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Biochem 2 > Lecture 15 - Nucleic Acid Synthesis > Flashcards

Lecture 15 - Nucleic Acid Synthesis Flashcards

1
Q

What is replication?

A

Copying of parental DNA to form daughter DNA molecules with identical nucleotide sequences

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2
Q

What is transcription?

A

Parts of the genetic message encoded in DNA are copied precisely into RNA

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3
Q

What is translation?

A

The genetic message encoded in mRNA is translated on the ribosomes into a polypeptide with a particular sequence of amino acids

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4
Q

Does DNA have parallel or anti-parallel strands?

A

Anti-parallel

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5
Q

What is the function of chromatin?

A

To package DNA in a more compact shape

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6
Q

What is Phe-tRNA used in?

A

Protein synthesis

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7
Q

What is a hammerhead ribozyme?

A

An RNA enzyme

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8
Q

Describe the conservative theory of DNA replication

A

The parental molecule is conserved, or remains intact

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9
Q

Describe the semi-conservative theory of DNA replication

A

The parental strands separate but they are conserved as strands

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10
Q

Describe the dispersive theory of DNA replication

A

The parental strands are fragmented and interspersed with new DNA

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11
Q

Does the conservative, semi-conservative, or dispersive theory occur in reality?

A

Semi-conservative

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12
Q

Describe the Meselson-Stahl experiment

A

1) E. coli cells were grown in only heavy nitrogen (N15) in order to label all of the nitrogens in DNA w/ heavy nitrogen
2) Cells were isolated and then transferred to a medium with only light nitrogen (N14) and grown for one generation and then DNA was extracted
3) Continued to grow cells in light nitrogen and DNA was extracted after each generation
4) DNA was analyzed by CsCl density centrifugation - DNA with heavy nitrogen will accumulate further down the tube (where its density matches the CsCl density) and light nitrogen will be higher up
5) Each subsequent generation has a bit more light nitrogen

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13
Q

What is the key enzyme in DNA replication?

A

DNA polymerase

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14
Q

Do prokaryotes or eukaryotes have a more complex method of DNA replication?

A

Eukaryotes

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15
Q

What are 3 properties of all polymerases?

A

1) Use dNTP’s as substrates
2) Require a primer and a template
3) Elongate in the 5’ to 3’ direction

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16
Q

What happens to the primer during DNA synthesis?

A

Primer is elongated using the template to direct the nucleotide to be incorporated in a base pairing sense (G + C and A + T)

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17
Q

What happens when a dNTP bonds to a primer?

A

Pyrophosphate is lost b/c the nucleotide only needs one phosphate

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18
Q

Why must bases be properly paired?

A

If not, it can exclude them from the active site of DNA polymerase

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19
Q

What is the function of RNA polymerase in DNA replication?

A

RNA polymerase opens up the DNA to make a loop at a specific point and can initiate elongation without a primer

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20
Q

What is the major difference between RNA polymerase and DNA polymerase?

A

RNA polymerase can initiate elongation without a primer

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21
Q

What are okazaki fragments?

A

Small fragments of single stranded DNA that have nucleotides of RNA at the 5’ end, which serves as a primer for DNA polymerase

22
Q

What happens to the leading strand during DNA synthesis?

A

It is elongated 5’ to 3’ continuously to the “end”

23
Q

What happens to the lagging strand during DNA synthesis?

A

It is synthesized as a series of small fragments that start whenever ~1000 nucleotides of single-stranded DNA is opened up by growth of the leading strand

24
Q

The RNA primer is removed by ____

A

RNase

25
Q

How are okazaki fragments joined into one continuous strand?

A

By DNA ligase

26
Q

Do okazaki fragments occur on one or both strands of DNA?

A

Can occur on both

27
Q

What are the 2 experiments that proved that DNA contained all the genetic information?

A

1) Avery-McLeod-McCarty experiment

2) Hershey-Chase experiment

28
Q

What 4 facts were proven in the Griffith experiment?

A

1) A mouse infected with the virulent bacterium died
2) A mouse infected with the mutant (no capsid) lived
3) A mouse infected with the heat killed batch also lived
4) A mouse infected with a mixture of the mutant strain and the heat killed batch died

29
Q

What questions arose from the findings of the Griffith experiment?

A
  • Was the non-virulent mutant resurrecting the heat killed bacteria?
  • Was something in the heat killed bacterium transforming the non-virulent to virulent?
30
Q

What did the Avery and McLeod experiment show (keeping in mind the results of the Griffith experiment)?

A
  • Only the fraction with nucleic acids caused the non-virulent bacteria to have virulent properties
  • DNA from the heat killed strain was recombined into the chromosome of the non-virulent strain, replacing a defective gene for capsid synthesis with a normal gene
31
Q

What was the question posed by the Hershey-Chase experiment?

A

Whether the protein or the DNA entered the cell on infection, and passed on the genetic info of the phage

32
Q

What did the Hershey-Chase experiment study?

A

A bacteriophage that infects E. coli

33
Q

Is the RNA that is produced from transcription an opposite or a duplicate of the DNA strands?

A

It is the opposite of one, and a duplicate of the other (except all of the T’s become U’s)

34
Q

What are 3 requirements of RNA polymerase for transcription?

A

1) NTP’s
2) Template (DNA)
3) Promoter and terminator

35
Q

_____ signals where the RNA polymerase is to start and stop

A

The DNA sequence

36
Q

What must happen after synthesis of the primary transcript for mature mRNA to be produced?

A

Processing

37
Q

What are the 2 main forms of RNA polymerase that exist in bacteria?

A

1) Core enzyme - carries out elongation of the RNA chain after sigma release
2) Holoenzyme - binds to the promoter site on DNA to initiate transcription

38
Q

Is a primer needed for transcription?

A

No, the holoenzyme recognizes and binds to the promoter sequence on the DNA

39
Q

What is the key protein factor of transcription and what is it required for?

A
  • Sigma

- Required for binding to the DNA at the promoter

40
Q

What must happen to the sigma protein for elongation to begin?

A

It must leave the complex

41
Q

Which sequences are recognized by the holoenzyme?

A

-10 and -35

42
Q

Which sequence facilitates the formation of the open complex and why?

A

-10 sequence because it is AT rich

43
Q

Does RNA polymerase travel at the same speed across the DNA sequence?

A

No, it speeds up and slows down depending on the DNA sequence

44
Q

What happens if the RNA polymerase pauses for too long?

A

Termination occurs

45
Q

What causes termination of transcription?

A

The DNA sequence, because it causes the enzyme to slow, and then other factors facilitate termination

46
Q

What are the 3 other factors (besides DNA sequence) that facilitate transcription termination?

A

1) Loop structure
2) Rho protein
3) Poly U

47
Q

What causes a loop structure?

A

Palindromic (same forwards and backwards) sequence in the new RNA

48
Q

What does a loop structure cause?

A

The RNA-DNA duplex being disrupted, weakening the complex and making dissociation of the RNA from DNA easier

49
Q

What is rho protein?

A

A termination factor that binds to the 5’ end of the RNA transcript and “chases” after the RNA polymerase, catching up to it when the RNA polyermase is paused and then destabilizes the RNA-DNA duplex causing dissociation of RNA from DNA

50
Q

What is poly U?

A

A sequence of 5-10 uridines in a row at the end of the RNA, destabilizing the RNA-DNA duplex making dissociation easier

51
Q

What are the 3 types of RNA polymerase that are needed for eukaryotic transcription and what does each do?

A

1) RNA polymerase 1 - makes rRNA
2) RNA polymerase 2 - makes mRNA for translation
3) RNA polymerase 3 - makes tRNA, some rRNA and other specialized RNA

52
Q

Does transcription or translation take up more energy?

A

Translation

Biochem 2 (40 decks)

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