Genes and Genomes Flashcards
(24 cards)
What are the basic steps in mRNA processing?
Chromosomal DNA has exons (protein coding sequences) interrupted by introns (non-coding sequences). During transcription the primary RNA transcript has the introns removed by splicing to form the mature mRNA. Exons can be located in the 3’ and 5’ ends of the mRNA transcript and can contain untranslated regions (UTRs).
What are the main differences in gene structure between prokaryotes and eukaryotes?
Eukaryotes typically have a complicated intron exon structure - often intron sequences are bigger than exons. In prokaryotes, introns are only found in rare genes, and exons are operons (where proteins are)
What is the functional/regulatory role of introns?
Introns encode proteins, non-coding RNAs, or nested genes, and they also contain regulatory sequences that control gene expression and transcription, crucial to cell behavior.
What are nested genes?
Genes contained within an intron of a larger host gene, which encode functional products (proteins or non-coding RNA)
What are transcriptional regulatory elements?
They control transcription, and can be located hundreds of kilobases away from the gene, upstream of the gene, or within non-coding exons or within introns of the gene.
What is the role of alternative splicing in extending the functional repertoire of the human genome?
Allows multiple proteins to be encoded by a single gene (20,000 human protein coding genes to specify 80,000 different proteins).
What is the point of non-coding sequences?
Although they don’t make proteins, they play important roles in gene regulation; some non-coding RNAs (tRNA and rRNA) have key roles in protein synthesis, and pre-mRNA splicing is a key role too.
What are the steps involved in repression of translation of mRNA by miRNA, and specific roles of Drosha, Dicer, and RISC.
The pri-miRNA gene is transcribed by RNA polymerase. The pri-miRNA is then processed and cleaved in the nucleus by Drosha, and it is released as pre-miRNA, which is a hairpin-like structure. It’s exported from the nucleus to the cytoplasm, where it’s further processed by Dicer, which cleaves it to make mature double-stranded miRNA. The RNA-induced silencing complex (RISC) is a protein complex that guides the miRNA to the 3’ end of its target mRNA, which leads to mRNA degradation or repression of translation.
How do miRNA and lncRNA differ in the way they regulate transcription?
Long non-coding RNAs (lncRNAs) are non-coding RNAs greater than 200 nucleotides that are major regulators of gene expression. miRNA binds to mRNA directly (either degrading it in response to a perfect match or blocking translation with an imperfect match) and lncRNA methylates the histones in a nucleosome complex, which blocks transcription.
What are the overall findings of the ENCODE project?
It advanced our understanding of defining the functional elements of the human genome by transcribing 75% of the human genome, and found that non-coding RNAs make up a lot of the genome. It found 20,000 protein-coding genes, 18,000 non-coding RNA, 75% of genome transcribed into RNA, and 8% of genome-binding transcription factors.
What role does lncRNA have in x chromosome inactivation.
The key element in x chromosome inactivation is a lncRNA specifically called Xist, which binds to the inactive X, blocking its transcription
What is the significance of the large number of lncRNA transcripts in humans compared to other organisms?
With the human genome encoding ~50,000 lncRNAs, and the fact that the number of lncRNAs is larger than the amount of protein-coding genes, it suggests that lncRNAs make a substantial contribution to the biological complexity of higher eukaryotes.
What are the roles of transposable elements in disease?
Transposable elements like SINEs (Short Interspersed Nuclear Elements) and LINEs (Long Interspersed Nuclear Elements) can move within a genome and can introduce mutations and affect expression (stimulation or inhibition) of genes at their integration sites. Most mutations are expected to be harmful in the cell, and have been associated with several inherited human diseases and hereditary cancers. Movement of transposable elements has played a major role in genome evolution.
What is the mechanism of retrotransposition in the formation of psuedogenes?
Retrotransposition is a process where retrotransposons, a type of transposable element, move within a genome by copying themselves into an RNA intermediate and then using reverse transcription by reverse transcriptase to create a new DNA copy at a new location. Pseudogenes are inactive gene copies when mRNAs are copied by reverse transcription, yielding a cDNA (complementary DNA) copy lacking introns. Retrotransposition of the cDNA into chromosomal DNA results in formation of a processed pseudogene.
What are histones?
small proteins containing a high proportion of basic amino acids that facilitate binding to negatively charged DNA molecules (form chromatin)
What are nucleosomes?
The basic unit of chromatin, consisting of DNA wrapped around histones octamers
Why do eukaryotes require complex packaging and prokaryotes do not?
Eukaryotes have condensed histones, which package long DNA into a tiny nucleus. Prokaryotes have much smaller and less DNA
What is the overall genomic organization of prokaryotes?
circular singular DNA
What is the organization of chromatin in nucleosomes?
A nucleosome core particle consists of base pairs of DNA wrapped around a histone core of 2H2A, H2B, H3, and H4 all sealed by 1 H1
What is the importance of chromatin condensation?
The extent of chromatin condensation varies during the cell cycle and controls gene expression
What are centromeres?
The middle of the chromosome - where sister chromatids remain attached during metaphase. The kinetochore is formed, which is the site where microtubules (spindle fibers) attach to chromosomes during mitosis.
What is the significance of sequence repeats in human kinetochores?
Kinetochores are characterized by heterochromatin containing highly repetitive A/T sequences called satellite DNA, which are required for chromosomal stability.
What are the roles of telomeres in eukaryotes and prokaryotes?
In eukaryotes only, they do chromosome maintenance (buffer for degradation) and replication with repetitive DNA and simple sequence repeats of TTAAGGG at the ends of chromosomes. Telomere DNA loops back on itself to form a circular structure and associate with a protein complex called shelterin to protect the ends of chromosomes. Prokaryotes don’t have telomeres because they have circular DNA.
What is epigenetic inheritance?
The transfer of information from parent to progeny that is not based on DNA sequences (like centromeres being defined by chromatin structure rather than DNA sequence). These changes are usually related to how genes are expressed and can be influenced by environmental factors.
