The Chemistry of Life Chapters 2 and 3

Atoms Smallest unit of matter that retains physical properties Smallest unit of matter that retains physical properties 3 Basic Parts 3 Basic Parts Proton Proton Neutron Neutron Electron Electron Nucleus gives an atom its mass Nucleus gives an atom its mass Electrons give an atom is behavior Electrons give an atom is behavior

Elements Made up of only 1 type of atom Made up of only 1 type of atom Isotopes have same number of p +, but different numbers of n 0, so atomic mass varies Isotopes have same number of p +, but different numbers of n 0, so atomic mass varies Form compounds Form compounds Chemical Bonds Chemical Bonds Formula tells the ratio of atoms in a compound Formula tells the ratio of atoms in a compound 98% of living things are made of CHNOPS 98% of living things are made of CHNOPS

Chemical Bonds The valence electrons are involved in the bond The valence electrons are involved in the bond Atoms are stable when their valence shell is filled Atoms are stable when their valence shell is filled

Covalent Bonds- atoms share valence electrons and are held together Covalent Bonds- atoms share valence electrons and are held together Non-metal to non-metal Non-metal to non-metal Molecule is the smallest part of a compound that retains the properties Molecule is the smallest part of a compound that retains the properties

Polarity Covalent bonds share electrons between atoms Covalent bonds share electrons between atoms Electrons shared equally result in a non- polar bond Electrons shared equally result in a non- polar bond Electrons shared unequally between the atoms create regions of positive charge and negative charge, though the molecule is neutral, results in a polar bond Electrons shared unequally between the atoms create regions of positive charge and negative charge, though the molecule is neutral, results in a polar bond Polar molecules can interact with each other and with ions Polar molecules can interact with each other and with ions Whole molecules can be polar or select bonds in a molecule can be polar Whole molecules can be polar or select bonds in a molecule can be polar

Ionic Bonds are a result of the transfer of valence electrons Ionic Bonds are a result of the transfer of valence electrons Atoms that lose electrons have more p+ than e- and are called positive ions (cations) Atoms that lose electrons have more p+ than e- and are called positive ions (cations) Atoms that gain electrons have more e- than p+ and are called negative ions (anions) Atoms that gain electrons have more e- than p+ and are called negative ions (anions) Metals form cations and non-metals form anions Metals form cations and non-metals form anions The positive ion is attracted to the negative ion and they stick together The positive ion is attracted to the negative ion and they stick together

Energy Comes in many forms Comes in many forms Kinetic, Potential, Chemical, Thermal, Radiant Kinetic, Potential, Chemical, Thermal, Radiant The ability to do work The ability to do work Can be converted from one form to another Can be converted from one form to another When atoms for chemical bonds energy can either be absorbed or released When atoms for chemical bonds energy can either be absorbed or released

Living Things and Energy All living things require energy All living things require energy 1000s of chemical reactions occur in living organisms a day 1000s of chemical reactions occur in living organisms a day Energy is either stored in bonds formed during a reaction or it is released by the reaction Energy is either stored in bonds formed during a reaction or it is released by the reaction Living organisms use this energy to carry out life processes Living organisms use this energy to carry out life processes Metabolism is all of the chemical reactions that occur in an organism Metabolism is all of the chemical reactions that occur in an organism

Activation Energy Energy required for a chemical reaction to occur Energy required for a chemical reaction to occur Can be a large amount Can be a large amount Catalysts lower the activation energy for a reaction Catalysts lower the activation energy for a reaction They are not used up and can be used repeatedly They are not used up and can be used repeatedly Enzymes are proteins or RNA that act as catalysts in living organisms- there are 1000s Enzymes are proteins or RNA that act as catalysts in living organisms- there are 1000s

Enzyme has a specific shape that will interact with a specific substrate Enzyme has a specific shape that will interact with a specific substrate Substrate is reactant being catalyzed fits in active site on enzyme Substrate is reactant being catalyzed fits in active site on enzyme Enzyme’s shape is changed when substrate bonds at active site Change in shape causes bonds in substrate to weaken and break Change in shape causes bonds in substrate to weaken and break Products are released by enzyme Products are released by enzyme Enzyme is unchanged and reacts anew with another substrate Enzyme is unchanged and reacts anew with another substrate Enzymes require very specific temperature and pH ranges Enzymes require very specific temperature and pH ranges Changes can cause the enzyme to denature Changes can cause the enzyme to denature

Enzyme Catalyzed Reaction

Oxidation Reduction Reactions AKA- Redox reactions AKA- Redox reactions Reactions that involve the transfer of electrons Reactions that involve the transfer of electrons LEO says GER LEO says GER Lose electrons oxidize Lose electrons oxidize Gain electrons reduce Gain electrons reduce Oxidation and Reduction are coupled together- something is oxidized because something else is reduced Oxidation and Reduction are coupled together- something is oxidized because something else is reduced

Water and Solutions Cells are mainly water and the water is an arena for the chemical reactions of life to occur Cells are mainly water and the water is an arena for the chemical reactions of life to occur Water is polar Water is polar H is slightly +, O is slightly – H is slightly +, O is slightly – Allows water molecules to interact with each other, ions, and other polar molecules Allows water molecules to interact with each other, ions, and other polar molecules Water is universal solvent because of its polarity- it dissolves a lot of stuff Water is universal solvent because of its polarity- it dissolves a lot of stuff

Hydrogen bonds form between water molecules allowing them to stick together Hydrogen bonds form between water molecules allowing them to stick together Hydrogen bonds form between H with a slight + charge and areas of – charge or with anions Hydrogen bonds form between H with a slight + charge and areas of – charge or with anions Can be formed or broken easily and repeatedly- weak independently, strong in great numbers Can be formed or broken easily and repeatedly- weak independently, strong in great numbers Many occur at one time in water Many occur at one time in water H bonds allow water to experience H bonds allow water to experience Cohesion- water molecules stick together Cohesion- water molecules stick together Adhesion- water molecules stick to other things Adhesion- water molecules stick to other things

When ionic compounds are dissolved in water they ionize- break apart into cations and anions When ionic compounds are dissolved in water they ionize- break apart into cations and anions

Water is less dense as a solid than as a liquid Water is less dense as a solid than as a liquid Ice floats- pond ecosystems are conserved even in winter Ice floats- pond ecosystems are conserved even in winter Water has a high specific heat capacity Water has a high specific heat capacity Water absorbs large amounts of heat with little temperature change Water absorbs large amounts of heat with little temperature change

Solutions Solutions are homogeneous mixtures Solutions are homogeneous mixtures All substances are evenly distributed throughout All substances are evenly distributed throughout Composed of solute and solvent Composed of solute and solvent Solute is what is dissolved (less of this) Solute is what is dissolved (less of this) Solvent does the dissolving (more of this) Solvent does the dissolving (more of this) Can have different concentrations Can have different concentrations How much solute is dissolved in the solvent How much solute is dissolved in the solvent Saturated- the max amount of solute is dissolved Saturated- the max amount of solute is dissolved

Aqueous solutions have water as the solvent Aqueous solutions have water as the solvent Essential for life Essential for life Aqueous solutions are essential for cells Aqueous solutions are essential for cells Blood is an aqueous solution Blood is an aqueous solution Many organisms live in aqueous solutions- The ocean! Ponds! Lakes! Rivers! Your gut! Many organisms live in aqueous solutions- The ocean! Ponds! Lakes! Rivers! Your gut!

Acids and Bases Water can ionize (split into ions) Water can ionize (split into ions) H 2 O H + + OH - H 2 O H + + OH - OH - is the hydroxide ion OH - is the hydroxide ion H + is a proton H + is a proton Water can also accept a proton (H + ), forming hydronium ion (H ) Water can also accept a proton (H + ), forming hydronium ion (H ) H + + H 2 O H H + + H 2 O H This occurs all of the time in water This occurs all of the time in water

Acids and bases are determined by the ratio of hydronium ions to hydroxide ions Acids and bases are determined by the ratio of hydronium ions to hydroxide ions Acids H > OH- Acids H > OH- Bases H < OH- Bases H < OH- Compounds that are acids donate a H+ and it will react with H 2 0 to form H 3 O + Compounds that are acids donate a H+ and it will react with H 2 0 to form H 3 O + Bases produce OH- which will increase their concentration Bases produce OH- which will increase their concentration

pH scale is a way to measure the concentration of H 3 O + pH scale is a way to measure the concentration of H 3 O + It is a logarithmic scale- so each number is a ten-fold difference in concentration of H 3 O + It is a logarithmic scale- so each number is a ten-fold difference in concentration of H 3 O +

Buffers are chemical substances that can absorb excess acids or bases to maintain pH Buffers are chemical substances that can absorb excess acids or bases to maintain pH Very important job Very important job Enzymes (biological catalysts) can only function in specific pH ranges Enzymes (biological catalysts) can only function in specific pH ranges Cells must regulate their pH Cells must regulate their pH

Biochemistry The study of the chemistry that allows life to exist and flourish The study of the chemistry that allows life to exist and flourish Biochemistry is centered around the element Carbon Biochemistry is centered around the element Carbon Organic compounds are those that contain carbon Organic compounds are those that contain carbon Inorganic compounds do not generally contain carbon Inorganic compounds do not generally contain carbon

Carbon Carbon has 4 valence electrons and needs 8 Carbon has 4 valence electrons and needs 8 Forms covalent bonds to complete its valence shell Forms covalent bonds to complete its valence shell Carbon is special because is will bond with up to 4 other carbon atoms Carbon is special because is will bond with up to 4 other carbon atoms Can form rings, straight chains, and branched chains Can form rings, straight chains, and branched chains

A covalent bond is formed when two atoms share 2 electrons A covalent bond is formed when two atoms share 2 electrons Represented with a straight line Represented with a straight line Carbon can form single, double, and triple bonds Carbon can form single, double, and triple bonds Carbon can form almost endless compounds as a result Carbon can form almost endless compounds as a result

Functional Groups Organic molecules all contain Carbon- so what makes one compound different from another- Functional Groups Organic molecules all contain Carbon- so what makes one compound different from another- Functional Groups Functional Groups are specific clusters of atoms attached to a carbon compound Functional Groups are specific clusters of atoms attached to a carbon compound Each functional group has specific properties that it gives the compound Each functional group has specific properties that it gives the compound

Large Carbon Molecules Monomers are small, simple molecules that can be bonded together to form polymers Monomers are small, simple molecules that can be bonded together to form polymers Macromolecules are made from polymers Macromolecules are made from polymers

Condensation and Hydrolysis Reactions Monomers are bonded together through condensation reactions Monomers are bonded together through condensation reactions With the addition of each monomer a water molecule is lost With the addition of each monomer a water molecule is lost

Polymers can be broken down into polymers through hydrolysis reactions Polymers can be broken down into polymers through hydrolysis reactions A water molecule must be added in order to split one monomer away from the polymer A water molecule must be added in order to split one monomer away from the polymer

Energy Currency Remember chemical bonds contain energy Remember chemical bonds contain energy Breaking or making a bond can either absorb or release energy Breaking or making a bond can either absorb or release energy Some compounds have a lot of energy stored in their bonds Some compounds have a lot of energy stored in their bonds This energy can be used to power cell functions This energy can be used to power cell functions

Adenosine Triphosphate (ATP) is a high energy compound Adenosine Triphosphate (ATP) is a high energy compound Bond between the second and third phosphate is hydrolyzed to release energy for cellular functions, leaving ADP and P Bond between the second and third phosphate is hydrolyzed to release energy for cellular functions, leaving ADP and P ATP + H 2 O  ADP + P + Energy ATP + H 2 O  ADP + P + Energy ADP + P + energy  ATP + H 2 O ADP + P + energy  ATP + H 2 O

Molecules of Life Carbohydrates, Lipids, Proteins, Nucleic Acids Carbohydrates, Lipids, Proteins, Nucleic Acids Each type has different properties and responsibilities Each type has different properties and responsibilities All have C, H, O; some also have N, P, S All have C, H, O; some also have N, P, S Put together in different ratios Put together in different ratios

Carbohydrates Roles include energy source and structural components Roles include energy source and structural components Made of C, H, O in a 1:2:1 ratio (CH 2 O) n Made of C, H, O in a 1:2:1 ratio (CH 2 O) n Monomer- monosaccharide Monomer- monosaccharide Glucose (simple sugar), galactose (milk), fructose (fruits) Glucose (simple sugar), galactose (milk), fructose (fruits) Disaccharides are made by a condensation rxn joining 2 monosaccharide Disaccharides are made by a condensation rxn joining 2 monosaccharide Glucose + Fructose  Sucrose Glucose + Fructose  Sucrose

Polymers are polysaccharides- large molecules made by joining many monosaccharides Polymers are polysaccharides- large molecules made by joining many monosaccharides Animals store excess sugar as Glycogen Animals store excess sugar as Glycogen Plants store excess sugar as Starch Plants store excess sugar as Starch Cellulose is a polysaccharide made by plants that gives cell walls strength and rigidity Cellulose is a polysaccharide made by plants that gives cell walls strength and rigidity Can be broken down by hydrolysis reactions Can be broken down by hydrolysis reactions

Proteins Have a diversity of structures, resulting in a wide range of functions Have a diversity of structures, resulting in a wide range of functions Account for ~50% dry mass of cells Account for ~50% dry mass of cells Act as enzymes, play roles in defense, storage, transport, cell communication, movement, structural support Act as enzymes, play roles in defense, storage, transport, cell communication, movement, structural support Each protein has a unique 3-D shape Each protein has a unique 3-D shape Composed of mainly C, H, O, N Composed of mainly C, H, O, N

Monomer is amino acid Monomer is amino acid There are 20 amino acids used to build thousands of proteins There are 20 amino acids used to build thousands of proteins Amino Acids have same basic structure Amino Acids have same basic structure Amino group, central C, Carboxyl group, and R group (variable- distinguishes 1 aa from another) Amino group, central C, Carboxyl group, and R group (variable- distinguishes 1 aa from another) Polymer is polypeptide Polymer is polypeptide Long chain of amino acids Long chain of amino acids Held together by peptide bonds Held together by peptide bonds Covalent bonds formed via condensation rxn Covalent bonds formed via condensation rxn

1 or more polypeptide chain(s) fold into complex shapes 1 or more polypeptide chain(s) fold into complex shapes Shape is essential to function Shape is essential to function Chains held together via interactions like hydrogen bonds Chains held together via interactions like hydrogen bonds Enzymes are important group of proteins Enzymes are important group of proteins Act as biological catalysts Act as biological catalysts Enzyme has a specific shape that will interact with a specific substrate Enzyme has a specific shape that will interact with a specific substrate Substrate is reactant being catalyzed fits in active site on enzyme Substrate is reactant being catalyzed fits in active site on enzyme

Lipids Function as long term energy storage, in membranes, water proof coverings, steroids (hormones) as chemical messengers Function as long term energy storage, in membranes, water proof coverings, steroids (hormones) as chemical messengers Have C, H, O- higher ratio of C and H to O Have C, H, O- higher ratio of C and H to O Long chains of C and H store more energy Long chains of C and H store more energy

Fatty Acids Fatty Acids Carboxyl Group connected to a long carbon chain Carboxyl Group connected to a long carbon chain Carboxyl group is polar and therefore hydrophilic Carboxyl group is polar and therefore hydrophilic Hydrocarbon chain is non-polar and hydrophobic Hydrocarbon chain is non-polar and hydrophobic Fatty acids that have each C bonded to 4 things are called saturated Fatty acids that have each C bonded to 4 things are called saturated Fatty acids that have double bonds between some C atoms are called unsaturated Fatty acids that have double bonds between some C atoms are called unsaturated

Triglycerides have 3 fatty acids joined to a glycerol head Triglycerides have 3 fatty acids joined to a glycerol head Saturated triglycerides have a high melting point and are solid at room temp- butter, fats, red meat Saturated triglycerides have a high melting point and are solid at room temp- butter, fats, red meat Unsaturated triglycerides are usually liquid at room temp- Plant oils (olive, sunflower, etc) Unsaturated triglycerides are usually liquid at room temp- Plant oils (olive, sunflower, etc)

Phospholipids- 2 fatty acids bonded to a glycerol head and a phosphate group Phospholipids- 2 fatty acids bonded to a glycerol head and a phosphate group Form water-tight barriers, such as cell membrane (lipid bi- layer) Form water-tight barriers, such as cell membrane (lipid bi- layer) Waxes are long chains of fatty acids bonded to large alcohol groups Waxes are long chains of fatty acids bonded to large alcohol groups Help plants retain water and earwax protects ear from invaders Help plants retain water and earwax protects ear from invaders

Steroids are made of 4 carbon rings and functional groups attached Steroids are made of 4 carbon rings and functional groups attached Hormones are steroids that have important roles transmitting chemical messages and roles in the cell membrane (cholesterol) Hormones are steroids that have important roles transmitting chemical messages and roles in the cell membrane (cholesterol)

Nucleic Acids Function to store and transfer information in cells, including hereditary material Function to store and transfer information in cells, including hereditary material Composed of C, H, O, N, P Composed of C, H, O, N, P Monomer- Nucleotide Monomer- Nucleotide Three parts: 5-C sugar, Nitrogenous base, Phosphate group Three parts: 5-C sugar, Nitrogenous base, Phosphate group ATP ATP Polymer- Nucleic Acid Polymer- Nucleic Acid DNA, RNA DNA, RNA