Transposable Elements

• Genetics studies heredity and variation in organisms
• Molecular genetics studies the structure and function of genes at a molecular level

Transposable Elements Overview

• Transposons are DNA segments
• Transposons move within a cell's genome
• The genome is a collection of DNA in a cell
• Exists in all organisms
• Transposons replicate themselves
• They are selected based on how well they are at replicating themselves within other cell genomes.
• A major force for genetic evolution
• In eukaryotes, transposons split into two types based on propagation methods
  • DNA transposons
  • Retrotransposons
• In prokaryotes, there are simpler DNA transposons known as insertion sequences
• All transposons have repeat sequences at their borders
• Everything within the repeats is the transposable element

DNA Transposons

• Found in eukaryotes and prokaryotes
• Class II transposons
• Use a 'cut and paste' or 'copy and paste' mechanism
• Mediated by transposase enzyme
  • Transposase cuts out transposable elements and inserts them elsewhere.
  • This process also breaks and reforms phosphodiester bonds
• Yellow highlights the repeat-sequence boarder.
• Genetic recombination moves DNA transposons around the genome
  • Genetic recombination is the process of breaking DNA and putting it back together
• They are "Jumping genes”
• In replication, there will be 2 copies and one moves to the new site.

Retrotransposons

• Only found in eukaryotes
• Class I transposons
• Uses "copy and paste" via RNA intermediate
• Codes for reverse transcriptase enzyme
  • Reverse transcriptase uses RNA to make DNA
• The original retrotransposon stays put when it makes an RNA copy, it then makes a DNA copy from that

Transposons and Humans

• ~2% of the human genome codes for proteins (3.2 x 109 base pairs)
• ~44% of the human genome is transposable elements
  • Most of the transposable elements are not active
• 0.2% of the human genome consists of active transposons
• Transposable elements are larger by portion of the genome than protein coding genes
• The fact that transposable elements are active allows natural selection to take place

Viruses Overview

• Viruses are biological particles that can infect cells
• They do not follow the definition of life because they can't replicate or generate metabolic energy independently
• Viruses use the host's machinery for replication and energy
• They have very simple genetic systems
• Most viruses have genes that encode proteins that help them manipulate the host
• Viruses are categorized by genome and structure type

Virus Basic Structure

• All viruses have:
  • Nucleic acid core : hereditary material
  • Proteins outside

Bacteriophages

• Viruses that infect bacteria
• The head is similar in structure to viruses
• The phage infects the bacteria
• All proteins are encoded by the genome
• The two types of bacteriophages are virulent and temperate
• Of interest because they are simple and can teach us about bacterial genetics
• T even bacteriophages
  • Are virulent
  • Do not incorporate into the host genome
  • Cuts up the host genome during lifecycle
  • Always lyses bacteria during its normal cycle
    • Releases more viruses

Transduction

• Sometimes results in generalized transduction
  • Transduction: a change in bacterial genetics from a virus
  • Generalized transduction: pieces of the cut-up host genome integrate into virions (viral particles) and carry to a new bacterial cell
    • This process is random and can be any piece of host DNA

Lambda Phage

• Temperate bacteriophage
• Incorporates into host genome as part of the lysogenic cycle
• Imperfectly excises genome at low rate
• Can perform both lysogenic or lytic cycles based on environmental conditions
  • Specialized transduction: viral genome incorporates at specific locations, so a fragmented host genome will be specific (not random)
• Lysogenic cycle: each new bacteria has the virulent genome inside
  • slow process and does not cost the virus anything
• Lytic cycle: very similiar to virulent bacteriaophage process
  • can cause generalized transduction
• The switch from Lysogenic to Lytic is not random
  • Environmental factors like nutrient depletions often determine the viral cycle

Viruses Infecting Animals

• Diverse group categorized by:
  • Nucleotide use in the genome
  • Viral structure
  • Species/Tissue tropism
• Animal viruses likely evolved from cellular DNA

HIV

• Human Immunodeficiency Virus
• A retrovirus that Infects T-Cells
  • It has Tissue Tropism
• Double stranded RNA genome
• Causes AIDS
• Structure
  • Protein coded particle containing the genome
  • Enveloped virus
  • Has a membrane for interacting with the outside of new host cells

HIV Genome

• Highly Organized
• Forming Secondary Structures to create 3D RNA which is important for handling machinary

HIV Lifecycle

• Reverse transcriptase happens like in retrotransposons
• Integrase mediates step 3 (integrated into host genome)
• new viruses will be made at some point
• Retroviruses make up 8% of our gnome
• The Reverse transcriptase enzyme: -Is responsible for reverse transcription -Can catalyse a number of steps in the life cycle -Has 3 domains: - Uses RNA as template to make DNA - Degrades orginal RNA template leaving single stranded DNA - DNA-dependant DNA polymerase
• In order to turn RNA to DNA, this enzyme does all of it!
• Good drug target because it doesn’t exist in human cells.
• AIDS -Harmfull to TCells - harming patients immune system.

SARS-CoV2 (COVID-19)

• Very different than HIV
• The COVID-19 Viruses are:
  • Corona viruses
  • Sense strand Viruses COVID-19 lifecycle is similar to the HIV virus
• Structure
  • Similar to HIV with a membrane bound envelope.

SARS-CoV2 (COVID-19) Lifecycle

• Targets then fuses with a target cell.
• Because this is a positive-sense strand RNA it is translated right away
• Turns from + strand to - strand RNA to make more + strand RNA for template for translation.
• Different Genomes Handled the same way:
  • Compare and contact the cycle compared to the HIV cycle where there is no latent phase built in
  • tries to make new visions immediately
• Results in Spike in number of viral genomes.
• Has initial infection thats always 14 days instead of years like HIV so there is a longer/shorter form.

Bacterial Genetics

• A subfield of genetics that studies bacteria which are a huge amount of biomass and has great value for showing model of Eukaryotic genetics works.
• Has DNA organization and mechanisms for gene transfer
• Was found to causes dysentery in infants:
  • Was found by Thomas Escherich in 1885 It is normally found in our gut: -Involved in making vitamin K. E. Coli cells:
  • Can be infected.
  • Grow well.
  • Can be cloned.
  • Perform Conigation

E. Coli Characteristics

• Gram Negative
• Some have Plasmid, some have a single circular chromosome
• The E Coli stats are as follows:
  • 4.6 million base pairs, 4288 coding protein genes, 7 ribosome rRNA genes and 66 tRNA genes.

Gene Transfer & Genetic Recombination

• In Bacteria, DNA isnt transferred like it Eukaryotes,
• Bacteria are a to increase genetic diversity by natural selection and differs depending on setting. Genetic recombinational allows more gene variations
• A Wild type can grow on a defined media unlike mutants or auxotrophs
• Antibiotic are commonly used in media and used as gene transfer
• 3 ways genes transfer in bacteria, all can’t perform the all: -Transformation can be performed in laboratories. -Transduction -Conjugation

Transformation

• Involves uptake of an environmental DNA strand.
• Transforming principle came up in griffith principle and transformation is not very natural in the wild only 1 percents.
• Plasmids
  • E. coli must chemically modified to used plsmids to make cells competent
  • R plasmids that make Antibiotic resistance.

Transduction

• Gene transfer from sources, specifically bacteriaphages
• Brings in DNA , then chops up the whole genetic code of the either the virulent phage of lytic cycle. When the virus infects a new cell, it transfers the new gene that turns non-functional ones now functional.
  • This Process is accidental.
  • Phage likely does not function in it does take up material from the host
• Transfer may involve:
  • Generalised transduction
  • Specialised transduction

Conjugation

• Involves a transfer of DNA between Bacterial cells
• Mutants such I strains 1 and 2, When combined create every gene due to the way transfers happen.

Plasmids

• F plasmid, coding transfer and pilus where pili is an external structures, these transfer by being F pillus which moves DNA by brings the genes along into the help to complete life cycle.