RNA structure + transcription Flashcards
Semester 1 year 1
Describe the structure of RNA nucleotides
-ribose, base, phosphates
Where do the bases and phosphates join the ribose in RNA?
-bases join at the 1’ carbon
-phosphates join at the 5’ carbon
Where do the phosphates of a nucleotide join to the adjacent RNA ribose?
At the 3’ carbon
What is a nucleoside?
When the phosphate group has been removed
What are the RNA base names and their corresponding nucleoside names?
-uracil –> uridine
-adenine –> adenosine
-guanine –> guanosine
-cytosine –> cytidine
What is the difference between ribose and deoxyribose?
Ribose has an OH group, whereas deoxyribose only has an H group
Where are the phosphate and hydroxyl groups typically in cellular RNA?
-5’ phosphate group
-3’ hydroxyl group
What forms as a result of intramolecular base-pairing within RNA?
Short helices - many are stem-loops (secondary structure)
Are RNA helices normally regular or irregular and why?
Irregular - can have different base pairs from C-G and A-U
Describe the major and minor groove in RNA
-major groove is narrow
-many interactions with RNA involve the minor groove - molecules can access base pairings
What are the Watson and Crick base pairings and how many bonds does each form?
Cytosine and guanine - 3 hydrogen bonds
Uracil and adenine - 2 hydrogen bonds
What is the “wobble” base pair and what is its importance?
Guanine and uracil - important for decoding information
Describe the tertiary structure of RNA
-interactions connect regions of RNA that are separated in secondary structure
-folds into 3 dimensions
-a minor motif
What is a minor motif?
Consists of 2 adjacent A residues in the minor groove that interact with the edge of a G-C base pair
How is RNA made?
-by (DNA-dependent) RNA polymerases (RNAP)
-nucleotide triphosphates (NTPs) selected by base-pairing with the template strand and added to the 3’ end of the extending RNA strand
What does the RNAP active site contain?
A short RNA/DNA heteroduplex - a double stranded nucleotide structure containing 1 DNA and 1 RNA
What regions start and end RNA polymerase action?
Promotor and terminator
What are regulatory sequences?
Sequence of DNA that’s bound by a protein that promote the activity of polymerases
-typically found upstream to promotor regions
Which direction does RNA polymerase move in?
5’ carbon to 3’ carbon
What are the subunits of an E. coli RNA polymerase enzyme and what are they for?
2 alpha subunits (identical) - where it binds to transcription factors
2 beta subunits (different) - used in making RNA
Omega subunit - for assembly + stability
Where does DNA bind to E. coli RNA polymerase?
Between the 2 beta subunits - DNA binding groove
In prokaryotes, what do sigma factors do?
-provide specificity to the RNAP for the gene promotor
-RNAPs can start transcription without additional primase activity
-sigma factor released from RNAP as it moves away from promotor
How many RNA polymerases are in eukaryotic cells + what do they do?
RNA polymerase I - synthesise rRNA
RNA polymerase II - synthesis mRNA + noncoding RNAs
RNA polymerase III - synthesises tRNA + 5S rRNA
How is RNA polymerase II assembled onto gene promotors and why is it needed?
-eukaryotic cells don’t express sigma factors
-general transcription factors (gTF) complexes are required to put RNAP II onto promoters
