Month: December 2009

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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.

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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

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(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.

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Avogadro’s constant

아보가드로의 숫자

온도와 압력이 같을 때 서로 다른 기체라도 부피가 같으면 같은 수의 분자를 포함한다는 법칙.

분자량을 그램으로 정의한 물질 1g·mol 속의 분자 개수는 6.0221367×1023개로 이 숫자를 아보가드로 수 또는 아보가드로 상수(常數)라 한다. 예를 들어 산소의 분자량이 32.00이므로 산소 1g·mol은 32.00g이고 6.0221367×1023개의 산소분자로 이루어진다.

1g·mol이 차지하는 부피는 0℃, 1기압인 표준상태에서 약 22.4ℓ로 아보가드로 법칙에 따라 모든 기체에서 같은 값을 갖는다.

1811년에 수년간 투린대학교 고등물리학교수를 지낸 아메데오 아보가드로가 이 법칙을 처음 제안했으나 1858년 이탈리아의 화학자 스타니슬라오 카니차로가 이 법칙을 바탕으로 화학의 논리적 체계를 세운 뒤에야 비로소 이 법칙이 일반적으로 받아들여지게 되었다.

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그렇다면 Avogadro는 누규?

아메데오 아보가드로(1776/ 8/ 9 ~1856/ 7/ 9)은 이탈리아의 물리학자, 화학자이다. 본명은 로렌초 로마노 아메데오 카를로 아보가드로 디 콰레그나 에 디 세레토(이탈리아어: Lorenzo Romano Amedeo Carlo Avogadro di Quarequa e di Cerreto)이다.

1776년 토리노에서 태어났다. 그의 아버지는 당시 사르데냐 왕국 피에몬테 지방에서 법률가와 의회의원으로 활동하였다. 아보가드로 역시 법률공부를 하여 1796년 법학 박사 학위를 취득하였다. 그 후 법률가로 활동하면서 1800년초 부터 수학과 물리학을 독학으로 공부하여 전기 등에 대한 논문을 발표하였다. 그 결과 1806년 토리노 대학교의 조교수가 되었고 1809년에는 왕립 베르첼리 대학의 자연 철학 교수가 되었다. 1815년에 결혼하여 6명의 자녀를 두었다. 1820년에는 토리노 대학교의 수리물리학 교수가 되었다. 또한 도량형 위원회 등 정부 기관에 관여하기도 하였다.

아보가드로는 외국어에 능통하여 그의 논문에는 프랑스어 논문이 많았으나, 살아있을 때에는 다른 화학자들과의 소극적인 접촉과 그의 연구를 그 스스로 인용하는 버릇으로 인해서 국내외에서 유명하지는 않았다.그는 1850년에 토리노 대학교 교수 자리에서 은퇴하였고, 1856년 토리노에서 사망하였다.

Reference:http://ko.wikipedia.org/wiki/아메데오_아보가드로

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왜 화학에서는 복잡하게 mole이나 아보가드로 숫자를 알아야할까..

화학자들을 어떤 물질을 만드느냐에 집중하기도 하지만, reactant가 얼마나 있어야 product가 얼마만큼 나오는지 알려고 한다. 이런 화학실험이 대부분 산업공장에서 이루어지기 때문이다. 몇가지 간단한 공식으로, 구입해야 하는 reactant의 양과 원하는 product의 양을 계산할수 있다.

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Atoms, ions and molecules are very tiny particles and it is impossible to measure out a dozen or even a hundred of them. Instead, chemists weigh out a very large number of particles. This number is the 6.0221367×1023, ions or molecules. An amount of substance containing 6.0221367×1023 particles is called a mole (abbreviated to mol).

So, a mole of the element aluminium is 6.0221367×1023 atoms of aluminium and a mole of the element iron is 6.0221367×1023 atoms if iron.

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Cell organelle

동물성 세포의 각 기관들을 나타낸 그림이다.

Nucleus (핵)안에는 chromosome염색체를 가지고 있고 세포안의 모든 활동/화학작용(chemical reaction/metabolism) 에 대한 정보가 들어있다. 이 염색체는 부모로부터 유전된(inherited) 물질로써 세포가 분열(cell division)할때 완벽하게 복제(copy/duplicate/clone/replicate)된다.

단백질(Protein)을 합성하는 과정중 염색체의 gene을 베껴오는데, 이것을 RNA라고 한다. DNA와 RNA의 다른점중 한가지는 DNA는 핵안에만 있어야 하고, RNA는 이것을 cytoplasm으로 베껴나온 카피라고 할수있다. 도서관에서 빌려나오지 못하는 책을 복사하는 것과 같은것이다.  Gene만 복사했기때문에 DNA에 비해서는 월등히 짧으며 필요한 protein를 만드는데 사용할 정보만 들어있다.

베껴나온 RNA는 Endoplasmic Reticulum(ER)에 붙어있는 Ribosome (Rough E.R) 들이 해석해내어 protein의 초본을 만들고, 이것을 polypeptide라고 한다. 이 이유는, RNA를 해석한대로 amino acid(아미노산)이 순서대로 붙게되는데 3D의 입체적인 구조와 모양을 지니지 못했기때문에 그 기능을 다 할수없다. 그래서 polypeptide라고 하며, 만들어진 polypeptide는 Golgi Body로 보내저 입체적인 구조와 모양을 가지게 된다. Golgi Body(Apparatus)의 역활은 즉 packaging(포장)과 modification(변형)이다.

Ribosome이 붙어있지 않은 Smooth E.R 부분 에서는 세포막에 쓰여질 lipid, cholesterol 와 steroid를 만드는데 쓰인다.

Mitochondrion에서는 세포의 기관들이 일을할때 쓰이는 energy (ATP)를 만드는 역활을 가지고 있다.

Peroxisome 안에는 lysosome이 들어있고, 주변에 membrane으로 둘러싸여져 있다.  Membrane 으로 묶어둔 이유는 lysosome이 enzyme이기 때문이다. 세포안에 들어온 균(bacteria, virus, antigen 등)을 녹이거나 늙어서 없어져야할 세포기관을 녺이는 데 쓰인다. – 세포가 자폭할때 쓰이기도 함.

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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..!)

A 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. :)

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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.

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(연습) LV3 NCEA Q: DNA Replication

DNA REPLICATION

NCEA Type Questions

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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.

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Food web

This is a diagram of a food web. Almost all animals must eat other organisms to obtain energy. Animals do not generally eat just one thing, nor are they eaten by only one thing. This means that each organism, through feeding, is interconnected to many different organisms. A food web shows how all species in a community are connected.

Let’s think about the organisms in an environment. If any one species is disturbed, then all species will undergo changes in its population. Eg. If small fish numbers go down then snail and cockle numbers will go up. Big fish and seabird numbers will go down.

An animal can be both a predator and a prey. For example, a small fish may eat certain types of snails, but he may also be eaten by a duck. So the small fish is both predator and prey in this food web..

Almost all animals must eat other organisms to obtain energy. Animals do not generally eat just one thing, nor are they eaten by only one thing. This means that each organism, through feeding, is interconnected to many different organisms. A food web shows how all species in a community are connected.

We, humans, often upset the balance of different populations in natural ecosystems, or change the environment so that some species find it difficult to survive. We reduce the amount of land available for animals and plants by: building; quarrying; farming; dumping waste.

Our activities may pollute: water ‐ with sewage, fertiliser or toxic chemicals; air ‐ with smoke and gases such as sulfur dioxide; land ‐ with toxic chemicals, such as pesticides and herbicides, which may be washed from land into water.

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What’s for dinner?

Ecology is the study of organisms and their relationship with their surroundings. Ecologists study the interaction between an organism and its environment. Some ecologists study a specific species or habitat. They might study the behaviour of a single species to see how it interacts with other organisms and the environment. Or, an ecologist might study many different species that either depend on each other (a food web, for example), or compete with each other for food and space

Every organism needs to obtain energy in order to live. For example,plants get , energy from the sun, some animals eat plants, and some animals eat other animals.

A food chain is the sequence of who eats whom in a biological community (an ecosystem) to obtain nutrition.

  • The arrows indicate the direction of energy flow.
  • The food chain moves food from one organism to another, giving energy to the organism digesting the food.

Eg. Buttercup → Bee → Thrush → Hawk. Plankton → Herrings → Salmon →Seals → Killer whales

  • All food chains start with the sun which provides energy for plants.
  • Photosynthesis by plants converts light energy to food. Plants are considered producers because they make their own food.
  • The producers above are grass, buttercup, rosebush and plankton.
  • Animals, including humans, cannot make their own food. As a result, they must get their energy from other sources, usually plants and other animals. Thus, animals are considered consumers.

As you can see in the diagram, food chain is the sequence of who eats whom in a biological community (an ecosystem) to obtain nutrition. Every organism needs to obtain energy in order to live. For example, plants get energy from the sun, some animals eat plants, and some animals eat other animals.