How proteins and enzymes are synthesized

Protein Synthesis

Gene expression

This  is  the  process  by  which  the genetic  code  -  the  nucleotide  sequence  -  of  a gene  is  used  to  direct  protein  synthesis  and produce  the  structures  of  the  cell.  Genes  that code  for  amino  acid  sequences  are  known  as 'structural genes'. 

The  process  of  gene  expression  involves  two main stages: 

-Transcription
-Translation

Transcription:  the  production  of  messenger RNA  (mRNA)  by  the  enzyme  RNA  polymerase, and  the  processing  of  the  resulting  mRNA molecule. 

Translation:  the  use  of  mRNA  to  direct  protein synthesis, and  the  subsequent  post-translational processing of the protein molecule. Some  genes  are  responsible  for  the  production of  other  forms  of  RNA  that  play  a  role  in translation,  including  transfer  RNA  (tRNA)  and ribosomal RNA (rRNA). 

 Gene Control Sites

  Start site. A start site for transcription.   

  A promoter. A region  a few hundred nucleotides  'upstream' of the gene (toward the  5' end). It is  not transcribed into  mRNA, but plays a role in controlling the transcription  of the  gene. Transcription factors bind to  specific nucleotide sequences  in the promoter region  and assist  in the binding of RNA polymerases. 

  Enhancers. Some transcription factors (called activators) bind to  regions called 'enhancers' that increase the  rate  of transcription. These  sites may be thousands  of nucleotides from the coding sequences or within an intron. Some enhancers are conditional and only work in  the presence of other factors as  well as transcription  factors. 

  Silencers. Some transcription factors (called repressors) bind  to regions  called 'silencers' that depress the rate  of transcription. 

Note:  The  term  'gene  expression'  is  sometimes used to  refer  to  the transcription  phase alone. 

Coded RNA includes;

  Exons. Exons code for amino acids and collectively  determine the amino  acid sequence  of  the protein product. It is these  portions  of the gene that are represented  in final mature mRNA molecule.

  Introns. Introns  are  portions  of  the gene that do not  code for amino acids, and are  removed (spliced) from the mRNA molecule before  translation.


Molecular basis of gene expression

  Transcription


This  is  the  process  of  RNA  synthesis, controlled  by  the  interaction  of  promoters  and enhancers.  Several  different  types  of  RNA  are produced,  including  messenger  RNA  (mRNA), which  specifies  the  sequence  of  amino  acids  in the  protein  product,  plus  transfer  RNA  (tRNA) and  ribosomal  RNA  (rRNA),  which  play  a  role  in the translation process.

Transcription involves four steps:

1.  Initiation. The DNA molecule unwinds and separates to  form a  small  open complex. RNA polymerase binds to the promoter of the  template strand.

2.  Elongation. RNA polymerase moves along  the template  strand, synthesising an mRNA molecule. In prokaryotes RNA polymerase is a holoenzyme  consisting of a number of subunits, including a sigma factor  (transcription factor)  that recognises the promoter. In eukaryotes there are three RNA polymerases:  I,  II and III. The process  includes a proofreading mechanism.

3.  Termination. In prokaryotes there are two ways in  which transcription is terminated. In  Rho-dependent termination, a protein factor called "Rho"  is responsible for  disrupting the complex involving the template strand, RNA polymerase and RNA molecule.  In Rho-independent  termination, a loop forms at the end of  the  RNA molecule, causing it to detach itself.  Termination in eukaryotes is more  complicated, involving  the  addition of additional adenine nucleotide at the 3'  of the  RNA transcript (a  process referred to  as polyadenylation). 

4.  Processing. After transcription the RNA molecule is  processed in a number of ways:  introns are removed and the exons  are  spliced together  to form a mature mRNA molecule consisting  of a single protein-coding sequence. RNA synthesis involves the normal base pairing rules, but the base thymine is replaced with the base  uracil. 

  Translation 

In  translation  the  mature  mRNA  molecule  is used  as  a  template  to  assemble  a  series  of amino  acids  to  produce  a  polypeptide  with  a specific  amino  acid  sequence.  The  complex  in the  cytoplasm  at  which  this  occurs  is  called  a ribosome.  Ribosomes  are  a  mixture  of ribosomal  proteins  and  ribosomal  RNA  (rRNA), and  consist  of  a  large  subunit  and  a  small subunit.

Translation involves four steps: 

1. Initiation. The small subunit of the ribosome binds at the 5' end of  the  mRNA molecule and  moves  in a  3' direction until it meets a start codon  (AUG). It then forms a complex with the large unit of  the ribosome complex and an initiation tRNA molecule. 

2. Elongation. Subsequent codons on the mRNA molecule  determine which tRNA molecule linked to an amino acid binds to  the mRNA. An  enzyme  peptidyl transferase links the amino acids together using peptide bonds. The process continues, producing a chain  of amino acids as  the ribosome moves along the  mRNA molecule. 

3. Termination. Translation  in terminated when the  ribosomal complex  reached one or more stop codons  (UAA, UAG, UGA).  The ribosomal complex  in eukaryotes is  larger  and more complicated than in prokaryotes. In addition, the processes  of transcription and translation are divided in  eukaryotes  between the nucleus  (transcription) and the  cytoplasm (translation), which provides more opportunities for the regulation  of gene expression.   

4.  Post-translation  processing of  the protein 

  Gene regulation

This is a label for the cellular processes that control the rate  and manner of  gene  expression.  A complex set of  interactions  between genes,  RNA molecules,  proteins (including transcription factors) and other components of  the expression system determine  when and where specific genes are activated and the amount of protein  or RNA product produced. 

  Some genes  are  expressed continuously, as they produce proteins  involved in basic metabolic functions; some genes are  expressed as part of the process of cell differentiation; and some genes are expressed as a result of  cell differentiation. Mechanisms  of gene regulation  include: 

  Regulating the rate of transcription.  This is the most economical  method of regulation. 

  Regulating the processing  of RNA molecules, including alternative splicing to produce  more than one protein product  from a single gene. 

  Regulating the stability  of mRNA molecules. 

  Regulating the rate of translation. Transcription  factors  are  proteins  that  play  a role  in  regulating  the  transcription  of  genes  by binding  to  specific  regulatory  nucleotide sequences.