RNA Primer

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.

Okazaki fragment 설명방법

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

(답) NCEA L3: DNA Replication Q [1]

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.

DNA and Gene Expression

Function of chromosomes

When a cell is not dividing, its chromosomes become very long and thin. Along the length of chromosome is a series of chemical structures called genes. The chemical which forms the genes is called DNA. Each gene controls some part of the chemistry of the cell. It is these genes which provide the instructions. One gene may instruct the cell to make the pigment which is formed in the iris of brown eyes. On one chromosome there will be a gene which causes the cells of the stomach to make the enzyme pepsin. When the chromatids separate at mitosis, each cell will receive a full set of genes. In this way, the chemical instructions in the zygote are passed on to all cells of the body. All the chromosomes, all the instructions are faithfully reproduced by mitosis and passed on complete to all the cells.

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‘Chromosome’과 ‘DNA’의 의미를 제대로 알고 사용해야한다. Chromosome이란 세포의 핵안에 있는 유전물질(genetic material)을 말한다. DNA는 Deoxyribonucleic Acid의 약자인데… 이것을 생각해보면 분명 화학적 의미를 가지고 있다는걸 알게된다. DNA는 즉, chromosome을 이루고 있는 molecule의 집합이고, nucleic acid/nucleotide 로 이루어져 있다.

(NCEA시험이든 CIE시험이든 이 두단어를 제대로 구분하지 못하고 쓰지 못하면 점수를 획득할수 없다!)

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Genes

Chromosomes consist of a protein framework, with a long DNA molecule coiled round the framework in a complicated way. Its the DNA part of the chromosome which controls the inherited characters and it is sections of the DNA molecule which constitute the genes. The gene which causes brown eyes will have no effect in a stomach cell and the gene for making pepsin will not function in the cells of the eye.

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(다시 DNA로 돌아와서..!)

DNA molecule is a long chain of nucleotides.  A nucleotide is a 5 carbon sugar molecule joined to a phosphate group and an organic base.

In DNA, the sugar is Deoxyribose and the organic base is either

  • A = adenine
  • T = thymine
  • C = cytosine
  • G = Guanine

The sequence of bases forms a code which instructs the cell to make particular proteins. Proteins are made from amino acids linked together. The type and sequence of the amino acids joined together will determine the kind of protein formed. It is the sequence of bases in the DNA molecule which decides which amino acids are used and in which order they are joined. Each group of three bases stands for one amino acid.

A gene, then, is a sequence of triplets of the four bases, which specifies an entire protein. Most proteins contain a thousand or more bases.

The chemical reaction which take place in a cell determine what sort of a cell it is and what its functions are. These chemical reactions are controlled by enzymes. Enzymes are proteins. Therefore the genetic code of DNA, in determining which proteins, particularly enzymes are produced in a cell, and determines the structure and function of the enzymes.

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Replication of DNA

(기억할것! Replication은 Mitosis 과정중 일어난다.)

The DNA in a chromosome consists of 2 chains of nucleotides held together by chemical bonds between the bases. The size of the molecule ensures that adenine always pairs with thymine and cytosine pairs with guanine. The double strand is twisted to form a helix.

Before cell division can occur, the DNA of the chromosome has to replicate – to make identical copy of it-self. To do this, enzymes make the double strands of DNA unwind and separate into two single strands rather like undoing a zip.

Nucleotides are brought to the unzipped DNA and joined to the exposed bases with the aid of enzymes. The adenine of an arriving nucleotide always joins to the thymine of the DNA, and cytosine to the guanine.

The new nucleotides join up to form a chain attached to the exposed strand. This happens all the way along each DNA strand. Since this is happening in both strands of DNA strand, the double helix is replicated and the full set of genetic instructions is passed to both daughter cells at cell division.

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수많은 궁굼증을 해소해야만 이해할수 있는 Gene expression! 공부하면 할수록 어려운 부분이긴 하지만 결코 넘지 못할 산은 아니다. :)

Cell Division

Mitosis : Cell division in body cells (somatic cells)

When a cell is not dividing there is not much detailed structure to be seen in the nucleus. Just before cell division, a number of long, thread-like structures appear in the nucleus. These threads are called chromosomes.

Each chromosome is seen to be made up of two parallel strands, called chromatids. When the nucleus divides into two one chromatid from each chromosome goes into each daughter nucleus. The chromatids in each nucleus now become chromosomes and later they will make copies of themselves ready for the next cell division. The process of copying is called replication. It is called replication because it makes the exact copy of itself.

Mitosis has specific function in producing new cells for growth or replacement.

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Meiosis: Cell division in sex cells(sperm/egg) of reproductive organs.

In a cell which is going to divide and produce gametes, the diploid number of chromosomes shorten and thicken as in mitosis. The pairs of homologous chromosomes, lie alongside each other and when the nucleus divides for the first time. It is the chromosomes and not the chromatids which are separated. This results in only half the total number of chromosomes going to each daughter cell.

(연습) LV3 NCEA Q: DNA Replication

DNA REPLICATION

NCEA Type Questions

………………………………………………….

Part A:

1. Describe the function of DNA polymerase.

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

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

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

–> Model Answer to this question

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Part B: DNA is made up of two polynucleotide chains.

1. What group of biochemical compounds are composed of nucleotides?

2. What component molecules make up a nucleotide?

3. Where in a human cell does replication of DNA occur?

4. Draw and show what is meant by semi-conservative replication.

5. What percentage of DNA in the second generation cell would have come from the parent cell?

–> Model Answer to this question

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Part C:

1. Describe the process of DNA replication.

2. DNA replication is described as a semi-conservative process. Explain what is meant by semi-conservative.

–> Model Answer to this question

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*Try to practice writing essay type questions. NCEA external examination questions will be asking you to ‘Discuss’ or ‘Explain’ about a topic.

DNA란….!

Chromosome(염색체):  http://www.tiricosuave.com/images/chromosome.jpg

Structure of DNA: http://www.scq.ubc.ca/wp-content/dna.gif

모든 세포는 핵(nucleus)를 가지고 있는데 이 안에 들어있는것이 Chromosome이다. 앞서 설명했던 것과 같이 chromosome은 DNA로 이루어져있다. DNA는 두개의 긴 테이프가 사다리로 연경되어 나선형으로 돌고있는 형태를 취하고 있으며, 세포가 활성을 유지하기 위해 필요한 모든 정보를 지니고 있다.

만일, DNA에 구조상 결함이 있거나 DNA의 양이 충분하지 못할경우 세포의 기능은 물론 분열(Cell Division: Mitosis, Meiosis 참고)에 지장을 초래한다. 이 이유는, 세포가 분열할때 DNA는 본래의 DNA와 똑같은 두개의 DNA를 복제하는데, 이 복제가 무슨 이유에서든 일어날 수 없으면 그 세포는 두개의 세포로 나누어 질수 없거나 chromosome의 갯수(number)가 부족하게 된다.

Chromosome의 number가 달라질경우 이 세포는 죽음으로 이루게 되거나, 잘못된 세포로 임신을 하게되면 기형아기가 태어난다.

Deoxyribonucleic acid (DNA)

  • Nucleic acid (there are two nucleic acid found in living organisms, which is RNA and DNA)
  • Contains the genetic instructions used in the development and functioning of all known living organisms
  • Storage of information
  • DNA is like blueprints or a recipe, or a code,
  • It contains the instructions needed to construct other components of cells (eg. proteins)
  • DNA segments that carry this genetic information are called genes
  • Involved in regulating the use of this genetic information.

Cancer

불치의 병으로 여겨졌던 질병이었지만 이제 암의 완치율이 증가하고 있는 이유는 조기발결을 위한 검진, 수술의 개선, 방사선요법의 출현과 약물요법의 발달이라고 볼수있다. 암에 대해서 많이 들어보기도 했고 암환자들의 이야기도 방송에 자주 출연하지만 과학과목을 듣는 학생들 조차도 암이 어떤 질병이고 어떻게 발생하는지 잘 모르고 있다.

오늘은 ‘암'(Cancer) 에대해서 설명할텐데 전문용어가 많이 나오기때문에 한국어와 함께 영어를 써야할것 같다. :) 모르는 단어는 물어보시길…

인체의 구성단위는 세포(cell)이다. 인체의 성장은 세포의 분열(cell division)으로 이루어진다. 세포의 분열은 성인이 될때까지 지속되는데, 성인이 되더라도 모발(hair), 피부(skin), 위장관의 상피(villi), 생식기관(reproductive organ), 골수(bone marrow)등 신진대사(metabolism)가 활발한 기관에서는 여전히 왕성한 게포분열을 보인다.

각 장기(organ)를 이루고 있는 세포군(tissue)은 장기의 이익을 도모하려는 합목적적인 기능을 발휘하며, 필요이상의 세포분열은 정상적으로라면 제어되야한다.

미성숙한 세포(pre-mature)는 분열에 따라 자신이 소속된 장기의 특이한 고유기능을 가지게되면서 성숙(mature)해진다. 세포가 성숙해지는 시기가 오면 세포의 분열이 멈추게 된다. 예를들자면 자극전달의 기능을 가진 신경세포나 운동을 담당하는 근육세포는 영구히(permanently) 분열이 정지된다. 산소운반의 기능을가진 적혈구도 일단 골수(bone marrow)에서 성숙해지면 분열할수가 없다. 간세포의 경우는 조금 다른데, 정상시에는 분열하지 않다가 손상을 입게되면 (damage) 매우 왕성하게 분열한다.

암은 한개 또는 여러개의 비정상적인 세포로 부터 발생하며, 비 정상적인 세포분열을 제어하는 조정으로부터 벗어나 자동적으로 분열을 계속하는 특징을 가졌고 미성숙한 세포와 유사한 분열을 고수한다.

이때문에, 자신이 소속한 장기에서 이탈하여 다른 장기로 전이하고 정착하면서 상당한 크기로 분열하게 되면 장기전체를 파멸로 이끌게된다. 예를들면 장(intestine)에있는 세포가 허파(lung)으로 옮겨가 허파의 tissue사이에 장세포가 이전되 허파기관을 망가트려 놓는 것이다.

암을 쉽게 발견하지 못하는 이유는, 암중에는 분열 및 성장이 매우 더딘 종류가있어 수년내지 십수년간 전혀 증상을 초래하지 않는 경우도 있다. 그중에 하나가 전립선암(Prostate cancer)이다. 그러나 대부분 정상조직보다 분열이 빠르며, 이거슬 저지할수 있는 면역기전(Immune system)이나 방어기전(Defensive system) 이 무너지면 급속히 자라기 시작한다. 어떤암들은 두배로 성장하는 시간이 하루종도 밖에 안된다.

암의 중요한 특징을 몇가지 들수 있는데, 첫째로 정상조직보다 빨리 자라서 딱딱한 종괴로 발견되며, 둘째로 암조직과 정상조직과의 경계가 불분명하고, 세째로 원방부위에서 타부위로 전이되는 성향이 있다.

일반적으로는 성장속도가 느린 암일수록 크게 자라지 않는 한, 전이가 드물고, 성장속도가 빠른 암일수록 조기에 전이가 가능하다.

전이되는 대표적인 경로는 혈액을 통하여 간,폐,골(brain)등으로 가거나 임파관(Lymph vessels)를 통하여 임파선으로 갈수 있고, 인접 장기에 직접 침윤해 갈 수도 있다.

For animal lovers! – Did you know?!

(This is helpful for Year13 Biology – Animal Behaviour)

  • Domestic dogs can determine the age, gender, sexual activity, and exact identity of another dog simply by sniffing the scent marks it leaves behind.
  • Rats can smell a cat. The mere whiff of cat odour causes a rat’s blood pressure to rise dramatically, even if it has never encountered a cat before in its life.
  • Birds recognize each other by smell just as mammals do.
  • Nesting birds change the way they smell so that predators cannot sniff them out. Usually ground-nesting birds and ducks coat their feathers using a substance known as a preen wax, which repels water and inhibits the growth of feather-degrading bacteria.
  • Rats smell in stereo. With just one sniff, the rodents can workout the direction a smell is coming from. That is because the waft of an odour reaches each nostril 50milliseconds apart, a tiny but significant different that allows the rat to workout from and where the smell is emanating. When one nostril is blocked, a rat’s ability to sniff out the direction of a smell is greatly reduced.
  • Wasps and bees have such good noses that they are being used to quality-check the freshness of supermarket food. They are also being trained to sniff out the chemical ingredients of bombs or the odours produced by people with certain diseases.

From ‘Moths that drink elephants tears – And other zoological curiosities” by Matt Walker. Matt Walker is a writer and senior editor with New Scientist, the world’s leading weekly science and technology magazine.

There are lots of interesting books at libraries. Make sure you read heaps and build answers to your questions! :)

DNA Replication Process Steps (2)

  • Helicase: The enzyme splits and unwinds the 2-strnaded DNA molecules.
  • DNA Polymerase III : Extends RNA primer with short length of complementary DNA.
  • RNA Polymerase: Synthesizes a short RNA primer which is later removed.
  • DNA Polymerase I: Digests RNA primer and replaces it with DNA.
  • DNA Ligase: Joins neighbouring fragments together into longer strands.

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Leading strand

•Leading strand is the new strand that grows continuously toward the replication fork.

• The new strand is 5’–>3’ direction. It is also complementary to 3’–>5’ parent strand.

•DNA polymerase reads the parent strand in 3’ to 5’ direction, while building the new strand in opposite (5’–>3’) direction.

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Lagging strand

Okazaki Fragment: The lagging strand is formed in fragments, between 1000 and 2000 nucleotides long – called Okazaki fragments.

•Since new nucleotides can only be added at the 3’end, each new half-strand is synthesized in the 5’–>3’ direction.

•At the 5’end of the old strand, the new strand is synthesized in separate bits called Okazaki fragments. These grow addition at their 3’ends and are then joined up by DNA ligase.

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You should be able to explain the steps involved in DNA Replication & role of the enzymes in DNA replication.

To help you with the understanding of this concept watch this Youtube video: http://www.youtube.com/watch?v=teV62zrm2P0