Bio200 Activity 3 10-2 DNA Replication KEY v2 PDF

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Biology notes for the 3rd midterm and the final exam for that year....

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DNA Replication, Fall 13 KEY A POGIL exercise developed by Dr. A. Schivell

Crowe

MODEL 1: The circle is an E. coli chromosome at the beginning of DNA synthesis. The original DNA strands are called "parental strands". In this model, DNA is black and RNA is gray. Each shape represents a different enzyme.

"Replication Bubble"

"replication fork"

T I

Leading strand 5'

M E

5' Lagging strand

3'

DNA Replication, Fall 13 KEY A POGIL exercise developed by Dr. A. Schivell

Crowe

1.Which parental strand acts as a template for synthesis of a new complementary DNA strand? - neither strand - both strands - only one strand

5'

2. a. Label the 5' and 3' ends of the new strands in the middle panel of Model 1. b. On what end of a DNA strand are new nucleotides added? 3' end c. Draw a sketch of a "new nucleotide" before it is added by a polymerase: They should draw an "activated deoxyribonucleotide" (dNTP) 3. a. Match each enzyme's shape with its function and fill in the column on the left. Shape:

Function: Enzyme that synthesizes the largest part of the new DNA strands Enzyme that forms a phosphodiester bond without adding a new nucleotide

Enzyme Name: DNA polymerase III

Enzyme that synthesizes a short RNA primer

Primase

Ligase

Enzyme that replaces RNA nucleotides with DNA polymerase I DNA Enzyme that breaks H-bonds between strands Helicase of the parent DNA helix b. Use the following root "translations" to help you define each enzyme: Roots: Enzyme names: - "lig-" is a latin prefix meaning "bind" ligase - DNA polymerase - helicase - "prim-" is a latin prefix meaning "first" primase - ligase - primase - "poly-" means "many", "-mer" is "unit" DNA polymerase - "heli-" means "coil or spiral" helicase c. Fill in the Enzyme Name column in the table above with one of the enzymes. One enzyme will be used twice. d. Go back and label the shapes on the model with their enzyme names. e. The enzyme that does the majority of DNA synthesis is called DNA polymerase III. The enzyme that replaces RNA nucleotides with DNA is called DNA polymerase I. Add I and III in the table above and in the model.

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DNA Replication, Fall 13 KEY Crowe A POGIL exercise developed by Dr. A. Schivell 4. DNA polymerase can add nucleotides using the bottom strand as a template in the diagram below on the left, but cannot add nucleotides using the bottom strand as a template in the diagram on the right. DNA polymerase can use this:

but not this:

a. Can RNA polymerase use one or both of the templates above when adding nucleotides? _Both__ b. RNA polymerase has an enzymatic ability that DNA polymerase does not have. What is it? (write in less than one sentence): can start a new strand of RNA (does not need a 3' end to add onto). 5. a. One new DNA strand at each replication fork is made in pieces, while the other one is made continuously. Explain why this has to be the case in 1-2 sentences. Because of the antiparallel nature of the template (parental) strands, when helicase separates them, one new strand will be synthesized "toward" the fork, whereas the other will be made in a direction "away" from where the strands are separating. Therefore the latter new strand will need to be made in sequential pieces. b. In the middle panel of Model 1, label the continuously made strand the "leading strand". Label the strand made in pieces the "lagging strand".

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DNA Replication, Fall 13 KEY A POGIL exercise developed by Dr. A. Schivell

Crowe

MODEL 2: This model shows one entire eukaryotic linear chromosome. The original chromosome is shown before replication. The same chromosome is shown about 30 minutes after the process of DNA synthesis has begun in each of four different cells (no enzymes are shown). The chromosomes are aligned by sequence and gray = new DNA. "original" chromosome * * * * cell # 1

2

3

4

6. Based on Model 2, decide if each statement is most likely True or False. False DNA synthesis can start anywhere on a chromosome. False DNA synthesis starts only at one place on a chromosome. True DNA synthesis starts at specific locations on a chromosome. False DNA synthesis starts at every location at exactly the same time. 7. Using asterisks, indicate the specific locations where synthesis can start on the original chromosome. These are called "Origins of Replication" 8. a. The protein that binds to origin sequences is called an "initiator protein". Do you think that initiator proteins are expressed constitutively? Why or why not? Note: constitutively = at all times No. If initiator proteins were expressed consititutively, then DNA would replicate all the time. b. What is the most likely role of initiator proteins? Initiator proteins most likely "attract" and bind to the five proteins needed for DNA replication (the enzymes from Model 1). 9. In transcription and translation, the terminator and stop codons were used (respectively) to end the processes at the correct location. Keeping in mind the goal of DNA replication, what stops the process of DNA synthesis? The end of the chromosome or running into another replication fork 10. When do cells need to replicate their DNA? Only if they are going to divide 4

DNA Replication, Fall 13 KEY A POGIL exercise developed by Dr. A. Schivell On Your Own:

Crowe

1. Watch the videos marked "DNA Replication" on our website on the "Movies" page. You may need to watch them several times to get a sense of how the replication enzymes work together at a replication fork. a. Which part of the DNA is phosphodiester backbone, red or yellow? red b. Which part of the DNA represents the nitrogenous bases, red or yellow? yellow c. Determine which strand is the leading strand and which is the lagging strand. d. Try to identify as many enzymes as possible in the animation. 2. A cartoon of one replication bubble is shown below. On one template strand on one fork, the newly made strands are shown. Draw in the rest for the rest of the bubble and label the 3' and 5' ends as well as the leading and lagging strands. (Arrow indicates 3' end) 5’ Leading 5’ 3’

3’

5’ ’ Lagging

3’ 5’

Lagging 3’ 5’

5’

Leading 3’

3’

3’ 5’

5’

3. Drawn in detail below is a region of parental DNA with two replication forks approaching from either direction. Explain what enzymes will be needed and diagram how the replication will be completed when the two forks meet. You will need DNA pol III to finish the main DNA synthesis, DNA pol I to replace the RNA, and ligase to seal the last phosphodiester bond. But you will NOT need prim

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DNA Replication, Fall 13 KEY A POGIL exercise developed by Dr. A. Schivell

Crowe

4. On planet Mandoid, DNA polymerase III adds nucleotides onto the 3’ end of a growing nucleic acid just like on Earth. However, Mandoid DNA polymerase III CAN start a new DNA strand on its own (it does not need an existing 3’ end to add to). Lagging 5’

3’ 5’

5’ 3’

3’ 5’

3’

a. The diagram above shows a single replication fork of a chromosome on Mandoid. Draw in the leading and lagging strands and label them (‘leading’ and ‘lagging’). Include 5’ and 3’ labels! b. Which of the following enzymes or molecules involved in DNA replication on Earth will ALSO be found on planet Mandoid? (Circle ALL that apply) - DNA pol I

- ligase

- primase

- helicase

5. E. coli, a prokaryote, has a single origin of replication on its one chromosome. The E. coli chromosome is about 5 million base pairs long. Human chromosomes are on average 20 times longer. Do you think human chromosomes have a single origin or many? Why? Human chromosomes probably have many origins since their chromosomes are so long. This way they can replicate chromosomes more rapidly.

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