Intro to Genes and Genomes Dynamics Flashcards
Why is the structure not sufficient to define function?
99.9% of our ~25000 genes are identical
Why is NGS more common than PCR for the purpose of genome sequencing?
it is much more fast-paced and uses pre-defined adapters
What is coronavirus?
the largest RNA virus that forms enveloped and spherical particles of around 100-160nm in diameter
Describe the coronavirus genome
positive sense, ssRNA genome of ~30kB
What is the distribution of the ORFs in the coronavirus genome?
ORF1a is expressed in much higher levels but both are required to make a replicate
What does polyadenylation do?
stabilise the 5’ end of RNA (capping with poly-A tail)
What does spike protein do?
interact with ACE2 to enter into the host and replicate and propagate the genome
What is an ORF?
a span of DNA or RNA between the start and stop codons
How many frames are used to check if the RNA sequence contains a stop codon?
3
What would happen if there was a stop codon present in RNA?
the polymerase would be terminated
What would mutations in one locus of DNA likely affect?
the reading frames of another gene if both genes were being encoded by the same locus
What do most naturally arising S antibodies and MAbs do?
target the receptor binding domain (RBD)
What are the MAb fab and Fc domains responsible for?
- fab = antigenic recognition
- Fc = immune effector functions
What percentage of the human genome encodes for proteins?
less than 5%
What are possible functions of intergenic regions?
- encoding of regulatory RNA (miRNA)
- long-range elements that control the folding and topology of DNA organisation
- gene regulation
Why are promoters generally more obvious than enhancers?
due to their larger consensus sequences
How can enhancers work to regulate genes from far away?
by chromosomal loops and structures within the DNA
How is the gene regulatory machinery stabilised?
by chromosomal loops
What percentage of genes undergo alternative splicing in the brain?
30%
What are the introns removed during splicing used for?
to make pre-miRNA
What are dicer proteins used for?
recruiting the pre-miRNA; they cleave the pre-miRNA to retain the targeting miRNA
What happens to the targeting miRNA?
it can associate with other proteins to form the activated RISC that grabs the target mRNA and degrades it
What is the RISC?
RNA-induced silencing complex
When are RNA and DNA complimentary?
during transcription (bubble) and reverse transcription (RNA-dependent DNA polymerase e.g. telomerase)
What is RNA interference?
a biological process in which RNA molecules are involved in sequence-specific suppression of gene expression by dsRNA, through translational or transcriptional repression
What are miRNAs?
genome-encoded short RNAs that regulate gene expression by translational repression and/or degradation of cognate mRNAs
How do miRNAs regulate gene expression?
by suppressing the availability of mRNA by degradation or physically stopping the ribosome from proceeding to full translation
Why doesn’t miRNA act at the DNA level?
due to compartmentalisation
What are the key differences between miRNA and siRNA?
- siRNA is derived from the introduction of exogenous dsRNA to the cells while miRNA is generated from the expression of the endogenous non-coding RNA
- siRNA is present in lower animals and plants but not mammals and miRNA is present in all plants and animals
- siRNA is highly specific with only one mRNA target while miRNA can inhibit translation of multiple mRNA targets due to its lower specificity when pairing
- siRNA primarily provides viral defence and genome stability while miRNA functions as an endogenous gene expression regulator
How can special complimentary RNA oligos be re-engineered?
in the form of siRNA or shRNA to introduce them into cells to target and degrade target genes of interests
What are oligos?
short, single- or double-stranded synthetic RNA sequences that can serve as the starting point for many molecular biology and synthetic biology applications
What are RGENs?
programmable genome engineering tools adapted from CRISPR/Cas system
What does Cas9 form?
a sequence-specific endonuclease that targets a sequence that is 23bp in length, ending with two guanines (GG) i.e. can essentially cleave any region of the genome
What can CRISPR do?
effectively knockout/delete the gene of interest and replace it with a specific mutant of interest
What can CRISPR be used for?
narrowing down not just what the gene does, but potentially how the gene and the protein encoded would execute their functions at the biochemical and molecular levels
What is a syntenic group?
a set of loci in two different species which is located on the same chromosome in each (not necessarily in the same order)
Give examples of rearrangements to the genome during evolution
- chromosome translocations
- meiosis
What can meiosis do?
separate 2 loci resulting in the loss of synteny between them
What may conserved chromosomal domains be important for?
chromosomal function
What predicts evolutionary relationships?
similarities in genetic loci and their order
What do speculative positive selection pressures do?
- minimise random mutations of genes
- increase gene duplications
- increase chromosomal rearrangement
What are selection pressures?
external agents which affect an organism’s ability to survive in a given environment
What do negative and positive selective pressures do respectively?
- negative = decrease the occurrence of a trait
- positive = increase the proportion of a trait
What is the centromere?
part of the chromosome important for mitosis and meiosis; the region where the cell’s spindle fibres attach
What is heterochromatin and what does it consist of?
a highly condensed form of DNA and mostly consists of repetitive DNA sequences and non-coding RNA transcripts
What is euchromatin and what does it consist of?
the opposite of heterochromatin and is made up of repeating units called nucleosomes which each contain a segment of DNA wound around eight histone proteins
What are very active in the pufferfish (Fugu) genome?
transposable elements
What are SINEs and LINEs?
short (SINE) and long (LINE) interspersed retro-transposable elements that invade new genomic sites using RNA intermediates
Where are SINEs and LINEs found?
almost all eukaryotes (although not in S. cerevisiae)
When does equal crossover between homologous chromosomes occur?
when sister chromatids crossover during meiosis
What is unequal crossover?
a type of gene duplication or deletion event that deletes a sequence in one strand and replaces it with a duplication from its sister chromatid in mitosis or from its homologous chromosome during meiosis
What is slipped strand mispairing/replication slippage and what does it involve?
a mutation process which occurs during DNA replication that involves denaturation and displacement of the DNA strands resulting in mispairing of the complimentary bases
What is GC content?
the percentage of nitrogenous bases in a DNA or RNA molecule that are either guanine (G) or cytosine (C)
What are CpG islands?
short interspersed non-methylated DNA regions with a high concentration of phosphate-linked CG pairs
