Chapter 14 - RNA Molecules & RNA Processing

Question 1

In bacteria, ___ often begins before ___ is completed.

Answer 1

Translation; transcription

Question 2

A male fly that is ___ for a mutation in the fru gene is ___.

Answer 2

homozygous; bisexual

Question 3

Which of the following would most likely contain genes with the greatest number of introns?
A. E. coli cells
B. Yeast cells
C. Human cells
D. Mitochondria
E. Bacteriophage lambda

Answer 3

C. Human cells

Question 4

Jr. Scientist has identified sequences on an mRNA from a vampire bat that she thinks are important for proper association of the mRNA with a ribosome. These sequences must be part of which portion of the mRNA?
A. 5’ Untranslated Region
B. 3’ Untranslated Region
C. Intron
D. Open-Reading Frame (ORF)
E. None of the above

Answer 4

A. 5’ Untranslated Region

Question 5

Crick was the first to propose that there’s a direct relationship between DNA and amino acid sequences; in other words, they are ____. This assumption is fairly accurate for ___ and ___.

Answer 5

colinear

bacteria and viruses

Question 6

With ___, the number of nucleotides is ___ to the number of amino acids.

Answer 6

collinearity; proportional

Question 7

_-__ is an experiment used to demonstrates that eukaryotic DNA and proteins are not ___.

The experiment includes ___ dsDNA, and then ___ DNA with mRNA (specifically, the (specifically the __ DNA strand); then viewing ___ made by the ssDNA with the mRNA. The ___ portion represents noncoding sequences in ssDNA known as ____).

Answer 7

R-looping; colinear.

denaturing; annealing; nonsense/complimentary; loops.

looped; introns

Question 8

___ (aka expressed sequences) are regions of DNA that are transcribed and appear in mature ___. ___ (aka intervening sequences) are DNA regions that are not part of the mature ___. The latter are mostly found in ___, but a limited number have been found in some __ and __.

Answer 8

Exons; RNA.

Introns; RNA.

eukaryotes; bacteria; viruses

Question 9

In general, ___ size and complexity are correlated to organismal complexity with ___ containing the most and largest. An example is the ___ protein which has 4K amino acids (__K nucleotides - 3 per codon); but the gene is > __M nucleotides long.

Answer 9

intron; vertebrates

dystrophin; 12K; 2M

Question 10

Introns are very ___ relative to ___.

Answer 10

large; exons

Question 11

Name the 4 major classes of introns. Which of the 4 is the “major”?

Answer 11

Group I, Group II, Nuclear pre-mRNA; and Transfer RNA

nuclear pre-mRNA

Question 12

These introns are found in some rRNA, are self-splicing, and have catalytic/enzymatic activity. They are commonly found in rRNA genes of protozoans, mitochondria of some fungi, and a few bacteriophages.

Answer 12

Group I introns

Question 13

These introns are found in protein-coding genes of mitochondria/chloroplasts and some bacteria, and are self-splicing (have catalytic/enzymatic activity).

Answer 13

Group II introns

Question 14

__ __ introns are found in nuclear protein-coding genes; and they’re mechanism of self-splicing is similar to Group __ introns, but requires a complex of –RNAs and a protein called a ____.

Answer 14

Nuclear pre-mRNA; group II; snRNAs; splicosome

Question 15

These introns utilize a splicing mechanism that was not covered in lecture.

Answer 15

Transfer RNA introns.

Question 16

A gene is a __ __ that contains three things: a __, __ __ sequences, and a ___. The __ __ sequences include all __ and __.

Answer 16

transcription unit; promoter; RNA coding; terminator.

RNA coding; introns; exons

Question 17

The definition “DNA sequences that code for a polypeptide” is not sufficient to describe a gene because a gene has a ___ promoter, a __ promoter, the __ __ frame, and a ___; plus, the mRNA it codes for has ___ and ___.

Answer 17

regulatory; core; open reading; terminator; exons; introns

Question 18

T or F: DNA can directly encode information for the synthesis of proteins.

Answer 18

Depends: True for bacteria, false for eukaryotes since RNA synthesis includes slicing and dicing before translation.

Question 19

mRNA was discovered by experiments using ___ that resulted in the synthesis of a very ___ RNAs with a nucleotide composition very different from the bacterial ___.

Answer 19

bacteriophage; unstable; genome

Question 20

There are __ primary regions to the mRNA of both prokaryotes and eukaryotes: a _‘__ (does not code for AA); a __ region (called ___ or ___ by GenBank) that begins with a __ __ of - - - and ends with __ of __ possible __ __; and a _‘__ which affects the mRNA’s stability.

Answer 20

3

5’UTR [untranslated region];
coding; ORF [open-reading frame]; CDS [coding sequence]; start codon; AUG; 1 of 3; stop codons
3’UTR

3’UTR

Question 21

The 5’UTR of bacterial mRNA have a __-___ sequence that serves as a binding site for ___.

Answer 21

mRNA; Shine-Dalgarno; ribosomes

Question 22

In prokaryotes, transcription and translation occur ___. ___ attach at the _’ end (specifically the __-___ sequence) and begin ___ before transcription is complete [note: mRNA is not ___ before transcription begins].

Answer 22

simultaneously; ribosomes; 5’; Shine-Dalgarno; translation; modified

Question 23

Changes occur to eukaryotic mRNA including changes to the _’ end, the _’ end, and the __-__ regions before ever leaving the ___.

Answer 23

5’; 3’; protein-coding; nucleus

Question 24

In eukaryotes, a _’ __ is added to mRNA after transcription. This includes adding a modified __ nucleotide to the __; a __ group is added to the ‘-OH of at least the first nucleotide after the __ (corresponding to the +). The __ is required for translation and also impacts the ___ of the molecule.

Answer 24

5’ cap

guanine; end; methyl; 2’; cap/guanine; +1

cap; stability

Question 25

5’CAP of mRNA:
__ is added post-transcription; it’s attached by a _’ - _’ bond with 3 __ (not just one); it has a methyl group aded to the _’ carbon.

Additionally, a __ group is added to the _‘__ of the +1 nucleotide (and sometimes a few more).

Answer 25

Guanine; 5’ - 5’; phosphates; 7

methyl; 2’OH

Question 26

Because of the unique features of the 5’ cap in eukaryotic mRNA, the molecule has two of what? Why?

Answer 26

It has two 3’ ends.

The 5’end of the +1 nucleotide is bound to the 5’ end of the methylated guanine (with 3 phosphates between them) in a ‘mirrored’ arrangement leaving the 3’ end at the end of the molecule.

Question 27

In eukaryotes, -RNA is ___ after ___ with the addition of a _’ __, a ’ __- __; and removal of ___.

Answer 27

mRNA; modified; transcription; 5’ cap; 3’ poly-A tail; introns

Question 28

___ is a process wherein 50 - 250 adenine bases are added to mRNA (__-transcription) with an enzyme complex that includes ___ ___. It starts with ___ of the 3’ end ~ 10 - 30 nucleotides downstream from a consensus sequence (in the _’ __ __). Its purpose includes __ and assisting with ___.

Answer 28

Polyadenylation; post-transcription; polyadenylate polymerase.

cleavage; 3’UTR

stability; translation

Question 29

How might you isolate eukaryotic mRNA in a lab?

Answer 29

Exploit polyadenylation: fix thymine to a plate, incubate with mixed sample; wash, denature/elute.

Question 30

mRNAs coding for what protein lack a poly(a) tail? Why might that be?

Answer 30

mRNAs that code for histones.

Poly(A) tails help with mRNA stability. Since histone mRNAs are only transcribed during S phase, they don’t need to remain stable any longer than S phase.

Question 31

RNA __ (removal of introns) usually occurs after addition of the __ and after __, but before being ___ to the ___.

Answer 31

splicing; cap; polyadenylation; transported; cytoplasm.

Question 32

3 sequences are needed to splice mRNA: (1) a _’ splice site (usually indicated by a GU consensus sequence); (2) a _’ splice site (usually indicated by a AG consensus sequence); and (3) a __ __ located 18 - 40 nucleotides upstream of the _’ splice site (YNYYR_Y consensus sequence wherein the _ is the __ __).

Answer 32

5’;
3’;
branch point; 3’; A; branch point

Question 33

T or F: the GU consensus sequence of the 5’ splice cite and AG consensus sequence of the 3’ splice cite are part of exons to be joined after splicing.

Answer 33

False - they are part of the intron and are therefore spliced out.

Question 34

The __ __ in mRNA is part of the ___ to be spliced and removed.

Answer 34

branch point; intron

Question 35

Small __ __ (AKA snRNPs) are used in mRNA processing.
Splicing of pre-mRNA requires a __ and –RNAs complexed with snRNPs that interact with the pre-mRNA. The –RNAs are ___ to some of the pre-mRNA - this enables the pre-mRNA to be held close enough to the ___ for splicing reactions to occur.

Answer 35

ribonucleoprotein particles

spliceosome; snRNAs;
snRNAs; complimentary; spliceosome

Question 36

Splicing occurs in 2 distinct steps:

(1) pre-mRNA is cleaved at _’ spice site (freeing __ 1); the ’ end of the intron loops to the “” in the __ point to form a __) and forming a novel _’ to ’ phosphodiester bond (“” has 3 bonds)
(2) pre-mRNA is cleaved at the _’ spice site while __ 1 is joined to __ 2; the intron is released as a __; the __ point bond breaks; and the intron is __ by nucleases.

Answer 36

5’; exon
5’; “A”; branch; lariat
5’ to 2’; “A”

3’; exon; exon
lariat
branch
degraded;

Question 37

List the 3 phosphodiester bonds of the adenine in the break point of pre-mRNA introns?

Answer 37

1. a bond between its 5’ carbon and the 3’ carbon of the preceding nucleotide
2. A bond between its 3’ carbon and the 5’ carbon succeeding nucleotide.
3. A bond between its 2’ carbon and the 5’ carbon of the guanine from GU consensus sequence.

Question 38

The self-splicing mechanism of group __ introns is similar to nuclear pre-mRNA introns (__ mediated) which suggests an ___ connection. The enzymatic/catalytic activity depends on the complexity of the ___ structure of the RNA. This catalytic form of RNA is commonly called __ a due to the fact that it’s an RNA-based __ (not protein-based).

Answer 38

II; spliceosome; evolutionary

secondary

ribozyme; enzyme

Question 39

Different proteins derived from the same gene are called ___ or ___ and are the result of __ __ pathways (i.e. they result from one __ unit making one pre-mRNA that is ___ different ways to yield different proteins). This overcomes the issue of more ___ than ___ to produce them.

Answer 39

isoforms; variants; alternative processing
transcription; spliced.

proteins; genes

Question 40

A single gene can yield multiple types of mRNA by all of the following mechanisms EXCEPT:
A. alternative splicing of the exons of the pre-mRNA
B. use of alternative 3’ cleavage and polyadenylation sites in the pre-mRNA.
C. shuffling the order of the exons in the mRNA relative to their order in the DNA.
D. Examples of all of the above have been found.

Answer 40

C. shuffling the order of the exons in the mRNA relative to their order in the DNA.

Question 41

Another form of alternative processing (splicing) is utilization of multiple _’ ___ sites. It may result in alternate forms of an ___, but it might not if __ is downstream of the __ codon in the open __ __.

Answer 41

3’ cleavage

exon; cleavage; stop; reading frame (ORF)

Question 42

The importance of alternative splicing:
It is estimated that up to 60% of human genes have ___ due to alternative splicing (note: __ also refer to proteins from __-__ genes).

Answer 42

isoforms

isoforms; closely-related

Question 43

Many genetic diseases are the result of mutations that affect __ __.

In fact, 15% of single-base mutations leading to disease result in __ errors in the ORF (functionally equivalent to a __-__ mutation).

Some intron mutations can also affect the __ site, but most don’t.

Answer 43

alternative splicing.

splicing; frame-shift

splice site

Question 44

Another alternative processing pathway is RNA ___ wherein the coding sequence is changed after transcription either by ___, ___ and/or ___ substitutions. There are 2 major mechanisms; the first uses gRNAs that are partially ____ to the RNA to be edited and function to ‘stretch and add’ nucleotides (usually to correct a __-__ mutation). The second involves __ activity to __ nucleotides from one to another (e.g. C ➭ U via deamination) which can change a regular codon to a __ codon and result in a shortened ___.

Answer 44

editing; insertion; deletion; nucleotide.

complimentary; frame-shift

enzymatic; convert; stop; polypeptide

Question 45

tRNAs are also known as __ molecules because they join the __ __ to the corresponding __ of the mRNA. Each tRNA is specific for one of the 20 common __ __. Most organisms have 30 - 40 or more tRNAs encoded by __ genes.

Answer 45

adapter; amino acid; codon

amino acids.

different

Question 46

tRNAs contain numerous modified ___ (modified by __ activity). These modifications are made __ synthesis.

Answer 46

bases; enzymatic

after

Question 47

Most organisms have several copies of -RNA genes that are transcribed by RNA polymerase __ as a large precursor molecule that incorporates several -RNA genes. The molecule is then __, __ modified, and __ to produce the mature -RNA. Very few have ___, but it’s not common.

Answer 47

tRNA; III; tRNA

cleaved, chemically modified; trimmed; tRNA

introns

Question 48

> 90% of all RNA in a cell is -RNA.

There are multiple ___ of -RNA genes. In prokaryotes, the genes tend to be ___; in eukaryotes, the genes tend to be ___ (since so much is needed).

Answer 48

rRNA

copies; rRNA.

dispersed; clustered

Question 49

There are four rRNA genes; 3 of the genes are ___ together and transcribed as one ___ molecule by RNA polymerase __: 18S (a __ subunit); 28S and 5.8S (both __ subunits).
The remaining gene is __ from the other 3 and produces rRNA 5S (the __ of the four), and it’s transcribed by RNA polymerase __.
The “S” refers to ___ units and is based on __ during centrifugation; and importantly, it is not ___.

Answer 49

clustered; precursor; I
small; large

separate; smallest; III

Svedburg; movement; additive

Question 50

T or F: rRNA is spliced in a manner similar, but separate, from mRNA.

Answer 50

False; it’s processed, but not spliced.

Question 51

What evidence suggests that RNA was the first genetic material, and as opposed to what? What was the missing puzzle piece that overwhelmingly supports this theory?

Answer 51

It seemed to be the most logical explanation over proteins or DNA.

Couldn’t figure out how RNA could ‘produce’ proteins without enzymes (which are proteins themselves - chicken v. egg); it was the discovery of ribozymes that satisfied this missing piece.

Question 52

__ can inhibit translation of mRNA if it contains ___ sequences. No known mechanism explained this phenomenon in the late 90s, but it did lead to the discovery of 3 classes of small RNAs: __ __ RNAs (degrade mRNA or __ translation); __ RNAs (termed “__” RNA by Crick; interacts with the environment to regulate gene expression); and __-__ RNAs.

Answer 52

dsRNA; complimentary

small interfering; block
microRNAs; “junk”; Piwi-interacting (piRNA)

Question 53

RNAi evolved as a protective mechanism against ___ and ___. It’s triggered by __ molecules.

The __ molecules are chopped by ___ (an ___); then the bits are unwound producing –RNA and –RNA.

Both RNAs combine with proteins to form __-__ __ __ (RISC), and are __ to mRNA (which causes ___ or ___).

Answer 53

protective; viruses; transposons; dsRNA.

dsRNA; Dicer; enzyme;; siRNA and miRNA.

RNA-induced silencing complex; complementary; degradation; interference/inhibition.

Question 54

___ (abbreviation for RNA ___) have been exploited for lab work as a tool to __ gene expression.

Answer 54

RNAi; interference; block