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Molecular Biology > 8-DNA Replication > Flashcards

8-DNA Replication Flashcards

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1
Q

From which nucleotide end does the polymerase attach new nucleotides?
Which its direction?

A

DNA polymerase attaches new nucleotide to 3’ carbon of previous nucleotide
( 5’..3’ direction)

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2
Q

How many and which are the types of replication?

Which pattern does the DNA follow?

A
  • The semiconservative model
  • The conservative model
  • The dispersive model

DNA replication is semiconservative because each daughter DNA helix is composed of one conserved strand and on new strand.

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3
Q

Which and how many are the components needed for DNA synthesis?

A

Four components are required for DNA synthesis:

  1. dNTPs: dATP, dTTP, dGTP , dCTP
  2. DNA template
  3. DNA polymerase
  4. Mg2+ (optimizes DNA polymerase activity)
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4
Q

What is the DNA polymerase’s I function?

From where does the required energy derive from?

A
  1. DNA polymerase I catalyses formation of phosphodiester bond between 3’-OH of the deoxyribose (on last nucleotide) and the 5’-phosphate of the dNTP

Energy for this reaction is derived from the release of two of the three phosphates of the dNTP.

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5
Q

What is the speed of DNA polymerase and what is the wrong rate?

A
  • rate ≤ 800 dNTPs/second

- low error rate

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6
Q

What comes first: Proofreading OR Repair

A

Proofreading occurs during the replication process

Repair occurs when the replication process has been completed

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7
Q

Name 5 common polymerases for mammals

A
  • Polymerase a (alpha)
  • Polymerase b (beta)
  • Polymerase γ (gamma)
  • Polymerase δ (delta)
  • Polymerase ε (epsilon)
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8
Q

Which polymerases can be found in the nucleus?

A

All polymerases are there except from polymerase γ (gamma) that is found in mitochondria

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9
Q

Which polymerases are responsible for DNA replication?

A

DNA Replication: All polymerases are responsible for replication except from polymerases β (beta) and ε(?) (epsilon)

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10
Q

Which polymerases can proofread?

A

Proofreading: All polymerases can proofread except from polymerases α (alpha) and β(beta)

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11
Q

Are polymerases the same for all organisms?

A

Note: Polymerases vary by species.

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12
Q

How many replication origins are in prokaryotes during DNA replication?

A

there is only ONE replication origin

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13
Q
  • In which phase do eukaryotes replicate their DNA?
  • What chromosomes do eukaryotes have in comparison to prokaryotes?
  • What is the speed of DNA replication in eukaryotes?
  • How many days woud take to replicate the DNA if eukaryotes had one replication origin?
  • How many replication origins do eukaryotes have?
A
  • Eukaryotes replicate their DNA only in S-phase
  • Eukaryotes have larger chromosomes
  • Replication speed 2,600 npm
  • From a single origin, bidirectional replication would take 8.5 days
  • The chromosome must have some 7,000 origins of replication (see slide17)
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14
Q

What is gyrase and which is its function?

A

Gyrase (a type of topoisomerase) relaxes the supercoiled DNA

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15
Q

How a primosome is built?

A

• DNA primase next binds to helicase producing a complex called a primosome (primase is required for synthesis)

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16
Q

Which type of DNA polymerase adds nucleotides after the RNA primer?

A

Type III

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17
Q

Which type of DNA polymerase adds nucleotides in the gap which is created when a RNA primer is removed?

How the two chains are binded?

A

Type I

with DNA ligase

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18
Q

What SSB proteins do?

A

Protein molecules that hold the single stranded DNA template, after the helicase enzyme occurred in order to prevent these two ( complimentary) strands to bind again with hydrogen bonds.

19
Q

INFO:

  • Leading strand: synthesized 5’ to 3’ in the direction of th replication fork movement(continuous)
  • Lagging strand: requires a single RNA primer, synthesized 5’ to 3’ BUT in the opposite direction of the fork’s movement (semidiscontinuous)
A

-

20
Q

How the fragments that are synthesized in the lagging strand (semidiscontinuous) are called ?

A

‘’Okazaki Fragments’’

21
Q

INFO:• DNA ligase seals the gaps between Okazaki fragments with a phosphodiester bond

A

-

22
Q

How can a polymerase detect a wrong-set base?

A

• Correct nucleotide has greater affinity (helps the polymerase ) for moving polymerase than incorrect nucleotide

23
Q

What happens to the unpaired bases?

A

• DNA polymerase has separate catalytic site that removes unpaired residues at terminus

24
Q

Which is the structure of the DNA polymerase that is responsible for repairing?

A

DNA Polymerase ( this type that is responsible for repairing has 2 catalytic sites

25
Q

INFO:• Defective copy of mismatch repair gene predisposed to cancer (see slide 30)

A

-

26
Q

How can DNA be damaged?

A
  • Chemical mutagens
  • Radiation
  • Free Radicals
27
Q

What Free Radicals are?

A

Free Radicals are molecules with only one electron. Due to the fact that they have ONLY 1 electron they try to steal another electron from other molecules and this initiates all the trouble to human body

28
Q

INFO:
 Despite 1000’s of alteration that occurs to DNA each day, few are retained as mutations
 Efficient repair mechanisms
 Importance of DNA repair highlighted by:
-Number of genes devoted to DNA repair
-Mutation rates rise with inactivation or loss of DNA repair gene
 Defects in DNA repair associated with several disease states

A

-

29
Q

What is error-prone repair?

A

 Error-prone DNA polymerases when a wrong in the base-pairing occurs, they put whatever bases they think of in order for the DNA to be replicated and not die.

30
Q

How are cells being protected by DNA damage?

A
  • Polymerase base Selection
  • Proofreading
  • Mismatch repair
31
Q

What is Recombination and polymerase bypass?

A

This term we use in DNA damage. If the DNA damage is too severe the DNA is not repaired, not replicated and the cell will be triggered to die by apoptosis.Polymerase bypass is itself often mutagenic

32
Q

Name some characteristics of prokaryotic cells

A 
Prokaryotic		
•	Circular
•	Very small
•	1 chromosome per cell
•	Some enzymes and proteins 
are associated with the DNA
•	Not housed in a nucleus
33
Q

Name some characteristics of eukaryotic cells

A 
•	Linear
•	Fairly long
•	Several chromosomes per cell
•	Histone proteins—‘’spools’’
Same in ALL eukaryotes
•	Housed in a nucleus
•	Nucleosome—2 loops of DNA wrapped around 8 histone proteins.
34
Q

What is the role of the following:
G2 delay
G1 arrests
S-phase arrest

A

G2 delay: protects against mitotic errors

G1 arrests: prevents replication errors

S-phase arrest: replicon initiation inhibition; prevents replication errors

35
Q

Which protein monitors repair of damaged DNA?

What happens if damage is too severe?

A
  • The protein p35 monitors repair of damaged DNA

* If damage too severe, p35 promotes programmed cell death (apoptosis)

36
Q

INFO: • Mutations in genes encoding DNA repair proteins can be inherited overall increase in mutations as errors or damage to DNA no longer repaired efficiently

A

-

37
Q

Which are the 4 Bsic Rules in DNA damage?

A
  1. Surveillance
  2. Recognition
  3. Signalling
  4. Repair
38
Q

What is the cause of Aicardi–Goutières syndrome (AGS)

Which are the symptoms?

A
  • 16 mutations in the SAMHD1 gene are responsible for this syndrome
  • This results in a less function SAMHD1 protein

Symptoms:
• This disease usually presents at the age of four months
• Characterized by the neurological symptom of cerebral calcification (accumulation of calcium

-White matter abnormalities (White matter disease is a disease that affects the nerves that link various parts of the brain to each other and to the spinal cord. These nerves are also called white matter.)

• Cerebral atrophy(Atrophy of any tissue means loss of cells. In brain tissue, atrophy describes a loss of neurons and the connections between them.)

39
Q

which are the consequences in telomerase defects?

A
  • Defects in the Telomerase activity is known to lead to abnormal cell proliferation and cancer
  • Abnormal function pf Telomerase also causes premature aging syndromes due to short Telomers
40
Q

What is a telomere?

A

• Telomere is a ribonucleoprotein that is an enzyme that adds DNA sequence repeats (Telomers)

41
Q

Name some syndromes that are connected with short telomeres.

A

Werner syndrome

  • Ataxia telangiectasia,
  • Ataxia-telangiectasia like disorder,
  • Bloom syndrome,
  • Fanconi anemia,
  • Nijmegen breakage syndrome.
42
Q

INFO: Mice engineered to block the gene that produces telomerase, unless they are given a certain drug, aged at a much faster rate and died at about six months, instead of reaching the average mouse lifespan of about three years

A

-

43
Q

INFO:
Cancer:

  • When cells approaching finite limit in cell cultures, the time to senescence (stop dividing) can be extended by the inactivation of the tumor suppressor proteins- p53 and Retinoblastoma protein (Rb)
  • Many cancer cells are considered as immortal because telomerase activity allows them to divide virtually forever, which is why they can form tumors.
A

-

Molecular Biology (9 decks)

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