BIO - Review of Chemistry [LESSON]
Review of Chemistry
pH
The pH of a solution is the concentration of hydrogen ions (H+). The pH scale is an inverse logarithm that ranges from 0 to 14: anything below 7.0 (ranging from 0.0 to 6.9) is acidic, and anything above 7.0 (from 7.1 to 14.0) is basic. The lower the pH, the higher the concentration of H+. In simple terms, an acid is a substance that increases the concentration of hydrogen ions (H+) in a solution, usually by dissociating one of its hydrogen atoms. A base provides either hydroxide ions (OH–) or other negatively-charged ions that react with hydrogen ions in solution, thereby reducing the concentration of H+ and raising the pH. Each step of the pH scale is 10x more basic than the one below it.
Click the arrow to answer the question.
For example, how many times more basic is pH 9 than pH 6?
10 x 10 x 10 = 1000 times more basic
Energy
Energy is a core concept in AP Biology and we will encounter this throughout many units. Here, we will review some of the key ideas from your chemistry course. Energy is a property of objects which can be transferred to other objects or converted into different forms but cannot be created or destroyed. Organisms use energy to survive, grow, respond to stimuli, reproduce, and for every type of biological process. Matter always wants to attain the lowest energy state and will stay there unless there is an input of energy. The higher the energy, the more unstable the matter is. Likewise, the lower the energy, the more stable the matter is.
*Important misconception to address: It REQUIRES an input of energy to break a bond. Forming bonds RELEASES energy. Please be sure that you understand this moving forward!
Click on the letters A, B, and C in the following Energy Activity graphic to learn more about an energy diagram.
Atomic Structure
Atoms consist of three basic particles: protons, electrons, and neutrons. The nucleus (center) of the atom contains the protons (positively charged) and the neutrons (no charge). The outermost regions of the atom are called electron shells and contain the electrons (negatively charged). Atoms have different properties based on the arrangement and number of their basic particles. Since matter seeks the lowest energy configuration, they are happiest when they have a full valence shell. For most atoms, this is eight (8) electrons in the outer shell.
Electrons fill energy shells in a consistent order. Under standard conditions, atoms fill the inner shells (closer to the nucleus) first, often resulting in a variable number of electrons in the outermost shell. The innermost shell has a maximum of two electrons, but the next two electron shells can each have a maximum of eight electrons. This is known as the octet rule which states that atoms are more stable energetically when they have eight electrons in their valence shell, the outermost electron shell.
In AP Biology, we are concerned with the following SIX atoms: Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus, and Sulfur (CHONPS). These are the atoms that will appear in our biomolecules and are the most abundant in the body.
Bonding
According to the octet rule, elements are most stable when their outermost shell is filled with electrons. This is because it is energetically favorable for atoms to be in that configuration. However, since not all elements have enough electrons to fill their outermost shells, atoms form chemical bonds with other atoms, which helps them obtain the electrons they need to attain a stable electron configuration. When two or more atoms chemically bond with each other, the resultant chemical structure is a molecule. The familiar water molecule, H2O, consists of two hydrogen atoms and one oxygen atom, which bond together to form water. Atoms can form molecules by donating, accepting, or sharing electrons to fill their outer shells.
Ionic Bonding:
Some atoms are more stable when they gain or lose an electron (or two) and form ionic bonds to result in a full outermost electron shell. Since the number of electrons does not equal the number of protons, each ion has a net charge. Cations are positive ions that are formed by losing electrons (the number of protons is now greater than the number of electrons). Negative ions are formed by gaining electrons and are called anions (more electrons than protons). Please watch the brief video below for a look at ionic bonding.
Watch the Ionic Bonding video below.
Covalent Bonding:
The image above depicts a covalent bond that forms when atoms share electrons. Typically, atoms will share electrons when they have similar electronegativities. The electronegativity of an atom is the magnitude of the “pull” it has on electrons of other atoms. Atoms that are more electronegative are “greedy” and will attempt to steal electrons away from others. This will enable us to determine the polarity of a covalent bond. Please watch the brief video below for a look at covalent bonding.
Watch the video below about Covalent Bonds.
Polarity
There are two types of covalent bonds: polar and nonpolar. In a polar covalent bond, the electrons are unequally shared by the atoms because they are more attracted to one nucleus than the other. The relative attraction of an atom to an electron is known as its electronegativity: atoms that are more attracted to an electron are considered to be more electronegative. Because of the unequal distribution of electrons between the atoms of different elements, a slightly positive (δ+) or slightly negative (δ-) partial charge develops.
Nonpolar covalent bonds form between two atoms of the same element or between different elements that share electrons equally. For example, molecular oxygen (O2) is nonpolar because the electrons will be equally distributed between the two oxygen atoms. The four bonds of methane are also considered to be nonpolar because the electronegativities of carbon and hydrogen are nearly identical.
Now you try to identify these types of bonds using the Polarity Activity practice below.
Intermolecular Forces
Not all attractions between atoms are ionic or covalent; weaker attractions can also form between molecules or between two parts of a larger molecule. These are typically referred to as intermolecular forces. Two types of these weak intermolecular forces that are extremely important in AP Biology are hydrogen bonds and van der Waals interactions (often used interchangeably with London dispersion forces from your chemistry class, though there are technically slight differences). Without these two types of bonds, life as we know it would not exist.
Hydrogen bonds provide many of the critical, life-sustaining properties of water and also stabilize the structures of proteins and DNA. When polar covalent bonds containing hydrogen are formed, the hydrogen atom in that bond has a slightly positive charge (δ+) because the shared electrons are pulled more strongly toward the other element and away from the hydrogen atom. Because hydrogen has a slightly positive charge, it's attracted to neighboring negative charges. The weak interaction between the δ+ charge of a hydrogen atom from one molecule and the δ- charge of a more electronegative atom is called a hydrogen bond. Individual hydrogen bonds are weak and easily broken; however, they occur in very large numbers in water and in organic polymers, and the additive force can be very strong. For example, hydrogen bonds are responsible for bringing together the two strands of a DNA double helix. In the image below, the hydrogen bonds are shown as dotted lines with the reference number “1.” It is important to note that hydrogen bonds are the strongest intermolecular force.
van der Waals attractions can occur between any two or more molecules and are dependent on slight fluctuations of the electron densities, which can lead to slight temporary partial charges (dipoles) around a molecule. For these attractions to happen, the molecules need to be very close to one another. Even though van der Waals attractions exist between every molecule, the cumulative effects are only significant in nonpolar molecules since no other attractions such as hydrogen bonding occur.
Functional groups
Functional groups are very important in biochemistry. The term "function" relates to what something does. So, functional groups in chemistry play a role in how a chemical "works," or what it does. If we understand the nature of the functional groups contained in a molecule, we also understand the chemical nature of the organic molecules that contain them.
The functional groups we will focus on in this course are:
Each of the functional groups above gives the molecules in which they are found specific characteristics. If the functional groups contain atoms that are very electronegative, the functional groups may be polar. In contrast, if the atoms are not as electronegative, the functional groups may exhibit nonpolar characteristics. Compounds composed of only carbon and hydrogen are called hydrocarbons. Although they are not technically considered a functional group, hydrocarbons give molecules specific properties as well.
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