Second Lesson: Chemical Bonding

Greetings to all you curious science minds!  Today I would like to continue off of the previous post's topic and discuss some more basic chemistry.  Again, I am always surprised by how little this is understood between biology students.  (This is made especially evident nearly every time I have tutored for organic chemistry).

Since we now have a basic understanding of what exactly an atom is, we can now discuss how they combine to form molecules that make up the basis of everything around us.  If an atom loses an electron, which of course is negatively (-) charged, then the atom is said to be positively charged (+).  Likewise, when a given atom loses an electron that electron is gained by another atom which makes that atom overall negatively charged (-).  Protons and neutrons are typically not transferred as easily as the small readily displaced orbiting electrons are.  


Any atom that has a charge is called an ion.  When two ions of opposite charge meet they are attracted to each other and will weakly bond together.  This type of bond is called an ionic bond. 

The more common type of bond used in biology is a covalent bond.  The reason why a covalent bond is more common is because a covalent bond is significantly stronger than an ionic bond.  Basically in a covalent bond, electrons are shared between two atoms instead of being transferred to forms ions.  There is a certain amount of electrons atoms usually want in order to be in their most stable state.  This depends on the location of the atom on the periodic table (usually 2 electrons for Hydrogen and about 8 for most other atoms in the second row), and atoms either form ionic bonds or share electrons in covalent bonds to reach this stable state.

The degree in which an electron is shared can vary also.  If an electron is equally shared between two atoms, it is called a nonpolar covalent bond.  If a given atom has a higher affinity for the electron in the covalent bond, it will be slightly more negative, likewise the other atom involved in the covalent bond will be slightly more positive.  This type of bond is called a polar covalent bond.  The amount of affinity an atom has for an electron is termed electronegativity.

The last type of bond I want to discuss is a hydrogen bond.  Basically, a hydrogen bond is when a given Hydrogen atom is partially shared between two other atoms.  Think of it as if a hydrogen atom forms a partially covalent bond between two atoms.  Typically, one atom holds onto the Hydrogen atom stronger than the other and is given the title of the Hydrogen Bond Donor.  The atom that is weakly bond to the Hydrogen atom is called the Hydrogen Bond Acceptor.  Think it as a clingy child versus an aloof older brother.  The clingy child (Hydrogen Bond Donor) wants to attached to his mother (the Hydrogen molecule).  On the other hand, the aloof older brother (Hydrogen Bond  Acceptor) is not as attached to his mother.  Hydrogen Bonds are very important in the structure of DNA which I will discuss in the next posting.

Intro Lesson

I will complete my B.S. degree in Microbiology with a minor in Chemistry in August, and over the last couple of years of my college science education, I have noticed that the most basic of principles are the least understood.  Almost every time I would begin a Biology science course, I was relearning the same basic concepts again and again regarding molecular biology.  That is what I hope to do with this blog.  I do not want to go into huge detail, but provide a refresher understanding to the general public regarding these important principles of Biology and Chemistry.

I am not a professional teacher, nor do I claim to be, though I do have some teaching experience.  I have tutored for organic chemistry for two and half years of college.  I have also been an Undergraduate Teaching Assistant for Molecular Biology twice now.

In order to understand molecular biology it is EXTREMELY important to understand the basic principles of chemistry.  Everything we see around us is made of atoms.  Within the nucleus of atoms are protons and neutrons.  Protons are positively charged and neutrons have no charge.  Surrounding the nucleus of atoms are negatively charged electrons.  Electrons are a lot smaller than their counterparts in the nucleus and fly around the nucleus in a circle pattern called an orbit.  Think of the orbit in a similar fashion to how the moon travels around the earth.  Usually, the number of protons equals the number of electrons, so the atom has no charge.   The periodic table represents all the known atoms, but Biology usually uses just a few of these atoms: Hydrogen, Oxygen, Sulfur, Phosphate, Nitrogen, Potassium, Sodium, and most commonly Carbon.  These atoms combine in various different ways to form everything we see around us, and in my next lesson I am going to discuss how this binding occurs.