Biology Fall 2009--Rozema
Unit 1: Biochemistry Notes
from Wednesday 9-23-09
*Textbook pages 35-38.
Matter & Energy:
-Matter is anything with mass and volume.
-Atoms are the most basic unit of matter.
-All “things” are composed of matter, except energy. This includes your cells, blood, entire body, pencil and desk.
-Energy is the ability to do work. This is a difficult concept to envision.
-The two categories of energy are potential and kinetic. Potential Energy, is that which is “stored” or not being used presently. Kinetic Energy, is that of “motion” or that which is being used presently.
-In this class we will focus primarily on chemical potential energy, or the energy stored within the bonds of molecules.
-An important energy molecule, within our bodies, is ATP (adenosine triphosphate), in which immense amounts of energy are stored within the phosphate bonds of the molecule.
-Matter and Energy continuously cycle throughout living systems, including our own bodies. This occurs as a result of occurring chemical reactions, larger processes such as movement of food and waste, movement of our own bodies. If everything is matter, and there is constant movement and exchange within our bodies (work which is being done through the use of energy), then there is constant movement and exchange of matter and energy within our bodies!
Valence Electrons & Bonding:
-Atoms are the basic unit of matter.
-Recall that atoms are composed of protons and neutrons at their centers (nuclei), and contain electrons orbiting around.
-The outermost electrons in any atom are called the valence electrons.
-A stable atom wants a full valence shell, however most atoms on our periodic table do not have a full valence shell, and thus are not stable.
-Atoms will bond with each other in order to share/gain more valence electrons, so that they may become stable and “happy”.
-This interaction of valence electrons, and drive to stability, is the basis for all chemical reactions.
-Remember that atoms are made with all of their electrons orbiting around the outside of their structure, and with protons on the inside. Also remember that electrons are negatively charged particles, and protons are positively charged particles.
-This means that when atoms come together to bond, they are trying to get close, even though their charges are the same (or alike). This is difficult, because like charges repel, and it is opposite charges that attract.
-In order to overcome this resistance, energy must be “put in” to bonding the atoms…. Because essentially those atoms are doing work!
-All of this energy being put in to bond these atoms is stored as chemical potential energy in their bonds. Because energy went IN to the bond, this is an endothermic reaction.
-In an endothermic reaction you would feel a loss of heat and temperature would drop.
-DEMO: acetic acid + sodium bicarbonate sodium acetate + carbonic acid
-If you break the bonds, you then are going to release all of that stored (potential) energy as kinetic energy. You can think of that stored energy literally exploding out.
-Because energy is exiting the system or bonds, this is an exothermic reaction.
-In an exothermic reaction you would feel an increase in heat and temperature would rise.
-DEMO: Dissociation of sodium hydroxide in distilled water.
Using the Periodic Table:
-Recall the periodic table of elements.
-There are lots of letters and numbers.
-The letters are the symbols for each different element.
-The numbers at the top of each column represents the “group number”. That means every element straight down that column is that group number.
-The “Group Number” also tells you how many valence electrons the element has. For example. If an element is group 5, it has 5 valence electrons.
-Also remember that atoms want to be stable and happy, this means they want that outer shell to have 8 valence electrons….. if an element has 5 then, it is not happy, it is unstable.
-What do atoms do if they are not stable and happy? They react!
-Let’s look at carbon. What group is carbon in? Carbon is in group 4, that means it has 4 valence electrons.
-I think we probably need to review Lewis dot structures and why we even use these things. Lewis dot structures allow us to see how many bonds an atom can make. Each dot represents 1 valence electron.
-For carbon, which has 4 valence electrons, I draw 4 dots around it. I just pretend there’s a little box around it, and I put one dot on each side. Remember though that our carbon needs 8 v.electrons to be happy. That means it is missing 4 dots (or valence electrons).
-Any time an atom is missing a valence electron, that means it can make a bond to gain one. So how many bonds can carbon form? 4!
-This allows carbon to bond with lots of different elements in living things.
Types of Biomolecules or Organic Molecules:
-Organic means that the molecule is made of primarily carbon.
-Organic in science does not mean pesticide free (like with food).
-We can also call them “bio” molecules because they are molecules that make up living things (hence bio = life or living).
-Types = Carbohydrates, Lipids, Proteins, Nucleic Acids.
-All living things are made of carbohydrates, lipids, proteins and nucleic acids.
-The most common elements in biomolecules are C, H, O, N, P and S.
-This means that you will find lots of those elements in carbohydrates, lipids, proteins and nucleic acids.