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Biology IB > DNA replication > Flashcards

DNA replication Flashcards

1
Q

Define helicase

A

The enzyme that unzips the DNA for replication

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2
Q

Define SSBP protein (AJT photo)

A

A protein that binds to the single-stranded DNA to avoid hydrogen bonds between the two diff strands
- prevents closing

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3
Q

(REVIEW) why is a DNA strand 5’ to 3’ and 3’ to 5’ (aka why are they anti-parallel?) [add another photo]

A

For the 5’ to 3’:
- The 5th carbon (phosphate atom) bonds to the third carbon of another

For the 3’ to 5’:
- no “horizontal flip” (my words) — MUST rotate
- to make the nitrogenous bases face each other
- make the hydrogen bonds
- The third carbon (the phosphate atom bonds to the 5th carbon

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4
Q

Descrjve the process of DNA replication (EDUT using book)

A
  • Zipper analogy
  • Helicase unwinds
  • SSBP attaches to nucleotides (gets removed during ?/)
  • primer attached to nucleotides at the same time before DNA polym/
  • DNA polymerase continuous adding with leading strand
  • Lagging opposite direction :(
  • okazaki fragments added to DNA replication
  • DNA polymerase moves in intervals bc of it
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5
Q

Describe DNA polymerase III [2]

A

An enzyme that adds nucleotides to the two old DNA strands during replication
- moves in 5’ to 3’ direction
- therefore, leading strand OK with direction
- however, NOT ok with lagging strand

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6
Q

Define RNA primer

A

a short genetic sequence of RNA that tells the DNA polymerase where to start

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7
Q

Define primase (?)

A

the enzymes that synthesize RNA primers (from free nucleotides?)

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8
Q

What is the direction of the semi-conservative model (aka old strand and new strand)

A

For leading:
- old strand: 3’ to 5’
- new strand: 5’ to 3’

For lagging:
- old: 5’ to 3’
- new: 3’ to 5’

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9
Q

Define DNA replication

A

DNA sequence is copied during S-Phase of cell cycle

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10
Q

Define DNA gyrase

A
  • enzyme that stabilizes DNA structure as it unwinds
  • why?: the compression of the wound/ not yet unwinded parts of the DNA unwinding
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11
Q

Define DNA polymerase III

A
  • enzyme
  • adds nucleotides in the 5’ to 3’ direction
  • (both lagging and leading)
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12
Q

define DNA ligase

A

joins okazaki fragments on lagging strand
- seals the nicks

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13
Q

Describe the PCR

A
  • synthetic (artificial) method of lengthening specific seuqences of DNA
  • useful when theres small amount of DNA available (e.g. crime scenes)
  • Taq DNA polymerase enzyme is used for PR
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14
Q

Describe Taq DNA polymerase

A
  • used for PCR
  • from thermus acquaticus, heat resistant bacterium
  • therefore, resists denaturation at high temperatures
  • copies up 1000 nucleotides at a minute
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15
Q

Describe the PCR process

A

1.) Denaturation
- DNA sample heated to 95*C
- to break hydrogen bonds and separate to 2 strands

2.) Annealing
- DNA sample cooled
- primers attach to the opposite ends of target seq

3.) Elongation (70C - 75C)
- heat-tolerant/ Taq DNA polymerase copies strands

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16
Q

What determines if a DNA strand is 5’ to 3’ or 3’ to 5’

A

which carbon in the pentose sugar is exposed

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17
Q

What is the role of the RNA primer?

A
  • To let the DNA polymerase know where to start
  • By adding a short nucleotide sequence wherein other nucleotides can bond to (?)
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18
Q

In which direction and where can the DNA helicase unwind?

A

Anywhere and both directions as long as its an A-T rich region

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19
Q

Why is the 3’ carbon the ONLY available carbon for bonding in DNA?

A

Because it has one bond left
- available for phopshodiester bond

20
Q

Give the alternative name for PCR

A

Thermocycle

21
Q

Define “vitro”

A

outside
- e.g.: PCR = vitro DNA replication

22
Q

What is the temperature in the denaturation process of PCR?

A

90-95*C

23
Q

Give the temperature for annealing phase of PCR

A

50-60*C

24
Q

Give the temperature for the elongation phase of PCR

A
  • 70-75*C
  • (for the Taq Polymerase)
25
Q

Give the purpose of the “Sanger Sequence”

A
  • To know the full genetic sequence
26
Q

What makes Sanger Sequence different from PCR?

A

the use of ddNTP

27
Q

Define ddNTP

A

dideoxyribonucleic tri-phosphate
- deoxyribose sugar without an Oxygen atom at 3’
- attached to 3 phos

28
Q

Give the different types of ddNTP

A

1.) ddATP
2.) ddTTP
3.) ddCTP
4.) ddGTP

29
Q

What does ddNTP do?

A

it stops the (further) genetic sequencing

30
Q

How does ddNTP terminate genetic sequencing?

A

It removes the oxygen carbon of 3’
- removes the bonding ability due to removal of oxygen’s additional bond

31
Q

What will happen to the DNA sample because of ddNTP?

A

Instead of 1 long DNA strand, we get multiple of diff lengths

32
Q

Describe the process of Sanger Sequencing

A

1.) DNA sample
- DNA strand split into 4 test tubes
- 1 ddNTP each
- attaches and stops the sequencing at random pts

2.) Gel electrophoresis
- separation of DNA by size
- in wells
- electric current: law of attraction, poles, mvmt.
- most neg: most long -> most positive: least long

3.) Analysis
- read from the bottom up
- determine the sequence

33
Q

How do the single strand binding proteins prevent repannealing

A

The pull away the backbones of the strands which breaks the hydrogen bonds

34
Q

What does the exonuclease do?

A

The exonuclease removes the RNA primers because of their different structure AND replaces them with DNA

35
Q

What is the function of DNA ligase

A

To seal the nicks

36
Q

Define dNTP

A

deoxyribonucleoside

37
Q

Distinguish nucleotide and dNTP

A

dNTPs:
- from the cytoplasm
- used by DNA polymerase III to make new strands
- Tri-phosphate
-loses two phosphate because of hydrogen and phosphodiester bond
- becomes nucleotide

Nucleotide:
- One phosphate only

38
Q

Why can’t lytic cycle become lysogenic?

A

Because of lysis (cell burst)

39
Q

Discuss the evidence provided by viral structure and function that suggests they evolved from living organisms

A
  • complexity in structure of some viruses would suggest bacteria ancestor
  • e.g. maybe from parasitic bacteria
  • retroviruses and some eukaryotic cells w/ reverse transcriptase
  • genetic material moved out of cells
  • obligate parasites, couldn’t exist without cells
  • viruses have similar genetic material as cells (DNA and RNA)
40
Q

Utline the stages in the production of mRNA by transcription

A
  • DNA is unwound by RNA POLYMERASE
  • new nucleotides attached to the anti-sense strand by RNA polymerase
  • complementary base pairing with example (e.g. A-U)
  • mRNA detaches from template and unwinds
41
Q

Give the alternative name for exonuclease

A

DNA polymerase I

42
Q

How do dNTPS become Nucleotides?

A

They bond to others nucleotides and lose 2 phosphate atoms for the hydrogen bond and the phosphodiester bond)

43
Q

Give the temperatures for PCR (BOOK)

A

1.) Heating: 90-95C
2.) Cooling: 54C
3.) Elongation: 72*C optimum for TAQ DNA polymerase

44
Q

Outline the process of DNA profiling [4]

A
  • DNA is obtained from material/individual (e.g. crime scene, hair, blood, mouth, swab, etc.)
  • *tandem repeats are copied by PCR ~13 times min.
  • gel electrophoresis separates by lengths
  • DNA patterns always the same and is unique to individual
  • [insert application here]
45
Q

Explain Chargaff Experiment (bruef)

A
  • Main Findings in Support of: Complementary base pairing + ** DNA IS THE GENETIC MATERIAL**
  • BEFORE: tetranucleotide — equal nitro base concentration.
  • DURING EXP: Sampled the nucleotide concentration of different orgs + viruses
  • AFTER: A-T and C-G very similar concentrations, DNA has variation

Biology IB (25 decks)

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