Reading...
Play button
Play button
Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
48 Cards in this Set
- Front
- Back
|
What are the three phases of replication?
|
initiation, elongation, termination
|
|
|
In DNA, nitrogenous bases are attached to the deoxyribose at the ____ position. What occurs at the 5' position?
|
1': It's where phosphates get added to the structure.
|
|
|
In DNA, the 3' and 5' spot are used for what?
|
They are involved in attaching one nucleotide to another via phosphodiester bonds.
|
|
|
If you are talking about the nitrogenous base and the sugar attached then it is called a _____.
|
nucleoside
|
|
|
If you are talking about the nitrogenous base, a sugar, and a phosphate group coming off of the 5' end then it is called a _____.
|
nucleotide (if using adenine, 1 phosphate group would be AMP--monophsphate; 2 would be ADP--diphosphate; 3 would be ATP--triphosphate)
|
|
|
Nucleotides on each strand are attached to each other via ________ linking how?
|
phosphodiester bonds; linking the 5' end of one deoxyribose to the 3' end of the adjacent sugar.
|
|
|
One strand of DNA is linked to the other by....
|
H bonds between the bases.
|
|
|
DNA strands run _______ to each other. What does this mean?
|
antiparallel; this means one strand runs 5'--->3' while it's complement runs 3'---->5'
|
|
|
When the bases form the rungs of the ladder....
|
they create a stacking energy that adds stability.
|
|
|
Replication of DNA is ________.
|
semiconservative, it is not duplicated.
|
|
|
All DNA polymerases (DNAPs) synthesize DNA in the ____ to ____ direction.
|
5'--->3'
|
|
|
Because the strands of DNA are antiparallel, replication on the two unwound strands has to proceed...
|
in opposite directions.
|
|
|
Phosphodiester bond hydrolysis provides....
|
energy (2 high energy bonds/nucleotide)
|
|
|
Initiation of replication begins at...
|
the oriC
|
|
|
DnaA-ATP is how many molecules long?
|
20-40
|
|
|
What does DnaA-ATP do?
|
They bind at the oriC and initiate melting at AT rich sites using ATP hydrolysis as energy.
|
|
|
What is DnaB?
|
It is a helicase (binds to help unwind DNA).
|
|
|
What does DnaB do?
|
It binds and help unwinds more oriC DNA, but it needs the help of DnaC and ATP hydrolysis.
|
|
|
What are SSB's?
|
Single strand DNA binding proteins.
|
|
|
What does SSB's do?
|
They bind to single stranded DNA to prevent it from rewinding (in the bubble area after the helicase has unwound it).
|
|
|
What are replisomes?
|
They contain replication proteins and they form in the bubble of unwound area in DNA.
|
|
|
Explain replication in prokaryotes.
|
It is bidirectional because it is a round plasmid.
|
|
|
Elongation rate of DNA is ____ and how does it vary?
|
1000 nucleotides/sec; It doesn't vary. That is how fast the DNA polymerase can replicate it, as long as it is at 37 degrees.
|
|
|
Regulation of DNA is at the....
|
initiation step.
|
|
|
How can cells divide faster than the time it takes to replicate the chromosome?
|
Because re-initiation of replication at new ori's can start before initial round of replication terminates.
|
|
|
What has to be replicated every time the cell divides?
|
the chromosome
|
|
|
For the cell to re-initiate (restart replication at a new oriC), what is required?
|
ATP. Reinitiation will not occur if unless the cells have enough dNTPs (deoxynucleotides) to complete a round of replication.
|
|
|
The leading strand orientation is ___--->___. Therefore the compliment strand is ___--->___.
|
It goes through the complex 3'--->5'; compliment is made 5'--->3'.
|
|
|
The lagging strand orientation is ___--->___. Therefore the compliment strand is ___--->___.
|
It goes through the complex 5'--->3'; compliment is made 3'--->5'.
|
|
|
The ____ strand is fed through backwards.
|
lagging
|
|
|
What makes replication occur?
|
DNA polymerase.
|
|
|
Both strands of DNA are replicated simultaneously from a single complex (replisome) containing.....
|
2 DNAP III core enzymes
|
|
|
DNA is threaded through the complex (replisome), then how does it move?
|
The replisomes remain stationary and DNA moves.
|
|
|
How are RNA primers used in the different strands?
|
In th leading strand they only need to be made once at the origin. In lagging strand they are continuously used with the okazaki fragments.
|
|
|
_____ are loaded on the strands after when primase is finished making primers.
|
Beta clamps
|
|
|
The Beta clamps keep the DNAPIII in.....
|
processive mode (from falling off).
|
|
|
On the lagging strand, _____ falls off once it meets the previously formed DNA on the okazaki fragment.
|
DNAPIII
|
|
|
What replaces the primers on the DNA strands?
|
DNA Polymerase I, but it leaves nicks in the DNA.
|
|
|
How are the nicks closed on the DNA strands?
|
ligase closes the nicks using ATP or NAD+ by activating the 5' ribose before it to make a covalent bond.
|
|
|
What is the final product of DNA replication?
|
Two concatenated chromosomes that are linked at the terC.
|
|
|
How are the two concatenated chromosomes separated?
|
A Type VI topoisomerase cuts the double stranded DNA at the terC. It then passes through one chromosome through the other and religates.
|
|
|
What are Type VI topoisomerases inhibited by?
|
Antibiotics such as ciprofloxicin.
|
|
|
What are the error rates for DNAP I or III and what causes it?
|
Low, at 10 ^ -10. This is due to proofreading and mismatch repair.
|
|
|
What is proofreading?
|
DNAP I and III have a 3'--->5' endonuclease activity that can go back and hydrolyze mistakes that were made.
|
|
|
What does DNAP V do? How does it replicate compared to DNAP I & III?
|
It is made after some DNA is extensively damaged. It is much faster than I or III.
|
|
|
What is mismatch repair?
|
A system used after proofreading to fix mistakes. It makes DNAP V and fixes it.
|
|
|
What is used in mismatch repair?
|
A few different proteins: MutS, a DNA binding protein that recognizes the wrong base pair; MutL is used as a linker protein; MutH, binds to hemimethylated GATC sequences.
|
|
|
How does mismatched repair work?
|
If all three proteins are set up correct, MutH will make a cut in the nonmethylated (lagging strand) and uses an endonuclease to eat up the DNA beyond the nick. Then DNA polymerase I refills is and ligase seals it.
|
