Chapter 2 pt 1. Atoms, Molecules, and Life. Gregory Ahearn. John Crocker. Including the lecture Materials of

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1 Chapter 2 pt 1 Atoms, Molecules, and Life Including the lecture Materials of Gregory Ahearn University of North Florida with amendments and additions by John Crocker Copyright 2009 Pearson Education, Inc..

2 The main steps of the scientific method Feedback falsifiable Results does not support hypothesis; revise hypothesis or pose new one Question Research Hypothesis M & M/Data Results: Experiment or additional observation Results supports hypothesis; make additional predictions and test them

3 If a hypothesis is correct, when we test it, we can expect a particular outcome We try to disprove hypothesis. Control groups are tested along with experimental groups to provide a comparison of results

4 Snowberry fly mimicking a jumping spider Figure 1.3Cx

5 Pounce rate (% of trials in which spider jumped on fly) Case study: spider mimicry Control group (untreated flies) Figure 1.3D Experimental group (wing markings masked)

6 Biosphere Ecosystem -abiotic factors -all organisms Community Population Organism ECOSYSTEM LEVEL Eucalyptus forest COMMUNITY LEVEL All organisms in eucalyptus forest POPULATION LEVEL Group of flying foxes ORGANISM LEVEL Flying fox ORGAN SYSTEM LEVEL Nervous system ORGAN LEVEL Brain Brain Spinal cord Nerve TISSUE LEVEL Nervous tissue CELLULAR LEVEL Nerve cell MOLECULAR LEVEL Molecule of DNA Figure 1.1

7 Organisms are made up of: organ systems organs tissues cells molecules ECOSYSTEM LEVEL Eucalyptus forest COMMUNITY LEVEL All organisms in eucalyptus forest POPULATION LEVEL Group of flying foxes ORGANISM LEVEL Flying fox ORGAN SYSTEM LEVEL Nervous system ORGAN LEVEL Brain Brain Spinal cord Nerve TISSUE LEVEL Nervous tissue CELLULAR LEVEL Nerve cell MOLECULAR LEVEL Molecule of DNA Figure 1.1

8 Each level of organization builds on the one below it At each level, new properties emerge Biological function starts at the chemical level ATOMS AND MOLECULES

9 2.1 What Are Atoms? Elements: substances that cannot be broken down by ordinary chemical means (ex/ carbon) all atoms belong to one of 96 types of naturally occurring elements life requires about 25 of these elements

10 2.1 What Are Atoms? Atoms: basic structural unit of matter consist of charged particles protons (+) neutrons (0) electrons (-) smallest particle of an element each element has a unique number of protons (atomic number)

11 Atoms of the same element with different numbers of neutrons are called isotopes of the element. Some isotopes spontaneously break apart, forming different kinds of atoms and releasing energy in the process. Such isotopes are radioactive. Example: radioactive uranium isotopes decay and form lead in the process

12 Atoms are electrically neutral because they have and equal number of positive protons and negative electrons 2 Protons Nucleus 2 Neutrons 2 Electrons Helium atom

13 Electrons are arranged in shells Electrons orbit around atomic nuclei at specific distances called electron shells the outermost shell determines the chemical properties of an atom Outermost electron shell (can hold 8 electrons) Electron HYDROGEN (H) Atomic number = 1 First electron shell (can hold 2 electrons) CARBON (C) Atomic number = 6 NITROGEN (N) Atomic number = 7 OXYGEN (O) Atomic number = 8

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15 Electrons can move from electron shell to electron shell. Electrons move from an inner to an outer shell when absorbing energy. Electrons move from an outer shell to an inner shell when releasing energy. All life depends on this energy. 1 An electron absorbs energy 2 The energy boosts the electron to a higher-energy shell energy The electron drops back into lower-energy shell, releasing energy as light light +

16 Energy Capture and Release Life depends on electrons capturing and releasing energy Electron shells correspond to energy levels Energy exciting an atom causes an electron jump from a lower- to higher-energy shell Later, the electron falls back into its original shell, releasing the energy

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20 2.2 How Do Atoms Form Molecules? Molecules: two or more atoms of one or more elements held together by interactions among their outermost electron shells Atoms interact with one another according to two basic principles: An inert atom will not react with other atoms when its outermost electron shell is completely full or empty. A reactive atom will react with other atoms when its outermost electron shell is only partially full.

21 Atoms Interact Atoms will react with other atoms if the outermost shell is partially full (such atoms considered reactive) Example: Oxygen, with 6 electrons in outermost shell (can hold 2 more electrons)

22 Atoms Interact Reactive atoms gain stability by electron interactions (chemical reactions) Electrons can be lost to empty the outermost shell Electrons can be gained to fill the outermost shell Electrons can be shared with another atom where both atoms have full outermost shells

23 Atoms Interact Hydrogen and oxygen atoms gain stability by interacting with each other Single electrons from each of two hydrogen molecules fill the outer shell of an oxygen atom

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25 Atoms combine with each other to fill outer electron shells (e.g. hydrogen and oxygen have unfilled outer electron shells, and thus, can combine to form the water molecule). The water molecule, with a filled outer electron shell, is more stable than either the hydrogen or oxygen atoms that gave rise to it. The results of losing, gaining, or sharing electrons are chemical bonds attractive forces that hold atoms together in molecules.

26 2.2 How Do Atoms Form Molecules? A molecule may be depicted in different ways. H H H H H C C C C H H H H O H (a) All bonds shown CH3 CH2 CH2 CH2 OH (b) Bonds within common groups omitted OH (c) Carbons and their attached hydrogens omitted (d) Overall shape depicted Fig. 2-4

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28 Types of bonds Ionic bonds: formed by passing an electron from one atom to another One partner becomes positive, the other negative, and they attract one another. Na+ + Cl becomes NaCl (sodium chloride) Positively or negatively charged atoms are called ions. + cation - anion

29 Ions and Ionic Bonds Atoms that have lost electrons become positively charged ions (e.g. sodium: Na+) Atoms that have gained electrons become negatively charged ions (e.g. chlorine: Cl-) Oppositely charged ions are attracted to each other are bound into a molecule by ionic bonds

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31 Ions and Ionic Bonds Salt crystals are repeated, orderly arranged sodium and chloride ions

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34 Types of bonds (continued) Covalent bonds: bond between two atoms that share electrons in their outer electron shell For example, an H atom can become stable by sharing its electron with another H atom, forming H2 gas.

35 Covalent Bonds Atoms with partially full outer electron shells can share electrons Two electrons (one from each atom) are shared in a covalent bond

36 Covalent Bonds Covalent bonds are found in H2 (single bond), O2 (double bond), N2 (triple bond) and H2O Covalent bonds are stronger than ionic bonds but vary in their stability

37 Covalent Bonds Most biological molecules contain covalent bonds

38 Covalent bonds produce either nonpolar or polar molecules. Nonpolar molecule: atoms in a molecule equally share electrons that spend equal time around each atom, producing a nonpolar covalent bond

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40 Nonpolar covalent bonding in hydrogen Same charge on both nuclei + (uncharged) + Electrons spend equal time near each nucleus (a) Nonpolar covalent bonding in hydrogen Fig. 2-6a

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42 Polar Covalent Bonds Atoms within a molecule may have different nuclear charges Those atoms with greater positive nuclear charge pull more strongly on electrons in a covalent bond

43 Polar Covalent Bonds In diatomic molecules like H2, both atoms exert the same pulling force on bond electrons: the covalent bond is nonpolar

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45 Polar Covalent Bonds In molecules where atoms of different elements are involved (H2O), the electrons are not always equally shared: these covalent bonds are polar

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47 Polar Covalent Bonds A molecule with polar bonds may be polar overall H2O is a polar molecule The (slightly) positively charged pole is around each hydrogen The (slightly) negatively charged pole is around the oxygen

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50 Types of bonds (continued) Hydrogen bonds: weak electrical attraction between positive and negative parts of polar molecules Example: the negative charge of oxygen atoms in water molecules attract the positive charge of hydrogen atoms in other water molecules

51 Hydrogen Bonds Polar molecules like water have partially charged atoms at their ends Hydrogen bonds form when partial opposite charges in different molecules attract each other The partially positive hydrogens of one water molecule are attracted to the partially negative oxygen on another

52 Hydrogen Bonds Polar biological molecules can form hydrogen bonds with water, each other, or even within the same molecule Hydrogen bonds are rather weak but can collectively be quite strong

53 Hydrogen bonds H (+) H (+) H (+) O ( ) H (+) O ( ) hydrogen bonds Fig. 2-7

54 2.2 How Do Atoms Form Molecules?

55 Free Radicals Some cellular reactions produce free radicals Free radical: a molecule whose atoms have one or more unpaired electrons in their outer shells

56 Free Radicals Free radicals are highly unstable and reactive Free radicals steal electrons, destroying other molecules Cell death can occur from free radical attack

57 Free Radicals Free radicals are involved in causing heart disease, Alzheimer s, cancer, and aging Antioxidants like vitamins C and E render free radicals harmless