Lecture 2 RNA Structure, Function, and Transcription Flashcards
What is transcription?
DNA directed RNA synthesis from a DNA template by a DNA-dependent RNA polymerase
DNA to message is….?
Nuclear
Protein synthesis is?
Cytoplasmic
mRNA translocation happens from where and to where?
Nucleus to cytoplasm
Unbranched polymer of nucleotide 5’ monophosphates are linked by?
3’-5’ phosphodiester bonds
RNA contains…?
Ribose instead of deoxyribose
In RNA what nucleotide replaces which nucleotide?
Uricil replaces thymidine
Do not understand
“Can fold upon itself to form intrastrand helical regions. The filded 3D
structure of RNA, like the folded proteins, can have multiple biological
functions.”….
List as many different types of RNAs
Pre-RNA
mRNA
tRNA
rRNA
snRNA
snoRNA
miRNA
snoRNAs and miRNAs are extensively characterized small _________ RNAs?
small non-coding regulatory RNAs
snoRNAs and miRNAs have distinct and central _______ _____ in cells.
Regulatory roles
Both snoRNA and miRNA share ______ and ______ exist.
characteristics and functionality exist
What two things does snoRNAs and miRNAs likely share?
Functional and evolutionary relationship
What are the major types of RNA?
Ribosomal RNA - 80%
Transfer RNA - 15%
Messenger RNA - 5%
What characteristic allows functional RNAs to be involved in a wide range of cellular processes?
Ability to form unique 3D structures that act similarly to proteins
What two things are required for RNA synthesis?
-DNA template
-RNA polymerase
-Mg2+ (included in the rxn equation)
What polymerase is used for DNA template to DNA?
DNA polymerase
What polymerase is used for DNA template to RNA?
RNA polymerase
What polymerase is used for RNA template to RNA?
RNA replicase
What polymerase is used for RNA template to DNA?
Reverse transcriptase
What is responsible for catalyzing RNA synthesis?
RNA polymerase
What are the subunits of prokaryotic RNA polymerase?
Theres a total of 6.
-Alpha-2
-Beta
-Beta prime
-Sigma
-Omega
What is the purpose of a prokaryote sigma subunit (RNA polymerase)?
Recognizes the promoter region of DNA that precedes the structural gene
What is the purpose of a prokaryote omega subunit of RNA polymerase?
Binds to promotor region, may serve to control efficiency of RNA synthesis. The overall function is not very clear.
What antibiotic is able to inhibit the beta subunit of RNA polymerase?
Rifampin
What are the steps in general transcription?
Initiation
Elongation
Termination
RNA polymerase will bind to…
Promoter region using omega factor
The promoter seeks out what specific sequences?
CAAT, GC, TATA
DNA coding strand uses which strand?
Sense strand
Non-coding strand uses which strand?
Anti sense strand.
Note Non-coding strand is the template.
Which strand is used in the 3’ - 5’ direction for RNA chain to be synthesized 5’ - 3’?
Anti-sense to make the coding strand
What happens to show transcription is happening?
A 15-20 basepair (be) bubble formed and 1 strand is read.
Elongation starts with a _____, then continues
purine
Termination uses what two things?
Rho independent or Rho dependent
Polymerase 1 synthesizes what and where?
Located in the nucleolus, producing all rRNAs except 5S rRNA.
Note: It is insensitive to alpha amanitin (mushroom toxin)
Polymerase II synthesizes what and where is it?
Located in the nucleus and codes for all protein coding nuclear pre-mRNAs
Note: Recognizes promoter sequence and EXTREMELY sensitive to alpha amanitin toxin
Polymerase III is where and what does it synthesize?
In the nucleus; Synthesizes. TRNA, 5sRNA and miRNA or snRNAs
Note: Moderately sensitive to alpha amanitin toxin
Mitochondrial polymerase synthesizes…?
mitochondrial RNA; In. Mitochondria
B-thalassemia involves a mutation of _______ before b-hemoglobin gene
TATA box. Note: affects rate of transcription and rate of protein production
________ regions in Eukaryotic promotes effect regulation of _____ ________
Enhancer ; gene expression
Binding to ______ will increase the rate and frequency of transcription
Enhancer region
What are suppressor regions?
Site of binding of regulatory proteins that stop transcription
Where are cell signaling factors?
100 - 5000 be upstream from promoter
What is the purpose of modifications?
- Stability of mRNA
-Determine protein variation from a single message (splicing)
-Guide for translocation of mature mRNA to cytoplasm
What are the types of processing for mRNA?
- 5’ cap
- 3’ poly-A tail
- Splicing
What is 5’ cap?
A 7-methyl-guanosine to 5’ end
What is a 3’ poly-A tail?
Numerous adenosines added for stability
What is splicing?
Removal of introns
Alpha amanitin (mushroom toxin) will inhibit…?
Eukaryotic poly II and poly III
What antibiotic will bind to template preventing elongation?
ACTINOMYCES D
What are two inhibitors of reverse transcription?
Azidothymidine (AZT) and dideoxyinosine (ddl)
What is thalassemia?
A form of inherited autosomal recessive blood disorder characterized by abnormal formation of hemoglobin.
What ethnicity is highly likely of carrying the thalassemia gene?
Mediterranean = 20%
US carrier = 7%
What is alpha thalassemias?
Production of defective alpha globin chain
- 4 alleles, mostly deletion
What is beta thalassemias?
Production of defective beta globulin chain
What are possible mutations in beta thalassemias?
Promoter mutation
Splicing mutation
Capping and tailing mutations
Nonsense and frame shift mutation
What happens to defective proteins in beta thalassemias?
They are destroyed
