The replication bubble and antiparallel elongation

Biology Homework

Study Guide Chapter 16- Molecular basis of Inheritance-Answers

16.1 DNA is the genetic material____________________________________________

1. What specific research done by (A) Rosalind Franklin and (B) Chargaff did Watson use to deduce that DNA was a double helix?

(A) sugar-phosphate backbone was on the outside of the DNA molecule and nitrogenous bases must face the interior of the molecule

(B) A pairs with T and C pairs with G

16.2 DNA Replication____________________________________________

2. Watson and Crick’s model for DNA replication is based on its structure. Their model follows:

A. The parent DNA molecule has two__complementary__strands of DNA.

B. In the first step of replication the DNA strands are __separated__by an enzyme.

C. Each parent strand serves as a __template__that determines the order of nucleotides along the newly forming complementary strand.

E. Each daughter DNA molecule consists of one_parent_strand and one __new__ strand.

3A. Compare a conservative model for DNA replication and a semi-conservative model.

Conservative = at the end of replication the two parent strand would come back together and the new strands would come together = one original parent DNA molecule one new DNA molecule

Semiconservative = at the end of replication each DNA daughter molecule has one parent strand and one new strand

3B. Which model correlates with Watson and Crick’s DNA replication hypothesis?

Semiconservative

Getting Started: Origins of Replication

4. Where is the replication of a DNA molecule initiated?

Origin(s) of replication

5. Proteins called __helicases___ recognize the specific nucleotide sequence of the start site and attach to the DNA, separating the two strands creating a____replication bubble__________.

6. At the ends of each replication bubble are ____replication forks___.

7. T/F: Replication occurs at only one end of each replication bubble. If this statement is FALSE, correct it to make it TRUE!

Replication occurs at both replication forks (both ends) of a replication bubble.

8. T/F Eukaryotic chromosomes can have only one replication origin. If FALSE, fix the statement to make it TRUE!

Eukaryotic chromosomes have many origins of replication. Having many replication bubbles speed DNA replication!

Elongating a New DNA Strand

9. After an enzyme separates the parent DNA strands, new DNA nucleotides are added to the newly forming DNA strand by an enzymes called DNA polymerase III (DNA Pol III).

Antiparallel Elongation

10. The two strands of DNA are antiparallel, one strand runs 5’( 3’ other strand runs 3’ ( 5’.

A. Define antiparallel: Parallel but having opposite directions.

B. What do the numbers 3’ and 5’ represent?

(We discussed this in chapter 5) The carbons of the deoxyribose ring in the sugar-phosphate backbone of DNA. Counting the carbons of the ring clockwise from the nitrogenous base, 3' specifies the 3rd carbon in the ring and 5' specifies the 5th carbon in ring.

11A.To what end of the strand (3’ or 5’) does the DNA Polymerase III (DNA Pol III) enzyme add nucleotides?

3’ end of the strand ONLY

11B. Why can this enzyme add new nucleotides to this end of the newly forming DNA strand and not the other end?

The DNA Polymerase III requires an OH group to catalyze the addition of a new nucleotide. The 3’ end of the DNA strand has an OH group, whereas the 5’ end of the DNA strand does not.

11C. Strands can only be made in the 5’ to 3’ direction. The second number (3’) represents where the DNA Pol II is adding new nucleotides. Which of the following would you use to represent this situation: 5’ ( 3’ or 3’ ( 5’

5’ ( 3’

Reviewing the functions of the enzymes and proteins of DNA Synthesis

12. How do the following proteins: helicase and single stranded binding proteins assist in replication of DNA?

Helicase- unwinds the DNA helix

s.s. binding- bind to template DNA strands to keep them single stranded during replication

13. Can DNA Pol III initiate the synthesis of a new DNA strand? If no, what does initiate this process?

No, a primase enzyme adds 5-10 RNA nucleotides to initiate the process, then DNA pol III can add nucleotides.

14. How many primers are needed to synthesize the leading strand? Lagging strand?

1 primer for leading strand, many for lagging strand

15. What is the function of DNA polymerase I (DNA Pol I) in DNA synthesis?

Removes RNA primers

16. What is the function of DNA ligase in DNA synthesis?

Ligates (seals together) the okazaki fragments of the lagging strand

Draw a replication fork to assist you in answering the next 2 questions.

Label the two parent template strands and their 5’-3’ or 3’-5’ orientation to one another.

17A. DNA Pol III synthesizes a new complementary strand along the 3’ ( 5’ parent molecule template strand in the 5’(3’ or 3’(5’ direction?

5’ ( 3’ ALWAYS, this is the ONLY way to make DNA strands!

B. This new DNA strand is synthesized continuously/discontinuously by elongating the new DNA in the mandatory 5’(3’ direction.

continuously

C. This strand is elongated toward/away from the replication fork.

toward

D. What name is given to the DNA strand synthesized by this mechanism: Leading or Lagging strand?

Leading strand

E. Describe how this strand is synthesized. Discuss ALL proteins and enzymes used to make the new strand. Start with helicase and end with the DNA ligase.

1. Helicase separates and unwinds the template strands of the DNA double helix.

2. Single Strand Binding (SSBs) proteins prevent the template strands from reconnecting.

3. Primase adds a short sequence of RNA nucleotides (called a primer). The primer is complementary to the DNA template strand.

4. DNA pol III adds nucleotides to 3’ end of the primer, synthesizing the new DNA strand in the 5’ ( 3’ direction. The DNA Pol III synthesizes the new DNA strand toward the replication fork.

5. RNA primers are removed by DNA pol I

6. DNA ligase ligates the primer fragment to the newly synthesized leading strand.

18A. DNA Pol III synthesizes a new complementary strand along the 5’ ( 3’ parent molecule template strand in the 5’(3’ or 3’(5’ direction?

5’ ( 3’ ALWAYS, this is the ONLY way to make DNA strands!

B. This new DNA strand is synthesized continuously/discontinuously by elongating the new DNA in the mandatory 5’(3’ direction.

discontinuously

C. This strand is elongated toward/away from the replication fork.

Away from

D. What name is given to the DNA strand synthesized by this mechanism: Leading or Lagging strand?

Lagging strand

E. Describe how this strand is synthesized. Discuss ALL proteins and enzymes used to make the new strand. Start with helicase and end with the DNA ligase.

1. Helicase separates and unwinds the template strands of the DNA double helix.

2. Single Strand Binding (SSBs) proteins prevent the template strands from reconnecting.

3. Primase adds a short sequence of RNA nucleotides (called a primer). The primer is complementary to the DNA template strand.

4. DNA pol III adds nucleotides to 3’ end of the primer, synthesizing the new DNA strand in the 5’ ( 3’ direction. The DNA Pol III synthesizes the new DNA strand away from the replication fork.

5. DNA pol III falls off the template DNA strand and stops synthesis of the new DNA strand when it runs into an RNA primer.

6. Primase makes a new primer near the replication fork

7. DNA pol III adds nucleotides to 3’ end the new primer

8. DNA pol III falls off template when it runs into a RNA primer

(steps 6-8 repeat…)

In the meantime….

7. RNA primers are removed by DNA pol I

8. DNA ligase ligates the Okazaki fragments of the newly synthesized lagging strand.

19.What is an Okazaki fragment? In what strand (leading or lagging) would you find such fragments?

DNA fragments that are made during lagging strand synthesis.

Proofreading and Repairing DNA

20A.Approximately how many nucleotides (base pairs: A, T, C and G) are in the human genome (46 chromosomes)?

6 billion base pairs!

20B. How often are nucleotide errors made during replication of a human genome?

1:100,000 base pairs = YIKES! lots of mistakes, good thing we have proofreading enzymes!!!

20C. Proofreading enzymes scan the newly synthesized DNA strands following replication looking for errors. After the DNA is proofread, how many neucleotide errors remain?

1: 10 billion base pairs

21. What physical agents is DNA constantly subjected to that could damage nucleotides?

UV sunrays, radiation, chemical mutagens

22. Most mechanisms for repairing DNA errors or damage take advantage of the base-paired structure of DNA. Describe this DNA repair process. include mention of the DNA cutting enzyme (nuclease).

Nucleotide excision repair:

EX: thymine dimmer cause by UV radiation

Nuclease cuts part of DNA strand with dimmer (damage)

DNA polymerase adds new nucleotides to replace the ones cut out

DNA ligase seals together the new DNA nucleotides to the ones of the old strand

16.3 DNA Packaging

23. Describe the first level of DNA packaging (include histone proteins, DNA, linker DNA, and nucleosomes) Also, what are some common names given to DNA packaged at this level?

DNA wrapped around histone proteins, DNA not wrapped around histone proteins is the linker DNA.

Common names = 10 nm fiber and “beads on a string”

24A. Describe the structure of the nucleosome.

DNA wrapped around histone proteins

24B. What chemical properties of histones and DNA enable these molecules to bind tightly together?

DNA negative charge

Histones positive charge

25. Second level of DNA packaging

Describe how DNA is packaged into the 30 nm fiber.

Linker DNA associates with histone protein H1

26. Third level of DNA packaging

Describe how DNA is packaged into the 300 nm fiber (include protein scaffold, looped domains).

30nm fiber associates with a non-histone protein scaffold, forming looped domains attached to the scaffold.

27. Fourth level of DNA packaging

Describe how DNA is packaged into the 700 nm fiber.

Protein scaffold with 30nm fiber attached folds on itself

28. What is the difference between euchromatin and heterochromatin? In which of these DNA configurations are gene repressed? expressed?

Euchromatin = DNA that is not condensed during interphase and available for transcription= these genes can be expressed

Heterochromatin = DNA that is condensed during intrephase and NOT available for transcription= these genes cannot be expressed