A length of DNA which contains the instructions for making a single protein or polypeptide is called a gene. A group of three bases, called a triplet, codes for one amino acid.
Transcription: Can be divided into more phases.
Phase 1: Initiation – Transcription factors(proteins) and RNA-Polymerase recognize specific DNA sequences, called promoters1, only to begin DNA synthesis in the direction 5′ to 3′.
NOTE: Only one strand is used, – the template strand – the 3′ -> 5′ strand.
Step 1. DNA Unwinds
Step 2: Hydrogen bonds between complimentary bases bases break.
Step 3: The enzyme RNA-polymerase II catalyses the synthesis of DNA. When a free nucleotide moves randomly next to an exposed base complementary to it, Hydrogen bonding occurs. This happens in the GI (Growth I) phase of the cell cycle.
Phase 2: Elgongation – RNA-Polymerase II synthesises a new strand according to base complementarity, the mRNA strand. The T(Thymine) bases on the DNA are now U(Uracil). At any given time, there could be dozens of polymerases comping the same length of DNA.
Incoming ribonucleoside triphosphates (ATP, CTP, UTP and GTP) provide the energy needed to drive this reaction forwards.
Step 4: The newly bonded nucleotide is joined to the growing mRNA molecule by phosphodiester bonds.
Phase 3: Termination – RNA-Polymerase recognises a specific DNA length, called a terminator2, and releases itself from DNA.
Step 5: The DNA molecule returns to the double helix, while the single stranded mRNA molecule is released. The mRNA molecule will be transported from within the nucleus, through the nuclear pores, into the cytoplasm – where translation of this gene into a protein will occur -.
Gene Expression = processes by which the information coded in a DNA sequence is translated into a product that has some effect on a cell or organism.
This part fits between Steps 1 and 2.
Eukaryotic RNA Polymerase requires General Transcription factors. Those are accessory proteins that assemble on the promoter, where they position the RNA polymerase and pull apart the DNA double helix to expose the double strand.
– The assembly process begins with the binding of the general transcription factor TTFIID to a short segment of DNA double helix composed primarily of T and A nucleotides; Because of its composition this part of the promoter is know as the TATA box.
This whole assembly of proteins on the promoter is called a transcription initiation complex.
To be translated, mRNA has to be exported to the cytoplasm. Before this happens it undergoes some changes: RNA capping, splicing and polyadenylation. The enzymes that take part in those processes are attached to RNA polymerase.
At this stage, the unprocessed mRNA is called pre-RNA.
- RNA capping – A methylated guanine nucleotide is added to the 5′ end.
- Polyadenylation refers to the addition of a series of Adenine(about 200) nucleotides to the 3′ end of mRNA.
Both those processes are meant to stabilize E.K. mRNA.
The last process a pre-mRNA molecule has to undergo is splicing. Coding mRNA is interrupted by long, non-coding, intervening sequences called introns.
RNA Splicing – Removal of introns by enzymes called snRNP (small ribonucleoprotein particles). The family of snRNAs that carry out splicing can be referred to as a spliceosome.
Only mature mRNA molecules are transported out of the nucleus, by a selective transport system mediated by NPCs (Nuclear pore complexes).
Waste RNA is degraded in the nucleus.
The types of RNA that can be produced during transcription can be:
- mRNA, messenger RNA, which encodes the genetic information required for making proteins
- rRNA, ribosomal RNA, which is a part of ribosomes
- tRNA, transfer RNA, which binds to specific amino-acids and holds them in place on the ribosome during translation
- snRNA, small nuclear RNA, which participates in RNA splicing during transcription
- microRNA and siRNA, interfering RNA, which are short sequences of non-coding RNA that mark RNA for destruction, thus regulating gene expression
- Xist, which is a long non-coding RNA whose role is to inactivate one copy of the chromosome X in women.
Translation: is the process of protein synthesis in the cell cytoplasm on the ribosome. It is called translation because the sequence of bases on the mRNA code is ‘translated’ into a sequence of amino-acids. It is also divided into three phases.
In translation, mRNA, tRNA and rRNA(or ribosome) are all required. mRNA is the template for making the protein and the ribosome is the site of translation. The role of tRNA is bringing amino-acid molecules to the site of translation.
Before use (protein synthesis) each amino-acid has to be linked to a specific transfer RNA. A specific enzyme will only link a particular amino-acid to a tRNA molecule(80 nucleotides long) with a particular anti-codon.
Phase 1: Initiation – The initiation begins as a tRNA molecule recognizes the codon3 AUG – coding for Methionine.
Step 1: mRNA moves into the cytoplasm and attaches to a ribosome. the first amino-acid tRNA binds to the firs codon by Hydrogen Bonding between complementary bases.
Phase 2: Elongation – During elongation, amino-acids are linked together and a polypeptide begins to form.
Step 2: Another amino-acid binds to the vacant codon in the ribosome.
Step 3: A peptide bond is formed between the attached amino acids
Step 4: As the mRNA moves through the ribosome, tRNA molecules which are not bound to amino acids are released. Another amino-acid tRNA binds to the vacant codon as in step 2 and steps 3 and 4 are afterwards repeated.
Phase 3: Termination – Steps 2, 3 and 4 in Phase 2 are repeated until a release factor (not tRNA) recognises a stop codon(UAA, UAG, or UGA) on the mRNA. A protein binding to the stop codon adds a water molecule to the end of the polypeptide chain. This causes the release of mRNA from the ribosome.
*It is to be noted that P.K. mRNAs usually carry multiple coding regions (multiple proteins) while, E.K. mRNAs carry only one.
- Cleavage of N-terminal of Methionine
- Cleavage of larger amino-acid blocks
- Phosphorylation/Dephosphorylation of the protein – acts as a switch between the active and inactive form of the protein.
- Glycolysation (sometimes) – Attaching of saccharide molecules to the polypeptide chain to form glycoproteins.
- Methylation or Acetylation of proteins
- Adding prosthetic groups or coenzymes.
Important notes about Translation:
- It is usual that multiple ribosomes (polyribosome or polysome) are attached to the same molecule of mRNA at the same time, and the rate of production of a certain protein is increased. Click to see an animation.
- Since there are four bases: Adenine, Guanine, Cytosine, and Uracil there are 64 existent triplets. However we know that there are only 20 amino acids. Therefore, an amino acid can be coded for by multiple different codons. This reduces the chance of a point mutation having a significant effect on the final polypeptide chain.
In an organism different genes are expressed in different cell types, even though they contain the same DNA. This is because of transcription factors – which makes the to differentiate.
Proteolysis – is a processes by which cells enzymatically break proteins down into their constituent amino acids. Proteolysis is used to regulate the amount of protein in each cell.
The enzymes involved in this processes are called proteases. They assemble into a complex called a proteasome, and act by hydrolyzing the peptide bonds.
Proteasomes only chop into bits the proteins that have been marked for destruction by a small protein called ubiquitin, reaction catalyzed by specialized enzymes.
Introns and Exons = Introns are DNA parts that are not coded for during translation, while exons are coded for. Usually introns make up 50% (+- 25%) of the whole gene. The same terms apply for pre-mRNA.
- Promoters are a length of DNA, present upstream a gene, that initiate translation. ↩
- Terminators are a length of DNA present at the end of a gene, which signals the end of transcription or translation. ↩
- A codon is a triplet on the mRNA molecule which code for one amino acid. An anti-codon is a triplet on the tRNA molecule complementary to a codon. ↩