Cell Bio Test3

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In multicellar organism cells differ in morphology & function
Cell differences are due to

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different proteins made by the cells
Different proteins are due to different genes being expressed in different cells

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Different genes are expressed because of

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difference in regulatory elements in different cells or in the same cell at different times
These regulatory elements may be induced internally by the cell (e.g. ova) or induced from external signals (e.g. hepatocytes)
Involves control of transcription, post-transcriptional processing, translation, post-translational processing)

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The primary method of gene control in eukaryotes is

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control of transcription
Involves DNA sequences: promoters, promoter proximal elements, enhancers, silencers

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The primary method of gene control in eukaryotes is control of transcription involving:

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Proteins: RNA RNA Polymerase complex, general transcription factors, mediator complex, specific transcription factors (activators & repressors)
Process involves changing histone-DNA binding or stabilizing RNA Polymerase binding
Normally have multiple factors controlling transcription of a single gene

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3 RNA Polymerases

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RNA Polymerase I
RNA Polymerase III (RNA Pol III)
RNA Polymerase II (RNA Pol II)

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RNA Polymerase I

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(RNA Pol I) – synthesizes pre-rRNA in nucleolus

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RNA Polymerase III (RNA Pol III)

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– synthesizes tRNAs, 5S rRNA, many small stable RNAs
e.g., signal peptide recognition 7S RNA

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RNA Polymerase II (RNA Pol II)

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synthesizes mRNA (& some snRNAs)

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Yeast RNA Polymerases are

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the model Complex structure-2 large subunits (RPB1, RPB2), 10-14 small subunits

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RNA Polymerase II
RPB1 has a ?? domain

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carboxy-terminal
(Tyr-Ser-Pro-Thr-Ser-Pro-Ser)

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RPB1 has a carboxy-terminal:
Yeast has -- copies, mammals --At least --copies required for viability in yeast

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26 yeast
52 mammals
10 required for viability in yeast

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Phosphorylation occurs at

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Ser & Tyr during transcription

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RNA Polymerase II initiates transcription only when

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C-terminal domain is un-phosphorylated
Initiation site corresponds to the 5’ end of the mRNA on the base (usually Adenine) to which the cap is added

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RNA Polymerase subunits are either

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enzymes or they modulate binding to control elements including promoters

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Eukaryotic promoters

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Base sequences to which RNA Polymerase complexes bind

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In multicellar organism cells differ in morphology & function
Cell differences are due to

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different proteins made by the cells
Different proteins are due to different genes being expressed in different cells

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Different genes are expressed because of

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difference in regulatory elements in different cells or in the same cell at different times
These regulatory elements may be induced internally by the cell (e.g. ova) or induced from external signals (e.g. hepatocytes)
Involves control of transcription, post-transcriptional processing, translation, post-translational processing)

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The primary method of gene control in eukaryotes is

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control of transcription
Involves DNA sequences: promoters, promoter proximal elements, enhancers, silencers

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The primary method of gene control in eukaryotes is control of transcription involving:

Back 19

Proteins: RNA RNA Polymerase complex, general transcription factors, mediator complex, specific transcription factors (activators & repressors)
Process involves changing histone-DNA binding or stabilizing RNA Polymerase binding
Normally have multiple factors controlling transcription of a single gene

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3 RNA Polymerases

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RNA Polymerase I
RNA Polymerase III (RNA Pol III)
RNA Polymerase II (RNA Pol II)

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RNA Polymerase I

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(RNA Pol I) – synthesizes pre-rRNA in nucleolus

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RNA Polymerase III (RNA Pol III)

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– synthesizes tRNAs, 5S rRNA, many small stable RNAs
e.g., signal peptide recognition 7S RNA

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RNA Polymerase II (RNA Pol II)

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synthesizes mRNA (& some snRNAs)

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Yeast RNA Polymerases are

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the model Complex structure-2 large subunits (RPB1, RPB2), 10-14 small subunits

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RNA Polymerase II
RPB1 has a ?? domain

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carboxy-terminal
(Tyr-Ser-Pro-Thr-Ser-Pro-Ser)

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RPB1 has a carboxy-terminal:
Yeast has -- copies, mammals --At least --copies required for viability in yeast

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26 yeast
52 mammals
10 required for viability in yeast

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Phosphorylation occurs at

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Ser & Tyr during transcription

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RNA Polymerase II initiates transcription only when

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C-terminal domain is un-phosphorylated
Initiation site corresponds to the 5’ end of the mRNA on the base (usually Adenine) to which the cap is added

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RNA Polymerase subunits are either

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enzymes or they modulate binding to control elements including promoters

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Eukaryotic promoters

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Base sequences to which RNA Polymerase complexes bind

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Eukaryotic Promoters

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Close to start site (numbered +1)

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Eukaryotic Promoters --Usually 2 or more of four core sequences

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Usually 2 or more of four core sequences
TATA box (consensus sequence: 5’-TATA(A/T)A-3’)
TFIIB recognition element (BRE)
Downstream promoter element (DPE)

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TATA box (consensus sequence: 5’-TATA(A/T)A-3’)

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25-35 base pairs upstream from initiation site (-35 to –25)
Associated with actively transcribed genes
Bound by TATA box binding protein (TBP)

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TFIIB recognition element (BRE)

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Just upstream from TATA box
G & C rich

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Downstream promoter element (DPE)

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~+30
Binds TFIID

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Initiator sequences

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(usually C @ -1, A @ +1)
Degenerate (highly variable) seq. (5’-YYA+1N(T/A)YYY-3’)

Strength of promoter associated with base sequence

Binds TFIID

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CpG islands:

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groups of CGs 20-200 bases upstream from initiation site

Multiple alternative 5’ ends

Associated with housekeeping genes (intermediate metabolism for example) that are transcribed at a steady, but low rate

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Non-promoter control elements

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Promoter proximal elements

Enhancers/silencers

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Promoter proximal elements

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DNA sequences within 100-200 base pairs upstream of promoter that are 10-20 base pairs long
Associated with most genes (often cell type specific)
Spacing not critical if changes are <20 base pairs

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Enhancers/silencers

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Sequences that may be thousands of base pairs from start site (upstream, downstream or in introns within the controlled gene)
Made up of 10-20 base pair long regions that are binding sites for DNA binding proteins

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Transcription factors: activators & repressors

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Proteins that recognize & bind to specific DNA base sequences
Recognize sequences by inserting into the major groove
Base sequences are usually ~ 20 base pairs long (2 turns)

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Activators contain specific domains

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==DNA binding domains have the amino acid sequence that recognizes as specific enhancer sequence
==Activation domain activates transcription by binding co-factors or polymerase complex
==Protein-protein binding domain for those factors which form dimers
==Usually long flexible regions join domains

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Repressors bind to

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silencer sequences in the same way activators bind enhancers Repressors usually have 2 domains (DNA binding & repression domain)
==Can mix DNA binding regions with different activating or repression domains to get different results

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DNA binding domains

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Defined by structural features (motifs) allowing DNA binding

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Eukaryotic transcription factors are classified by

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DNA binding domain motif
Usually an α-helical region (recognition helix) that binds to specific base sequences
Orientation often comes from adjacent regions in tertiary structure