Bacterial Diversity and Response to the Environment

Question 1

Classification requires

Answer 1

the presence of structures
that are conserved across all species.

Question 2

ALLknown forms of life have

Answer 2

ribosomes and even though there are differences between prokaryotes (archaea and bacteria) and eukaryotes, the basic
structure is conserved

Question 3

The most conserved sub-unit is the

Answer 3

16S subunit and this is the basis of classifying bacteria

Question 4

The rRNA genes are duplicated in the

Answer 4

genome as they are needed in large amounts as they form the
basis of the cell’s ability to produce proteins.

Question 5

Because of the conservation of the 16S
subunit the genes that encode 16S rRNA
are highly

Answer 5

conserved

Question 6

This conservation in sequence can be
exploited to sequence

Answer 6

16S rRNA genes

Question 7

Because there are defined areas of
conservation within the rRNA gene we can

Answer 7

design primers that will amplify the gene from many different species of bacteria and compare them by examining to areas of the
gene that are not so strictly conserved.

Question 8

Conservation can occur in areas that:

Answer 8

• Only bacteria exhibit
• Only eukaryotes exhibit
• Only archaea exhibit
• Or can be conserved across almost
  all life

Question 9

The basic idea of constructing
trees is that

Answer 9

they reflect similarity between sequences.

Question 10

Those with the greatest similarity
must be

Answer 10

closest related in evolution.

Question 11

Those with the least similarity
show the

Answer 11

greatest evolutionary divergence.

Question 12

There is a huge difference between
the number of organisms that can be
seen microscopically in any collection
and

Answer 12

those that can be cultiovated on nutrient media

Question 13

Only ~1% of bacteria collected are
able to

Answer 13

be cultivated

Question 14

• Only ~1% of bacteria collected are
  able to be cultivated
• The rest are

Answer 14

either in a dormant state, require other nutrients, or
require factors produced by other microorganisms

Question 15

Although we cannot culture many species of bacteria and
archaea, we can

Answer 15

classify them by using oligonucleotide
primers designed to the conserved regions of 16S rRNA

Question 16

Once amplified from a given environmental sample the
resulting DNA can be

Answer 16

inserted into a gene library and
large scale sequencing of the resultant 16S rRNA genes
can take place

Question 17

a problem: The species we can sample this way MUST have

Answer 17

the same conserved sequences of their 16S rRNA genes

Question 18

One of the starkest differences between
bacteria and archaea is

Answer 18

in the composition of the membrane.

Question 19

Like eukaryotes, bacteria have

Answer 19

ester linkages between the glycerophosphate head and the lipid tail

Question 20

Like eukaryotes, bacteria have ester
linkages between the glycerophosphate
head and the lipid tail while archaea have

Answer 20

ether linkages

Question 21

many archaea have lipid

Answer 21

monolayers rather than bilyaers

Question 22

archaea was orginially thought to only

Answer 22

habit ‘extreme’ environments such as hydrothermal vents, hot springs etc,

Question 23

archaea was orginially thought to only habit ‘extreme’ environments such as hydrothermal vents, hot springs etc, but now known to…

Answer 23

… be far more widespread – include environments such as the oceans and the mammalian gut.

Question 24

many of the archae are

Answer 24

extremophiles

Question 25

Methanopyrus which is capable of reproducing in temperatures up to

Answer 25

120°C

Question 26

Chemoautotrophic metabolism – produces

Answer 26

methane from reduction of CO2 by hydrogen

Question 27

Other Archaea are able to withstand

Answer 27

extremely low pH (acidophiles), high temperatures (thermophiles), or salinity (halophiles).

Question 28

13

Question 29

17-24 major groups (phyla) on the basis of their

Answer 29

genetic divergence

Question 30

Recent uses of environmental genomics suggest that there are around

Answer 30

50 phyla - most not culturable

Question 31

Some groups are

Answer 31

small and ‘obscure’ compared with familiar groups

Question 32

Proteobacteria and Gram positive contain

Answer 32

best-known species

Question 33

There is a huge amount of metabolic diversity within

Answer 33

groups

Question 34

* At the fundamental level there is little diversity within

Answer 34

plants and animals

Question 35

Photoautotrophy distributed among

Answer 35

5 phyla

Question 36

Extreme loss of capability in

Answer 36

chlamydia - atp parasite

Question 37

Traditional bacterial taxonomy:

Answer 37

* cell structure * ability to take up stains * biochemistry * Habitat

Question 38

But many bacteria have no

Answer 38

distinctive structures

Question 39

Many large morphological differences are due to

Answer 39

small genetic changes

Question 40

There has been a large amount of

Answer 40

horizontal gene transfer

Question 41

the vast majortiy cannot be

Answer 41

cultures

Question 42

One way of classifying bacteria is in terms of the

Answer 42

GC content of their genomes

Question 43

as a general rule those bacteria that live intracellulary have low

Answer 43

gc content whilst those in soil have high gc content

Question 44

GC content varies from

Answer 44

16.6% in Carsonella ruddi to 74.9% in Anaeromyxobacter dehalogenans.

Question 45

Phylogenetic analysis can be confused by

Answer 45

the presence of horizontal gene transfer by either conjugation, transduction, or transformation.

Question 46

Gram negative bacteria e.g. proteobacteria have an

Answer 46

outer and inner membrane which surround a periplasmic space

Question 47

A separate family of bacteria are

Answer 47

gram positive

Question 48

The Gram stain attaches to

Answer 48

Gram-positive bacteria but as this layer is shielded in Gram-negative bacteria the stain is easily washed away with ethano

Question 49

notable gram-positive bacteria include:

Answer 49

Bacillus. staphylococcus, and clostridium.

Question 50

proteobacteria are the largest...

Answer 50

... group (phylum) of bacteria

Question 51

proteobacteria include many of the

Answer 51

familar species important in medicine, agriculture, and industry

Question 52

proteobacteria is metabolically very

Answer 52

diverse

Question 53

all proteobacteria are

Answer 53

gram negative

Question 54

proteobacteria is divided into

Answer 54

5 groups

Question 55

important members of proteobacteria?

Answer 55

* Purple sulphur bacteria * Nitrosomonas – Rhizobium, Agrobacterium, Beggiatoa, Pseudomonas * Purple non-sulphur bacteria * E. coli

Question 56

Regardless of the type of metabolism all have

Answer 56

common elements

Question 57

all bacteria require a

Answer 57

- a carbon source (CO2 or organic). - an energy source (light, organic compounds, or inorganic compounts) - Electron donor with higher energy than the electron acceptor.

Question 58

Energy gained by

Answer 58

using electrons with high energy

Question 59

Energy gained by using electrons with high energy and

Answer 59

converting the energy into useful biological energy via ATP synthesis which can then be used to drive biosynthetic pathways.

Question 60

The redox tower illustrates the

Answer 60

comparative redox potential of redox pairs

Question 61

Chemoheterotrophs exhibit

Answer 61

the most familiar means of obtaining energy and converting carbon into useable compounds

Question 62

like animals and fungi chemoheterotrophs require

Answer 62

the intake of ready made organic compounds in order to grow

Question 63

They cannot fix

Answer 63

carbon dioxide themselves

Question 64

Carbon sources are converted to

Answer 64

a useable energy source (glucose) which then goes through glycolysis

Question 65

Chemoheterotrophs can range from

Answer 65

obligate anaerobes to obligate aerobes.

Question 66

what kind of anaerobe is e. coli ?

Answer 66

E. coli is a facultative anaerobe.

Question 67

what are photoautotrophs also known as?

Answer 67

purple sulphur bacteria

Question 68

how do photoautotrophs obtain energy?

Answer 68

energy is obtained by light but rather than the electron donor being water as in the case of normal photosynthesis, the electron donor in this case is hydrogen sulphide

Question 69

photoautotrophs crucially

Answer 69

fix carbon dioxide

Question 70

the pigmentation of Photoautotrophs is produced by

Answer 70

bacteriochlorophylls and carotenoids

Question 71

it is the absorption spectra that are responsible for

Answer 71

the colours of photoautotrophs

Question 72

elemental sulphur is further oxidised to

Answer 72

SO4^2-

Question 73

Beggiatoa species live in

Answer 73

sulphur springs, the soil, and mud at the bottom of lakes

Question 74

Beggiatoa exist as

Answer 74

filaments of around 50 cells

Question 75

Beggiatoa can grow as

Answer 75

chemoheterotrophs or as chemoautotrophs

Question 76

Chemoautotrophy depends on a cell using

Answer 76

the energy from oxidation of inorganic compounds (e.g. H2S, Fe2+) rather than energy from light in order to drive splitting of water molecules and the fixation of carbon dioxide.

Question 77

The levels of hydrogen sulphide required by purple sulphur bacteria are

Answer 77

toxic to purple non-sulphur bacteria

Question 78

Photoheterotrophs use light and an autotrophic mechanism to

Answer 78

fix carbon dioxide but they are also capable of photoheterotrophy

Question 79

Light is used as the energy source but

Answer 79

organic carbon compounds are used as the carbon source rather than just carbon dioxide

Question 80

Rhodobacter obtains hydrogen from

Answer 80

small fatty acids it has obtained by heterotrophic nutrition

Question 81

The hydrogen is then used as an

Answer 81

electron donor to drive the photosynthetic reaction centre

Question 82

Cyanobacteria formally known as

Answer 82

blue green algae. however, they are bacteria, not algae

Question 83

cyanobacteria are the ancestral bacteria which

Answer 83

were endosymbiosed by eukaryotic cells and evolved into chloroplasts in algae and plants

Question 84

As cyanobacteria are the ancestors of chloroplasts their

Answer 84

photoautotrophic metabolism is the same as in plants

Question 85

In cyanobacteria, light energy is harvested by

Answer 85

pigments (chlorophyll)

Question 86

Light energy is harvested by pigments (chlorophyll), water molecules are

Answer 86

split, and the resultant electrons are passed along an electron transport chain generating ATP

Question 87

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