L12/13: Nucleic acids - Genomes, CRISPR Flashcards
What is a gene?
- A gene is a sequence of bases in a region of the DNA that can code for a protein or RNA
- Unit of hereditary information consisting of a DNA sequence.
Describe the bacterial genome.
- Circular, double-stranded
- Haploid
- all DNA in the cell is tightly wound (supercoiled)
- Genome size (# of base pairs) is small - cells are small
Describe the genome in eukaryotes.
- DNA is wound around proteins called histones and wound into chromatin
- Linear, double-stranded
- Diploid
What is a genome?
- All the genetic material of a cell/organism
What is a genotype?
- The genetic make-up of a cell/organism
- All the genes in the cell
What is a phenotype?
- Observable characteristics/traits.
- All the genes that are expressed in the cell due to conditions.
Describe the sequence of the composition of the human genome.
- Genomes are complex; contain both coding and non-coding regions of DNA
- only a portion of the human genome codes for proteins (exons, 2.5%)
Genome vs. Transcriptome
GENOME:
- all the genetic material in an organism passed from parent to offspring
TRANSCRIPTOME:
- the genes actively being transcribed into mRNA in a given cell, developmental state, etc.
- the entire RNA sequence in a cell.
- the subset of all the genes present in the genome.
What does CRISPR stand for?
- Clustered Regularly Interspaced Short Palindromic Repeats
What is bacterial immunity?
- Scientists observed that some bacteria could resist and survive a virus attack
How was bacterial immunity possible?
- CRISPR DNA
- Some bacteria are able to sample and see DNA from viral genes in special CRISPR arrays.
How did CRISPR get discovered?
- Bacteria can get infected by viruses called bacteriophage
- When the cell survives, part of the viral genome is copied in the bacterial genome (i.e short interspaced repeats of sequences of 20-50 bases each)
- Bacterial cell gets infected again, the cell they use RNA (copied from repeats) and a protein Cas9 to edit out the viral DNA
What is the difference between spacers and repeats?
- the SPACER is the small section of viral DNA that is captured and inserted into the CRISPR array
- the spacer is always paired up w/ a repeat DNA sequence that is made from the bacterial genome
- the CRISPR array itself is a permanent part of the bacterial genome and can therefore be passed to offspring cells.
What are CRISPR arrays?
- Contain all of the viral DNA samples together in a single repeated array
- each spacer sequence is taken from a different virus
- the CRISPR array is a storage bank that records previous encounters with viruses that infect the bacterial cell
What is Cas9?
- A protein whose gene is found on another part of the bacterial genome.
- An enzyme that cuts foreign DNA
What are the steps in CRISPR?
STEP 1:
- The Cas9 enzymes start scanning all DNA they encounter (including their own) looking for a specific PAM sequence that is unique to viral DNA
- if it finds a PAM sequence, it starts the process of checking the DNA with the crRNA it is carrying.
STEP 2:
- the Cas9 opens the viral DNA and checks it against the crRNA samples it is carrying.
- if it matches, it forms complementary base pairing
STEP 3:
- Once the crRNA and viral DNA are “locked-in”, the Cas9 cuts up the viral DNA (i.e. the Cas9 enzyme is a type of enzyme called a nuclease - cuts nucleic acids)
Describe CRISPR and gene editing.
- the crRNA is custom made to match whatever we want to target in the host DNA.
- this type of CRISPR system is also modified in other ways to ensure that the Cas9 recognizes only the target DNA sequence.
- But, there is no guarantee that this won’t happen, which is why most scientists are still wary of testing this out on humans.
