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Genetics > Exam 2: Coding and Noncoding RNA > Flashcards

Exam 2: Coding and Noncoding RNA Flashcards

1
Q

what was the nature of the defect that cause hemophilia in the family of Tsar Nicholas

A

there was a splice site mutation in the gene (F9) on X chromosome for hemophilia which resulted in an intron not being removed and thus not spliced correctly. Consequence is a piece of RNA left that should not be there resulting in a few aas added (1 or 2 nucleotides added). Not a coding change but change in nucleotide at splice jxn so spliceosome doesn’t recognize splice site and cannot splice correctly

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2
Q

number of nucleotides in a gene should be proportional to

A

the number of aas in the encoded protein (collinearity)

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3
Q

t/f: mRNA is longer than dna

A

false; dna is much longer than mRNA demonstrated through hybridization

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4
Q

the concept of conlinearity

A

suggests that a continuous seq of nucleotides in dna encodes a continuous seq of aas in a protein’ the number of nucleotides in the gene is proportional to the number of aas in the protein

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5
Q

is the coding seq in a gene always continuous?

A

no, coding seqs in a gene may be interrupted by noncoding seqs; the noncollinearity of euk genes was discovered by hybridizing DNA and mRNA (mix dna and its complementary rna, separate, reanneal with its complementary strand or with rna, and noncoding regions of dna are seen as loops)

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6
Q

the coding seq (exons) of most euk genes are disrupted by _

A

noncoding introns

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7
Q

dna is transcribed into rna, and introns are removed via

A

rna splicing

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8
Q

what are the 2 mechanisms of splicing

A
  1. self-splicing (w/in the intron contain info to catalyze self-splice)
  2. splicesomal machinery within cells
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9
Q

the gene includes:

A
  • dna seqs that code for all exons and introns
  • those seqs at the beginning and end of the rna that are not translated into a protein, including the entire transcription unit: the promoter, the rna coding seq, and the terminator
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10
Q

structure of a mature mRNA

A
  • mature mRNA contains a 5’ UTR (leader seq for ribosome to attach and start translation)
  • protein-coding region
  • 3’UTR (site of miRNA binding)
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11
Q

3’UTR almost always has a

A

poly A tail attached to it and usu where miRNAs bind

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12
Q

pre-mRNA processing includes:

A
  • the addition of the 5’ cap (protection/orientation; a nucleotide with 7-methylguanine; 5’-5’ bond is attached to the 5’ end of the RNA)
  • the addition of the poly A tail (50-250 adenine nucleotides added to the 3’ end of the mRNA
  • need to be added before leaves nucleus along w/ splicing of introns*
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13
Q

unprocessed mRNA contains:

A

exons, introns, lack of 5’ cap and 3’ poly A tail

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14
Q

addition of 5’ cap function:

A

facilitates binding of ribosome to 5’ end of mRNA, increases mRNA stability

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15
Q

3’ cleavage and addition of poly A tail function:

A

increases stability of mRNA, facilitates binding of ribosome to mRNA

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16
Q

RNA splicing function

A

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

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17
Q

RNA editing function

A

alters nucleotide seq of mRNA

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18
Q

t/f: most euk mRNAs have a 5’ cap

A

true

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19
Q

t/f: most euk mRNAs have a 3’ poly A tail

A

true; pre-mRNA is cleaved, at the position downstream of the consensus seq in the 3’ UTR, and adenine nucleotides are added (branch point the “A” 18-40 nucleotides upstream of 3’ splicing site)

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20
Q

what is the significance of the boundaries at the 5’ and 3’ ends

A

the consensus seqs in the 5’ and 3’ show that there can be different nucleotides alluding that we still don’t know everything bc the info encoded there is for the spliceosome for its recognition

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21
Q

the spliceosome consists of

A

5 RNAs, which organizes the set of proteins (brains), and 300 proteins that does the work (enzymatic)

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22
Q

t/f: consensus seqs are not cut sites

A

true

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23
Q

splicing of pre-mRNA requires _

A

consensus seqs; critical consensus seqs are present at the 5’ splice site and 3’ splice site

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24
Q

RNA splicing takes places w/in the

A

spliceosome; the spliceosome subunits are arranged around the 5 spliceosome RNAs and assembles sequentially as the steps occur

25
Q

pre-mRNA processing: nuclear organization

A

intron removal, mRNA processing, and transcription take place at the same site in the nucleus

26
Q

minor splicing

A

achieved by the minor spliceosome; non-canonical splicing (U12-type introns)

27
Q

self-splicing introns in some rRNAs in:

A

protists and in mitochondrial genes in fungi

28
Q

euk cells have alternative pathways for processing pre-mRNA which results in:

A
  • pre-mRNA can be spliced in different ways to produce different mRNAs
  • w/ multiple 3’ cleavage sites, there are 2 or more potential sites for cleavage and polyadenylation; use of the different sites produces mRNAs of different lengths
  • conclusion: both alternative splicing and multiple 3’ cleavage sites produce diff mRNAs from a single pre-mRNA*
29
Q

example of pre-mRNA and tissue type dependence

A

pre-mRNA encoded by the gene for calcitonin undergoes alternative processing depending on the tissue

30
Q

what is rna editing

A

coding seq altered after transcription (post-transcriptional)

31
Q

how does rna edited occur

A

unedited mRNA pairs with guide RNA, guide RNA serves as a template for the addition, deletion, or alteration of bases.
rna editing is carried out by guide RNAs and guide RNAs add nucleotides to the mRNA that were not encoded by the DNA

32
Q

what are the general steps to pre-mRNA processing (6)

A
  1. introns, exons, and a long 3’end are all transcribed into pre-mRNA
  2. 5’ cap is added
  3. 3’ end is cleaved, 10 nucleotides downstream of the consensus seq
  4. polyadenylation at the cleavage site = poly A tail
  5. introns are removed
  6. mature mRNA is produced
33
Q

dicer functions how again?

A

dicer cleaves double-stranded RNA and pre-miRNA into short double-stranded RNA fragments called siRNA and miRNA (mechanism of gene regulation)

34
Q

transcription and processing of miRNAs occur via (3 steps)

A
  1. miRNAs transcribed by RNA polymerase II (pri-microRNA) which are processed in pre-microRNA
  2. pre-microRNA is transported to cytoplasm and processed by Dicer into mature miRNA (22 nucleotides)
  3. mature miRNA is incorporated into a ribonuclear particle to form RISC which mediates gene silencing
35
Q

what are small interfering RNA (siRNA)

A

aka as short interfering RNA or silencing RNA; class of double-stranded RNA molecules (20-25 bp) similar to miRNA by interfering with the expression of specific genes with complementary nucleotide seqs by degrading mRNA after transcription, preventing translation

36
Q

RNA silencing leads to

A

the degradation of mRNA or to the inhibition of translation or transcription

37
Q

origin of siRNA:

A

mRNA, transposon, or virus

38
Q

origin of miRNA:

A

RNA transcribed from distinct gene

39
Q

siRNA cleavage of:

A

RNA duplex or single-stranded RNA that forms long hairpins

40
Q

miRNA cleavage of:

A

single-stranded RNA that forms short hairpins of double-stranded RNA

41
Q

siRNA size:

A

21-25 nucleotides

42
Q

miRNA size:

A

21-25 nucleotides

43
Q

siRNA action:

A

degradation of mRNA, inhibition of transcription, chromatin modification

44
Q

miRNA action:

A

degradation of mRNA, inhibition of translation, chromatin modification

45
Q

siRNA target:

A

genes from which they were trancribed

46
Q

miRNA target:

A

genes other than those form which they were transcribed

47
Q

small noncoding RNAs (snoRNA)

A

primarily guide chemical modifications of other RNAs, mainly rRNAs, tRNAs, and small nuclear RNAs (spliceosomal RNAs)

48
Q

what are the 2 main classes of snoRNAs

A
  1. C/D box snoRNAs (methylation)
  2. H/ACA box snoRNAs (pseudouridylation)
    * adds nucleotides/changes charge*
49
Q

importance of long noncoding RNAs

A

less than 2% of the human genome encodes proteins but most of our dna still gets transcribed thus lncRNAs must not be ‘junk’ because it would be a burden (much energy consumed in transcription) on the cell. it would be selectively advantageous to get rid of these noncoding RNAs to save energy so we they are not unimportant, we just don’t know what it does

50
Q

why are we optimistic with lncRNAs

A

therapeutic notion; continued study w/ noncoding transcriptome has promise in understanding normal physiology and disease

51
Q

what are the 2 modified bases found in tRNAs

A
  1. ribothymine (from uracil add methyl group)
  2. pseudoruradine (arrangement of ribose sugar to diff atom) most common in rRNAs
    * changing atoms/atom arrangement causes change in charge; essential for tRNA function*
52
Q

all tRNAs possess a common secondary structure called the _ structure which is important for

A

common secondary structure called the cloverleaf structure. contain info for enzymatic and catalytic fcn ie cleavage, splicing (self), base addition, and base modification
modifications are important for maintaining secondary structure and enzymatic fcn

53
Q

anticodon is

A

the anticodon comprises three bases and interacts with a codon in mRNA

54
Q

for euks rRNAs, they contain a distinct seq for

A

clearly different evolution trajectory

55
Q

ribosomal RNA is processed after

A

transcription

56
Q

prok and euk rRNA are produced from precursor RNA transcripts that are:

A

methylated, cleaved, and processed to produce mature rRNAs

57
Q

describe CRISPR

A

CRISPR RNAs is a family of DNA seq found in genomes of proks (bacterial defense mech) and these seqs are derived from DNA fragments of bacteriophages that previously infected prok. they are used to detect and destroy DNA from similar future invaders and thus play a role in antiviral (antiphage) defense sys of proks

58
Q

2 distinct functions w/in sequence of dna describes

A

an operon

Genetics (37 decks)

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