Nucleic Acid Structures and Functions - Biochemistry

This question presents us with a portion of the coding strand of a gene, and asks us to determine the corresponding sequence of nucleotides in the mRNA that would be transcribed from this gene.

To begin, it is very important to recognize that the sequence given to us in the question stem is the coding strand. This is to distinguish it from the template strand.

For any given gene, there is a template strand and a coding strand. These two strands are complementary to one another and run in opposite directions. The template strand is the one that is transcribed to give rise to a complementary mRNA molecule that will go on to be translated into a polypeptide. Hence, it is called the template strand because it provides the template for the production of mRNA, and subsequently a protein.

The coding strand, on the other hand, is not transcribed. Instead, the coding strand gets its name because its sequence is identical to the sequence of the pre-mRNA (before introns are removed). The exception to this is that the coding strand contains thymine nucleotides, whereas the pre-mRNA contains uracil in place of thymine. The reason why these two have the same sequence is because both of them are complementary to the template strand. Sometimes, the template strand is also referred to as the antisense strand, while the coding strand is referred to as the sense strand.

It is important to realize this distinction because, without it, one might arrive at the incorrect answer. Because this is the coding strand (sense strand), the mRNA product will have an identical sequence, with the exception of uracil in place of thymine.

Coding strand:

mRNA strand:

DNA and RNA share many common characteristics, as they are both nucleic acids. One of the key differences is that DNA use a deoxyribose sugar while RNA uses a ribose sugar. It should be noted that while RNA is typically assumed to be single stranded, it can still exhibit complementary base pairing. As a result, the guanine and cytosine base pairing can still take place.

DNA is negatively charged because of the sugar-phosphate backbone. Histones are rich in lysine residues because they are positively charged and are ideal for DNA to wrap around. If the lysines became glutamates, the histone would overall have a negative charge, causing the DNA to bind weakly to each histone. The function of introducing negative supercoils would be reduced, and ubiquitination would not be affected.

The deoxyribose–phosphate backbone of DNA is on the outside (hydrophylic) of the helix while the hydrophobic bases are inside. The classical B form, found in chromosomal DNA, and predicted by Watson and Crick, is a right-handed helix with 10 bases per turn of helix. The number of bases is different in Z and A DNA helix conformations.

There are 3 conformations of the DNA molecule. The B form is in chromosomal DNA, the A form is representative of DNA-RNA hybrids. The Z form of DNA appears in poly GC (poly guanine, cytosine) sequences.

Phosphate groups attach to the 5' carbon of the nucleosides forming nucleotides. Phosphodiester bonds of DNA form between the 3'-hydroxyl group of the deoxy pentose of one nucleotide and the 5'-hydroxyl group of the deoxy pentose of another nucleotide.Deoxythymidine is the deoxynucleotide with thymine as its base. It can be mono-, di, or tri- phosphorylated as deoxythymidine mono-, di- or triphosphate.

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.

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.

Reverse transcriptase synthesizes DNA in the 5' to 3' direction, using RNA as a template (hence it is the reverse of transcription). Restriction enzymes act only on DNA, not RNA, and they can cut bacterial as well as viral DNA—indeed, they can provide protection against viruses—and are found in archaea. Restriction enzymes can recognize specific sequences of nucleotides at restriction sites and cut DNA at these sites. Restriction enzymes do not create covalent bonds between adjacent exons after intron excision, rather this is done by tRNA splicing ligase.

Xanthine oxidase is an enzyme important in purine catabolism. Nucleotides from DNA degradation are metabolized to uric acid by xanthine oxidase.In diseases with high levels of nucleotide production, uric acid levels are also high and produce symptoms of gout (uric acid is deposited abnormally in tissues). Gout is treated with inhibitors of xanthine oxidase such as allopurinol, reducing the levels of uric acid and the symptoms of gout.

tRNA carries the anticodon. tRNA is a transfer ribonucleic acid; it is a type of RNA molecule that decodes the mRNA sequence to form a protein. The anticodon is the part of the tRNA structure that complements the mRNA codon, dictating the identity of the amino acid carried by the tRNA and required to build the proper polypeptide chain.

The presence of an group on the 2’ carbon if ribose does indeed make any phosphodiester bonds at this site subject to hydrolysis. RNA can sometimes form double-helices, such as in tRNA. mRNA is constantly being degraded in the cytoplasm, and so it has a very short half-life relative to the life of the cell. RNA’s hairpin turn structures are composed of only one molecule which has doubled back on itself, rather than two separate molecules.

B DNA has a wide and deep major groove and a narrow and deep minor groove. All other statements regarding B DNA are true.