nucleotide

Examples of nucleotide in the following topics:

• Nucleotide and Nonnucleotide Reverse Transcriptase Inhibitors

  • They mimic, respectively, nucleosides or nucleotides but lack a free hydroxyl group at the 3' end.
  • Nucleoside and nucleotide inhibitors are also called competitive substrate inhibitors.
  • Non-nucleotide inhibitors are non-competitive inhibitorsof reverse transcriptase.
  • The mechanisms for resistance against the nucleoside (nucleotide) inhibitors are two.
  • Resistance to the non-nucleotide inhibitors is caused by mutations in the inhibitor binding site of the enzyme.

• DNA Replication in Prokaryotes

  • The addition of nucleotides requires energy; this energy is obtained from the nucleotides that have three phosphates attached to them, similar to ATP which has three phosphate groups attached.
  • There are specific nucleotide sequences called origins of replication where replication begins.
  • It also requires a free 3'-OH group to which it can add nucleotides by forming a phosphodiester bond between the 3'-OH end and the 5' phosphate of the next nucleotide.
  • This means that it cannot add nucleotides if a free 3'-OH group is not available.
  • The replication fork moves at the rate of 1000 nucleotides per second.

• Transcription in Prokaryotes

  • Yet there are only four different nucleotides in DNA or RNA, so a minimum of three nucleotides are needed to code each of the 21 (or 22) amino acids .
  • The only difference is that in RNA all of the T nucleotides are replaced with U nucleotides.
  • The nucleotide on the DNA template strand that corresponds to the site from which the first 5' RNA nucleotide is transcribed is called the +1 nucleotide, or the initiation site.
  • Conversely, nucleotides following, or 3' to, the template strand initiation site are denoted with "+" numbering and are called downstream nucleotides.
  • A codon is made of three nucleotides.

• The Structure and Sequence of DNA

  • The monomeric building blocks of DNA are deoxyribomononucleotides (usually referred to as just nucleotides), and DNA is formed from linear chains, or polymers, of these nucleotides.
  • The nucleotide is named depending on which nitrogenous base is present.
  • In polynucleotides (the linear polymers of nucleotides) the nucleotides are connected to each other by covalent bonds known as phosphodiester bonds or phosphodiester linkages.
  • Each nucleotide is made up of a sugar, a phosphate group, and a nitrogenous base.
  • Once at least one phosphate is covalently attached, it is known as a nucleotide.

• DNA Sequencing Techniques

  • DNA sequencing techniques are used to determine the order of nucleotides (A,T,C,G) in a DNA molecule.
  • Using radiolabeled nucleotides also compounded the problem through safety concerns.
  • From the color of the resulting flouresence, a computer can keep track of which nucleotide was present as the terminating nucleotide.
  • Each sequencing reaction is a modified replication reaction involving flourescently-tagged nucleotides, but no chain-terminating dideoxy nucleotides are needed.
  • Sanger sequence can only produce several hundred nucleotides of sequence per reaction.

• DNA Sequencing Based on Sanger Dideoxynucleotides

  • Sanger sequencing is based on the incorporation and detection of labeled ddNTPs as terminal nucleotides in DNA amplification.
  • This method is based on amplification of the DNA fragment to be sequenced by DNA polymerase and incorporation of modified nucleotides - specifically, dideoxynucleotides (ddNTPs).
  • The classical chain-termination method requires a single-stranded DNA template, a DNA primer, a DNA polymerase, normal deoxynucleotidetriphosphates (dNTPs), and modified nucleotides (dideoxyNTPs) that terminate DNA strand elongation .
  • These chain-terminating nucleotides lack a 3'-OH group required for the formation of a phosphodiester bond between two nucleotides, causing DNA polymerase to cease extension of DNA when a ddNTP is incorporated.
  • Technical variations of chain-termination sequencing include tagging with nucleotides containing radioactive phosphorus for radiolabelling, or using a primer labeled at the 5' end with a fluorescent dye.

• DNA Replication in Eukaryotes

  • Only the nucleotide complementary to the template nucleotide at that position is added to the new strand.
  • For example, when DNA polymerase meets an adenosine nucleotide on the template strand, it adds a thymidine to the 3' end of the newly synthesized strand, and then moves to the next nucleotide on the template strand.
  • This short stretch of RNA nucleotides is called the primer.
  • Eventually, the RNA nucleotides in the primer are removed and replaced with DNA nucleotides.
  • Once all the template nucleotides have been replicated, the replication process is not yet over.

• DNA Repair

  • If it is the correct base, the next nucleotide is added.
  • Once the incorrect nucleotide has been removed, a new one will be added again.
  • Mutations, variations in the nucleotide sequence of a genome, can also occur because of damage to DNA.
  • The most common nucleotide mutations are substitutions, in which one base is replaced by another.
  • Nucleotide excision repairs thymine dimers.

• DNA and RNA

  • DNA and RNA are made up of monomers known as nucleotides.
  • The nucleotides combine with each other to form a polynucleotide: DNA or RNA.
  • Each nucleotide is made up of three components:
  • A nucleotide is made up of three components: a nitrogenous base, a pentose sugar, and one or more phosphate groups.
  • Two types of pentose are found in nucleotides, deoxyribose (found in DNA) and ribose (found in RNA).

• Initiation of Transcription in Prokaryotes

  • The nucleotide pair in the DNA double helix that corresponds to the site from which the first 5' mRNA nucleotide is transcribed is called the +1 site, or the initiation site.
  • Nucleotides preceding the initiation site are given negative numbers and are designated upstream.
  • Conversely, nucleotides following the initiation site are denoted with "+" numbering and are called downstream nucleotides.
  • The transcription initiation phase ends with the production of abortive transcripts, which are polymers of approximately 10 nucleotides that are made and released.