Conjugation of ubiquitin molecules to a protein activates the ubiquitin proteasome system, which is required by cells to break down proteins into their component amino acid residues to be reallocated in protein building as necessary. While the other modifications may contribute to some degradation pathway, ubiquitin is classically considered a marker of protein destruction via the proteasome system. 

Polyadenylation is the process in which a "Poly-a tail," or a tail of adenine bases, is added to the 3' end of an mRNA. The other processes listed do not carry out this function.

Epigenetics are changes to the genome that result in phenotypic variation that have nothing to do with changes in the actual DNA sequence. All listed answers occur independently of DNA sequence, except for "different exon sequences," which is the actual sequence of an exon. This referces to alternative splicing, an is not related to the modification of DNA or histones.

Methylation and acetylation of histones occurs on lysine residues, thereby decreasing or increasing gene expression, respectively. Methylation increases the affinity for histones and DNA, where acetylation decreases the affinity for histones and DNA. Gene expression is in part controlled by modification of histone proteins, rather non-histone chromosomal proteins. 

The correct answer is an increase in gene expression. Histone acetylation removes positive charges on the histones, reducing the affinity of DNA for histones. Remember that DNA is negatively charged due to the phosphate groups on its backbone. DNA and histones are attracted to each other because histones are positively charged due to being rich in basic amino acid residues. Acetylation relaxes the tightly bound DNA allowing transcription factors to bind promoter regions. DNA deacetylation and methylation supress gene transcription by making DNA and histones associate more tightly together, decreasing the ability of transcription factors and/or RNA polymerase to bind the DNA. Histone modifications such as acetylation, deacetylation, and methylation do not directly affect the amount of DNA. If a histone is acetylated on a part of the DNA which codes for the genes for ribosome production, then an increase in ribosomal production and assembly could occur, but genes coding for ribosomes are greatly outnumbered by other genes, and thus, this is not the usual result of acetylating histones. 

Proto-oncogenes are genes that have the ability to become oncogenes (genes that cause cancer). There are many ways to activate proto-oncogenes. Gene duplication can cause an increase in the expression of a particular protein, which can lead to cancer. Exposure to mutagens can cause a mutation on a proto-oncogene, which causes it to become activated. Chromosomal translocations can relocate proto-oncogenes to areas where they are expressed more rapidly. Most proto-oncogenes are involved in cell cycle regulation. Irregular expression of these genes can allow the cell to progress through the cell cycle too rapidly, resulting in unregulated cell division and tumor formation.

Oncogenes can be thought of as cancerous genes, or rather a gene that has the potential to cause cancer. They typically occur when a normal proto-oncogene undergoes a mutation. Proto-oncogenes normally code for growth and development in cells, and tightly regulate these processes. If mutated, these newly cancerous genes can stimulate unregulated growth, a symptom characteristic of cancerous cells.

DNA helicases use ATP to break the hydrogen bonds that separate complementary strands of DNA. During DNA replication, DNA helicases move along the DNA backbone with the replication fork and are responsble for unwinding the DNA at the fork.

RNA polymerase is an enzyme that transcribes RNA from DNA; it is not essential for DNA replication. This enzyme is easy to confuse with primase, whose primary function is to synthesize the RNA primers necessary for replication. DNA polymerase add nucleotides during replication, synthesizing the daughter strand from the parental template. Helicase is responsible for separating double-stranded DNA. Single-strand binding proteins are needed to keep DNA from reannealing after it has been denatured by helicase.

DNA replicates in a semiconservative process. Parental strands are used as templates to synthesize daughter strands, which remain adhered to the parental template creating hybrid molecules of old and new DNA.

The original DNA molecules is "unzipped" by helicase to create the replication fork. DNA polymerase then begins to recruit nucleotides to bind to the exposed template, building the new DNA strand along the parental strand.