Chapter 14 - RNA Molecules and RNA Processing

Question 1

What are exons?

Answer 1

RNA coding regions in eukaryotic genes

Question 2

What are introns?

Answer 2

Non-coding regions of eukaryotic genes that interrupt exons

Removed posttranscriptionally

Tend to be longer than exons, so they contain more non-coding nucleotides

Question 3

What are pre-mRNAs?

Answer 3

mRNA right after transcription before it is fully processed

Still contains introns until they are spliced out posttranscriptionally

Question 4

What is a gene?

Answer 4

DNA sequence that encodes an RNA molecule

Question 5

What is mRNA and its function?

Answer 5

Messenger RNA

Functions as a template for protein synthesis

Carries genetic information from the DNA to a ribosome, where it helps it assemble amino acids into peptide chains

In prokaryotes, mRNA is directly transcribed because there are very few introns (if any)

In eukaryotes, pre-mRNA is transcribed and modifications occur to splice out introns, leaving you with mature mRNA

Question 6

What are codons?

Answer 6

Groups of three nucleotides that are translated into amino acids

Found in mRNA

Question 7

What are the three regions of mRNA?

Answer 7

5’ untranslated region (UTR)

Protein-coding region

3’ untranslated region (UTR)

Question 8

What is the 5’ untranslated region?

Answer 8

Sequence of nucleotides at leading end of mRNA strand that does not code for any amino acids

In prokaryotes, 5’ UTR has a Shine-Dalgarno sequence, which is a sequence that serves as the binding for a ribosome to begin translation
- Sits about 7 nucleotides upstream of start codon
- Complementary sequence on ribosome that bidns to Shine-Dalgarno sequence

Question 9

What is the protein-coding region of mRNA?

Answer 9

Region that contains codons that are translated into amino acids and later proteins

Goes from start codon to stop codon

Question 10

What is the 3’ untranslated region of mRNA?

Answer 10

Area at 3’ end of strand that does not trnaslate into amino acids

Helps with stability of RNA molecule

Can help regulate translation

Question 11

How do transcription and translation occur in prokaryotes?

Answer 11

Simultaneously

Question 12

How do transcription and translation occur in eukaryotes?

Answer 12

Transcription takes place in the nucleus and translation occurs in the cytoplasm

After pre-mRNA is transcribed and is traveling to the cytoplasm is when posttranscriptional modifications occur to all three regions of mRNA

Question 13

What are the 4 types of posttranscriptional modifications that happen to pre-mRNA?

Answer 13

Addition of 5’ cap

Poly(A) tail

Formation of m-6-methyladenosine

RNA splicing

Question 14

What is the 5’ cap, how is it added, and what is its function?

Answer 14

Consists of a modified guanine and several methyl groups on 5’ end of nucleotides

Modified guanine is added by cleaving a phosphate from the first rNTP that has all three phosphates and adding the guaning in its place

Added immediately after transcription

Functions in the initiation of translation, increases the stability of the strand and influences the removal of introns

Question 15

What is the poly(A) tail, how is it added, and what is its function?

Answer 15

Addition of adenines to the 3’ end of pre-mRNA strand

Not encoded in DNA

Occurs through process of polyadenylation

At the end of transcription, cleavage of mRNA occurs at cleavage site and poly(A) tail is added to where cleavage occurred

Poly(A) tail confers stability of mRNA molecule and protects strand from exonucleases
- Helps in mRNA attaching to ribosome
- Helps mRNA get exported to cytoplasm for translation

Question 16

Where is m-6-methyladenosine formed and what is its function?

Answer 16

Found near stop codon in 3’ UTR

Influences splicing and aids in mRNA degradation and translation

Question 17

What is RNA splicing and where/when does it occur?

Answer 17

Removal of introns

Takes place in the nucleus right before mRNA is shuttled to cytoplasm

Tends to occur co-transcriptionally (while transcription is occurring)
- While transcription is occurring at 3’ end, introns are being removed from already transcribed areas

Question 18

What is the splicing code made up of?

Answer 18

5’ splice site (consensus sequence)

Adenosine that sites just upstream of 3’ splice site - called the branch point

3’ splice site

Question 19

Where does splicing occur?

Answer 19

Spliceosome - large protein complex

Question 20

What are the steps to RNA splicing?

Answer 20

5’ end of intron is cut and attaches to branch point
- Looped formation is called a lariat
- Phosphate binds to adenosine through a phosphodiester bond
- Adenosine comes from the m-6-methyladenosine that is attached before

3’ splice site is cut

3’ end of exon 1 and 5’ end of exon 2 covalently bond together

Intron lariat is released

Enzyme that releases lariat chews intron up and degrades it

Result is mature mRNA, which is shuttled to cytoplasm

Question 21

What is the purpose of snRNAs in the spliceosome?

Answer 21

Interactions between snRNAs and pre-mRNA facilitate splicing

Question 22

What is trans-splicing?

Answer 22

Sometimes several pre-mRNAs are spliced together to form mature mRNA

Question 23

What are the 3 alternative routes of splicing?

Answer 23

Self-splicing introns

Alternative splicing

Multiple 3’ cleavage sites

Question 24

What happens with self-splicing introns?

Answer 24

Found primarily in eukaryotes and in mitochondria

Splicing occurs without enzyme

Results in secondary structures forming in pre-mRNA - hairpins and lariats

Allow exons to meet up, intron destabilizes, and intron and secondary structures disappear

Question 25

What happens with alternative splicing?

Answer 25

Same pre-mRNA can be spliced in many different ways to yield many different mRNAs, amino acid sequences and later proteins

Produces a different combination of exons/mRNA

Order of the exons almost never changes
- But can lose exons in between others

May be the reason why genome size does not indicate organism complexity becase multiple proteins can be created from a single gene depending on what exons are kept vs spliced

Question 26

What happens with multiple 3’ cleavage sites?

Answer 26

There can be multiple sites on the 3’ pre-mRNA that can be cut, resulting in different length mRNA strands

Question 27

What happens with RNA editing?

Answer 27

Protein coding region is altered after transcription

Translated amino acid downstream is different than what is coded to begin with

Guide RNA serves as template for addition, deletion, or alteration of base pairs in pre-mRNA

Question 28

What do transfer RNAs (tRNAs) do?

Answer 28

During translation, tRNAs transport amino acids to the ribosome and interact with the codons of the mRNA

Each tRNA attaches itself to a specific amino acid and then carries it to the ribosome

Within the ribosome, tRNA has a sequence that is the anticodon that pairs to the codon on the mRNA
- Anticodon is complementary to codon on mRNA

Each tRNA is capable of carrying only one specified amino acid

Question 29

What is the structure of tRNA?

Answer 29

Cloverleaf structure
- Have many inverted sequences that allow them to fold and form hairpins and loops

Acceptor arm (top)
- Forms stem with 5’ and 3’ ends of tRNA molecule
- Where amino acid is going to bind (at overhanging CCA site of 3’ end)

TψC arm (right)

Anticodon arm (bottom)
- Anticodon pairs with codon on mRNA sequence

DHU arm (left)

Question 30

How are tRNA genes processed?

Answer 30

All prokaryotic and eukaryotic tRNAs undergo posttranscriptional processing

No general way they are processed - some are transcribed as part of a larger precursor molecule which is later cleaved at different sites
- Some have introns that are removed (always at 3’ end of anticodon)

Question 31

What happens with rRNA gene processing?

Answer 31

Genes for rRNAs can be found in multiple copies throughout the genome

All copies are nearly identical

rRNAs always processed after transcription in both prokaryotes and eukaryotes

Question 32

How does rRNA processing occur in bacteria?

Answer 32

2 rRNAs that make up large subunit, 1 makes up small subunit

Each rRNA is transcribed into a single precursor

Precursor is methylated at multiple sites and cleaved to produce all 3 rRNAs

Cleavage also results in one mature tRNA

Question 33

How does rRNA processing occur in eukaryotes?

Answer 33

3 rRNAs make up large subunit, 1 makes up small subunit

Encoded in 2 genes
- 2 of the large and small is in one gene, other large is in another gene

Same process as in bacteria, but small nucleolar RNAs (snoRNAs) help modify rRNAs
- Each rRNA is transcribed into a single precursor
- Precursor is methylated at multiple sites and cleaved to produce all 3 rRNAs
- Cleavage also results in one mature tRNA

Question 34

What are the 2 categories of other varieties of RNAs?

Answer 34

Small RNAs

Long noncoding RNA (lncRNA)

Question 35

What do small RNAs do and what types are there?

Answer 35

Serve many functions: gene regulation, expression, viral defenses, suppression of transposons, help in modification of chromatin structure
- Also used to study gene function and treating diseases

Types:
- Small interfering RNA (siRNA)
- microRNA (miRNA)
- Piwi-interacting RNA (piRNA)
- CRISPR RNA (crRNA)