Unit 3: The Chemistry of Life The study of matter & the changes it undergoes. Unit 3: The Chemistry of Life Chapter 3: Matter & Energy

Matter & It’s Combinations: Matter (sec. 3.1) What is matter? anything that has mass & volume What is matter made of? elements Mass = amount of substance (NOT weight… weight includes the effect of gravity) Volume = amount of space taken up by substance

Matter & It’s Combinations: Elements What is an element? a substance made of only one type of atom & can’t be broken into simpler substances ex. = carbon, hydrogen, nitrogen, oxygen, phosphorous, sulfur, etc. What are elements made of? atoms What is an element? substance that is made of only one type of atom, can’t be broken into simpler substances by ordinary chemical means. Examples: CHNOPS What are elements made of? atoms

What are the 6 Most Abundant Elements in Biological Matter? CHNOPS makes up 99% of mass of ALL living things Along w/ CHNOPS… Ca & K make up the 8 most abundant elements in the HUMAN body…

Matter & It’s Combinations: Atoms What is an atom? smallest part of an element that has all the element’s chemical & physical properties ex. carbon, hydrogen, nitrogen, oxygen, phosphorous, sulfur, etc. What are atoms? Atoms are the smallest part of an element that has all the element’s chemical & physical properties Examples =oxygen, carbon, nitrogen, hydrogen, silicon, gold Represented by a symbol (as well as name)

What Makes Up an Atom? subatomic particle location charge symbol proton nucleus (center of atom) positive p+ neutron neutral (no charge) n0 electron orbit around nucleus (located in energy levels) negative e- 17 p+ 18 n0 Central region called the nucleus Consists of: protons, p+ positive charges (determines element & its properties) neutrons, n0 (neutral/no charge), Most of the mass of an atom (p = 1 amu n = 1 amu, about 0.001 amu heavier than proton) Electrons, e- Negatively charged particles orbit around nucleus, Located in discrete energy levels = shells Often called electron “cloud” (outer most = valence shell) smallest part of atom 0.0005 amu In its neutral state, an atom has an equal number of protons and electrons…so, it has no charge.

Matter & It’s Combinations: Atoms Atoms found in their neutral state have no charge. Why? equal # of protons & electrons What would happen if an atom: gained an electron? negative charge lost an electron? positive charge What do we call an atom that has a charge? ion 17 p+ 18 n0 Central region called the nucleus Consists of: protons, p+ positive charges neutrons, n0 (neutral/no charge), Most of the mass of an atom (p = 1 amu n = 1 amu, about 0.001 amu heavier than proton) Electrons, e- Negatively charged particles orbit around nucleus, Located in discrete energy levels = shells Often called electron “cloud” (outer most = valence shell) smallest part of atom 0.0005 amu In its neutral state, an atom has an equal number of protons and electrons…so, it has no charge.

Matter & It’s Combinations: Atoms How do we classify atoms? The Periodic Table families (groups) columns elements have similar chemical properties b/c same # of valence electron periods rows # of protons & electrons increases (+1 as move left to right)… filling up outer energy level periodic table = tool used to organize info about the elements. Shows atomic number (# protons) and atomic mass (# protons + neutrons). Families (groups) vertical (up and down) columns elements have similar chemical properties. Same # of valence electrons Periods rows from left to right # of protons & electrons increases (by 1 each time you move from left to right filling up outer energy (valence) level

Using the Periodic Table of the Elements to Determine Atomic Structure # of protons (determines element & its properties) 16 also # of electrons bigger of the 2 #s periodic table = tool used to organize info about the elements. Shows atomic number (# protons) and atomic mass (# protons + neutrons). Atomic number: number of protons in nucleus (Because atoms are neutral: # electrons = # protons) Determines the element & its properties Atoms of the same element always have the same atomic number Atomic Mass: total mass of protons and neutrons within an atom’s nucleus (bigger of the 2 numbers) To figure out # of neutrons… atomic mass – atomic number = neutrons protons + neutrons

Bohr Model of Atomic Structure # protons (+) equals # electrons (-) Electrons in shells # of valence electrons determines type of bonding argon outermost (valence) shell

Atomic Structure: Electrons & Energy Levels electrons in energy levels (“shells”) around nucleus 1st shell  holds up to 2 electrons other shells  up to 8 electrons (fill before go to next) Na 17 p+ 18 n0 As the # of electrons in atoms increases, more energy levels are needed to hold them. Each level can hold only a specific number of electrons. 1st  2 2nd  8 3rd  8 For Na (sodium), how many more electrons can the 3rd shell hold? Seven more How many more electrons can the 3rd shell hold?

What Affects the Bonding of Atoms? # of valence electrons If valence level is: not full atom is unstable & will bond with electrons from other atom(s) to fill outer level (by sharing, gaining, or losing) full atom is stable & won’t bond # of electrons in outermost (valence) shell governs bonding behavior Some atoms already have full valence energy levels (& are stable) do not readily combine with other elements to form compounds If not full, stability can be achieved by forming bonds with other atoms by gaining, losing, or sharing electrons. 3 main bond types: 1. covalent 2. ionic 3. metallic

What is a Covalent Bond? atoms are held together by shared electrons 2+ atoms share electrons to form a compound. single pair shared = single covalent bond 2 pairs shared = double covalent bond A water molecule is made up of two hydrogen atoms and one oxygen atom. Oxygen is in the 6th column of the periodic table so we know it has 6 electrons in its outermost shell. To be balanced Oxygen needs to gain two electrons or lose six. Hydrogen needs to gain one electron to be balanced. Each hydrogen can form a covalent bond and share its electron.

What is an Ionic Bond? Atoms & Bonding Interactive atoms are held together when they lose or gain electrons oppositely charged ions attract forming compounds Ex. Na+ & Cl-  NaCl (table salt) held together when atoms lose or gain electrons charged atom = ion lose  positive gain  negative opposite charges attract forming compounds (salts) Ex. NaCl (table salt) The number of positive or negative charges on an ion is shown as a superscript after the symbol for an atom or group of atoms Hydrogen ions (H+), Hydroxide ions (OH-) Sodium ions (Na+), Chloride ions (Cl-)

What are Molecules/Compounds? combinations of 2 or more atoms bonded together ex. = O2, H20, C6H12O6, NaCl, HCl, C6H12O6 What is a molecule? Combination of 2 or more atoms are joined by a covalent bond Examples… oxygen O2, hydrogen H2, water H2O Compounds substance with two or more atoms of different elements combined chemically; Elements combine in a fixed proportion (Can have properties unlike those of the elements from which it is made) Examples water 2 hydrogen and 1 oxygen table salt 1 sodium and 1 chlorine sucrose

Chemical Formulas & Equations tell kinds & #s of atoms in one molecule of substance shown with subscripts Ex. H2O chemical equations represent chemical reactions coefficients Ex. 2Mg + O2 2MgO (yields) Formula Tell kinds and numbers of atoms in one molecule (or smallest unit) of a substance Subscripts tell the number of atoms of the element to the upper left (of the subscript). Ex. H2O Tells us 2 atoms of H & 1 of O in one molecule of water (if no subscript, then it is understood to be 1) Chemical Equations Represent chemical reactions, obey the law of conservation of matter –what goes in must come out Coefficients tell how many of the molecules they precede are involved. Eg. 2Mg + O2  2MgO Read as magnesium plus oxygen yields magnesium oxide Substances to the left of the arrow are reactants, and substances to the right are products In this reaction, 2 atoms of magnesium react with 2 atoms of oxygen to produce 2 molecules of magnesium oxide.

Hydrogen Ions Determine pH pH  concentration of H+ ions in a solution expressed as 1.0 x 10-x (absolute value of) exponent tells pH scale: 0 - 14, quantifies acidity of solutions. acid  pH <7 neutral pH = 7 base  pH >7 pH  concentration of H+ ions in a solution Expressed as 1.0 x 10-x exponent tells pH value. Ex. A substance with a pH of 7 has an [H+] of 1.0 x 10-7 The pH scale ranges from 0 to 14 and quantifies the acidity of solutions Acidic solutions have a pH less than 7 Lower pH = higher concentration of H+ (lower concentration of OH-), greater the acidity Basic solutions have a pH greater than 7 Higher pH = higher concentration of OH- (lower H+), greater the alkalinity (base) Neutral solutions have a pH of 7 (ex. pure water) For every increase in pH value, the concentration of H+ ions increases tenfold. Ex. A substance with pH of 6 contains 10 times as many hydrogen ions as a substance with pH of 7 Organisms – and tissues within organisms have specific pH requirements Copyright C Pearson Education, Inc., publishing as Benjamin Cummings

Biological Chemistry (sec. 3.2) inorganic molecules simple structure H20, 02, NH3, CO2 inorganic even though it contains carbon an exception to the rule

Biological Chemistry organic molecules contain: carbon & usually hydrogen complex structure Carbon has 6 electrons (4 in the valence shell), needs 4 more electrons, usually forms covalent bonds… not only can it bond w/ different elements, but can also bond w/ other carbon atoms, which explains why C-compounds can be so complex

Biological Chemistry: Monomers & Polymers What is a monomer? small molecule What is a polymer? large molecule made of repeated monomers

What are the 4 major types of organic biological macromolecules? amino acid polypeptide (protein) nucleotide nucleic acid (DNA & RNA) monosaccharide polysaccharide fatty acids & glycerol Lipid carbohydrates lipids (fats) proteins nucleic acids

Carbohydrates monomer = monosaccharides polymer = polysaccharides simple sugars All have same empirical formula CH2O C6H12O6  glucose polymer = polysaccharides starches, cellulose sugar cellulose starch major source of energy (& energy storage) in the body Contain C,H,O in a ratio of 1:2:1 Ratio of H:O is 2:1 just like H2O Ex. C6H12O6 Monomer = Monosaccharides All have the same empirical formula CH2O. C6H12O6  glucose Polymer = some sugars (disaccharides), Starches, Cellulose Formed by dehydration synthesis of monosaccharides Isomers are molecules with the same formula, but have different molecular structures. monosaccharide + monosaccharide disaccharide

Functions of Carbohydrates energy source, energy storage, support (plant cell walls) cellulose major source of energy (& energy storage) in the body Contain C,H,O in a ratio of 1:2:1 Ratio of H:O is 2:1 just like H2O Ex. C6H12O6 Monomer = Monosaccharides All have the same empirical formula CH2O. C6H12O6  glucose Polymer = some sugars (disaccharides), Starches, Cellulose Formed by dehydration synthesis of monosaccharides Isomers are molecules with the same formula, but have different molecular structures.

Lipids oil fat building blocks (not monomers) = fatty acids & glycerol lipid (fat) molecule = triglyceride Building blocks (not monomers) = fatty acids & glycerol Long-term energy storage, cell membrane, hormones, insulation, nerve transmission Formed by dehydration synthesis of glycerol & fatty acids Forms the letter E

Functions of Lipids long-term energy storage, cell membrane, hormones, insulation, nerve transmission Building blocks (not monomers) = fatty acids & glycerol Long-term energy storage, cell membrane, hormones, insulation, nerve transmission Formed by dehydration synthesis of glycerol & fatty acids Forms the letter E

Saturated vs. Unsaturated Fats unsaturated has double bonds saturated has only single bonds Saturated (animal fats) Consist of SINGLE bonds…has the maximum number of hydrogens bonded to the carbons, and therefore is "saturated" with hydrogen atoms. (solid @ room temp) Unsaturated (plant fats) Consist Of at least 1 DOUBLE bond… doesn’t have max # of hydrogens bonded to the carbons, & therefore is “unsaturated” w/ H atoms (liquid @ room temp) In cellular metabolism, unsaturated fat molecules contain somewhat less energy (i.e., fewer calories) than an equivalent amount of saturated fat. …healthier

Proteins monomer = amino acid polymer = polypeptide/protein meat,/ fish/ eggs/ nuts/ beans monomer = amino acid amino group  NH2 acid group  -COOH “variable”/replaceable group  R polymer = polypeptide/protein muscle Amino Acids = Building blocks of (polypeptides & then) proteins AA have a central carbon atom which is attached to a hydrogen atom, an amine group (-NH2), a carboxyl acid group (-COOH), and a Variable/replaceable group (R)  R: one of 20 different atoms or group of atoms There are 20 different types of amino acids found in the natural world. proteins make up muscle, enzymes, hormones, meats/fish/eggs/nuts/beans Enzymes make reactions happen Protein function is dependent on structure hormone

There are 20 different amino acids found in the natural world.

Functions of Proteins structure, enzymes, transport materials in & out of cells, hormones, muscle hormone muscle Amino Acids = Building blocks of (polypeptides & then) proteins AA have a central carbon atom which is attached to a hydrogen atom, an amine group (-NH2), a carboxyl acid group (-COOH), and a Variable/replaceable group (R)  R: one of 20 different atoms or group of atoms There are 20 different types of amino acids found in the natural world. proteins make up muscle, enzymes, hormones, meats/fish/eggs/nuts/beans Enzymes make reactions happen Protein function is dependent on structure

Nucleic Acids monomers = nucleotides polymers = nucleic acids (entire structure) monomers = nucleotides sugar-phosphate backbone nitrogenous bases DNA = Adenine, Thymine, Cytosine, Guanine RNA = Uracil (instead of Thymine) polymers = nucleic acids DNA & RNA Monomers = nucleotides made of sugar-phosphate backbone & 1 of 4 nitrogenous bases (In DNA… Adenine, Thymine, Cytosine, Guanine & in RNA… Uracil instead of Thymine) Polymers = nucleic acids (DNA & RNA) DNA = Deoxyribonucleic Acid Stores info for putting amino acids together to make proteins The basis of genes & heredity RNA = Ribonucleic Acid Helps to synthesize (build) proteins Why do living things need DNA? so they can pass on genetic code & continue the species

Functions of Nucleic Acids DNA = Deoxyribonucleic Acid genetic “blueprint” RNA = Ribonucleic Acid helps to synthesize proteins Why do living things need DNA? So they can pass on genetic code & continue the species. Monomers = nucleotides made of sugar-phosphate backbone & 1 of 4 nitrogenous bases (In DNA… Adenine, Thymine, Cytosine, Guanine & in RNA… Uracil instead of Thymine) Polymers = nucleic acids (DNA & RNA) DNA = Deoxyribonucleic Acid Stores info for putting amino acids together to make proteins The basis of genes & heredity RNA = Ribonucleic Acid Helps to synthesize (build) proteins Why do living things need DNA? so they can pass on genetic code & continue the species

Organic Biological Macromolecules Elements Contained Monomer (building blocks) Polymer Function carbohydrates (sugar, starch, cellulose) C, H, O Ratio 1 : 2 : 1 monosaccharide (simple sugars such as glucose) polysaccharide (such as starch & cellulose) Energy source, energy reserve, plant cell walls lipids (fats, oils, & waxes) (# of H is much greater than # of O) Fatty acids & Glycerol (Built from 2 types of simpler molecules… NOT monomers.) Not applicable Energy reserves, cell membrane, hormones, insulation, nerve transmission protein C, H, O, N, S Amino acids (20 different A.A.) polypeptides (proteins) Structure, enzymes, transport materials in & out of cells hormones, muscle nucleic Acids (DNA & RNA) C, H, O, N, P Nucleotides (sugar-phosphate backbone & nitrogenous bases) nucleic acids (DNA & RNA) Carries genetic code (“blueprint for organism) & directs protein synthesis A monomer is a molecule that is able to bond in long chains. Polymer means many monomers. Sometimes polymers are also known as macromolecules or large-sized molecules. Usually, polymers are organic (but not necessarily). Enzymes are catalysts & help reactions occur