Related Textbook Readings:
-
For General Biology (BIO 1114) Class only: Johnson and Losos (2008) Chapter 3 and Chapter 4
-
For General Zoology (Z00 1114) Class only : Hickman, et al. (2006) Chapter 2 (all) and Chapter 5 starting with "Gene Theory" and stopping before "DNA Coding"
- IMPORTANT NOTE FOR GENERAL ZOOLOGY STUDENTS. Your textbook authors presume your high school background has prepared you with sound knowledge of simple middle school and/or high school level introductory level chemistry. Therefore, they do not include this review material in your textbook. You must know introductory basic chemistry including such things as elements, bonds, compounds, acids/bases, etc. I must also assume that you know this material, and it will be covered on your exam. However, if you do not, or you just need a review, I will provide you with reading sources, video tape presentations, and computer-assisted learning resources. Examine the general objectives for this unit above to determine whether you feel you have that background knowledge or need further review. Please make no mistake by underestimating how important this knowledge is in your educaiton.
Basic Structure of Matter
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.
| Table 3.2-1. 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.
Reminder about Textbook Study
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. (For general zoology students only, recall that you must know the basic chemistry that is the basis for understanding chemistry of life. That material, as previously mentioned, is available for you to study outside of class. It will be included on the lecture exam, so be sure to check the general objectives at the start of these Notes on the Web to make sure you know these materials.)
The "Testing Yourself" questions will be helpful for general biology students, although many more detailed questions will be included in the lecture exam. Similarly, study questions in the zoology textbook will be helpful review for general zoology students, but again, they are not comprehensive.
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.
An In-class or Lab Day Exercise.
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).
Alpha-ringed glucose
Link to Dynamic Graphics Site for DNA
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.
An Interactive Animated Nonlinear Tutorial by Eric Martz
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.
- If you are using your home computer, here is a link to MDL Information Systems, Inc. where you can download Chime. Just follow the instructions there and then come back to the tutorial webpage. Note, you may have to close your browser and reopen it after you download Chime.
- At college, you may use the Murray State College
computers in the Library/Science Building at the following location:
- Room LS 119
- A part of our legal agreement requires
that you read the following "Chemscape
Chime Network License Agreement":
- Chemscape Chime is owned by MDL Information Systems, Inc. and is protected by United States and international copyright and other intellectual property laws. Your use of Chemscape Chime is governed by the terms of MDL's End User License Agreement for Chemscape Chime. By using Chemscape Chime, you indicate that you have read MDL's End User License Agreement for Chemscape Chime and agree to be bound by its terms and conditions.
- If the computer you use in LS 119 has not yet had Chemscape Chime installed, please ask me for an "Installation Instructions for Chemscape Chime" sheet that is written specifically for the college network.
Links to Relevant Websites with Tutorials and/or Self-study Questions
Radioactive Isotope Dating Techniques
Visit the web site at the following link and complete the tutorials and on a) the virtual isochron dating of rocks and minerals and b) the virtual radiocarbon dating of carbon remains of formerly living things.
