Gene Regulation and 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 to promote formation of euchromatin and increase gene expression. Acetylation of histones "relaxes" DNA coiling around histones by reducing the affinity between histones and DNA. This allows transcription factors to bind promoter regions and promote increased gene expression via transcription.

The correct answer is that mediator is a coactivator of transcription and serves to recruit transcription factors and RNA polymerase II. Mediator does not directly initiate transcription; however, by protein-protein interactions, it recruits the necessary proteins to sites of transcription.

Upstream signaling, such as from a toll-like receptor, causes IKK to phosphorylate IkB, signaling for its ubiquitin-mediated degradation. Since NFkB is no longer bound by its inhibitor, IkB, it translocates to the nucleus where it binds specific motifs in the genome to recruit other transcriptional machinery and initiate transcription.

The correct answer is recruiting DNA polymerase. DNA polymerase is involved in DNA replication, not transcription. Pioneer transcription factors can bind specific DNA motifs and promote euchromatin formation, allowing other transcription factors to bind the less organized DNA. Transcription factors can recruit other transcription factors and the RNA polymerase holoenzyme to promoters to promote gene-specific transcription.

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).

Activation of the lac operon is necessary for the transport and metabolism of lactose sugars by E. coli. Lactose sugars actively work to remove a repressor that statically inhibits transcription; however, high concentrations of glucose (and, thus, low concentrations of cAMP) will prevent these genes from being transcribed rigorously. In order for the lac operon to be active at high levels, lactose must be present and glucose must be absent.

The lac operon is a system designed to only express particular proteins when the concentration of glucose is low and the concentration of lactose is high. The common cellular response to a low concentration of glucose is to increase the concentration of cAMP in order to activate various alternative metabolic pathways. Both a high concentration of cAMP and a high concentration of lactose are necessary to get sustained expression of the lac operon. When glucose levels begin to rise, the cAMP concentration will begin to fall and the operon function will deteriorate.

lac I is the gene that encodes for the repressor of the lac operon. If there is no repressor, the cell will constantly express the genes present in the lac operon whether or not the typical conditions are present.

A mutation of the gene encoding -galactosidase permease (lac Y) would prevent lactose from entering the cell. A mutation in the gene encoding -galactosidase (lac Z) would prevent the breakdown of lactose. A mutation in the promoter region would prevent RNA polymerase from binding.

Prokaryotic organisms often have functionally related genes joined together on the chromosome under the direction of a single promoter. These structures are called operons. Operons have additional sequences, called operators that can be bound by either repressor or activator proteins, which will repress or activate transcription of the operon. One commonly studied example is the lac operon, whose genes encodes products required for lactose metabolism.