Genomics - GRE Subject Test: Biochemistry, Cell, and Molecular Biology

Recombination frequencies are used to map genes on chromosomes by determining their relative distances from other genes. If a distance is large, there is a higher chance that a recombination event can occur between these two genes. Linkage occurs when genes are so close to one another that the genes always segregate together (recombination never occurs between them). The only answer that makes sense is that high recombination frequencies lead to the conclusion that two genes are far apart.

A low recombination frequency would indicate that the gene loci are close together, and a recombination frequency of zero would indicate linked genes.

The larger the recombination frequency, the larger the distance between two genes. By looking at the data, we know that genes W and X are close to one another. Also, genes X and Y are close to one another. Gene Z, however, seems to be far away from both W and Y (but closer to W). We can represent these distances relatively in a picture:

W - - - X (3)

X - - Y (2)

Y - - - - - - - - - - - - - Z (13)

Z - - - - - - - - W (8)

The most likely explanation is that W, X, and Y are close to one another and Z is located slightly farther away on whichever side W is closest. A spatial map would look something like this:

Z - - - - - - - - - - W - - - X - - Y

If the genes were linked, there would be an incredibly small recombination frequency. If the genes were on opposite ends of the chromosome or on separate chromosomes, the recombination frequency would approach the maximum of 50%.

Because the recombination frequency is relatively intermediate, we can conclude that the distance between the genes does not fall at either extreme. The genes are neither very close, nor very far apart.

The correct answer is that rRNA genes have both highly conserved and highly variable regions. Molecular typing is the process of identifying species from a microbiome by analysis of common molecules or genes. All organisms including eukaryotes, prokaryotes, and archaea, (but not viruses) have multiple rRNA genes. Given that rRNA genes have highly conserved regions, it allows researchers to identify transcripts/genes as rRNA genes in unknown species. Comparing the sequences of the variable regions of the rRNA genes allows researchers to identify the species of the organism from which it is derived.

An orthologous gene is one that is descended from a common ancestral sequence. So, when two sequences from different species are compared, they are orthologs if they have the same evolutionary history. A paralogous gene is the case in which a similar gene sequence is derived from a genome duplication event, and do not have a evolutionary relationship. These genes often develop different functions, unlike orthologs.

Tandem arrays are used for extremely important genes, like ribosomal RNA genes that are vital for organism function. The arrays serve to allow massive parallelized encoding of these genes, because many copies are required.

The correct answer is rRNA genes and ITS have highly conserved regions and highly divergent regions. Both prokaryotes and eukaryotes have rRNA genes and ITS, making these ideal targets for molecular typing. In order to amplify, then sequence these regions for evolutionary comparisons, universal primers are designed to anneal within the highly conserved regions and amplify through the highly divergent regions. The divergent regions of rRNA genes and ITS allow for specie to specie comparison and identification.

When two sequences have less than 20% identity, it is almost impossible to align them and identify that they are actually orthologs. This is especially the case in huge genome data sets, in which it is impossible to find matching sequences by hand.

The key factors that distinguish pseudogenes are that they are sequences that result from a duplication event in the genome, but have since mutated without selection pressure and have become nonfunctional.

Organisms with large genomes tend to have very high levels of transposons. For instance, this is the case in our own genomes. It is hypothesized that in some organisms, there is a breakdown of systems that control insertion of transposons into the genome, resulting in large expansions.

Genetic linkages are determined by frequencies of recombination. These are measures of how often chromosomal crossovers will take place between two genes. The closer the loci of the two genes are on a chromosome, the less likely a crossover event will separate the two genes. If the recombination frequencies are sufficiently low, the genes are considered to be linked.

Genetic linkage has nothing to do with genes coding for the same mRNA, sharing a promoter, or overlapping one another. Linked genes still code for distinctly separate traits/proteins and have different loci (don't overlap).

Transposable elements are portions of the DNA that are free to move around the genome and are generally considered non-coding DNA. This can be potentially dangerous, however. Transposable elements can insert themselves in the coding regions of genes, thus making them non-functional. This can lead to disease. Both eukaryotic and prokaryotic genomes contain transposable elements.

Class I transposable elements are RNA-mediated elements of a single evolutionary origin, and are found in yeast, which only have class I elements, and in eukaryotes, which have both class I and class II elements. Bacteria only have class II elements, and hence are not included in the correct answer to this question.

Barbara McClintock named the transposons that are defective, and serve as sites of chromosomal breakage where other transposons insert (the associator, Ac) the dissociators. These were likely transposons that lacked the transposase that catalyzes their movement.

Two transposons flanking an antibiotic resistance gene can easily move between bacteria and confer new resistance. A mix of transposons and new genes such as this is called a composite transposon. Recall that bacteria exchange genetic information via conjugation, transduction, and transformation.

LTR stands for Long Terminal Repeats, which are 250-500 base pair repeats located on the ends of a transposon. These repeats encode a series of proteins, most significantly transposase. These are very likely to be early evolutionarily stages of retroviruses.

Non-LTR retrotransposons use an endonuclease that nicks thymine-rich host DNA, which eventually leads to incorporation of the transposon by host DNA repair functions. These other methods are all associated with different specializations of transposon.

The only difference between most LTR retrotransposons and retroviruses are that retroviruses can encode an envelope protein. Phylogenetic analyses have shown that retrotransposons and retroviruses are extremely closely related, and may be direct ancestors of one another.

Movement of transposons is very commonly controlled by RNA interference. The RNAi system cuts up problematic RNAs, and uses these small pieces to target transposons for destruction.