In The Gno

I found this article today from ScienceDaily.  It is a short read, but quite interesting.  Thought I’d pass it along!  Cheers…

http://www.sciencedaily.com/releases/2009/07/090716201127.htm

All living things contain DNA.  In fact, DNA is the universal genetic code for life.  DNA stands for deoxyribonucleic acid.  But where does this name come from?  The “deoxyribo…” bit relates to the name of the five-carbon sugar that is the first of three parts of a DNA nucleotide.  This sugar molecule is named a deoxyribose sugar.  The “nucleic” bit is termed so because DNA is usually contained and replicated in the nucleus of a cell.  Even microscopic bacteria have DNA as their genetic code.  Bacteria are single-celled organisms that lack a nucleus.  But if bacteria don’t have nuclei, how can they contain DNA?

The answer is that their DNA is packaged differently than human DNA.  Typically, bacteria contain one long, circular bacterial chromosome tightly coiled into a nucleoid “region.”  Plasmids, or small, circles of DNA, are usually present in bacteria which may contain genes that give bacteria a unique resistance to certain drugs.  The manner in which disease-causing bacteria become to resist antibiotics is an interesting example of genetics and evolution in action.

Bacteria are fun, little creatures if you have ever seen one under a microscope.  They are also the most widespread of all living organisms on Earth – even more widespread than humans.  Although microscopic, their size is no relation to the important role they play in ecosystems and at the organismal level.

Bacteria are decomposers that play the role of recyclers in nonliving components of the environment such as soil.  They are also present on and in many other living organisms.  In animals, for instance, bacteria exist as normal flora.  Some examples include the bacteria that exist in the digestive system of cows that help break down cellulose, as well as harmless strains of bacteria like Escherichia coli that thrive in the human colon.  E. coli is actually important to our health because they naturally make vitamin K.

The strains of bacteria that can make you sick are called pathogenic bacteria.  In medical language, pathogenic means disease-causing.  Pathogenic bacteria can cause vomiting, diarrhea, urinary tract infections, respiratory illness, pneumonia, and many other diseases.

Some pathogenic bacteria are naturally resistant to antibiotics by means of genetic variation.  This presents emerging problems with antibiotic use.  The first of many is that antibiotics should only be prescribed for a bacterial infection.  The second problem relates to their proper use.  Antibiotics are routinely prescribed every day to rid bodies of bacterial infection; however, if not taken properly, problems result.

Antibiotics must be taken exactly as prescribed.  This means that if you are prescribed an antibiotic to be taken every twelve hours for ten days, you take it every twelve hours for the full ten days.  Do not stop taking the drug when you “feel better.”  Doing so could potentially create a future bacterial population resistant to that antibiotic.  The next time you take that same drug, it won’t work as well or won’t work at all.

Here’s the simple answer to how it works.  As I said, some disease-causing bacteria are naturally resistant to antibiotics by means of genetic variation.  This just means that some bacteria have resistance genes and some don’t.  When an antibiotic is taken, it slowly begins to kill the bacteria.  A doctor will (hopefully) prescribe the proper dose for the pertinent infection.  If the entire course of antibiotics is taken, theoretically ALL of the bacteria will be killed.

If you stop taking an antibiotic, there will be bacteria left alive.  If among those bacteria that survived, there exists even one bacterium that has this natural resistance, it will reproduce in a manner (called binary fission) which perpetuates identical daughter cells.  Because they are identical cells, they also now have a copy of their parent’s genetic material which contains…you guessed it…the genes for this antibiotic resistance.

Most bacteria can multiply exponentially in a very short time period.  The problem this presents is that when disease-causing bacteria survive and multiply, it creates a population largely made of bacteria with this natural resistance to antibiotics.  If bacteria contain genes resistant to more than one drug, it is termed multidrug-resistant which is where superbugs like MRSA (methicillin-resistant staphylococcus aureus) and VRE (vancomycin-resistant enterococcus) get their names.

So, my suggestion to you is that next time you are prescribed antibiotics, follow instructions on the label.  I hope I have armed you with more interesting and relevant information about DNA and genetics today.  I will expand more later on the topic of bacteria and how useful they are in genetic engineering.  But for now, I’m Pyrimidiva, reminding you that what you “know” is not as important as what you “gno.”

Blood type is a special type of inherited trait that is governed by multiple alleles, or gene variants.  Most often referred to as the ABO blood group, these three alleles (A, B, and O) can produce four phenotypes from six genotypes.  Of the three possible alleles, A and B are always dominant to O.  In addition, A and B are codominant; this means if inherited together, both alleles will be expressed.  Like any other inherited trait, only one allele will be donated from each parent.  Possible combinations (genotypes) are AA, AO, BB, BO, AB, and OO.  The phenotypes that result from these are (1) Type A blood for AA and AO genotypes, (2) Type B blood for BB and BO genotypes, (3) Type AB blood for the AB genotype (remember the codominant alleles), and (4) Type O blood for the OO genotype.

Another interesting snippet about blood types is how they are physically expressed.  A blood type is expressed by the presence of certain sugars on the surface of red blood cells.  Individuals with Type A blood have only carbohydrate A on their red blood cell surfaces.  Likewise, red blood cells with carbohydrate B at the surface will dictate Type B blood.  Type AB blood contains both carbohydrates and Type O has neither.

In this manner, blood types are extremely important in situations such as transfusions where foreign blood will enter the body.  Donated blood must only contain blood cells that match the type of carbohydrate present in the recipient’s blood.  If donated blood cells contain a foreign carbohydrate, the recipient will make antibodies against donor cells causing them to clump together, or agglutinate, putting the recipient at risk.  Clumping can eventually cause a blockage that could lead to reduced or nonexistent blood flow and possible death.  The laboratory process of blood typing is performed in much the same way, except a blood sample is first withdrawn from the individual, then the antibodies for type A and B are mixed with the sample.  Blood type is then determined based on clumping reactions.

Most people know what their blood type is, but if you don’t, you can still try to figure it out with a nifty visual tool called a Punnett square.  The Punnett square is named after its inventor, a pioneer in the genetics field, Reginald C. Punnett.  This tool is used to determine possible combinations of alleles; alternatively, it is used to predict the probability of certain genotypes that can result from a genetic cross.  Here’s how it works:

This is a simple Punnett square that shows a monohybrid cross, a cross involving only one trait (in this case, blood type).  The first parent, represented horizontally at the top of the Punnett square, has Type A blood with an AA genotype.  The second parent, represented vertically along the left side of the Punnett square has Type B blood with a BO genotype.  Again, this parent has Type “B” blood because the allele B is always dominant to O (as is A).

Back to our Punnett square…  You can see the combinations from this cross show that there is a 50% chance that the offspring will be Type AB and a 50% chance that the offspring will be Type A (A masks O).  This is also expressed as a 1:1 ratio between AB and AO genotypes.  Any combination of alleles can be depicted by drawing a Punnett square.  If you know your parents’ blood types, this is one method you could use to figure out your own possible blood type.

One unique situation is for crosses resulting in the OO genotype, which is the only allelic combination that yields Type O blood.  The only time a person will end up with Type O blood is if each parent has at least one O allele to donate.  Obviously, if both parents have Type O blood, all of their children will have Type O blood as well.  However, parents with genotypes AO (Type A blood) or BO (Type B blood), can still produce offspring with Type O blood.  See the Punnett square to learn why:

As you can see, this cross predicts a 1:1:1:1 ratio between genotypes.  So, there is a 25% chance of a child with these two parents having Type O blood, even though neither parent actually has Type O blood.

For this same reason, parents can be carriers of a disease without being afflicted.  This is how recessive genetic disorders are passed from parents (with no disease) to their children.  Let me draw you one last Punnett square so it will be easy to visualize what I am trying to explain.  In this example, “r” will represent any number of recessive inherited diseases like Cystic Fibrosis, Sickle Cell Anemia, and Tay Sachs, and “R” will represent the dominant allele that will mask the disease.

Notice again, that both parents (just like in the blood type example) must have at least one copy of the recessive allele.  This means both parents are heterozygous for this trait (See Genotypes and Phenotypes).  If these two people mate, there is a 25% chance that their offspring will get the disease.  This is the reason why genetic counseling and prenatal screening is usually recommended if it is suspected that either.  On the other hand, if only one parent is a carrier (Rr), there is no chance their children will be afflicted.  Draw your own Punnett square and see if you can figure out why.  (Hint: the cross is RR x Rr and remember that in order to express a genetic disease, there must be two copies of the recessive allele.)

I’m Pyrimidiva, and I hope you have enjoyed my topic on blood types as much as I enjoyed writing it. Stay tuned for more posts on genetic diseases and remember, what you “know” is not as important as what you “gno.”

Electron microscopy of chromosomes

These terms might sound scary, but there is a simple explanation for each.  A phenotype is merely how a gene is expressed.  For instance, a dimpled chin is an example of a trait that is governed by genetics.  Your phenotype is determined by whether or not you have a dimple in your chin.  Some people call this a “cleft chin.”  If you have a dimpled chin, you express the trait.  Essentially, your phenotype is a “YES – I have a dimpled chin.”  By the way, this means the trait is dominant. A recessive trait, no dimpled chin for instance, is one in which the trait is hidden; hence, the term recessive.  A genotype, on the other hand, is the actual hereditary information of an individual.  This means that a genotype represents the copies of the alleles one inherits for a particular trait.

Dominance rules in patterns of inheritance are pretty straightforward.  If an individual inherits two recessive alleles, the trait will always be hidden or masked.  This individual would be considered a recessive homozygote.  Recessive alleles are usually written with lowercase letters.  So, if we say that the letter “d” represents the trait for “dimpled chin,” then someone that inherits two recessive alleles (one from each parent) has the genotype of “dd,” and is said to be homozygous recessive.

Consequently, if an individual inherits two dominant alleles, the trait will always be expressed.  This is also known as homozygous dominant.  Dominant alleles are written with (you guessed it) capital letters, so someone with two dominant alleles (DD) for the dimpled chin trait will surely have a dimpled chin.  So, what happens if someone inherits one dominant and one recessive allele, effectively “Dd”?  This means that they are heterozygous for the trait; however, they will always express it.  The reason for this is because dominant alleles are exactly that – dominant.  Even in the presence of a recessive allele, a dominant trait will always be expressed.

One last note on recessive alleles and traits…  They are more significant than merely being “hidden.”  In some cases where, two copies of a recessive allele can mean that a person will inherit a genetic disease.  Some commonly known recessive inherited diseases are Cystic Fibrosis, Sickle Cell Anemia, and Tay Sachs.  These are examples of autosomal disorders, which are diseases that are linked to the 22 pairs of chromosomes that do not determine our gender.  Interestingly enough, there are also dominant inherited disorders which are quite lethal.  We will explore genetic diseases and autosomal vs. sex-linked disorders at a later date.

I hope you have enjoyed reading about the expression of traits and dominance rules.  Remember, what you “know” is not as important as what you “gno.”

Genetics, the science of heredity, is a diverse field rich in many topics of study and research including genes and DNA, chromosomes, related diseases or conditions, and patterns of inheritance.  Roots of genetics can be traced back to the 1800s when an Austrian monk named Gregor Mendel first began studying inheritance patterns using garden-variety pea plants.  The results of his studies provided important groundwork for modern genetic science and are much of the reason why the science of genetics has prospered to date.  Mendel’s work provided basic laws establishing the rules for inheritance patterns and those laws, in turn, can be applied to many genetic situations including blood types and sex-linked traits.

Although many ideas on inheritance patterns pre-date Mendel, his work first demonstrated that (what we now know as genes) were the discrete, independently inherited units of heredity.  Mendel’s experimental organism of choice was the common garden pea, Pisum sativum.  He chose seven discrete pea plant characteristics:  Seed shape, seed color, flower color, pod shape, pod color, flower position, and stem height.  Each characteristic studied had two distinct forms, such as tall or short stem height, or smooth or wrinkled seed shape.  Mendel studied his plants for near eight years.

Mendel experimented with his pea plants by performing genetic crosses, usually monohybrid (involving only one trait) or dihybrid (involving two traits).  He experimented with true-breeding varieties, applied mathematics, and kept detailed results on his crosses.  Because of his diligence, use of math, and excellent choice of experimental organism, his studies eventually led to two important laws in genetics.

1.     Mendel’s Law of Segregation – each pair of alleles, or variants of genes, separate during gamete (egg and sperm) formation so that each gamete (egg and sperm) receives one member of a pair

2.     Mendel’s Law of Independent Assortment – during gamete (egg and sperm) formation, alleles (gene variants) in one gene pair segregate into gametes independently of other alleles (gene variants)

There is a lot of new vocabulary in the definition of these two laws, but one of the most important concepts is that Mendel’s experiments cements the idea that (1) we get one copy of a gene from one parent and another copy of the same gene from the other parent, and (2) human characteristics are inherited independently of other characteristics – for instance, hair color has nothing to do with eye color.

We will visit Mendel’s laws in more detail at a later date.  I’m Pyrimidiva, and I hope you have enjoyed our presentation on Mendelian Genetics.  For now, remember that what you “know” is not as important as what you “gno.”

Recall that a single nucleotide monomer, the individual building blocks of genes, is basically made of a sugar, phosphate group, and nitrogenous base.  The monomer itself, as previously mentioned, is usually referred to by the same name as the base it contains.  This is why the linear sequences of genes are sometimes explained as strings of GAACACCTG or TAACGAATTCGCC or any other millions of possible combinations.  Genes may be several hundreds of nucleotides long or even up to several thousand.

Genes are what actually contain the chemical instructions that tell our body to make certain proteins.  When gene segments of DNA are “read” by RNA (ribonucleic acid), they are decoded in triplet.  This means that RNA reads nucleotides in segments of three.  When RNA “reads” a gene’s instructions, each triplet of nucleotides, called a codon, equates to a particular amino acid.  There are twenty possible amino acids that may be produced.

For instance, when RNA “reads” the codon “TTT” it will translate that into an amino acid called Phenylalanine.  Individuals who lack a necessary enzyme to properly metabolize phenylalanine are afflicted with a rare disorder called phenylketonuria (PKU).  PKU screening is now routinely performed at birth in all United States hospitals.  On the other hand, if RNA “reads” the codon “GAG“, it will translate that into an amino acid called Glutamic acid.  Glutamic acid is the origin of the unique flavor given to certain ethnic foods.  This flavor has recently been named “umami” (Japanese for “yummy”) and has formally been added to the other four traditional flavors:  Sweet, salty, bitter, and sour.  Glutamic acid is believed to play a role in cognitive functions such as learning and memory.  Further, it is a key molecule in the process of cellular respiration, the crucial metabolic process that converts what we eat into energy.

Amino acids are the building blocks of proteins.  So as RNA “reads” a gene, several strings of amino acids are produced.  The end result is called a polypeptide.  One or more polypeptides makes a protein.  Because amino acids are all chemically different, they give proteins unique sizes, shapes, and structures.  Some proteins are enzymes that help lower the amount of energy it takes to start a chemical reaction.  Some proteins are transporters of certain substances within our circulatory system (like hemoglobin that carries oxygen).  Some proteins are chemical messengers, or hormones.  There are many other types of proteins in our bodies, and all play a vital role in proper body function and survival.

DNA is the inherited genetic material that controls gene expression through protein synthesis.  This is a fancy way of saying that DNA is a chemical form of a genetic blueprint.  The genetic instructions contained in DNA are housed in genes.  Genes are smaller segments that, when strung together, comprise a DNA molecule.  Genes are actually unique linear sequences of nucleotide monomers named for the nitrogenous base they contain.

Wait – nucleotide monomers and nitrogenous bases?  This blog is supposed to demystify genetics by explaining concepts and ideas in everyday language, but sometimes that is difficult to do without a deeper understanding of chemistry.

Yes, there is much chemistry intertwined in biology; in fact, they go hand in hand.  Without going into too much unnecessary detail, a nucleotide monomer is a chemical unit that is made of a sugar with five carbon atoms (aptly named a “five-carbon sugar” or “pentose sugar”), a phosphate atom bonded to four oxygen atoms (called a phosphate group), and one of four possible nitrogen-containing bases called adenine (A), cytosine (C), thymine (T), or guanine (G).  They are called bases because these chemical compounds, collectively made mostly of carbon, nitrogen, and hydrogen atoms, have basic properties as opposed to acidic properties.

Acids and bases are a deeper lesson in chemistry; right now it is more important to focus on the fact that the four bases (A, C, T, or G) are categorized into two types:  Purines and pyrimidines.  Purines are chemically a double-ringed structure, whereas pyrimidines form a single ring.  Adenine and guanine are classified as purines, while cytosine and thymine are pyrimidines.

DNA double helix

One strand of DNA might look like a straight ladder cut down the middle, making the left side of the ladder and the right side of the ladder.  One strand complements the other in a way that is also related to chemical structure.  The component nucleotide bases (the rungs of the ladder) of a DNA strand (one half of the ladder) pair with each other by chemically bonding to the nucleotide bases of the second DNA strand (the other half of the ladder).  Together, the two DNA strands unite to form what looks like one single ladder.

Watch a video on the unique structure of DNA

For genes to properly function, the nucleotides must pair up correctly.  They do this by adhering to a strict set of base-pairing rules that were discovered by pioneers in the science of genetics, James Watson and Francis Crick.  Base-pairing rules dictate that a purine always pairs with a pyrimidine.  In other words, adenine (A) always pairs with thymine (T), and cytosine (C) always pairs with guanine (G).  When nucleotide bases pair correctly, that is, when A pairs with T, or C pairs with G, the rungs on two halves of the ladder (single DNA strands) come together to form a single ladder.  The ladder appears twisted due to complex chemical bonding, such as weak hydrogen bonds or ionic and covalent bonding, between the various elements in the DNA molecule itself.  The “twisted ladder” shape of DNA is what gives the molecule its unique name – the double helix.

Welcome, and thank you for reading this blog – In The Gno – where “gno” is Latin root for knowledge.  Are you a college student researching data or facts for an essay?  Maybe you are an expecting parent – in which case congratulations would be in order – and searching for information regarding heredity or genetic disorders.  You may even be a grade school or high school student, or you simply want to increase your knowledge about genes, chromosomes, and the chemistry of what makes us human.  No matter whom you are, the intent of this site is to introduce, simplify, and explore the exciting world of genetics, patterns of inheritance, and that lovely stuff called DNA!

What is DNA anyway?  As you may remember from high school biology, DNA is an acronym for that long word deoxyribonucleic acid (dee-ocks-ee-rhy-bow-noo-clay-ic acid) which is nothing more than a molecule that contains our own unique genetic code – a set of chemical instructions that tell our cells to manufacture proteins that make us look, think, feel, and behave the way we do.  There are many different versions of how to define DNA depending on where you decide to look, but this serves as a very basic, down-to-earth definition.  In technical terms, DNA is part of molecular biology, the study of life at the molecular level.  Much has already been revealed about DNA through years of scientific research, including the completion of mapping the human genome – the primary goal of the Human Genome Project.  However, there is still much to learn in the field of genetics; the amount of information that we do not know far outweighs what we do know.

Fortunately, what has already been learned about DNA and genetics lets us focus on an entire treasure chest of information including:

• Mendelian genetics and the laws of inheritance
• Genes, alleles, and human characteristics
• Chromosomes and cellular reproduction
• Genetic crosses (dating back to experimental genetics)
• Genotypes and phenotypes
• Inherited disorders and genetic testing
• Chemistry of DNA and how it is passed from parents to offspring
• Role of viruses and bacteria in DNA technology
• Gene cloning and gene therapy
• DNA analysis
• Genetically modified organisms (GMO) and what they mean to you
• Genomics (the study of whole sets of genes and their interactions)
• and much, much more…

Please check back periodically for updates to In The Gno.  If you would like to see an article about any topics or subtopics from the list above, or any other related topic not listed, feel free to let us know in our comments section.  And remember, what you “know” is not as important as what you “gno.”