Making polypeptides
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DNA is more or less inert, it acts simply to store information.  For that information to be used, it must be transformed first into RNA; this process is known as transcription. 

It is called transcription because there is no "change in language"; information is encoded through the sequence of bases in both DNA and RNA.  Transcription is mediated by DNA-dependent, RNA polymerases.

When the information is to be used to produce a polypeptide, the RNA is known as a messenger RNA or mRNA.    The information in the mRNA will then be translated from a nucleotide into polypeptide sequence. 

The sequence of nucleotides is related to the final sequence of the polypeptide by the genetic code.   The genetic code is not the information itself, but the algorithm by which nucleotide sequences encode polypeptide sequences.

The code consist of codons, which are nucleotides, read three at a time. 

Since there are 4 possible nucleotides, there are 43 (or 64) possible codons. 

Since cells only use 20 amino acids, the code is redundant - certain amino acids are encoded for by more than one codon. 

  
There are also three codons, UAA, UAG and UGA that do not encode an amino acid, and act as "stops" or periods. 
 

 

In general (but not always), the first AUG in the mRNA, which encodes the amino acid methionine, serves to mark the start of translation. 

There are a number of hypotheses on the origin of the genetic code, from the frozen accident model, to one in which interactions between RNAs and amino acids play an important role.
 

Whichever is the case, it is clear that the genetic code is nearly universal, and in those organisms (and organelles) where it is different, the differences are minor (see here). 

It would seem that the genetic code is a homologous trait between all organisms. 

 

 
  • How can DNA be inert, and yet store information? 
  • What does it mean to say the genetic code is an algorithm?
  • What types of gene products does DNA encode?
 

Translation involves a complex cellular organelle, the ribosome, which together with a number of accessory factors, including transfer  or tRNAs, reads the code in an mRNA and produces the appropriate polypeptide.

  
 

Ribosomes are composed of roughly equal amounts of ribosomal RNA (rRNA) and ribosomal polypeptides.  An active ribosome is composed of a small and a large ribosomal subunit. 

The complete ribosome has a molecular weight of ~3 x 106 daltons.  A catalytic rRNA, a ribozyme, lies at the heart of the ribosome - it catalyzes the addition of amino acids to the growing polypeptide chain. 

 
 

The cytoplasm of cells is packed with ribosomes. In rapidly growing bacterial cell, approximately 25% of total cell mass is ribosomes.

Although structurally similar, there are characteristic differences between the ribosomes of bacteria and eukaryotes.

This is important from a practical perspective.  For example, a number of antibiotics selectively inhibit translation by bacterial, but not eukaryotic translation.

Both chloroplasts and mitochondria have ribosomes of the bacterial type.

This is yet another piece of evidence that chloroplasts and mitochondria are descended from bacterial endosymbionts.

A David S. Goodsell image.

 

The small and large subunits of the ribosome remain separated until they find an mRNA.

Together with accessory factors, they associate with an mRNA and assemble into a functional ribosome, which then translates the mRNA.

When the ribosome reaches the end of the region of the RNA that encodes the polypeptide (defined by a stop codon), it is released, disassembles and is ready to start another cycle.

  
 
 

A key translation accessory factors are the transfer RNAs or tRNAs.

These are small, L-shaped RNAs.  There are specific tRNAs for each amino acid.  For example, a tRNA specific for phenylalanine would be written tRNAPhe.

Enzymes, amino acyl tRNA synthetases, recognize specific tRNAs and catalyze the attachment of the appropriate amino acid to the tRNA's acceptor stem.

A codon in an mRNA are recognized by the anticodon in the tRNA molecule.
 
 

Initiating translation: To make the correct polypeptide, the ribosome must start translating an mRNA at a specific point, the start codon.  

The initial amino acid of the polypeptide in almost always a methionine and is encoded by a start codon (AUG).

Similarly, the end of the polypeptide is marked by a stop codon (UGA, UAA or UAG).

Accessory factors are associated with translation initiation, elongation and termination.

A tRNA associated with the elongation factor TU (EF-TU)

  

 
 

The mRNA moves through the ribosome, bringing one codon after another into place.

These are recognized by the amino acid-charged tRNAs.

 

Once in place, the ribosome catalyzes the formation of a peptide bond and the transfer of the growing or nascent polypeptide to the newly arrived amino acid-charged tRNA and the release of the now uncharged tRNA.

  

Here is a nice
translation tutorial
 
 

This process uses energy both to move the mRNA through the ribosome and to form the peptide bonds.

There are no tRNAs that recognize stop codons, so when the ribosome reaches a stop codon, it stalls as it waits for a charged tRNA, which will never arrive. 

Instead, a polypeptide known as a release factor, which looks very much like a tRNA, can bind instead.

This leads to the release of the polypeptide from the ribosome, and the disassembly of translation complex.

 
  • Aside from mRNA, which RNAs are involved in protein synthesis? 
  • Are these gene products?
  • How, in the most basic terms, do different tRNAs differ from one another?
  • How many different tRNA-amino acid synthetases do you think there must be in a cell?  
  • What could happen if a ribosome started translating an mRNA at the "wrong" place? 
  • Why doesn't the presence of release factor in the cell cause the premature termination of translation at non-stop codons?
  • Do you think release factors look like tRNAs by chance, or is there a reason?  
Use Wikipedia | revised 20-mar-08