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True or False: Both intron and exon sequences are transcribed into RNA.

TRUE: The introns are removed during processing of RNA into mRNA

--> This is called RNA splicing


True or False: Both replication and transcription use a DNA template to incorporate nucleotide triphosphates into a polynucleotide chain.



True or False: Both replication and transcription use enzymes that synthesize polynucleotides by forming 3'-5'-phosphodiester bonds in the 5' to 3' direction. Energy derived from hydrolysis of the α-β phosphodiester bond of incoming nucleotide



True or False: Only replication (not transcription) needs to unwind DNA

FALSE: Both need to unwind DNA in order to work


True or False: Only transcription (not replication) begins at specific sites in DNA

FALSE: BOTH start at specific sites


True or False: Both replication and transcription require the step-wise assembly of a multi-component protein complex to initiate



What do exons contain?

Exons include the codons PLUS the 5’- and 3’-untranslated sequences (UTRs)

--> Therefore, introns are the spaces between exons, NOT the spaces between genes!


True or False: Introns and Exons are about the same size

FALSE: Introns are usually much longer than exons


When are introns removed in short transcripts?

Often removed from the primary RNA (pre-mRNA) after polyadenylation


When are introns removed in long transcripts?

Often removed co-transcriptionally (during transcription)


What processes are done BEFORE any splicing occurs in RNA?

- Poly-A tailing (~200 A's) - 3' End
- G-capping - 5' End


Define splicing

Removal of the intron between 2 adjacent exons


Define alternative splicing

Production of different RNAs from the same gene by splicing the RNA in different ways (ex: splicing together of non-adjacent exons

--> About 95% of human genes are spliced in this way


Define trans-splicing

Exons from two different RNAs are spliced together. This occurs in only a few eukaryotes such as trypanosomes, C. elegans

Note: This DOESN'T HAPPEN in humans


How does splicing increase biodiversity?

- Allows for the emergence of new proteins over evolutionary time as a result of exon ‘shuffling’ during genetic recombination.
- This concept is supported by all the ‘domains’ that proteins have in common


How does splicing increase the "functional density" per gene?

It allows one gene to make many different kinds of RNAs and thus proteins (alternative splicing). Approximately 95% of human genes are thought to be alternatively spliced


How does splicing get directed in long transcripts?

Phosphorylation of the CTD tail of RNA Pol directs RNA processing
--> Splicing occurs co-transcriptionally for most primary mRNAs


True or False: RNA that turns into mRNA is the only kind of RNA that gets spliced

FALSE: More types of RNA can be spliced

--> However, we don't need to know about those


What is a transesterification?

A splicing event that involves 2 sequential phosphoryl-transfer reactions

--> Changes one type of phosphodiester bond to another type

--> These reactions link two exons together, while removing the intron as a lariat-like structure


In what situation would more than one intron be removed at a time?

In the case of alternative splicing, where both exons and introns might be spliced out

--> Typically, each splicing event removes only 1 intron


Describe how a lariat is formed and then released

- A specific Adenine nucleotide in the intron (highly conserved) attacks the 5’-splice site and cuts the sugar-phosphate backbone of the RNA
- The cut 5' -end of the intron becomes covantly linked to the A, creating a loop
- The free 3’-end of the 5’ exon reacts with the start of the next exon, joining the 2 exons and releasing the intron as the lariat


What three parts of the primary RNA transcript must the splicing machinery recognize?

i) The 5’ splice site (5’ of the intron to be spliced out)
ii) The 3’ splice site (3’ of the intron to be spliced out)
iii) The branch point


How does the splicing machinery solve the problem of short and highly variable consensus sites in the primary RNA transcript?

The cell has other information that helps select the splice sites


What 3 nucleotide “motifs” are invariant within an intron?

i) A GU at the 5’ end of the intron
ii) A branch site, which is always A, is found 20 – 50 NT from the 3’ splice site
iii) An AG at the 3’end of the intron

--> A pyrimidine-rich region near the 3’ end of the intron is found in most cases


Define: Ribonucleoprotein

Conains both RNAs and protein

i.e. : Ribosomes


True or False: The spliceosome is a large ________ particle

Ribonucleoprotein (RNP


What is snRNA?

-Small nuclear RNA
- The RNAs in spliceosomes are specialized RNAs known as small nuclear RNAs (snRNAs)
-These snRNAs are <200 nucleotides long


What are snRNAs made by?

Some snRNAs are made by RNA pol II and others by RNA pol III


What are the two specialized functions of snRNAs?

i) Recognize the splice sites by base pairing with the primary RNA transcript
ii) Catalyze the two transesterification reactions, i.e. snRNAs are enzymes


What is a snRNP?

They are the core units of the Spliceosome