2. Microbial phylogeny, structure and function

Question 1

Which are the three domains of life?

Answer 1

Bacteria & Archea (short prokaryotic cells nut have differences, in food archea are more “similar to eukaryota”)

And Eukarya

Question 2

What is phylogeny?

Answer 2

The evolutionary relationship between life forms. Based on physical or genetics characteristics.

Question 3

What is dendogram?

Answer 3

It’s a branching diagram representing categories based on the degree of similarity or the number of shared characteristics. The more distans the more difference the organisms have.

Question 4

Why do you search for the RNA I6S sequence? (3)

Answer 4

• Exisist in all organism
• Have both high and less conserved regions.
• Shows relationships as the n of differences is proportional to the n of stable mutations.

Question 5

What is a probe?

Answer 5

In DNA sequencing fragment of DNA or RNA used to detect presence of nucleotide complementary sequences.

Question 6

Describe G+ and G- bacteria?

Answer 6

G+, gets colored blue by gram coloring. Have several layers of peptidoglycan, a inner membrane and no outer membrane.

G-, gets colored red by gram coloring.
Only have few layers of peptidoglycan, surrounded by periplasm, a inner membrane and a outer membrane (LPS and protein)

Question 7

Describe spirochets

Answer 7

Spirochetes (G-)

Only sex genera – yet large impact on human and animal lives. Thin (often hard to see in microscope), mobile (swin). Both syphilis and borrelia (lymes disease) are caused by spirochete bacteria, other species are important symbionts in the stomach of cows and other ruminants.

Question 8

Describe archea

Answer 8

Many are extremophiles, i.e. thrive under environmental conditions in which other organism cannot survive. Common in marine environment (not only extreme milieus). Not so much known about archaea.

No known pathogenic archae

Question 9

What is extermophiles?

Answer 9

extremophiles, i.e. thrive under environmental conditions in which other organism cannot survive.

i.e. lives in extreme conditions.

Question 10

What are som e difference between archea, bacteria and eukarotes?

Answer 10

Archea:
Has membrane with branched hydrocarbon (properly what allows them to grow in extreme conditions) and some species can grow at >100 C

A + B
Has circular chromosome, no nuclear envelops, no organells.

A + E
Methionine is the initiator a.a. for protein synthesis. Has no peptidoglycan in the cell wall. No response to antibiotics. DNa is associated with histones. Contains several RNA polymerase.

Question 11

Desribe hyperthermophile and psychophile.

Answer 11

Extremes temperatures

90-113 C and 0-12 C

Question 12

Decribe acidophile and alkaliphile.

Answer 12

Extreme pH

-0.06-4 and 8.5-12

Question 13

Decribe barophile.

Answer 13

Extreme pressure

500-1000 atm

Question 14

Desribe halophile.

Answer 14

Extreme NaCl concentartions

15-32(sat)%

Question 15

Desribe eukaryota.

Answer 15

Includes algae, fungi and protozoa.

Two main types of cells
Prokaryote and eukaryote. Prokaryotic cells have a simpler internal structure than eukaryotic cells. Prokaryotes lack membrane-enclosed organelles.

Question 16

Describe plasmid/chromosome.

Answer 16

Plasmids are circular extra-chromosomal genetic elements (DNA, nonessential for growth, found in prokaryotes.)

DNA is arranged in cells to form chromosomes. In prokaryotes there is usually a single circular chromosome; whereas in eukaryotes, several linear chromosome exist.

Question 17

What is nucleus?

Answer 17

Membran-enclosed structure in euk cells that contains chromosomes.

Question 18

What is nucleiod?

Answer 18

is the aggregated mass of DNA that constitutes the chromosome of cells of bacteria and Archea.

Question 19

What is lysosome?

Answer 19

Vesicle contains hydrolytic enzymes which can break down many bio-molecules. Act as a waste disposal.

Breaks the beta1,4 links

Question 20

What is peroxisome?

Answer 20

metabolism of fatty acids and hydrogen peroxide

Question 21

What is the endosymbiosis theoru?

Answer 21

Mitocondria and chloroplast of eukoryotes contain their own genomes (DNA arranged in circular fashion, as in bacteria and ribosomes. rRNA and DNA sequencing technology indicate that these organelles are closely related to present day proteobacteria and cyanobacteria, respectively. Mitochondria and chloroplast were once free-living cells that established stable residency in cells of eukarya eons ago. The process by which this stable arrangement developed is known as endosymbiosis.

Question 22

What is morphology?

Answer 22

The shape of the microorganism.

Question 23

What is physiology?

Answer 23

Is the scientific study of normal mechanisms, and their interactions, which work within a living system.

Question 24

What is the VBNC concept?

Answer 24

Viable but nonculturable bacteria that are in a state of very low metabolic activity and do not dived but are alive and once resuscitated can become cultivatable.

Question 25

Decribe coccus/rod/spririlum/spirochete.

Answer 25

Coccus- round
Rod -rod
Spirillum - rod that is twisted
Sporpchete- corkscrew shaped

Question 26

What is significance of being small? (2)

Answer 26

The small size of prokaryotic cells affects physiology, growth rate and ecology… and evolution. Due to their small cell size most prokaryotes have – high surface area-to-volume ratio (more efficient nutrient and waste exchange with the environment. Favors fast growth.

Question 27

Describe the cytoplasmic membrane

Answer 27

The cytoplasmic membrane is a highly selective permeability barrier construct of lipids and proteins that forma a bilayer with hydrophilic exteriors and a hydrophobic interior.

Question 28

Desribe sterols and haponoid

Answer 28

In the membrane there is also other lipids, this strengtens the membrane as a results of theier rigid planar structure:
Sterols(euk) and hopanoids (bac and arc)

Question 29

Esther/ isopremen aechea ???

Answer 29

Unlike bacteria and eukaryote, in which ester linkage bond fatty acids to glycerol, archaea has a ether-linked lipids … and branched-chain (isoprene-derivation) lipid side-chains.

Question 30

Decribe monolayer and bilayer-

Answer 30

Monolayer has large biphytanyl

Bilayer has instead two groups of phospolipids with the fatty chains (non-polor side) together.

Question 31

What is the function of the membrane (3)?

Answer 31

1. Permeability barrier – prevents leakage and functions as a gateway from transport of nutrients into and out of the cell.
   The membrane also functions as an anchor for membrane proteins involved in transport, bioenergetics, and chemotaxis and as a site for energy conservation in the cell.
2. Protein anchor – site of many proteins involved in transport, bioenergetics and chemotaxis.
3. Energy conservation – site of generation and use of the proton motive force

Question 32

Describe the cell wall of prokaryotes.

What is

Answer 32

Strands of alternating repeats of N-acetylglucosamine and N-acetylmuramic acid, the latter cross-linked between strands by short peptides. Many sheets of peptidoglycan can be present, depending on the organism. Each peptidoglycan repeating subunits is composed of four amino acids (L-alanine, D-alanine, D-glutamic acid, and either lysine or diaminopimelic acid) and two N-acetyl-glucose-like sugars. Tetrapeptide cross-links formed by the amino acids from one chain of peptidoglycan to another provide the cell wall of prokaryotes with extreme strength and rigidity. (lipo)teichoic acid – glycerol/ribitol phosphate polymers covalently bonded to muramic acid (and for lipot, a the membrane) negatively charged.

! n-acetylglucosamine
n-acetylmutaomic - peptides
peptidoglucon
teichoic acids

Question 33

Describe the archea cell wall.

Answer 33

Lack of peptidoglycan, walls made out of other polysaccharides or protein. Pseudopeptidoglycan, S-layers and other cell walls. Pseudopeptidoglycan: N-acetyltalosaminuronic acid instead of the N-acetylmuramic acid of peptidoglucan. The backbone of pseudopeptidoglycan is linked by Beta-1,3 bonds instead of the beta-1,4 bonds of peptidoglycan.

! pseudopeptidoglycom
N-acetylialosaminoronic acids
beta1,3 ma beta14

Question 34

What is a protoplast?

Answer 34

Cells with no wall
some prokaryotes are free-living protoplast that survive without cell walls because they have unusually tough membranes or live in osmotically protected habitats, such as the animal body. Ex. Mycoplasma.

Question 35

Describe the outer membrane of G- bacteria.

Answer 35

The outer membrane of gram negative bacteria contain an outer membrane consisting of lipopolysaccharide (LPS), protein and lipoprotein. LPS =endotoxin. Lipopolysaccharides (LPS) is composed of lipid A, a core polysaccharide and an O-specific polysaccharide. Lipid A od LPS has endotoxin properties, which may cause violent symptoms in humans.

Question 36

Describe porins.

Answer 36

Protein called porins allows for permeability across the outer membrane by creating channels that traverse the membrane.

Question 37

Describe periplasm.

Answer 37

The space between the membranes is the periplasm, which contains various proteins involved in important cellular functions.

Question 38

Describe simple transport.

Answer 38

Transport is driven by the energy(H+) in the proton motive force.

Question 39

Describe group translocation

Answer 39

Transport through chemical modification of the transported substance driven by phosphoenolpyruvate

Question 40

Describe ABC system transport.

Answer 40

Transport by perplasmic binding proteins are involved and energy comes from ATP.

ABC transporters contain three interacting components. Transport requires energy from either the proton motive force, ATP, or some other energy-rich substance.

Question 41

Describe passive diffusion and faculative diffusion.

Answer 41

passive diffusion - molecules dissolve in the phospholipid bilayer, no membrane protein involved.

facilated diffusion – via transmembrane integral proteins.

Question 42

Describe uniporters, symporters and antiporters

Answer 42

One going through, two together, one going in and one going out.

Question 43

Describe translocases.

Answer 43

proteins are exported out of prokaryotic cells through the actions of proteins called translocases, which are specific in the types of proteins exported.

Question 44

Describe fimbriea and pili

Answer 44

Short protein filaments used for attachment are fimbriae. Longer filaments that are best known for their function conjugation are called pili.

Question 45

Describe PHAs and glycogen.

Answer 45

Poly-beta-hydroxyalkanoates (PHAs) and glycogen are produced as storage polymers when carbon is in excess. Poly-beta-hydroxybutyrate (PHB) is common storage material of prokaryotic cells.

Question 46

Describe endospores.

Answer 46

The endospores are a highly resistant differentiated bacterial cell produced by certain gram-positive bacteria. Endospore formation leads to highly dehydrated structure that contains essential macromolecules and a variety of substances such as calcium dipicolinate and small acid-soluble proteins (protect DNA) absent from vegetative cells.

Endospores differ significantly from vegetative, or normally functioning cells. Endospores can remain dormant indefinitely but germinate quickly when the appropriate trigger is applied.

! calcium dipicolinate

Question 47

Describe flagellum mobility.

Answer 47

Moving along. E.coli bacteria propel themselves by pushing fluid with a rear mounted flagellum, but other microbes have front-mounted flagella that “pull” the fluid. Pushers and pullers have clear but opposite effects on the overall viscosity of the fluid that host them according to experiments. Mobility in most microorganism is accomplished by flagella. In prokaryotes, the flagellum is a complex structure made of several proteins, most of which are anchored in the cell wall and cytoplasmic membrane. Flagella can occur in a variety of locations and arrangements. Each arrangement is unique to a particular species. The flagellum filament is made of a single kind of protein, flagellin. Rotates at the expense of the proton motive force – drives the flagellar motor. Flagella move the cell by roation, much like the propeller in a motor boat. An appreciable speed of about 60 cell lengths/seconds can be achived. Protons moving through the mot protein may exert forces on charges on the C and MS rings.

!Flagellin
Fili proteins
C and MS rings

Question 48

Describe chemo-phototaxis

Answer 48

Motile bacteria can respond to chemical and physical gradients in their environment. In the process of chemotaxis and phototaxis, random movement of prokaryotic cell can be biased, either toward or away from stimulus. By controlling the degree to which runs, or tumbles occur. The degree of runs/tumbles is controlled by the direction of rotation of the flagellum, which in turn is controlled by a network of sensory and response proteins. Positive chemotaxis is occurring toward an attractant when flagellar rotation results in net movement in the direction of increasing concentration of a chemical. In contrast, motile bacteria will move away from a repellent – negative chemotaxis.