SH4: Bacterial taxonomy, genomics and genetics

Question 1

What is taxonomy?

Answer 1

The science of classification. It is concerned with nomenclature and identification, and organising groups of organisms, defining the relationships between them.

Question 2

What is taxonomy?

Answer 2

The science of classification. It is concerned with nomenclature and identification, and organising groups of organisms, defining the relationships between them.

Question 3

Name a bacterium and virus that cause diarrhoea.

Answer 3

shigella dysenteriae/ E.coli

Question 4

A lower level than species is subspecies which show members of the same species differ in certain ways. Name these ways.

Answer 4

• Biological characteristics (biotypes or biovars)
• Expression of surface antigens (serotypes or serovars)
• Virulence -pathogenic or not (virotypes)
• Strains, pure cultures of mutants, isolates and variants

Question 5

How do they determine subspecies of organisms in hospitals?

Answer 5

The phenetic approach, which is looking at characteristics such as cell size, gram stain, shape

Question 6

How to scientists classify organisms into subspecies?

Answer 6

The phylogenetic approach, which is looking at evolutionary relationships

Question 7

What is the issue with the phenetic approach of classification?

Answer 7

Convergent evolution- a biological property can arise by more than one route meaning have evolved in different ways.

Question 8

What is numerical taxonomy

Answer 8

A way to quantitatively analyse variation within organisms and come up with relationships. Technique removes subjectivity, implying that not all features were equally as important for example gram stain is more important than cell shape.

Question 9

What are some chemical and molecular markers used in phenetic taxonomy?

Answer 9

• Cell wall composition – crosslinking in peptidoglycan
• Membrane lipid structure
• Proteins
• Nucleic acid composition
• Base pairs - looking at the percentage of G-C pairs
• Hybridisation – if DNA from different organisms mix easily, they are closely related

Question 10

What is genomics?

Answer 10

The branch of molecular biology concerned with the structure, function, evolution, and mapping of genomes based upon the sequence analysis.

Question 11

Using genomics, what can be told about a micro-organism by looking at its genome?

Answer 11

• Transcriptosome- can look at cells and see what RNA’s are being made, what genes are being expressed and when, how much and in response to stimulus
• Proteome- what proteins are being expressed, when, how much, in response to what stimulus
• Metabolic potential
• glycome (sugars)
• interactome- interactions between proteins and macromolecules

Question 12

Bacteria have plasmids. What are these?

Answer 12

Heterogeneous group of dsDNA molecules, separate from the chromosomes, encoding for additional features.

Question 13

What are the 2 types of virus specific bacteria?

Answer 13

1. Virulent/ lytic cycle - infects cell, grows, cell burst, virus infects other cells
2. Temperate – inserts itself into the genome of the bacteria cell, living harmlessly

Question 14

What are transposable elements (jumping genes)?

Answer 14

DNA that replicate themselves and are able to move within and between DNA molecules.

Question 15

What are insertion sequences?

Answer 15

Sequences that can ‘jump’ into a gene and inactivate it

Question 16

What are complex transposons?

Answer 16

Larger versions of insertion sequences that include more genetic information, like genes such as antibiotic resistance.

Question 17

What are some mechanisms of genetic exchange in bacteria?

Answer 17

• Transformation- uptake of DNA of dead cell released into the environment, fragments in the soil. This fragmented DNA is sampled by living bacteria and proteins of the surface of the bacteria take up the DNA from the dead species and recombine it with its own genome
• Transduction- a phage dependent process, where the phage carries the bacterial DNA from one infected cell to another
• Conjugation- plasmid dependent DNA transfer between bacteria. ‘conjugate’ plasmids initiate cell to cell contact; the DNA is transferred by rolling circle replication. (F+ plasmid induces the formation of a membrane protrusion called the ‘sex pilus’ off of the membrane of the bacterial cell to another. Either plasmid moves to the other cell, or the desired gene in the DNA is copied and moves across.)

Question 18

Name a bacterium and virus that cause diarrhoea.

Answer 18

shigella dysenteriae/ E.coli

Question 19

A lower level than species is subspecies which show members of the same species differ in certain ways. Name these ways.

Answer 19

• Biological characteristics (biotypes or biovars)
• Expression of surface antigens (serotypes or serovars)
• Virulence -pathogenic or not (virotypes)
• Strains, pure cultures of mutants, isolates and variants

Question 20

How do they determine subspecies of organisms in hospitals?

Answer 20

The phenetic approach, which is looking at characteristics such as cell size, gram stain, shape

Question 21

How to scientists classify organisms into subspecies?

Answer 21

The phylogenetic approach, which is looking at evolutionary relationships

Question 22

What is the issue with the phenetic approach of classification?

Answer 22

Convergent evolution- a biological property can arise by more than one route meaning have evolved in different ways.

Question 23

What is numerical taxonomy

Answer 23

A way to quantitatively analyse variation within organisms and come up with relationships. Technique removes subjectivity, implying that not all features were equally as important for example gram stain is more important than cell shape.

Question 24

What are some chemical and molecular markers used in phenetic taxonomy?

Answer 24

• Cell wall composition – crosslinking in peptidoglycan
• Membrane lipid structure
• Proteins
• Nucleic acid composition
• Base pairs - looking at the percentage of G-C pairs
• Hybridisation – if DNA from different organisms mix easily, they are closely related

Question 25

What is genomics?

Answer 25

The branch of molecular biology concerned with the structure, function, evolution, and mapping of genomes based upon the sequence analysis.

Question 26

Using genomics, what can be told about a micro-organism by looking at its genome?

Answer 26

• Transcriptosome- can look at cells and see what RNA’s are being made, what genes are being expressed and when, how much and in response to stimulus
• Proteome- what proteins are being expressed, when, how much, in response to what stimulus
• Metabolic potential
• glycome (sugars)
• interactome- interactions between proteins and macromolecules

Question 27

Bacteria have plasmids. What are these?

Answer 27

Heterogeneous group of dsDNA molecules, separate from the chromosomes, encoding for additional features.

Question 28

What are the 2 types of virus specific bacteria?

Answer 28

1. Virulent/ lytic cycle - infects cell, grows, cell burst, virus infects other cells
2. Temperate – inserts itself into the genome of the bacteria cell, living harmlessly

Question 29

What are transposable elements (jumping genes)?

Answer 29

DNA that replicate themselves and are able to move within and between DNA molecules.

Question 30

What are insertion sequences?

Answer 30

Sequences that can ‘jump’ into a gene and inactivate it

Question 31

What are complex transposons?

Answer 31

Larger versions of insertion sequences that include more genetic information, like genes such as antibiotic resistance.

Question 32

What are some mechanisms of genetic exchange in bacteria?

Answer 32

• Transformation- uptake of DNA of dead cell released into the environment, fragments in the soil. This fragmented DNA is sampled by living bacteria and proteins of the surface of the bacteria take up the DNA from the dead species and recombine it with its own genome
• Transduction- a phage dependent process, where the phage carries the bacterial DNA from one infected cell to another
• Conjugation- plasmid dependent DNA transfer between bacteria. ‘conjugate’ plasmids initiate cell to cell contact; the DNA is transferred by rolling circle replication. (F+ plasmid induces the formation of a membrane protrusion called the ‘sex pilus’ off of the membrane of the bacterial cell to another. Either plasmid moves to the other cell, or the desired gene in the DNA is copied and moves across.)