Introduction to genomes, transposable elements Flashcards
What’s a genome?
The entirety of an organism’s hereditary information. Usually DNA (but some viruses have RNA genomes).
What is the DNA content of the genome measured in?
measured in base pairs (bp)
Is there a correlation between DNA content and organism complexity?
No
What is a gene?
the entire nucleic acid sequence that is necessary for the synthesis of a functional product (polypeptide or RNA)
What is the difference between exons and introns?
Exons contain the coding region or Open Reading Frame (ORF), while introns separate the exons and are spliced out during mRNA processing.
What is the function of control regions in a gene?
Control regions include the promoter and cis-regulatory factors and regulate gene expression.
What is BLAST?
A tool used to find nucleic acid and protein sequence similarities
Proteins with ________ functions often contain similar
____________ sequences that encode functional domains
similar
amino acid
What is the main reason for differences in genome
size among species?
Differences in genome size among species are mostly due to different amounts of non-coding DNA and transposable elements.
What is the difference in gene density between lower and more complex eukaryotes?
Gene density is much greater in lower eukaryotes than in more complex eukaryotes.
What is a pseudogene?
A pseudogene is a non-functional DNA sequence that resembles a functional gene but cannot produce a functional protein or RNA product.
What is an Alu site?
Alu sites are just repetitive elements of DNA and they’re called Alu sites because they include a recognition site for a restriction enzyme called Alu 1.
What is the difference between orthologs and paralogs?
Orthologs are the same protein in different species, while paralogs are closely related proteins in the same species.
What are called genes that are represented once in the genome?
solitary or single-copy genes
What is the difference between solitary genes and duplicate genes?
Solitary genes are represented once in the genome, while duplicate genes occur in multiple copies.
A set of related genes formed by duplication of an original single-copy gene make up a:
gene family
What is DNA fingerprinting?
DNA fingerprinting compares individual differences in simple-sequence tandem arrays.
What is the difference between microsatellite DNA
and minisatellite DNA?
Microsatellite DNA repeat units are typically 1 to 4 bp (shorter and more abundant) in length and found in arrays of up to ≈600 bp in length, while minisatellite DNA repeat units are ≈14 to 100 bp in length (longer and less abundant) and found in arrays of 1 to 5 kbp in length.
What are transposable DNA elements?
DNA elements that move within genomes by different mechanisms.
What is the percentage of the human genome that consists of DNA transposons?
3%.
What is the percentage of the human genome that consists of retro-transposons?
40%.
How does a transposon increase its copy number?
If it moves from a replicated region to a non-replicated region, copy number will increase by one in one of the daughter chromosomes.
What are the two major classes of transposons?
DNA transposons
Retrotransposons
What is the meaning of LTR in eukaryotic LTR retrotransposons?
Long terminal repeats.
What does the protein coding region of eukaryotic LTR retrotransposons encode?
Reverse transcriptase, integrase, and other proteins.
What is the mechanism for generating retroviral genomic RNA from integrated retroviral DNA?
RNA polymerase II transcribes the integrated retroviral DNA into a full-length RNA molecule.
This primary transcript is then processed by enzymes, including polyadenylation (addition of a poly-A tail) by poly(A) polymerase, to create mature retroviral genomic RNA for packaging and translation.
What are LINEs?
nonviral DNA retrotransposons (Long interspersed nuclear element)
What does LINEs code for ?
2 proteins:
ORF1: encodes an RNA binding protein involved in nuclear transport of LINE RNA.
ORF2: encodes a reverse transcriptase and a nuclease.
How can recombination between repeated elements impact genes?
Recombination between repeated elements can shuffle exons and produce new genes with new combinations of existing exons.
What is a notable characteristic of the sequences carried by DNA transposons and LINEs during their movement?
DNA transposons and LINEs can carry unrelated flanking sequences with them when they move.
