RNA Metabolism Flashcards by Megan Carnahan

What has greater structural diversity: DNA or RNA?

RNA

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What process makes RNA?

transcription of DNA

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What are the 3 major types of RNA?

mRNA
rRNA
tRNA

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mRNA

messenger RNA
carries info from DNA

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rRNA

ribosomal RNA
makes ribosome that makes protein

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tRNA

transfer RNA
translates mRNA into amino acids

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siRNA

small interfering RNA
block gene expression by increasing mRNA breakdown and decrease in protein
made synthetically

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miRNA

microRNA
regulate mRNA
suppress translation
come from other RNA

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snRNA

small nuclear RNA
helps process mRNA

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snoRNA

small nucleolar RNA
helps process rRNA

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How is RNA synthesis similar to DNA synthesis?

same fundamental mechanism
same direction
uses a template

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How is RNA synthesis different from DNA synthesis?

no primer required
only copies small sections at a time
only 1 strand is a template strand

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RNA Polymerase

makes RNA and binds to promoter region in DNA

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RNA synthesis makes more errors than DNA synthesis. Why is this not as detrimental?

more copies of RNA and higher turnover

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What do the magnesium ions in RNA synthesis do?

one stabilizes the deprotonated 3’ OH
one coordinates incoming nucleotide

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DNA bubble

about 17 base pairs of DNA where active replication is ongoing

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What do promoters signal?

start point
level of expression
template strand

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sigma factor

determines the promotor to bind to

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sigma subunits

bind to different promoters
used under different conditions

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In DNA dependent synthesis, RNA polymerase and sigma factor bind together and then to what?

The promotor

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What opens the complex to start transcription in DNA dependent synthesis?

DNA bubble

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In the elongation phase of DNA dependent synthesis, sigma factor dissociates. What binds in its place?

NusA

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Can RNA polymerase be resused?

yes

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cAMP receptor protein

activator; turns on genes that metabolize non-glucose sugars

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Lac Repressor

shuts off genes that metabolize lactose

Protein regulation starts with?

RNA regulation

Rho independent termination

palindrome causes a hairpin to form multi-A sequence causes RNA polymerase to pause RNA breaks H bonds and leaves the polymerase

Rho dependent termination

rho helicase binds to rho utilization sequence and moves along the RNA strand separates RNA from DNA to allow RNA to leave requires ATP

RNA Polymerase 1 (eukaryotes)

makes pre-rRNA

RNA Polymerase 2 (eukaryotes)

makes pre-mRNA and some specialized uses proteins, enzymes, and transcription factors major promotor: TATA box conserved and have well-defined function

RNA Polymerase 3 (eukaryotes)

makes pre-tRNA and some specialized

TF2F

gives specificity

TF2B

recruits TATA binding protein and TF2F

TF2E

helicase that opens the bubble

TF2H

kinase that phosphorylates the C terminal domain

Actinomycin D

targets RNA polymerase as a drug antibiotic/anticancer

Rifampicin

targets RNA polymerase as a drug antibiotic used in TB treatment

Amanitin

mushroom toxin selective for eukaryotes

primary transcript

newly made RNA

What does RNA Splicing remove?

introns

During RNA processing, mRNA is given what two things?

a 5' cap and a 3' poly A tail

What kind of bond is the 5' cap ?

5'-5' phosphodiester bond

What is the purpose of the 5' cap?

to protect mRNA from degradation and help it bind to the ribosome

When does capping occur?

When RNA is being made

S-adenosyl-methionine (SAM)

methylates the terminal G and first few ribonucleotides in mRNA capping

How many adenosines does the poly A tail have?

80-250

In eukaryotes why is the poly A tail good?

serves as a binding site for proteins; prevents degradation

differential RNA processing allows a single gene to?

make multiple products

Multiple processing sites allows the cell type and environmental factors to?

determine the product

What does rRNA start as?

pre-rRNA

Which contains the 16s rRNA? The 18s?

16- bacteria 18- eukaryotes

Rnase D

removes from the 3’ end

Rnase P

removes from the 5’ end

All tRNA’s have 3’ terminal with the sequence?

CCA

Where do snoRNAs come from?

introns of other RNAs

Where do snRNAs come from?

larger pre-snRNAs

pri-miRNA is cleaved to?

pre-miRNA

pre-miRNA is cleaved to miRNA by what?

dicer and helicase

4 classes of introns

1. self-splicing, G nucleophile 2. self-splicing, A nucleophile 3. Spliceosome Catalyzed 4. Endonuclease Catalyzed

Self-splicing, G nucleophile

splicing occurs via 2 transesterifications 3’ OH of an external G acts as a nucleophile and breaks the strand 3’ OH of the new end attacks the 3’ end of the intron and removes it

Self-Splicing, A nucleophile

splicing occurs via 2 transesterifications 2’ OH of an internal A acts as a nucleophile and attacks the 5’ end of the intron 3’ OH of the new terminus attacks the 3’ end of the intron cutting it out

Spliceosome

has snRNPs 2’ OH attacks 5’ end 3’ OH attacks 3’ end

In Group 3 RNA Processing what do the introns contain?

GU at 5’ end AG at 3’ end

Endonuclease

used mostly in tRNA needs ATP cleaves the backbone at both ends of the intron

What is the main indicator of gene expression?

[mRNA]

What is the degradation rate for vertebrates? Bacteria?

Vertebrates- 3hrs bacteria- 1.5 min

What is mRNA degraded by?

ribonucleases

Reverse transcriptase makes DNA from?

RNA

Retroviruses

incorporate their genome into the host have a high error rate and high mutation rate

gag

viral structural proteins

pol

encodes reverse transcriptase, integrase, and protease

env

envelope proteins

What 3 reactions does reverse transcriptase catalyze?

1. DNA synthesis from viral RNA 2. Degradation of viral RNA 3. Complimentary strand synthesis

How does the double stranded DNA get inserted into the host?

with an integrase

HIV

lentivirus its reverse transcriptase has a high error rate and fast mutations leads to drug resistances

Why can’t we make a vaccine to HIV?

the envelope changes

Dolutegravir

integrase inhibitor

Zidovudine

nucleotide reverse transcriptase inhibitors

Efavirenz

NNRTI

Telomeres

made of TG repeats protects ends of chromosomes require a special enzyme to maintain their length

Telomerase

acts as reverse transcriptase; carries its own template;

T loop

TG strand inserts itself back into the double helix

Telomerase activity can enhance?

the ability of cells to continue to divide

Telomere length in fibroblast cells is inversely proportional to?

the age of the person they came from

Do somatic cells have telomerase activity?

Transcription

DNA -> RNA

Translation

RNA->Protein

Reverse Transcription

RNA -> DNA

RNA Metabolism Flashcards

(88 cards)