DNA replication

Examples of DNA replication in the following topics:

• DNA Replication in Prokaryotes

  • Prokaryotic DNA is replicated by DNA polymerase III in the 5' to 3' direction at a rate of 1000 nucleotides per second.
  • As the DNA opens up, Y-shaped structures called replication forks are formed.
  • A replication fork is formed when helicase separates the DNA strands at the origin of replication.
  • The DNA tends to become more highly coiled ahead of the replication fork.
  • Explain the functions of the enzymes involved in prokaryotic DNA replication

• Basics of DNA Replication

  • DNA replication uses a semi-conservative method that results in a double-stranded DNA with one parental strand and a new daughter strand.
  • Watson and Crick's discovery that DNA was a two-stranded double helix provided a hint as to how DNA is replicated.
  • In dispersive replication, after replication both copies of the new DNAs would somehow have alternating segments of parental DNA and newly-synthesized DNA on each of their two strands.
  • Meselson and Stahl were interested in understanding how DNA replicates.
  • The three suggested models of DNA replication.

• DNA Replication in Eukaryotes

  • As the DNA opens up, Y-shaped structures called replication forks are formed.
  • Once DNA replication is finished, the daughter molecules are made entirely of continuous DNA nucleotides, with no RNA portions.
  • Each origin of replication forms a bubble of duplicated DNA on either side of the origin of replication.
  • DNA polymerase halts when it reaches a section of DNA template that has already been replicated.
  • A replication fork is formed by the opening of the origin of replication; helicase separates the DNA strands.

• The DNA Double Helix

  • DNA has a double-helix structure, with sugar and phosphate on the outside of the helix, forming the sugar-phosphate backbone of the DNA.
  • This antiparallel orientation is important to DNA replication and in many nucleic acid interactions.
  • This is known as the base complementary rule because the DNA strands are complementary to each other.
  • During DNA replication, each strand is copied, resulting in a daughter DNA double helix containing one parental DNA strand and a newly synthesized strand.
  • Native DNA is an antiparallel double helix.

• Telomere Replication

  • As DNA polymerase alone cannot replicate the ends of chromosomes, telomerase aids in their replication and prevents chromosome degradation.
  • After DNA replication, each newly synthesized DNA strand is shorter at its 5' end than at the parental DNA strand's 5' end.
  • These telomeres protect the important genes from being deleted as cells divide and as DNA strands shorten during replication.
  • After sufficient rounds of replication, all the telomeric repeats are lost, and the DNA risks losing coding sequences with subsequent rounds.
  • A simplified schematic of DNA replication where the parental DNA (top) is replicated from three origins of replication, yielding three replication bubbles (middle) before giving rise to two daughter DNAs (bottom).

• DNA Repair

  • Most mistakes during replication are corrected by DNA polymerase during replication or by post-replication repair mechanisms.
  • DNA replication is a highly accurate process, but mistakes can occasionally occur as when a DNA polymerase inserts a wrong base.
  • Most of the mistakes during DNA replication are promptly corrected by DNA polymerase which proofreads the base that has just been added .
  • Errors during DNA replication are not the only reason why mutations arise in DNA.
  • DNA ligases catalyse the crucial step of joining breaks in duplex DNA during DNA repair, replication and recombination, and require either Adenosine triphosphate (ATP) or Nicotinamide adenine dinucleotide (NAD+) as a cofactor.

• Characteristics of Eukaryotic DNA

  • In addition, prokaryotes have plasmids, which are smaller pieces of circular DNA that can replicate separately from prokaryotic genomic DNA.
  • Mitosis, a process of nuclear division wherein replicated chromosomes are divided and separated using elements of the cytoskeleton, is universally present in eukaryotes.
  • Prokaryotes on the other hand undergo binary fission in a process where the DNA is replicated, then separates to two poles of the cell, and, finally, the cell fully divides.
  • A major DNA difference between eukaryotes and prokaryotes is the presence of mitochondrial DNA (mtDNA) in eukaryotes.
  • Eukaryotic DNA is stored in a nucleus, whereas prokaryotic DNA is in the cytoplasm in the form of a nucleoid.

• Noncoding DNA

  • Noncoding DNA are sequences of DNA that do not encode protein sequences but can be transcribed to produce important regulatory molecules.
  • In genomics and related disciplines, noncoding DNA sequences are components of an organism's DNA that do not encode protein sequences.
  • The amount of noncoding DNA varies greatly among species.
  • For example, over 98% of the human genome is noncoding DNA, while only about 2% of a typical bacterial genome is noncoding DNA.
  • However, many types of noncoding DNA sequences do have important biological functions, including the transcriptional and translational regulation of protein-coding sequences, origins of DNA replication, centromeres, telomeres, scaffold attachment regions (SARs), genes for functional RNAs, and many others.

• Steps of Virus Infections

  • Viral infection involves the incorporation of viral DNA into a host cell, replication of that material, and the release of the new viruses.
  • A virus must use cell processes to replicate.
  • The replication mechanism depends on the viral genome.
  • DNA viruses usually use host cell proteins and enzymes to make additional DNA that is transcribed to messenger RNA (mRNA), which is then used to direct protein synthesis.
  • To convert RNA into DNA, retroviruses must contain genes that encode the virus-specific enzyme reverse transcriptase, which transcribes an RNA template to DNA.

• Prokaryotic Reproduction

  • The DNA of a prokaryote exists as as a single, circular chromosome.
  • Prokaryotes do not undergo mitosis; rather the chromosome is replicated and the two resulting copies separate from one another, due to the growth of the cell.
  • The DNA transferred can be in the form of a plasmid or as a hybrid, containing both plasmid and chromosomal DNA.
  • The DNA may remain separate as plasmid DNA or be incorporated into the host genome.
  • In (b) transduction, a bacteriophage injects DNA into the cell that contains a small fragment of DNA from a different prokaryote.