Lectures 1-3 (Leonid Kulakov) - Bacterial Genetics Flashcards
What are the main properties of hereditary material
- Hereditary stability - ensures continuation through generations.
- Hereditary variability - ensures natural diversity.
Give two examples of a bacteriophage
- Bacteriophage lambda
- Bacteriophage-transposon Mu-1
What is the wild-type (WT) and give an example
An arbitrarily chosen strain and other strains of the species are compared with it e.g. E.coli K12
Define the term mutation
Any change in a DNA sequence compared with the WT.
Define the term genotype
Refers to genetic composition of an organism.
Define the term phenotype
The observable property of an organism.
What do bacterial genes encode
- Proteins/enzymes
- tRNA and rRNA
- Regulatory elements
What does it mean that bacterial genes and proteins are colinear
- 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.
What are bacterial genes encoding proteins with related functions often organised into
Oberon
What is the advantage of bacterial genes being organised into operons
Allows for coordinate expression/regulation of metabolic pathways.
Define the term genome
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.
Describe the bacterial genome
- 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).
Describe the bacterial chromosome
- 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.
Define the term plasmid
An extra-chromosomal and non-essential DNA molecule.
What is the major difference between a plasmid and the chromosome
The chromosome is essential for the survival of the bacterial cell whereas a plasmid is not.
What is the importance of plasmids
- 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.
What is an episome
A plasmid that is able to integrate into the chromosome.
What is the importance of mobile genetic elements
- 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.
What are the three different types of mutants
- 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.
Why are mutations important
- 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.
Define genetic recombination
Physical exchange of various mutations located on different DNA molecules.
Describe homologous recombination
- 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.
What are the features of homologous recombination
- 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.
Define the terms conjugation, transduction, and transformation
- Conjugation - genetic exchange between phylogenetically related bacteria.
- Transduction - bacterial genes delivered to new hosts by bacteriophages.
- Transformation - DNA is introduced into a bacterial cell.
What is the role of recombination
- 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.
Define the terms genome and bacterial genomics
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.
Describe the process of next generation genome sequencing
- 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.
Describe the process of Sanger DNA sequencing
- 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.
What are the general features of second generation sequencing
- 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
What is metagenomics and why do we do it
- Genome level study of the whole bacteria community.
- The diversity of microorganisms is enormous but only 1% of them can be cultured.
What does metagenomics involve
- Direct DNA isolation from the environment.
- Environmental DNA analysis allows access to 100% of genetic resources.
