MI 3.1 Test

How is a labeled DNA copy made?

A fluorescent tag, or a labeled nucleotide, is added to the mRNA. This dye used contains reverse transcriptase, which will build a complimentary strand of DNA (cDNA) based on the mRNA strand. The cDNA will be kept while the mRNA strand will discarded.

Tumor Suppressor Genes

A gene whose protein product inhibits cell division, thereby preventing the uncontrolled cell growth that contributes to cancer.

How is DNA applied?

A microarray already has single strands of DNA sequences from genes on it, so the cDNA will be pipetted onto the microarray so the single strands of cDNA can bind to the strands on the microarray.

Cancer

A multifactorial disorder that can be caused by multiple factors such as genetics, the environment someone lives in, their habits, and diet in which cells grow uncontrollably. Can be malignant or benign and may be able to be removed through rounds of chemotherapy and/or radiation. In some cases, a limb or organ may need to be removed.

Gene Expression Ratio 1

Expressed equally in normal and cancerous cells

Gene Expression Ratio >1

Expressed more in cancer cells

Gene Expression Ratio 0<1

Expressed more in normal cells

Describe the genetic mutations that you think occurred in the cancer cells that were responsible for the phenotypic differences between the normal and cancer cells you observed

I think a base pair deletion, addition, or change in cancer cells may occur to produce different phenotypic differences when compared to normal cells because cancer cells form a different shape than normal cells and have a different shaped nucleus.

How do you think a person's age can affect his or her chances of developing cancer?

I think a person's age can affect their chances of developing cancer due to their prolonged exposure to certain risk factors such as carcinogens, the increased likelihood of their DNA mutating, and due to a decreased immune system in which the function of the T-cells starts to decrease.

How does cancer spread or metastasize?

Cancer can metastasize through growing into nearby normal tissue, through moving into blood vessels or lymph nodes, through traveling to different parts of the body through the lymphatic system and bloodstream, through invading the blood vessel walls, and through creating its own blood supply through causing new blood vessel to form.

How do you think a person's lifestyle can affect his or her chances of developing cancer? Be specific.

I think a person's lifestyle can affect his or her chances of developing cancer because depending on their lifestyle, they can be more exposed to certain risks. As an example, someone who smokes a lot is more likely to develop lung cancer than a marathon runner who eats a balanced diet and practices healthy habits. In addition, a person's lifestyle can determine if they go to the doctors or not. An example of this would be of a person noticing an oddly shaped, discolored mole on their skin but not going to their dermatologist to get it checked out due to not having the time to.

What characteristics would you look for that would indicate the presence of cancer cells? Describe three distinct morphological differences you would expect to see between normal cells and cancer cells.

If I was inspecting tissue for the presence of cancer cells, I would check to see if there are any abnormal looking cells that are piled on top of each other with an abnormally shaped nucleus. In normal cells, they are organized and have distinct features that can be seen. In addition, normal cells are one size and they have one, small nucleus.

Gene Expression Ratio 0

Not expressed in cells

How does p53 prevent cancer cells from forming?

P53 prevents cancer cells from forming by stopping cells with damaged or mutated DNA by causing them to go through apoptosis since it is a tumor suppressor.

Signals

Signs

How is mRNA isolated?

Since mRNA has poly-A tails, the mRNA is "filtered" out of the other types of RNA by pouring the RNA solution over beads that contain poly-T tails. Since the poly-A tails and complimentary to the poly-T tails, they will bind together while the rest of the RNA is drained through the container containing the beads. Once the mRNA is isolated from the rest of the RNA (tRNA and rRNA), then buffer can be poured over the beads to separate the poly-A tails from the poly-T tails.

How can studying genes give us more information about cancer?

Studying genes give us more information about cancer because we can figure out if there are any specific mutations in genes that cause cancer. In addition, from the genetic coding, we can tell if a person may be more predisposed to developing a certain type of cancer.

What does a correlation coefficient of zero mean?

That the gene expression behave in an unrelated manner.

What does a positive correlation coefficient mean?

That the gene expressions behave in a similar manner.

What does a negative correlation coefficient mean?

That the gene expressions don't behave in a similar manner.

What does a correlation coefficient of one mean?

That the genes are expressed identically

Gene Expression Log Ratio >0 (positive)

The gene is induced by tumor formation (Present when a tumor is formed)

Gene Expression Log Ratio <0 (Negative)

The gene is suppressed by tumor formation (Present when there is no tumor)

Metastasis

The spread of cancer cells beyond their original site

What type of mutations might occur that cause proto-oncogenes to become oncogenes?

The type of mutations that may occur to cause proto-oncogenes to become oncogenes are translocations/transpositions, gene amplification, and point mutations.

Cytochrome P450 (CYP1A1)

This gene codes for a protein that is located in the endoplasmic reticulum. The protein catalyzes reactions involved in drug metabolism and synthesizes cholesterol, steroids, and other lipids. The expression of this protein is induced by some polycyclic aromatic hydrocarbons (PAHs), some of which are found in cigarette smoke.

Human carcinoembryonic antigen (CEACAM6)

This gene codes for a protein that is located in the extracellular matrix. This protein is involved with adhesion between cells and is thought to be a proto-oncogene and when over-expressed is an oncogene.

P53 tumor suppressor (TP53)

This gene codes for a protein that is located in the mitochondria and in the nucleolus. This protein is involved with cell cycle checkpoints. This gene is a tumor suppressor gene and is thought to be the "Guardian of the Genome."

SRY

This gene codes for a protein that is located in the nucleus. The protein that this gene codes for is testis-determining factor (TDF) which initiates male sex determination. This protein has no function in lung cells.

Glypican 3(GPC3)

This gene codes for a protein that is located in the plasma membrane and extracellular matrix. The gene controls cellular response to damage and may control cellular growth regulation and apoptosis. This gene is considered to be a tumor suppressor gene for lung cancer

Surfactant protein B (SFTPB)

This gene codes for an extracellular protein. This protein enhances the rate of spreading and increases the stability of pulmonary surfactant, a lipid-rich material that prevents lung collapse by lowering surface tension at the air-liquid interface in the alveoli of the lungs.

X-Rays

Use EM radiation in the form of x-rays to pass photons through the body, which will produce a 2D image of bones and dense structures.

MRI

Use magnet and radio waves to produce cross-sectional images of soft tissue by sending radio waves through the body.

Bone Scan

Use radioactive tracers to track any abnormal bone metabolism.

Dendogram

treelike diagram used to display results

Blood vessels

tubelike structures that carry blood throughout the body

Mutations

a random error in gene replication that leads to a change

Regulated

controlled

Oncogenes

genes that cause cancer by blocking the normal controls on cell reproduction

DNA Microarray Steps (7)

1) Collect Sample 2) Isolate RNA 3) Isolate mRNA 4) Make labeled DNA copy 5) Apply DNA 6) Scan microarray 7) Analyze microarray

What diagnostic procedures can detect cancer? (4)

1) X-rays 2) CT Scan 3) MRI 4) Bone scan

Why is cancer such a difficult disease to study?

Cancer is a difficult disease to study because it is caused by random mutations that need to be identified and because the patterns of how it spreads aren't the same for every single person.

When analyzing DNA microarray results, why are colors turned into ratios?

Colors are turned into ratios so the gene behavior in cancerous cells vs healthy cells can be easily analyzed.

Gene Expression Log Ratio 0

Gene isn't expressed at all

How are samples collected for a microarray?

Healthy and abnormal tissue are collected and placed into two seperate test tubes.

What is the difference between normal cell division and cancer cell division?

In normal cell division, cells receive a signal that tells them to stop going through cell division while in cancer cell division, the cancerous cells don't receive that signal and continue to divide.

How is the DNA Microarray scanned?

Place microarray onto microarray scanner and scan for green first to see genes in healthy cells. Then, scan for red to see genes in cancer cells. Merge both pictures to scan for genes shared between healthy and cancer cells. The red dots that appear on the yellow produce more genes, while the green dots on yellow show genes that are turned down

Cell division

Process by which a cell divides into two new daughter cells

CT Scans

Produces cross-sectional images by taking x-rays from different angles.

How is the microarray analyzed?

Protein analysis is used.

What are the roles of oncogenes and tumor suppressor genes in cancer?

Proto-oncogenes are genes that help cells to grow, however they can mutate into a "bad" gene called an oncogene, which will produce too many copies of cells. When the cell starts to grow out of control, it leads to cancer. Meanwhile, tumor suppressor genes slow down the cell division, repair any mistakes in the DNA, and cause cells to go through apoptosis. When these tumor suppressor genes don't work, cells can grow out of control and cancer can form.

What is RNA isolated?

Saline is added to the solution, which is then vortexed and centrifuged. Then, the supernatant is removed (this contains the RNA).

Summary paragraph of the process in which normal cells become cancer cells

When normal cells undergo cell division in the cell cycle, they are regulated by two different objects that helps the cells to grow. First, proto-oncogenes are used to help cells grow. However, these proto-oncogenes can go through mutations and turn into oncogenes, which cause cells to continuously divide without stopping, resulting in cancer. Second, tumor suppressor genes are used to slow down cell division. By doing so, they can repair any mutated or damaged DNA. In addition, they can send signals to abnormal cells and tell them to go through apoptosis so they won't become cancer cells. Despite these two processes, cells can still mutate into cancer. When they do, the cancer cells can either stay localized in a certain area, or they can spread to distant parts of the body. Cancer can spread in many ways, such as traveling through the blood vessels. When this happens and they spread, it is called metastasis. If a person has localized cancer in one area, it can be easier to cure. However, when it metastasis into a distant area, the cancer can only be treated rather than cured.

Apoptosis

programmed cell death

Cell cycle

series of events that cells go through as they grow and divide

Proto-oncogenes

the corresponding normal cellular genes that are responsible for normal cell growth and division