Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BLGY1232 > RNA and Genomes > Flashcards

RNA and Genomes Flashcards

1
Q

hnRNA

A

heterogeneous nuclear RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

RNA Pulse Labelling Experiment

A

1) grow mammalian cells in culture
2) pulse label, provide 32PO4 for only 10 minutes, RNA synthesised in this time is radioactively labelled
3) transfer the cells to a medium containing non-radioactive PO4 (chase)
4) extract RNA at intervals after the transfer and resolve on a gel
5) autoradiography of the gel shows the fate of the RNA labelled during the pulse period

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

RNA Pulse Labelling

Autoradiograph

A

0’ - 5S segment at bottom, 45S segment at the top, large blurred blob at top
5’ - 5.8 and 5 S segments at the bottom, some 45S at the top, a 28S region and an 18S smaller blob and further down
10’ - all of the 45S has gone, 28S, 18S, 5.8S and 5S regions smaller blob
15’-30’ - this remains the same from 15’ onwards

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

RNA Pulse Labelling

Conclusion

A
  • 5S element appears to be made immediately
  • the others (5.8,18,28 S) are transcribed in one big RNA and then cut down afterwards
  • the blob is thought to be mRNAs
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Eukaryotic Ribosomes

A
  • 80S ribosome composed of 40S and 60S subunits
  • the 40S subunit contains 18S rRNA
  • the 60S subunit contains 5S, 5.8S and 26-28S rRNA depending on the organism
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Formation of rRNA

A
  • in nucleolus
  • individual genes simultaneously transcribed by multiple polymerases to generate multiple transcripts
  • multiple genes encoding the same RNA
  • allows large numbers of rRNAs
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Eukaryotic Ribosome Biogenesis

45S

A

-transcribed by RNA polymerase I
ETS-18S-ITS-5.8S-ITS-26-28S
ETS - external transcribed spacer
ITS - internal transcribed spacer
-whole gene is transcribed into one 45S pre-rRNA including ETS and ITS
-nucleases digest this to produce the 5.8S, 18S and 26-28S rRNAs
-there are ~1000 of these identical genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Eukaryotic Ribosome Biogenesis

5S

A
  • transcribed by RNA polymerase III
  • many 5S DNA sequences one after the other, each separately transcribed
  • there are ~100 of these genes
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Eukaryotic Ribosome Biogenesis

Proteins

A
  • transcribed by RNA polymerase II

- 80 genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Why are there more copies of rRNA genes than ribosomal protein genes?

A
  • there are two rounds of replication for protein genes as they are transcribed and translated so to points at which amplification can occur
  • rRNA is only transcribed so need so only one opportunity for amplification
  • so you need more rRNA genes for the same amplification
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Eukaryotic RNA Polymerases and Alpha-Amanatin

A

RNA polymerase I - resistant to alpha amanatin at very high concentrations
RNA polymerase II - sensitive to alpha amanatin at 0.05μg/ml
RNA polymerase III - intermediate sensitivity 10-25μg/ml

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Eukaryotic Messenger RNA

A

Mature mRNA

5’-cap-AUG-codingsequence-UGA-polyAtail

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

R-Loop Analysis

A
  • clone gene
  • collect mRNA
  • mix cloned gene and mRNA
  • denature and re-anneal under conditions that favour the formation of DNA-RNA hybrids
  • found that there were regions in the DNA (loops) that weren’t present in the RNA
  • the looped out regions correspond to introns that are removed from the primary transcript
  • e.g. identification of introns in the adenovirus ‘hexon’ gene
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Splicing

A

1) intron bound by a SNURP
2) SNURP cuts at the GU at the beginning of the intron but holds on to both the intron and the exon
3) the 5’ end of the G residue at the beginning of the intron is ligated to the 2’-OH group of the A residue in the branch point forming a 2’-5’ phosphodiester bond
4) the SNURP proceeds to the AG at the end of the intron where it cuts
5) ligates the -3’ end of the first exon to the 5’- end of the second exon
6) the looped, discarder intron is called a lariat

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

SNURP

A

small, nuclear, ribonucleoprotein particle

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Intron Structure

A

-GU at the beginning of the intron
-A/U rich region
-branch point, CURAY
R - any purine
Y - any pyrimidine
-AG at the end of the intron

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Average Human Gene

A
  • 27kb long (DNA sequence)
  • encodes mRNA of only 2.2kb
  • contains 8-9 introns
  • the average exon is only 150bp long
  • the average intron is 3400bp long
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Longest Human Gene

A

the Duchenne Muscular Dystrophy gene is 2.4 million bp

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Alternative Splicing

A
  • one gene can encode more than one mRNA product

- when the human genome was sequencedit was found that there were many more mRNAs than genes

20
Q

Alternative Splicing

Drosophilia adh Gene

A
  • larval mRNA encodes a high activity alcohol dehydrogenase
  • in adult flies, the same gene is transcribed to synthesise a lower activity alcohol dehydrogenase by alternative splicing
21
Q

Why do eukaryotes have introns?

A
  • exons usually encode protein ‘modules’ and this enables new combinations to arise through shuffling of exons during evolution
  • we can see that in evolutionarily related genes in widely different taxa, the positions of introns are conserved
  • introns allow flexibility in encoding information - the human genome contains ~25000 genes but they encode >50000 different mRNAs by alternative splicing
  • introns may contain regulatory information - experiments in which introns are added or removed from genes show that generally the presence of introns leads to higher levels of gene expression
22
Q

Genome Size

Mad Cow Disease

A

0bp (protein)

23
Q

Genome Size

Cadang-Cadang

A

300nts (ssRNA)

24
Q

Genome Size

m13

A

7000nts (ssDNA)

25
Q

Genome Size

Lambda

A

48000bp

26
Q

Genome Size

E.coli

A

4.6Mbp

27
Q

Genome Size

Yeast

A

12Mbp

28
Q

Genome Size

Arabidopsis

A

125Mbp

29
Q

Genome Size

Drosophilia

A

165Mbp

30
Q

Genome Size

Human

A

3000Mbp

31
Q

Genome Size and Complexity

A
  • genome size is generally associated with complexity
  • there is a minimum number of genes required for a certain level of complexity
  • but an organism may have any amount of DNA on top of this
  • e.g. the largest known genome is 670 000 Mbp and is found in a single celled Amoeba dubia
32
Q

Genome Complexity Analysis

A

1) isolate DNA
2) shear into small fragments (~200bp)
3) denature so that each fragment is split into two single stranded molecules
4) allow to reanneal
5) the more DNA there is in the genome the longer it will take for all of the fragments to reanneal as the chance of a fragment finding its complimentary fragment is smaller than in a smaller genome

33
Q

DNA Reassociation Kinetics

Foldback

A
  • repetitive sequences that can fold and anneal with themselves
  • always reanneal fastest as they don’t have to locate a complimentary sequence
34
Q

DNA Reassociation Kinetics

Highly Repeated

A
  • the second fastest sequences to reanneal
  • highly repetitive so there are thousands of the sequence in the genome and the chances of a molecule annealing with the complimentary sequence are quite high
  • pairing slows down as with time there are fewer unpaired highly repeated molecules remaining
35
Q

DNA Reassociation Kinetics

Middle Repeatative

A
  • third fastest to reanneal
  • sequences present in hundreds of copies in the genome
  • reasonably abundant so don’t pair that slowly
  • rate of pairing slows down with time as there are less available sequences for remaining molecules to pair with
36
Q

DNA Reassociation Kinetics

Single Copy

A
  • sections of DNA that are only present once in the genome
  • this means that there is only one piece of DNA that the unpaired sequence can bind with
  • slowest to completely reanneal
  • only begin pairing when some of the other molecules have annealed and are no longer options
37
Q

What makes up the genome?

A
  • a few genes are present in multiple copies e.g. genes encoding rRNA has 500 copies in the human genome
  • the bulk of DNA does not encode genes
  • most can be traced to transposons
38
Q

Transposons

A
  • mobile genetic elements
  • characterised by terminal inverted repeats
  • the inverted repeats are sites recognised by a transposase enzyme
  • the specific transposase enzyme is encoded by the middle section of the transposon
  • the transposase cuts the transposon out of the genome and reinserts it elsewhere
  • this can sometimes leave small target site duplications
39
Q

Retroviruses

A

-5’ LTR - gag - pol - env - 3’ LTR -
LTR = long terminal repeat
gag = protein involved in integration of DNA copy of viral genome into the host
pol = encodes polymerase (reverse transcriptase) to copy the RNA viral genome into a DNA intermediate
env = encodes the protein capsid of the retrovirus

40
Q

Retrotransposons and Retroviruses

A
  • closely related

- retrotransposons are though to be derived from defective retroviruses

41
Q

LTR Retrotransposons

A

-5’ LTR - gag - pol - 3’ LTR -
LTR = long terminal repeat
gag = protein involved in integration of DNA copy of viral genome into the host
pol = encodes polymerase (reverse transcriptase) to copy the RNA viral genome into a DNA intermediate

-Ty / copia family

42
Q

Non-LTR Retrotransposons

A

-5’ region - gag - pol - 3’ region - polyA -
LTR = long terminal repeat
gag = protein involved in integration of DNA copy of viral genome into the host
pol = encodes polymerase (reverse transcriptase) to copy the RNA viral genome into a DNA intermediate

-Alu / L1 family

43
Q

Retrotransposon Replication

A

1) RNA polymerase II transcribes the retrotransposon into RNA
2) reverse transcriptase makes a DNA copy of the RNA transcript
3) the DNA copy integrates into the genome elsewhere

44
Q

Retrotransposons

A
  • highly repeated in the genomes of all complex eukaryotes
  • replicate and insert a COPY of themselves elsewhere in the genome, so accumulate over time
  • undergo rapid evolution as their reverse transcriptase is highly error prone, sometimes this results in an inability to replicate
  • non-LTR elements account for 33% of the human genome and LTR elements for 8%
  • in some plants (e.g. maize) LTR elements make up 60% of the genome
45
Q

Non-Reciprocal Recomination

A
  • allows repetitive sequences to become amplified
  • crossing over can occur without chromosomes being completely lined up as the same transposon sequence occurs more than once in a chromosome
  • as a result you end up with an increase in the number of copies of the transposon in one chromosome and a decrease in the other chromosome

BLGY1232 (19 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions