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
2
Q
Understanding life processes
A
microbes are excellent models for understanding cellular processes in unicellular AND multicellular organisms
3
Q
Applying that knowledge to the benefit of humans
A
microbes play important roles in medicine, agriculture, and industry
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
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
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)
7
Q
Everything except … are microbes
A
animals, fungi, plants
some are microbes
8
Q
Characteristics of living systems
A
- metabolism
- reproduction
- differentiation
- communication
- movement
- evolution
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
10
Q
Reproduction
A
generation of 2 cells from one
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
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
13
Q
Movement
A
via self-propulsion, many forms in microbes
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
15
Q
Growth
A
chemicals from the environment are turned into new cells under the genetic direction of preexisting cells
16
Q
Genetic functions
A
• replication • transcription • translation --> proteins (to growth)
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)
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
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
20
Q
Cells as catalysts and as coding devices
A
- cells carry out chemical reactions
- cells store and process information that is eventually passed on to offspring during reproduction through DNA and evolution
21
Q
Cells carry out chemical reactions
A
• enzymes - protein catalysts of the cell that accelerate chemical reactions
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
23
Q
Growth
A
the link between cells as machines and cells as coding devices
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
25
Microorganisms exist in nature in populations of interacting assemblages called
microbial communities
26
The environment in which a microbial population lives in its
habitat
27
Ecosystem refers to
all living organisms plus physical and chemical constituents of their environment
28
Microbial ecology is
the study of microbes in their natural environment
29
Microorganisms and their environments
* 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
30
Diversity and abundances of microbes are controlled by
resources (nutrients) and environmental conditions (eg temp, pH, O2)
31
The activities of microbial communities can affect the
chemical and physical properties of their habitats
32
Microbes also interact with their physical and chemical environment
• 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
33
Nutrition and cell chemistrys
* metabolism
* catabolic reactions (catabolism)
* anabolic reactions (anabolism)
* most knowledge of microbial metabolism is based on study of laboratory culture
34
Metabolism
the sum total of all chemical reactions that occur in a cell
35
Catabolic reactions (catabolism)
energy-releasing metabolic reactions
36
Anabolic reactions (anabolism)
energy-requiring metabolic reactions
37
Microbial metabolism
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
Biological molecules are produced by
anabolic reactions
39
Breaking down
catabolic reactions
40
Anabolic reactions generally require
• 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
The Calvin Cycle
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
Inputs of Calvin Cycle
* raw materials (CO2)
* free energy (hydrolysis of ATP to ADP plus Pi)
* electrons: oxidation of NADPH to NADP
43
Electron donors and electron acceptors
* 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
Redox tower
represents the range of possible reduction potentials
• top = reduced, donates electrons
• bottom = oxidized, accepts electrons
45
Redox reactions usually involve reactions
between intermediates - carriers
• electron carriers are divided into 2 classes
- prosthetic groups (attached to enzymes)
- coenzymes (eg NAD+, NADP)
46
NAD+ and NADH
facilitate redox reactions without being consumed
| • they're recycled
47
NAD+ reduction
enzyme I reacts with electron donor and oxidized form of coenzyme, NAD+
48
NADH oxidation
enzyme II reacts with electron acceptor and reduced form of coenzyme, NADH
49
Chemical energy released in redox reactions is
primarily stored in certain phosphorylated compounds
• ATP - the prime energy currency
• phosphoenolpyruvate
• glucose 6-phosphate
chemical energy also stored in coenzyme A
50
Long-term energy storage involves
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
Nitrogen fixation
another crucial anabolic reaction
N2 + 8H+ + 8e- + 16 ATP
--> nigrogenase (enzyme)
2NH3 + H2 + 16 ADP + 16Pi
52
Incorporating fixed nitrogen into amino acids
anabolism
NH4+ + α-ketoglutarate + NADPH + H+
--> glutamate dehydrogenase (enzyme)
L-glutamate + NADP+ + H20
53
Essentials of catabolism
* glycolysis
* respiration and electron carriers
* the proton motive force
* the Citric Acid Cycle
* catabolic diversity
54
Catabolic reactions tend to
release energy and reducing power
| eg glycolysis
55
Glycolysis net reaction
glucose + 2ADP + 2Pi + 2NAD+
-->
2 pyruvate + 2ATP + 2NADH + 2H+
* glucose consumed
* 2 ATPs produced
* fermentation products generated
56
Glycolysis
* 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
Substrate-level phosphorylation
energy rich intermediates
• Pi in
• ADP --> ATP
58
Oxidative phosphorylation
```
energized membrane (+in -out)
ADP + Pi --> ATP
```
59
Glycolysis: fermented substance is
both an electron donor and an electron acceptor
60
Glycolysis (Embeden-Meyerhof pathway)
a common pathway for catabolism of glucose
• anaerobic process
• 3 stages
61
Nutrition and cell chemistry
* 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
Carbon
* 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
Nitrogen
* typical bacterial cell ~12% nitrogen (by dry weight)
| * key element in proteins, nucleic acids, and many more cell constituents
64
Other macronutrients
* phosphorus (P)
* sulphur (S)
* potassium (K)
* magnesium (Mg)
* calcium (Ca)
* Sodium (Na)
65
Phosphorus (P)
synthesis of nucleic acids and phospholipids
66
Sulphur (S)
* sulphur-containing amino acids (cysteine and methionine)
| * vitamins (eg thiamine, biotin, lipoic acid) and coenzyme A
67
Potassium (K)
required by enzymes for activity
68
Magnesium (Mg)
* stabilizes ribosomes, membranes, and nucleic acids
| * also required for many enzymes
69
Calcium (Ca)
* helps stabilize cell walls in microbes
| * plays key role in heat stability of endospores
70
Sodium (Na)
required by some microbes
| eg marine microbes
71
Iron
* 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
Iron cont'd
```
(outside cell)
ferric (Fe3+) + hydroxamate
--> ferric hydroxamate
--> (inside cell)
--> + electrons (reduction), - hydroxamate
--> ferrous (Fe2+)
```
73
Growth factors
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
All living things need
* a source of raw materials
* a source of energy
* a source of reducing power
75
Living things can be classified according to
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
Classification based on metabolism
* chemoorganotrophs (chemoheterotrophs)
* photolithotrophs (photoautotrophs)
* chemolithotrophs (chemoautotrophs)
77
Sergei Winogradsky
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
Photolithotrophs
* energy from light
* obtain electrons from inorganic molecules
* carbon from inorganic sources (CO2, CH4) rather than organic molecules
79
Eg of photolithotrophs
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
Chemoorganotrophs
* energy obtained by catalyzing chemical reactions
| * obtain carbon from organic molecules
81
Eg of chemoorganotrophs
aniimals, fungi, E. coli
• ingest organic molecules
• obtain energy, reducing power, and carbon by breaking down these molecules
82
All macroorganisms are
chemoorganotrophs and/or photolithotrophs
• so are many microbes
• bacteria in particular use a very wide range of other metabolic options
83
Photoorganotrophs
= photoheterotrophs
• energy from sunlight
• reducing poewr, carbon (and some energy) obtained by beraking down organic molecules
84
Chemolithotrophs
= chemoautotrophs
• energy and reducing power obtained by catalyzing inorganic chemical reactions
• carbon obtained from CO2 or CH4
85
Thiobacillus ferrooxidans
```
• chemolithotroph
• lives in mine drainage
• lives on pyrite (FeS2)
• oxidizes Fe2+ to Fe3+
and sulfide to sulfate (produces sulphuric acid)
```
86
Biofilm from chemolithotrophic bacteria on
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
Microbes on mars
• presence of methanogenic microbes under the surface
88
How have all the different microbial metabolisms evolved?
• 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
The same principle allows individual bacteria to be very metabolically versatile
eg Rhodospirillum rubrum
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
