RNA is transcribed 5' to 3' ALWAYS, meaning that the template DNA strand is read from the 3' to 5' direction.

The 5’ UTR region is known as the leader sequence and runs upstream from the coding sequence. The 3’ UTR region is the trailer sequence and runs downstream to the coding sequence. The start codon runs after the 5’ UTR region and the stop codon is seen prior to the 3’ UTR region.

mRNA processing includes capping (5’ cap), polyadenylation (3’ Poly A tail), and splicing (removal of introns).

Eukaryotes are more complex cells than prokaryotes and have 3 different polymerases for the different RNA classes, while prokaryotes only have one RNA polymerase that handles RNA transcription for the whole cell. 

The ability of a gene to affect an organism is multiple ways is called pleiotropy. During post-transcriptional modification, introns are removed from the mRNA sequence and exons are spliced together to create the desired protein product. By splicing the gene in different ways, different proteins can be produced, which will affect different traits.

Consider the sentence: The man ran on the track, but fell.

By splicing different portions of the sentence, it can take on different meanings: The man ran. The man on the track fell. The man fell. The man ran, but fell.

Where pleiotropic genes affect more than one trait, polygenic traits are affected by multiple genes. Epistatic genes are regulated by the activation of other genes.

Out of the choices, only methylation of histones is commonly associated with the silencing of genes. Proteins known as histone methyltransferases bind a methyl group to amino acids in the histone, most commonly lysine or arginine. The result is a change in chromatin structure, most commonly blocking transcription sites and preventing expression.

Acetylation of histones is often found in activated genes. Phosphorylation of histones has been seen in DNA regulation, but it is unclear whether or not this modification affects the expression of genes.

Topoisomerases unwind supercoiling of DNA by breaking and rejoining DNA chains. 

Nucleotide excision repair (NER) is used to repair thymine dimers, which are caused by ultraviolet damage. It also repairs bulky DNA adducts caused by carcinogens.

DNA polymerase III has these two functions:

1. 5'-3' polymerase requiring a 3' hydroxide primer and a DNA template

2. 3'-5' exonuclease proofreading

Both DNA polymerase I and DNA polymerase III are prokaryotic only. DNA polymerase I excises RNA primers with a 5' to 3' exonuclease.

5'-3' exonuclease removal of primers by DNA polymerase I.

DNA polymerase I is prokaryotic only, it degrades RNA primer and fills in the gap with DNA.