Cell BIO Exam 2

Transcription of DNA to RNA

Overview of Gene Expression

• Gene expression is the process of turning DNA into protein through multiple steps.
• A DNA must be accessible for RNA polymerase to make an RNA copy.
• Transcription is the process of transcribing a piece of DNA into RNA.
• In eukaryotes, there are extra processing steps after transcription.
• After RNA is made, processing occurs before it is exported to the cytoplasm.
• In the cytoplasm, mRNA is used to make a protein.

Eukaryotic vs. Prokaryotic Transcription

• Transcription is similar in eukaryotes and prokaryotes, but eukaryotes have extra processing steps.
• In eukaryotes, RNA synthesized is called pre-messenger RNA, which is immature and needs processing.
• In prokaryotes, DNA acts as a template to make mature messenger RNA, which is directly used to make proteins.
• In prokaryotes, transcription and translation can occur simultaneously, called coupling, making it simpler than eukaryotic transcription.

The Transcription Process

• Transcription involves making an RNA complementary to the DNA.
• Template DNA is directly involved in RNA synthesis.
• The non-template strand is referred to as the coding strand.

DNA Template

• During transcription, only one of the two DNA strands is involved.
• The start of transcription on the DNA is the 3' end on the template DNA, where RNA polymerase binds.
• Multiple RNA polymerases transcribe the same DNA simultaneously.
• New RNA nucleotides are added to the 3' end.
• RNA and template DNA are antiparallel: if the RNA end is 5', the corresponding template end is 3'.

How RNA Polymerase Recognizes the Start of a Gene

• RNA polymerase needs to recognize the start of a gene to make an RNA out of specific genes or operons.
• This is done by locating a specific sequence on the template DNA called the promoter.
• Promoter sequences are in both eukaryotic and prokaryotic systems.
• In bacterial systems, these are represented by two different sections in the DNA.
• RNA polymerase needs the help of a protein called sigma factor to recognize promoters.
• Sigma factor helps RNA polymerase recognize the promoter on the gene.
• Once promoters are recognized, RNA polymerase slides downstream and starts transcription at the transcription start site, usually referred to as +1.

Termination of Transcription

• Terminator sequences at the end of the gene tell RNA polymerase to stop.
• Terminator sequences get transcribed and become part of the RNA.
• Example: Gene bio b with a promoter sequence before the start of the gene (+1).
• RNA sequence is complementary to the DNA template, with uracil (U) replacing thymine (T).
• The first transcribed nucleotide is the 5' end of the RNA.
• In bacterial transcription, the transcribed region contains the terminator sequence but not the promoter.

Eukaryotic Transcription

• In eukaryotic cells, promoters are specific sequences, such as -35 and -30 regions upstream of the start site.
• Sometimes, promoter sequences are found downstream within the gene, meaning some promoters will be part of the RNA. If this is the case, then questions asking about eukaryotic cells will be false.
• Transcription of eukaryotic genes is very complex, involving many proteins.
• The template is associated with RNA polymerase and many proteins.
• More than 200 proteins can be involved.
• Regulatory DNA sequences are also involved in transcription.
• These are recognized by transcription factors, regulators, and mediators.
• A protein (TF2D) binds to the double-stranded DNA.
• TF2D has a TATA-binding protein (TBP) that recognizes the TATA box promoter sequence.
• TF2D recruits other transcription factors like TF2B.
• RNA polymerase II recognizes the start of transcription with the help of these proteins.
• The RNA made is usually pre-messenger RNA, which needs to be processed.

Processing of Eukaryotic Pre-mRNA

• The 5' end of the RNA is capped for protection.
• The 3' end has multiple adenines (A) attached, called a poly-A tail, usually between 150 and 250 A's.
• RNA splicing removes parts of the RNA that will not be used to make a protein.
• RNA splicing involves many proteins, some carrying RNA called SNURBS.
• SNURBS help the protein bind to the RNA that needs to be spliced.

RNA Splicing

• Splicing joins exons together by removing introns.
• The removed intron forms a lariat structure.
• Multiple introns can be removed at the same time.
• Alternate splicing produces different messenger RNAs from the same gene by selectively removing different exons.
• Alternate splicing creates multiple different mRNAs by removing varying combinations of exons.
• Skipping of exons is allowed, but there is no rearrangement of the order of exons.
• Alternate splicing allows for the production of a larger number of proteins than the number of genes in the genome.
• Different cells can produce slightly different proteins from the same gene through alternate splicing. Fibroblast and hepatocytes produce fibronectin.

Export and Translation

• After processing, mature messenger RNA is exported out of the nucleus into the cytosol or cytoplasm.
• Transport through the nuclear pore is an intricate process involving multiple proteins.
• Once in the cytosol, the RNA is protected by its 5' cap and 3' tail.
• Initiation factors bind to the 5' end to help ribosomes bind to the mRNA, initiating translation.

Comparison with Prokaryotic Transcription

• Eukaryotic and prokaryotic transcriptions are similar.
• The processing of RNA (capping, poly-A tail, splicing) is not found in prokaryotes.