LS 204 Chapt. 4 Chemistry Biology is the study of living things, which involves chemical reactions (metabolism) Organisms are composed of macromolecules, molecules and atoms, which is Chemistry Knowledge of Chemistry is essential to understand Biology

Biological Hierarchy of Organisms Classification system to organize ** Fig. 4.1 Study biology to learn about all forms of life – including yourself  Level Subdisciplines Biosphere ecology Ecosystem ecology Community ecology Population population genetics, evolution, paleontology Organism anatomy & physiology Organ system anatomy & physiology Organ anatomy & physiology Tissue cell biology, microbiology, molecular genetics Cell cell biology, microbiology, molecular genetics Organelle cell biology, microbiology, molecular genetics Macromolecule/ molecule chemistry, biochemistry Atom chemistry

Hierarchy of life see Fig. 4.1

Goals Chapter 4 Chemistry Compare and contrast different states of matter Describe atomic structure Demonstrate use of the Periodic Table of Elements Explain ionic, covalent, and hydrogen bonding Describe polar molecules; their unique characteristics Discuss organic molecules, chemical reactions

Your starting point The most basic unit of a chemical substance is ___ Matter is defined as anything that _____ What are the three states of matter? _____ What are the 3 most common subatomic particles? Which subatomic particles interact during chemical reactions? What is the molecular formula for water? What are 3 common types of chemical bonds? What happens in anabolic reactions? What is meant by organic molecules? Are proteins organic or inorganic?

What is matter? Matter is ‘stuff’ which has mass (or weight) and takes up space. Mass is actual physical amount, whereas weight includes force of gravity. Three states of matter: solid, liquid, gas. Example for water: ice water steam/ vapor

Elements: The most basic chemical substances. Ex. iron, oxygen, carbon, helium. Some elements are pure; some function combined with others. Living organisms require about 20 elements: 95% of body is carbon, hydrogen, oxygen, nitrogen (C, H, O, N). 70% of the body is molecule water (H2O) Table 4.3 shows symbols for different elements (C = carbon; Na = sodium (natrium))

2. Atomic structure Atom = smallest complete unit of an element. Molecule = 2 or more atoms joined together (water = H2O) Macromolecule is bigger, more complex (a protein, carbohydrate)

Atomic structure Atoms contain subatomic particles: proton, neutron, electron are most important. Nucleus = middle of atom and contains protons (p+, positively charged) neutrons (n, neutral). Electrons (e-) are very tiny, negatively charged; move around the nucleus. Fig. 4.2 An atom is electrically neutral: the number of electrons = number of protons.

Electrons Electrons are negatively charged Electrons move in orbitals, multiple paths with different energy levels (shells): 1st shell can have only 2 e- and is closest to nucleus. 2nd shell can have 8 e- 3rd shell also can have 8 e- (gets more complex)

Atomic number Atomic number is unique for each element = number of protons (and number of electrons): Ex. H = 1; C = 6, O = 8 Question: Nitrogen has atomic number of 7: how many protons? how many electrons?

Atomic weight or mass Atomic weight and mass almost same = weight of 1 atom. 1 atomic mass unit (1 u) = the mass or weight of 1 proton; (1 neutron weighs the same), Weight of an electron is so tiny as to not be counted. Therefore, the atomic weight of an element = number of protons plus number of neutrons. All atoms of an element have the same atomic number (ex. C = 6). Different isotopes can have different numbers of neutrons, and atomic weights: Regular C = C12 = weight of 12 (has 6 neutrons); radioactive C14 has weight of 14 (8 neutrons)

3. Periodic table of elements (Fig. 4.3) Focus on the first 3 rows, main elements for biology. (handout has names of elements in addition to abbreviations) Table is a specific arrangement which helps understand chemical properties of atoms. H (1 proton), Helium (He) has 2 protons and 2 neutrons. Fig. 4.3 Oxygen has atomic number of 8 -> 2 electrons in 1st shell, 6 in outer shell. Rows = periods, represent the different shells: 1st (2 e-), 2nd (8 e-), 3rd (8 e-). Columns = groups; elements that share the same number of e- in the outermost shell, (and properties)

Hierarchy of life

4. Chemical interactions Electrons in atom’s outermost shell determine the reactivity of the element. Chemical bonding: two or more atoms join together to form molecules. Valency shell is the outermost e- shell: If shell is full, the atom is stable or inert (He has 2, Ne has 8, Ar has 8). These atoms do not usually enter into chemical reactions. If outer shell is not full, atom ‘wants’ to make that shell full; gains or loses or shares electrons with other atoms.

Ionic bonding ions have permanently gained or lost an e-; they are not electrically neutral. Na+ is sodium that has lost the 1 e- in its outermost shell. Cl- is chlorine that has gained 1 e- to add to the 7 it had for a full outermost shell. Two ions bond together to form NaCl = salt.

Covalent bonding is sharing electrons. H2 = hydrogen gas (H-H); each has 1 e- in outer shell, and ‘wants’ 2; sharing, each nucleus of 1 p+ has 2 e- part of the time. O2 = oxygen gas (O:O); each atom wants 2 e- to fill its outer shell (has 6); by sharing 2 e-, they each have full outer shell; this double sharing is called a double bond. H2O = water (H-O-H); O wants two e-, and shares 1 e- each with 2 different H atoms.

Hydrogen bonding is weak bonds Sharing between an H in 1 molecule and atom in another: important for biological molecules and macromolecules. O does not share fairly in H2O; it is big and tends to keep the e- near its nucleus. The O is more negative (d-) and the H is more positive (d+). Polarity (Fig. 4.9). Water molecules line up with the little + of one water with the little – of another.

hydrophilic = polar solutions (water) “water-loving” hydrophobic = nonpolar solutions (oil, hydrocarbons). ‘water-hating’

Molecules and compounds. Molecule = two or more atoms binding together: If two of the same element (O) -> a molecule of O2. If different elements H and O = a compound and a new name (ex. H2O is water). Molecular formula tells what atoms and how many are in a molecule: CO2 = carbon dioxide Structural formula is diagram of how atoms are joined – which ones together (Fig. 4.10). Important for understanding properties of complex molecules; example of 3 sugars different properties. C6H12O6 for glucose, fructose, galactose

Structural formulas of sugars C6H12O6 for glucose, fructose, galactose glucose galactose fructose

5. Chemical reactions Breaking and remaking covalent bonds is the basis of metabolism. Organic compounds contain C and H (and others): Carbon-based life form: Most macromolecules of animals, plants. Carbohydrates (CHO), proteins (also have S and N), lipids, nucleic acids (have N, P). Inorganic compounds do not have both C and H: ex. CO2, HCl; Fe(OH)3

5. Chemical reactions Energy from breaking down macromolecules of food and use it to make new molecules. Enzymes do the reactions Chemical equations: reactants -> products; some reactions are reversible. Anabolic reactions = synthesis; molecules -> macromolecules Catabolic reactions = decomposition; breakdown, digestion of macromolecules. Exchange reactions swap pieces: AB + CD -> AC + BD example.

Review questions Which subatomic particles are always in the nucleus? Which subatomic particles are not included in atomic mass? What is the difference between ionic and covalent bond? For oxygen, write the number of protons ___ and electrons ____ How many electrons in the outer shell of iodine?