Genetics: It Makes the World Go Round

Over the past week or so, I've become somewhat fascinated by genetics. Perhaps my background in mathematics is the cause, but I'm quite fascinated by the idea of simply building every idea out of another idea. 

To really understand genetics, we have to start out by going down to the molecular level. Every cell contains a nucleus, and within that nucleus, there's DNA. DNA is incredibly important to the body. It carries the information used to build an organism. But what makes it up?

DNA is composed of four different chemicals: guanine, adenine, thymine, and cytosine, which are typically abbreviated as their first letters. Within the strand itself, there are some rules these chemicals have to follow. A will always pair with T, and G will always pair with C. (Pair, by the way, means that they have been hydrogen bonded together. Picture a twisted ladder, and that's the shape of DNA. The rungs on the ladder can be thought of as hydrogen bonds between the two molecules. The sides of the ladder are actually made of sugar and phosphate bonded together.) 

Now, I read an excellent metaphor at the University of Utah website. It said that the letters of the strand can be thought of as letters of the alphabet. The letters come together to form words, and the words come together to form sentences. In the same way, different series of letters (for example, A T G T C A) can be thought of as coming together to form genes. 

Now, genes tell the cell to make certain proteins. Proteins, as we know, can give cells certain functions and abilities--for example, within a cell of the inner ear, they can allow the cell to work with other cells to hear sounds. Genes are composed of DNA, although there are many genes along a single strand of DNA. (There are approximately 25,000 genes within the human body!)

Of course, DNA isn't simply laying around the nucleus of the cell. It's packaged into units known as chromosomes. Chromosomes are simply big chunks of DNA with protein wrapped around it. Every human cell contains 23 pairs of chromosomes--46 in all. Each chromosome carries different DNA with different genes, which means that each one controls different traits. For example, the 23rd chromosome contains either an X and a Y chromosome or two X chromosomes. Whichever one of the pairs actually occurs defines the sex of the person.

This brings us into our next big topic, which is heredity. If you need a refresher, see my post on mitosis and meiosis before reading on. 

Because genes carry certain traits, and because each parent gives one set of 23 chromosomes to the child, a child will inherit certain traits from each parent. (Fans of the Harry Potter series will recognize that Harry inherited his father's hair and general appearance but his mother's eyes.) Because of this, each child has a different genotype (genetic makeup) and phenotype (physical appearance). When these children have children, they will pass on some genes from their mother and some genes from their father. This is how traits can pass through multiple generations.

Now, let's mix heredity and genes together. Genes are made up of what are called alleles. An allele can be either recessive or dominant. If it is dominant, its presence will be apparent in the child's phenotype regardless of whether another gene is present. If it is recessive, however, it will only be visible if it is paired with another recessive gene. Basically, dominant alleles are just that--dominant. They mask recessive alleles. 

Of course, it's possible for some interesting combinations to occur. If a person has two dominant alleles or two recessive alleles, they are known as homozygous. If they have a combination of  dominant and recessive alleles, they are heterozygous. Now, here is where inheritance becomes interesting. If two people, one who is homozygous dominant for a trait and another who is heterozygous for the same trait have a child, their child's phenotype will display the dominant allele. However, if they receive the recessive allele from their heterozygous parent, and they have a child with someone who also has a recessive allele for the same trait, then it is possible for their child to show the recessive trait! This is how traits can skip generations.

Well, I think that's all for now! Let me know if I mangled anything! 

Cells: They Reproduce

Well...I'm back. It's been a while.

DISCLAIMER: This material is confusing. I've done my best to explain it in a clear fashion, but there might be a few places where readers may get lost. My apologies! 

Recently, I've been studying the various ways in which cells divide and reproduce. There are two primary methods through which this is accomplished: mitosis and meiosis. On the surface, the differences are somewhat slight: one produces two cells with two pair of chromosomes; the other, four cells with only twenty-three chromosomes each. 

Now, I decided that I was going to stop starting paragraphs with, "Let's take a deeper look at each." With that said, I will instead finish this paragraph with: Let's take a deeper look at each.

To understand mitosis, one must comprehend the cell cycle. After one series of mitosis has ended, the daughter cells enter what is known as "G1," in which all that happens is growth of the cell. Then, during the next period of time, the chromosomes duplicate, causing this phase to be known as "synthesis." Another phase of growth, this time, "G2," occurs. The previous three phases are collectively known as "interphase."

Now, the mitotic cycle starts. This is where it gets really interesting. The chromosomes become visible under a microscope and the nucleolus dissolves. This period of time is known as "prophase." Now, the chromosomes appear in an X shape because their duplicates formed during the synthesis phase are joined in the middle, along what is known as the centromere. Next, the sister chromatids line up along the middle of a cell, known as the metaphase plate, as this time is called "metaphase." Then, the sister chromatids are pulled apart along the centromeres by fibers emitted from the centrioles (poles at both ends of the cell), and the chromosomes head to opposite ends of the cell in "anaphase." Finally, the cell's membrane splits the cell into two distinct cells. This is known as "telophase."

Meiosis has a few differences. First off, the goal of meiosis is to produce a cell with only twenty-three chromosomes so that it can share its chromosomes with another cell in order to produce a cell with unique genes that is then capable of developing into a baby of the species. Therefore, the cells undergo one more division than they do in mitosis.

Now, meiosis starts out just like mitosis does, with the chromosomes replicating and then condensing. However, the first difference comes in what is known as "Prophase I." Here, the condensed chromosomes pair up with their corresponding chromosomes (remember, each cell has a two sets of chromosomes). While they are paired up, enzymes cut sections of DNA from each chromosome and exchanges it with the other. This allows genes (more on those later!) to be transferred between the strands.

Then, the centrioles attach to the pairs of chromosomes--fibers from both centrioles to 23 chromosomes. The centrioles pull the chromosomes (as in metaphase), but instead of lining up along the metaphase plate, the chromosomes line up so that the pairs of chromosomes are divided by the plate. The pairs of chromosomes are now separated as one member of each pair is pulled to both sides of the cell. The sister chromatids, however, are still attached. The sister chromatids arrive at opposite ends of the cell, and nuclei form around them. Telophase I occurs and the cell divides into two cells, each with one set of 23 chromosomes that were duplicated during the synthesis phase.

So, quick recap: Originally, there were two pairs of 23 chromosomes. Each pair duplicated, creating four pairs. Then, the cell divided, creating two cells, each with two pairs of 23 chromosomes.

Now, the two cells basically perform mitosis again. The chromosomes condense into chromatids, line up along the metaphase pate, divide along the centromere, and a new membrane forms. Because each cell (which had two set of 23 chromosomes) has now divided into two, there are now four cells with one set of 23 chromosomes--the original goal of meiosis.

Well, that's that! See you again soon! 

The Longest Prezi You Will See in Your Life

Well...this one's a biggie.

It's pretty self-explanatory, so I won't say much more.

However, I will point out that my energy and focus was gone by the time I got around to the Calvin Cycle, so if typos and mistakes abound...you know why.

Have fun!

Green Humans? Why Not? on Prezi

The Joy of Making Bubbles with Enzymes

Well, we did a little experiment with enzymes to see just how they worked. Our setup was relatively simple: 3 mL of water and 3 mL of hydrogen peroxide. Our enzyme was simply yeast, and the object was to manipulate various variables with the reaction to see what the change would be. My attempt at explaining what was going on is that the yeast breaks off the oxygen from the hydrogen peroxide and releases the oxygen into the atmosphere. This created the pressure we measured with a pressure probe.

Here are the various graphs we managed to draw from the experiment. I'll explain the meaning of each as we go along. 

This graph shows the change in the rate of reaction as we changed the concentration of the enzyme. The slope of this graph is relatively constant, suggesting that the rate of reaction is directly related to the concentration of the enzyme.

This graph (although admittedly bizarre) shows the change of the rate of reaction as the pH level of the solution the reaction was occurring in changed. We used buffers to hold the pH at constant levels of 4, 7, and 10, and found that the highest rate of reaction was when the pH was the pH of water--7.

This graph shows the change of the rate of reaction as we changed the temperature of the solutions that the reaction was occurring in. We used four different temperatures, namely, 0, 25, 38, and 80 (all of which were measured in degrees Celsius). By looking at this graph, we can see that the greatest rate of reaction occurred at slightly warmer than room temperature, but that the enzymes' productivity fell dramatically as the heat increased too much. This was explained when we realized that the heat could cause the enzymes to become denatured (meaning that the shape changed).

Unpronouncable Words...And Lots of Them

As we've spent a large proportion of time recently discussing enzymes, I thought I'd put together a little post on a disorder of an enzyme: PKU. (I found most of this information in the Mayo Clinic article.)

Phenylketonuria (fen-ul-ke-toe-NU-re-uh) is a genetic defect that results in too much of the acid phenylalanine. It's caused by mutation within a gene that contains the instructions to make the enzyme that breaks it down. Amino acids are the fundamental building blocks of proteins, but too much of phenylalanine results in various health problems. People who have this excess of the phenylalanine, referred to as PKU, must carefully limit their diets so that they do not consume too much phenylalanine (which is found primarily in protein-rich foods).

At birth, babies within the U.S. and several other countries are screened for PKU. When it is caught soon after birth, serious complications can be prevented.

  

When a baby is born with PKU, he or she has no symptoms. Soon after, however, the various complications arise. These include:

• Mental retardation
• Behavioral or social problems
• Seizures, tremors or jerking movements in the arms and legs)
• Hyperactivity
• Stunted growth
• Skin rashes (eczema)
• Small head size (microcephaly)
• A musty odor in the child's breath, skin or urine, caused by too much phenylalanine in the body
• Fair skin and blue eyes, because phenylalanine cannot transform into melanin — the pigment responsible for hair and skin tone

Let's go a little deeper with the causes of PKU:

PKU is caused by a genetic mutation. The gene that is defective is the one that carries the information used to make an enzyme that breaks down phenylalanine. Because this particular amino acid is allowed to flourish, a hazardous buildup of the acid can occur when a patient eats foods such as milk, cheese, nuts, or meats (foods that are rich in protein). This buildup leads to potentially serious health problems.

Because PKU is a genetic disease, the defective gene must be passed on to a child from both the mother and the father. This typically happens when the parents do not know that they have the defective gene. (Think of Typhoid Mary. People who have the defective gene but not PKU are known as carriers.)

Well, I think that's all for now! Who knows? I might actually stay on top of blog posts this time!

(Ha ha! How funny that is!) 

Poisonous Thoughts

Mustard gas. What is it really?

An article I found gave me a few answers. It's a poison that is particularly bad for the skin and the eyes, but can also affect the lungs and other organs if it is inhaled. Although it is typically not fatal, it does have severe effects. However, these effects do not occur immediately after exposure; rather, symptoms take up to six hours to develop. This can be a problem because permanent damage can occur before the victim even knows that they need medical treatment!

Mustard gas is a so-called "blister agent," meaning that it is a chemical that can damage the skin, eyes, and lungs. In comparison with "nerve agents," (chemicals that prevent the nervous system from properly functioning) it is not as likely to become fatal. However, the amount to which a victim is exposed plays a role in the long-term effects. Long-lasting complications (such as cancer) can be traced back to mustard gas.

Another article gave me some more in-depth information on the processes of mustard gas. As an alkylating agents, it binds to nucleophilic molecules (molecules that share electrons with another molecule to bind with them) such as both types of nucleic acids as well as proteins and various parts of cell membranes. Obviously, this can be bad. For example, when it bonds with DNA, it can cause the strands of DNA to break or develop various other problems. When mustard gas bonds with RNA, it can alter the creation of proteins that are dependent upon the RNA, which results in the death of the cell.  Because mustard gas also binds to some proteins, it can change the shape of those proteins, which can alter the enzyme activity. Finally, mustard gas can also alter the structural proteins of the membrane of the cell or cause the lipids within the cell to be damaged, both of which can cause the death of the cell.

Can anything be done for people who have been exposed to mustard gas? Unfortunately, the answer is "not too much." It seems that decontamination is the primary method of treatment for exposure to mustard gas. There is no antidote (at least at the time of publication of the latter article) and, although thiols have been suggested as possible treatment, there is not a wide acceptance of this method.

Photosynthetic Imagination

Well, after complaints from my audience (meaning: me) about the high concentration of prezis, I've reverted to Power Points. Here's a little thing I threw together about an imaginary experiment (literally, a thought experiment).

Embedding is not working well (read: not working at all) so, for now, I'll give you a link to the presentation. Hopefully, I can get it embedded sometime!