Lecture 15 - Nucleic Acid Synthesis

Question 1

What is replication?

Answer 1

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

Question 2

What is transcription?

Answer 2

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

Question 3

What is translation?

Answer 3

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

Question 4

Does DNA have parallel or anti-parallel strands?

Answer 4

Anti-parallel

Question 5

What is the function of chromatin?

Answer 5

To package DNA in a more compact shape

Question 6

What is Phe-tRNA used in?

Answer 6

Protein synthesis

Question 7

What is a hammerhead ribozyme?

Answer 7

An RNA enzyme

Question 8

Describe the conservative theory of DNA replication

Answer 8

The parental molecule is conserved, or remains intact

Question 9

Describe the semi-conservative theory of DNA replication

Answer 9

The parental strands separate but they are conserved as strands

Question 10

Describe the dispersive theory of DNA replication

Answer 10

The parental strands are fragmented and interspersed with new DNA

Question 11

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

Answer 11

Semi-conservative

Question 12

Describe the Meselson-Stahl experiment

Answer 12

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

Question 13

What is the key enzyme in DNA replication?

Answer 13

DNA polymerase

Question 14

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

Answer 14

Eukaryotes

Question 15

What are 3 properties of all polymerases?

Answer 15

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

Question 16

What happens to the primer during DNA synthesis?

Answer 16

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

Question 17

What happens when a dNTP bonds to a primer?

Answer 17

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

Question 18

Why must bases be properly paired?

Answer 18

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

Question 19

What is the function of RNA polymerase in DNA replication?

Answer 19

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

Question 20

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

Answer 20

RNA polymerase can initiate elongation without a primer

Question 21

What are okazaki fragments?

Answer 21

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

Question 22

What happens to the leading strand during DNA synthesis?

Answer 22

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

Question 23

What happens to the lagging strand during DNA synthesis?

Answer 23

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

Question 24

The RNA primer is removed by ____

Answer 24

RNase

Question 25

How are okazaki fragments joined into one continuous strand?

Answer 25

By DNA ligase

Question 26

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

Answer 26

Can occur on both

Question 27

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

Answer 27

1) Avery-McLeod-McCarty experiment | 2) Hershey-Chase experiment

Question 28

What 4 facts were proven in the Griffith experiment?

Answer 28

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

Question 29

What questions arose from the findings of the Griffith experiment?

Answer 29

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

Question 30

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

Answer 30

- 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

Question 31

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

Answer 31

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

Question 32

What did the Hershey-Chase experiment study?

Answer 32

A bacteriophage that infects E. coli

Question 33

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

Answer 33

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

Question 34

What are 3 requirements of RNA polymerase for transcription?

Answer 34

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

Question 35

_____ signals where the RNA polymerase is to start and stop

Answer 35

The DNA sequence

Question 36

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

Answer 36

Processing

Question 37

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

Answer 37

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

Question 38

Is a primer needed for transcription?

Answer 38

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

Question 39

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

Answer 39

- Sigma | - Required for binding to the DNA at the promoter

Question 40

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

Answer 40

It must leave the complex

Question 41

Which sequences are recognized by the holoenzyme?

Answer 41

-10 and -35

Question 42

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

Answer 42

-10 sequence because it is AT rich

Question 43

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

Answer 43

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

Question 44

What happens if the RNA polymerase pauses for too long?

Answer 44

Termination occurs

Question 45

What causes termination of transcription?

Answer 45

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

Question 46

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

Answer 46

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

Question 47

What causes a loop structure?

Answer 47

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

Question 48

What does a loop structure cause?

Answer 48

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

Question 49

What is rho protein?

Answer 49

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

Question 50

What is poly U?

Answer 50

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

Question 51

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

Answer 51

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

Question 52

Does transcription or translation take up more energy?

Answer 52

Translation