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Physiology and Diversity of Prokaryotes
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© Heribert Cypionka, www.pmbio.icbm.de2
What is Physiology ?
Greek physis, nature, logos, word, logia, science (compare with Biochemistry)
What is Diversity ?Physiological and/or phylogenetic variance among communities or groups (compare with Morphology, Taxonomy)
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Class Schedule
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...Teaching
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The prokaryotic cell
and a bit about science
Heribert Cypionka
Brock: Chapters 1-4
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Prokaryotic cell
Brock/Madigan 10th ed.
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Prokaryotic cell
Life, life science
Size
Membrane(s)
Cell wall
Cytoplasm
Nucleoid, Plasmids
Ribosomes
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Building blocks of organisms
• Subatomic
• Chemical element
• Molecule
• Molecule aggregate
• Organelle
• Cell
• Tissue
• Organ
• Organism
(• • • Population, community, biotope, biosphere)
• (Quarks, ...) proton, electron
• Hydrogen, carbon, oxygen
• Water: H 2O, sugar: C 6H12O6, peptide
• Multi-enzyme complex
• Nucleus, mitochondrium
• bacterium, mouth mucosa cell
• Fat tissue
• Heart
• Bacterium, amoeba, lion, tree
Example
Living organisms consist of one or of many cells – m ost are unicellular.
© Heribert Cypionka, www.pmbio.icbm.de8Brock/Madigan 10th ed.
Definition of life
!
Complexity
Energy transformation
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© Heribert Cypionka, www.pmbio.icbm.de9 Brock/Madigan 10th ed.
Regulation upon intra- and extracellular signals
Complexity
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Brock/Madigan 10th ed.
Characteristics of life
!??
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Size - the relevance of being small
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Bacterium : Man : Earth
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Size 1-D, 2-D, 3-D
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Size relations bacteria : humans
Size relations
1-D: 10-7
2-D: 10-14
3-D: 10-21
Biological activity is proportional to the membrane surface.
For bacteria diffusion is a fast process.
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Size: area
Bacteria with a volume of 1 cm 3 have a surface area of ≈≈≈≈10 m2
Edge length Surfaceof 1 cm 3 cube
1 cm → 6 cm2
1 mm → 60 cm2
100 µm → 600 cm2
10 µm → 6000 cm2
1 µm → 6 m2
Most chemical reactions on earth are microbial metabolism.
Volume to area ratio
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Just for fun
Many natural water bodies contain about 106 bacteria per ml . How many of these will you see if you bring 10 µl w ater under a cover slip of 20 x 20 mm and count them through the 100-fold objective in a microscopic field of view with 100 x 100 µm?
Surface area : 106 x 6 x 0.25 µm2 = 1.6 x 106 µm2 = 1.6 mm 2 per ml
10 µl = 10-2 ml containing 104 bacteria under a cover slip
with 400 mm2. View field is only 0.01 mm2:
(0.01 / 400) x 104 = 0.25 per view field
Which surface area do the bacteria have in 1 ml of water?
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Why is the frog green?
No! But the correct answer does not give a rational e or meaning.
Biological Questions
... In order to hide from the stork!?
(Note that the correct answer is misssing on this s lide.)
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Scientific method
Why has a beetle wings?
Result: "A maybug without wings can not hear anymore."
Why have humans hands?
„Fly!"
What is the function of a bacterial membrane?
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Intelligence testContinue the series 3, 4, 6, 9, ...
42 - 32 - 1 = 6
62 - 42 - 11 = 9
92 - 62 - 21 = 24
242 - 92 - 31 = 464
4642 - 242 - 41 = 214 679
3 + 1 = 4
4 + 2 = 6
6 + 3 = 9
9 + 4 = 13
13 + 5 = 18
Simple explanations
Newton: "Nature is pleased with simplicity."
Einstein: "The supreme goal of all theory is to mak e the irreducible basic elements as simple and as few as possible without having to surrender the adequate representa tion of a single datum of experience."
Occam's Razor: When multiple explanations are avail able for a phenomenon, the simplest version is to be preferred .
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Simplicity
After Gott !
How simple is science?
Scientifically correct answer (with 90 % probability )
How long will Homo sapienssurvive on earth?
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J.R. Gott (1993) Nature 363:315-319
Gott, 1993
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Statistics
Which useful life does a thing have?
You don't even have to check the fill level!
From 100 tubes with tooth paste (rolls of toilet paper, bottles of after shave, sofas e.t.c.) about 5 % can be assumed to be in use newly (first 5 % of their useful life) or consumed almost completely (last 5 %). For 90 % holds true: they are between the first 5 % and last 5 % of their expected useful life.
5% 95%
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Statistics
When I know the age of a thing, I can assume normally :
The total lifetime of a 10-day-old thing is with 90% probability between 10/0.95and 10/0.05, i.e. 10.53 to 200 days.
With 90 % probability it has had between 5 % and 95 % of its lifetime .
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Homo sapiens
Homo sapiens exists since about 270 000 years
Geo 10/2001
Gott says: With 90 % probability we will survive further 14 200 years (270 000/0.95 – 270 000) to5.13 Million years (270 000/0.05 – 270 000) .
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Simplicity of science
Is Gott right?
Yes, why do you feel kidded?
Since 50 years mankind can exstinguish itself within a day. Exponential growth of natural population does last over few generations, and then tends to end abruptly...
Age is the only information used.
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Science
The scientific approach asks for simplicity .
Statistics requires the ignorance of details.
Our perception of diversity is based on simple statistics and an improper species term.
Biology is complex .
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Schätzen wir das ruhige Wahrnehmen noch richtig ein? - Reflexionen eines Mikrobiologen
"Es liegt wohl daran, dass die Natur unglaublich vie l reichhaltiger ist, als wir auf Grund unserer Suche n ach Gesetzmäßigkeiten erwarten." ... "Und wir sind dann sehr zufrieden damit, in der Welt nur das wahrzunehmen, was wir schon kennen."
_______________________________________________
Do we still esteem open-minded observation? -Reflexions of a microbiologist
"Probably this is due to the fact that nature is muc h more ample than we expect on our search for regularities." ... "And then we are very satisfied to realize in our world only what we already know."
Norbert Pfennig on the symposium held at H.G. Schle gel's retirement
Arbeitsberichte Naturwissenschaften 15, Deutsches I nstitut für Fernstudien, Univ. Tübingen 1993
Pfennig
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Membranes
● Properties, permeability, “function“
● Building blocks
● Differences between Bacteria, Archaea, Eukarya
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© Heribert Cypionka, www.pmbio.icbm.de29 Brock/Madigan 10th ed.
© Heribert Cypionka, www.pmbio.icbm.de30 Brock/Madigan 10th ed.
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Membranes
● Thickness 2.5 + 3 + 2.5 = 8 nm
● Sidedness: defined by the proteins
● Semi-permeable (?)
● Stands a membrane potential of 160 mV
(Calculate the electrical field strength per mm!)
● Permeable for uncharged small molecules, i.e.
● Impermeable for the rest, if not mediated by transport proteins
? ? ?
www.biologie.uni-hamburg.de/b-online
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Membrane – building blocks
(You should know the building blocks and bonding types)
Cypionka, Grundl. der Mikrobiologie
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© Heribert Cypionka, www.pmbio.icbm.de33 Brock/Madigan 10th ed.
(You should know these reactive groups)
Functional groups
Form these by removal of water
© Heribert Cypionka, www.pmbio.icbm.de34 Brock/Madigan 10th ed.
Causes bending
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Brock/Madigan 10th ed.
© Heribert Cypionka, www.pmbio.icbm.de36 Brock/Madigan 10th ed.
Ester lipid
Ether lipid [Archaea]
Isoprene [Archaea]
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© Heribert Cypionka, www.pmbio.icbm.de37 Brock/Madigan 10th ed.
Sterol ring structure
Cholesterol[Eukaryotes]
Hopanoid (Diploptene)[Bacteria]
© Heribert Cypionka, www.pmbio.icbm.de38 Brock/Madigan 10th ed.
Archaeal lipids (1)
Compare stability of eubacterial and archaeal lipid s
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© Heribert Cypionka, www.pmbio.icbm.de39 Brock/Madigan 10th ed.
Archaeal lipids (2)
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Cell wall
● Properties, permeability, “function“
● Building blocks
● Differences between Bacterial groups and Archaea
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Cell wall properties
● Jute bag around a balloon
● Pressure resistant (0.3 bar osmotic pressure)
● Shaping the cell
● Not a barrier for diffusing molecules
● Diaminopimelic acid as cross-linker
● Occurence of D-amino acids
© Heribert Cypionka, www.pmbio.icbm.de42 Brock/Madigan 10th ed.
Bacterial cell walls
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© Heribert Cypionka, www.pmbio.icbm.de43 Brock/Madigan 10th ed.
Gram-negative cell
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Murein building blocks
Cypionka, Grundl. der Mikrobiologie
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Diaminopimelic acid Lysine
© Heribert Cypionka, www.pmbio.icbm.de46 Brock/Madigan 10th ed.
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© Heribert Cypionka, www.pmbio.icbm.de47 Brock/Madigan 10th ed.
Cell wall of a Gram-positive bacterium(glycerol or ribitol phosphate)
© Heribert Cypionka, www.pmbio.icbm.de48 Brock/Madigan 10th ed.
Cell wall of a Gram-negative bacterium
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© Heribert Cypionka, www.pmbio.icbm.de49 Brock/Madigan 10th ed.
Lipopolysaccharides typical for the cell wall of Gram-negative bacteria
KDO = KetodeoxyoctonateHexoses
LPS (Lipid A) active as Endotoxin (“although the major function is structural“)
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Cypionka, Grundl. der Mikrobiologie
Cell walls of Gram-negative and Gram-positive Bacteria and Archaea
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S-layers are the outermost component of the cell wall of many bacteria and most of archaea. S-layer proteins form natural two-dimensional protein crystals covering the cell completely and confering stability in addition to other structures of the cell envelope.
www.biochem.mpg.de/baumeister/membran/S-layers
S-Layer
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Gram-Test with KOH
3 % KOH causes lysis of Gram-negative cells and releases DNA
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- Flagella,Fimbriae
- Capsules
-Spores
Cell surface structures
(not a surface structure)
(Indian Ink contrasting)
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Spiroch(a)ete and Spirilli
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Movement analysis by means of PICOLAY
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Slime capsules
Alga in a horse trough
Symbiose? ‘ Symbiosis‘! Parasites? Predators?
Mafia!
Capsule visualisation by means of indian ink (negative contrast)
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Cells without cell wall?
Mycoplasma
Thermoplasma
Brock/Madigan 10th ed.
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Nucleoid
- Mostly 1 chromosome
- Many with plasmids
Brock/Madigan 10th ed.
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Building blocks of nucleic acids
(You should know ATP and the and bonding types)
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Hydrogen bonds G= C, A=T
Brock/Madigan 10th ed.
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- H2O!
N-Glycosidic linkage, anhydride, ester
Brock/Madigan 10th ed.
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DNA
Brock/Madigan 10th ed.
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DNA
large groove
small groove
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Hydrogen bonds, primary and secondary structure
Brock/Madigan 10th ed.
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How much information is encoded in DNA?
E. coli: 1.3 mm DNA = 4 million base pairs
about 4 000 proteins encoded
2 bits per base
8 million bits = 1 MB
For comparison: Human genome
1 m DNA, about 25 000 genes
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Chemical Composition of a bacterial cell
Compound Percent Per cell ( ≈≈≈≈10-15 l)of dry mass
Number of Different molecules molecules
H2O 500 1011 1
Proteins 50 106 1000
Cell wall 20 1 1
RNA 15 104 1000 (Ribosomes) (mRNAs)
DNA 3 1 1
Lipids 5 106 50
Small org. compds. 5 106 200(Amino acids, ATP...)
Inorg. Ions (K+) 1 108 20
H+ (pH≈8) 0 6 1
Cytoplasm