Chapter 13 Flashcards by Julia Nauman

Evidence suggests RNA was the original genetic material: Ribozymes

Cut out parts of their own sequence

Connect RNA molecules

Replicate

Catalyze formation of peptide bonds between proteins

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rRNA

B&E, cytoplasm

Function: Structural & functional components of the ribosome

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mRNA

B&E, nucleus & cytoplasm

Carries genetic code for proteins

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tRNA

B&E, cytoplasm

Helps incorporate amino acids into polypeptide chain

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snRNA

Eukaryotic, nucleus

Processing of pre-mRNA

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SnoRNA

Eukaryotic, nucleus

Processing and reassembly of rRNA

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MiRNA

Eukaryotic, N&C

Inhibits translation of mRNA

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siRNA

E, N&C

Triggers degradation of other RNA molecules

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piRNA

Eukaryotic, N&C

Suppresses the transcription of transposable elements in reproductive cells

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crRNA (CRISPR)

Prokaryotic

Assists in destruction of foreign DNA

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Transcription needs 3 things

A DNA Template
Raw materials (ribonucleotide triphosphates)
Transcription apparatus: proteins

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How did they find the Christmas trees structure?

Deoxyribonuclease= loss trunk
Ribonuclease= loss of branches

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Transcription Unit

Stretch of DNA that encodes an RNA molecule and sequences necessary for its transcription.

Includes RNA coding sequence, promotor, and terminator

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RNA coding sequence

sequence of DNA nucleotides that copied into an RNA molecule.

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Promotor

DNA sequence where transcription apparatus binds, determines which strand to use and transcription start site

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Terminator

sequence that signals where to end transcription

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RNA is synthesized from ____________________. In RNA synthesis, nucleotides are added to the ____ of the RNA molecule (phosphodiester bond).

Ribonucleoside triphosphates (rNTPs)

3’-OH

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Does initiation of RNA synthesis require a primer?

Bacterial RNA polymerase

2x alpha
1x beta
1x beta prime
Stabilizing enzyme w

The core enzyme catalyzes elongation of RNA molecule by the addition of RNA molecules

The sigma factor

controls the binding of RNA polymerase to the promoter.

Without sigma, RNA polymerase initiates transcription at random point along DNA.

Sigma + core enzyme =

holoenzyme

RNA polymerase 1 transcribes…

Larger rRNAs

RNA polymerase 2 transcribers…

pre-mRNA, snoRNA

Some:
snRNAs
mi RNAs

RNA polymerase 3 transcribes…

t RNA, small rRNAs,

some:
snRNAs
miRNAs

Plant only RNA polymerase

4- some siRNAs | 5- heterochromatin formation

Initiation

when the transcription apparatus assembles on the promoter and begins the synthesis of RNA

Elongation

DNA is threaded through RNA polymerase, the polymerase unwinds the DNA and adds new nucleotides, one at a time, to the 3′ end of the growing RNA strand

Termination

recognition of the end of the transcription unit and the separation of the RNA molecule from the DNA template. RNA released for RNA polymerase. RNA separated from DNA RNA polymerase detach from DNA

Important steps in initiation

1. promotor recognition 2. formation of transcription bubble 3. creation of first bonds between rNTPs 4. Escape of the transcription apparatus

Bacterial promoters

sequences recognized by the transcription apparatus (holoenzyme) & required for transcription. Tells where to start, what strand to use, and what direction to transcribe. Consensus sequences: sequences that possess similarity. -10 consensus: 10bp upstream of start site Pribnow box: -5'TATAAT3' -3'ATATTA5' -35 consensus sequence: TTGACA

Termination: Rho-dependent

Use rho factor 1. DNA sequence of the terminator itself 2. DNA sequence upstream of the terminator that encodes a stretch of RNA that is unusually rich in cytosine nucleotides and devoid of any secondary structures. Rut site= rho utailization site

Termination: Rho-independent termination

hairpin structure formed by inverted repeats, followed by a string of uracils. Because hairpin/weak U-A bonds, destabilizes RNA-DNA binding String of U causes RNA polymerase to pause giving time for the hairpin to form.

Promoters: What initiates transcription? (E)

Basal transcription apparatus (aka RNA polymerase & general transcription factors)

Promoters: Transcriptional Activator Proteins (E)

Bring basal transcription apparatus to the promoter and increase transcription above rates of the basal apparatus

Promotors: RNA polymerase 2 (E)

mRNA synthesis

Core Promoter TATA box TATAAAA (E)

located upstream of gene has consensus sequences -25- -30 bp, binded by general transcription factors

Regulatory Promoter

Variety of different consensus sequences Transcriptional activator proteins bind and modify transcription

Overall, remember that initiation has

RNA polymerase 2 + general transcription factors | TATA binding protein

What is the difference between core promoter and regulatory promoter?

The regulatory promoter is farther upstream. AND Transcription factors bind to the core promoter, transcriptional activator proteins bind to regulatory promoters

RNA polymerase 1 Termination requires...

a termination factor like rho which binds to DNA sequence

RNA polymerase 3 termination is

similar to rho-independent except no hairpin structure (inverted repeats). Strings of uracils signal termination.

RNA polymerase 2 termination

When Rat1 reaches polymerase

What suggests archaea is related to eukaryotes

RNA polymerase similar to eukaryotes than eubacteria Acraea promoters have similar TATA box found in eukaryotic promoters Archaea posses a TATA binding protein