genomic 2nd exam Flashcards
- Which of the following in not a good reason to consider the yeast, Saccharomyces cerevisiae, as a general model for biological study?
a. It is haploid.
b. It reproduces by budding.
c. It can grow and reproduce very quickly.
d. It shares complex internal cell structure of plants and animals without the high percentage of non-coding DNA.
e. It is easily cultured.
b. It reproduces by budding.
additional:
the properties that make yeast particularly suitable for biological studies include rapid growth, dispersed cells, the ease of replica
plating and mutant isolation, a well-defined genetic system, and most important, a highly versatile DNA
transformation system.1 Being nonpathogenic, yeast can be handled with little precautions. Large
quantities of normal bakers’ yeast are commercially available and can provide a cheap source for
biochemical studies.
- Contrast the coding capacity (gene density) of the yeast, Saccharomyces cerevisiae, to that of a typical prokaryote and to a human genome. How does the yeast genome differ from an E. coli genome?
-S. cerevisiae 38.3% GC with 70.3% coding capacity
GC content for euk’s tends to higher than for non-coding regions
High GC correlate with region of increased recombination (similar to tRNA and rRNA bacterial genes)
Yeast telomers: higher AT and less recomb
-S. cerevisiae 70.3% coding capacity lower than bacteria (>85-90%)
One gene per 2 kb DNA
C. elegans: one gene per 6 kb DNA
Humans: one gene per 30 kb DNA
- What are yeast artificial chromosomes (YACs), and what have experiments with YACs suggested to explain that the four smallest yeast chromosomes (I, III, VI, IX) have highest recombination frequencies and unusual architecture?
yeast artificial chromosomes (YACs) are genetically engineered chromosomes derived from the DNA of the yeast, Saccharomyces cerevisiae, which is then ligated into a bacterial plasmid. By inserting large fragments of DNA, the inserted sequences can be cloned and physically mapped using a process called chromosome walking.
The four smallest chromosomes (I, III, VI, and IX) exhibit average recombination frequencies some 1.3 to to 1.8 times greater than the average for the genome as a whole. it was suggested that high levels of recombination have been selected for on these very small chromosomes to ensure at least one crossover per meiosis, and so permit them to
segregate correctly.
Extra: It is known that artificial chromosomes (or chromosome fragments) of approximately 150 kb in size are mitotically unstable), which raises the related questions of whether there is a minimal size for yeast
chromosomes and how the smallest chromosomes have achieved their current size. The organization of chromosome I is very unusual: The 31 kb at each of its ends are very gene-poor, and Bussey et al. have suggested that
these terminal domains may act as “fillers” to increase the size, and hence the stability, of this smallest yeast chromosome
- What is the evidence to suggest that the yeast, Saccharomyces cerevisiae, evolved through a massive genome duplication event?
* Lecture note: Easiest to see near centromeres Many syntenic regions within genome Indicate large segment duplications e.g., paralogous regions of V and X, IV and II, and II and XIV Synteny in Yeast Genome Whole genome duplication Return to normal state via mutations, rearrangements, gene loss 8 to 16 chromosomes with loss of 90% of duplicated genes
- online source:
(syntenic paralogs)
1. Number of chromosomes was doubled.
2, Despite Whole Gene Duplicate, current S. cerevisiae genome:
13% larger than K. waltii genome.
10% more genes.
Gene loss:
large segmental deletions individual gene deletions.
Balanced between two paralogs act primarily on one of them.
Analysis of DCS blocks show:
average size of lost segment: 2 genes.
average balance: 43%-57%.
- Intergenic DNA in Eukarya was originally considered “junk DNA,” but that view has drastically changed. So, why is it no longer considered “junk?” If not useless, what are some of the functions?
intergenic DNA have sometimes been called junk DNA suggesting that they have no function. However, it has been known for a long time that these regions do contain functionally important elements such as promoters and enhancers. Also intergenic regions may contain as yet unidentified genes such as noncoding RNAs. Though little is known about them, they are thought to have regulatory functions.
lecture:
There’s an expression about having junk in your trunk, but the real junk — that is, junk DNA — is actually in each of our faces. According to findings of Axel Visel and his fellow researchers at California’s Lawrence Berkeley National Laboratory, even the faces which most of us consider to be the most attractive or handsome are created with junk DNA.
Short sequences of DNA, called distant-acting enhancers, account for much of the variation in the faces of humans, according to Vixel and his colleagues. These DNA sequences are located in non-coding genome regions, but are important in influencing the activity of genes associated with our faces.
Visel states that these distant-acting enhancers (also known as “transcriptional enhancers”)”are part of the 98 percent of the human genome” that has been considered for a long time to be “junk” DNA, though it’s becoming more and more apparent that this junk DNA really contains many important functions in determining things such as variations in the faces of humans.
- Telomeres are turning out to be very important. Give two “functions” of telomeres considered important. Considering their importance, one might think that their sequence and associated proteins might be highly conserved. Is that the case? Explain.
A telomere is a repeating at the end of the body’s chromosomes. The telomere can reach a length of 15,000 base pairs. Telomeres function by preventing chromosomes from losing base pair sequences at their ends. They also stop chromosomes from fusing to each other. However, each time a cell divides, some of the telomere is lost (usually 25-200 base pairs per division). When the telomere becomes too short, the chromosome reaches a “critical length” and can no longer replicate. This means that a cell becomes “old” and dies by a process called apoptosis. Telomere activity is controlled by two mechanisms: erosion and addition. Erosion, as mentioned, occurs each time a cell divides. Addition is determined by the activity of telomerase.
- Comparative genomics and molecular barcode comparison should provide clear insight into the origins of human pathogens and their evolutionary history along with their non-human cousins. Why hasn’t this worked well so far in understanding the history of tuberculosis in humans?
Still do not know how oldthe TB complex is
Molecular clock estimatesvary greatly – confusing
Open to more research andinterpretation
- The discovery of the mimivirus was a big surprise. What characteristics of the mimivirus are unique to viruses? Make arguments for and against the statement that it is “alive.”
Mimivirus has large size and large genome
Mimivirus the genome contains 911 potential protein-coding genes, or open reading frames
Mimivirus appears to contain many ORFs previously identified in members of the nucleocytoplasmic large DNA virus (NCLDV) group.
I believe Mimivirus is not alive Mimivirus even it contains a much more complete repertoire of translation-associated genes than does any other known virus. but Mimivirus may have evolved from a more independent ancestor. or Over time Mimivirus lost some genes associated with translation as it became more dependent on its host. The translation-like genes that we see in its genome today are relics of a previously intact translation machinery. Mimivirus, in other words, may represent evidence in support of the regressive model of virus origins
- When comparing many genomes at once, it becomes apparent that there is a trend for certain amino acids to decrease (pro, ala, glu, gly) and other amino acids to increase (cys, met, his, ser, and phe) with evolutionary time. What is the only discernable difference between these two groups of amino acids?
Decreasing group proposed to be 1st a.a. to be incorporated into genetic code
Accumulating group probably entered code later
- Describe “segmented genomes” in the viral world.
RNA viruses have smaller genome sizes than DNA viruses because of a higher error-rate when replicating, and have a maximum upper size limit. Beyond this limit, errors in the genome when replicating render the virus useless or uncompetitive. To compensate for this,
(* segment genomes:)
RNA viruses often have segmented genomes – the genome is split into smaller molecules – thus reducing the chance that an error in a single-component genome will incapacitate the entire genome. In contrast, DNA viruses generally have larger genomes because of the high fidelity of their replication enzymes.[81] Single-strand DNA viruses are an exception to this rule, however, as mutation rates for these genomes can approach the extreme of the ssRNA virus case
- You compare the genomes of humans and mice and find large segments in many of their chromosomes showed synteny. What can you conclude about the relationship of the two species?
Both species came from the same origin that diverged approximately thousands of years ago. one might evolved from another through chromosome fusion.
- One of the first comparative genomics analyses was to compare Escherichia coli stains K12 and O157:H7. How does the genome of a single species of a bacterium like E. coli vary?
- One of the findings from the comparison in #13 was the concept of “genomic islands.” What are they? What functions do they encode in their DNA?
Compare genomesDNA Sequencing: overall differenceFred Blattner, Univ Wisconsin
Goal of research: better diagnosis and treatment
O157:H7 is 5.5 Mbp circular chromosome
K12 is 4.6 Mbp circular chromosome
Difference is ~0.9 Mbp (~20% of K12 size)
Comparison shows they share a conserved 4.1 Mbp “backbone” (~89% of K12; 75% of O157:H7)
O157:H7 has 1.34 Mbp “O-islands” not in K12
1,387 genes not found in K12
Many predicted “virulence” genes (toxins, etc)
K12 has 0.53 “K-islands” not found in O157:H7
528 genes not found in O157:H7
Only ½ of O- and K-island genes with known function
The 2 sets of islands DO NOT have same base compositions (i.e., %G+C)
Many island genes have orthologs in other species and in viruses
Only 25% (911/3,574) produce identical proteins
75% vary by at least 1 amino acid
Is this difference trivial?
Difference between wild type (wt) hemoglobin and cystic fibrosis protein (CFTR) differ from disease-causing versions by ONE amino acid
Could pathogenicity between K12 and O157:H7 be due to such small changes too?
- Comparative genomic analysis of Mycobacterium leprae with Mycobacterium tuberculosis reveals much about the evolution of M. leprae in becoming an obligate intracellular parasite of humans. What are the major changes since the two species diverged? Which one has the smaller genome? What hypothesis might best explain why it is smaller?
Contrast with M. tuberculosis striking
Only 50% protein coding
Over 1,000 pseudogenes
Since divergence: leprae has lost 2000 genes and 1Mb DNA
M. leprae has smaller genome.
it might be because there are much more pseudogenes.
- What specific mechanisms can lead to changes in the size of an organism’s genome? (How exactly do genomes gain or lose DNA?)
*Genomes get larger – more genes advantageous Chromosome duplication,
Fuse with another genome
Accumulate viral DNA
Horizontal gene transfer, HGT
*Genomes can get smaller
Massive gene loss
- In conducting metagenomic studies, we use the concept “phylotype” rather than “species” when determining the diversity of prokaryotes in a given sample or environment. Compare and contrast the concept of phylotype and species.
*species (plural: species): the basic unit of biological classification
often defined as a group of organisms capable of interbreeding and producing fertile offspring
Bacteria and Archaea has a species problem. Differing measures are often used, such as similarity of DNA, morphology, or ecological niche.
*phylotype: a biological with evolutionary relationship to other organisms
taxon-neutral, thus one can choose the phylogenetic level at which the phylotype is described, e.g. species, genus, class, 97% genetic identity of 16S rRNA (or operational taxonomic unit, OTU)
