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Biochemistry (Cole) > Lecture 27 DNA RNA and DNA Replication > Flashcards

Lecture 27 DNA RNA and DNA Replication Flashcards

1
Q

Did watson and crick do any experiments of their own?

A

No they borrowed data from man sources including:

  • Chargaff (base compositions of DNA)
  • Franklin and Maurice wilkins (x-ray diffraction studies)
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2
Q

DNA bases

A
  • Adenine
  • Guanine
  • Thymine
  • Cytosine
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3
Q

RNA bases

A
  • Adenine
  • Guanine
  • uracil
  • cytosine
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4
Q

Purines

A

Adenine

Guanine

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5
Q

Pyrimidines

A

Thymine
Cytosine
Uracil

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6
Q

In DNA or RNA is the 2prime hydroxly group absent?

A

DNA (deoxyribonucleic acid)

RNA the hydroxyl group is present

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7
Q

Why is rna easily degraded in akaline conditions?

A

It has both hydroxyl groups present

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8
Q

DNA is extremely stable

A

Extracted from many mammals (mammoth)

Why we can clone animals

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9
Q

Why do we take special care with RNA samples?

A
  • RNA from fingertips can degrade sample
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10
Q

Chargaffs rule

A
  • A= T (form double bonds)

- G= C (form tripple bonds)

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11
Q

What end of DNA has the free phosphate group?

A
  • 5’ end
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12
Q

What end of DNA has the free hydroxyl group?

A
  • 3’ end
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13
Q

Depending on what organism you are looking at the DNA can be organized differently.

A
  • All DNA is double helix parallel but can be linear or in chromosomes
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14
Q

Why can transcription and translation occur simultaneously in Prokaryotes?

A
  • DNA is organized in a linear or contiguous fashion

- and because no nucleus

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15
Q

Exons

A
  • blocks or regions of sequence that will give rise to the protein sequence
  • Exons are separated by regions that do not code for protein (introns) and regions at the 5’ and 3’ ends that do not encode the protein called untranslated regions (UTRS)
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16
Q

What happens to introns after the DNA is copied

A
  • they are removed by splicing
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17
Q

Alternative splicing

A
  • in eukaryotic organisms primary transcripts are often spliced in multiple combinations of exons
  • Gives rise to a family of possible proteins that can different functions, regulation and or tissue specificity
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18
Q

Prokaryote DNA condensation

A
  • condensed by a set of polyamines and proteins in back and forth loops
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19
Q

Eukaryotes DNA condensation

A
  • DNA first condensed into nucleosomes with each involving ~200 bp of DNA and a set of core histone proteins
  • Nucleosomes (beads on string) packaged to chromatin
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20
Q

Euchromatin

A

-relaxed transcriptionally active structure

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21
Q

Heterchromatin

A
  • highly condensed and generally not transcriptionally active
22
Q

Chromatin/Nucleosome over view

A

DNA-> wraps around core histone dimers –> nucleasome twists around –> chromatin –> condenses into chromosome

23
Q

Chromosome

A
  • contain DNA information that we inherit
24
Q

How many mutations in base pairs does it take to cause disease?

A
  • one bp mutation
25
Q

DNA replication

A
  • antiparallel orientation of the strands
  • strands are complementary
  • each strand can act as a template for the synthesis of a new strand
26
Q

What phase of the cell cycle does DNA replication take place in?

A
  • M phase
27
Q

Central dogma of genetic information flow

A

DNA –> RNA –> Protein

28
Q

RNA Genome of viruses

A

RNa –> DNA –> RNA –> Protein

29
Q

What enzyme catalyzes DNA replication?

A
  • DNA polymerase
30
Q

All replication reactions proceed in what direction

A
  • 5’ to 3’
31
Q

DNA polymerase shape

A
  • hand with DNA sitting in it
32
Q

DNA polymerase

A
  • reads template strand and places opposing base pair
  • synthesizes new strand in the 5’ to 3’ direction
  • Requires a template strand and a strand to build off of with a free 3’-OH group
  • Contains a 5’ to 3’ polymerase activity and a 3’-5’ exonuclease activity
  • self correcting enzyme
33
Q

Exonuclease

A
  • removes incorrect base pairs

- proof reading function

34
Q

Where does the energy come from to add nucleotides to the template strand?

A
  • hydrolysis of the pyrophosphate bond
35
Q

What direction is the proof reading exonuclease of DNA polymerase?

A

3’ to 5’

36
Q

What are the origins of replication rich in?

A
  • AT
37
Q

What is the shape of DNA replication?

A
  • replication fork
38
Q

Leading strand

A
  • daughter strand that is synthesized continuously

- moves toward the replication fork

39
Q

Lagging strand

A
  • Daughter strand that is synthesized discontinuously
  • away from replication fork
  • Leaves okazaki fragments
40
Q

RNA primer strands

A

-short sequences of DNA

41
Q

What enzyme makes the RNA primers?

A
  • DNA primase
42
Q

What can DNA primase do that DNA polymerase can’t

A
  • start a new polynucleotide chain by joining two nucleoside triphosphate together
43
Q

DNA primase

A
  • synthesizes a short polynucleotide in the 5’ to 3’ direction and then stops making the 3’ end of this primer available for the DNA polymerase that produce Okazaki fragment
44
Q

How many nucleotides is the RNA primer?

A
  • about 10 nucleotides
45
Q

What joins Okazaki fragments?

A
  • DNA ligase
46
Q

DNA ligase

A
  • uses ATP to convert 5’ phosphate group into diphosphate

- uses hydrolysis to seal bond

47
Q

What does DNA helicase do?

A
  • unwind/unzip DNA so it can be translated
48
Q

What prevents DNA from binding back together?

A
  • single strand DNA binding proteins (helix-destablizing proteins)
49
Q

What do sliding clamp and clamp loader do?

A
  • Position DNA polymerase onto the DNA
50
Q

What happens to clamp loader once the DNA polymerase binds to DNA

A
  • clamp loader is ejected
51
Q

Sliding clamp

A
  • Assists DNA polymerase in its movement
52
Q

Werner syndrome

A
  • premature aging syndrome
  • cells with an altered werner protein may divide more slowly or stop dividing earlier than normal, causing growth problems.
  • Mutation in DNA helicase
  • Cells divide more slowly or stop dividing

Biochemistry (Cole) (25 decks)

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