Lecture 7 Flashcards
An interaction between two similarly sized molecules will result in a?
Lesser change in stability.
Active site in an enzyme?
The area where the substrates fits in.
The substrate of an enzyme?
It
Why to enzymes need to be folded up correctly?
To bring all the active sites together.
Allosteric proteins?
The shape of a protein can be controlled by the cell by attaching to that protein and changes its shape, somewhere other than the active site.
phosphodiester bond?
When two of the hydroxyl groups in phosphoric acid reacts with hydroxyl groups on other molecules to form two ester bonds.
RNA vs DNA?
•2’ OH RNA instead of 2’H DNA
•Uracil RNA instead of thymine DNA.
•A ribose sugar group RNA instead of a deoxyribose DNA.
Which interaction contributes to DNA stability?
Base stacking by ID-ID interactions.
Why do major grooves exist that exposes the interior of the DNA?
To be able to read the information along the DNA without pulling the strands apart.
Sigma Factor?
Transcription Factor?
RNA Polymerase?
Synthesizes RNA from a DNA template strand from the 5’ to 3’ end.
How does the 2’ carbon differ in DNA vs RNA?
There is no oxygen in the 2’ carbon in DNA and will not form a hydroxyl group while it will in RNA.
What does a gene contain?
A promotor, an RNA coding sequence, and a terminator.
A gene is read by?
RNA polymerase that reads from the 3’ to 5’ end. It starts in the promoter sequence.
What direction do base building occur?
From the 5’ to 3’ end.
Downstream?
The direction that the polymerase moves.
Upstream?
The other side of the direction of polymerase.
Where does RNA polymerase bind to?
The sigma factor on the promotor.
Where in the template strand does transcription start?
In the first +1 nucleotide.
Sigma factor?
To find the promotor and bind directly do it and waits for the RNA polymerase to come.
The region of a promoter in bacteria?
-10 box and -35 box.
RNA polymerase always moves towards?
Downstream towards the 3’ region of the template strand.
Why is it important that the sigma factor is not-symmetrical?
It knows the difference between the -35 and -10 box, so it can properly orientate itself .
The region of the promotor in eukaryotes is?
The -35 to the TATA box (-10).
Are there sigma factors in eukaryotes?
No, it takes about 30 proteins to do the same job.
The Job of the terminator is to?
Stop RNA polymerase from reading past it.
Ester bond?
A linkage between an atom that is double bonded to an oxygen atom and that atom bonds with an alkyl or aryl group.
RNA transcript is produced by?
Polymerization of ribonucleoside triphosphates.
Initiation?
Elongation?
Termination?
How many nucleotides from the 3’ end of the TATA box does transcription begin?
25 nucleotides.
How many general transcription factors assemble at the promotor of a gene?
At least 6.
Transcriptional activator proteins bind to where?
Enhancers.
Mediator complex?
Ribonucleotides?
Pyrophosphate?
Two phosphate atoms in the form of P-O-P
Alternative splicing?
When certain exons are spliced out for RNA variation.
Glycosidic bond?
A carbohydrate bonding with another molecule.
How do proteins recognize the nucleotides in a DNA strand?
A protein has one order of donors and acceptors while the nucleotide bases has one order of donors and acceptors. They must line up correctly to get together.
First level of transcription regulation?
How strongly does the sigma and transcription factors interact with the DNA strands.
Strong promotors help?
Easily starts transcription.
RNA Processing:
•5’ Capping
•Poly-A Tails
•Splicing of introns
Do you shuffle exons?
No
In bacteria, where in the RNA strand is the start codon?
Exactly on the active site.
