

A

The interaction between two organisms in which one organisms lives within the other

101
Q

Describe the endosymbiotic hypothesis (who wrote it, what does it mean, and what 3 things is it the origin of?)

A

-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

102
Q

True or false: In endosymbiosis, the bacteria eventually lose the ability to live independently

A

True

103
Q

List the 3 pieces of evidence for the Endosymbiotic Hypothesis

A

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

104
Q

Describe the Hydrogen Hypothesis

A

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)

105
Q

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

A

2.4 billion; 1.3 billion years

106
Q

Describe The Great Oxygenation Event

A

-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

107
Q

Define the Gaia Hypothesis

A

A self-regulating Earth is controlled by the community of living organisms

108
Q

Define panspermia and give an alternative name for it

A

-The theory that life exists throughout the universe and is distributed by meteoroids, asteroids, and SSSBs (small solar system bodies)
-Also called exogenesis

Microbiology (42 decks)

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