Genetics, DNA, and Molecular Biology - GRE Subject Test: Biology

Nucleosomes are the basic, repeating units of eukaryotic chromatin. They consist of chromosomal DNA wrapped around special DNA-binding proteins called histones. There are many examples of non-chromosomal DNA, such as plasmids, but they do not contain nucleosomes. Nuclear import is controlled by importin proteins.

Histones are proteins that bind and package DNA. The strand of DNA is wound around histone proteins, condensing it to fit in the nucleus and acting to moderate gene expression. Chromatin is the term given to the complex of DNA associated with histones. A nucleosome is the smallest repeating unit of chromatin, formed from eight histone proteins and two loops of coiled DNA. Telomerase is an enzyme responsible for maintaining the integrity of the telomeres.

Euchromatin is the name given to chromatin that appears lighter when viewed under a microscope. It is actually relatively decondensed chromatin that is available for active transcription. Because it is decondensed it is more accessible to RNA polymerase and, therefore, easier to transcribe. In contrast, heterochromatin is tightly wound, dense DNA that is inaccessible by RNA polymerase and is considered inactive.

Translation is the process of synthesizing proteins from mRNA transcripts and does not directly involve DNA or chromatin.

Chromatin is not present in all eukaryotic and prokaryotic DNA; most prokaryotic DNA is circular and does not require the complex folding of eukaryotic chromatin. Chromatin exists in more compacted states than 10nm. In particular, the 30nm version is commonly recognized as heterochromatin (DNA that is not being actively transcribed). Packaging can also be more condensed during certain stages of mitosis. Nucleosomes are the smallest units of chromatin and are strands of DNA wrapped in proteins known as histones.

Patterns of methylation and acetylation of these histones have been shown to repress and activate gene expression, respectively, and are important factors in regulating gene expression and epigenetics.

DNA repair can, and does, occur during replication. An easy example of this is the proofreading function of several DNA polymerases. This function is carried out due to the enzymes containing an exonuclease function that allows them to excise incorrect base pairs. p53 is an incredibly important protein that is expressed heavily when DNA damage is detected. It is responsible for activating both DNA repair pathways and apoptotic pathways, preventing the cell from passing replication and cell cycle checkpoints. If the DNA damage is irreparable, the cell may undergo apoptosis.

The correct answer is homology directed repair. Using flanking homologous regions upstream and downstream of the double stranded break, the cell is able to determine the precise sequence that is in the damaged region and repair that sequence.

DNA ligase catalyzes the formation of phosphodiester bonds between the elements of the DNA backbone. DNA polymerases function in replication of DNA, whereas exonucleases and endonucleases break apart DNA strands by disrupting phosphodiester bonds.

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.

Before replication, the DNA helix must be unwound so that the strands can be replicated by DNA polymerase. This unwinding is accomplished by DNA helicase, which interferes with the hydrogen bonds between nucleotide pairs. This intervention creates a small separation between the two strands, known as the replication fork. DNA polymerase binds to the replication fork and recruits nucleotides to build the new DNA strand.

Topoisomerase is responsible for cleaving phosphodiester bonds in order to release torsional tension in the DNA backbone. DNA ligase synthesizes phosphodiester bonds, both on the daughter strand of DNA and in the regions cleaved by topoisomerase. Primase is responsible for synthesizing RNA primers that serve to help recruit and bind DNA polymerase in the replication fork.

In order for DNA polymerase to begin synthesizing base pairs, an RNA primer is needed to assist the binding of DNA polymerase to the DNA template strand. This primer is synthesized by the enzyme primase. Because DNA polymerase always needs an RNA primer before it can bind, primase must synthesize RNA primers on both the leading and lagging strands.

RNA polymerase transcribes molecules of RNA from DNA sequences during transcription, and is not involved in DNA replication.

DNA replication occurs during the S phase of the cell cycle, significantly before prophase of mitosis. During prophase chromosomes are condensed into easily segregated forms, but replication has already occurred. The S phase is the intermediate period of interphase in the cell cycle. The G2 phase follows the S phase, and is subsequently followed by the M phase (mitosis).

The short fragments synthesized on the lagging strand are known as Okazaki fragments. DNA replication does occur in the 5' to 3' direction; this is also the reason that the lagging strand must be synthesized away from the replication fork. DNA is denatured (separated) at the replication fork by an enzyme known as helicase, which breaks the hydrogen bonds between base pairs to allow DNA polymerase and other replication proteins to bind to single-strand DNA.

DNA polymerase I replaces the RNA primer gap with DNA nucleotides. This polymerase is unique in that it has 5' 3' exonuclease activity. This RNA primer is created by primase, it is removed and replaced with DNA by DNA polymerase I, and the remaining nick is sealed by DNA ligase. Bacterial DNA polymerase III, in contrast, is the main polymerase for bacterial elongation. The function of DNA polymerase II is not completely understood. The remaining answer choices are not involved in prokaryotic DNA replication.

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.

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.

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 question informs us that the mutational defect in the gene involves the enzyme's ability to load copper onto apoceruloplasmin. Healthy individuals are able to load copper to apoceruloplasmin, creating serum-soluble ceruloplasmin. With this process disrupted in an individual with Wilson's Disease, we would expect that less ceruloplasmin would be produced because copper could not be transported. We would expect to see reduced serum levels of the complete protein, and high levels of copper building up in hepatocytes and circulatory serum.

The addition of a number of nucleotides that is not a multiple of three shifts the reading frame of the codons in the gene. One base pair was inserted early in the strand, thus shifting the codon reading frame +1 to the right.

Missense and nonsense mutations imply base pair substitutions, which did not occur in the diagram. Similarly, nothing was duplicated, and repeat expansion would require multiple repetitions of a short DNA sequence.