Lecture 5 Flashcards
Recall the CENTRAL DOGMA
DNA -> RNA (transcription) -> protein (translation)
ALL cells use this
In Eukaryotes:
-DNA undergoes transcription, pre-mRNA undergoes 5’ capping, RNA splicing, 3’ polyA tail in NUCLEUS; mRNA is exported out of nucleus, translated to protein outside nucleus
In Prokaryotes:
-DNA undergoes transcription - mRNA - translated to protein; NO nucleus
EVERY cell processes information like this
Information processing (how a cell goes from DNA to protein)
RNA processing
RNA splicing
5’ cap
3’ PolyA tail
ONLY in eukaryotes
Eukaryotes vs Prokaryotes
Eukaryotes are LARGER, possess introns/exons, RNA processing, and nucleus (prokaryotes don’t have those)
Product of a gene is NOT always turned into a protein
Cells can regulate how much is made into protein (usuallly at transcription)
A cell can express different genes at
Different rates
Gene expression
1st step is transcription
What determines where RNA polymerase starts transcribing DNA?
Transcription of a gene produces an RNA complementary to one strand of DNA
The promoter
Transcription proceeds in a 5’ to 3’ direction using a
3’ to 5’ template
Bacterial promoters and terminators have specific
Nucleotide sequences that are recognized by RNA polymerase
Transcription in Bacteria
starts on a sequecnce call the Promoter: It is NOT a continuous strand of bases, occurs in segments (UNLIKE replication origin)
Transcription starts at the +1 (this is where the first nucleotide is added
In eukaryotes, the promoter is NOT in
RNA
Signals in the nucleotide sequence of a gene tell bacterial RNA polymerase
Where to start and stop transcription
Sigma Factor
Transcription factor that helps the RNA polymerase (one of the main differences between prokaryotic and eukaryotic)
Recognizes the Promoter
Terminator
Where transcription stops
Ends up in molecule of RNA (promoter does NOT)
Eukaryotic promoters
Contain sequences that promote the bindings of the general transcription factors
TBP binds to the TATA box and bends
The DNA molecule
General transcription Factors
found in EVERY single cell and initiate transcription
Regulatory Transcription factors
Regulate transcription (activators, repressors)
Vary on cell type
Some genes are transcribed using one DNA strand as a template, and others are transcribed from
The other DNA strand
How does RNA polymerase differ from DNA polymerase?
DNA is transcribed into RNA by the enzymes RNA POLYMERASE
-Helicase opens the helix in RNA, too; opens as it goes, closes behind it; NO primer for transcription of RNA
How do RNA and DNA differ from each other?
The chemical structure of RNA differs slightly from that of DNA
-RNA uses ribose (has one more OH), DNA uses deoxyribose (one less OH)
RNA uses uracil (one less methyl)
DNA uses thymine (one more methyl)
uracil forms a base pair with adenine
Messenger RNAs
mRNA
Code for proteins
NOT translated to proteins
Ribosomal RNAs
rRNAs
Form the core of the ribosome’s structure and catalyze protein synthesis
MicroRNAs
miRNAs
Regulate gene expression by associated with RISC complex then binding to certain mRNA that it carries a message for and destroys that mRNA
TransferRNAs
tRNAs
Serve as adaptors between mRNA and amino acids during protein synthesis
Other noncoding RNAs
Used in RNA splicing, gene regulation, telomere maintenance, and many other processes
RNA can fold into structures that are held together by
H bonds
How does transcription Proceed?
TO begin transcription, eukaryotic RNA polymerase II requires a set of general transcription factors:
- TATA and TFIID recognize promoter
- Recruit TFIIB
- TFIIB binds, recruits TFIIE and TFIIH and RNA polymerase II
- TFIIH breaks H-bonds and acts as a helicase (does NOT stay the whole time like helicase does in DNA)
- DNA melts, transcription factors dissociate
RNA polymerase I
most rRNA genes
RNA polymerase II
All protein-coding genes, miRNA, plus genes for other noncoding RNAs (e.g. those of teh spliceosomes)
RNA polymerase III
tRNA genes, 5S rRNA gene, genes for many other small RNAs
Eukaryotic vs. Prokaryotic Initiation
Eukaryotic
-TATA, TBP, TFIID recognize promoter, recruit TFIIB, binds to promoter, recruits TFIIE, TFIIH, polymerase II, TFIIH unwinds helix (closes right behind), DNA melts, transcription factors dissacoiate
Prokaryotic:
-Sigma factor binds to RNA polymerase, RNA polymerase binds to promoter at start site, begins RNA synthesis, sigma factor is released, polymerase calmps firmly on DNA, RNA synthesis terminated at stop site, polymerase and completed RNA released
Phosphorylation of the tail of RNA polymerase II allows RNA-processing proteins to
Assemble
TFIIH functions
1) Helicase
2) Phosphorylation
- Melt DNA, open up, phosphorylate
Phosphorylation acts as a docking site
ONLY RNA polymerase II does this (other proteins not made by RNA polymerase II do NOT have a cap)
Eukaryotic mRNA molecules are modified by capping and polyadenylation
Capping: Occurs on 5’ ends, message is capped BEFORE trancription is even done
Tail: Poly-A tail is added at the EN of transcription (after message is completed)
Major function of PolyA tail and 5’ cap
1) Stabilizes message/prevents being eaten by nucleases
2) Translate; helps DNA to realize that these are processed and don’t need to be destroyed
There is ALWAYS s string of sequences at BOTH ends that are
NOncoding (start codon is NEVER right at the end)
Special nucleotide sequences in a premRNA transcript signal the beginning and the end of an intron
pre-mRNA hasn’t been fully processed
There are very soncerved sequences that tell us where these sections are
Start codon is NEVER at the end, always separated by UTR
An intron in a pre-mRNA molecule forms a branched structure during RNA splicing
Red “A” 100% conserved base; any mutations are fatal
3’ ydroxyl group attacks 5’ end
Lariat (bundle of introns that results from 3’ hydroxyl attacking 5’ end) will be degraded so you can reuse the bases
Splicing is carried out by a collection of RNA-protein complexes called
snRNPs
RNA portion of snRNP base-pairs with sequences that signal splicing
It is the RNA that recognizes sequences in the introns
Active site created by two things (U2 and U6)
Excised intron in the form of a lariat
Exon junction complex
Small nuclear ribonucleic proteins:
RNA protein complexes
Spliceosome
One of largest complexes in cell
Binds at ends to bring together
Some pre-mRNAs undergo alternative splicing to produce different mRNAs and proteins from the same
Gene
We can alternatively splice messages (splice 2 out, get completely different protein)
90% of proteins are alternatively spliced
Mix and match
Most protein-coding human genes are broken into multiple
Exons and introns
Prokaryotes do NOT have introns and exons
Drosophila gene: 38000 different genes (record for alternative splicing)
Eukaryotic and bacterial genes are organized
Differently
A specialized set of RNA binding proteins signals that a complete mRNA is ready for export to the
Cytosol
Ribosomes are out in the cytoplasm
Will bind to proteins (proteins tell the cell message hass been processed)
Transport through nuclear pore => protein exchange (switch out for translation initiation factors)
When a message is processed, it associates with a bunch of proteins that tell the cell if the information has been processed
Transported through nuclear pore
Protein exchange in nuclear pore
