Basic Chemistry Biochemistry Chapter 2 1 Outline Basic

Basic Chemistry & Biochemistry Chapter 2 1

Outline • Basic Chemistry – – – • Chemical Bonds – • • • Elements Atoms Ions, Molecules & Compounds Ionic, Covalent, & Hydrogen Bonding Properties of Water Acids, Bases & Buffers Molecules of Life – Carbohydrates, Lipids, Proteins, Nucleic acids, ATP 2

Basic Chemistry • There are 92 naturally-occurring elements. – About 96% of human body is composed of just four elements. v Oxygen v Carbon v Hydrogen v Nitrogen 3

Atoms • An atom is the smallest unit of matter that retains an element’s physical and chemical properties. – Positively-charged protons and neutral neutrons are located in the nucleus. – Negatively-charged electrons orbit the nucleus in shells. 4

Figure 2. 1 The structure of an atom. Nucleus Helium atom 2 protons (p+) 2 neutrons (n 0) 2 electrons (e–) (a) Planetary model (b) Orbital model KEY: Proton Neutron © 2015 Pearson Education, Inc. Electron cloud

Second electron shell First electron shell 1 p+ 6 n 0 7 p+ 7 n 0 Hydrogen (H) Atomic number = 1 Mass number = 1 or 2 Atomic mass = 1. 01 Carbon (C) Atomic number = 6 Mass number = 12 or 13 Atomic mass = 12. 01 Nitrogen (N) Atomic number = 7 Mass number = 14 or 15 Atomic mass = 14. 01 Fourth electron shell Third electron shell 8 p+ 8 n 0 Oxygen (O) Atomic number = 8 Mass number = 16, 17, or 18 Atomic mass = 16. 00 Fifth electron shell 11 p+ 12 n 0 17 p+ 18 n 0 19 p+ 20 n 0 Sodium (Na) Atomic number = 11 Mass number = 23 Atomic mass = 22. 99 Chlorine (Cl) Atomic number = 17 Mass number = 35 or 37 Atomic mass = 35. 45 Potassium (K) Atomic number = 19 Mass number = 39, 40, or 41 Atomic mass = 39. 10 Atomic number = number of protons in an atom Mass number = number of protons and neutrons in an atom (boldface indicates most common isotope) Atomic mass = average mass of all stable atoms of a given element in daltons 53 p+ 74 n 0 Iodine (I) Atomic number = 53 Mass number = 127 Atomic mass = 126. 90

Ions, Molecules & Compounds • • • During ionization, atoms give up or take on an electron to stabilize their outer shells An ion is an atom that has a positive or negative charge; has gained or lost an electron A molecule consists of two or more atoms bonded together, sharing electrons 7

Ionic Bonds • Ions are particles that carry a positive (+) or negative (-) charge – The attraction between oppositely charged ions forms an ionic bond v Example: bones & teeth; ions deposited into a matrix 8

Elemental Sodium: 11 protons, 11 electrons Na Na Atom Electron donated (a) Sodium: 1 valence electron Ion

Elemental Chlorine: 17 protons, 17 electrons Electron accepted Cl Cl Atom Ion (b) Chlorine: 7 valence electrons

Na Cl (c) Ionic bond in sodium chloride (Na. Cl)

Covalent Bonds • In covalent bonds, atoms share electrons instead of losing or gaining them; strongest bonds – – A single bond is formed when atoms share a single pair of electrons A double bond is formed when atoms share two pairs of electrons 12

Figure 2. 7 Formation of covalent bonds. Reacting atoms H Resulting molecules H H Hydrogen atom (a) Formation of a single covalent bond O O Oxygen atom H or Molecule of hydrogen gas (H 2) O or O Key to why we are carbon-based life forms: Carbon can make four bonds with other atoms Molecule of oxygen gas (O 2) (b) Formation of a double covalent bond H H H C H H Hydrogen atoms Carbon atom Molecule of methane gas (CH 4) (c) Formation of four single covalent bonds © 2015 Pearson Education, Inc. or

Hydrogen Bonding • Nonpolar & Polar Covalent Bonds – – • Nonpolar covalent bond: both atoms share electrons equally Polar covalent bond: unequal sharing of electrons Polar covalent bonds lead to hydrogen bonding – – Example: H 2 O, water. Electrons in water molecule – spend more time circling larger oxygen atom than smaller hydrogen atom; leads to charge distribution across the whole molecule Hydrogen bonding in water imparts very special characteristics to water that are extremely important for life; water is the most important molecule for life Hydrogen bonding in other biological molecules will be extremely important for structure/function relationships 14

Figure 2. 8 Molecular models illustrating the three-dimensional structure of carbon dioxide and water molecules. Non-polar covalent bond (a) Carbon dioxide (CO 2) δ– Polar covalent bond δ+ δ+ (b) Water (H 2 O) © 2015 Pearson Education, Inc.

Hydrogen Bonding between Water Molecules Water is a polar molecule with the oxygen end being slightly negative and the hydrogen end being slightly positive. 16

H H O d– d– Water molecule d– d– H H O d– Na+ – d d– d– Hydrated sodium ion Na+ H O Cl– H d+ Crystal of Na. Cl d+ d+ Cl– d+ d+ d+ Hydrated chloride ion

Properties of Water Critical for Life • • • Water is liquid at room temperature. Water is a solvent for polar molecules. Water molecules are cohesive. Water temperature rises and falls slowly. Water has a high heat of vaporization. Frozen water is less dense than liquid water. 18

Density of Ice vs. Liquid Water 19

Acids and Bases • • Acids dissociate in water and release hydrogen ions (H+). Bases take up hydrogen ions (H+) or release hydroxide ions (OH-). – Buffers prevent large changes in amounts of acids and bases in body by taking up excess hydrogen ions or hydroxide ions. 20

HCl H+ KOH Cl– (a) Acid K+ OH– (b) Base KCl K+ Cl– (c) Salt

The p. H Scale 22

Molecules of Life • Organic Compounds – – – Molecules containing carbon Carbon can make four bonds with many types of atoms including itself; can form large molecules Result: many different types of organic molecules each with a unique structure and therefore function 23

Molecules of Life • Four categories of molecules are unique to cells. – Carbohydrates. – Lipids. – Proteins. – Nucleic Acids. v ATP 24

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Carbohydrates • Carbohydrates function for quick and shortterm energy storage – Monosaccharide (simple sugar). v Glucose. – Disaccharide. v Sucrose: Glucose + Fructose 26

Glucose All atoms written out Standard shorthand

Figure 2. 14 Carbohydrates. (a) Simple sugar (monosaccharide) (b) Double sugar (disaccharide) (c) Starch (polysaccharide) Dehydration synthesis H 2 O Hydrolysis Glucose Fructose Sucrose (d) Dehydration synthesis and hydrolysis of a molecule of sucrose © 2015 Pearson Education, Inc. Water

• Complex Carbohydrates Polysaccharides. – Glycogen – storage form of carbohydrates in animals 29

Lipids (Fats) • Lipids contain more energy per gram than any other biological molecule; long-term energy storage – – Do not dissolve in water v Absence of polar groups Types of Lipids v Fatty acids v Triglycerides v Phospholipids v Steroids v Animal origin, solid at room temperature v Plant origin, liquid at room temperature 30

Saturated and Unsaturated Fatty Acids • A fatty acid is a carbon-hydrogen chain ending with -COOH – – Saturated fatty acids: contain only single bonds between the carbon atoms; saturated with hydrogen Unsaturated fatty acids: contain one or more double bonds in the carbon chain; not saturated with hydrogen 31

Ester linkage Palmitic acid (C 15 H 31 COOH) + (Saturated) Stearic acid (C 17 H 35 COOH) + (Saturated) Oleic acid (C 17 H 33 COOH) + (Monounsaturated) (c) Triglyceride (fat) molecule

Fatty Acid Stacking 33

Figure 2. 16 Examples of saturated and unsaturated fats and fatty acids. Structural formula of a saturated fat molecule. (a) Saturated fat. At room temperature, the molecules of a saturated fat such as this butter are packed closely together, forming a solid. © 2015 Pearson Education, Inc. Structural formula of an unsaturated fat molecule. (b) Unsaturated fat. At room temperature, the molecules of an unsaturated fat such as this olive oil cannot pack together closely enough to solidify because of the kinks in some of their fatty acid chains.

Phospholipids • Phospholipids contain a phosphate head and fatty acid tails. – Polar head and non-polar tails v Soluble in water 35

Polar head Phosphate group Polar heads Nonpolar tails Cell membrane Polar heads Nonpolar tails (b) Simplified way to draw a phospholipid (a) Chemical structure of a phospholipid (c) Arrangement of phospholipids in a portion of a cell membrane

How Detergents Work 37

Steroids • Steroids are lipids with a backbone of four fused carbon rings – Examples: cholesterol, estradiol, testosterone, cortisol 38

Hydrocarbon tail 4 rings Hydroxyl group Cholesterol Estradiol (an estrogen or female sex hormone) Testosterone (a male sex hormone) Cortisol

Proteins • Proteins are macromolecules with amino acid subunits – An amino acid has a central carbon atom bonded to a hydrogen and three groups. Ø Polypeptide – Single chain of amino acids 40

Figure 2. 17 Amino acid structures. Amine group Acid group (a) Generalized structure of all amino acids. © 2015 Pearson Education, Inc. (b) Glycine is the simplest amino acid. (c) Aspartic acid (d) (an acidic amino acid) has an acid group (—COOH) in the R group. Lysine (a (e) Cysteine (a basic amino acid) has an acid) has a amine group sulfhydryl (—NH 2) in the (—SH) group in R group. the R group, which suggests that this amino acid is likely to participate in intramolecular bonding.

Proteins 43

Essential Amino Acids 44

Levels of Protein Organization • • Primary Structure – Linear sequence of amino acids Secondary Structure – Polypeptide takes on orientation in space Tertiary Structure – Final three-dimensional shape Quaternary Structure – Proteins with more than one polypeptide 45

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Proteins (Cont. ) • Enzymes: proteins that catalyze chemical reactions; most names end in the suffix -ase – – – Are catalysts- help reactions to occur but are not part of the product or changed by the reaction Master molecules of metabolism Highly specific Very efficient Subject to a variety of cellular controls 48

Figure 2. 20 A simplified view of enzyme action. Energy is absorbed; bond is formed. Substrates (S) e. g. , amino acids Water is released. H 2 O Product (P) e. g. , dipeptide Peptide bond Active site Enzyme-substrate complex (E-S) Enzyme (E) © 2015 Pearson Education, Inc. 1 Substrates bind at active site, temporarily forming an enzyme-substrate complex. 2 The E-S complex undergoes internal rearrangements that form the product. Enzyme (E) 3 The enzyme releases the product of the reaction.

Nucleic Acids • Nucleic acids are huge macromolecules composed of nucleotides. – A nucleotide is constructed of a phosphate, a pentose sugar, and a nitrogenous base. – Deoxyribonucleic acid (DNA) v Information storage on how to make proteins – Ribonucleic acid (RNA) v Helper molecule for DNA related to protein synthesis 50

Figure 2. 21 a Structure of DNA. Deoxyribose Phosphate sugar Adenine (A) (a) Adenine nucleotide (Chemical structure) © 2015 Pearson Education, Inc.

Figure 2. 21 Structure of DNA. Deoxyribose Phosphate sugar Adenine (A) KEY: Thymine (T) Adenine (A) (a) Adenine nucleotide (Chemical structure) (b) Adenine nucleotide (Diagrammatic representation) Cytosine (C) Guanine (G) Hydrogen bond Deoxyribose sugar Phosphate (c) Computer-generated image of a DNA molecule © 2015 Pearson Education, Inc. (d) Diagram of a DNA molecule

(ATP) Adenosine Triphosphate • ATP is the primary cellular energy carrier – Energy currency of cells – Breaks down to adenosine diphosphate (ADP) and a molecule of inorganic phosphate, releasing energy to drive cellular metabolism 53

Figure 2. 22 a ATP—structure and hydrolysis. Adenine High energy bonds P P P Ribose Phosphates (a) Adenosine triphosphate (ATP) © 2015 Pearson Education, Inc.

Figure 2. 26 Release of Energy for Cell to Do Work Adenosine H 2 O Hydrolysis of ATP produces useful energy for the cell Adenine (A) Adenosine P P P (ATP) Triphosphate H 2 O Adenosine P P (ADP) Energy for ATP synthesis comes from food or body stores of glycogen or fat Ribose The structure of ATP. The breakdown and synthesis of ATP. The breakdown (hydrolysis) of ATP yields energy for the cell. The reaction is reversible, meaning that ATP may be resynthesized using energy from other sources. © 2014 Pearson Education, Inc. P

Need to Know Main chemical elements in the body 1. – – Life is based on the chemistry of carbon, hydrogen, nitrogen, and oxygen Know difference between ions and molecules Chemical bonds 2. – – Know difference between ionic, covalent, and hydrogen bonding Know the reason why life is based on carbon Properties of water 3. – – Understand how hydrogen bonding contributes to the unique properties of water Understand how the unique properties of water allow for life 56

Need to Know (Cont. ) Acid-Base balance and buffers 4. – Understand importance of acid-base balance and how buffers work 57

5. Need to Know (Cont. ) Molecules of life- built by putting subunits together – Carbohydrates v v – Carbon-oxygen ring structures Know the most important subunit is glucose Types: mono, di, polysaccharides Quick energy, short-term storage of energy Lipids v v Know the subunits- three fatty acid chains bond to one glycerol molecule to make triglyceride Long carbon-hydrogen chains Long-term energy storage Types: fatty acids, triglycerides, phospholipids, steroids, other 58

Need to Know (Cont. ) 6. Molecules of life (Cont. ) – Proteins: v v v Carbon-nitrogen chains (amino acids) with side groups Know the subunits are amino acids- 20 different kinds- 10 essential, 10 non-essential Functions of proteins Level of structural organization; interaction of structure with function Enzymes for biochemical regulation 59

Need to Know (Cont. ) 7. Molecules of life (Cont. ) – Nucleic Acids- ex. DNA- subunits are nucleotides v v Nucleotide are make of nitrogenous base + pentose sugar + phosphate group Storage of how to make every protein- also called genetic material (DNA)- subunits of DNA are nucleotides- adenine, thymine, cytosine, guanine Protein making blueprint is RNA (to be discussed in a later chapter) Energy currency of the cell is ATP; proteins can get energy from it to do work 60