Difference between revisions of "FArhad"

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Day 6
 
Day 6
Today we talked about the genome and genome sequencing. The first type of genome sequencing was hierarchal sequencing where there are certain landmarks in the genome which are used for genome sequencing. The other method is called shotgun sequencing. longer sequences get subdivided into smaller fragments, and subsequently reassembled to give the overall sequence.98% of the RNA produced does not even leave the nucleus. The walls of the nucleus act as as a purifier.they are like a simple on off switch. we also talked about bacteria that have a self defence against
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      Today we talked about the genome and genome sequencing. The first type of genome sequencing was hierarchal sequencing where there are certain landmarks in the genome which are used for genome sequencing. The other method is called shotgun sequencing. longer sequences get subdivided into smaller fragments, and subsequently reassembled to give the overall sequence.98% of the RNA produced does not even leave the nucleus. The walls of the nucleus act as as a purifier.they are like a simple on off switch. we also talked about bacteria that have a self defence against
  
  
  
 
Day 7   
 
Day 7   
We talked about recombinant DNA. Recombinant DNA is DNA that is artificially created from two or more sources and is incorporated into a single recombinant molecule. Recombinant DNA (rDNA) is a form of DNA that does not exist naturally, but is created by combining DNA sequences that would not normally occur together.  
+
      We talked about recombinant DNA. Recombinant DNA is DNA that is artificially created from two or more sources and is incorporated into a single recombinant molecule. Recombinant DNA (rDNA) is a form of DNA that does not exist naturally, but is created by combining DNA sequences that would not normally occur together.  
 
Most of the bacteria have a restriction enzyme which cuts up foreign DNA. Therefore it is sometimes difficult to splice DNA.
 
Most of the bacteria have a restriction enzyme which cuts up foreign DNA. Therefore it is sometimes difficult to splice DNA.
 
This process of splicing  can create new types of organisms. This is what synthetic biology is based on. Usually a bacteria called E.coli is used for this as it is not dangerous to experiment on. Synthetic bio. Has many applications. It is used to study particular sequences that are very tiny(the sequence is put in the bacteria and amplified), to express phenotypes, to increase the quantities of proteins , etc.  
 
This process of splicing  can create new types of organisms. This is what synthetic biology is based on. Usually a bacteria called E.coli is used for this as it is not dangerous to experiment on. Synthetic bio. Has many applications. It is used to study particular sequences that are very tiny(the sequence is put in the bacteria and amplified), to express phenotypes, to increase the quantities of proteins , etc.  

Revision as of 11:24, 31 May 2010

Journal


Day 1 After a very long time I had again opened my mind to biology. The last time I had studied biology was in the 10th grade and for the first half hour of the class everything pretty much went over my head. It had been a long time since I had heard these words and they actually sounded like Greek to me. But slowly everything I had learned in the past came back to me. In the first class we discussed about general information regarding the first theories of evolution and how they were replaced by others as we come to this day. WE also talked about DNA and its purpose.


Day 2 Today we talked about mendel’s laws of segregation and independence. A very important point is that you don’t need to be a scientist or have a PhD. to discover things. We got to know how genes are passed down from one generation to another. Also alleles are outputs of genes (allele=pea being round or wrinkled.) The terminology used may take some time to get used to. It is amazing to actually see a cell splitting into 2. We then talked about chromosomes and how they decide the characteristics of a person.

If Genome=book,

Then DNA=volume,

And Chromosome=library

We also saw a video that talked about where gen. engineering would be about 30 yrs. from now. another important thing to consider is the ethics of the topic. Is creating new species good or bad for the world? Is it really progress or just an illusion of progress that we are blindly following that will lead us to our end???...


Day 3 Today we started off with seeing how gene mutation is not a good thing. For eg. Cigarette smoking causes the gene p53 to permanently mutate thus causing lung cancer.we then talked about the basic requirements for being genetic material, which are as follows 1 information storage-Dna has 4 proteins that can be arranged in any way creating different codes 2 accurate replication-there is a chance of 1 ni a million that the gene is defective, and if it’s so it gets disposed. 3 it must be expressed as a phenotype- A phenotype is any observable characteristic or trait of an organism: such as its morphology, development, biochemical or physiological properties, or behavior 4 it should be able to change –i.e. every individual has different characteristics therefore DNA is different DNA is like a symbol for bio like an atom for chem. DNA stands for dioxyribose nucleic acid. It consists of a sugar phosphate backbone and ATGC base pairs. The base pairs are what create code of the DNA for creating proteins. (Sugar=dioxy ribose, base pairs=nucleic acid)

A=adenine

T=thymine

G=guanine

C=cytosine

The proportion of A & T is always equal. Similarly G=C. DNA replication is called semi conservative replication. In this process the DNA is split into its 2 separate helical structures (unzipped )and each of the single helix join to the respective base pair. Thus forming 2 similar DNA 2ble helixes. All somatic cells (non sex cells) have the same amount DNA specific organism. On the other hand sex cells (e.g. sperm) there is only half the total amount of DNA. The other half is in the sex cells of the mate. Thus the child gets 1 half each of the parents’ genes. Also genetic engineering is not creation of genes but just modifying the original genes to create a different protein.


Day 4 Today we talked about proteins. Proteins are polymers of amino acids. There are 20 types of amino acids, 8 of which cannot be produced by man. Thus they need to be consumed.the shape of he protein is very sensitive to the environment.(eg. An egg on heating becomes solid. There are 2 types of proteins based on their function: -Structural proteins ( hair, muscle collagen, etc.) -Enzymes enzymes are surfaces for reactions to occur. They act as catylists for reactions in the body. Enzyme names usually end with the letters “ase” eg .polymerase. proteins are also present in the nucleus.thus the DNA contains the gene and the proteins in the nucleus are the phenotype.


Day 5

       As we talked yesterday gene= DNA and the protein= phenotype(expression). Today we talked about the process of protein creation using DNA. In the nucleus one of the helix of the DNA gets replicated to form RNA(RNA=1/2DNA).RNA is the set of instructions for producing protein. The RNA travels outside the nucleus and goes to the ribosome. The ribosome is like the factory for producing proteins. There are free proteins in the cell in pairs of 3 called codons that act as input for the ribosome. The protein pair is selected according to the code in the RNA(ATC produces a certain protein.) There are 20 types of proteins and only 4 codes in the RNA. Thus the RNA is in pairs of 3 to create enough no of codes for the 20 proteins.
In DNA only 1 of the 2 helix is used for production, however it is a double helix for easy replication. When DNA is replicated, each of the daughter DNA has 1 of the helix of the parent DNA. Also the other helix decides where in the body the protein is used. 


Day 6

      Today we talked about the genome and genome sequencing. The first type of genome sequencing was hierarchal sequencing where there are certain landmarks in the genome which are used for genome sequencing. The other method is called shotgun sequencing. longer sequences get subdivided into smaller fragments, and subsequently reassembled to give the overall sequence.98% of the RNA produced does not even leave the nucleus. The walls of the nucleus act as as a purifier.they are like a simple on off switch. we also talked about bacteria that have a self defence against


Day 7

      We talked about recombinant DNA. Recombinant DNA is DNA that is artificially created from two or more sources and is incorporated into a single recombinant molecule. Recombinant DNA (rDNA) is a form of DNA that does not exist naturally, but is created by combining DNA sequences that would not normally occur together. 

Most of the bacteria have a restriction enzyme which cuts up foreign DNA. Therefore it is sometimes difficult to splice DNA. This process of splicing can create new types of organisms. This is what synthetic biology is based on. Usually a bacteria called E.coli is used for this as it is not dangerous to experiment on. Synthetic bio. Has many applications. It is used to study particular sequences that are very tiny(the sequence is put in the bacteria and amplified), to express phenotypes, to increase the quantities of proteins , etc.


Day 8 Isolating genes was always done from the phenotype to theto the DNA, but that changed while trying to cure muscular dystrophy The doctor tried to sequence the gene from the dNA to the phenotype. This is called reverse genetics. He found that a small gene on the x chromosome was missing. This gene was responsible for production of distrophin which connects the muscle fiber to the cells. Distrophin can be replaced by urotrophin , which can be produced by a drug. Thus the problem was cured. In the nucleus mRNA of about 14,600 base pairs is formed, most of which ars not required. the introns remove about 79 peaces from the mRNA by gene splicing in the nucleus itself. The DNA library is a volume of the genome. Hybrid DNA is a combination of 2 DNA from 2 different places. The geme and a vecter is combined and introduced into the bacteria. the bacteria takes the new gene and adds it to the original gene. The bacteria is allowed to grow and half the DNA of the new bactrria is introduced so that the full(double helix) DNA is fished out. Thus hybrid DNA is created.


Day 9 Today we talked about transgenetics which is DNA of more than 1 species. The the method used is called gene splicing which was first done by Boyle. While working with fruit flies he found that a certain gene called the homiobox genes were responsible for descision of what grows where. Thus by changing this gene he could change the position of different body parts. Thus started synthetic biology which was literally engeneering biology.


Day 10 Today we talked about creating a hypothetical bacteriaof our own. We also given a talk on hybrids and new creatures. The concept of hybrids has existed since many ages. The available technology and advancements in biology has made it possible to create such hybrids. Radical plastic surgens do exactly this. They add extra parts to the body through surgery.


Day 11 Today we saw a video of craig venter on ted talks. He was talking about his recent discoveries in biotechnology and how they went about doing it. We also talked about different bioartists and their approach to biology


Day 12 Today we went to NCBS for the first time.we had gone to meet the person who would help us create the new bacteria and understand how to go about doing it.


Day 13



My assignments

Living sculpture: (living furniture)

Most of the furniture that we use in places like the lawn or at the beach are made of wood that has been cut from living trees. this living sculpture has both a use and aesthetics.instead of cutting trees why not grow the according to the shape you need.

"Tree shaping.jpg"

Hypothetical bacteria: (Pressure sensitive Thermo Bacteria)

The Srishti School of art design and tech. has created bacteria that emits heat when pressure is applied on it. It consists of tiny turbine like particles on it’s cell walls. When pressure is applied the cell produces an enzyme that causes the turbines to spin. These cells are tightly packed together in a tiny porous container. The activated turbines hit each other producing heat. The collected heat is magnified by the bacteria and is concentrated at the point of pressure. The temp ranges from 100 to 500 degrees. Bact 0.jpg Bact1.jpg The porous container itself is a living organism which concentrates all the heat on the point where the pressure is and spreads the heat across the area where pressure is. both the bacteria live along with each other as symbiotes. The heat producing bacteria feeds on the nutrients supplied by outer shell which is made of sugars and fatty acids. On the other hand the outer shell depends on the thermo bacteria for its shape and heat. Using some amount of the heat produced by the thermo bacteria, the porous outer structure converts cellulose into simple sugars which is food for both the organisms has pores that are about 0.01 nm in diameter all over it which are used to vent out all the extra heat in the form of steam (water is one of the byproducts of converting cellulose into sugar.) The organism reproduces by binary fission. When the shell is overloaded with the bacteria it expands until it breaks into 2 pieces. The 2 pieces join to themselves to form 2 separate structures. The outer structure does not break unless there is an internal pressure applied and it immediately joins when it breaks and grows to its normal size in 5 hours to incorporate more bacteria. The bacteria can be killed using an electric charge of 20 volts (D.C.), thus its growth can be controlled. This organism can be used for security purposes, as they are too small to be seen and produce enough heat to burn the body. If the amount of heat given out (number of collisions between spindles) can be controlled it can be used for various reasons e.g. Cooking, hot tubs, heated chairs, etc. And being organisms that can reproduce, they don’t need to be replaced.


Imagenary machine:(Projector bacteria)