chapter 8 part 3

Question 1

what part of the mRNA transcript becomes the mature mRNA

Answer 1

exons

Question 2

are introns in bacterial genes?

Answer 2

rarely - not really

Question 3

are there introns in archaeal gene?

Answer 3

occasionally

Question 4

2 methods for removing introns

Answer 4

1. spliceosome complex
2. self-splicing

Question 5

how are group I and II introns removed

Answer 5

self-splicing

Question 6

how are pre-mRNA introns removed

Answer 6

spliceosome complex

Question 7

how are rRNA and tRNA introns removed

Answer 7

enzymatic activity

Question 8

why does intron splicing have to be precise?

Answer 8

to remove nucleotides accurately, errors would lead to inccorect protein sequences

Question 9

who is responsible for the discovery of “split genes”

Answer 9

Roberts and Sharp - 1993 Nobel prize

Question 10

R-looping

Answer 10

DNA gene is isolated, denatured, and hybridized to mature mRNA from the same gene
- regions of DNA where introns are present have no complementary region within the mRNA and loop out visibly

Question 11

intron splicing signals

Answer 11

• 5’ splice site
• 3’ splice site
• branch site

Question 12

5’ splice site

Answer 12

has consensus sequence with an invariant GU dinucleotide

Question 13

3’ splice site

Answer 13

11 nucleotide consensus w/ pyrimidine-rich region and nearly invariant AG

Question 14

branch site

Answer 14

20-40 nucleotides upstream of 3’ end of intron
- pyrimidine-rich
- contains invariant adenine called branch point adenine near 3’ end of consensus

Question 15

splicing action of spliceosome

Answer 15

• 5’ splice site cleaved first
• variant intron structure formed when 5’ intron binds to branch point adenine
• 3’ splice site cleaved
• exons ligated together

Question 16

are introns always removed by the spliceosome in order?

Answer 16

no

Question 17

composition of spliceosome

Answer 17

small nuclear ribonucleoprotein particles (snRNPs U1-U6)

Question 18

is the composition of spliceosome steady?

Answer 18

no, always changing through steps of splicing

Question 19

how are spliceosome components recruited to splice sites

Answer 19

SR proteins that bind to exotic splicing enhancers to ensure accurate splicing

Question 20

what is the function of the carboxyl terminal domain (CTD) of RNA polymerase II?

Answer 20

assembly platform and regulator pre-mRNA processing machinery

Question 21

gene expression machines

Answer 21

proteins that carry out capping, intron splicing, and polyadenylation associate with CTD of pol II

Question 22

CTD and RNase

Answer 22

degrades residual transcript resulting from 3’ cleavage and trigger termination of transcription

Question 23

how many proteins are produced for one gene

Answer 23

can be many due to alternative mRNA processing

Question 24

3 transcription-associated mechanisms that explain more proteins than genes

Answer 24

1. pre-mRNA spliced in alternative patterns
2. alternative promoters can initiate transcription at different start points
3. alternative sites for polyadenylation

Question 25

how many human genes are thought to undergo alternative splicing

Answer 25

70%

Question 26

human calcitonin/calcitonin gene-related peptide and alternative splicing

Answer 26

- gene has 6 exons, 2 alternative polya sites - thyroid cells: exon 4 polya site to produce calcitonin - neuronal cells: splice exon 4, use exon 6 polya site to produce CGRP

Question 27

Drosophila Dscam gene

Answer 27

- 24 exons: 4, 6, 9, and 17 have alternative sequences - more than 38,000 dif polypeptides can be produced

Question 28

alternative promoters

Answer 28

occur when 1+ sequence upstream of a gene can initiate transcription

Question 29

alternative polyadenylation

Answer 29

requires 1+ polyadenylation signal in a gene

Question 30

group I introns and self-splicing

Answer 30

takes place via 2 transesterification reactions that excise intron and ligate exon ends

Question 31

what are group I and group II introns?

Answer 31

large, self-splicing ribozymes that catalyze own excision - group I: bacteria, simple eukaryotic, plants - group II: archaea, bacteria, mitochondrial and chloroplast

Question 32

group II introns and self-splicing

Answer 32

form very complex secondary structures and their self-splicing takes place in a lariat-like manner

Question 33

how are bacteria and eukaryotic rRNAs transcribed?

Answer 33

in large precursor molecules that are cleaved into smaller molecules by the removal of spacer sequences between the rRNA genes

Question 34

what do rRNAs do after processing

Answer 34

fold into complex secondary structures and join ribosomal proteins to form ribosomal subunits

Question 35

what do all tRNAs have in common?

Answer 35

similar structure, but dif nucleotide sequences

Question 36

overview of bacterial tRNA production

Answer 36

some produced simultaneously with rRNAs, others transcribed as large pre-tRNA transcript and cleaved into ind. molecules

Question 37

overview of eukartyouic tRNA production

Answer 37

each tRNA gene individually transcribed

Question 38

how many organisms do tRNAs usually produce?

Answer 38

30-40, fewer than 61 due third-base wobble

Question 39

what do bacterial tRNAs required before assuming their function role?

Answer 39

processing

Question 40

processing of bacterial tRNAS

Answer 40

- CLEAVAGE from large precursor molecule to small - TRIM nucleotides from 3' and 5' ends - CHEMICALLY MODIFY certain nucleotides - fold into 3D STRUCTURE - postranscriptional ADDITION of bases (CCA at 3' end)

Question 41

3D structure of tRNA

Answer 41

4 double-stranded stems, 3 of which capped by single-stranded loops

Question 42

do eukaryotic tRNAs undergo processing?

Answer 42

yes, may also include small introns that are removed

Question 43

RNA editing

Answer 43

responsible for post-transcriptional modifications to nucleotide sequence and protein produced of some mRNAs

Question 44

guide RNA

Answer 44

takes part in a kind of RNA editing, and adds uracils to mRNA

Question 45

base substitution

Answer 45

replacing one base with another

Question 46

frequent base substitution

Answer 46

replacing cytosine with uracil

Question 47

example of base substitution

Answer 47

production of 2 different apolipoprotein B proteins from single gene in human liver and intestinal cells - intestinal: produces premature stop codon, produces smaller protein than liver

Question 48

cis-splicing

Answer 48

connecting exons from single mRNA

Question 49

trans-splicing

Answer 49

connecting exons from multiple different mRNAs

Question 50

intragenic splicing

Answer 50

exons from single mRNA, often repeated exons

Question 51

intergenic splicing

Answer 51

exons from more than 1 type of mRNA