Basic and Biochemistry for Human Anatomy & Physiology I

Notes on the Web
Basic and Biochemistry for Human Anatomy & Physiology I
Bruce G. Stewart

Your objectives for these Notes on the Web and associated readings and exercises are: To define and compare matter and energy and to differentiate between kinetic and potential energy; To define and explain the fundamental structure of elements including subatomic particles, atoms and their structures;

Note: The following is simply a little introduction to the materials we will study in Chapter 3. You must read and study the textbook chapter itself to fulfill the objectives described previously.

Matter. A basic definition is anything that takes up space and has mass. Mass is the amount of matter in an object while weight is the gravitational force exerted on that mass. While not the same, they are terms that are often used almost interchangably since their values are so consistent under the same (or nearly the same) for an object under the gravitational pull of the Earth. Energy is the capacity to do work. To major categories of energy include kinetic energy (energy in the form of movement) and potential energy (stored energy). We will be interested in learning about various kinds of potential energy described by Marieb (2004) and Marieb and Hoehn (2007) including chemical energy, electrical energy, and radiant (=electromagnetic) energy.

Elements. All matter on Earth is composed of a limited number of basic substances called elements. An element can be defined as a substance that (a) cannot be broken down into simpler substances by chemical means, and (b) is composed of atoms all of which have the same number of protons in their nucleus. Physical scientists have discovered 92 naturally occurring elements in the universe. Each has its own specific set of chemical and physical properties. For our purposes here, we need not learn all of these, nor do we have to learn theoretical concepts that deal with why they are structured the way they are. We only need to know some details about a limited number of elements that are related to the biological concepts of this course.

Elements have names, and the names can be represented by standard symbols. The symbols are typically the first one or two letters of the English name for the element; however, some are symbolized by letters from their more ancient Latin names. For example, O=Oxygen, N=Nitrogen, C=Carbon, and H=Hydrogen. However, K=Potassium (for the Latin name, kalium) and Na=Sodium (for the Latin name, natrium).

Atoms. Atoms are defined as the smallest part of an element that maintains the properties of that element. Democritus of ancient Greece proposed that all matter must be made of some undivisible unit. Atoms, in fact, can be divided, but not by normal chemical means. Furthermore, if nuclear methods are used to divide an atom, it no long possesses the chemical and physical properties of the original element. To understand the difference between chemical versus nuclear means, we need first learn about the parts of an atom. Study your textbook thoroughly for this. The main elements that we will encounter in our discussions are given in the following Table 2-1.

>Table 2-1. Some Important Elements in Living Things
Element Name	Chemical Symbol	Atomic Number	Number of Outer Shell Electrons	Examples of Function
>Carbon	>C	>6	>4	Basic structure of all organic compounds
>Oxygen	>O	>8	>6	Part of most classes of biological molecules; required in aerobic metabolism
>Hydrogen	>H	>1	>1	Abundant element in biological molecules; H⁺ (ionic form) very important in many ways
>Nitrogen	>N	>7	>5	Important in structure of proteins, nucleic acids, and many other types of molecules
>Sulfur	>S	>16	>6	Important part of cysteine, an amino acid in many proteins
>Phosphorus	>P	>15	>5	Component of nucleic acids; important part of cell membrane molecules called phospholipids; part of ATP the universal energy molecule
>Iron	>Fe	>26	>2	A central component of hemoglobin
>Sodium	>Na	>11	1	Important in Sodium/Potassium pumps in cell membranes of nerve cells and muscle cells; important in many physiological aspects such as maintenance of osmotic balances
>Calcium	>Ca	>20	>2	Abundant in bones; important in nerve function and muscle function
>Potassium	>K	>19	>1	Important in Sodium/Potassium pumps in cell membranes of nerve cells and muscle cells; activates many enzymes
>Chlorine	>Cl	>17	>7	Important ion in many solutions of living things
>Iodine	>I	>53	>7	Trace element, but critical component of vertebrate thyroid hormone
>Fluorine	>F	>9	>7	Trace component in bones and teeth
>Zinc	>Zn	>30	>2	Trace element; part of some enzymes

Molecules. Most types of elements have atoms that can chemically react with other atoms to form compounds. When they do so, they form molecules. Molecules are distinctive structures composed of atoms that are chemically bonded to each other. Each kind of compound is composed of molecules that have a particular number and arrangement of atoms. For example, water is a compound composed of two atoms of hydrogen and one atom of oxygen. Its chemical formula can be represented as: H₂O. Water molecules also have a particular size and shape. Your textbook shows many illustrations for the shape and/or arrangements of different molecules. There you can study the nature of compounds, their chemical and physical properties, and the types of chemical bonds that are important in their formation and structure.

As for most other topics, your textbooks have excellent presentations of the materials on chemistry of life, including generous excellent illustrations. Check the general objectives above to make sure that you have covered all of the topics in the textbook readings.

As with all materials throughout the semester, you will have opportunities to ask questions or ask that any relevant material from your assignments be discussed in class and/or in threaded discussions on Internet.

We will do an in-class or lab day exercise in which you will building a physical 3-D model of an alpha-ringed glucose molecule). Extremely positive student feedback on this indicates that this exercise helps them grasp the concepts of molecules with three dimensional structures and bond angles that cannot be easily learned from a flat drawing only. The following drawing shows the specific molecular arrangement you will build. Memorize this graphic and be able to draw it from memory if asked.

DNA (deoxyribonucleic acid) is perhaps the most famous of all organic molecules of life. Understanding its structure is the first step for educated people to be able to grasp subsequent processes and patterns in life, such as inheritance, gene function, genetic disease, biological diversity, evolution, DNA forensic science, and many others. Your textbook, like any good high school or college-level introductory biology textbook has this information regarding DNA. However, it is often difficult (as mentioned previously for the the glucose molecule) for students to visualize 3-D structures that are represented in 2-D space (that is, that are drawn on a flat piece of paper!). The following link will take you to a web site that allows you to manipulate a DNA molecule and its various parts in 3-D computer graphics space. I highly recommend that you use this in your study of DNA structure.

>Visit this site and explore Number 2 through Number 5 on his list of links. Spend some time there until you understand the nature of DNA structure thoroughly. If your browser does not already have it, you will need to download Chemscapes's Chime's latest version to view these images.

The next links lead to web sites that have information similar to the chemistry or life chapter your textbook, but it always helps to see the same information presented in different ways. Also, the questions (problem sets) are very good to use for self-testing to see how well you understand much of the material that will be covered on your major lecture exam.

This site also requires some specialized "plugins" like Chemscape to view their graphics. If you can view them, great. If not, you might try downloading (if you are at your home computer) to appropriate plugins. If you cannot do this, don't worry. It is presented here as an optional resource only.

An Outline of Basic Terms and Related Information as a Study Aid (Minimum Knowledge)

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