Transcription

RNA polymerase reads in the ________

3' to 5' builds new strand 5' to 3'

pre-tRNA

A tRNA precursor containing additional transcribed bases at the 5' and 3' ends compared to the mature tRNA. Some pre-tRNAs also contain an intron in the anti-codon loop.

Operon

A unit of genetic function common in bacteria and phages, consisting of coordinately regulated clusters of genes with related functions.

Pribnow box

Also known as the -10 sequence, consists of a sequence TATAAT that is used as a promoter for DNA transcription.

Splicosome

An enzyme that splices introns out of RNA. Made of splicing factors. SF1

Rho-independent transcription termination

Once termination sequence is transcribed --> transcribed mRNA forms a hairpin (stem) loop (GC rich) followed by multiple *uracils* --> Causes RNAP termination and complex dissociates

Pol II promoters

-GC Box (-100 nt) proximal control element -CAAT box (-80 nt) proximal control element -TATA box (-30 nt) core promoter

RNA Polymerase in Prokaryotes

-One RNA polymerase only for all genes -Core-enzyme made up of 5 subunits, 2 large beta units, 2 alpha units, and 1 omega unit -When paired with a delta factor it becomes a Holo-enzyme

mRNA maturation

1. Addition of poly-A tail - increases stability of mRNA 2. Addition of 5' cap - facilitates binding of 5' end to ribosome 3. UTRs - sequence that does not encode any amino acids 4. Splicing/alternative splicing - removes noncoding introns. alternative splicing allows multiple proteins to be produced (different mRNAs can be produced from the same pre-mRNA) 5. Function of spliceosome (U proteins) - large protein complex that splices pre-mRNA, contains 5 sRNP particles

Capping of mRNA

1. The terminal γ-phosphate of the mRNA is hydrolyzed. 2. The GMP portions of GTP is added to the 5' diphosphate end of the mRNA. and pyrophosphate is released 3. S-adenosyl methionine (adoMet) methylates the guanine at position 7, releasing S-adenosyl homocysteine 4. The 2' hydroxyls of the 1st 2 riboses of mRNA are sometimes methylated 5. The completed "cap" binds a cap-binding complex (CBC), and mRNA can be accepted by ribosomes for translation. The cap/CBC are tethered to the CTD of RNA Pol II

TATA box

A DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex.

regularoty gene

A gene that codes for a protein, such as a repressor, that controls the transcription of another gene or group of genes. Operons in prokaryotes (lactose operon)

general transcription factors

A set of proteins that bind to the promoter of a gene whose combined action is necessary for transcription. Detach after RNA pol II is added and has CTD phosphorylated

enhancers and silencers

Found upstream, within, or downstream of gene Enhancers increase transcription levels; silencers decrease them Modulate transcription from a distance Act to increase or decrease transcription in response to cell's requirement for gene product

poly-A tail

Modified end of the 3' end of an mRNA molecule consisting of the addition of some 50 to 250 adenine nucleotides. 5' end is also capped but not with poly A This serves to protect from 3'-5' exonuclease activity

RNA splicing

Process by which the introns are removed from RNA transcripts and the remaining exons are joined together.

catabolite activator protein (CAP)

Protein that functions in catabolite repression. When bound with cAMP, CAP binds to the promoter of certain operons and stimulates transcription.

RNA polymerase in Eukaryotes

RNA polymerase I - rRNA RNA polymerase II - mRNA (coding genes) RNA polymerase III - tRNA

alternative splicing

Splicing of introns in a pre-mRNA that occurs in different ways, leading to different mRNAs that code for different proteins or protein isoforms. Increases the diversity of proteins.

CTD of RNA Pol II

The carboxy-terminal domain (CTD) of RNA polymerase II is that portion of the polymerase that is involved in the initiation of DNA transcription, the capping of the RNA transcript, and attachment to the spliceosome for RNA splicing.

pre-rRNA

The precursor to mature 18S, 5.8S, and 28S ribosomal RNAs. The mature rRNAs are processed from this long precursor RNA molecule by cleavage, removal of spacers from the ends of the cleaved products, and modification of specific bases.

CPSF (cleavage and polyadenylation specificity factor)

binds to signal poly A

PAP (poly A polymerase)

adds poly-A tail

Transcription steps

helicase and topsisomerase unwind DNA double helix RNA polymerase II binds to TATA box within promoter region of gene preRNA synthesized from DNA template strand

template strand of DNA

the DNA strand that is transcribed into mRNA and has the complementary sequence to the mRNA

mRNA branch point

the adenine nucleotide near the end of an intron that will be used in transesterification for exons. Branches to the phosphate group of the previous exon. Allowing the previous exon to attach to the phosphate of the successive exon.

coding strand

the strand of DNA that is not used for transcription and is identical in sequence to mRNA, except it contains uracil instead of thymine