SM 11 Flashcards
(21 cards)
There is a coding and a template strand for transcription.
How are coding strand and RNA template similar?
coding strand is the DNA strand that has the same 5’ to 3’ sequence as the RNA to be made (with T instead of U).
The start of transcription is designated
+1
What are the different types of RNA polymerases?
- RNA polymerase I (RNAP I) transcribes ribosomal RNA (rRNA) genes.
- RNA polymerease II (RNAP II) transcribes protein coding genes into messenger RNA (mRNA), and many non-protein-coding RNA genes including small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), micro RNAs (miRNAs) and long non-coding RNAs (lncRNA).
- RNA polymerase III (RNAP III) transcribes transfer RNA (tRNA), 5S rRNA, and some snRNA, snoRNA and miRNA genes.
- Mitochondria have a single RNA polymerase (POLRMT) that is similar to the single prokaryotic RNA polymerase.
Eukaryotes also have two non-template dependent RNA polymerases that synthesize RNA polymers, polyadenylate polymerase and poly ADP-ribose polymerase (PARP)
rRNA and tRNA genes are linked as multiple copies in
tandem repeats b/t genes containing the terminator of one gene and the promoter for the next gene
What percent of our DNA is retrotransposns from ancient retroviruses?
30%. Consist of All and L1. They are mostly silent. Though L1 still encodes retrotransposae and is cap of retrotransprition in the genome. It can disrupt or change gene expression.
Satellite DNAs are clustered in discrete areas, such as centromeres. They are gene ______
poor.
How is rRNA processed?
Ribosomal RNAs are transcribed as a single 45S transcript containing 28S, 18S and 5.8S RNAs. 5S rRNA is synthesized separately by RNAP III. 45S transcripts are cut by endoribonucleases to remove internally transcribed spacers (ITS), the ends of the individual rRNAs are trimmed by exonucleases and some of the bases are modified to pseudouridine or 2’-O-methylated ribonucleotides. As this processing occurs, ribosomal proteins previously synthesized bind to the rRNA and ribosome assembly occurs. Small and large subunit are assembled and leave the nucleus through pore separately.
Made in nucleolus
How is tRNA processed?
RNAP III transcribes transfer RNA (tRNA) genes.
Processing of tRNA. tRNAs are synthesized as longer molecules that are trimmed at their ends to form the mature tRNA. Uracil residues at the 3’ end are removed and replaced by the sequence CCA. Some tRNAs also have a small intron in the anticodon loop that is removed. All tRNAs have extensive base modification, primarily dihydrouracil, pseudouracil, ribothymidine and other methylated bases.
After processing, the tRNAs are aminoacylated and transported into the cytoplasm through nuclear pore complexes.
Made throughout nucleus.
Describes structure of RNA pol II.
Upstream it has TATA box. In genes that are constitutively expressed, there is usually not a TATA box, and it is replaced by a GC-rich sequence. There can also be a CAAT box ~70-80 bps upstream. These sequences are recognition binding sites for transcription factors (TFs), which in turn interact with each other and RNAP II
Initiation of transcription by Pol II
Begins with recruitment of basal transcription machinery when TF bind to TATA and CAAT box, recruiting RNA pol and other factors. Pol II has a tail called carboxyterminal domain of CTD. That CTD acts as scaffold to bind a bunch of TF/other proteins. This is the pre-initiation complex.
What happens when gene gets signal to transcribe.
Phosphorylation occurs on the tail which signals pol to move along gene and transcribe RNA. it recruits other factors that allow it to change chromatin in front of it and bring in other TF for regulation. This is the mediator complex. It binds to pre-initiation complex and brings in other regulators. These are called enhancers which pos (activator) or neg (repressor) regulate transcription.
Elongation stops at the stop codon. T/F
F. Elongation proceeds past the stop codon and through the 3’ untranslated region. After passing a sequence called the polyadenylation signal, the polymerase encounters a non-specific termination signal and the transcript is released from the polymerase complex.
How is chromatin activated/inactivated?
To activate chromatin you add acetyl groups to histones (from acetyl CoA)
To inactivate you add methyl to histones (from SAM)
What does JMJD do?
remove methyls
What are heterogenous nuclear RNA or pre-mRNA (assembled with proteins into hnRNPs)
all primary RNAP II protein coding transcripts. includes transcripts that will become mRNA and other transcripts that will be long non-coding RNAs.
How does tissue/developmental stage specific expression work?
It is regulated by promoter elements. Depending on which TF present we can only activate genes when the TF are present. Ex: In fibroblasts the TF to make insulin will not be present.
What are the steps of mRNA processing?
- 5’ capping is the first processing event for pre-mRNA. A 7-methylguanosine “cap” is added “backwards” to the 5’ end of the pre-mRNA
- Splicing. The intron-exon junctions are recognized by snRNPs and other sequence specific RNA-binding proteins to form a spliceosome. U1 SnRNP binds to splice donor site. U2 snRNP binds to branch site. Then U4/U5/U6 binds and then U5SNP binds to both splice door and acceptor. The spliceosome contains the catalytic activity required for cutting and rejoining the mRNA. Cryptic splice site utilization due to mutations in the RNA sequence can produce mRNAs that encode abnormal proteins.
- Poly(A) addition. After termination of transcription, the 3’ end of the pre-mRNA is cut A2UA3 is recognized and a 40-200 nucleotide long polyadenosine tail is added by poly(A) polymerase. The poly(A) “tail” immediately interacts with a specific poly(A)-binding protein that helps to stabilize the tail against degradation by nucleases.
Why is it important that the exon junction complex be present?
So that only processed mRNA is transported.
How is miRNA processed?
Primary miRNAs are capped at the 5’ end and polyadenylated. A “Microprocessor Complex” associates with the individual primary miRNAs and cuts them from the long precursor. These are now called pre-miRNAs. Some miRNAs are then modified by RNA editing which deaminates adenosines to inosines. The pre-miRNA is transported to the cytoplasm where it is cleaved by an RNase called Dicer to give a RNA duplex of 22 nucleotides. One strand of the duplex is then incorporated into a RNA-induced silencing complex (RISC) which will regulate everything downstream.
Give example of gene rearrangement
the rearrangement of immunoglobulin genes in B cells to produce antibodies
When is the following mechanism used:
amplified DNA is excised and forms small unstable chromosomes call double minutes that can integrate into the genome resulting in amplification of the genes involved?
drug resistance in some tumors
