3.4 RNA Processing

Ribosomal RNA (rRNA)

noncoding RNA found in all ribosomes that aid in translation; they're concentrated in the nucleolus

How do prokaryotes have one mRNA strand code for multiple proteins?

if it's a polycistronic mRNA, it can code for multiple proteins

What is the benefit of alternative splicing?

it's designed to manage the influence of introns on a primary transcript and its eventual translation into different protein products

Transfer RNA (tRNA)

noncoding RNA that carries individual amino acids for use in translation

What is a transesterification reaction with respect to RNA processing?

the bonding of the guanine and adenine bases takes place via a chemical reaction in which a hydroxyl group on a carbon atom of the adenine "attacks" the bond of the guanine nucleotide at the splice site

Primary Transcript

the initial RNA transcript that comes off the template DNA strand

RNA splicing

the process of intron removal from the primary transcript

What is the third step of RNA processing?

the removal of noncoding introns (also known as RNA splicing, that is catalyzed by a complex of RNA and protein known as the spliceosome)

What is the benefit of introns?

they create an added complexity that allows for different protein products via alternative splicing

Where does RNA processing occur?

in the nucleus

What are the four functions of the 5' cap?

1) Facilitating splicing 2) RNA stability 3) Allowing for Export out of the Nucleus 4) Recognized by the ribosomes and is then translated

What are the steps of intron splicing?

1) a spliceosome brings a specific sequence within the intron into proximity with the 5' end of the intron (the 5' splice site) 2) the proximity enables a reaction that cuts the RNA at the 5' splice site and the cleaved end of the intron connects bac on itself, forming a loop and tail called a lariat 3) the spliceosome brings the 5' splice site close to the splice site at the 3' end of the intron 4) the 5' splice site attacks the 3' splice site, cleaving the bond that holds the lariat on the transcript and attaching the ends of the exons to each other

What are the four functions of polyadenylation?

1) protecting 3' end of the RNA 2) alternative processing generates different msgs; in transcription, defines the end of the exon 3) RNA export 4) translation

Alternative splicing allows for: A) different polypeptides to be made from a single gene B) increased stability of a mature mRNA C) enhanced recognition of an mRNA by a ribosome D) multiple genes to be used to code for a single polypeptide chain

A) different polypeptides to be made from a single gene

RNA processing occurs in the: A) nucleus B) plasma membrane C) cytoplasm D) nucleus and cytoplasm

A) nucleus

An intron is: A) a type of transfer RNA B) an RNA sequence that is removed during the processing of an RNA molecule in the nucleus C) part of an RNA transcript that is not present in the DNA template D) a polypeptide that is excised out of a larger protein post-translationally E) part of an intact, mature mRNA that leaves the nucleus

B) an RNA sequence that is removed during the processing of an RNA molecule in the nucleus

Arrange the descriptions of the steps in RNA splicing in order from earliest to latest. Consider the steps in RNA splicing. 1. Exon ends are covalently joined together. 2. Components of the spliceosome bind conserved regions in the intron and bring them together in close proximity. 3. Acceptor splice site is cut. 4. Donor splice site is cute, and the end of the intron is joined covalently to the branch site. A) 3, 1, 2, 4 B) 3, 2, 4, 1 C) 2, 4, 3, 1 D) 3, 4, 1, 2 E) 2, 3, 1, 4

C) 2, 4, 3, 1

Alternative splicing means that: A) some transcripts are spliced correctly and others incorrectly B) some transcripts are spliced while others are not C) alternating introns are removed D) different spliced forms contain different combinations of exons

D) different spliced forms contain different combinations of exons

The type of RNA that physically interacts with a ribosome, providing the sequence information for a specific protein, is abbreviated: A) snRNA B) rRNA C) tRNA D) siRNA E) mRNA

E) mRNA

What are five types of noncoding RNA and their functions?

Five types of noncoding RNA are (1) ribosomal RNAs (rRNA), which are found in all ribosomes and aid in translation; (2) transfer RNAs (tRNA), which carry individual amino acids for use in translation; (3) small nuclear RNAs (snRNA, which are involved in eukaryotic gene splicing, polyadenylation, and other process in the nucleus; (4) microRNAs (miRNA), which inhibit translation; and (5) small interfering RNAs (siRNA), which destroy RNA transcripts.

What is an isoform?

Gene isoforms are mRNAs that are produced from the same locus but are different in their transcription start sites, protein coding DNA sequences and/or untranslated regions, potentially altering gene function.

When does translation happen in prokaryotes?

It happens immediately because there's no nuclear envelope to divide time and space. so even as the RNA strand is still being coded, translation can begin

What is the second step of RNA processing?

Polyadenylation--the addition of the poly(A) tail to the 3' end of the primary transcript

When a region of DNA that contains the genetic information for a protein is isolated from a bacterial cell and inserted into a eukaryotic cell in a proper position between a promoter and a terminator, the resulting cell usually produces the correct protein. But when the experiment is done in the reverse direction (inserting eukaryotic DNA into a bacterial cell), the correct protein is often not produced. Why is this the case?

The eukaryotic DNA sequence contains introns, which the bacterial cell cannot splice out properly. Thus, the correct protein is not produced from the information in the bacterial RNA transcript.

small interfering RNA (siRNA)

a type of small double-stranded regulatory RNA that becomes part of a complex able to cleave and destroy single-stranded RNA with a complementary sequence

What are three mechanisms of RNA processing in eukaryotes?

Three mechanisms of RNA processing (chemical modification of the primary transcript to generate the finished mRNA) in eukaryotic cells are as follows: i. Addition of the 5' cap. This modified nucleotide (7-methylguanosine) allows the mRNA to be recognized by the ribosome complex and helps stabilize the mRNA. ii. Addition of the poly(A) tail. This modification is important in mRNA transcription termination as well as in the export of the mRNA into the cytoplasm. Like the 5' cap, the poly(A) tail helps stabilize the mRNA. iii. RNA splicing. Splicing is the process by which introns are removed from a primary RNA transcript. A single transcript with multiple introns may be spliced in different ways to generate different mRNAs and different protein products with different functions. Thus, this alternative splicing is one more layer contributing to the diversity of the genetic information stored in DNA.

Spliceosome

a complex of RNA and protein that catalyzes RNA splicing

Nucleolus

a distinct, dense, non-membrane-bound spherical structure within the nucleus that contains the genes and transcripts for ribosomal RNA

Alternative Splicing

a process in which primary transcripts from the same gene can be spliced in different ways to yield different mRNAs and therefore different protein products

Introns

a sequence that is excised from the primary transcript and degraded during RNA splicing

Exons

a sequence that is left intact in mRNA after RNA splicing

Polycistronic mRNA

a single molecule of messenger RNA that is formed by the transcription of a group of functionally related genes located next to one another along bacterial DNA

RNA processing

chemical modification that converts the primary transcript into finished mRNA, enabling the RNA molecule to be transported to the cytoplasm and recognized by the translational machinery

Small nuclear RNA (snRNA)

noncoding RNA found in eukaryotes and involved in splicing, polyadenylation, and other processes in the nucleus

microRNA (miRNA)

small, regulatory RNA molecules that can cleave or destabilize RNA or inhibit its translation

What is the structural importance of the 5' cap and the 3' end?

the 5' cap and the poly(A) tail help to stabilize the RNA transcript and protect the two ends of the transcript until it is translated in the cytoplasm

What is the first step of RNA processing in eukaryotes?

the 5' end of the primary transcript is modified by the addition of a 5' cap, which is how the ribosome recognizes it. the 5' cap is attached via a triphosphate bridge

Messenger RNA (mRNA)

the RNA molecule that combines with a ribosome to direct protein synthesis; it carries the genetic "message" from the DNA to the ribosome

Polyadenylation

the addition of a long string of consecutive A-bearing ribonucleotides to the 3' end of the primary transcript

5' cap

the modification of the 5' end of the primary transcript by the addition of a special nucleotide attached in an unusual chemical linkage

Poly(A) tail

the nucleotides added to the 3' end of the primary transcript by polyadenylation