Chapter 15

Question 1

What did Alfred Hershey and Barbara Chase discover via their experiment?

Answer 1

1. ) Genes are composed of DNA

2. ) The overall pattern of which DNA is replicated.

Question 2

What were Alfred Hershey and Barbara Chase’s test subjects?

Answer 2

• They were working with a virus called a T-2 Phag (infects bacteria) and they have a moon lander shape.
• This allows them to sit a top of the bacteria and drill a little hole and inject their genes into the host bacterium.

Question 3

What is a summary of the Alfred Hershey and Barbara Chase experiment?
- What did Reedy give on a background for what was occurring as well.

Answer 3

1.) the Phag links to the bacteria’s surface and injects its genes into the bacteria.
2.) This in turn creates for production of the new virus within the host bacteria cell.
3.) Finally, when the virus is completed it exists the host bacteria
( what Ready explained as the synopses)
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1.) They generated two different sets of viruses, one set they label the DNA with a radioactive tracer (32P) they did this because DNA has a large phosphate backbone and this would stand out with the tracer.
2.) The other set of T-32 phag was labeled with radio active 35S (sulfur, which is present in many amino acids, thus proteins) but isn’t present in DNA.
3.) They took each population of T-32 phag and separately injected them into bacteria.
4.) At this point the T-32 phag had injected the host with it’s genes and then they agitated the phag to knock it off.
5.) They then pelleted everything in the centrifuge, which causes the genes to fall inside the test tube so their Gene structure could be tested (DNA. vs Proteins) .
6.) Radioactive DNA was found in the Pellet, while the proteins were found in the solution. ( thus meaning genes were composed of DNA).

Question 4

What was Alfred Hershey and Barbara Chase hypothesis?

Answer 4

What ever the parasitic type organism was injecting into the cell (DNA) this is what would be seen in it’s offspring’s genes ( Virus Genes) that were released into the host bacteria cell.

Question 5

Describe the structure of a DNA molecule?

Answer 5

• 5 prime carbon (deoxyribose, with a phosphate attached to its 5 prime carbon end.
• Obv a Phosphate group.
• A nitrogenous base bonded to carbon 1 on deoxyribose.

Question 6

What holds differing nucleotides together?

Answer 6

• Phosphodiester linkage (covalent bond), formed via a condensation reaction.
• That bonds the hydroxide bonded to the third prime carbon on the deoxyribose to a 5 prime phosphate group.

Question 7

3 prime vs. 5 prime end?

Answer 7

• DNA is polar, who knew!!
• The side with a phosphate group extending from the top is the 5 prime end ( phosphate isn’t bonded with anything) and the side with a hydroxide extending is the 3 prime end ( again not bonded to anything).

Question 8

What is the complementary base pairing to:
5’- A,T,G,C,A,A,C-3’ ?
How is the double helix form following complementary base pairing (not super deep)

Answer 8

1. ) 3’-G,T,T,G,C,A,T-5’

2. ) The structure twist to form the double helix.

Question 9

What did Watson and Crick suggest about how DNA is replicated?

Answer 9

• Semiconservative replication, the original parental strand, following replication is torn in half and used to complementary base pair with the new single strands.
• yielding two new DNA hybrids ( half new and half old).

Question 10

What is conservative replication?

Answer 10

• enzymes would read the DNA and somehow leave it intact somehow, and make a new identical DNA that was identical

Question 11

What is Dispersive replication?

Answer 11

• The two strands of DNA pulled apart and then are chopped into pieces
• New DNA is synthesized to stich it back together.
• Forming new DNA w the old strands, and new,
• but is differing in semiconservative as it is continous

Question 12

How did they test which type of DNA replication could was most correct?
What were their findings

Answer 12

• ## Meselson and Stahl ( 1958) **
• They could change the weight of DNA by growing bacteria in media with different isotopes of Nitrogen * (15, 14).
• ## DNA is nitrogen heavy, therefor nitrogen 14 media would produce lighter DNA.
• Grew E.coli in a nitrogen 15 media culture
  2.) They removed the bacteria once it had grown and labeled it generation 0 and stuck it in the fridge.
  3.) then they replaced the Nitrogen 14 media and allowed them to grow for one generation.
  4.) Then they extracted the cells and labeled them generation 1.
  5.) They allowed the cells to grow for anther generation within the same media, took a sample and fridged in labeling it Generation two.
  ——————————————————————–
• Once they had their samples they separated the DNA via a process called density gradient centrifuge.
  ///////////////////////////////////////////////////////////////////////
  #2.)
• Semiconservative

Question 13

What is DNA centrifuge?

Answer 13

The molecular weight of DNA is lighter than the other cell material, like proteins and cell walls. By spinning the sample with centrifuge, we separate the cell material from the DNA, which gives us a cleaner DNA sample.

Question 14

What type of DNA replication would it be if you saw the offspring containing only the nitrogen 15 and 14 in separate strands in generation1?

Answer 14

• conservative DNA replication

Question 15

What type of DNA replication would it be if you saw the offspring containing the nitrogen 15 and 14 in hybrid forms strands generation 2?

Answer 15

• dispersive DNA replication.

Question 16

What type of DNA replication would it be if you saw the offspring containing the nitrogen 15 and 14 in 2 hybrid forms and two sperate nitrogen 15, 14 strands generation 2?

Answer 16

semi-conservative DNA replication.

Question 17

What is the Replication bubble?

Answer 17

• The site where DNA replication is occurring

Question 18

When looking at the DNA replication bubble, what is the replication fork?

Answer 18

• ## where DNA molecule splits from its conjoined strands to the singular strand ( one per side)

Question 19

What is the site in which DNA replication bubble forms?

Answer 19

• origin of replication
• Bacteria have one
• Eukaryotes are much larger and typically have multiple origins of replication .
• Each origin of replication bubble has two forks.

Question 20

What is the new growing strand referred to as?

What is the original strand referred to as?

Answer 20

• Daughter strand

- Parental strand

Question 21

What is the function of DNA polymerase?

Answer 21

• Enzyme, Carry out the formation of phosphodiester linkages

Question 22

t/f you can only add nucleotides to the 5’ end of a chain?

Answer 22

• false, you can only add to the three’ end, Usssshhhhaaaa ussssshhhhhaaaa

Question 23

What direction does the daughter strand grow in?

Answer 23

• She grows in the 5’-3’ direction.

Question 24

How is the parent stand’s nucleotides read?

Answer 24

DNA polymerase reads the parent strand in the 3’ - 5’ direction.

Question 25

What type of nutrient is needed to carry out the replication process of DNA?

Answer 25

- proteins

Question 26

What is the first step in the process of replicating DNA, and what things make it possible to be carried out?

Answer 26

1. ) the two original strands must separated via an enzyme helicase. 2. ) helicase binds to one strand and origin of replication. Then, moves in one direction and begins splitting apart the DNA strands. - ------------------------------------------------------------ 3. ) Once split apart the strands have a tendency to join back together so.... Single-stand DNA-binding proteins (SSBP's) stabilize single strands, thus preventing the two from coming back together. 4. ) because DNA has a tendency to get jumbled up following when it is split, Topoisomerase binds to the double stranded DNA in front of helicase and makes little Knicks in sugar backbone thus preventing the twisting tendency. - ---------------------------------------------------------------------- 5. ) Shortly after DNA has been split via helicase, Primase (3) pulls up behind it ( if you know what I mean do this with your homie) and sits on a parental stand. 6. ) Primase (3) sits on a very short RNA that serves as a primer (initiating site.) . RNA primer complementary base pairs ( remember thymine=uracil and it also has a '5-3'-OH) with the split DNA, thus allowing DNA polymerase (3) to come in and take care of base pairing and relive the RNA primer.

Question 27

- At the DNA replication fork how many strands are there? | - What happens on each half of the DNA as it is split for replication and polymerase comes in?

Answer 27

- Two - The leading stand: DNA polymerase synthesizes DNA in the direction of the parent strand: 5'-3'. - Lagging strand: On the other half of the fork, DNA polymerase, it will also synthesis it in the same direction 5'-3' - ------------------------------------------------------------------------- - Because there parent strands are ran in opposite directions; their daughter strands are read in opposite directions. - Therefore, the leading strand moves in the same direction as helicase, meaning the daughter strand can be produced in one long continuous fashion.

Question 28

What is the difference between the lagging strand and the leading strand.

Answer 28

- They both synthesis (make or add to the 3') DNA in the '5-3' direction and synthesis and read in the 3'-5' direction. ------------------------------------------------------------------------------ - The leading strand: - Moves in the same direction as helicase and DNA polymerase. - Daughter strand is produced in one long continuous fashion. -------------------------------------------------------------------------- The lagging strand: - moves in the opposite direction of Helicase & polymerase. - made in choppy pieces and is later stitched together.

Question 29

In what direction does DNA read the parental strand?

Answer 29

3'-5'

Question 30

What is different about the lagging stand and leading strand?

Answer 30

- The lagging strand is moving in the opposite direction and there for isn't moving with helicase and polymerase. -

Question 31

Describe the order of events taking place in the lagging strand?

Answer 31

-This process essentially happens shortly after the the leading strand moves. - Then, primase sits down of the TEMPLATE strand and synthesis a short RNA primer that is used a template for DNA polymerase (3). - This allows DNA polymerase (3) to make the new strand accordingly. ----------------------------------------------------------------------------- - Every time helicase moves it reveals a new strand SEGMENT of the new template. - Each segment is known as an Okazaki fragment. --------------------------------------------------------------------------- - DNA polymerase(1) one then binds to the RNA component of the Okazaki fragment. - It chews away at the Ribonucleotides and replaces it with deoxyribonucleotides. --------------------------------------------------------------------- Finally, DNA ligase pulls up to the function and binds the end of one Okazaki fragment to the beginning of anther via phosphodiester bonds. - This process is carried out in the opposite direction but same ' direction as the leading strand.

Question 32

Describe the order of events taking place in the leading strand?

Answer 32

- DNA gets sat down. - DNA is split - Helicase sits down, on one of the single strands. - Topoisomerase moves in front of the helicase, preventing it from unwinding. They both move in one direction unzipping the DNA as they go. - -------------------------------------------------------------- - Then, bitch ass primase sits down of the TEMPLATE strand and synthesis a short RNA primer that is used a template for DNA polymerase (3). - This allows DNA polymerase (3) to make the new strand accordingly. - Importante* because DNA polymerase is moving slower then helicase/topoisomerase, this allows the daughter strand to be made in one long strand.

Question 33

What is the contents of an Okazaki fragment?

Answer 33

- RNA primer with the new Daughter strand being formed as a result.

Question 34

Which functional components of forming DNA just are used for the lagging strand?

Answer 34

- DNA polymerase (1)

Question 35

Describe the function and location of the Following: | Helicase, SSBP's, topoisomerase, Primase, DNA Polymerase (3), Sliding Clamp, DNA Polymerase (1), DNA ligase?

Answer 35

Helicase: Catalyzes the breakdown of hydrogen molecules between base pairs. SSBP : stabilizes the single stranded DNA topoisomerase: enzymes that alter the supercoiling of double-stranded DNA. (In supercoiling the DNA molecule coils up like a telephone cord, which shortens Primase: enzyme that catalyzes the synthesizes of the RNA primer on the Okazaki fragment. DNA Polymerase (3): Extends an Okazaki fragment. Sliding Clamp: Holds DNA polymerase in place with the DNA strand is extended. DNA Polymerase (1): Removes RNA primer and replaces it with DNA. DNA ligase: Catalyzes the formation of Okazaki fragments into a continuous strand.

Question 36

What is a replisome?

Answer 36

All the events of DNA replication at one fork.

Question 37

How many forks are on each replication bubble?

Answer 37

2 | 1 per side

Question 38

What happens following the DNA helicase falling off and exposing the last fragment of DNA on the lagging strand? - ---------------------------------------------------------------------- 2. )- How does the lagging strand protect itself from degradation and or the shorting of it's chromosome?

Answer 38

- RNA primase sits down, but not on the very end. This is because it must be offset by several bases. - Thus, this leaves an exposed unreplicated end that is particularly unstable.. - This in turn would lead to a shortening of the chromosome at the end of every round. - ------------------------------------------------------------------------- 2. ) Telomerase, an enzyme that carries around its own RNA template that is complementary to the exposed lagging strand region. - This allows for the extension of telomere region of the lagging DNA strand, so its chromosomes aren't cut into.

Question 39

What is the exposed lagging strand region known as?

Answer 39

- Telomere region.

Question 40

Describe the order of events in regards to telomerase?

Answer 40

- Telomerase binds to the telomere region and begins to complementary base pair. - Following, the strand is extended as a result. - Then, DNA polymerase (3) pulls up to the function and binds the final Okazaki fragments. - ----------------------------------------------------------------------------- - All of the original strand has been replicated, but your left with a hanging region.

Question 41

T/F most cells express telomeres?

Answer 41

False, most do not.

Question 42

What is telomere length indicative of?

Answer 42

age, the more replications and shorter the length of the telomere is a good sign as to what a persons age is.

Question 43

What is cellular senescence and what triggers it?

Answer 43

- It is when the telomere becomes too short and this triggers cellular death or inactivation.

Question 44

What is the advantage of a cell that expresses telomeres?

Answer 44

- That cell can extend its telomere and live continuously.

Question 45

What is mismatch repair? How can you see a mismatch? How is it corrected/is it corrected?

Answer 45

- When a single base doesn't match the complementary strand, therefore it needs to be removed and replaced. - ---------------------------------------------------------------------------- - There is usually a bump in the DNA phosphate backbone. - ---------------------------------------------------------------------------- - DNA polymerase proofs the DNA strand and replaces what errors may have occurred. - ( It is pretty accurate, but definitely shy of 100%

Question 46

When do most errors in complementary base pairing occur?

Answer 46

- During DNA replication.

Question 47

What are the hMSH genes?

Answer 47

- They serve as secondary double checkers to DNA polymerase. | - Discovered by Dr. Henry Lynch at the Creighton Medical Center.

Question 48

What happens when there is a physical change in the structure of the DNA, lets just same form UV radiation, what has to happen?

Answer 48

- The UV radiation likely caused a Thymine Dimer which put a kink in the DNA strand. - This kink can block DNA polymerase, Helicase, ect. during DNA replication. - -------------------------------------------------------------------------- So... NUCLEOTIDE EXESISION REPAIR pulls up like Bob The Builder. - Then, senses what kinds of bumps are in the DNA back bone and chops that shit out.