Molecules of Life Chapter 2 Part 1

2.1 Impacts/Issues Fear of Frying All living things consist of the same kinds of molecules, but small differences in the ways they are put together have big effects on health Artificial trans fats found in manufactured and fast foods raise cholesterol and increase risk of atherosclerosis, heart attack, and diabetes

Video: Fear of frying

Fear of Frying Trans fats are made by adding hydrogen atoms to liquid vegetable oils

trans fatty acid Figure 2.1 Trans fats. Left, the particular arrangement of hydrogen atoms around two carbon atoms (yellow box) makes a trans fat very unhealthy as a food. Right, french fries and other fast foods are often cooked with trans fats. Fig. 2-1, p. 20

2.2 Start With Atoms All substances consist of atoms Atom Fundamental building-block particle of matter Life’s unique characteristics start with the properties of different atoms

Subatomic Particles and Their Charge Atoms consist of electrons moving around a nucleus of protons and neutrons Electron (e-) Negatively charged subatomic particle that occupies orbitals around the atomic nucleus Charge Electrical property of some subatomic particles Opposite charges attract; like charges repel

Subatomic Particles in the Nucleus Core of an atom, occupied by protons and neutrons Proton (p+) Positively charged subatomic particle found in the nucleus of all atoms Neutron Uncharged subatomic particle found in the atomic nucleus

An Atom

an atom Figure 2.2 Atoms consist of electrons moving around a core, or nucleus, of protons and neutrons. Models cannot show what atoms really look like. Electrons zoom around in fuzzy, three-dimensional spaces about 10,000 times bigger than a nucleus. Fig. 2-2a, p. 21

Elements: Different Types of Atoms Atoms differ in numbers of subatomic particles Element A pure substance that consists only of atoms with the same number of protons Atomic number Number of protons in the atomic nucleus Determines the element

Elements in Living Things The proportions of different elements differ between living and nonliving things Some atoms, such as carbon, are found in greater proportions in molecules made only by living things – the molecules of life

Same Elements, Different Forms Isotopes Forms of an element that differ in the number of neutrons their atoms carry Changes the mass number, but not the charge Mass number Total number of protons and neutrons in the nucleus of an element’s atoms

Radioactive Isotopes Radioisotope Radioactive decay Isotope with an unstable nucleus, such as carbon 14 (14C) Radioactive decay Process by which atoms of a radioisotope spontaneously emit energy and subatomic particles when their nucleus disintegrates

Carbon 14: A Radioisotope Most carbon atoms have 6 protons and 6 neutrons (12C) Carbon 14 (14C) is a radioisotope with six protons and eight neutrons When 14C decays, one neutron splits into a proton and an electron, and the atom becomes a different element – nitrogen 14 (14N)

Radioactive Tracers Researchers introduce radioisotope tracers into living organisms to study the way they move through a system Tracers Molecules with a detectable substance attached, often a radioisotope Used in research and clinical testing

Why Electrons Matter Electrons travel around the nucleus in different orbitals (shells) – atoms with vacancies in their outer shells tend to interact with other atoms Atoms get rid of vacancies by gaining or losing electrons, or sharing electrons with other atoms Shell model Model of electron distribution in an atom

Shell Models

Figure 2.3: Animated! Shell models. Each circle (shell) represents all orbitals at one energy level. Atoms with vacancies in their outermost shell can interact with other atoms. Fig. 2-3 (top), p. 22

Figure 2.3: Animated! Shell models. Each circle (shell) represents all orbitals at one energy level. Atoms with vacancies in their outermost shell can interact with other atoms. Fig. 2-3 (a-c), p. 22

1 proton 1 2 1 electron first shell hydrogen (H) helium (He) 6 8 10 second shell carbon (C) oxygen (O) neon (Ne) Figure 2.3: Animated! Shell models. Each circle (shell) represents all orbitals at one energy level. Atoms with vacancies in their outermost shell can interact with other atoms. 11 17 18 third shell sodium (Na) chlorine (Cl) argon (Ar) Fig. 2-3 (a-c), p. 22

1 proton 1 2 1 electron first shell hydrogen (H) helium (He) A) The first shell corresponds to the first energy level, and it can hold up to 2 electrons. Hydrogen has one proton, so it has one vacancy. A helium atom has 2 protons, and no vacancies. The number of protons in each shell model is shown. 6 8 10 second shell carbon (C) oxygen (O) neon (Ne) B) The second shell corresponds to the second energy level, and it can hold up to 8 electrons. Carbon has 6 protons, so its first shell is full. Its second shell has 4 electrons, and four vacancies. Oxygen has 8 protons and two vacancies. Neon has 10 protons and no vacancies. 11 17 18 third shell sodium (Na) chlorine (Cl) argon (Ar) C) The third shell, which corresponds to the third energy level, can hold up to 8 electrons, for a total of 18. A sodium atom has 11 protons, so its first two shells are full; the third shell has one electron. Thus, sodium has seven vacancies. Chlorine has 17 protons and one vacancy. Argon has 18 protons and no vacancies. Figure 2.3: Animated! Shell models. Each circle (shell) represents all orbitals at one energy level. Atoms with vacancies in their outermost shell can interact with other atoms. Stepped Art Fig. 2-3 (a-c), p. 22

Animation: Shell models of common elements

Ions The negative charge of an electron balances the positive charge of a proton in the nucleus Changing the number of electrons may fill its outer shell, but changes the charge of the atom Ion Atom that carries a charge because it has an unequal number of protons and electrons

Ion Formation

electron gain Chlorine atom 17p+ 17 17e– charge: 0 Chloride ion 17 electron loss Sodium atom 11p+ Figure 2.4: Animated! Ion formation. (A) A sodium atom becomes a positively charged sodium ion (Na+) when it loses the electron in its third shell. The atom’s full second shell is now its outermost, so it has no vacancies. (B) A chlorine atom becomes a negatively charged chloride ion (Cl–) when it gains an electron and fills the vacancy in its third, outermost shell. 11 11e– charge: 0 Sodium ion 11 11p+ 10e– charge: +1 Fig. 2-4, p. 23

Figure 2.4: Animated! Ion formation. (A) A sodium atom becomes a positively charged sodium ion (Na+) when it loses the electron in its third shell. The atom’s full second shell is now its outermost, so it has no vacancies. (B) A chlorine atom becomes a negatively charged chloride ion (Cl–) when it gains an electron and fills the vacancy in its third, outermost shell. Fig. 2-4a, p. 23

electron gain Chlorine atom 17p+ 17 17e– charge: 0 Chloride ion 17p+ Figure 2.4: Animated! Ion formation. (A) A sodium atom becomes a positively charged sodium ion (Na+) when it loses the electron in its third shell. The atom’s full second shell is now its outermost, so it has no vacancies. (B) A chlorine atom becomes a negatively charged chloride ion (Cl–) when it gains an electron and fills the vacancy in its third, outermost shell. 17p+ 17 18e– charge: –1 Fig. 2-4a, p. 23

Figure 2.4: Animated! Ion formation. (A) A sodium atom becomes a positively charged sodium ion (Na+) when it loses the electron in its third shell. The atom’s full second shell is now its outermost, so it has no vacancies. (B) A chlorine atom becomes a negatively charged chloride ion (Cl–) when it gains an electron and fills the vacancy in its third, outermost shell. Fig. 2-4b, p. 23

electron loss Sodium atom 11p+ 11 11e– charge: 0 Sodium ion 11 11p+ Figure 2.4: Animated! Ion formation. (A) A sodium atom becomes a positively charged sodium ion (Na+) when it loses the electron in its third shell. The atom’s full second shell is now its outermost, so it has no vacancies. (B) A chlorine atom becomes a negatively charged chloride ion (Cl–) when it gains an electron and fills the vacancy in its third, outermost shell. 11 11p+ 10e– charge: +1 Fig. 2-4b, p. 23

electron gain Chlorine atom 17p+ 17 17e– charge: 0 Chloride ion 17 electron loss Sodium ion 11p+ 11 charge: +1 10e– Sodium atom 11 11p+ 11e– charge: 0 Figure 2.4: Animated! Ion formation. (A) A sodium atom becomes a positively charged sodium ion (Na+) when it loses the electron in its third shell. The atom’s full second shell is now its outermost, so it has no vacancies. (B) A chlorine atom becomes a negatively charged chloride ion (Cl–) when it gains an electron and fills the vacancy in its third, outermost shell. Stepped Art Fig. 2-4, p. 23

Animation: How atoms bond

Animation: PET scan

Animation: The shell model of electron distribution

Animation: Subatomic particles

Animation: Atomic number, mass number

Animation: Electron arrangements in atoms

Animation: Isotopes of hydrogen

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Animation: Electron distribution

2.3 From Atoms to Molecules Atoms can also fill their vacancies by sharing electrons with other atoms A chemical bond forms when the electrons of two atoms interact Chemical bond An attractive force that arises between two atoms when their electrons interact

From Atoms to Molecules Group of two or more atoms joined by chemical bonds Compound Type of molecule that has atoms of more than one element

Referring to a Molecule

Same Materials, Different Results

Animation: Building blocks of life

Ionic Bonds and Covalent Bonds Depending on the atoms, a chemical bond may be ionic or covalent Ionic bond A strong mutual attraction formed between ions of opposite charge Covalent bond Two atoms sharing a pair of electrons

An Ionic Bond: Sodium Chloride

ionic bond 11 17 sodium ion (Na+) chloride ion (Cl–) p. 24

Covalent Bonds Molecular hydrogen (H—H) and molecular oxygen (O=O)

molecular hydrogen (H2) 1 1 molecular hydrogen (H2) 8 8 molecular oxygen (O2) p. 24

Polarity A covalent bond is nonpolar if electrons are shared equally, and polar if the sharing is unequal Polarity Any separation of charge into distinct positive and negative regions

Polar and Nonpolar Covalent Bonds Having an even distribution of charge When atoms in a covalent bond share electrons equally, the bond is nonpolar Polar Having an uneven distribution of charge When the atoms share electrons unequally, the bond is polar

Importance of Polar Molecules A water molecule (H-O-H) has two polar covalent bonds – the oxygen is slightly negative and the hydrogens are slightly positive – which allows water to form hydrogen bonds

p. 25

1 8 1 water (H2O) p. 25

Hydrogen Bonds Hydrogen bond Attraction that forms between a covalently bonded hydrogen atom and another atom taking part in a separate covalent bond

hydrogen bond p. 25

Importance of Hydrogen Bonds Hydrogen bonds form and break more easily than covalent or ionic bonds – they do not form molecules Hydrogen bonds impart unique properties to substances such as water, and hold molecules such as DNA in their characteristic shapes

Animation: Ionic bonding

Animation: Examples of hydrogen bonds

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Animation: Sucrose synthesis

Animation: Covalent bonds

2.4 Water All living organisms are mostly water, and all chemical reactions of life are carried out in water Hydrogen bonds between water molecules give water unique properties that make life possible Capacity to dissolve many substances Cohesion (surface tension) Temperature stability

Polarity and the Unique Properties of Water

Figure 2.7: Animated! Water. (A) Polarity of a water molecule: Each of the hydrogen atoms has a slight positive charge, and the oxygen atom has a slight negative charge. (B) The many hydrogen bonds (dashed lines) that keep water molecules clustered together impart special properties to liquid water. (C) Visible effect of cohesion: a wasp drinking (not sinking). Cohesion imparts surface tension to liquid water, which means that the surface of liquid water behaves a bit like a sheet of elastic. Fig. 2-7a, p. 26

slight negative charge Figure 2.7: Animated! Water. (A) Polarity of a water molecule: Each of the hydrogen atoms has a slight positive charge, and the oxygen atom has a slight negative charge. (B) The many hydrogen bonds (dashed lines) that keep water molecules clustered together impart special properties to liquid water. (C) Visible effect of cohesion: a wasp drinking (not sinking). Cohesion imparts surface tension to liquid water, which means that the surface of liquid water behaves a bit like a sheet of elastic. slight positive charge slight positive charge Fig. 2-7a, p. 26

Figure 2.7: Animated! Water. (A) Polarity of a water molecule: Each of the hydrogen atoms has a slight positive charge, and the oxygen atom has a slight negative charge. (B) The many hydrogen bonds (dashed lines) that keep water molecules clustered together impart special properties to liquid water. (C) Visible effect of cohesion: a wasp drinking (not sinking). Cohesion imparts surface tension to liquid water, which means that the surface of liquid water behaves a bit like a sheet of elastic. Fig. 2-7b, p. 26

Figure 2.7: Animated! Water. (A) Polarity of a water molecule: Each of the hydrogen atoms has a slight positive charge, and the oxygen atom has a slight negative charge. (B) The many hydrogen bonds (dashed lines) that keep water molecules clustered together impart special properties to liquid water. (C) Visible effect of cohesion: a wasp drinking (not sinking). Cohesion imparts surface tension to liquid water, which means that the surface of liquid water behaves a bit like a sheet of elastic. Fig. 2-7c, p. 26

Animation: Structure of water

Water and Solutions Polar water molecules hydrogen-bond to other polar (hydrophilic) substances, and repel nonpolar (hydrophobic) substances Hydrophilic (water-loving) A substance that dissolves easily in water Hydrophobic (water-dreading) A substance that resists dissolving in water

Water and Solutions Water is an excellent solvent Solvent Solute Liquid that can dissolve other substances Solute A dissolved substance

Water and Solutions Salts, sugars, and many polar molecules dissolve easily in water Salt Compound that dissolves easily in water and releases ions other than H+ and OH- Example: sodium chloride (NaCl)

Water and Solutions Water molecules surround the atoms of an ionic solid and pull them apart, dissolving it

Animation: Spheres of hydration

Temperature Stability Temperature stability is an important part of homeostasis Water absorbs more heat than other liquids before temperature rises Hydrogen bonds hold ice together in a rigid pattern that makes ice float Temperature Measure of molecular motion

Cohesion Cohesion helps sustain multicelled bodies and resists evaporation Cohesion Tendency of water molecules to stick together Evaporation Transition of liquid to gas Absorbs heat energy (cooling effect)

2.5 Acids and Bases Water molecules separate into hydrogen ions (H+) and hydroxide ions (OH-) pH A measure of the number of hydrogen ions (H+) in a solution The more hydrogen ions, the lower the pH Pure water has neutral pH (pH=7) Number of H+ ions = OH- ions

Acids and Bases Acid Base Substance that releases hydrogen ions in water pH less than 7 Base Substance that releases hydroxide ions (accepts hydrogen ions) in water pH greater than 7

A pH Scale

— 0 battery acid — 1 gastric fluid — 2 acid rain lemon juice cola more acidic vinegar — 3 orange juice tomatoes, wine — 4 bananas beer bread — 5 black coffee urine, tea, typical rain — 6 corn butter milk — 7 pure water blood, tears egg white — 8 seawater baking soda — 9 detergents Tums Figure 2.9: Animated! A pH scale. Here, red dots signify hydrogen ions (H+) and blue dots signify hydroxyl ions (OH–). Also shown are approximate pH values for some common solutions. This pH scale ranges from 0 (most acidic) to 14 (most basic). A change of one unit on the scale corresponds to a tenfold change in the amount of H+ ions. Figure It Out: What is the approximate pH of cola? Answer: 2.5. toothpaste — 10 hand soap milk of magnesia more basic — 11 household ammonia — 12 hair remover bleach — 13 oven cleaner — 14 drain cleaner Fig. 2-9, p. 27

Animation: The pH scale

Acid Rain Sulfur dioxide and other airborne pollutants dissolve in water vapor to form acid rain

Buffer Systems Most molecules of life work only within a narrow range of pH – essential for homeostasis Buffers keep solutions in cells and tissues within a consistent range of pH Buffer Set of chemicals that can keep the pH of a solution stable by alternately donating and accepting ions that contribute to pH

CO2 and the Bicarbonate Buffer System CO2 forms carbonic acid in water CO2 + H2O → H2CO3 (carbonic acid) Bicarbonate buffer system Excess H+ combines with bicarbonate H+ + HCO3- (bicarbonate) ↔ H2CO3

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3D Animation: Dissolution