Brainscape's Knowledge GenomeTM

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


See full index

MCB 1 > RNA (new) > Flashcards

RNA (new) Flashcards

1
Q

What enzyme do we need to regulate in Transcription of Eukaryotes

A

RNA polymerase II

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

RNA polymerase II

A
  • Cannot initiate transcription
  • Only elongation of existing RNA strand
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Initiation complex of Euk. Transcription

A
  • TFII A/B/D/E/F/H
  • RNA polymerase II
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What regulates Initiation of Euk. Transcription

A

Mediator Complex
- Enhance or block transcription initiation by receiving signals from activators or repressors.

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

Spacer DNA

A
  • Long undefined sequences of DNA (100s/1000s nucleotides)
  • Between the regulatory sequences
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What is the main way Euk. Transcription is Regulated

A

Packing/Unpacking of heterochromatin and Euchromatin
since in packed DNA TATA box is not available

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What causes unpacking of DNA to euchromatin

A

Prime activator proteins which recruit co-activators

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

2 Pathways after Prime activator

A
  • Chromatin Remodeling Complex
    OR
  • Histone Modifying Enzyme
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Co-Activator Chromatin Remodeling Complex

A
  • Recruited by Activator protein
  • Surrounds large area of DNA (4/5 nucleosomes and loosens them
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Co-Activator Histone Modifying Enzyme

A
  • Recruited by Activator protein
  • Covalently modifies Histones by histone acetylation
  • Positive charge is lost weakening interaction with DNA and loosening it
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What happens when DNA unfolds and Core promoter is seen

A

1) Activator protein binds to enhancer sequence
2) Activator protein recruits Histone acetyltransferase acetylating lysine residues
3) Histone Kinase also recruited phosphorylating serine on histones for more repulsion

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

Histone Code

A

Pattern of modifications happening to loosen DNA by histone kinase and histone acetyltransferase

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

What does Histone code recruit and what does it do

A

Chromatin Remodeling complex
- Stabilizes the less condensed chromatin, keeping the DNA accessible.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

TFIID role in Histone Code

A

TFIID also binds the histone code as well as core promoter
So it can engage the initiation of Transcription

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

Ways repressor proteins can act

A
  • Block binding of Activator
  • Binds to silencer sequence and competes with bound activator
  • Repressor and activator compete for mediator complex
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Co-repressors

A
  • Chromatin remodeling complex
  • Histone deacetylase & Histone methyltransferase
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Specific Transcription factors

A
  • Help regulate gene expression by binding to specific DNA sequences called Response Elements
  • Usually Dimeric
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Regulation of Specific Transcription factors

A
  • Protein Synthesis (under transcriptional control itself)
  • Ligand binding (Nuclear-R)
  • Covalent Mod. (undoable)
  • Dimerization
  • Unmasking (removing inh.)
  • Stimulation of Nuclear Entry
  • Release from membrane (because they are anchored)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Regulation of Euk. Gene expression by UTR binding

A
  • RNA Binding proteins (RBP)
  • Bind UTR regions
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

UTR binding example

A

IRE & IREBP in iron starvation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

IRE & IREBP in Iron Starvation

A
  • Cytosolic Aconitase (IREBP)
  • Binds IRE of 5’ UTR of mRNA coding Ferritin, and stabilizes 3’ end for transferrin-R
  • Represses translation of mRNA strand of Ferritin
  • No Ferritin so less storage, more Transferrin-R
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

IRE & IREBP in Iron Excess

A
  • Iron binds Cytosolic Aconitase (IREBP) bound to IRE on mRNA
  • Aconitase removed and no more repression
  • Ferritin Made
  • Aconitase off of 3’ exposes poly-A and causes instability
  • No Transferrin-R made
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What transcribes miRNA and how many are there

A

RNA Polymerase II
(500-2000 genes across different species)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

miRNA main functions summary

A

Inhibitory
- Cleavage of mRNA into 2 pieces
- Destabilization of mRNA by shortening poly-A tail
- Less efficient translation of mRNA to proteins by ribosomes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Biogenesis of Pri-miRNA (primary)

A
  • Synthesized in Nucleus from microRNA genes
  • Introns of protein coding genes or non coding RNA genes
  • Almost all synthesized by RNA polymerase II
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Structure of Pri-miRNA

A
  • Self-complementarity (fold back on themselves)
  • 35bp (ds) stem and single stranded loop (not strict pairing)
  • 5’ cap structure and 3’ poly-A tail
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Pri-miRNA Motifs

A
  • Basal UG motif
  • Flanking CNNC motif
  • Mismatched GHG motif
  • Apical UGU motif
28
Q

Biogenesis of Pre-miRNA

A
  • From Pri-mRNA
  • By Microprocessor (heterotrimeric complex)
  • Exported to cytoplasm by Exportin5 and GTPase
29
Q

Microprocessor

A

Primary to Pre-mRNA
- Enzyme drosha (ribonuclease III) cuts pri-mRNA at 22nd nucleotide of ssloop
- 2 Proteins: DGCR8

30
Q

Biogenesis of miRNA

A
  • By heterotrimeric complex from pre-miRNA
  • Dicer enzyme (ribonuclease III) + TARBP proteins
  • Loop is lost and dsRNA formed
31
Q

miRNA activation

A
  • Binding to Ago protein using guide strand
  • Forms RNA induced silencing complex (RISC)
  • Other strand (passenger) is degraded
32
Q

How does Ago protein decide which strand to chose as guide from mi-RNA

A

Prefers one with A or U at 5’end or less stable 5’end

33
Q

RNA editing - miRNA formation modification

A
  • ADAR enzymes catalyze deamination of Adenine to Inosine within the pri-mRNA transcript
  • Inosine is structurally similar to guanine and is read as guanine by machinery
  • Causes either Destabilization and degradation of pri-mRNA or an edited mature miRNA with altered specificity
34
Q

What does RNA editing + Alternative cleavage make?

A

IsomiRs

35
Q

What is edited more frequently RNA transcripts of miRNA genes or protein coding genes?

A

miRNA since they have a regulatory role

36
Q

Mitrons

A
  • Form from introns of protein coding genes
  • When intron is spliced it escapes degradation and remains in nucleus
  • Debranched and forms pre-miRNA
37
Q

Seed region

A
  • Small part of miRNA sequence that is important for finding its target mRNA
  • First base very important for its specificity: usually Adenine
38
Q

Where does miRNA bind mRNA

A

At 3’ UTR

39
Q

TNRC6 outcomes

A
  • TNRC6 brings proteins to break down mRNA (main way)
  • TNRC6 can also stop its translation to protein without degradation (less efficient)
40
Q

miRNA vs siRNA

A
  • miRNA: reduce expression of target gene
  • siRNA: completely eliminate the expression of a target gene
41
Q

DNA methylation

A
  • By SAM
  • Changes activity of DNA segment without changing the sequence
  • Usually in CpG dinucleotides (5th carbon of c then g on backbone)
  • Silences genes
42
Q

Importance of Cytosine deamination in methylation

A
  • Usually C deamination forms Uracil
  • But, methylated C deamination forms Thymine
  • This is one of the most frequent mutations
43
Q

Pioneer TFs

A

Weirdly prefer methylated sites on DNA rather than the usual TFs that prefer unmethylated

44
Q

Cassette Exon

A

Can be removed with introns or remain as part of the mRNA

45
Q

Alternative 3’/5’ splicing

A

Exon is longer or shorter at the 3’/5’ splice site

46
Q

Mutually exclusive exons

A

2 exons next to each other with an intron in between, but only 1 can remain in the final mRNA so 1 has to be spliced out

47
Q

Alternative Promoter

A
  • More than one promoter on a strand
  • If first promoter is used whole thing is transcribed
  • If second promoter is used the previous part is not incorporated in the pre-mRNA
48
Q

How are some introns spliced and some not in other cells?

A

We have Negative & Positive control with Splicing repressors and Splicing activators which binds intron splice sites

49
Q

Alternative Poly-A site

A
  • Resting B Cell: Low Cstf so weak poly-A site not recognized (membrane bound IgM)
  • Active B Cell: High Cstf recognizes weak poly-A site and early cleavage
    (free IgM)
50
Q

mRNA degradation methods

A
  • Poly-A tail removal/shortening
  • Decapping
    (allows exonucleases to act)
51
Q

RNA editing

A

Example that mRNA coding for ApoB-100 has base CAA
- In liver: No RNA editing so full mRNA translated
- In intestines: RNA editing by deamination and C forms U. (UAA)
Early stop codon and truncated protein formed ApoB-48

52
Q

Non-Sequence Specific Approach

A

Measuring overall gene expression in a sample
1) mRNA reverse transcribed to cDNA (dsDNA)
2) SYBR Green dye used to bind cDNA
3) Fluorescence only when bound to cDNA
4) PCR amplifies cDNA making more and hence more fluorescence detected

53
Q

Advantages of Non-Sequence Specific Approach

A
  • The SYBR Green dye can be used for any genes being studied
  • It is a non-specific DNA binding dye
54
Q

Disadvantages of Non-Sequence Specific Approach

A
  • Lack of specificity may lead to detection of non-specific amplification products
  • Primers can form complex with dye giving signal (false signal)
55
Q

Probe

A

Short ssDNA oligonucleotide complementary to target gene

56
Q

Probe parts

A
  • Reporter molecule (5’): Fluorophore
  • Quencher molecule (3’): Absorbs emitted fluorescence
57
Q

Sequence specific approach when Probe is intact

A

1) Reporter excited by λ1 emitting λ2
2) λ2 absorbed by Quencher
3) No signal is detected

58
Q

Sequence specific approach when Probe is Degraded

A

1) During PCR, DNA polymerase with 5’ exonuclease activity cuts probe
2) Reporter, Nucleotides & Quencher released
3) Fluorescence can be detected

59
Q

Advantages of Sequence specific approach

A
  • Always reliable
  • If probe not digested then no signal
60
Q

Disadvantages of Sequence specific approach

A

A difference Probe is needed for each gene we want to analyze

61
Q

Threshold intensity

A

Amount of PCR product that can be reliably detected during efficient phase

62
Q

Threshold cycle

A

Cycle number at which the amount of PCR product reaches the threshold intensity

63
Q

Types of Quantification

A
  • Relative Quantification
  • Absolute Quantification (uses standard calibration curve)
64
Q

DNA Microarray/Chip

A

Solid surface (glass/silicone) where thousands of known DNA sequences (probes) representing genes are immobilized in an organized grid/array

65
Q

DNA Microarray method

A

1) RNA extracted from sample
2) Reverse Transcription to cDNA
3) cDNA labelled with fluorescent dye
4) Placed on microarray
5) If cDNA binds probes it means the gene was expressed
(analysis of genome wide expression)

MCB 1 (3 decks)

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