Midterm1 Flashcards
When is the chromatin the less packed? Mitosis or Interphase?
Interphase
Why is the chromatine very packed during mitosis?
To be more easily manipulated
What form a nucleotide?
- 5 C sugar
- At leat 1 gr. Phosphate
- Base ( A C T G)
3’ end of the double helix expose a A gr, while 5’ end expose a B gr.
3' = OH 5' = phoshpate
What is the kind of bound between nucleotides from 2 different strands in the alpha helix?
How many bounds do make AT and CG?
H bounds.
AT : 2
CG: 3
What’s the difference between purine and pyrimidine?
Purine = 2 rings (AG) Pyrimidine = 3 rings ( CT)
Why are the bases always bound 1 pyrimidine and 1 purine?
To have a similar pair length, so the sugar-phosphate backbone is at a constant distance
Which groove allow more accessibility to the base?
Major groove
What is the genetic code?
The correspondance between the four nucleotides alphabet and the 20 acid aa.
How many pairs of nucleotides there is in the human genome?
3,2 x 10^9 pairs
What’s the difference between heterochromatin and euchromatin?
Which one is more accessible?
Heterochromatin is highly packed DNA.
Euchromatin is less condensed DNA.
Therefore, Euchromatin is more accessible.
What is the nucleolus?
Zone of the nucleus DNA which has a highly transcriptional activity (present a lot of RNA)
T\F
Nuclear membrane scaffold proteins and microtubules outside nucleus.
T
When are chromosomes more visible?
During metaphase (alignement au centre) in mitosis.
What the form difference between EUK chromosome and PROK?
Euk chromosomes are linear (telomere, centromere), while Prok chromosome are circular.
What’s the role of centromere?
- Attaches chromatides
2. Coordinates attachement to mitotic spindle during mitosis, with specifically modified histones.
What is the composition of chromatine?
DNA, histone and other proteins.
What is the composition of nucleosomes?
Histones
How many nucleotides there is on a nucleosome and between one another?
53 nucleotides wrapped on the histone and 147 naked nucleotides between each other, so 200 nucleotides from the beginning on a nucleosomes to the next.
What part of histones stick out to allow modification of histones and stabilization of chromatine fiber?
AMINO terminal tails (N).
What is the favorite position of CG and AT on the histone core?
CG: minor groove OUTSIDE
AT: minor groove INSIDE
What is the use of a ATP-dependent chromatin remodeling complex?
To move DNA on the histones so parts would. me more accessible, using ATP
True or False?
Histones can be partly removed and replaced OR completely removed and replaced.
True
What is the function of histone H1?
Specifically locks DNA on a nucleosomes.
T\F
Heterochromatin is inaccessible for RNA pol.
T
Heterochromatin is too tightly packed.
What is the histone tail modification that activates gene and the one that turns it off?
- Acetylation of histone tail : activates gene (C–O-CH3)
- Methylation of histone tail: turn the gene off (CH3)
(acetyl lysine, or monomethyl lysine)
What is the function of reader proteins?
Bind writer proteins on covalent modification on histone tails. (Specify active gene in the cell)
T\F
Heterochromatin spread can be prevented by barrier proteins.
T
T\F
The longer loops in chromatine fiber are more easily accessible and typically encode active genes.
T
True or False?
Interphase chromosomes of all EUL are arranged in loops, because they are more accessible for RNA pol.
T
T\F
The position of chromatin in the nucleus is not specific to gene expression.
F
Chromatin can move to specific sites in the nucleus to alter genes expression.
What’s the sens of DNA synthesis?
5’ to 3’
What molecule is release when a nucleotides is add on the 3’ end while DNA synthesis?
pyrophosphate ( 2 phosphate covalently joined)
Where does the PRIMER strand END in the DNA pol?
The primer strand ends in the ACTIVE BINDING SITE of DNA pol.
How are nucleotides attached on the DNA-DNA pol complexe?
- Free nucleotides bind on the E (Editing) site
- Nucleotides are transferred on the P (Polymerizing site)
- Nucleotides attach on growing strand (5’-3’)
How many forks of replication is there while DNA synthesis process?
2 replications forks, one for each new strands.
True of False?
Lagging DNA strand is synthesized continuously.
False.
Lagging strand is synthesized discontinuously, and there is gaps between DNA fragments that are joined later.
What is the sens of DNA pol exonuclease activity?
3’ to 5’
T\F
The rate of DNA pol exonuclease activity is inversely proportional to the rate of synthesis activity
F
The rate of DNA pol exonuclease activity is always stable, but the rate of synthesis activity is inversely proportional to the exonuclease activity, because if there is a lot of mistakes, DNA can no longer elongates, so synthesis slow down.
In what site of DNA pol misspaired nucleotides are removed?
In the E site (editing site)
True or False
The combination of polymerazation and exonuclease activity is a very effective mechanism,
True.
Combined with strand-directed mismatch repair, there is only 1 in 10^10 mistakes by nucleotides added.
What is the purpose of DNA primase? It what sens?
DNA primase synthesizes RNA primer for DNA pol in the LAGGING strand, so DNA pol can synthesizes another strand of DNA. The activity of DNA primase is 5’-3’, just like DNA pol.
What’s the purpose of DNA ligase and how does it work?
DNA ligase binds Okazaki fragment by removed 5’ Phosphate ends.
What molecule use DNA helicase to work?
ATP
What is the position of the lagging strand and the leading strand on the DNA helicase?
Lagging strand: THROUGH the helicase
Leading strand: AROUND the helicase
How many subunits form helicase?
6 identical subunits.
What are base-paired haripins?
It’s when single-stranded region of DNA binds to itself.
What are SSBP?
Single stranded binding proteins bind to single stranded DNA to prevent it to bind to itself by H bonds and favorise continuation of DNA elongation. They are removed by DNA pol.
What is the function of the clamp loader and the sliding clamp?
Clamp loader: use ATP to open the locking ring so DNA can passes through it
Locking sliding ring: keep the DNA pol on strand to prevent it to falling
ATP hydrolysis locks sliding clamp around DNA and releases clamp loader.
So, what enzymes are implied in DNA synthesis?
- DNA pol
- Helicase
- DNA primase
- SSBP (single-strand binding protein)
- Sliding clamp and clamp loader
- DNA ligase
- Topoisomerase I
- Telomerase
What’s the purpose of DNA topoisomerase I?
Detwist DNA before helicase arrives by cutting phosphodiester link in sugar backbone of DNA strand.
What’s the link between the sugarbackbone of DNA?
Phosphodiester link
T\F
The energy of re-unition of sugar backbone after topoisomerase has passed is spontaneous.
True
The energy of the phosphodiester link is reversible
What’s the difference between topoisomerase I and topoisomerase II?
Topoisomerase I cuts 1 strand of DNA(EUK), while Topoisomerase II cuts the 2 strands of circular DNA (PROK).
What are initiator proteins?
They formed the replication origin complex, which bends DNA to allow helicase and primase to bind to DNA.
True or False
Helicase is triggered by initiar proteins.
False
Helicase will bind to DNA grâce aux initator proteins, but it willl need to be triggered by something else to start synthesis.
What controls release of DNA helicase?
DNA methylation.
If DNA is methylated, DNA is ready for initiation.
Is hemimethlation suffisant for initiation?
Nope
In the GSM cycle, where is the helicase released?
At the end of S phase (S\G2)
Is histones information preserved from one strand of DNA to the other?
Yes
Why continual rounds of replication make the ends of DNA shorter and shorter?
Because there is no DNA pol coming from further to remove RNA pol.
What’s the purpose of Telomerase?
Telomerase provides its own template for DNA pol to repeat over and over to make end on DNA pol.
What is the use of telomerase overhang?
Protects from degradation.
What is the difference between DNA and RNA?
- sugar: DNA miss one OH
2. bases: DNA= thymine (methyl group), RNA = uracile (no methyl group)
What kind of RNA pol makes what kind of RNA?
mRNA: pol II (proteins)
rRNA: pol I (ribosome)
t RNA pol III (adaptors for mRNA and aa)
What RNA has to release to initiate transcription?
Promotor and sigma factor
What are the 2 well-known specific DNA sequence that coordinate assembly of the RNA polymerase complexe?
TTGACA 35 nucleotides before, and TATAAT ( TATA BOX) 10 nucleotides before the start of transcription.
What are the name of transcription factors for RNA polymerase II and what are their uses?
TFII
- TBP (TATA box Binding Protein) binds to the other subunit of TFII D and locates at the TATA box
- TFII B binds to TFII D-TATA box complex
- TFII E, F, H and RNA pol bind too
- Complex is then stuck on the promotor and can’t go
- Sigma factor is released, and C terminal domain of RNA pol is phosphorylated
Which supercoil is more easy to separate?
Negative supercoil (underwound)
T\F
There is only introns in EUK
T
Where is located the G cap and the poly-A tail?
5’: methyl G cap
3’: poly-A tails
Why is there no splicing in prok?
No introns, no cap, no poly-A tails, no nuclear membranes, but can be operon.. So transcription and translation can happen at the same time.
In what order is the mRNA made in EUK?
5’ G-cap, mRNA, poly-A tail.
A protein of intron binds to 5’ exon sequence or 3’ exon sequence?
A is covalently attache to 5’ intro sequence.
What are the proteins involved in introns splicing? How do they work?
- U1 on 5’ exon sequence
- BBP-U2AF recognize branch point A
- U4\U6 and U5 bring BBP-U2AF to U1
- U4 \U6 break appart and removes UI
- Complex holds on the 3’ end of the exon RNA
=removal of the intron - EJC binds and is left where the intro was
