Lecture 5. GA in yeast Flashcards
Open Reading Frame (ORF)
An ORF contains the genetic instructions (a sequence of DNA) for producing a protein without interruptions from stop codons
Key Features: It starts with a start codon (e.g., AUG) and ends with a stop codon (e.g., UAA, UAG, UGA).
Code for location of a gene on a chromosome
YDR130c:
“Y” refers to yeast (for Saccharomyces cerevisiae).
“D” refers to chromosome IV (the fourth chromosome).
“R” indicates the right arm of the chromosome.
“130” indicates that this ORF is the 130th gene from the centromere on that arm.
“c” says the gene is located on the Crick (or Template) strand of DNA (or the “w” for Watson or (Coding) strand).
Gene Duplication types
Gene duplication is a significant source of genetic diversity in yeast, producing gene families with related functions.
Orthologs are genes in different species that evolved from a common ancestral gene (so have same/similar function), while paralogs are genes within the same genome that arose from a duplication event (same species, same gene duplicated to have different functions). Homologs is the general term for genes related by descent, encompassing both orthologs and paralogs
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Ortholog: Genes in different species that do the same job because they came from a common ancestor.
Example: The FOXP2 gene, involved in speech, is found in both humans and mice. Although they are different species, they both perform a similar function (helping with speech or vocalization). -
Paralog: Genes in the same species that are similar because one gene was copied. They might do different jobs now.
Example: In humans, the globin genes (like alpha-globin and beta-globin) are paralogs. They are similar because they originated from the same gene, but they now have different roles in carrying oxygen in the blood. -
Homolog: Genes that are similar because they come from a common ancestor.
Example: The gene for hemoglobin in humans and the gene for hemoglobin in elephants are homologous because both genes evolved from a common ancestor.
Aneuploidy
a condition where a cell has an abnormal number of chromosomes, either missing chromosomes (hypoploidy) or having extra chromosomes (hyperploidy) than the typical diploid number. It can happen due to errors during cell division, such as meiosis or mitosis, resulting in the gain or loss of whole chromosomes.
In Eukaryotes. Can occur naturally or under stress conditions, and it often leads to altered gene expression, affecting the cell’s physiology positive but can also be negative.
Yeast Deletion Strains
Strains of Saccharomyces cerevisiae where specific genes are deleted to study their function by observing changes in the organism’s phenotype.
Gene Deletion Method: Achieved through homologous recombination, where a disruption cassette (containing a selectable marker) is introduced to replace the target gene in the yeast genome.
Homologous recombination ensures precise gene replacement, making it possible to delete specific genes and analyze their function.
- Homologous recombination is a process by which genetic material is exchanged between two similar or identical DNA molecules. It occurs naturally in cells during DNA repair, genetic variation, and cell division, but it can also be used in the lab for genetic modifications.
- Deletion Strains: Organisms where specific genes are removed to study their function by observing phenotypic changes.
Antisense Transcription
The transcription of the antisense strand blocks sense transcription (protein coding mRNA) by causing chromatin changes, such as histone deacetylation at the promoter of the sense gene. This leads to a condensed chromatin structure that inhibits transcription by blocking access to the transcription machinery and production of sense strand.
So it antisense transcription blocks this not the produces antisense strand itself
Genome-wide RNA-seq Analysis
a high-throughput sequencing method used to study the entire transcriptome of an organism. It provides a detailed snapshot of gene expression under specific conditions.
