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Transcription and Translation
How are Genes Expressed?
Gene expression is the process by which DNA directs the synthesis of proteins (or, in some cases, just RNAs). The expression of genes that code for proteins includes 2 stages: transcription and translation. Not all proteins are enzymes (ex. keratin, the structural protein of animal hair & insulin).
Just as specific sequences of letters communicate information in a language like English, both nucleic acids and proteins are polymers with specific sequences of monomers that convey information. The monomers in DNA or RNA are 4 types of nucleotides, which differ in their nitrogenous bases. Genes are typically hundreds or thousands of nucleotides long, each gene having a specific sequence of nucleotides. Each polypeptide of a protein also has monomers arranged in a particular linear order, but its monomers are amino acids.
How do Prokaryotes and Eukaryotes Differ?
There is a difference in the flow of genetic information within the cells.
Bacteria do not have nuclei, so nuclear membranes do no separate bacterial DNA and mRNA from ribosomes and other protein-synthesizing equipment.
This lack of compartmentalization allows translation of an mRNA to begin while its transcription is still in progress.
Eukaryotic cells DO have nuclei.
The presence of a nuclear envelope separates transcription from translations in space and time.
Transcription occurs in the nucleus, but the mRNA must be transported to the cytoplasm for translation.
What is Transcription?
Transcription occurs in all organisms.
Transcription is the synthesis of RNA using information in the DNA.
The two nucleic acids are written in different forms of the same language, and the information is simple transcribed, or “rewritten,” from DNA to RNA.
DNA strand serves as a template for assembling a complementary sequence of RNA nucleotides.
This type of RNA molecule is called messenger RNA (mRNA) b/c it carries a genetic message from the DNA to the protein-synthesizing machinery of the cell.
Before eukaryotic RNA transcripts from protein-coding genes can leave the nucleus, they are modified in various ways to produce the final, function mRNA.
The transcription of a protein-coding eukaryotic gene results in pre-mRNA, and further processing yields the finished mRNA.
The primary transcript, also called pre-mRNA, is an initial RNA transcript from any gene. Can refer to tRNA, rRNA, or mRNA.
For each gene, only one of the two DNA strands is transcribed.
This strand is called the template strand, b/c it provides the pattern, or template, for the sequence of nucleotides in an RNA transcript.
For any given gene, the same strand is used as the template every time the gene is transcribed.
The strand that is used as a template is determined by the orientation of the enzyme that transcribes genes.
Depends on the particular DNA sequences associated with each particular gene.
RNA polymerase runs on the template strand of DNA in the 3’ → 5’ direction but synthesizes mRNA in the 5’ → 3’ direction, just like DNA polymerase.
An mRNA molecule is complementary rather than identical to its DNA template b/c RNA nucleotides are assembled on the template according to base-pairing rules.
Like a new strand of DNA, the RNA molecule is synthesized in an antiparallel direction to the template strand of DNA.
Ex. Template strand runs (3’ → 5’), then the mRNA strand runs from (5’ → 3’).
Specific sequences of nucleotides along the DNA mark where transcription of a gene begins and ends.
The DNA sequence for RNA polymerase to attach to and initiates transcription is called promoter.
In bacteria, the sequence that ends transcription is called the terminator
Transcription moves in the “downstream” direction, and thus the promoter sequence in DNA is said to be upstream from the terminator.
The stretch of DNA downstream from the promoter that is transcribed into an RNA molecule is called a transcription unit.
The promoter of a gene includes within it the transcription start point - the nucleotide where RNAP begins synthesizing the mRNA - and typically extends several dozen or more nucleotide pairs upstream from the start point.
In eukaryotes, a collection of proteins called transcription factors mediate the binding of RNAP and the initiation of transcription.
The transcription initiation complex is the completed assembly of transcription factors and RNA polymerase bound to a promoter.
TATA box is a crucial promoter DNA sequence that plays a role in forming the initiation complex at a eukaryotic promoter.
The Promoter is the landing pad for RNA polymerase and transcription factors.
The Start Point is the first nucleotide that gets copied into RNA.
The Transcription Unit is the full DNA segment that is transcribed, including the coding region.
Transcription Factors help initiate the process by guiding RNA polymerase to the promoter.
As RNAP moves along the DNA in a process called elongation, it untwists the double helix, exposing 10-20 DNA nucleotides at a time.
The enzyme adds nucleotides to the 3’ end of the growing RNA molecule.
As the process continues, the new RNA molecule peels away from the DNA template
At the same time, the DNA double helix re-forms
Many RNA polymerases can be working on the same gene simultaneously, increasing the amount of mRNA produced from a single gene.
This means more protein can be produced
This is important because proteins need to be produced in large amounts (i.e. enzymes & structural proteins)
The mechanism of termination differs between bacteria and eukaryotes.
Bacteria needs a terminator sequence in the DNA, which acts as a termination signal for the RNAP to detach from DNA and release the transcript (requires no further modification before translation).
In eukaryotes, RNAP transcribes a sequence on the DNA called polyadenylation signal sequence (AAUAAA), which is recognized by proteins that bind to the RNA. These proteins will then cut the mRNA free from RNAP.
How is mRNA Prepared to Transition into Translation?
Enzymes in eukaryotic nucleus modify the pre-mRNA before the genetic message is dispatched to the cytoplasm.
Both ends of the mRNA is altered in this method of RNA processing
At the 5’ end, which is synthesized first, received a 5’ cap, a modified form of guanine nucleotide added onto the 5’ end after the first 20-40 nucleotides have been transcribe.
The 3’ end is modified after exiting the nucleus.
An enzyme adds 50-250 more adenine nucleotides to the AAUAAA sequence, forming a poly-A tail.
Functions of the 5’ cap and poly-A tail:
Help facilitate the export of the mature mRNA from the nucleus.
Help protect mRNA from degradation by hydrolytic enzymes.
Help ribosomes attach to the 5’ end of mRNA
The untranslated regions (UTRs) at the 5’ and 3’ end of mRNA do not get translated into protein, but they help with ribosome binding.
Sequence of DNA nucleotides that codes for a polypeptide are not continuous, but are split into segments.
Noncoding segments are called introns.
Exons are segments that will be eventually translated and expressed.
During RNA splicing, introns are removed from the mRNA and the exons join together.
This transforms the mRNA into a continuous coding sequence.
Removal of introns is done by a large complex made of proteins and small RNAs called a spliceosome.
This binds to the introns, which releases them, and the introns are rapidly degraded.
Afterwards, the spliceosome joins together the two exons.
What is Translation?
Translation occurs in all organisms.
Translation is the synthesis of a polypeptide using the information in the mRNA.
During this stage, there is a change in language.
The cell must translate the nucleotide sequence of an mRNA molecule into the amino acid sequence of a polypeptide.
The sites of translation are ribosomes, molecule complexes that facilitate the orderly linking of amino acids into polypeptide chains.
During translation, the sequence of codons along an mRNA molecule is decoded/translated, into a sequence of amino acids making up a polypeptide chain.
They are read by the translation machinery in the 5’ → 3’ direction.
Each codon specifies which one of the 20 amino acids will be incorporated at the corresponding position along a polypeptide.
The translator between the mRNA and amino acid language is the transfer RNA (tRNA).
Its function is to transfer amino acids from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome.
The anticodon is the nucleotide triplet at one end of a tRNA molecule that base-pairs with a particular complementary codon on an mRNA molecule.
Codon chart reads off of the mRNA codons, not the anticodon
Ribosomes read the mRNA codons, not the anticodon
What is the Function of Codons?
There are four nucleotide bases to specify 20 amino acids.
Only 4 amino acids could be specified, one per nucleotide base.
Since there are four possible nucleotide bases in each position, this would give us 16 (that is, 4²) possible arrangements.
This is still not enough to code for all 20 amino acids.
Triplets of nucleotide bases are the smallest units of uniform length that can code for all the amino acids.
If each arrange is 3 consecutive nucleotide bases specifies an amino acid, there can be 64 (that is, 4³)
This is more than enough to specify all the amino acids.
A triplet code is a genetic information system in which a series of three-nucleotide-long words specifies a sequence of amino acids for a polypeptide chain.
The mRNA nucleotide triplets are codons, a three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal.
It is the basic unit of the genetic code.
Written in the 5’ → 3’ direction.
The term codon is also used for DNA nucleotide triplets along the non-template strand.
These codons are complementary to the template strand & thus identical in sequence to the mRNA.
61 of the 64 triplet codons code for amino acids.
The other three codons act as “stop” signals, or termination codons, marking the end of translation.
The codon AUG has duel functions:
1.) Codes for the amino acid methionine (Met, or M)
2.) Functions as a “start” signal, or initiation codon.
AUG signals the protein-synthesizing machinery to begin translating the mRNA at that location.
Because AUG also stands for methionine, polypeptide chains all begin with Met when they are synthesized.
But an enzyme may subsequently remove this starter amino acid from the chain.
