Question

1. How does transcription and translation differ in Eukaryotes and in prokaryotes.

2. How is DNA transcription different from prokaryotes and Eukaryotes?

3. What is a gene?

Answer 1

1. Location: Eukaryotic transcription occurs in the nucleus while prokaryotic transcription occurs in the cytoplasm (by virtue of the fact they don’t have a nucleus). Because of this, transcription and translation often occur simultaneously in prokaryotes. This isn’t possible in eukaryotes because the mRNAs must be exported from the nucleus before ribosomes can get at them.

• RNA Polymerase: Prokaryotes have one RNA polymerase that handles all transcription while eukaryotes have 3. The prokaryotic RNA polymerase is much simpler structurally than the eukaryotic polymerases.
• Initiation: Transcription initiation is also much simpler in prokaryotes. Prokaryotes have different proteins called σσ factors which bind to promoter sequences and start transcription (they are part of the RNA polymerase, which is often considered as its “core” polymerase + a σσ factor). Different σσ factors bind different promoters and are responsible for a different set of genes, often functionally related. An expression is highly regulated at this level. In eukaryotes, the RNA polymerase itself can’t actually initiate transcription. Instead, a variety of other proteins and transcription factors are required to help recruit the RNAP to the promoter (this is partly because eukaryotic DNA is coiled around histones so needs to be “opened up” for a polymerase to bind it). B/c of the variety of factors at play, regulation is also much more complex.
• Termination: Prokaryotic termination is relatively simple with only two different mechanisms, Rho-dependent, and Rho-independent termination. In eukaryotes, termination is dictated by a terminator sequence and a poly-A signal. In addition, I believe each of the 3 eukaryotic polymerases has different mechanisms of termination.
• mRNA structure: This may sort of bleed into translation stuff but prokaryotic transcripts are often polycistronic, meaning a single transcript encodes multiple proteins (ribosomes can bind in the middle of a transcript). Prokaryotic mRNAs also don’t usually have a 5′ cap and poly-A tail the way eukaryotes do. They protect their mRNAs from RNase degradation by coupling transcription to translation. That being said, prokaryotic mRNAs do usually have higher turnover rates. In contrast, eukaryotic transcripts typically encode a single protein, as translation initiation requires a 5′ cap for the ribosome to recognize. They also have a poly-A tail and generally, have more extensive mRNA processing. For example, prokaryotes don’t usually have introns while they are frequently present in eukaryotes, thus requiring “splicing” in eukaryotes.

2. Eukaryotes and prokaryotes follow a common path through transcription. For instance, both go through an initiation, elongation, and termination phase. There are some conserved domains that are found between prokaryotic polymerase and eukaryotic polymerase II. For instance the bridge helix, which is involved in translocation of the Polymerase in prokaryotes and eukaryotes, is conserved, however, the bridge helix in prokaryotes is always bent whereas the bridge helix is straight in eukaryotes⁶. Another conserved domain is the rudder (the loop that is closest to the active center). The active center is also conserved in both prokaryote and eukaryotes. There are however some marked differences between the two. Prokaryotic transcription is much simpler than eukaryotic transcription. For instance, prokaryotes have only one RNA polymerase that carries out the complete process of transcription. Eukaryotes, on the other hand, have three polymerases (Pol I, Pol II, and Pol III) that carry out different processes involved in the synthesis of proteins. Furthermore, each eukaryotic polymerase carries out its necessary functions at different locations in the cell. Prokaryotic transcription is carried out in the cytoplasm, where transcription is coupled with translation

• 1. In eukaryotes, one mRNA = one protein.
  (in bacteria, one mRNA can be polycistronic, or code for several proteins).

  2. DNA in eukaryotes forms a stable, compacted complex with histones. In bacteria, the chromatin is not in a permanently condensed state.

• 3. Eukaryotic DNA contains large regions of repetitive DNA, whilst bacterial DNA rarely contains any "extra" DNA.

• 4. Much of eukaryotic DNA does not code for proteins (~98% is non-coding in humans); in bacteria often more than 95% of the genome codes for proteins.

  5. Sometimes, eukaryotes can use controlled gene rearrangement for increasing the number of specific genes. This happens rarely in bacteria.

  6. Eukaryotic genes are split into exons and introns; in bacteria, genes are almost never split.

  7. In eukaryotes, mRNA is synthesized in the nucleus and then processed and exported to the cytoplasm; in bacteria, transcription, and translation can take place simultaneously off the same piece of DNA.

3. Gene, unit of hereditary information that occupies a fixed position (locus) on a chromosome. Genes achieve their effects by directing the synthesis of proteins. A gene is the basic physical and functional unit of heredity. Genes are made up of DNA. Some genes act as instructions to make molecules called proteins.  Every person has two copies of each gene, one inherited from each parent. Most genes are the same in all people, but a small number of genes (less than 1 percent of the total) are slightly different between people. Alleles are forms of the same gene with small differences in their sequence of DNA bases. These small differences contribute to each person’s unique physical features.