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Bio 226 > Topic 6 > Flashcards

Topic 6 Flashcards

1
Q

What is the central dogma of biological change of DNA to protein?

A

Information stored in DNA is unidirectionally transferred to RNA molecules during transcription and to proteins during translation

Slides 3-7
Slide 17 as we understand it today

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2
Q

Can RNA self replicate?

Can it be retrotranscribed to DNA?

A

RNA can replicate itself
RNA dependant RNA polymerase activity in RNA viruses

RNA can be retrotranscribed to DNA
Retrotranscriptase activity in retroviruses

Slides 9-12

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3
Q

Who is the original self replicator?

A

RNA
can store info (primary function of DNA)
Can transduce DNA messages into protein (primary function of RNA)
Can read info and catalyze reactions as ribozimes (primary function of proteins)

Slide 18

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4
Q

Overview the processes of transcription and translation in prokaryotes and eukaryotes on slides 20-21

A

Ok

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5
Q

How is the information in the DNA mechanistically transmitted to proteins in cells?

A

Transcription/RNA processing/translation

  1. Gene expression (RNA synthesis)
  2. mRNA processing (5’ capping, polymerization of poly A tail, intron splicing)
  3. mRNA transport
  4. mRNA translation

Slide 24

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6
Q

How is RNA synthesized?

A

RNA is synthesized in the nucleus, transported to the cytoplasm
Pulse chase labeling
Labeled RNA is exclusively in the nucleus
Later the labeled RNA is found in the cytoplasm
RNA synthesized in the nucleus and then transported to the cytoplasm

Slide 25

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7
Q

What are the 5 different RNA molecules involved in translation?

A 
Messenger RNA (mRNA)- intermediates that carry generic info from DNA to ribosomes 
Small nuclear RNA (snRNA)- structural components of spliceosomes
Transfer RNA (tRNA)- adaptors between amino acids and the codons in mRNA
Ribosomal RNA (rRNA)- structural and catalytic components of ribosomes 
Micro RNA (miRNA)- short single stranded RNAs that block expression of complementary mRNAs

Slide 26

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8
Q

What are the features of RNA synthesis?

A

Similar to DNA synthesis except the precursors are ribonucleoside triphosphates (not deoxy), only one strand of DNA is used as template, RNA chains can be initiated de novo, uracyl instead of thymine

The RNA molecule will be complementary to the DNA template (antisense) strand and identical to the DNA nontemplate (sense) strand (except that uridine replaces thymidine)

RNA synthesis is catalyzes by RNA polymerases and ALWAYS proceeds in the 5’->3’ direction

Slide 27-34

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9
Q

What are the stages of transcription in prokaryotes?

A
  1. RNA chain initiation
  2. RNA chain elongation
  3. RNA chain termination

Slide 35

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10
Q

What is the first stage of transcription?

A

RNA polymerase binding to promoter
Initiation
After binding of RNA polymerase holoenzyme to promoter, localized unwind of 2 DNA strands by RNA polymerase to provide single stranded template
Formation of phosphodiester bonds between the first few ribonucleotides in the nascent RNA chain

Slides 36-39

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11
Q

What is the second stage of transcription?

A

Elongation
Rewinds the 2 DNA strands after done replicating new RNA strand

Slide 40

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12
Q

What is the 3rd stage of transcription?

A

Termination
Intrinsic mechanism
RNA being released

Rho dependant terminators- require a protein factor (ρ)
Ribosomes occupy transcript, cannot bind, stop codon in mRNA triggers release of attached ribosomes opening room for rho to bind, rho migrates on RNA and reaches polymerase where it rewinds the DNA closing the bubble

Rho independent terminators- do not require ρ

Slides 41-49

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13
Q

What are the 3 post transcriptional modifications (editing) of mRNAs?

A

Intron splicing
5’ capping
3’ poly-adenylation

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14
Q

What are the differences between prokaryotic and eukaryotic transcription?

A

One RNA polymerase vs 3 RNA polymerases
Sigma factors vs multi subunit general transcription factors
Co transcriptional translation vs spatially separated transcription and translation
Simple transcript vs processed (cap, introns/Exons, poly A tail)
DNA (almost naked) vs chromatin

Slide 51

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15
Q

What are the challenges in eukaryotic transmission?

A

Harder to locate the promoter, genome is bigger, genes are more spaced out
Transcription and translation are decoupled- they take place in different cellular components (nucleolus and cytoplasm)
Eukaryotic DNA is wrapped up around proteins- histones that need to be removed/moved for transcription to occur
Eukaryotic transcription is more complex- holoenyme has more subunits, transcriptional factors are required to recruit the polymerase and there are several types of RNA polymerases

Slide 52

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16
Q

What is RNA polymerase II?

A

transcribes mRNA and some functional RNAs
Assisted by transcriptional factors, protein complexes that help it recognize and initiate transcription at the promoter
Many RNA pol promoters contain TATA box, but not all promoters
TATAless promoters use other elements to direct RNA pol II

Slide 54-55

17
Q

How is transcription initiated in eukaryotes?

A

TFIID vins the promoter at the TATA box via TBP
Other TFs associate leading to the formation of the pre initiation complex
RNA polymerase starts synthesis and leaves the promoter and TFIID behind
This is coupled to the phosphorylation of RNA pol at the c terminus domain (CTD)

Slide 56

18
Q

What is the 7 methyl guanosine cap?

A

Protects mRNA from nucleases
Recognition signal for translation machinery

Slide 58

19
Q

What are the co transcriptional processing of RNA during elongation splicing and poly A polymerization?

A

Splicing- RNA splicing machinery, process of removing introns, must be very precise, branch point adenine

Poly A polymerization- poly A tail added

Slides 57-62
Slide 70

20
Q

What is the 3’ poly (A) tail?

A

Mediates mRNA transport across the nuclear envelope

Enchanted mRNA stability in the cytoplasm

Slide 61

21
Q

How does protein diversity arise from transcription of a limited number of genes?

A

Splicing and generation of alternative transcripts explains the diversity

Slide 65-66

22
Q

What are introns?

A

Noncoding sequences that interrupt coding sequences, or exons
Introns are excised from the RNA transcripts prior to their transport to the cytoplasm
Located between coding sequences
Introns are removed from the pre-mRNA and are not present in the processed mRNA
Exons (expresses regions) are composed of the sequences that remain in the mature mRNA after splicing

Slide 67-69

23
Q

What is the biochemistry of exon splicing?

A

2 consecutive transesterification reactions transfer the phosphodiester bonds from exon-intron boundaries to exon-exon

Slide 71

24
Q

What are the 2 main mechanisms of splicing evolved in eukaryotes?

A
  1. Self splicing- primary transcript with enzymatic activity (ribozyme)
    Slide 76 example
  2. RNA/protein complex mediated splicing- enzymes/snRNAs needed to recognize and mediate intron excision (spliceosome)

Slide 72

25
Q

What is spliceosome dependant spicing?

A

RNA/protein structure
Excises introns from nuclear pre-mRNA
5 snRNAs: U1, U2, U4, U5, U6
Some snRNAs associate with proteins to form SNRP (small nuclear ribonucleoproteins)

Slide 73

26
Q

What is the spliceosome assembly and function?

A

To facilitate the reaction, the RNA in the SNRPs bind the transcript to bring the exons in close proximity
The intron sequences are removed with the formation of a loop (lariat)

Slide 74-75

27
Q

What are all 6 functional RNAs?

A

tRNA- carry amino acids to ribosome for protein synthesis
rRNA- RNA components of ribosome
snRNA- involves in splicing of eukaryotic RNAs into mRNAs
miRNA- micro RNA processes from larger RNA regulate translation and RNA stability
siRNA- small interfering RNA that are part of RNAi pathway, help prevent transposon and viral mobilization
piRNA- piwi RNAs small RNAs that help prevent transposon and viral mobilization by silencing at the level of chromatin

Slide 77

Bio 226 (9 decks)

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