Introduction:
A microarray is a tool that helps scientists look at thousands of genes at a time. This enables them to see to what extent the genes are expressed in certain tissues. Microarrays are commonly used to compare tissues. The mRNA extracted from the samples are labeled with colors such as red and green. The mRNA is then applied to the DNA chips and the spots on the microarrays show which genes are expressed. Whichever color appears on a certain spot shows whether the gene is on in that sample. Combinations can create (for example with red and green) yellow spots revealing that the gene is on in both of those samples. Intensity is also important because a dull red spot and a bright red spot are two different things. The bright one shows that the gene is turned on more than the dull one. A helpful analogy is to think of the spots like lights with dimmer switches. This can be applied to cancerous and noncancerous tissues to see which genes are on in each showing the difference between the two. We will be studying the expression of six different genes in normal lung and cancerous lung cells. The end results will show us which genes have been expressed to produce more RNA in cancerous lung cells and which genes have been repressed from producing mRNA in normal lung cells.
Monday, November 15, 2010
Monday, October 25, 2010
Records Put On Record
Introduction:
Every person in the world has their own unique DNA fingerprint DNA fingerprinting can help to identify and compare individuals. Much of every individuals DNA is the exact same. This makes it difficult to distiguish different people. Microsatellites are used to make this identification easier. Microsatellites are short pieces of DNA that repeat many times in one's DNA sequence. Any biological material can be used for DNA fingerprinting such as, body tissues, body fluids, and hair. Even some dired material such as blood stains can be used. To create this DNA fingerprint from the DNA restriction enzymes must be used.
Restriction enzymes act like small DNA scissors. These enzymes recognizes specific base pairs that tell it to cut the DNA at that point. The spots in which the enzymes make the cuts are called restriction sites. This can result in many different pieces or fragments along one DNA strand. Once the DNA has been cut it can be seperated by the size of the fragments. This seperation is created by using a process called Agarose gel electrophoresis. This process consists of inserting the DNA into an agrose gel slab and passing an electircal current through it. The DNA fragment (which are negatively charged) are attracted to the postively charged end. This is the point in the process that creates the seperation. The bigger DNA fragments are unable to pass through the gel as easily as the small fragments consequently causing them to not travel as far. All of the fragments that are the same size come togethor to form bands. Once the gel is stained we can see these bands. This final result of the way that they line up is the DNA fingerprint.
Results/Observation:
Lane 4 or sample number 3 ended up matching the the crime scene DNA from lane 1. All of the other lanes had differing results with the strips being at different places along the gel. The crime scene matched perfectly to sample 3 which happened to be the sample from Katie Records.
Discussion:
The gel ended up working correctly and the restriction enzyme obviously did its job as the molecular scissors. The smaller pieces moved farther along the gel as expected compared to the larger fragments that didn't make it as far. Some possible sources of error could have been the loading dye not weighing down the sample and the DNA floating out and mixing with the other DNA. Another source of error could have occurred when undergoing the difficult task of inserting the samples into the small slots in the gel. Although some incidents did occur, we were able to work past these and receive the correct results.
Sources:
McGuigan, Brendan. "What Is DNA Fingerprinting?." wiseGeek. wiseGeek, 08/9/2010. Web. 25 Oct 2010. <http://www.wisegeek.com/what-is-dna-fingerprinting.htm>.
Every person in the world has their own unique DNA fingerprint DNA fingerprinting can help to identify and compare individuals. Much of every individuals DNA is the exact same. This makes it difficult to distiguish different people. Microsatellites are used to make this identification easier. Microsatellites are short pieces of DNA that repeat many times in one's DNA sequence. Any biological material can be used for DNA fingerprinting such as, body tissues, body fluids, and hair. Even some dired material such as blood stains can be used. To create this DNA fingerprint from the DNA restriction enzymes must be used.
Restriction enzymes act like small DNA scissors. These enzymes recognizes specific base pairs that tell it to cut the DNA at that point. The spots in which the enzymes make the cuts are called restriction sites. This can result in many different pieces or fragments along one DNA strand. Once the DNA has been cut it can be seperated by the size of the fragments. This seperation is created by using a process called Agarose gel electrophoresis. This process consists of inserting the DNA into an agrose gel slab and passing an electircal current through it. The DNA fragment (which are negatively charged) are attracted to the postively charged end. This is the point in the process that creates the seperation. The bigger DNA fragments are unable to pass through the gel as easily as the small fragments consequently causing them to not travel as far. All of the fragments that are the same size come togethor to form bands. Once the gel is stained we can see these bands. This final result of the way that they line up is the DNA fingerprint.
Results/Observation:
Lane 4 or sample number 3 ended up matching the the crime scene DNA from lane 1. All of the other lanes had differing results with the strips being at different places along the gel. The crime scene matched perfectly to sample 3 which happened to be the sample from Katie Records.
Discussion:
The gel ended up working correctly and the restriction enzyme obviously did its job as the molecular scissors. The smaller pieces moved farther along the gel as expected compared to the larger fragments that didn't make it as far. Some possible sources of error could have been the loading dye not weighing down the sample and the DNA floating out and mixing with the other DNA. Another source of error could have occurred when undergoing the difficult task of inserting the samples into the small slots in the gel. Although some incidents did occur, we were able to work past these and receive the correct results.
Sources:
McGuigan, Brendan. "What Is DNA Fingerprinting?." wiseGeek. wiseGeek, 08/9/2010. Web. 25 Oct 2010. <http://www.wisegeek.com/what-is-dna-fingerprinting.htm>.
Tuesday, October 5, 2010
Petroleum No More
Introduction/Procedure
Enzymes which are generally proteins, speed up the rate of chemical reactions. They have specific three dimensional structures and reduce the energy needed to carry out a chemical reaction (otherwise known as the activation energy). Since the enzymes reduce the amount of activation energy the reaction occurs at a quicker pace. Enzymes do not chemically react with the substrate so they can continually help to convert reactants to products. Changes in pH and salinity negatively affect the enzymes productivity. Another factor in the speed of the reaction is heat. More heat, therefor faster moving enzyme and substrate molecules, causes more collisions and speeds up the reaction. Most enzymes function best at medium temperatures however there are of course exceptions. The enzymes "natural habitat" is a good reflection of what are optimal temperatures for the enzymes to operate under. Another component to the speed of reaction is concentration of molecules. Until the point of excess, enzymes will speed up the reaction if there are more molecules. This knowledge of enzymes will help us in our lab because we are using cellobiase, (an enzyme) to break down cellobiose to glucose. Also our knowledge of how pH, temperature, and concentration affect reactions will come into consideration when we analyze how these affect our break down of cellobiose. This ability to break down celluloses into glucose is used by biofuel industrys in search of an alternative to petroleum. The glucose can be converted to ethonol which can be used to power engines. In our lab we are not trying to solve the worlds pollution problems, merely trying to understand the process. We are going to use cellubiase to break down cellubiose into glucose. During the process we will take part of the solution at different times in the reaction and attempt to use a stop solution to take "snap shots" of the process. Using p-nitro to turn the glucose a color visible to human eyes, we will be able to see glucose in the making. I predict this will be a successful lab but precision will be necessary throughout.
Results/Observations
During the experiment every later interval progressively became a stronger yellow color. In the beginning the yellow was hard to see and closer to a clear color. Towards the end the last tube that we transfered it into turned a very strong yellow color. This was also true when we replaced the enzyme with mushroom extract. The results seemed to be nearly identical to the previous days tubes.
Discussion:
This means that the experiment did end up working. The cellobiose inside the main tube was being broken down into glucose and the results were obvious. It also proved that the mushroom acted just like cellobiase in that it also produced the glucose. Although our lab ended up working errors could have occurred during the process such as maybe a certain mushroom doesn't act like cellobiase. If it didn't break down the cellobiose then the p-nitro would have no glucose to turn yellow and we would have to results to look at.
Enzymes which are generally proteins, speed up the rate of chemical reactions. They have specific three dimensional structures and reduce the energy needed to carry out a chemical reaction (otherwise known as the activation energy). Since the enzymes reduce the amount of activation energy the reaction occurs at a quicker pace. Enzymes do not chemically react with the substrate so they can continually help to convert reactants to products. Changes in pH and salinity negatively affect the enzymes productivity. Another factor in the speed of the reaction is heat. More heat, therefor faster moving enzyme and substrate molecules, causes more collisions and speeds up the reaction. Most enzymes function best at medium temperatures however there are of course exceptions. The enzymes "natural habitat" is a good reflection of what are optimal temperatures for the enzymes to operate under. Another component to the speed of reaction is concentration of molecules. Until the point of excess, enzymes will speed up the reaction if there are more molecules. This knowledge of enzymes will help us in our lab because we are using cellobiase, (an enzyme) to break down cellobiose to glucose. Also our knowledge of how pH, temperature, and concentration affect reactions will come into consideration when we analyze how these affect our break down of cellobiose. This ability to break down celluloses into glucose is used by biofuel industrys in search of an alternative to petroleum. The glucose can be converted to ethonol which can be used to power engines. In our lab we are not trying to solve the worlds pollution problems, merely trying to understand the process. We are going to use cellubiase to break down cellubiose into glucose. During the process we will take part of the solution at different times in the reaction and attempt to use a stop solution to take "snap shots" of the process. Using p-nitro to turn the glucose a color visible to human eyes, we will be able to see glucose in the making. I predict this will be a successful lab but precision will be necessary throughout.
Results/Observations
During the experiment every later interval progressively became a stronger yellow color. In the beginning the yellow was hard to see and closer to a clear color. Towards the end the last tube that we transfered it into turned a very strong yellow color. This was also true when we replaced the enzyme with mushroom extract. The results seemed to be nearly identical to the previous days tubes.
Discussion:
This means that the experiment did end up working. The cellobiose inside the main tube was being broken down into glucose and the results were obvious. It also proved that the mushroom acted just like cellobiase in that it also produced the glucose. Although our lab ended up working errors could have occurred during the process such as maybe a certain mushroom doesn't act like cellobiase. If it didn't break down the cellobiose then the p-nitro would have no glucose to turn yellow and we would have to results to look at.
Wednesday, September 22, 2010
Genetic Jewelry
Intro/Procedure:
DNA, short for deoxyribonucleic acid, is in all living things. It carries genetic information responsible for features such as skin, eye color, height, blood type, exc. Every one of our cells carries these instructions. The DNA is found in the nucleus of all cells except red blood cells.The shape of DNA is a double helix with bases on the inside and phosphates on the outside. The bases (adenine, guanine, cytosine, and thymine) are paired together. Adenine always pairs with thymine and guanine always pairs with cytosine. Everyone's DNA is 99.9% the same and it's that .1% that makes the difference and unique qualities of individuals. A section of the DNA, genes, carry the information to make proteins. DNA can be used for testing for traits, cloning, crime scene investigations, and more. Our lab is an attempt to precipitate or extract our own DNA and then put it into a necklace. To extract the DNA we first must get some of our cells. After loosening cheek cells and putting them in saline solution which keeps the cells "happy", we use a lysis buffer to break open the membrane (phospholipids). We then use protease (an enzyme that breaks down proteins) to kill possible threats to the DNA (DNAse and Histone). After hot water is used to speed up this process cold ethonal precipitates the DNA.
Results/Observations:
We were successfully able to extract DNA from our cells and put it into a necklace. When doing the lab little could be seen inside the tube until the ethonal was added. Once the ethonal was added and we swished the tube around the DNA strands became visible.
Discussion:
There is not much to analyze other than the DNA was precipitated due to protease successfully killing anything that may have harmed the protein and then the ethonal worked and the DNA became present. Although the lab worked, things such as using wrong amounts of protease or ethonal could have ruined the results. Overall this was a fun, successful,and not too difficult lab.
DNA, short for deoxyribonucleic acid, is in all living things. It carries genetic information responsible for features such as skin, eye color, height, blood type, exc. Every one of our cells carries these instructions. The DNA is found in the nucleus of all cells except red blood cells.The shape of DNA is a double helix with bases on the inside and phosphates on the outside. The bases (adenine, guanine, cytosine, and thymine) are paired together. Adenine always pairs with thymine and guanine always pairs with cytosine. Everyone's DNA is 99.9% the same and it's that .1% that makes the difference and unique qualities of individuals. A section of the DNA, genes, carry the information to make proteins. DNA can be used for testing for traits, cloning, crime scene investigations, and more. Our lab is an attempt to precipitate or extract our own DNA and then put it into a necklace. To extract the DNA we first must get some of our cells. After loosening cheek cells and putting them in saline solution which keeps the cells "happy", we use a lysis buffer to break open the membrane (phospholipids). We then use protease (an enzyme that breaks down proteins) to kill possible threats to the DNA (DNAse and Histone). After hot water is used to speed up this process cold ethonal precipitates the DNA.
Results/Observations:
We were successfully able to extract DNA from our cells and put it into a necklace. When doing the lab little could be seen inside the tube until the ethonal was added. Once the ethonal was added and we swished the tube around the DNA strands became visible.
Discussion:
There is not much to analyze other than the DNA was precipitated due to protease successfully killing anything that may have harmed the protein and then the ethonal worked and the DNA became present. Although the lab worked, things such as using wrong amounts of protease or ethonal could have ruined the results. Overall this was a fun, successful,and not too difficult lab.
Monday, September 6, 2010
Food For Thought
Introduction/Procedure
Bacteria the most abundant life form on earth, was discovered in 1676 by Anton van Leeuwenhoek. Bacteria are prokaryotes, or single celled organisms. It is often referenced with disease and other negative effects. A few devastating break outs of disease due to bacteria such as the Bubonic plague have put a bad picture in our head. Thus many antibiotics have been created to help prevent any future tragedies. The truth is very little bacteria can harm you. The human body is full of bacteria that actually help you to survive. Bacteria are even present in many of the foods we eat. One of these foods is yogurt. In our lab our purpose is to make yogurt and use Koch’s postulates. Yogurt is essentially milk with added bacteria. The bacterium added to the milk takes in the milk sugars (lactose) and creates lactic acid. This lactic acid drops the pH causing the milk to curdle. We are going to attempt to use Koch’s postulates to prove or disprove which microbes cause the “yogurtness disease”. I hypothesize that this will prove correct and microbes will be the cause.
Results/Observations
Tube 1: Positive control, milk, smells like sour milk, texture is liquid.
Tube 2: Negative control, yogurt, smooth texture, smells like yogurt.
Tube 3: Milk and e. coli, milk, smells terrible, liquid texture.
Tube 4: Milk and ampicillin, smells like milk, liquid texture.
Discussion
Tube one had no chance of turning into yogurt because it was just sour milk. The negative control turned into yogurt. Milk and e. coli didn't become yogurt because e. coli isn't the right type of bacteria to make the milk curdle. Milk and ampicillin stayed milk because antibiotics don't help either. Some possible sources of error could have been a contamination where other unwanted bacteria gets in the tubes.
Results/Observations
Tube 1: Positive control, milk, smells like sour milk, texture is liquid.
Tube 2: Negative control, yogurt, smooth texture, smells like yogurt.
Tube 3: Milk and e. coli, milk, smells terrible, liquid texture.
Tube 4: Milk and ampicillin, smells like milk, liquid texture.
Discussion
Tube one had no chance of turning into yogurt because it was just sour milk. The negative control turned into yogurt. Milk and e. coli didn't become yogurt because e. coli isn't the right type of bacteria to make the milk curdle. Milk and ampicillin stayed milk because antibiotics don't help either. Some possible sources of error could have been a contamination where other unwanted bacteria gets in the tubes.
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