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Microbial Physiology and Growth > Week 2 - Diversity of Microbial Metabolisms > Flashcards

Week 2 - Diversity of Microbial Metabolisms Flashcards

1
Q

Microbiology revolves around 2 themes

A
  • understanding basic life processes

* applying that knowledge to the benefit of humans

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2
Q

Understanding life processes

A

microbes are excellent models for understanding cellular processes in unicellular AND multicellular organisms

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3
Q

Applying that knowledge to the benefit of humans

A

microbes play important roles in medicine, agriculture, and industry

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4
Q

The importance of microorganisms

A
  • oldest form of life
  • largest mass of of living material on Earth
  • carry out major processes for biogeochemical cycles
  • can live in places unsuitable for other organisms
  • other life forms require microbes to survive
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5
Q

Evolution and the extent of microbial life

• life on Earth through the ages

A

• Earth if 4.6 billion years old
• first cells appeared between 3.8 and 3.9 billion years ago
• the atmosphere was anoxic until ~ 2 billion years ago
- metabolisms were exclusively anaerobic until evolution of oxygen-producing phototrophs
• life was exclusively microbial until ~ 1 billion years ago

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6
Q

The extent of microbial life

A

• microbes found in almost every environment imaginable
• global estimate of 5x10^30 cells
- most microbial cells are found in oceanic and terrestrial subsurfaces
• microbial biomass is significant and cells are key reservoirs of essential nutrients (eg C, P, N)

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7
Q

Everything except … are microbes

A

animals, fungi, plants

some are microbes

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8
Q

Characteristics of living systems

A
  • metabolism
  • reproduction
  • differentiation
  • communication
  • movement
  • evolution
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9
Q

Metabolism and compartmentalization

A

chemical transformation of nutrients
• a cell is a compartment that takes up nutrients from the environment, transforms them, and releases wastes into the environment
• the cell is an open system

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10
Q

Reproduction

A

generation of 2 cells from one

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11
Q

Differentiation

A

synthesis of new substances or structures that modify the cell (only in some microbes)
• some cells can form new cell structures such as a spore, usually as a part of a cellular life cycle

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12
Q

Communication

A

generation of, and response to, chemical signals (only in some microbes)
• many cells communicate or interact by means of chemicals that are released or taken up

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13
Q

Movement

A

via self-propulsion, many forms in microbes

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14
Q

Evolution

A

genetic changes in cells that are transferred to offspring
• cells contain genes and evolve to display new biological experiences
• phylogenetic trees show the evolutionary relationships between cells

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15
Q

Growth

A

chemicals from the environment are turned into new cells under the genetic direction of preexisting cells

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16
Q

Genetic functions

A 
• replication
• transcription
• translation
--> proteins
(to growth)
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17
Q

Catalytic functions

A
  • energy conservation ADP + Pi –> ATP
  • metabolism: generation of precursors of macromolecules (sugars, amino acids, fatty acids, etc.)
  • enzymes: metabolic catalysts

(to growth)

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18
Q

Microbial cell

A
  • a dynamic entity that forms the fundamental unit of life
  • cytoplasmic cell membrane - barrier that separates the inside of the cell from the outside environment
  • cell wall - present in most microbes, confers structural strength
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19
Q

What do we mean by diversity?

A
  • morphological diversity
  • genetic (evolutionary) diversity
  • metabolic diversity
  • macroorganisms (animals and plants) are morphologically very diverse, but very similar by other criteria
  • microbes aer genetic and metabolically diverse
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20
Q

Cells as catalysts and as coding devices

A
  1. cells carry out chemical reactions
  2. cells store and process information that is eventually passed on to offspring during reproduction through DNA and evolution
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21
Q

Cells carry out chemical reactions

A

• enzymes - protein catalysts of the cell that accelerate chemical reactions

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22
Q

Cells store and process information that is eventually passed on to offspring during reproduction through DNA and evolution

A
  • transcription - DNA produces RNA

* translation - RNA makes protein

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23
Q

Growth

A

the link between cells as machines and cells as coding devices

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24
Q

Microorganisms and their environments

A
  • microorganisms exist in nature in populations of interacting assemblages called microbial communities
  • the environment in which a microbial population lives in its habitat
  • ecosystem refers to all living organisms plus physical and chemical constituents of their environment
  • microbial ecology is the study of microbes in their natural environment
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25
Q

Microorganisms exist in nature in populations of interacting assemblages called

A

microbial communities

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26
Q

The environment in which a microbial population lives in its

A

habitat

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27
Q

Ecosystem refers to

A

all living organisms plus physical and chemical constituents of their environment

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28
Q

Microbial ecology is

A

the study of microbes in their natural environment

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29
Q

Microorganisms and their environments

A
  • diversity and abundances of microbes are controlled by resources (nutrients) and environmental conditions (eg temp, pH, O2)
  • the activities of microbial communities can affect the chemical and physical properties of their habitats
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30
Q

Diversity and abundances of microbes are controlled by

A

resources (nutrients) and environmental conditions (eg temp, pH, O2)

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31
Q

The activities of microbial communities can affect the

A

chemical and physical properties of their habitats

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32
Q

Microbes also interact with their physical and chemical environment

A

• ecosystems greatly influenced (if not controlled) by microbial activities
• microorganisms change the chemical and physical properties of their habitats through their activities
- for example, removal of nutrients from the environment and the excretion of waste products

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33
Q

Nutrition and cell chemistrys

A
  • metabolism
  • catabolic reactions (catabolism)
  • anabolic reactions (anabolism)
  • most knowledge of microbial metabolism is based on study of laboratory culture
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34
Q

Metabolism

A

the sum total of all chemical reactions that occur in a cell

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35
Q

Catabolic reactions (catabolism)

A

energy-releasing metabolic reactions

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36
Q

Anabolic reactions (anabolism)

A

energy-requiring metabolic reactions

37
Q

Microbial metabolism

A

catabolism (wastes out)
–> ATP and smaller molecules (amino acids, nucleotides)
• nutrients in
–>
anabolism (heat out)
–> larger molecules (for cytoplasmic membrane, cell wall, ribosomes, etc)
–> catabolism

lots of heat out during catabolism
some heat lost during anabolism

38
Q

Biological molecules are produced by

A

anabolic reactions

39
Q

Breaking down

A

catabolic reactions

40
Q

Anabolic reactions generally require

A

• raw materials
macronutrients (CHONPSK)
micronutrients (trace elements - CoZnMo)

  • energy - most anabolic reactions are energetically “uphill)
  • reducing power (a source of electrons) - most anabolic reactions require a net of electrons - often supplied by reduced cofactors such as NADH, NADPH, FADH2
41
Q

The Calvin Cycle

A

a key anabolic pathway to plants and many bacteria
• fixes CO2 to produce sugars
• incredibly important for the biosphere - the key enzyme Ribulose bisphosphate carboxylase (Rubisco), may be the most abundant protein on the planet

42
Q

Inputs of Calvin Cycle

A
  • raw materials (CO2)
  • free energy (hydrolysis of ATP to ADP plus Pi)
  • electrons: oxidation of NADPH to NADP
43
Q

Electron donors and electron acceptors

A
  • the redox tower represents the range of possible reduction potentials
  • the reduced substance at the top of the tower donates electrons
  • the oxidized substance at the bottom of the tower accepts electrons
  • the farther the electrons “drop” the greater the amount of energy released
44
Q

Redox tower

A

represents the range of possible reduction potentials
• top = reduced, donates electrons
• bottom = oxidized, accepts electrons

45
Q

Redox reactions usually involve reactions

A

between intermediates - carriers
• electron carriers are divided into 2 classes
- prosthetic groups (attached to enzymes)
- coenzymes (eg NAD+, NADP)

46
Q

NAD+ and NADH

A

facilitate redox reactions without being consumed

• they’re recycled

47
Q

NAD+ reduction

A

enzyme I reacts with electron donor and oxidized form of coenzyme, NAD+

48
Q

NADH oxidation

A

enzyme II reacts with electron acceptor and reduced form of coenzyme, NADH

49
Q

Chemical energy released in redox reactions is

A

primarily stored in certain phosphorylated compounds
• ATP - the prime energy currency
• phosphoenolpyruvate
• glucose 6-phosphate
chemical energy also stored in coenzyme A

50
Q

Long-term energy storage involves

A

insoluble polymers that can be oxidized to generate ATP

examples in prokaryotes
• glycogen
• poly-β-hydroxybutyrate and other polyhydroxylalkaoates
• elemental sulfur

examples in eukaryotes
• starch
• lipids (simple fats)

51
Q

Nitrogen fixation

A

another crucial anabolic reaction

N2 + 8H+ + 8e- + 16 ATP
–> nigrogenase (enzyme)
2NH3 + H2 + 16 ADP + 16Pi

52
Q

Incorporating fixed nitrogen into amino acids

A

anabolism

NH4+ + α-ketoglutarate + NADPH + H+
–> glutamate dehydrogenase (enzyme)
L-glutamate + NADP+ + H20

53
Q

Essentials of catabolism

A
  • glycolysis
  • respiration and electron carriers
  • the proton motive force
  • the Citric Acid Cycle
  • catabolic diversity
54
Q

Catabolic reactions tend to

A

release energy and reducing power

eg glycolysis

55
Q

Glycolysis net reaction

A

glucose + 2ADP + 2Pi + 2NAD+
–>
2 pyruvate + 2ATP + 2NADH + 2H+

  • glucose consumed
  • 2 ATPs produced
  • fermentation products generated
56
Q

Glycolysis

A
  • 2 reaction series are linked to energy conservation in chemoorganotrophs: germentation in respiration
  • differ in mechanism of ATP synthesis
  • fermentation - substrate-level phosphorylation, ATP directly synthesized from an energy-rich intermediate
  • respiration - oxidative phosphorylation, ATP produced from proton motive force formed by transport of electrons
57
Q

Substrate-level phosphorylation

A

energy rich intermediates
• Pi in
• ADP –> ATP

58
Q

Oxidative phosphorylation

A 
energized membrane (+in -out)
ADP + Pi --> ATP
59
Q

Glycolysis: fermented substance is

A

both an electron donor and an electron acceptor

60
Q

Glycolysis (Embeden-Meyerhof pathway)

A

a common pathway for catabolism of glucose
• anaerobic process
• 3 stages

61
Q

Nutrition and cell chemistry

A
  • nutrients - supply of monomers (or precursors of) required by cells for growth
  • macronutrients - nutrients required in large amounts
  • micronutrients - nutrients required in trace amount
62
Q

Carbon

A
  • required by all cells
  • typical bacterial cell ~50% carbon (by dry weight)
  • major element in all classes of macromolecules
  • heterotrophs use organic carbon
  • autotrophs use inorganic carbon
63
Q

Nitrogen

A
  • typical bacterial cell ~12% nitrogen (by dry weight)

* key element in proteins, nucleic acids, and many more cell constituents

64
Q

Other macronutrients

A
  • phosphorus (P)
  • sulphur (S)
  • potassium (K)
  • magnesium (Mg)
  • calcium (Ca)
  • Sodium (Na)
65
Q

Phosphorus (P)

A

synthesis of nucleic acids and phospholipids

66
Q

Sulphur (S)

A
  • sulphur-containing amino acids (cysteine and methionine)

* vitamins (eg thiamine, biotin, lipoic acid) and coenzyme A

67
Q

Potassium (K)

A

required by enzymes for activity

68
Q

Magnesium (Mg)

A
  • stabilizes ribosomes, membranes, and nucleic acids

* also required for many enzymes

69
Q

Calcium (Ca)

A
  • helps stabilize cell walls in microbes

* plays key role in heat stability of endospores

70
Q

Sodium (Na)

A

required by some microbes

eg marine microbes

71
Q

Iron

A
  • key component of cytochromes and FeS proteins involved in electron transport
  • under anoxic conditions - generally ferrous (Fe2+) form; soluble
  • under oxic conditions - generally ferric (Fe3+) form; exists as insoluble minerals
  • cells produce siderophores (iron-binding agents) to obtain iron form insoluble mineral form
72
Q

Iron cont’d

A 
(outside cell)
ferric (Fe3+) + hydroxamate
--> ferric hydroxamate
--> (inside cell) 
--> + electrons (reduction), - hydroxamate
--> ferrous (Fe2+)
73
Q

Growth factors

A

organic compounds required in small amounts by certain organisms
• eg vitamins, amino acids, purines, pyrimidines

vitamins
• most commonly required growth factors
• most function as coenzymes

74
Q

All living things need

A
  • a source of raw materials
  • a source of energy
  • a source of reducing power
75
Q

Living things can be classified according to

A

their metabolism, on the basis of where they get these things from
(in the case of raw materials classification is usually on the basis of carbon source)

76
Q

Classification based on metabolism

A
  • chemoorganotrophs (chemoheterotrophs)
  • photolithotrophs (photoautotrophs)
  • chemolithotrophs (chemoautotrophs)
77
Q

Sergei Winogradsky

A

the concept of chemolithotrophy
• demonstrated that specific bacteria are linked to specific biogeochemical transformations (S and N cycles)
• proposed concept of chemolithotrophy - oxidation of inorganic compounds linked to energy conservation

78
Q

Photolithotrophs

A
  • energy from light
  • obtain electrons from inorganic molecules
  • carbon from inorganic sources (CO2, CH4) rather than organic molecules
79
Q

Eg of photolithotrophs

A

plants and cyanobacteria
• energy from sunlight used to generate ATP and split water

2H20 –> O2 + 4H+ + 4e-

  • electrons used to reduce NADP to NADPH
  • NADPH and ATP required for the calvin cycle
80
Q

Chemoorganotrophs

A
  • energy obtained by catalyzing chemical reactions

* obtain carbon from organic molecules

81
Q

Eg of chemoorganotrophs

A

aniimals, fungi, E. coli
• ingest organic molecules
• obtain energy, reducing power, and carbon by breaking down these molecules

82
Q

All macroorganisms are

A

chemoorganotrophs and/or photolithotrophs
• so are many microbes
• bacteria in particular use a very wide range of other metabolic options

83
Q

Photoorganotrophs

A

= photoheterotrophs
• energy from sunlight
• reducing poewr, carbon (and some energy) obtained by beraking down organic molecules

84
Q

Chemolithotrophs

A

= chemoautotrophs
• energy and reducing power obtained by catalyzing inorganic chemical reactions
• carbon obtained from CO2 or CH4

85
Q

Thiobacillus ferrooxidans

A 
• chemolithotroph
• lives in mine drainage
• lives on pyrite (FeS2) 
• oxidizes Fe2+ to Fe3+ 
and sulfide to sulfate (produces sulphuric acid)
86
Q

Biofilm from chemolithotrophic bacteria on

A

basalt from 1500m depth - Columbia River Basin, USA
• chemolithotrophs growing deep below the earth’s surface may account for a significant proportion of the earth’s biomass

87
Q

Microbes on mars

A

• presence of methanogenic microbes under the surface

88
Q

How have all the different microbial metabolisms evolved?

A

• microbes generally use a “mix and match” approach, combining a limited number of basic metabolic pathways in different ways

  • eg photoautotrophs, photolithotrophs, and chemolithotrophs all use the Calvin cycle to fix CO2
  • although the ATP and reducing power required are obtained in different ways
89
Q

The same principle allows individual bacteria to be very metabolically versatile
eg Rhodospirillum rubrum

A

a purple non-sulfur bacterium that lives in muddy sediments in lakes and ponds
• adjusts its metabolism according to the availability of light, oxygen, organic compounds and sulfide - it can be a photoorganotroph, an aerobic chemoorganotroph, or an aerobic chemoorganotroph, or a lithotroph using the calvin cycle to fix CO2

Microbial Physiology and Growth (5 decks)

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