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Cell and Molecular Bio > DNA replication-12 > Flashcards

DNA replication-12 Flashcards

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1
Q

Recap questions: What are nucleic acids made up of?

What are the 3 major components?

A

Polymeric molecules made up of repeating units of nucleotides

  1. Phosphate
  2. Pentose sugar
  3. Nitrogenous base (A,C,G,TU,C)
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2
Q

What is RNA made up of?

A

RNA is a polymeric molecule made up of one or more nucleotides

Each nucleotide is made up of a base (adenine, cytosine, guanine and uracil), a ribose sugar and a phosphate

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3
Q

In terms of structure:

What is the difference between DNA and RNA?

A
  1. The sugar is ribose in RNA rather than deoxyribose as in DNA
    (deoxyribose has one fewer OH group compared with ribose on 2nd carbon position

Remember RNA is more reactive and less stable than DNA because of the C-OH group on the 2nd Carbon position and DNA is more stable and less reactive due to the C-H group on the 2nd Carbon position

  1. The DNA base Thymine is replaced with Uracil in RNA
  2. RNA is single stranded and DNA is double
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4
Q

What is the backbone of DNA made up of? how are the bases paired?

A

2 nucleotides in a ladder-like structure which is twisted (double helix)

The sugar and phosphate make up the backbone, while the nitrogen bases are found in the center and hold the 2 strands together

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5
Q

What allows the DNA strands to run in opposite directions?

A

Due to base pairing, the DNA strands are complementary to each other, run in opposite directions and are called anti parallel strands

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6
Q

Describe the structure of ATP:

A

Chemically, ATP is an adenosine binds to 3 phosphate groups

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7
Q

What are the bonds that link phosphate groups in ATP?

A

3 phosphate groups are linked to one another by 2 high energy bonds called phosphoanhydride bonds

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8
Q

How is ATP (adenosine triphosphate) converted into ADP (adenosine diphosphate) via hydrolysis?

A

1 phosphate group is removed by the of breaking

a phosphoanhydride bond in hydrolysis

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9
Q

How is energy released from ADP to AMP? (adenosine monophosphate)

A

Energy is released when a phosphate is removed from ADP to form AMP

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10
Q

Recap: Describe the structure of DNA once it has replicated during the interphase:

A

When DNA has replicated during the interphase, it has not formed the condensed structure of chromosome. They remain as loosely coiled chromatin

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11
Q

Recap: What is the purpose of the nuclear membrane still being intact during the interphase?

A

Nuclear membrane is still intact to protect the DNA molecules from undergoing mutation

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12
Q

Recap: Why is DNA replication described as semiconservative?

A

Because each new double helix has one original strand one new strand

new double helix= original + new strand

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13
Q

What are the basic requirements for DNA replication?

A
  1. Substrates- the 4 deoxynucleoside triphosphates (dNTPs)
    - dATP, dTTP, dGTP, dCTP are needed
    - cleavage of the high energy phosphate bond provides the energy for the addition of the nucleotide
  2. Template- DNA replication cannot occur without a template
    - each strand of parental DNA serves as a template
  3. Other proteins
    - topoisomerase (prevent supercoiling)
    - SSB (single stranded binding protein) keep DNA separated
  4. Replication enzymes
    Helicase, Primase, DNA polymerase, Ligase
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14
Q

Name and state the function of 4 replication enzymes used in the DNA replication process:

A
  1. Helicase-Unwinds the DNA
  2. Primase- provides an RNA primer
  3. DNA polymerases- matches the correct nucleotides then joins adjacent nucleotides to each other
  4. Ligase-joins adjacent DNA strands together (fixes “nicks”)
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15
Q

What is the function of DNA polymerases?

A

it catalyzes DNA synthesis, extends an existing DNA or RNA strand paired with a template strand
(zips the strand together, RNA and DNA)

they do not initiate synthesis of new strands

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16
Q

Where does DNA polymerase extend the DNA? How does it do this?

A

DNA polymerase requires a free 3’-OH group to which it can add nucleotides by forming a phosphodiester bond between the 3’-OH end of the sugar and the 5’ phosphate of the next nucleotide.

DNA polymerase cannot add nucleotides if a free 3’-OH group is not available

Synthesis of DNA is always in 5’ to 3’ direction

17
Q

During initiation, Where does the DNA replication begin? What binds there?

A

DNA replication begins at a location on the double helix known as origin of replication (ori) where certain initiator proteins bind and trigger unwinding DNA

18
Q

What is the difference in Eukaryotes and Prokaryotes in terms of their ori ?

A

Prokaryotes have a single circular molecule of DNA and therefore have a single origin of replication

Eukaryotes often have multiple origins of replication on each chromosomes

19
Q

Steps of DNA replication, Initiation stage:

What occurs here?

A
  1. Ori (origin of replication) is where DNA replication begins, initiator proteins bind and trigger the unwinding of DNA
  2. Once Ori has been located, helicases and other proteins (SSB-single stranded binding protein, keep strands separated) keep the single strands from rejoining
  3. Helicase unwinds the double helix by breaking the hydrogen bonds that exist between complementary base pairs
  4. Replication fork- is the area where the replication of DNA will take place, 2 strands of DNA are exposed once the double helix is opened
  5. Synthesis of RNA primers, to begin synthesis, a short fragment of RNA called a primer, must be created and paired with the template DNA strand
    - Elongation occurs after this
20
Q

What are the advantages of unwinding the DNA helix?

A

Much of DNA’s sequence-specific information is accessible only when the double helix is unwound

21
Q

What is the function of the enzyme primase?

A

Synthesizes primers which are created and paired with the DNA template strand

Primase produces RNA molecules, it is a type of RNA polymerase

22
Q

Steps of DNA replication, Elongation stage:

What occurs here?

A
  1. The existing strand is a template for the new strand
    for example, if the existing strand is an A, the new strand receives a T
  • The DNA helix is antiparallel
  • one strand is oriented in the 5’ to 3’ direction and the other is oriented in the 3’ to 5’ direction
  1. Leading strand (Parent strand) that is replicated continuously toward the replication fork, runs in the 3’ to 5’ direction, with one primer as the starting point, 3’-OH group immediately available for synthesis of leading strand
  2. Lagging strand is replicated discontinuously from 5’ to 3’ away from the replication fork
  3. DNA synthesis occurs in small sections, new segments of DNA are called Okazaki fragments and each require a DNA primer
  4. DNA polymerase 1 - RNA primers present on newly formed strands need to be replaced by DNA after synthesis of an Okazaki fragment.
  5. After primer removal is completed the lagging strand contains gap-s and nicks between the adjacent Okazaki fragments
    - DNA ligase- seals breaks in the sugar-phosphate backbone between the adjacent Okazaki fragments
    - The 2 newly synthesized double-helix molecules are identical to each other and to the original DNA molecule

-DNA replication has occurred resulting in 2 newly synthesized DNA fragments

23
Q

What is the difference between a lagging strand and a leading strand?

A

Leading strand also known as the parent strand replicated continuously from 3’ to 5’ towards the replication fork

Lagging strand is replicated discontinuously from 5’ to 3’ away from the replication fork

24
Q

What is the role of the lagging strand?

How does DNA synthesis occur here?

A

Lagging strand is replicated discontinuously from 5’ to 3’ away from the replication fork

  • DNA synthesis occurs in small sections
  • these new segments of DNA are called Okazaki fragments and each one requires its own RNA primer
25
Q

Steps of DNA replication, Termination stage:

What occurs here?

A
  1. Replication in bacteria is bidirectional from one origin and 2 replication forks must meet an on point call “ter” (termination sequences- direct termination of replication)
  2. In eukaryotes, all the bubbles merge and yield two completed double stranded daughter DNA molecules
  3. All the RNA primers will be removed and all Okazaki fragments will be connected by DNA pol 1 and ligase
26
Q

Explain how DNA replication may occur in bacteria?

practice exam style question

A
  1. Initiation, locate the ori (origin of replication) in prokaryotes there is only one ori because it has a single circular DNA

2.

27
Q

What is the result of too many damages on the DNA caused by environmental factors and normal metabolic processes inside the cell?

A

This may result in cells becoming apoptotic

  • too many DNA damages trigger an apoptotic signaling cascade
  • forcing the cell into programmed cell death

Further damage
Cell may become malignant-cancer, develop immortal characteristics and begin uncontrolled division

28
Q

What are Endogenous and Exogenous causes of DNA damage?

A

Endogenous causes:
Reactive Oxygen Species (ROS) produced from normal metabolic by-products

Exogenous causes:
Environmental factors
Radiation 
UV light 
High energy radiation 
Mutagenic chemicals 
Plant toxins 
viruses
29
Q

Describe how the structure of DNA may be changed due to damage:

A

Single-stranded or double-stranded breaks in the DNA sugar-phosphate backbone

The nucleotide bases have been chemically modified

DNA cross-links- a covalent linkage between 2 nucleotides of DNA

30
Q

Damage to the DNA may cause the cell to be malignant and cause cancer,

How do cells detect DNA damage and repair them?

A

In the cell cycle there are checkpoints which act as a kind of assessment to DNA damage are activated

Cell’s corresponding DNA repair mechanisms respond to DNA damage

31
Q

What, Why and How does Cancer work?

A

What -
Cancer is uncontrolled cell growth

How-
Cancers are a result of a cell accumulating mutations that ultimately cause a loss of control over the cell cycle

Why-
Gene mutation

32
Q

Cancer results from gene mutation,

What are the two classes of checkpoint genes?

A
  1. Proto-oncogenes- code for proteins that promote the cell cycle and prevent apoptosis (uncontrollable death of cells)
  2. Tumor suppressor genes- code for proteins that inhibit the cell cycle and promote apoptosis (uncontrollable cell growth)

Mutations in these checkpoint genes cause the cell to lose control of the cycle, resulting in cancer

33
Q

What are environmental factors that cause cancer?

A 
Radiation 
Tobacco smoke 
Pollutants 
Viruses 
Dietary choices
Life style
34
Q

Focus points of this deck/ topic

A

Distinguish the differences between the structures of DNA and RNA
Explain the process of DNA replication
Describe the major enzymes involved in DNA replication

Cell and Molecular Bio (13 decks)

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