Nucleic Acid Structures - Biochemistry

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.

The helix-turn-helix motif has two helices at a particular angle, with one of them, the recognition helix, fitting into a major groove. Zinc fingers have sheets and helices held together via zinc complexes. Beta sheets have hydrogen bonds along their strand backbones. The helix-loop-helix motif has one helix folded and packed against another. In the leucine zipper, two helices are coiled up to where they are "unzipped" to form a Y.

The backbone of DNA is made up of alternating phosphate groups and sugar groups, linked together via phosphodiester bonds. The nitrogenous bases jut off of the backbone and form bonds with nitrogenous bases on other strands of DNA to become double stranded. A nucleotide consists of a sugar, nitrogenous base, and one or more phosphate groups.

The anticodon is a part of tRNA that is capable of finding its complementary codon on mRNA. This allows the tRNA to carry its specific amino acid to a ribosome when necessary in the production of proteins.

The clover-like structure of tRNA is held together by hydrogen bonds between nitrogenous bases of the molecule. Without them, this tertiary structure would not be possible.

In RNA the four bases are: adenine, uracil, guanine, and cytosine. The bases in DNA are similar, except uracil is replaced with thymine. In RNA, adenine will always pair with uracil, and guanine will always pair with cytosine. Remember, a purine (adenine, guanine) will always pair with a pyrimidine (cytosine, uracil or thymine).

The glycosidic bonds of B DNA are in the anti conformation. This means that the nucleotide and sugar are on opposite sides of the N-glycosidic bond.

The function of snRNA is to participate in the splicing of RNA exons. Micro RNA binds to complementary mRNA to inhibit translation. Small interfering RNA binds to mRNA to facilitate its degradation. mRNA functions as a template for protein synthesis. Transfer RNA (tRNA) carries amino acids to the ribosome during translation.

The function of snRNA is to participate in the splicing of RNA exons. Micro RNA binds to complementary mRNA to inhibit translation. Small interfering RNA binds to mRNA to facilitate its degradation. mRNA functions as a template for protein synthesis. Transfer RNA (tRNA) carries amino acids to the ribosome during translation.

The TATA box and/or the Hogness box are regions on DNA that function as promoter sites. RNA polymerase scans DNA for these regions and when it sees one, it recognizes that it should begin transcription of the following gene.

Primase is an enzyme used in the replication of DNA. DNA polymerase synthesizes DNA in a 5' to 3' direction, so it needs a free 3' end to begin its replication from. The primase constructs an RNA substrate with a free 3' end, that binds complementary to the unwound and single-stranded DNA template that is about to be replicated.

After DNA Polymerase 1 replaces the RNA primers with DNA. DNA ligase then comes along and uses an ATP for energy as it connects the 3' and 5' ends of the DNA gap, completing the replication of the template strand.

A codon is a set of three nucleic acids on the messenger RNA that codes for an amino acid. The start codon is AUG. In this strand, AUG is the first codon, the second is UUA, and the third is GCG.

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.