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Chapter 2 The chemical Basis of Life Introduction Why study chemistry in an Anatomy and Physiology class? • body functions depend on cellular functions • cellular functions result from chemical changes • biochemistry helps to explain physiological processes, and develop new drugs and methods for treating diseases Introduction cont. • Chemistry = the study of matter • Biochemistry= the study of the chemistry of life • Matter = anything that occupies space and has mass – composed of elements – (i.e. solids, liquids, gases) Structure of Matter Structure of Matter • Elements – composed of chemically identical atoms – bulk elements – required by the body in large amounts – trace elements – required by the body in small amounts • Atoms – smallest particle of an element – the least complex level of organization Subatomic Particles • Proton = a positively charged particle in the nucleus of an atom – Mass=1 • Neutron = an electrically neutral particle in the nucleus of an atom – Mass=1 • Electron = an electrically negative particle that revolves around the nucleus – Mass = 0 Elements • • • • Element = a basic chemical substance composed of atoms Elements are represented by a 1 or 2 letter symbol 120 elements exist in nature Approximately 26 are naturally occurring in humans. – most abundant=carbon (C), Hydrogen (H), Oxygen (O) Nitrogen (N), Phosphorus (P) = CHONP – Referred to a bulk elements (Know Table 2.2 and 2.3 for the test) Elements You need to Know Know this table Elements cont. • Atoms are neutral in charge - The number of protons is equal to the number of electrons. • The Atomic Number (A#) of an atom represents the number of protons in its nucleus. • The Atomic Mass (AM) of an atom is equal to the number of protons plus the number of neutrons in its nucleus – Average weight of common isotopes Isotopes • Isotopes = atoms of an element that have the same A#'s but different AW's (i.e. same # of protons, different # of neutrons) – Any sample of an element is likely to contain multiple isotopes – The nuclei of some isotopes are stable – The nuclei of other isotopes are unstable and break apart to become more stable • When the nucleus of an atom breaks apart, it releases radioactive energy • Radioactive isotopes have many biological uses (i.e. Carbon Dating) Molecules and Compounds • Molecule – particle formed when two or more atoms chemically combine • Compound – particle formed when two or more atoms of different elements chemically combine • Molecular formulas – depict the elements present and the number of each atom present in the molecule – water (H2O), glucose (C6H12O6) Bonding of Atoms • The electrons of an atom are arranged in orbits, shells, or energy levels around the central nucleus • A characteristic number of electrons fill each shell – 2 electrons fill the first shell (closest to nucleus) – 8 electrons fill the second shell – 8 electrons fill the third shell Bonding of Atoms cont. • The way in which atoms react with one another (i.e. their chemical properties) is based on the electrons in their outermost shell = Valence Electrons • The outermost shell of an atom is called its valence shell Electron Shells (valence) Bonding of Atoms cont. • Atoms form bonds with other atoms to fill their outermost or valence electron shell (energy level) – "Rule of Octets" = except for the first energy level (which contain 2 electrons), atoms react with other atoms so they will have 8 electrons in their valence shell – All 8 slots filled=inert, non reactive – Less that 8 slots filled= atom seeks a stable energy level with a full shell Example Problem #1 Fluorine has an Atomic Number of 9. Draw an atom of fluorine. How and why will fluorine react? Example Problem #1 Fluorine has an Atomic Number of 9. Draw an atom of fluorine. How and why will fluorine react? Since atoms are stable with 8 electrons in their valence shell, + 9p fluorine will tend to 0 9n bind with atoms that have one electron to donate - Example Problem #2 Argon has an Atomic Number of 18. Draw an atom of argon. How and why will argon react? Example Problem #2 Argon has an Atomic Number of 18. Draw an atom of argon. How and why will argon react? Since Argon has a full valence shell, it - will not tend to bond to other + 18p atoms and be 0 18n relatively inert - - - - - - Ions • Ions = atoms that have lost or gained electrons to fill their valence shell – anion = a negatively charged ion (Cl-) – cation = a positively charged ion (Na+) – An attraction exists between oppositely charged ions and an ionic bond results (i.e. Na+Cl-) • Formed when electrons are transferred from one atom to another Ionic Bond • An ionic bond results due to the attraction that exists between oppositely charged ions and (i.e. Na+Cl-) – They are formed when electrons are transferred from one atom to another Ionic Bond Covalent Bond • A covalent bond is formed by the equal sharing of electrons between atoms – very strong bond – i.e. H2 and O2 • Atoms tend to make the same number of covalent bonds – Same number of slots on the valence shell – Structural formula – More than one elector can be bound • Double, triple bonds Covalent Bond • • • • Hydrogen atoms form single bonds Oxygen atoms form two bonds Nitrogen atoms form three bonds Carbon atoms form four bonds H―H O=O N≡N O=C=O Covalent Bond Structural Formula Structural formulas show how atoms bond and are arranged in various molecules Polar Bond • Polar Bond=A polar covalent bond is formed by the unequal sharing of electrons between atoms – strong bond – results in molecules that are polar • one end of the molecule is slightly positive, one end of the molecule is slightly negative – i.e. water (H2O) Hydrogen Bond • Hydrogen Bonds= a weak attraction between the positive end of one polar molecule and the negative end of another polar molecule – formed between water molecules – important for protein and nucleic acid structure – Examples include interaction between water molecules and DNA chains – These bonds are easily broken and put back together (very weak) Types of Chemical Reactions • Synthesis Reaction – more complex chemical structure is formed A + B AB • Decomposition Reaction – chemical bonds are broken to forma simpler chemical structure AB A + B Types of Chemical Reactions cont. • Exchange Reaction – chemical bonds are broken and new bonds are formed AB + CD AD + CB • Reversible Reaction – the products can change back to the reactants A + B ↔ AB Acids, Bases, and Salts • Electrolytes – substances that release ions in water NaCl Na+ + Cl- • Acids – electrolytes that dissociate to release hydrogen ions in water HCl H+ + Cl- • Bases – substances that release ions that can combine with hydrogen ions NaOH Na+ + OH- • Salts – electrolytes formed by the reaction between an acid and a base HCl + NaOH H2O + NaCl Acid and Base Concentrations • pH scale - indicates the - concentration of hydrogen ions in - solution • Neutral – pH 7 - indicates equal concentrations of H+ and OH- • Acidic – pH less than 7 - indicates a greater concentration of H+ • Basic or alkaline – pH greater than 7 - indicates a greater concentration of OH- Chemical Constituents of Cells Inorganic Substances • Inorganic Substances are small compounds that do not contain both the atoms C and H – Examples include oxygen, carbon dioxide (CO2) water, salts, acids & bases Water • Water is a polar molecule that demonstrates hydrogen bonding and therefore it possesses very unique characteristics – Water is an excellent solvent (universal?) – Many solutes are dissolved in our body's water (i.e. polar substances dissolve in polar water) – Many ionic compounds (i.e. NaCl) dissociate or break apart in water Water cont. • Water participates in many chemical reactions (in our cells and fluids) – Dehydration (synthesis) is when water is removed from adjacent atoms (of molecules) to form a bond between them – Hydrolysis (degradation) is when water is used to break bonds between molecules • Water is an excellent temperature buffer – absorbs and releases heat very slowly • Water is the most abundant component in cells (about 70%) Water cont. • Water provides an excellent cooling mechanism – It requires a lot of heat to change water from a liquid to a gas (i.e. high heat of vaporization). If water does change forms and evaporate, it leaves a cool surface behind • Water serves as a lubricant – mucus – internal organs – joints Inorganic Substances cont. • Oxygen (O2) – gas that is transported in the blood – used to release energy from nutrient molecules • Carbon Dioxide (CO2) – a by-product of cellular respiration • Inorganic salts – Abundant in body fluids – Source of necessary ions (Na+, Cl-, K+, Ca2+, etc…) – Play important roles in metabolism Organic Substances • Organic Substances= contains the atoms carbon (and hydrogen) • Small molecules (monomers or building blocks) are covalently bonded together to form large polymers or macromolecules • Water is usually involved in the formation and breakage of bonds between monomers – Dehydration Synthesis = removal of water to form a covalent bond between monomers – Hydrolysis = using water to break bonds between monomers Organic Substances cont. • The four major classes found in cells include: – carbohydrates – lipids – proteins – nucleic acids Carbohydrates • • • • • Provide Energy to cells Supply materials to build cell structures Water-soluble Contain C, H, O Carbohydrates (sugars)= contains C, H, and O in a 1:2:1 ratio (usually) – glucose = C6H12O6 Carbohydrates • Monomers (building blocks) are monosaccharides – glucose, fructose • Hexoses = simple 6-C sugars – glucose – fructose – galactose • Polymers are formed by dehydration synthesis Monosaccharide Monosaccharide cont. Carbohydrates cont. Disaccharides: 2 monosaccharides covalently bonded together – maltose = glucose + glucose – lactose = glucose + galactose – sucrose = glucose + fructose Carbohydrates cont. • Polysaccharides: many glucose molecules covalently bonded together – starch = plant storage carbohydrate – glycogen = animal storage carbohydrate; stored in liver and skeletal muscle – cellulose=plant starch Carbohydrates cont. • Polymers are broken down by hydrolysis resulting in monosaccharides • Function = energy source / energy storage! CELLULAR RESPIRATION OVERVIEW glucose + oxygen energy + H2O + CO2 (ATP) Lipids • Lipids= contain C, H, and O, but much less O than in carbohydrates • Soluble in organic solvents • Insoluble in water • Types of lipids – Fats – Phospholipids – Steroids Fats • Monomers (building blocks) = triglycerides (glycerol + 3 fatty acids) • Function = energy store/ energy source • Saturated fats=have only single bonds between the carbons in their fatty acid chains – are solid at room temperature – are animal fats – are nutritionally "BAD" fat – include bacon grease, lard, butter Fats • Unsaturated fats= have one or more double bond between the carbons in their fatty acid chains – are liquid at RT (oils) – are plant fats – are nutritionally "GOOD" fat – include corn and olive oil Fatty Acids Triglycerides Phospholipids • Phospholipids= triglyceride with the substitution of a polar phosphate group (PO4-) for one fatty acid chain • One glycerol, 2 fattyacids, 1 phosphate • Function = major cell membrane component Steroids • Steroids= four interconnected carbon rings – Example is cholesterol • Function = compose cell membranes; chemical messengers (hormones) Proteins • Monomers = amino acids – Structure=amino group, carboxyl group, side chain (R group) – 20 different types of Amino Acids (R groups differ) Proteins cont. • Polymers are formed by dehydration synthesis between the amino group of one amino acid and the carboxyl group of a 2nd amino acid • Bond formed = a peptide bond Peptide Bond Proteins cont. • Length of amino acid chains may vary – peptide = 2-100 aa's – polypeptide = 100-thousands aa's without a function – protein = 100-thousands of aa's with a specific function Functions of Proteins • Structure – • Transport – • hemoglobin Movement – • keratin in hair, nails and skin actin and myosin in muscles Chemical messengers – – hormones neurotransmitters • Defense – antibodies • Catalysts – enzymes=Biological catalysts, that increase the rate of chemical reactions without being consumed by the reaction Denaturation of Proteins • Denaturation of Proteins= the loss of 3dimensional conformation (shape) of a protein. This results in loss of function • Reasons for denaturation – extreme pH values – extreme temperature values – harsh chemicals (disrupt bonding) – high salt concentrations Protein Structure • Primary (1o) = sequence of amino acids • Secondary (2o) = twisting of amino acid chain; due to hydrogen bonding; • Tertiary (3o) = folding of the amino acid chain; due to ionic bonds, disulfide bridges, and hydrophobic interactions; • Quaternary (4o) = interactions between different amino acid chains (See the four amino acids chains that compose hemoglobin on page 518). Primary Structure Secondary Structure Tertiary Structure Quaternary Structure Nucleic Acids • Monomers = nucleotides • Nucleotide structure = 3 parts – pentose sugar (5-C) – phosphate group – nitrogenous base • purine (double ring) • pyrimidine (single ring) • Polymers are formed by bonding between the sugar of one nucleotide and the phosphate group of a second nucleotide = sugar/phosphate backbone Nucleic Acids Deoxyribonucleic Acid = DNA • Structure – Sugar = deoxyribose – Bases = adenine (A), thymine (T), cytosine (C), guanine (G) – double stranded (resembles ladder); strands held together by H-bonds between bases on opposite strands • A complements T (2 hydrogen bonds) • C complements G (3 hydrogen bonds) Nucleotides DNA cont. • double helix (ladder is twisted) • Function = genetic material (i.e. genes, chromosomes) • DNA contains all necessary information needed to sustain and reproduce life! DNA Structure: One Strand DNA Structure: Two Strands DNA Structure cont. Ribonucleic Acid = RNA • Structure – Sugar = ribose – Bases = A,G,C, and uracil (replaces thymine) – single stranded. • Function = transport DNA code during protein synthesis RNA vs. DNA