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Molecular Cell Biology LSCI > Midterm1 > Flashcards

Midterm1 Flashcards

1
Q

When is the chromatin the less packed? Mitosis or Interphase?

A

Interphase

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2
Q

Why is the chromatine very packed during mitosis?

A

To be more easily manipulated

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3
Q

What form a nucleotide?

A
  1. 5 C sugar
  2. At leat 1 gr. Phosphate
  3. Base ( A C T G)
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4
Q

3’ end of the double helix expose a A gr, while 5’ end expose a B gr.

A 
3' = OH
5' = phoshpate
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5
Q

What is the kind of bound between nucleotides from 2 different strands in the alpha helix?
How many bounds do make AT and CG?

A

H bounds.
AT : 2
CG: 3

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6
Q

What’s the difference between purine and pyrimidine?

A 
Purine = 2 rings (AG)
Pyrimidine = 3 rings ( CT)
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7
Q

Why are the bases always bound 1 pyrimidine and 1 purine?

A

To have a similar pair length, so the sugar-phosphate backbone is at a constant distance

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8
Q

Which groove allow more accessibility to the base?

A

Major groove

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9
Q

What is the genetic code?

A

The correspondance between the four nucleotides alphabet and the 20 acid aa.

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10
Q

How many pairs of nucleotides there is in the human genome?

A

3,2 x 10^9 pairs

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11
Q

What’s the difference between heterochromatin and euchromatin?
Which one is more accessible?

A

Heterochromatin is highly packed DNA.
Euchromatin is less condensed DNA.
Therefore, Euchromatin is more accessible.

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12
Q

What is the nucleolus?

A

Zone of the nucleus DNA which has a highly transcriptional activity (present a lot of RNA)

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13
Q

T\F

Nuclear membrane scaffold proteins and microtubules outside nucleus.

A

T

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14
Q

When are chromosomes more visible?

A

During metaphase (alignement au centre) in mitosis.

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15
Q

What the form difference between EUK chromosome and PROK?

A

Euk chromosomes are linear (telomere, centromere), while Prok chromosome are circular.

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16
Q

What’s the role of centromere?

A
  1. Attaches chromatides

2. Coordinates attachement to mitotic spindle during mitosis, with specifically modified histones.

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17
Q

What is the composition of chromatine?

A

DNA, histone and other proteins.

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18
Q

What is the composition of nucleosomes?

A

Histones

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19
Q

How many nucleotides there is on a nucleosome and between one another?

A

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.

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20
Q

What part of histones stick out to allow modification of histones and stabilization of chromatine fiber?

A

AMINO terminal tails (N).

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21
Q

What is the favorite position of CG and AT on the histone core?

A

CG: minor groove OUTSIDE
AT: minor groove INSIDE

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22
Q

What is the use of a ATP-dependent chromatin remodeling complex?

A

To move DNA on the histones so parts would. me more accessible, using ATP

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23
Q

True or False?

Histones can be partly removed and replaced OR completely removed and replaced.

A

True

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24
Q

What is the function of histone H1?

A

Specifically locks DNA on a nucleosomes.

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25
Q

T\F

Heterochromatin is inaccessible for RNA pol.

A

T

Heterochromatin is too tightly packed.

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26
Q

What is the histone tail modification that activates gene and the one that turns it off?

A
  1. Acetylation of histone tail : activates gene (C–O-CH3)
  2. Methylation of histone tail: turn the gene off (CH3)

(acetyl lysine, or monomethyl lysine)

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27
Q

What is the function of reader proteins?

A

Bind writer proteins on covalent modification on histone tails. (Specify active gene in the cell)

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28
Q

T\F

Heterochromatin spread can be prevented by barrier proteins.

A

T

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29
Q

T\F

The longer loops in chromatine fiber are more easily accessible and typically encode active genes.

A

T

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30
Q

True or False?

Interphase chromosomes of all EUL are arranged in loops, because they are more accessible for RNA pol.

A

T

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31
Q

T\F

The position of chromatin in the nucleus is not specific to gene expression.

A

F

Chromatin can move to specific sites in the nucleus to alter genes expression.

32
Q

What’s the sens of DNA synthesis?

A

5’ to 3’

33
Q

What molecule is release when a nucleotides is add on the 3’ end while DNA synthesis?

A

pyrophosphate ( 2 phosphate covalently joined)

34
Q

Where does the PRIMER strand END in the DNA pol?

A

The primer strand ends in the ACTIVE BINDING SITE of DNA pol.

35
Q

How are nucleotides attached on the DNA-DNA pol complexe?

A
  1. Free nucleotides bind on the E (Editing) site
  2. Nucleotides are transferred on the P (Polymerizing site)
  3. Nucleotides attach on growing strand (5’-3’)
36
Q

How many forks of replication is there while DNA synthesis process?

A

2 replications forks, one for each new strands.

37
Q

True of False?

Lagging DNA strand is synthesized continuously.

A

False.

Lagging strand is synthesized discontinuously, and there is gaps between DNA fragments that are joined later.

38
Q

What is the sens of DNA pol exonuclease activity?

A

3’ to 5’

39
Q

T\F

The rate of DNA pol exonuclease activity is inversely proportional to the rate of synthesis activity

A

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.

40
Q

In what site of DNA pol misspaired nucleotides are removed?

A

In the E site (editing site)

41
Q

True or False

The combination of polymerazation and exonuclease activity is a very effective mechanism,

A

True.

Combined with strand-directed mismatch repair, there is only 1 in 10^10 mistakes by nucleotides added.

42
Q

What is the purpose of DNA primase? It what sens?

A

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.

43
Q

What’s the purpose of DNA ligase and how does it work?

A

DNA ligase binds Okazaki fragment by removed 5’ Phosphate ends.

44
Q

What molecule use DNA helicase to work?

A

ATP

45
Q

What is the position of the lagging strand and the leading strand on the DNA helicase?

A

Lagging strand: THROUGH the helicase

Leading strand: AROUND the helicase

46
Q

How many subunits form helicase?

A

6 identical subunits.

47
Q

What are base-paired haripins?

A

It’s when single-stranded region of DNA binds to itself.

48
Q

What are SSBP?

A

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.

49
Q

What is the function of the clamp loader and the sliding clamp?

A

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.

50
Q

So, what enzymes are implied in DNA synthesis?

A
  1. DNA pol
  2. Helicase
  3. DNA primase
  4. SSBP (single-strand binding protein)
  5. Sliding clamp and clamp loader
  6. DNA ligase
  7. Topoisomerase I
  8. Telomerase
51
Q

What’s the purpose of DNA topoisomerase I?

A

Detwist DNA before helicase arrives by cutting phosphodiester link in sugar backbone of DNA strand.

52
Q

What’s the link between the sugarbackbone of DNA?

A

Phosphodiester link

53
Q

T\F

The energy of re-unition of sugar backbone after topoisomerase has passed is spontaneous.

A

True

The energy of the phosphodiester link is reversible

54
Q

What’s the difference between topoisomerase I and topoisomerase II?

A

Topoisomerase I cuts 1 strand of DNA(EUK), while Topoisomerase II cuts the 2 strands of circular DNA (PROK).

55
Q

What are initiator proteins?

A

They formed the replication origin complex, which bends DNA to allow helicase and primase to bind to DNA.

56
Q

True or False

Helicase is triggered by initiar proteins.

A

False
Helicase will bind to DNA grâce aux initator proteins, but it willl need to be triggered by something else to start synthesis.

57
Q

What controls release of DNA helicase?

A

DNA methylation.

If DNA is methylated, DNA is ready for initiation.

58
Q

Is hemimethlation suffisant for initiation?

A

Nope

59
Q

In the GSM cycle, where is the helicase released?

A

At the end of S phase (S\G2)

60
Q

Is histones information preserved from one strand of DNA to the other?

A

Yes

61
Q

Why continual rounds of replication make the ends of DNA shorter and shorter?

A

Because there is no DNA pol coming from further to remove RNA pol.

62
Q

What’s the purpose of Telomerase?

A

Telomerase provides its own template for DNA pol to repeat over and over to make end on DNA pol.

63
Q

What is the use of telomerase overhang?

A

Protects from degradation.

64
Q

What is the difference between DNA and RNA?

A
  1. sugar: DNA miss one OH

2. bases: DNA= thymine (methyl group), RNA = uracile (no methyl group)

65
Q

What kind of RNA pol makes what kind of RNA?

A

mRNA: pol II (proteins)
rRNA: pol I (ribosome)
t RNA pol III (adaptors for mRNA and aa)

66
Q

What RNA has to release to initiate transcription?

A

Promotor and sigma factor

67
Q

What are the 2 well-known specific DNA sequence that coordinate assembly of the RNA polymerase complexe?

A

TTGACA 35 nucleotides before, and TATAAT ( TATA BOX) 10 nucleotides before the start of transcription.

68
Q

What are the name of transcription factors for RNA polymerase II and what are their uses?

A

TFII

  1. TBP (TATA box Binding Protein) binds to the other subunit of TFII D and locates at the TATA box
  2. TFII B binds to TFII D-TATA box complex
  3. TFII E, F, H and RNA pol bind too
  4. Complex is then stuck on the promotor and can’t go
  5. Sigma factor is released, and C terminal domain of RNA pol is phosphorylated
69
Q

Which supercoil is more easy to separate?

A

Negative supercoil (underwound)

70
Q

T\F

There is only introns in EUK

A

T

71
Q

Where is located the G cap and the poly-A tail?

A

5’: methyl G cap

3’: poly-A tails

72
Q

Why is there no splicing in prok?

A

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.

73
Q

In what order is the mRNA made in EUK?

A

5’ G-cap, mRNA, poly-A tail.

74
Q

A protein of intron binds to 5’ exon sequence or 3’ exon sequence?

A

A is covalently attache to 5’ intro sequence.

75
Q

What are the proteins involved in introns splicing? How do they work?

A
  1. U1 on 5’ exon sequence
  2. BBP-U2AF recognize branch point A
  3. U4\U6 and U5 bring BBP-U2AF to U1
  4. U4 \U6 break appart and removes UI
  5. Complex holds on the 3’ end of the exon RNA
    =removal of the intron
  6. EJC binds and is left where the intro was

Molecular Cell Biology LSCI (2 decks)

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