Nucleic Acid Structures - Biochemistry

Unmethylated cytosine spontaneously deaminates to uracil. Over time, methylated cytosine is spontaneously deaminated to thymine. Random deamination of methylcytosines causes mutation, creating hot spots. The vast majority of DNA methylations in mammals occurs at CpG (cytosine-phospate-guanine) sites.

A null mutation is one that deactivates a gene entirely. Point mutations are those that occur within a single, small site in a gene. Inversion involves the reversal of orientation of a DNA segment. Deletion occurs when a whole part of a chromosome is removed, joining two ends that were far apart. Translocation involves the exchange of genetic material from two chromosomes that are not homologous.

The silencing of a gene is most often accomplished via methylation of the DNA. The methyl groups are added to the gene's promoter region and thus, the DNA is not read by transcriptional enzymes.

In order to silence a gene by methylation, methyl groups are added to the promoter region of DNA. This area is upstream of the coding sequence and is responsible for initiation of transcription. Thus, methylating the promoter region inhibits further transcription of the gene.

The only two bases that can be methylated are cytosine and adenine.

Alkylating agents and can also cause cancer, but they lead to methylation and mismatch mutations rather than the formation of pyrimidine dimers.

The pentose phosphate pathway (also known as the hexose monophosphate shunt or HMS), mainly serves to produce for anabolic reduction reactions and ribose-5-phosphate for nucleic acid production.

A nucleoside is composed of both a nitrogenous base as well as a sugar. Cytosine and adenine are just nitrogenous bases. Guanosine monophosphate (or GMP) is also composed of a phosphate group, which designates it as a nucleotide. The only nucleoside is adenosine.

The phosphodiester bonds in DNA occur between the 3' and 5' hydroxyl groups on deoxyribose. (This is related to DNA's 5' to 3' directionality as DNA polymerase can only synthesize DNA by adding nucleotides to the 3' hydroxyl group).

The beta-N-glycosidic bond attaches the nitrogen on the purine or pyrimidine base to the 1' anomeric carbon on the deoxyribose sugar. Phosphodiester linkages connect the 3' and 5' sugar hydroxyl groups on adjacent nucleotides.

Phosphorus on both orthophosphate and pyrophosphate is surrounded by 10 electrons. This does not satisfy the octet rule in either case, so that answer choice is false, and therefore the correct answer. With four negative charges close by, pyrophosphate is very unstable, and releases a lot of energy when cleaved. Finally, the two orthophosphates formed from a single pyrophosphate gain an additional resonance structure.

The type of bond that holds the phosphate group to the sugar in DNA's backbone is called a phosphodiester bond. Hydrogen bonds connect bases to one another and glycosidic bonds occur between deoxyribose groups and the base groups.

The type of loop of tRNA at the anticodon sequence is indeed hairpin. Hypoxanthine is occasionally found in tRNA anticodons (as its nucleoside, inosine). tRNA anticodons and mRNA codons are indeed antiparallel (this is central to their functioning). However, just because an anticodon has guanine in position one, doesn’t mean in cannot code with any of the four codons to make the same amino acid; the amino acid produced will be subject to whatever combination of bases is present, as detailed in the genetic code.

The two pyrimidine bases are cytosine and thymine. Purine bases are larger in structure than pyrimidines and possess a two-ring nitrogenous base. In RNA, uracil is also a pyrimidine. One way to help us remember which nitrogenous bases are which is to use the mnemonic CUT. Pyramids (like pyrimidines) are "sharp" and thus they CUT, Cytosine, Uracil and Thymine.

DNA nucleotides have a maximum absorbance at 280 260nm. Pyrimidines Purines have a larger structure than purines pyrimidines, since purines have two rings in their structures, and the pyrimidines have only one. All DNA nucleotides have tautomeric forms, and the lactim or enol lactam or keto form is more common. The structure of adenine is identical to guanine with the exception of one additional amino group on carbon #2 and a double bonded oxygen replacing the amino group on carbon #6.

Thymine and uracil a both pyrimidines with similar structure but a key difference at the 5' carbon. While this location is methylated in thymine, there is no functional group there in uracil.

Adenine and guanine are purines (contain two rings). Thymine, cytosine, and uracil are pyrimidines (contain one ring). In normal base pairing, a purine matches to a pyrimidine. Adenine matches to thymine in DNA (uracil in RNA), and cytosine matches to guanine. Ribulose is a carbohydrate.

In DNA and RNA, there are two types of nitrogenous bases: pyrimidines and purines. A pyrimidine contains one carbon-nitrogen ring with two nitrogen atoms. A purine consists of a pyrimidine fused with an imidazole ring. Adenine and guanine are purines. Cytosine, thymine, and uracil are pyrimidines.

When purines are broken down, they go through the intermediates hypoxanthine and xanthine, then are converted to uric acid. Xanthine oxidase is the enzyme that converts xanthine to uric acid. Treatments for gout are suicide inhibitors of xanthine oxidase, lowering the production of uric acid and building up the intermediates. This is preferable, because unlike uric acid, the intermediates are highly soluble.

Okazaki fragments are found in the lagging strand, and are linked by DNA ligase. These short fragments of DNA are formed because DNA polymerase III (the main polymerizing enzyme complex) can only add nucleotides the the 3' end of a DNA strand. Since DNA strands are antiparallel, this is unavoidable.