Understanding DNA Replication, Transcription, and Genetic Code

The Central Dogma of Molecular Biology

Replication - General Characteristics:

• DNA replication is semiconservative: each strand in the DNA double helix acts as a template for the synthesis of a new, complementary strand. The new two daughter molecules of DNA have a new strand and an old one.
• DNA polymerase III: is the enzyme that adds nucleotides to the growing DNA chain, incorporating only those that are complementary to the template. DNA polymerase III has the following characteristics:
  • It can only read a template in 3’-----5’ direction so the new strand grows in 5’----3’ direction.
  • It needs a pre-existing strand of nucleotides called a primer which provides a 3’-OH end to bind new nucleotides.
  • It is able to repair the mistakes by removing the wrong nucleotides that are accidentally added to the chain.
  • The addition of nucleotides requires energy.

Replication - Initiation: Replication starts at specific locations on the DNA, which are called origins of replication and are recognized by their sequence. In Eukaryotic cells, there are several origins of replication in a single chromosome while in bacteria there is only one. Specialized proteins recognize the origin, bind to this site, and open up the DNA, making up what we call a replication bubble. As the DNA opens, two Y-shaped structures called replication forks are formed. Replication is bidirectional, so forks will move in opposite directions. Enzymes called helicases are involved in unwinding the DNA helix in the replication fork as replication proceeds.

Replication - Elongation: As DNA polymerase can only read the strand of 3’-----5’ polarity, it copies the two strands in two different ways; To determine the polarity we take as a reference the direction of the replication fork. Formation of the leading strand: the strand with 3’-----5’ polarity will be “read” continuously: A primase will produce a primer (short RNA fragment) with 5’----3’ polarity and DNA polymerase III will add DNA nucleotides to the 3’ end of the primer producing a new strand of DNA in the direction of the replication fork with 5’---3’ polarity. Formation of the lagging strand: the strand with 5’-----3’ polarity can't be “read” continuously by the DNA polymerase III since this enzyme only works in the opposite direction. In this case, primase will produce several separated primers in the opposite direction to the replication fork; that way the DNA polymerase will elongate these primers reading the template from 3’----5’ direction and producing discontinuous fragments of DNA with 5’---3’ polarity (Okazaki fragments). At the end of the process DNA polymerase I will eliminate the primers and will replace them by DNA, and a ligase will bind all DNA fragments together to form a continuous DNA strand.

Termination: Replication finishes when two bubbles of replication meet.

Transcription: Process by which the genetic information contained in a gene (fragment of DNA which codifies for a protein) is copied into a messenger RNA. Characteristics:

• The process is carried out by an enzyme called RNA polymerase.
• RNA polymerase is going to synthesize a complementary strand to DNA 3’--------5’ strand, so the mRNA will have 5’-----------3’ polarity and will carry the same message as the 5’---3’ DNA strand, called the coding strand.

Genetic Code: The genetic code is the relationship between the codons of mRNA and the amino acids. Characteristics:

• It is universal: all living things have the same genetic code.
• A triplet of mRNA nucleotides (codon) corresponds to a specific amino acid.
• Every codon of mRNA binds a complementary anticodon in tRNA.
• As we have 61 possible codons and just 20 different amino acids many amino acids are represented by more than one codon. For instance, there are six different codons which codify for leucine amino acid.

Transcription: It is the process by which the cell converts the message of mRNA (message of a gene) into proteins. The intermediary between the mRNA codon and the amino acid is the transfer RNA; One side of tRNA has three nucleotides that bind the mRNA codon (anticodon) and other side of the tRNA loads the specific amino acid for that codon. After transcription, the mRNA travels to the cytoplasm where a ribosome will read its message from 5’ to 3’; when the ribosome has read a codon “jumps” to the next codon until the whole mRNA message is translated into a sequence of amino acids.

Table of DNA and RNA- DNA: More stable, Two strands, Thymine, In 2C there is an H (deoxyribose), Single function, One 3D structure. RNA: More stable, One strand, Uracil, In 2C there is an OH (ribose), More functions, Different 3D structures. RNA (Ribonucleic Acid): Types

• Messenger RNA (mRNA): it is a linear strand with 5’------ 3’ polarity, which carries DNA message to the ribosomes to be transformed into proteins. The process by which DNA information is copied into mRNA is called Transcription.
• Transfer RNA (tRNA): transports the amino acid to the ribosome to include it in the new protein.
• Ribosomal RNA (rRNA): it is a structural component of the ribosomes, organelles which transform mRNA message into proteins. The template strand is from: 3-----5, The coding strand is from: 5--- 3 and the mRNA is: 5----3.