Day: December 17, 2009

Discuss how DNA replicates. In your discussion, you should explain:

• How replication begins.
• The roles of the main enzymes involved.
• Leading and lagging strands
• Okazaki fragements
• The source of materials for replication

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Click to see model answer to this question

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2009년부터 NCEA시험이 이런식으로 출제될 것이다. 올해, 학교들마다 NCEA시험문제유형을 몰라 준비되지 못한 학생들이 많았다. (2009년 Year13에게 엄청 미안하다.ㅎㅎ 지.못.미.)

여태까지 배운내용을 정리하면서 완성도 높은 답안지를 작성해 놓자. 이 문제와 완전 같은 문제가 나올것이라고는 생각하지 않는다. 하지만, 연말 NCEA external을 위해 마지막 점검을 할때 도움이 될거라 믿는다.

Okazaki fragment에 RNA primer가 필요한 이유.

DNA replication begins with a partial unwinding of the double helix at an area known as the replication fork. This unwinding is accomplished by an enzyme known as DNA helicase. This unwound section appears under electron microscopes as a “bubble” and is thus known as a replication bubble.

As the two DNA strands separate (“unzip”) and the bases are exposed, the enzyme DNA polymerase moves into position at the point where synthesis will begin.

The start point for DNA polymerase is a short segment of RNA known as an RNA primer. The very term “primer” is indicative of its role which is to “prime” or start DNA synthesis at certain points. The primer is “laid down” complementary to the DNA template by an enzyme known as RNA polymerase or Primase.

Because the original DNA strands are complementary and run anti-parallel, only one new strand can begin at the 3′ end of the template DNA and grow continuously as the point of replication (the replication fork) moves along the template DNA. The other strand must grow in the opposite direction because it is complementary, not identical to the template strand. The result of this side’s discontiguous replication is the production of a series of short sections of new DNA called Okazaki fragments (Okazaki는 DNA의 조각들을 발견하고 연구한 일본 과학자의 이름). To make sure that this new strand of short segments is made into a continuous strand, the sections are joined by the action of an enzyme called DNA ligase which LIGATES the pieces together by forming the missing phosphodiester bonds.

The last step is for an enzyme to come along and remove the existing RNA primers and then fill in the gaps with DNA. This is the job of yet another type of DNA polymerase which has the ability to chew up the primers (dismantle them) and replace them with the deoxynucleotides that make up DNA. Here is a link with a diagram of the overall process of DNA replication of Okazaki Fragments.

나는 Yr13 Biology를 공부하는 학생들에게 Okazaki fragment가 시험에 나오든 안나오든 무조건 이해하고 설명하는 방법을 익히기를 심하게(?) 권유한다. 이유는 역시 경험해본바, 이해하지 않고는 한해한해 고달플수 있기때문이다. Health Science, Biomedicine, Pharmacy, Chiropractic등 생물과목을 듣는 학과에 입학하게 되면 1학년 부터 세포학과목과 Genetic과목을 들을텐데 DNA Replication을 제대로 이해하지 못하면 과목 한번 통과하기가 산넘어 산이다..어쩌면 에베레스트 등반만큼 어려운 길이 될수도 있다.

어쩌면 내 두뇌가 그다지 명석하지 못해서 그랬을수도 있다. 어쨌거나 배워두면 이래저래 WIN WIN 게임인데, 이왕 배우는거 기쁜맘으로(!!) 제대로 배우고 가는게 좋지 않을까?

The overall unzipping process is in one direction, from the bottom of the diagram up to the top.  However, there are 2 chains. As the new DNA chains only grow in the 5′ to 3′ direction they must grow in opposite directions.

The 2 strands of the original DNA molecule run in opposite directions.

* 이부분에서 헷갈리는건 5’과 3’의 존재다. Carbon number를 세어보도록 하자.

The deoxyribose sugar is a 5carbon sugar. Each of the carbon atoms in the sugar is given a number. These 5 carbon sugars are connected by phosphates and the end that finishes with carbon 5 exposed is the 5’end, the other is the 3′ end. In reality each sugar has a base attached so we have a chain of nucleotides. A complete DNA molecule is a double helix with the two strands running in opposite directions.

The incoming nucleotide units can join only to the exposed 3′ end thus a new DNA chain can grow only in the 5′ to 3′ direction. The strand that has its 5’end exposed is called the leading strand and grows continuously, towards the replication fork. The other strand (lagging strand) cannot start from the exposed 3′ end so instead it starts growing from a carbon 5 at the fork. It then grows away from the  fork toward the 3′ end. As the fork unravels, exposing more bases, another Okazaki fragment starts forming at the fork and grows toward where the previous Okazaki fragment started from. When they meet they join up to eventually form a single lagging strand.

ref: University Busary Biology;1996;Terry Bunn and Max Thompson

NCEA Type Questions: DNA REPLICATION

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Part A:

1. Describe the function of DNA polymerase.

Model Answer: DNA Polymerase links the nucleotides by bonding the phosphate group of one nucleotide to the sugar molecule of the adjacent nucleotide, forming the side of a new DNA molecule.

2. Describe the significance that the 3′ and 5′ ends have in the process.

Model Answer: New nucleotide can only be added at the 3′ end, so each new half strand is synthesized in the 5′-3′ direction. At the 5’end, the strand is extended into separate parts(Okazaki fragments) which grow by addition at their 3’ends and are joined by DNA ligase. The new strand at the 3’end is the leading strand and that at the 5′ end is the lagging strand.

3. Discuss the ways in which complementary strands are formed.

Model Answer: Both (leading and lagging) strands are formed by DNA replication with new nucleotides being added according to the base pairing rule. Eg. Adenine with Thymine, and Guanine with Cytosine. The complementary on leading strand is formed by adding new separate nucleotides, where as the complementary strand on lagging strand is formed by adding Okazaki fragments in the opposite direction, because the new strand cannot be synthesized in the 5′ direction. DNA ligase is used to join the bases and DNA polymerase is also used to form both strands.

4. Explain why the process is necessary for the growth of living organisms.

Model Answer: The DNA replication process allows the genetic material to be copied exactly so cell growth and repair can take place. This division is constantly taking place so damaged cells can be replaced and the organism can grow. It is important in mitosis, cell division. The DNA replication process during Mitosis allows new cells to be formed, that have identical genetic material through semi-conservative replication.

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*여기 써있는 답보다 길게 써도 되지만 내용은 같아야함.