Gene Structure

Topics to be Covered
• Introduction
• Gene structure
–Promoter
–Terminator
–Splice site

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 Terminology
• Genome – entire
genetic material of an
individual
• Transcriptome – set of
transcribed sequences
• Proteome – set of
proteins encoded by the
genome

Terminology
• Only one strand of DNA serves as a
template for transcription.

• Different genes are transcribed from

different strands

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 From Gene to Protein

Eukaryotic Gene Structure

5’ - Promoter Exon1 Intron1 Exon2 Terminator – 3’
UTR splice splice UTR

transcription
Poly A

translation

protein

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 Prokaryotic Gene Structure
Promoter CDS Terminator
UTR UTR

Genomic DNA

transcription

mRNA

translation

protein
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Topics to be Covered
• Introduction
• Gene structure
–Promoter
–Terminator
–Splice sites

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 Promoter
• Promoter determines:

1. Which strand will serve as a template.

2. Transcription starting point.

3. Strength of polymerase binding.

4. Frequency of polymerase binding.

Prokaryotic Promoter
• One type of RNA polymerase.
• Pribnow box located at –10 (6-7bp)
• –35 sequence located at -35 (6bp)

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 Eukaryote Promoter
• 3 types of RNA polymerases are employed in
transcription of genes:
– RNA polymerase I transcribes rRNA
– RNA polymerase II transcribes all genes coding for
polypeptides
– RNA polymerase III transcribes small
cytoplasmatic RNA, such as tRNA.

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Eukaryote Promoter
• Goldberg-Hogness or TATA located at –30
• Additional regions at –100 and at –200
• Possible distant regions acting as enhancers or
silencers (even more than 50 kb).

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 Promoter

• Promoters sequences can vary

tremendously.
• RNA polymerase recognizes hundreds of
different promoters

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Promoter
• Strong promoter resemble the consensus
sequence.
• Mutations at promoter sites can influence
transcription.

Human gene
Beta globin
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 Promoter
• Conclusions:
1. Promoters are very hard to predict.

2. Promoter prediction must be organism-

dependent (and even polymerase-dependent).

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Termination Sites
• The newly synthesized mRNA forms a stem
and loop structure (lollipop).
• A disassociation signal at the end of the gene
that stops elongating and releases RNA
polymerase.
• All terminators (eukaryotes and prokaryotes)
form a secondary structure.

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 Termination Sites
• The terminator region pauses the
polymerase and causes disassociation.

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Splice Sites
• Eukaryotics only
• Removing internal parts of the newly
transcribed RNA.
• Takes place in the cell nucleus (hnRNA)

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 Splice Sites
• Conserved splice sites are shared by both
the exon and the intron.
• Different signals on the donor site (3’) and
on the acceptor site (5’).

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Splice Sites

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 Alternative splicing
• Different splice patterns from the same
hnRNA sequence. Different products from
the same gene
• Different organs, different stages of
development in the same cell.
• Exact splice sites are difficult to predict

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