Chapter 13: The Genetic Code and Transcription

The structure of DNA consists of a linear sequence of deoxyribonucleotides. This sequence dictates the components proteins, which are the end product of most genes. The question then becomes, how is this information decoded into a protein?

  1. The information present of one of the two DNA strands (template strand) is transferred into an RNA complement through the process of transcription. This RNA then acts as a messenger (mRNA) bearing the coded information.
  2. The mRNA then associates with ribosomes to decode the information and produce proteins in the process of translation.

13.1 The genetic code exhibits a number of characteristics

  1. Genetic code is written in linear form using the ribonucleotide bases of mRNA as its “letters” The RNA code is derived from the complementary bases of the template DNA.
  2. Each “word” of the RNA is written as a three letter code called a codon. This codon specifies one amino acid.
  3. The code is very clear and specifies one specific amino acid.
  4. The code is degenerate, meaning that more than one code can specify a particular amino acid.
  5. The code contains “start” and “stop” codons to initiate and terminate translation.
  6. Once translation begins, the codons are read one after another with no breaks in between.
  7. After translation starts, any single ribonucleotide at a specific location within the mRNA is part of only one codon.
  8. With minor exceptions, the same coding is used by almost all viruses, prokaryotes, archae, and eukaryotes.

13.4 The coding dictionary reveals several interesting patterns among the 64 codons

Deciphering the genetic code has revealed 61 triplet-codon amino acid assignments. The three remaining codons are termination signals and do not specify an amino acid.

The Ordered Nature of the Code

Chemically similar amino acids often share one or two “middle” bases in the triplet encoding them.

Hydrophobic amino acids, like valine and alanine, have either a U or C in their second position.

Hydrophilic amino acids, like serine or threonine, are specified with either a G or C in the second position.

Initiation, Termination, and Suppression

Experiments show that the initial amino acid inserted into all proteins is a form of methionine. Initiation is a highly specific process. Only one codon, AUG, codes for methionine and it is often termed the initiator codon.

Three other codons serve as termination codons (UAG, UAA, and UGA) but do not code for an amino acid. They are not recognized by the tRNA performing translation, so the process ends when they are reached.

13.8 Transcription synthesizes RNA on a DNA template

During the studies of DNA, it was clear that proteins were the products of many genes. The central question was, how DNA is able to specify a protein made of amino acids.

The process begins with the transfer of the information stored in DNA to RNA. This process is termed transcription. It results in an mRNA molecule complementary to the strand of DNA from which it was written. Each triplet in this mRNA is complementary to the anticodon of its corresponding tRNA. The tRNA inserts the correct amino acid during the process of translation.

Observations that led to the discovery of RNA as an intermediate include:

  1. DNA is associated with chromosomes in the nucleus of the cell, but protein synthesis occurs outside of the nucleus.
  2. RNA is synthesized in the nucleus of the cell and is chemically similar to DNA.
  3. Following synthesis, RNA migrates to the cytoplasm.
  4. The amount of RNA is proportional to the amount of new protein in the cell.

13.10 RNA Polymerase directs RNA synthesis

In 1959, the enzyme RNA polymerase was discovered. It has the same substrate requirements as DNA polymerase, but had the ribose sugar in it rather than the deoxyribose sugar. No primer is required to initiate synthesis.

Promoters and Template Binding

Transcription results in the synthesis of a single-stranded RNA molecule complementary to only one of the two DNA strands. The initial step is called template binding; in it, RNA polymerase subunits recognize specific DNA sequences called promoters. The helix becomes denatured and unwound locally, making the template accessible to the enzyme action. Transcription begins at the transcription start site.

Promoter sequences govern the efficiency of initiation and transcription. The type of promoter (strong or weak) determines the variation of initiation times. Mutations in these sites can lead to reducing or enhancing the initiation of gene expression.

Initiation, Elongation, and Termination of RNA Synthesis

Once it has bound to the promoter, RNA polymerase catalyzes initiation and the insertion of the first ribonucleotide at the start of the DNA template. Ribonucleotide complements are inserted and linked together as transcription proceeds. Chain elongation will proceed under the direction of an enzyme. Transcription will proceed down the entire gene until it encounters a specific nucleotide sequence that acts as a termination sequence. Termination sequences are especially important to prokaryotes because of the proximity of one gene’s end and the beginning of the next one.

13.11 Transcription in eukaryotes differ from prokaryotic transcription in several ways

Much of the knowledge of transcription comes from studies of prokaryotes. Most of the processes are similar, but some noticeable differences exist:

1. Transcription occurs in the nucleus under the direction of three separate forms of RNA polymerase

2. Initiation of transcription of eukaryotic genes requires the compact chromatin fiber be uncoiled and the DNA made accessible to the enzymes.

Initiation of Transcription in Eukaryotes

Eukaryotic RNA polymerase exists in three unique forms; each transcribes different types of genes. Each enzyme is larger and more complex than the prokaryotic form

*from another text

Protein Synthesis

A. Two main processes of protein synthesis.

1. Transcription - mRNA forms from the DNA code in the nucleus and moves to the

ribosome.

2. Translation - tRNA matches its anticodon the codons on mRNA creating an amino acid chain.

B. Transcription

1. Making RNA

2. One gene on a DNA strand “unzips” and is copied with RNA bases.

3. Transcription begins at a promoter on the DNA, a sequence of bases on the

DNA that tells the RNA to begin binding.

C. Translation - mRNA is translated into a protein.

1. mRNA arrives at the ribosome.

  • 3 bases of mRNA = codon

2. tRNA comes to a ribosome and its anticodon matches to codons on mRNA.

  • Each tRNA codon codes for a specific amino acid even though some codons may coded for the same amino acid.

3. Amino Acids break off to form protein