Lectures 1-3 (Leonid Kulakov) - Bacterial Genetics

Question 1

What are the main properties of hereditary material

Answer 1

• Hereditary stability - ensures continuation through generations.
• Hereditary variability - ensures natural diversity.

Question 2

Give two examples of a bacteriophage

Answer 2

• Bacteriophage lambda

- Bacteriophage-transposon Mu-1

Question 3

What is the wild-type (WT) and give an example

Answer 3

An arbitrarily chosen strain and other strains of the species are compared with it e.g. E.coli K12

Question 4

Define the term mutation

Answer 4

Any change in a DNA sequence compared with the WT.

Question 5

Define the term genotype

Answer 5

Refers to genetic composition of an organism.

Question 6

Define the term phenotype

Answer 6

The observable property of an organism.

Question 7

What do bacterial genes encode

Answer 7

• Proteins/enzymes
• tRNA and rRNA
• Regulatory elements

Question 8

What does it mean that bacterial genes and proteins are colinear

Answer 8

• In bacteria and bacteriophages the sequence of nucleotides in the gene corresponds exactly with the sequence of amino acids in the protein.
• Introns are not normally present in prokaryotic genes.

Question 9

What are bacterial genes encoding proteins with related functions often organised into

Answer 9

Oberon

Question 10

What is the advantage of bacterial genes being organised into operons

Answer 10

Allows for coordinate expression/regulation of metabolic pathways.

Question 11

Define the term genome

Answer 11

It is the whole hereditary composition of an organism that is presented by the DNA (RNA for some viruses). It includes both introns and exons.

Question 12

Describe the bacterial genome

Answer 12

• Haploid genome as most genes are presented in one copy.

- There are partial diploids as some genes are present in two copies (on plasmids and during conjugation process).

Question 13

Describe the bacterial chromosome

Answer 13

• The DNA is packed in loops back and forth.
• The condensed DNA forms a nucleoid.
• The DNA is concentrated in part of the cell but it is not separated by a nuclear membrane.

Question 14

Define the term plasmid

Answer 14

An extra-chromosomal and non-essential DNA molecule.

Question 15

What is the major difference between a plasmid and the chromosome

Answer 15

The chromosome is essential for the survival of the bacterial cell whereas a plasmid is not.

Question 16

What is the importance of plasmids

Answer 16

• Can be transferred between bacterial cells and can therefore spread antibiotic resistance throughout a large population of bacteria cells.
• Codes for antibiotic resistance and utilisation of various compounds.

Question 17

What is an episome

Answer 17

A plasmid that is able to integrate into the chromosome.

Question 18

What is the importance of mobile genetic elements

Answer 18

• Insertion elements and transposons can move to new locations inside the bacterial genome.
• They can move between the chromosome and plasmid inside the bacterial cell and cause mutations in the DNA. This is important in evolution.

Question 19

What are the three different types of mutants

Answer 19

• Auxotrophy mutants are microorganisms which are not able to synthesise a particular organic compound required for its growth.
• Prototrophy mutants are microorganisms which are able to synthesise the organic compound required for its growth.
• Non-conditional mutants do not display the mutant phenotype under any conditions.

Question 20

Why are mutations important

Answer 20

• Ultimate source of natural variability.
• Source for selection.
• Used to elucidate gene/protein function.
• Identify site of action of various agents.
• Widely used in biotechnology.

Question 21

Define genetic recombination

Answer 21

Physical exchange of various mutations located on different DNA molecules.

Question 22

Describe homologous recombination

Answer 22

• Two homologous DNA molecules align
• A cut is produced in both molecules randomly at matching loci.
• The fragments are joined together to form new combinations.

Question 23

What are the features of homologous recombination

Answer 23

• The enzymes involved can use any pair of homologous sequences as substrates.
• Some types of sequences may be favoured over others.
• The frequency of recombination is not constant throughout the genome but instead it is influenced by local and global effects.

Question 24

Define the terms conjugation, transduction, and transformation

Answer 24

• Conjugation - genetic exchange between phylogenetically related bacteria.
• Transduction - bacterial genes delivered to new hosts by bacteriophages.
• Transformation - DNA is introduced into a bacterial cell.

Question 25

What is the role of recombination

Answer 25

• Produces greater variety in offspring by generating new genetic combinations.
• Due to recombination, selection can remove deleterious mutations from a population.
• Has a role in repairing damaged DNA.
• Role is transposition and horizontal gene transfer -phages, F-plasmids, and mobile elements.

Question 26

Define the terms genome and bacterial genomics

Answer 26

Genome - the whole hereditary composition of an organism that is presented in the DNA (RNA for some viruses). Includes both genes and non-coding sequences.
Bacterial genomics - the study of the organisms entire genome as opposed to the investigation of single genes and their function.

Question 27

Describe the process of next generation genome sequencing

Answer 27

• Started by cutting the DNA into short sections to be sequenced and attaching oligonucleotides called adapters to the ends of the resulting fragments.
• The adapter at one end of each DNA fragment attaches it to a solid substrate, and the adapter at the other end anneals to a primer used to initiate the polymerase chain reaction.
• Due to thousands of DNA fragments being sequenced at the same time, these methods are sometimes called massively parallel sequencing techniques.

Question 28

Describe the process of Sanger DNA sequencing

Answer 28

• Carried out by chain termination by dideoxynucleotide.
• Firstly, a double strand of DNA is denatured into single strands.
• A primer is annealed to one of the template strands.
• The 3’ end of the primer is located next to the DNA sequence of interest.
• Either this primer or one of the nucleotides should be fluorescently labelled.
• This is then mixed with DNA polymerase, the four deoxynucleoside triphosphates, and dideoxynucleoside triphosphates.
• DNA synthesis will continue until a dideoxynucleoside phosphate is added to the growing chain.

Question 29

What are the general features of second generation sequencing

Answer 29

• High throughput number as a large number of DNA molecules are processed in parallel.
• No cloning.
• PCR amplification is required.
• Was-and-scan sequencing process
  Flooding in reagents
  Incorporation of nucleotides
  Stopping; treating of new base to remove label
  Long process

Question 30

What is metagenomics and why do we do it

Answer 30

• Genome level study of the whole bacteria community.

- The diversity of microorganisms is enormous but only 1% of them can be cultured.

Question 31

What does metagenomics involve

Answer 31

• Direct DNA isolation from the environment.

- Environmental DNA analysis allows access to 100% of genetic resources.