Chapter 14

What is the difference between the different types of RNA? What is the same?

All types of RNA have the same structure, they are all still RNA, they simply differ in function.

What is the function of the 3' untranslated region?

The 3' untranslated region is a sequence of nucleotides at the 3' end of the mRNA that is not translated into proteins. However, it does affect translation of the mRNA molecule as well as the stability of the mRNA

What is the function of the 5' cap?

The 5' cap functions in the initiation of translation and mRNA stability. And also protects from degradation.

What is the function of the 3' cleavage and the addition of the poly A tail?

- 3' cleavage and addition of poly A tail: increases stability of mRNA, facilitates binding of ribosome to mRNA, also prevents degradation, long length of poly A tail increases longevity, necessary for the mRNA to be transported out of the nucleus in the case of eukaryotes.

Name the four post-transcriptional modifications made to the mRNA (pre-mRNA) to make it mature?

- Addition of the 5' cap - 3' cleavage and addition of poly A tail - RNA splicing - RNA editing

What is the function of the addition of the 5' cap?

- Addition of the 5' cap: facilitates binding of the ribosomes to 5' end of mRNA, increases mRNA stability, enhances RNA splicing, protects 5' end after synthesis, keeps exonuclease from breaking down 5' end

What is the function of the RNA editing?

- RNA editing: Alters nucleotide sequence of mRNA

What is the function of the RNA splicing?

- RNA splicing: removes noncoding introns from pre-mRNA, facilitates export of mRNA to cytoplasm, allows for multiple proteins to be produced through alternative splicing

What major structures compose a eukaryotic gene?

- TATA box: recruits polymerase, its in the promoter - Exons - Introns - stop codon Transcription start site -3' cleavage site -Poly(A) consensus sequence: recruits enzymes that will cleave RNA and add Poly A tail

What are the three regions in a mRNA?

-5' Untranslated region - Protein-coding region - 3' Untranslated region Untranslated regions are also known as UTR's

What is the difference between the Shine-Dalgarno sequence (AGGAGG), and the Kozak sequence (gcc)gccRccAUGG

-The Shine-Dalgarno sequence is in prokaryotes and contains the start codon - The Kozak sequence is in eukaryotes and contains the start codon

What is the function of the Poly (A) tail?

A poly(A) tail is added to the 3' end of the pre-mRNA. It affects mRNA stability. And also helps transport the mRNA out of the cytoplasm.

Which of the following statements about bacterial mRNA transcripts is true? A. The Shine-Dalgarno box associates with an RNA component in the large subunit of ribosomes. B. Transcription and translation take place simultaneously in bacterial cells C. Unlike eukaryotes, bacterial mRNA transcripts do not typically contain untranslated regions D. Most of the bacterial genes contain a large number of introns and a small number of exons. E. None of these is the correct answer

B

Which of the following statements regarding gene structure is false? A. The number of the introns found in organisms is species specific B. The number if exons is always less than the number of introns in a gene. C. The amino acid sequence of a polypeptide can be precisely predicted by the nucleotide sequence of the gene that encodes it D. Intron cleavage and exon splicing are both mediated by protein enzymes. E. All of the above statements are NOT false

B

How do the mRNA's of bacterial cells and the pre-mRNAs of eukaryotic cells differ? How do the mature mRNA's of bacterial and eukaryotic cells differ?

Bacterial mRNA is translated immediately upon being transcribed. Eukaryotic pre-mRNA must be processed and exported from the nucleus. Bacterial mRNA and eukaryotic pre-mRNA have similarities in structure. Each has a - 5' untranslated region as well as a 3' untranslated region - Protein coding-regions (however euk. are dispersed with introns) Eukaryotic mRNA have a 5' cap and poly(A) tail, unlike bacterial mRNA's. Bacterial mRNA also contain the Shine-Dalgarno consensus sequence. While euk. have Kozak sequence.

Why did we think the human genome had 100000 genes?

Because the body produced 100000 proteins. But later we found the genome contains only about 25,000 genes and via RNA splicing we could produce many different proteins.

The list of events below describes intron removal and splicing during pre-mRNA processing. Please select the choice that lists the events in correct sequential order. 1. Attachment of snRNP U1 to the 5′ splice site 2. Transcription of the DNA template into the pre-mRNA molecule 3. Release of lariat structure 4. Splicing together of exons 5. Transesterification reaction at the branch point adenine a. 1, 2, 3, 4, 5 b. 4, 1, 3, 5, 2 c. 2, 1, 5, 3, 4 d. 3, 5, 1, 2, 4 e. 5, 3, 4, 1, 2

C

How many introns are present on a gene that consists of 5 exons? A. 7 B. 6 C. 5 D. 4 C. None of the above answers is correct

D

RNA editing relies on _______ to perform its function A. piwi RNA B. transfer RNA C. Micro RNA D. Guide RNA

D

Which of the following best defines the term translation? A. Using proteins as a template to make RNA B. Using DNA as a template to make RNA C. Using DNA as a template to make DNA D. Using RNA as a template to make a protein E. Using RNA as a template to make DNA

D

Explain the process of the making of Poly A tails

During transcription the consensus sequence is going to be transcribed. Once transcribed it recruits the enzyme that will cleave the mRNA, and then its going to add a string of A's. It does this without a template. Adenine is the only base that can be transcribed without a template that is how we get poly A tails.

What is the function of the exon?

Exons are transcribed regions that are not removed in intron processing. They include the 5' UTR, coding regions that are translated into amino acid sequences, and the 3'UTR.

What is the rule for exon order?

Exons will always be in increasing order, but can skip numbers. While out of order exons would increase protein diversity there is no history of that ever happening.

How would the deletion of the Shine-Dalgarno sequence affect a bacterial mRNA?

In bacteria, the small ribosomal subunit binds to the Shine-Dalgarno sequence to initia6e translation. If the Shine-Dalgarno sequence is deleted, the the translation initiation cannot take place, preventing protein synthesis.

What is the function of the Intron?

Introns are non-coding sequences of DNA that intervene within the coding regions of a gene

What are the roles of introns and exons in RNA splicing?

Introns=interfere Exons=expressed - Exons will always appear first and last with an intron in the middle, such that we will always have 1 fewer introns than we do exons. There is a a 5' consensus sequence at the E-I border, and a 3' sequence at the I-E border. The enzyme will look at these sequences to find the splice site, and cut there.

What does it mean that a messenger RNA is mature?

It is ready for translation

What is the function of the 5' untranslated region?

It leas upstream of the translation start site. The eukaryotic ribosome binds at the 5' cap of the mRNA molecule and scans to the first methionine codon (AUG). The region 5' of this start codon is the 5'UTR.

Explain why RNA splicing is a neutral energy process?

No energy required makes it possible to have self splicing introns.

Do all exons have to show up in the mRNA sequence?

No. There is no rule that all exons have to show up in the mRNA, this is called alternative splicing (only in eukaryotes). Usually the mRNA will always have the first and last exon, as those carry the start and stop codon. But via alternative splicing we can have mRNA's with only one exon, two exons, an elongated exon, or just the 2nd exon. (rare) giving the genome a high degree of expression.

What is the process of formation of the Lariat in RNA splicing?

Once the enzyme recognized the splice sites, it will clip the 5' site causing it to form a lariat structure. We now have a branch site where we can "park" the 5' end of the intron that is being removed by forming a bond with usually an adenine. We cut the 3' end of the intron. Now we join the 3' end of exon one with the 5' end of exon two. Now we have mature mRNA that is ready for translation.

Are the 5' untranslated regions (5'UTR) of eukaryotic mRNA's encoded by sequences in the promoter, exon, or intron of the gene? Explain.

The 5' UTR is located in the first exon of the gene. It is not part of the promoter because promoters for RNA polymerase 2 (which transcribes pre-mRNA) are not normally transcribed, and the 5' UTR is in the mRNA. It is not located in an intron because introns are removed during processing of pre-mRNA, and the 5' UTR is part of the mRNA.

What is the function of the promoter?

The DNA sequence that the transcription apparatus recognizes and binds to initiate transcription

What is the function of the AAUAAA consensus sequence?

The consensus sequence lies near the 3' end of the pre-mRNA. It determines the location of the 3' cleavage and poly (A) tail addition to the pre-mRNA molecule.

What are the functions of Long non-coding (IncRNA)?

The function is really unknown but some: -Control gene expression, (cell cycle regulation, chromosome stability, chromatin structure) -The reason why one X chromosome becomes a bar body. -Dosage compensation

Discuss the importance of collinearity in mRNA processing

The idea of collinearity is that the genes we see end up in the mRNA, which ends up in the proteins. The start codon is always first from genes through proteins, exons stay in their order. This precise info in genome makes transcription to mRNA possible, the precise info in mRNA makes translation possible.

Explain how introns can self-splice.

The intron is positioned in such a way, that the 5' and 3' splice sites are right next to, or in close proximity to each other. This causes a nucleophilic attack, phosphodiester bonds are broken, and one phosphodiester bond is made bringing exon one and exon two together. Whether we have a group one intron (process is internal to structure) or group two (process more external) the process is more or less the same.

Explain the process of editing with guide RNA.

The preedited mRNA pairs up with the guide mRNA. The guide mRNA has all these folds that, when stretched out will produce breaks wherever there were folds, the breaks can be filled in with RNA dependent RNA polymerase. Now you have a mature RNA that has been edited with a different sequence than the original preedited mRNA.

Both thyroid cells and brain cells produce the protein calcitonin, but brain cells produce calcitonin-gene-related peptide (CGRP). What causes this difference in the proteins?

The thyroid cells have exon 1, 2, 3, and 4. While the brain cells have exons 1, 2, 3, 5, and 6

What is the function of the transcription start site?

The transcriptions start site is the location of the first transcribed nucleotide of the mRNA and is located 25 to 30 nucleotides downstream of the TATA box

Describe the relationship of U1, 2, 4, 5, and 6 in RNA splicing

U1 binds to I-E border U2 binds through the branch point. Interaction of U1, U4, U5, and U6 causes formation of branch point, the breaking of the exon-intron phosphodiester bond, and breaking of intron-exon phosphodiester bond, and the formation of the phosphodiester bond between exon 1 and exon 2. This is a energy neutral process.

Why does RNA splicing have to be so specific and precise?

We have to cut pre- mRNA at precise points in order to not cause insertions or deletions, generating a frame shift, eliminating the pre-mRNA from producing the protein of interest in translation.

What are tRNA's

mRNA do not recognize and bind directly to amino acids, they depend on tRNA that serve as adaptor molecules that can recognize and bind to a codon at on site of their surface and to an amino acid at another.

What are rRNA's?

type of RNA that combines with proteins to form ribosomes

What are CRISPER RNA's?

RNA's used in anti-phage defense

What are micro RNA (miRNA) and small interfering RNAs (siRNA)?

RNA's used in gene silencing

What is the spliceosome composed of?

protein and DNA