It’s Alive! Marieb Chapter 2: Part A (Chemistry Comes Alive) Student Version © 2013 Pearson Education, Inc.

Major concepts in this chapter What are they? Energy vs. Matter Major concepts in this chapter What are they? How do they work in the body? Lets compare their properties: Energy Matter • - • © 2013 Pearson Education, Inc.

Matter—anything that has mass and occupies space 3 states of matter © 2013 Pearson Education, Inc.

Energy can be converted from Capacity to do work Types of energy —energy in action —stored (inactive) energy Energy can be converted from © 2013 Pearson Education, Inc.

Forms of Energy energy Stored in bonds of chemical substances Results from movement of charged particles Directly involved in moving matter Travels in waves (e.g., visible light, ultraviolet light, and x-rays) © 2013 Pearson Education, Inc.

Energy may be converted from one form to another Energy Conversions Energy may be converted from one form to another Energy conversion is inefficient Some energy is “lost” as heat (partly unusable energy) Gasoline is ___________ energy; we can only remove 8 - 10% of the available energy to do work Lance Armstrong’s muscles are 23% efficient © 2013 Pearson Education, Inc.

The Energy Name Game! A ? B ? © 2013 Pearson Education, Inc.

Name the Energy! © 2013 Pearson Education, Inc.

Potential vs Kinetic Energy … Ole! Video Potential vs Kinetic Energy … Ole! © 2013 Pearson Education, Inc.

Challenge Yourself! What Type of Energy? Potential or Kinetic? © 2013 Pearson Education, Inc.

Composition of Matter: Elements Matter is composed of elements Elements cannot be broken into simpler substances by ordinary chemical methods Each has its own unique properties © 2013 Pearson Education, Inc.

Composition of Matter Atoms Atomic symbol We will use the term atom rather than element Atomic symbol One- or two-letter chemical shorthand for each element © 2013 Pearson Education, Inc.

The Periodic Table Lanthanides Actinides © 2013 Pearson Education, Inc.

Major Elements of the Human Body Four elements make up ?% of body mass Element Carbon Hydrogen Oxygen Nitrogen Atomic symbol C H O N Know these symbols! © 2013 Pearson Education, Inc.

Lesser Elements of the Human Body 9 elements make up 3.9% of body mass Element Calcium Phosphorus Potassium Sulfur Sodium Chlorine Magnesium Iodine Iron Atomic symbol Ca P K S Na Cl Mg I Fe Yep, you need to know these too! © 2013 Pearson Education, Inc.

Trace Elements of the Human Body Occur in very minute amounts 11 elements make up < 0.01% of body mass Many are part of, or activate, enzymes For example: Element Chromium Copper Fluorine Manganese Silicon Zinc Atomic symbol Cr Cu F Mn Si Zn These are important but you won’t find them mentioned as often. Don’t worry about these symbols. © 2013 Pearson Education, Inc.

How Important Are These Elements? This is a generic form of _____________ © 2013 Pearson Education, Inc.

© 2013 Pearson Education, Inc. Table 2.1.1

© 2013 Pearson Education, Inc. Table 2.1.2

Atoms are composed of subatomic particles Atomic Structure Atoms are composed of subatomic particles Protons and neutrons are in the nucleus Electrons orbit the nucleus in an electron cloud © 2013 Pearson Education, Inc.

Atomic Structure: The Nucleus Almost entire mass of the atom Neutrons Carry no charge (Neutral!) Protons Carry positive charge Mass = 1 amu © 2013 Pearson Education, Inc.

Atomic Structure: Electrons Electrons in orbitals within electron cloud Circle outside the nucleus Carry negative charge Much smaller than protons or neutrons Number of protons and electrons are always equal © 2013 Pearson Education, Inc.

Figure 2.1 Two models of the structure of an atom. Nucleus Nucleus Helium atom Helium atom 2 protons (p+) 2 protons (p+) 2 neutrons (n0) 2 neutrons (n0) 2 electrons (e–) 2 electrons (e–) Planetary model Orbital model Proton Neutron Electron Electron cloud © 2013 Pearson Education, Inc.

Different atoms contain different numbers of subatomic particles Identifying Elements Different atoms contain different numbers of subatomic particles Hydrogen has 1 proton, 0 neutrons, and 1 electron Lithium has 3 protons, 4 neutrons, and 3 electrons © 2013 Pearson Education, Inc.

Figure 2.2 Atomic structure of the three smallest atoms. Proton Neutron Electron Hydrogen (H) (1p+; 0n0; 1e–) Helium (He) (2p+; 2n0; 2e–) Lithium (Li) (3p+; 4n0; 3e–) © 2013 Pearson Education, Inc.

Combining Matter: Forming Molecules Most atoms chemically combined with other atoms to form molecules Molecule Two or more atoms bonded together (e.g., H2 or C6H12O6) © 2013 Pearson Education, Inc.

Most matter exists as mixtures Three types of mixtures Two or more components physically intermixed Three types of mixtures Solutions Colloids Suspensions © 2013 Pearson Education, Inc.

Types of Mixtures: Solutions Homogeneous mixtures Most are true solutions in body Gases, liquids, or solids dissolved in water Usually transparent, e.g., atmospheric air or salt solution Solvent Usually a liquid; usually water Solute(s) For example: If glucose is dissolved in blood, glucose is the ; blood is the © 2013 Pearson Education, Inc.

How Do We Make Solutions? Can be expressed as Percent of solute in total solution (solvent assumed to be water) Parts solute per 100 parts solvent Milligrams per deciliter (mg/dl) (weight per volume) Molarity, or moles per liter (M) 1 mole of an element or compound = Its atomic or molecular weight (sum of atomic weights) in grams 1 mole of any substance contains 6.02  1023 molecules of that substance (Avogadro’s number) © 2013 Pearson Education, Inc.

Colloids and Suspensions Colloids (also called emulsions) Heterogeneous mixtures, e.g., cytosol Large solute particles do not settle out Suspensions Heterogeneous mixtures Large, visible solutes settle out © 2013 Pearson Education, Inc.

Figure 2.4 The three basic types of mixtures Solution Colloid Suspension Solute particles are larger than in a solution and scatter light; do not settle out. Solute particles are very large, settle out, and may scatter light. Solute particles are very tiny, do not settle out or scatter light. Solute particles Solute particles Solute particles Example Example Jello Whole Blood Example Mineral water Plasma Settled red blood cells Unsettled Settled © 2013 Pearson Education, Inc.

What About Those Electrons? Electrons have potential energy Each shell corresponds to a specific level of potential energy Shells that are farther from the nucleus contain electrons with more potential energy Up to seven electron shells (energy levels) can exist Atoms are most stable when their outermost (valence) shell is full Atoms will interact with other atoms to fill their outermost shells (via chemical bonds) Octet rule (rule of eights) Except for the first shell (full with two electrons) atoms interact to have eight electrons in their valence shell © 2013 Pearson Education, Inc.

Chemically Inert Elements Valence shell fully occupied or contains eight electrons Stable and unreactive because of this The “loners” © 2013 Pearson Education, Inc.

Figure 2.5a Chemically inert and reactive elements. Chemically inert elements Outermost energy level (valence shell) complete 8e 2e 2e Helium (He) (2p+; 2n0; 2e–) Neon (Ne) (10p+; 10n0; 10e–) © 2013 Pearson Education, Inc.

Chemically Reactive Elements Outer shell not full Tend to gain, lose, or share electrons (form bonds) with other atoms to achieve stability The “party animals” - like to interact with other atoms © 2013 Pearson Education, Inc.

Figure 2.5b Chemically inert and reactive elements. Chemically reactive elements Outermost energy level (valence shell) incomplete 4e 1e 2e Hydrogen (H) (1p+; 0n0; 1e–) Carbon (C) (6p+; 6n0; 6e–) 1e 6e 8e 2e 2e Oxygen (O) (8p+; 8n0; 8e–) Sodium (Na) (11p+; 12n0; 11e–) © 2013 Pearson Education, Inc.

Types of Chemical Bonds We will discuss three major types: © 2013 Pearson Education, Inc.

Attraction of opposite charges results in an ionic bond Ionic Bonds Ions are formed An atom gains or loses electrons and becomes charged The transfer of valence shell electrons from one atom to another forms ions One becomes an anion (negative charge) Atom that gained one or more electrons One becomes a cation (positive charge) Atom that lost one or more electrons Attraction of opposite charges results in an ionic bond © 2013 Pearson Education, Inc.

Figure 2.6a–b Formation of an ionic bond. (17p+; 18n0; 18e–)) (11p+; 12n0; 10e–)) — + Sodium atom (Na) (11p+; 12n0; 11e–) Chlorine atom (Cl) (17p+; 18n0; 17e–) Sodium ion (Na+) Chloride ion (Cl–) Sodium chloride (NaCl) Sodium gains stability by losing one electron, and chlorine becomes stable by gaining one electron. After electron transfer, the oppositely charged ions formed attract each other. © 2013 Pearson Education, Inc.

Most ionic compounds are salts When dry, salts form crystals instead of individual molecules Example is NaCl (sodium chloride) © 2013 Pearson Education, Inc.

Figure 2.6c Formation of an ionic bond. Cl– Na+ Large numbers of Na+ and Cl– ions associate to form salt (NaCl) crystals. © 2013 Pearson Education, Inc.

Do Salts Exist In the Body? Rarely, because most dissolve in water! Most ionic bonds are easily broken by water; ions are released Their ions do exist in the body = Exceptions: Calcium phosphate in bone Kidney stones (ouch!) Gall stones (also ouch!) © 2013 Pearson Education, Inc.

most salt crystals dissolve in water Ionic Bonds are Weak - most salt crystals dissolve in water © 2013 Pearson Education, Inc. Figure 2.12

Common Ions You Need To Know OH- Hydroxide PO43- Phosphate HCO3- Bicarbonate NH4+ Ammonium H+ Hydrogen (proton) Na+ Sodium K+ Potassium Ca2+ Calcium Cl- Chloride I- Iodide COO- Carboxyl © 2013 Pearson Education, Inc.

Formed by of two or more valence shell electrons Covalent Bonds Formed by of two or more valence shell electrons Allows each atom to fill its valence shell at least part of the time © 2013 Pearson Education, Inc.

Figure 2.7a Formation of covalent bonds. Reacting atoms Resulting molecules + or Structural formula shows single bonds. Hydrogen atoms Carbon atom Molecule of methane gas (CH4) Formation of four single covalent bonds: Carbon shares four electron pairs with four hydrogen atoms. © 2013 Pearson Education, Inc.

Figure 2.7b Formation of covalent bonds. Reacting atoms Resulting molecules + or Structural formula shows double bond. Oxygen atom Oxygen atom Molecule of oxygen gas (O2) Formation of a double covalent bond: Two oxygen atoms share two electron pairs. © 2013 Pearson Education, Inc.

Figure 2.7c Formation of covalent bonds. Reacting atoms Resulting molecules + or Structural formula shows triple bond. Nitrogen atom Nitrogen atom Molecule of nitrogen gas (N2) Formation of a triple covalent bond: Two nitrogen atoms share three electron pairs. © 2013 Pearson Education, Inc.

Two Different Types of Covalent Bonds Non-polar Covalent bonds Electrons equally shared Polar Covalent Bonds Electrons UNequally shared Come in single, double, or triple forms More lines means more electrons shared © 2013 Pearson Education, Inc.

Single, Double, and Triple Covalent Bonds © 2013 Pearson Education, Inc.

Chemical and Structural Formulas C2H5OH Chemical Formula (chemist’s shorthand) Structural Formula Sometimes you only see the “skeleton” of a molecule! © 2013 Pearson Education, Inc.

What Do I Mean? © 2013 Pearson Education, Inc.

More “Shorthand” - The Missing Atoms © 2013 Pearson Education, Inc.

More “Shorthand” - The Missing Atoms This is Cholesterol © 2013 Pearson Education, Inc.

Here Are The Missing Atoms! © 2013 Pearson Education, Inc.

Nonpolar Covalent Bonds Electrons shared equally Which bonds are nonpolar? C - C C - H If we have a lot of these bonds in a biological molecule, the molecule is non-polar (Most lipids= fats!) It would be oily, greasy, and hate water (hydrophobic = ) © 2013 Pearson Education, Inc.

Polar Covalent Bonds Unequal sharing of electrons produces polar bonds Examples of polar covalent bonds: C - O N - H O - O N - O O - H A molecule with lots of polar covalent bonds loves to interact with the polar covalent bonds in water Hydrophilic = Most biological molecules are polar. Carbohydrates • Some lipids Proteins Nucleic acids © 2013 Pearson Education, Inc.

Water Is A Polar Molecule δ– δ– δ+ δ+ δ+ δ+ V-shaped water (H2O) molecules have two poles of charge—a slightly more negative oxygen end (δ–) and a slightly more positive hydrogen end (δ+). © 2013 Pearson Education, Inc.

Figure 2.9 Ionic, polar covalent, and nonpolar covalent bonds compared. Ionic bond Polar covalent bond Nonpolar covalent bond Complete transfer of electrons Unequal sharing of electrons Equal sharing of electrons Separate ions (charged particies) form Slight negative charge (δ–) at one end of molecule, slight positive charge (δ+) at other end Charge balanced among atoms δ– δ+ δ+ Sodium chloride Water Carbon dioxide © 2013 Pearson Education, Inc.

Let’s Watch A Video or Two or Three…! http://bit.ly/VkdqRJ http://bit.ly/SouL10 © 2013 Pearson Education, Inc.

Hydrogen Bonds Attractive force between a + charged hydrogen atom of one molecule and an - charged atom of another molecule Common between molecules with polar bonds such as water Also found within a molecule, holding it in a three-dimensional shape © 2013 Pearson Education, Inc.

Figure 2.10a Hydrogen bonding between polar water molecules. δ+ δ+ δ− Hydrogen bond (indicated by dotted line) δ+ δ+ δ+ δ− δ− δ+ δ− δ+ δ+ δ+ δ+ δ− The slightly positive ends (δ) of the water molecules become aligned with the slightly negative ends (δ−) of other water molecules. © 2013 Pearson Education, Inc.

Figure 2.10b Hydrogen bonding between polar water molecules causes water to be “strong”. A water strider can walk on a pond because of the high surface tension of water, a result of the combined strength of its hydrogen bonds. © 2013 Pearson Education, Inc.

DNA Has Lots Of Hydrogen Bonds Sugar: Deoxyribose Base: Adenine (A) Phosphate Thymine (T) Sugar Phosphate Adenine nucleotide Thymine nucleotide Hydrogen bond Deoxyribose sugar Sugar- phosphate backbone Phosphate Adenine (A) Thymine (T) Cytosine (C) Guanine (G) © 2013 Pearson Education, Inc.

Water vs. Ice © 2013 Pearson Education, Inc.

Hydrogen Bond Videos http://www.youtube.com/watch?v=LK7ERiCy5b8 http://www.youtube.com/watch?v=PyC5r2mB4d4 © 2013 Pearson Education, Inc.

Chemical Groups In Biological Molecules Hydroxyl Amino Phenyl © 2013 Pearson Education, Inc.

Chemical Groups In Biological Molecules Methyl Carboxyl Phosphate © 2013 Pearson Education, Inc.

Chemical Groups In Biological Molecules Hydrocarbon chain © 2013 Pearson Education, Inc.

Polar Or Non-polar Molecule? © 2013 Pearson Education, Inc.

Polar Or Non-polar Molecule? © 2013 Pearson Education, Inc.

Polar Or Non-polar Molecule? © 2013 Pearson Education, Inc.

Occur when chemical bonds are formed, rearranged, or broken Chemical Reactions Occur when chemical bonds are formed, rearranged, or broken Represented as chemical equations using molecular formulas Chemical equations contain Reactant(s) = what you start with Chemical composition of the product(s) = what you end up with © 2013 Pearson Education, Inc.

Examples of Chemical Equations Reactant(s) H + H  4H + C  Product(s) H2 (Hydrogen gas) CH4 (Methane) © 2013 Pearson Education, Inc.

Types of Chemical Reactions Synthesis (combination) reactions Decomposition reactions Exchange (swapping) reactions © 2013 Pearson Education, Inc.

Synthesis Reactions A + B  A-B Example: Atoms or molecules combine to form larger, more complex molecule Always involve bond formation Anabolic reaction SMALLER TO BIGGER Example: © 2013 Pearson Education, Inc.

Figure 2.11a Patterns of chemical reactions. Synthesis reactions Smaller particles are bonded together to form larger, more complex molecules. Example Amino acids are joined together to form a protein molecule. Amino acid molecules Peptide bond Protein molecule © 2013 Pearson Education, Inc.

Decomposition Reactions A - B  A + B Molecule is broken down into smaller molecules or its constituent atoms Reverse of synthesis reactions Involve breaking of bonds Catabolic reaction BIGGER TO SMALLER Example: © 2013 Pearson Education, Inc.

Figure 2.11b Patterns of chemical reactions. Decomposition reactions Bonds are broken in larger molecules, resulting in smaller, less complex molecules. Example Glycogen is broken down to release glucose units. Glycogen Glucose molecules © 2013 Pearson Education, Inc.

Exchange Reactions A-B + C  A-C + B Also called displacement reactions Involve both synthesis and decomposition Bonds are both made and broken SWAPPING ATOMS © 2013 Pearson Education, Inc.

Figure 2.11c Patterns of chemical reactions. Exchange reactions Bonds are both made and broken (also called displacement reactions). Example ATP transfers its terminal phosphate group to glucose to form glucose- phosphate. + Adenosine triphosphate (ATP) Glucose + Adenosine diphosphate (ADP) Glucose- phosphate © 2013 Pearson Education, Inc.

Oxidation-Reduction (Redox) Reactions Let’s talk about these later when we discuss metabolism in detail… © 2013 Pearson Education, Inc.

Reversibility of Chemical Reactions Almost all biochemical reactions are reversible A + B  AB AB  A + B Chemical equilibrium occurs when a reaction is reversible Many biological reactions appear irreversible Due to energy requirements Due to removal of products © 2013 Pearson Education, Inc.

Rate of Chemical Reactions Affected by  Temperature   Rate  Concentration of reactant   Rate  Particle size   Rate Catalysts:  Rate without being chemically changed or part of product Enzymes are biological catalysts © 2013 Pearson Education, Inc.

The Law of Mass Action © 2013 Pearson Education, Inc.

The Law of Mass Action © 2013 Pearson Education, Inc.

The Law of Mass Action © 2013 Pearson Education, Inc.