Biology
Chapter 2:1-9 The Chemical Basis of Life - Atoms and Reactions
Homework
Biology Homework Chapter 2: Atoms and Molecules
Homework
- Reading Preparation
- WebLecture
- Study Activity
- Preparation work for chat
- Online Quiz
- Lab Instructions
Reading Preparation
Textbook assignment: Chapter 2: The Chemical Basis of Life, sections 1-9.
Study Notes
- 2.1 The holistic approach looks at the big picture and the reductionist approach breaks things down into components to simplify analysis. We start with a reductionist approach. On the assumption that all matter (anything with mass and volume) is made of atoms arranged in molecules, and changes to matter (such as the growth and reproduction that are characteristics of living things) involve changes in that arrangement, we should be able to explain life functions in terms of physical change (change of state from solid to liquid to gas) in the 25 or types of matter (elements) that make up organic molecules. Molecules that contain more than one type of atom are compounds. There are diatomic molecules such as H2 that are not compounds, even though they have more than one atom, because the atoms are from the same element.
- 2.2 Trace elements are present in very small quantities, abut are essential to health, and are often part of minerals or vitamins that make certain chemical reactions possible.
- 2.3 All atoms are made of the same types of components: positively charged and massive protons, uncharged and massive neutrons, negatively charged and very light electrons, and hundreds of subatomic particles we don't have to worry about in this class. They vary because of differences in the number of protons (determines element) and electrons (determines charge) and neutrons (determines isotope mass). Be sure to read the Weblecture and do the My Biology exercises until you have these differences mastered.
- 2.4 Not all atomic arrangements are stable (at the lowest possible energy level). Unstable atoms break down, throwing out part of the nucleus, in a process called radioactivity. Since this activity emits energy in forms that can be detected, radioactive versions of elements common to organic processes can be used to trace the flow of those elements in a chemical reaction, or even in a human body.
- 2.5 Atoms can only combine with one another by changing their electron arrangement, so the organization of electrons in shells around the outside of the atom is crucial to determining what kinds of compounds the atoms of a particular element can form.
- 2.6 Some arrangements of electrons in shells are more stable than others. Covalent bonds occur when atoms of the same or different elements share electrons in order to "fill up" their outer shells and reach a higher level of stability.
- 2.7 Ionic bonds occur when one atom swipes the electrons from the atom of another element. Each atom then has an electric charge: the one with extra electrons is negative, the one with fewer electrons than protons is positive. Since these opposite charges attract, the atoms are held together. Can ionic bonds occur between atoms of the same element?
- 2.8 In particular, when hydrogen combines with oxygen, nitrogen, or fluorine, the single electron of the hydrogen spends most of its time around the other atom, leaving the hydrogen's positively charged proton nucleus bare. In other elements in polar bonds, some of the positive charge of the nucleus will be shielded by the remaining electrons. The exposed hydrogen nucleus forms hydrogen bonds that are than other types of non-ionic polar bonds, which is why it is so important.
- 2.9 A chemical reaction is any process where atoms rearrange their bonds to form new associations. These reactions can combine individual atoms into a new molecule (synthesis), break apart molecules into individual atoms (dissociation), or rearrange atoms from one molecular set to another molecular set (rearrangement). Notice in the two formulae given as examples of chemical reaction that the number and types of atoms is preserved. In the formation of glucose from carbon dioxide and water, there are as many carbon atoms in the products as there were in the reactants. Chemical reactions can only rearrange atoms; they can never change an atom from one element to another (radioactivity does that). But this gives us an advantage when figuring out what is going on in a chemical reaction. If we can account for all the atoms that went into the reaction, we're done.
Web Lecture
Read the following weblecture before chat: The Chemical Basis of Life: Atoms
Take notes on any questions you have, and be prepared to discuss the lecture in chat.
Study Activity
Use the PhET molecular polarity simulation to explore how an atom's electronegativity (attraction for electrons) can change the nature of a chemical bond.
- In the Two Atoms simulation,
- Set the electronegativities for Atom A and Atom B equal (half way between less and more) and note there is no dipole.
- Change Atom A to the least electronegative, and Atom B to the most. The dipole arrow should appear pointing toward the greatest electronegativity. What happens to the dipole arrow as you change these values?
- Reset to neutral (central) electronegativities and display partial charges, then vary the electronegativity values again. What happens to the partial charges?
- Reset and display the bond characters. What happens to the bond characters as you change the electronegativities?
- Reset and display the electrostatic potential. What happens to the location and intensity of the positive and negative zones of the molecule as you change the electronegativity of each atom?
- Reset and display the electron density (the likelihood that electrons are in a particular region). How does the location of electrons change when you change the electronegativity of an atom?
- What happens when you put either of these two molecules in an electric field?
- Play with the Three Atoms simulation in a similar way.
- Think about the implications for a water molecule (B atom high electronegativity, A and C atoms low electronegativity, A and C at an angle to B).
- Display the electric field and observe how it changes if you increase the electronegativity of one of the A or C atoms.
- Set the conditions for carbon dioxide (low B electronegativity, high A and C electronegativity, A-B-C in a straight line) and observe the differences in electrical fields. Is the overall CO2 molecule polar the way the water molecule is?
Optional External Web site reading: The University of North Carolina Chemistry Department has a public tutorial on →atoms← that you may find interesting.
Chat Preparation Activities
- Essay question: The Moodle forum for the session will assign a specific study question for you to prepare for chat. You need to read this question and post your answer before chat starts for this session.
- Mastery Exercise: The Moodle Mastery exercise for the chapter will contain sections related to our chat topic. Try to complete these before the chat starts, so that you can ask questions.
Chapter Quiz
- No quiz yet: the Chapter Quiz opens when we finish the chapter.
Lab Work
Read through the lab for this week; bring questions to chat on any aspect of the lab, whether you intend not perform it or not. If you decide to perform the lab, be sure to submit your report by the posted due date.
- Lab Instructions: Water
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