5/18/2012. The Chemical Elements. The Chemistry of Life Chapter 2. Atoms, Ions and Molecules. Water and Mixtures. Energy and Chemical Reactions

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1 The hemistry of Life hapter 2 Atoms, Ions and Molecules Water and Mixtures Energy and hemical Reactions rganic ompounds The hemical Elements Element simplest form of matter to have unique chemical property An element can not be broken down or converted to something else Atoms particles that make elements basic structural units of matter Biochemistry the study of the molecules that compose living organisms periodic table elements arranged by atomic number elements represented by one or two letter symbols carbohydrates, fats, proteins, and nucleic 21 acids elements have biological role 96% of body weight Atomic Structure The nucleus consists of neutrons and protons eutrons have no charge Protons have a positive charge Electrons are found orbiting the nucleus Electrons negative charge The # protons and electrons for an atom is always equal (by definition: a complete atom) electrically eutral Atomic Structure Atomic number = # Protons Atomic weight = # Protons # eutrons Isotopes: Atoms with same atomic # but different atomic weights e.g., atoms all have 8 protons but might have different # of neutrons Atoms composed of subatomic particles: Proton positive charge eutron no electrical charge Electron negative charge ucleus entral part of atom omposed of protons and neutrons Electrons move around the nucleus eutron (n 0 ) Proton (p ) Electron (e ) ucleus Lithium (Li) 6 1

2 Electrons of an atom occupy regions of space called electron shells which circle the nucleus For atoms with atomic numbers of 18 or less, the following rules apply: The first shell can hold up to 2 electrons The second shell can hold up to 8 electrons The third shell can hold up to 8 electrons 7 Valence shell (electron) outermost shell More energy farther electrons are from nucleus Lower shells are filled before next shell accepts Electrons 8 Ions ations Anions 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. energy 1 An electron absorbs energy 3 2 The electron drops back into lowerenergy shell, releasing energy as light The energy boosts the electron to a higherenergy shell light Fig. 23 Ion An atom that gains or loses electrons to become stable An electrically charged atom ation A positively charged ion Formed when an atom loses electrons Anion A negatively charged ion Formed when an atom gains electrons 11p 12n 0 Sodium atom (a) 17p 18n 0 hlorine atom (l) 10 hemical Bonds A molecule may be depicted in different ways. (a) All bonds shown (b) Bonds within common groups omitted hemical bonds: hold molecules TABLE 2.3 together, or attract one molecule to another Types of hemical Bonds Types of hemical Bonds Ionic bonds (c) arbons and their attached hydrogens omitted ovalent bonds ydrogen bonds (d) verall shape depicted Fig

3 Ionic Bonds Ionic Bonds An attraction between a cation and an anion Ionic Bond: formed by transfer of >1 elecrons from one atom to another Formed when electrons are transferred from one atom to another atom one donates one receives! 11p 17p 12n 0 18n 0 a l Sodium ion (a ) Sodium chloride hloride ion (l ) 13 one donates one receives! Figure 2.5a ovalent Bonds ovalent Bonds: atoms share an electron Single Formed when atoms share electrons!!!! 2 ydrogen atom ydrogen atom ydrogen atoms form single bonds xygen atoms form two bonds itrogen atoms form three bonds arbon atoms form four bonds ydrogen molecule = = = 15 Figure 2.7a onpolar /Polar ovalent Bonds onpolar covalent bond Electrons shared equally ydrogen Bonds ydrogen bond a weak attraction between a slightly positive hydrogen atom in one molecule and a slightly negative oxygen in another. Water molecules are weakly attracted to each other by hydrogen bonds (a) Polar covalent bond Electrons shared unequally relatively weak bonds very important to physiology protein structure (b) Figure DA structure 218 3

4 ydrogen Bonds Polar molecule Water Water s polar covalent bonds and its V shaped molecule gives water unique properties why its important to life!!!!!!!! 1. Solvency (lots of things dissolve it it) 2. ohesion (same molecules stick together) 3. Adhesion (water sticks to charged surface) 4. hemical reactivity (involved in lots of reax & can form ions) 5. Thermal stability Figure 2.10a AcidBase oncentration (p) Acidic: p p Scale Basic: p eutral: p 7.00 A change of one number represents a 10 fold change in concentration Milk, Pure water Bread, saliva (7.0) Egg white Wine, black Bananas, ( ) (8.0) vinegar coffee Gastric juice tomatoes ( ) (5.0) ( ) (4.7) Lemon juice 1 M (2.3) ydrochloric Acid (0) eutral ousehold bleach ousehold (9.5) ammonia ( ) ven cleaner, lye (13.4) 1 M sodium hydroxide (14) p 4.0 is 10 times as acidic as p of Figure 2.13 rganic Molecules and arbon rganic ompounds 4 valence electrons binds with other atoms that can provide it with four more electrons to fill its valence shell i.e., can form many bonds!!!!!!!!!!!!!! carbon atoms bind readily with each other carbon backbones forms long chains, branched molecules and rings 4 categories of carbon compounds carbohydrates lipids proteins ucleic acids forms covalent bonds with hydrogen, oxygen, nitrogen, sulfur, and other elements carbon backbone carries a variety of functional 223 groups 224 4

5 Functional Groups Decoposition Reactions small clusters of atoms attached to carbon backbone determines many of the properties of organic molecules ame and Symbol ydroxyl ( ) Methyl ( 3) arboxyl ( ) Amino ( 2) Structure ccurs in Sugars, alcohols Fats, oils, steroids, amino acids Amino acids, sugars, proteins Amino acids, proteins Large molecule breaks down into two or more smaller ones AB A B Starch molecule Phosphate ( 2P 4) P ucleic acids, ATP Glucose molecules (a) Decomposition reaction Synthesis Reactions Dehydration Synthesis Two or more small molecules combine to form a larger one A B AB Amino acids AKA condensation reaction A hydroxyl group is removed from one monomer and a hydrogen from the next Monomer 1 Monomer 2 Dimer (a) Dehydration synthesis 2 Protein molecule (b) Synthesis reaction Figure 2.15a 228 ydrolysis rganic Molecules: arbohydrates Splitting a polymer (lysis) by addition of a water molecule a covalent bond is broken All digestion reax consists of hydrolysis reactions Dimer Monomer 1 Monomer 2 quickly mobilized source of energy all digested carbohydrates converted to glucose hydrophilic organic molecule general formula ( 2 ) n n = number of carbon atoms for glucose, n = 6, so formula is (b) ydrolysis

6 arbs: Monosaccharides arbs: Disaccharides Simplest carbohydrates simple sugars 3 important monosaccharides glucose, galactose and fructose same molecular formula produced by digestion of complex carbohydrates Glucose 2 Galactose 2 Fructose 2 2 composed of 2 monosaccharides Sucrose 2 Lactose 2 Maltose Figure 2.16 arbs: Polysaccharides long chains of glucose 3 polysaccharides of interest in humans Glycogen: energy storage in animals made in liver, muscles, brain, uterus, and vagina Starch: energy storage polysaccharide in plants only significant digestible polysaccharide in the human diet an Provide support!! ellulose: structural molecule of plant cell walls (fiber) hitin: hard covering of arthropods rganic Molecules: Lipids hydrophobic organic molecule composed of carbon, hydrogen and oxygen form hydrocarbon chains More energy than carbs! Types: 1. oils, fats and waxes 2. phospholipids 3. steroids 234 Fatty Acids hain of 4 to 24 carbon atoms carboxyl (acid) group on one end, methyl group on the other and hydrogen bonded along the sides Lipids Triglycerides Formed by condensation of 1 glycerol and 3 fatty acids Dehydration Synthesis lassified saturated carbon atoms saturated with hydrogen unsaturated contains = bonds without hydrogen polyunsaturated contains many = bonds Palmitic acid (saturated) 3 ( 2 )

7 ( 2) 5 3 5/18/2012 Phospholipids Steroids structural foundation of cell membrane fatty acid tails are hydrophobic phosphate head is hydrophilic P 2 3 itrogencontaining group (choline) Phosphate group Glycerol ydrophilic region (head) holesterol precurser from which other steroids are synthesized synthesized only by animals especially liver cells important component of cell membranes ( 2) 5 ( 2) 12 3 Fatty acid tails ydrophobic region (tails) required for proper nervous system function (a) (b) 238 rganic Molecules: Proteins Representative Amino Acids protein a polymer of amino acids amino acid central carbon with 3 attachments amino group (2), carboxyl group () and radical group (R group) 20 amino acids differ only in functional (R) group Some nonpolar amino acids Methionine 2 2 S 3 Tyrosine Some polar amino acids ysteine 2 S Arginine Essential A.A.s 2 ( 2) (a) ote: they differ only in the R group 240 Structure of Proteins Protein Functions Structure (muscles, Amino acids ommunication (hormones/receptors) Peptide bonds Primary structure Sequence of amino acids joined by peptide bonds Tertiary structure Folding and coiling due to interactions among R groups and between R groups and surrounding water Membrane Transport channels in cell membranes carrier proteins on cell membranes Alpha helix Beta sheet hain 1 hain 2 Secondary structure Alpha helix or beta sheet formed by hydrogen bonding Beta chain eme groups Alpha chain Alpha Quaternary structure chain Association of two or more polypeptide chains with each other Beta chain Muscle activity Enzymes Immunity/Protection (recognition/antibodies/clotting proteins) Movement (oxygen in blood) Denature 241 ell adhesion 242 7

8 ucleic Acids Long chains (polymers) of nucleotides 3 components of nucleotides 1. nitrogenous base 2. sugar (monosaccharide) 3. one or more phosphate groups DA (deoxyribonucleic acid) constitutes genes instructions for synthesizing all of the body s proteins transfers hereditary information from cell to cell and generation to generation RA (ribonucleic acid) 3 types 243 8

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