Chapter 14 - RNA Molecules & RNA Processing Flashcards
In bacteria, ___ often begins before ___ is completed.
Translation; transcription
A male fly that is ___ for a mutation in the fru gene is ___.
homozygous; bisexual
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
C. Human cells
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
A. 5’ Untranslated Region
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 ___.
colinear
bacteria and viruses
With ___, the number of nucleotides is ___ to the number of amino acids.
collinearity; proportional
_-__ 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 ____).
R-looping; colinear.
denaturing; annealing; nonsense/complimentary; loops.
looped; introns
___ (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 __.
Exons; RNA.
Introns; RNA.
eukaryotes; bacteria; viruses
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.
intron; vertebrates
dystrophin; 12K; 2M
Introns are very ___ relative to ___.
large; exons
Name the 4 major classes of introns. Which of the 4 is the “major”?
Group I, Group II, Nuclear pre-mRNA; and Transfer RNA
nuclear pre-mRNA
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.
Group I introns
These introns are found in protein-coding genes of mitochondria/chloroplasts and some bacteria, and are self-splicing (have catalytic/enzymatic activity).
Group II introns
__ __ 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 ____.
Nuclear pre-mRNA; group II; snRNAs; splicosome
These introns utilize a splicing mechanism that was not covered in lecture.
Transfer RNA introns.
A gene is a __ __ that contains three things: a __, __ __ sequences, and a ___. The __ __ sequences include all __ and __.
transcription unit; promoter; RNA coding; terminator.
RNA coding; introns; exons
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 ___.
regulatory; core; open reading; terminator; exons; introns
T or F: DNA can directly encode information for the synthesis of proteins.
Depends: True for bacteria, false for eukaryotes since RNA synthesis includes slicing and dicing before translation.
mRNA was discovered by experiments using ___ that resulted in the synthesis of a very ___ RNAs with a nucleotide composition very different from the bacterial ___.
bacteriophage; unstable; genome
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.
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
The 5’UTR of bacterial mRNA have a __-___ sequence that serves as a binding site for ___.
mRNA; Shine-Dalgarno; ribosomes
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].
simultaneously; ribosomes; 5’; Shine-Dalgarno; translation; modified
Changes occur to eukaryotic mRNA including changes to the _’ end, the _’ end, and the __-__ regions before ever leaving the ___.
5’; 3’; protein-coding; nucleus
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.
5’ cap
guanine; end; methyl; 2’; cap/guanine; +1
cap; stability
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).
Guanine; 5’ - 5’; phosphates; 7
methyl; 2’OH
Because of the unique features of the 5’ cap in eukaryotic mRNA, the molecule has two of what? Why?
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.
In eukaryotes, -RNA is ___ after ___ with the addition of a _’ __, a ’ __- __; and removal of ___.
mRNA; modified; transcription; 5’ cap; 3’ poly-A tail; introns
___ 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 ___.
Polyadenylation; post-transcription; polyadenylate polymerase.
cleavage; 3’UTR
stability; translation
How might you isolate eukaryotic mRNA in a lab?
Exploit polyadenylation: fix thymine to a plate, incubate with mixed sample; wash, denature/elute.
mRNAs coding for what protein lack a poly(a) tail? Why might that be?
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.
RNA __ (removal of introns) usually occurs after addition of the __ and after __, but before being ___ to the ___.
splicing; cap; polyadenylation; transported; cytoplasm.
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 __ __).
5’;
3’;
branch point; 3’; A; branch point
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.
False - they are part of the intron and are therefore spliced out.
The __ __ in mRNA is part of the ___ to be spliced and removed.
branch point; intron
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.
ribonucleoprotein particles
spliceosome; snRNAs;
snRNAs; complimentary; spliceosome
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.
5’; exon
5’; “A”; branch; lariat
5’ to 2’; “A”
3’; exon; exon
lariat
branch
degraded;
List the 3 phosphodiester bonds of the adenine in the break point of pre-mRNA introns?
- a bond between its 5’ carbon and the 3’ carbon of the preceding nucleotide
- A bond between its 3’ carbon and the 5’ carbon succeeding nucleotide.
- A bond between its 2’ carbon and the 5’ carbon of the guanine from GU consensus sequence.
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).
II; spliceosome; evolutionary
secondary
ribozyme; enzyme
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.
isoforms; variants; alternative processing
transcription; spliced.
proteins; genes
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.
C. shuffling the order of the exons in the mRNA relative to their order in the DNA.
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 __ __.
3’ cleavage
exon; cleavage; stop; reading frame (ORF)
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).
isoforms
isoforms; closely-related
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.
alternative splicing.
splicing; frame-shift
splice site
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 ___.
editing; insertion; deletion; nucleotide.
complimentary; frame-shift
enzymatic; convert; stop; polypeptide
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.
adapter; amino acid; codon
amino acids.
different
tRNAs contain numerous modified ___ (modified by __ activity). These modifications are made __ synthesis.
bases; enzymatic
after
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.
tRNA; III; tRNA
cleaved, chemically modified; trimmed; tRNA
introns
> 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).
rRNA
copies; rRNA.
dispersed; clustered
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 ___.
clustered; precursor; I
small; large
separate; smallest; III
Svedburg; movement; additive
T or F: rRNA is spliced in a manner similar, but separate, from mRNA.
False; it’s processed, but not spliced.
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?
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.
__ 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.
dsRNA; complimentary
small interfering; block
microRNAs; “junk”; Piwi-interacting (piRNA)
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 ___).
protective; viruses; transposons; dsRNA.
dsRNA; Dicer; enzyme;; siRNA and miRNA.
RNA-induced silencing complex; complementary; degradation; interference/inhibition.
___ (abbreviation for RNA ___) have been exploited for lab work as a tool to __ gene expression.
RNAi; interference; block
