physiology and diversity of prokaryotes · 3 5 © heribert cypionka, prokaryotic cell...

1

© Heribert Cypionka, www.pmbio.icbm.de1

Physiology and Diversity of Prokaryotes

Download: www.pmbio.icbm.de... Teaching...


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)

2


Class Schedule

www.pmbio.icbm.de

...Teaching


The prokaryotic cell

and a bit about science

Heribert Cypionka

Brock: Chapters 1-4

3


Prokaryotic cell

Brock/Madigan 10th ed.


Prokaryotic cell

Life, life science

Size

Membrane(s)

Cell wall

Cytoplasm

Nucleoid, Plasmids

Ribosomes

4


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

5

© Heribert Cypionka, www.pmbio.icbm.de9 Brock/Madigan 10th ed.

Regulation upon intra- and extracellular signals

Complexity



Characteristics of life

!??

6


Size - the relevance of being small


Bacterium : Man : Earth

7


Size 1-D, 2-D, 3-D


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.

8


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


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?

9


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.)


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?

10


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 .


Simplicity

After Gott !

How simple is science?

Scientifically correct answer (with 90 % probability )

How long will Homo sapienssurvive on earth?

11


J.R. Gott (1993) Nature 363:315-319

Gott, 1993


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%

....................................................................................................

12


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 .


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) .

13


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.


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 .

14


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


Membranes

● Properties, permeability, “function“

● Building blocks

● Differences between Bacteria, Archaea, Eukarya

15



16


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


Membrane – building blocks

(You should know the building blocks and bonding types)

Cypionka, Grundl. der Mikrobiologie

17


(You should know these reactive groups)

Functional groups

Form these by removal of water


Causes bending

18




Ester lipid

Ether lipid [Archaea]

Isoprene [Archaea]

19


Sterol ring structure

Cholesterol[Eukaryotes]

Hopanoid (Diploptene)[Bacteria]


Archaeal lipids (1)

Compare stability of eubacterial and archaeal lipid s

20


Archaeal lipids (2)


Cell wall

● Properties, permeability, “function“

● Building blocks

● Differences between Bacterial groups and Archaea

21


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


Bacterial cell walls

!

22


Gram-negative cell


Murein building blocks


23


Diaminopimelic acid Lysine


24


Cell wall of a Gram-positive bacterium(glycerol or ribitol phosphate)


Cell wall of a Gram-negative bacterium

25


Lipopolysaccharides typical for the cell wall of Gram-negative bacteria

KDO = KetodeoxyoctonateHexoses

LPS (Lipid A) active as Endotoxin (“although the major function is structural“)



Cell walls of Gram-negative and Gram-positive Bacteria and Archaea

26


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


Gram-Test with KOH

3 % KOH causes lysis of Gram-negative cells and releases DNA

27


- Flagella,Fimbriae

- Capsules

-Spores

Cell surface structures

(not a surface structure)

(Indian Ink contrasting)


Spiroch(a)ete and Spirilli

28


Movement analysis by means of PICOLAY


Slime capsules

Alga in a horse trough

Symbiose? ‘ Symbiosis‘! Parasites? Predators?

Mafia!

Capsule visualisation by means of indian ink (negative contrast)

29


Cells without cell wall?

Mycoplasma

Thermoplasma



Nucleoid

- Mostly 1 chromosome

- Many with plasmids


30


Building blocks of nucleic acids

(You should know ATP and the and bonding types)


Hydrogen bonds G= C, A=T


31


- H2O!

N-Glycosidic linkage, anhydride, ester



DNA


32


DNA

large groove

small groove


Hydrogen bonds, primary and secondary structure


33


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


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

physiology and diversity of prokaryotes · 3 5 © heribert cypionka, prokaryotic cell...

Documents