Chemical Basis for Life

Chemical Basis for Life
Unit 2 Chemical Basis for Life

Chapter 6 Chemistry in Biology

Section 1: Atoms, Elements, & Compounds (p
Section 1: Atoms, Elements, & Compounds (p ) Section 2: Chemical Reactions (p ) Section 3: Water & Solutions (p ) Section 4: The Building Blocks of Life (p )

Atoms, Elements, and Compounds
Section 1 Atoms, Elements, and Compounds

Objectives Living things consist of atoms of different elements
Ions form when atoms gain or lose electrons Atoms share pairs of electrons in covalent bonds

The atom The atom is the smallest basic unit of matter
Atoms are very small Smallest components of an element that retains its properties Elements are made of countless atoms of the element Each atom has the same properties as the element Atoms have a nucleus Neutrons that are neutral & Protons that are positive are in the nucleus Electrons that are negative orbit around the nucleus

The atom There are three parts of a an atom Subatomic particle Charge
Location Proton Positive Nucleus Neutron Neutral Electron Negative Surrounding nucleus Protons are positively charged and found in the nucleus Neutrons have no charge; they are neutral; They are found in the nucleus as well Electrons are negatively charged and orbit around the nucleus The atomic # identifies the element; Tells you the amount of protons Protons tells you the amount of electrons. They are oppositely charged and need to “cancel” eachother out Atomic mass tells you the average amount of protons and neutrons in the nucleus So to find neutrons, subtract the atomic # (amount of protons) from the atomic mass

Elements An element is one particular type of atom, and it cannot be broken down into a simpler substance by ordinary chemical means Gold Aluminum Helium Give a brief overview of the periodic table Show the noble gases, and what makes them so noble Show metals & nonmetals

Atoms & Elements

Key Elements CHOPSN In biology, there are SIX very important elements
Carbon Hydrogen Oxygen Phosphorus Sulfur Nitrogen CHOPSN Hydrogen (59%), Oxygen (24%), Carbon (11%), Nitrogen (4%), make up 80% of the components of the cell These make up biomolecules Carbon is very important b/c we are CARBON-BASED lifeforms Carbon also acts as a “building block” Organic chemistry is the chemistry of carbon-carbon bonds

How are elements different
The number of protons determines the identity of an element Carbon: 6 protons Oxygen: 8 protons The number of electrons determines the property of an element Carbon: 6 electrons, 4 on OUTSIDE Oxygen: 8 electrons, 6 on OUTSIDE Remember the # of protons, AKA the atomic #, identifies the element Go over energy levels (2 electrons in the first level, 8 electrons in the second, 8 to 18 in the third, etc)… 2n^2 is the equation Show the electron cloud model Show the electron dot (Bohr’s) model

Carbon diagrams Do both the electron cloud model, and the electron dot (Bohr’s) model

Chemical Party

Lonely Atoms Atoms rarely are found alone in nature
They will do ANYTHING to get to 8 electrons on the outside Steal Dump Share Stealing/Dumping = Ionic bond Sharing = Covalent bond

Compounds A compound is a substance made of atoms of different elements bonded together Result of sharing, stealing, or dumping electrons Atoms bonded in a specific ratio The specific ratio is very important If ratio gets changed it is something completely different Example: H2O = Water …. H3O = Hydronium ion All compounds have very different properties from eachother and of their individual components Example: H2O = water and it puts out water… Hydrogen and Oxygen individually both fuel fires

Carbon Compounds (more about this later)
Carbon can form many various bonds to form Carbohydrates Proteins Nucleic acids Lipids Talk about organic chemistry These are very important Biomolecules/macromolecules

Ionic Bond Ionic bonds are formed through the electrical force between oppositely charged ions Opposites attract! Ex: Salt aka sodium chloride (NaCl) Positive sodium (Na+) Negative chloride (Cl-) Ionic bonds steal and dump These bonds occur between metals and nonmetal elements

NaCl – ionic bond Do NaCl ionic bond example
Have class figure out how many particles in Na (11 protons, 11 electrons… energy level is 2,8,1) Have class figure out how many particles in Cl (17 protons, 17 electrons… energy level is 2, 8, 7) Draw electron cloud and then electron dot of both Na and Cl Show how Na give 1 electron to Cl Its easier to give 1 electron than taking 7, right? Now add positive charge to Na and negative charge to Cl Opposites attract

Ions Ions are atoms that have gained or lost one or more electrons.
Results in a change in electrical charge Gain e becomes negative Lose e becomes positive Ions are the elements involved in ionic bonds In previous slide sodium was a positive ion, which was denoted Na+ Chlorine was a negative ion, denoted Cl-

Ions, cont. Very important to organisms
Hydrogen ions (H+) needed to produce chemical energy in cells Calcium ions (Ca2+) needed for all muscle movement in your body Chloride ions (Cl-) needed for many chemical signals in the brain We cannot function w/o these ions

Covalent Bond Not all atoms easily gain or lose their electrons!
Some atoms share their electrons instead! Covalent Bond: forms when atoms share a pair of electrons Usually a very strong bond Atoms may have several covalent bonds to share several electrons Remember ionic bonds dump or steal electrons to form ions, and then the oppositely charged ions attract… opposites attract Covalent bonds share electrons instead of dumping and stealing These bonds are between 2 non-metals Are pretty strong bonds

H2O – covalent bond Show H2O example
Have class come up with particles in Hydrogen (1 proton, 1 electron… energy level 1) Have class come up with particles in Oxygen (8 protons, 8 electrons… energy level 2, 6) Draw electron cloud & electron dot of each Show how they combine

CO2 – covalent bond Show CO2 example
Have class come up with particles in Carbon (6 proton, 6 electron… energy level 2, 4) Have class come up with particles in Oxygen (8 protons, 8 electrons… energy level 2, 6) Draw electron cloud & electron dot of each Show how they combine

Covalent Bond, cont. Molecule: two or more atoms held together by covalent bonds Ex: carbon dioxide (CO2) Carbon atoms needs 4 electrons to fill outer level, oxygen needs two Carbon shares with 2 oxygen!

Ions, Ionic Bonds, & Covalent Bonds

Ionic Bonds Covalent Bonds

Review What are atoms? How are the particles that make up atoms diagrammed? What are the similarities between covalent and ionic bonds?

Section 2 Chemical Reactions

Objectives Bonds break and form during chemical reactions.
Chemical reactions release or absorb energy. So we have done a little with reactions already. Showing the different bonds that may result Who remembers the different bonds we have covered and what they are? Covalent… Sharing of electrons between 2 nonmetals Ionic… dumping/stealing of electrons between a metal and a non metal Hydrogen bond… a weak bond between hydrogen and a electronegative element such as oxygen

Evidence of a chemical reaction
Temperature change Formation of a solid (precipitate) Color change (sometimes) Odor (sometimes) Formation of gas Give examples of a chemical reaction… Light Temperature change Color change (sometimes) Odor change (sometimes) Etc.

Chemical Reactions Chemical Reaction... Gummy bear torture
Poor gummy bear… Example of a chemical reaction Magnesium oxide demo HCl demo

Chemical Reactions Bonds break & form during chemical reactions
Plant/Animal cells break down sugars to get usable energy Cells build protein molecules by bonding amino acids together Chemical reactions change substances into different substances by breaking and forming chemical bonds So bonds break and form during chemical reactions Chemical reactions have 2 or more reactants that form something different, which is at least 1 product Show example of a reaction

Chemical Reactions Reactants are the substance changed during a chemical reactions Oxygen (O2) & Glucose (C6H12O6) Products are the substances made by a chemical reaction Carbon Dioxide (CO2) & Water (H2O) 6O2 + C6H12O CO2 + 6H2O Here is a example of a chemical equation This is cellular respiration which we will be getting into in a upcoming chapter The reactants are oxygen and glucose The products are carbon dioxide and water The inverse of this equation (6CO2 + 6H2O -> 6O2 + C6H12O6) is photosynthesis Reactants Products

Reactants & Products

It’s all about the energy
Energy is needed to break bonds in molecules Bond energy is the amount of energy that will break a bond between two atoms. Every atom has different bond energy A SPECIFIC amount of energy is needed to break bonds in an oxygen molecule A SPECIFIC amount of energy is needed to break bonds in a glucose molecule Energy is released when bonds are formed The amount of energy released is equal to the energy that breaks the same bond Energy needed to break apart water molecule = energy released when hydrogen & oxygen atoms bond to form a water molecule To break bonds we need energy Every atom has it’s own unique bond energy Bond energy is the amount of energy that will break a bond between 2 atoms When bonds are formed, energy is released, which is equal to the amount of energy it took to break the bonds

Chemical Reactions All chemical reactions involve changes in energy
Energy added to the reactants breaks their chemical bonds When new bonds form in the products, energy is released Energy is both absorbed and released during a chemical reaction! Some release more energy than they absorb (Generous) Some absorb more energy than they release (Greedy) To break bonds energy must be added When bonds form energy is released In a chemical reaction, energy is both released and absorbed However some will release more energy then they absorb. They are generous reactions. Some absorb more energy than they release. They are greedy reactions.

Chemical Reactions, cont.
Generous chemical RXNs that release more energy than they absorb = Exothermic reaction Excess energy is the difference in bond energy between the reactants and products Excess energy is often released as heat or light Cellular respiration releases usable energy for your cells & heat! The generous reactions that release more energy than they absorb are call exothermic reactions Or in biology they are called exergonic Remember binomial nomenclature… Exo means outside… Exoskeleton is skeleton on the outside This excess energy that is released is the difference in bond energy between reactants and products This excess energy is often released as heat or light. A example of exergonic reaction is cellular respiration

Chemical Reactions, cont.
Greedy chemical RXNs that absorb more energy than they release = Endothermic reaction In photosynthesis, plants absorb energy from sunlight and use that to make sugars and carbohydrates

Exothermic VS. Endothermic graphs
Draw a exothermic graph, labeling reactants, products, activation energy, and energy released. Draw a endothermic graph with the same

But how does a rxn start? Some energy must first be absorbed by the reactants in ANY chemical reaction The amount of energy needed will vary Activation energy is the amount of energy that needs to be absorbed for a chemical reaction to start Push a rock up a hill Activation energy is the energy that needs to be overcome for the reaction to start Look at the picture Explain the boulder example

Activation energy Activation Energy

Catalysts & Enzymes A catalyst is a substance that lowers the activation energy needed to start a chemical reaction. Special proteins called enzymes are the biological catalysts that speed up the rate of chemical reactions in biological processes. Activation energy is the energy that needs to be overcome for the reaction to start Look at the picture Explain the boulder example

Enzymes

Review What are the parts of a chemical reaction?
How can energy changes be related to chemical reactions? What is the importance of enzymes in living organisms?

Section 3 Water and Solutions

Objectives Life depends on hydrogen bonds in water.
Many compounds dissolve in water. Some compounds form acids or bases.

THE IMPORTANCE OF WATER
CELLS Organisms’ bodies, (their _____________), are made up of mostly ____________________ The water in cells gives the cell _______________ and ___________________ materials within organisms. All of the processes necessary for an organism’s life take place within the ______________________________ of the cell WATER STRUCTURE TRANSPORTS Our cells are made mostly of water Water gives cells structure & helps transport materials within All processes necessary for an organism take place within the watery environment of the cell This watery environment is called the aqueous environment of a cell What does aqueous sound like? Aqua What does aqua mean? Aqua means water Breaking words apart is so important in biology WATERY ENVIRONMENT

PROPERTIES RELATED TO HYDROGEN BONDS ______________________
HIGH SPECIFIC HEAT 2. COHESION 3. ADHESION ______________________ 2. ______________________ 3. ______________________ Specific heat is the amount of energy it takes to raise the temperature 1 degree Celsius Cohesion is attraction among the same molecules Adhesion is attraction among different molecules

Hydrogen Bonding

HYDROGEN BONDS O H H POLAR UNEQUAL ELECTRONS HYDROGEN POSITIVE
Negative Charge POLAR O Water is a “______________” molecule Form when atoms in a molecule have ____________ pulls on the _____________ they share. Opposite charges of polar molecules can interact to form ____________________ bonds. An attraction between a slightly _______________ hydrogen atom and a slightly ______________ atom. (Usually _______________________________) Hydrogen bonds are part of the structures of _______________ and of ______________ UNEQUAL ELECTRONS H H Positive Charge Positive Charge HYDROGEN Shared Electrons POSITIVE NEGATIVE OXYGEN OR NITROGEN PROTEINS DNA

COHESION Cohesion: the attraction among __________________ of the same substance. Cohesion from hydrogen bonds makes water molecules _____________________. Cohesion produces __________________, ( “skin on water” ) MOLECULES STICK TOGETHER SURFACE TENSION Attraction among the same molecule Water has cohesion to other water molecules

ADHESION Adhesion: the attraction among __________________ of ______________ substances. For example, water molecules stick to other things. Water in a test tube, (water is attracted to the ____________) MOLECULES DIFFERENT ? GLASS Adhesion is attraction among molecules of different substances Show penny demo (water droplets on a penny)

MOLECULES DISSOLVE IN WATER
Materials such as ________________ and ____________ cannot be transported form one part of an organism to another unless they are dissolved in blood, plant sap, or other water based fluids. ______________: Mixture of a substance that is the same throughout. ___________: Substance that is present in the greater amount and dissolves another substance. ___________: Substance that dissolves in a solvent. MOLECULES DISSOLVE IN WATER SUGARS OXYGEN SOLUTION SOLVENT Water is a polar molecule It means that part of it is partially negative, and another part is partially positive Solution is a mixture of a substance that is the same throughout A solvent is a substance that is present in the greater amount and dissolve the other substance Solute is the substance that is being dissolved Think of the north and south poles, they are opposite Water being polar can dissolve other polar substances such as sugars & ionic compounds b/c weaker attraction between polar & nonpolar than 2 polar Water doesn’t dissolve oil/fats/lips Example of a cup of water and table salt Example of a cup of water and vegetable oil SOLUTE

Mixtures Heterogeneous Homogeneous
A mixture with easily separated parts with their distinct properties A mixture that it the SAME throughout and hard to tell individual characteristics

ACIDS AND BASES BASE: Compounds that
Some compounds form ______________ or _____________ because they _______________ into _______________ when they dissolve in ___________. BASE: Compounds that remove H+ ions from a solution ACIDS BASES BREAK UP IONS WATER ACID: Compounds that release a proton a hydrogen ion(H+) – when it dissolves in water Acids & bases break up into ions when they dissolve in water Acids release a proton (H+) when it dissolves in water Bases remove protons (H+) from solution

soap More acidic More basic neutral
The pH scale is a scale from 0 to 14 7 Neutral To the left of 7 is acidic, 0 being the strong acid To the right of 7 are bases, 14 being the most basic The pH scale is logarithmic, which means each # you move up or down on the scale, there is a difference of 10 fold in relative basicity/acidity More acidic More basic neutral

pH Scale examples

Review How does the structure of water make it a good solvent?
What are the similarities and differences between solutions and suspensions? What are the differences between acids and bases?

The Building Blocks of Life
Section 4 The Building Blocks of Life

Objectives Carbon atoms have unique bonding properties.
Four main types of carbon-based molecules are found in living things.

BUILDING BLOCKS OF CELLS
PROTEIN P ____________________ LIPIDS R L ____________________ CARBOHYDRATES O I C ____________________ ATP T P A A ____________________ So these are the building blocks of cells These are the important macromolecules N NUCLEIC ACID E I R T ____________________ A I D B P N

Carbohydrates Carbohydrates are molecules composed of carbon, hydrogen, and oxygen Include sugars & starches Can be broken down to provide useable energy for cells Major part of plant cell structure The most basic carbs are simple sugars, monosaccharides Polysaccharides are polymers of monosaccharides Carbohydrates provide energy used by your cells Examples are sugars (sucrose is table sugar or candy; fructose is fruit sugar; glucose) & starches (grains, potatoes, rice, bread) Carbohydrates such as complex starches are major part of plant structure Monosaccharides are simple sugars and the most basic carbs Polymers of monosaccharides are called polysaccharides.. Mono means 1, poly means multi.

CARBOHYDRATES USED BY CELLS FOR __________ ___________ AND __________ ____________. SIMPLE CARBS = _______________________________ COMPLEX CARBS = _____________________________ _____________________________ ENERGY SOURCE ENERGY STORAGE ONE OR TWO SUGAR MOLECULES LONG CHAINS OF SUGAR MOLECULES Ex) Starches such as potato, pasta, bread ________________________________ Note only are carbs used as an energy source, but also for energy storage Simple carbs are just one or two sugar molecules whereas complex carbs are very long sugar chains

Proteins Proteins are the most varied of the carbon-based molecules in organisms Have a role in movement, eyesight, digestion, etc. A protein is a polymer made of monomers called amino acids Amino acids are molecules that contain carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur Organisms use 20 different amino acids to build proteins The body makes 12 of the 20, the other 8 come from food Proteins vary greatly Their roles are vary greatly Amino acids are the monomer that is the building block for proteins Therefore proteins are the polymer of amino acids Amino acids contain many of those important elements that we talked about a week or two ago. Remember CHOPSN? There are a total of 20 amino acids that we use as building blocks for proteins However our body can only readily make 12 of the 20. We get the other 8 from foods we ingest. The 12 that we make are called the 12 nonessential amino acids, because we make them The 8 that we do not make are considered essential, because it is essential you supplement your body with them

These are the 20 amino acids
The ones with the arrows next to them are 8 essential (body doesn’t make them) amino acids The ones without the arrows are the 12 nonessential (body does make them) amino acids

PROTEIN CELLS MAKE UP _________________.
INVOLVED IN ALL _______ ____________. BUILDING BLOCKS = _________ __________. _________________= TYPE OF PROTEIN THAT STARTS AND SPEEDS UP CHEMICAL REACTIONS IN CELLS. LIFE PROCESSES AMINO ACIDS ENZYME Amino acids make up proteins, and proteins make up our cells Very important, and are involved in all life processes That means they have many functions and tasks Enzymes are proteins that speed up and help start chemical reactions in cells Enzymes are catalysts

Lipids Lipids are nonpolar molecules that include fats, oils, and cholesterol Contain chains of carbon bonded to oxygen & hydrogen Some broken down for useable energy Others are part of a cell’s structure Fatty acids are chains of carbon atoms bonded to hydrogen atoms. Saturated fatty acids have single carbon-carbon bonds Unsaturated fatty acids have double carbon- carbon bonds Lipids are made of CHO (carbon, hydrogen, oxygen; some of those IMPORTANT elements again) Lipids are nonpolar Since they are nonpolar that means they cannot be dissolved in water Include fats, cholesterol, and oil If you have a glass of water and put some vegetable oil in there what happens? It floats because water cannot dissolve it Cells use them for structure and for energy Fatty acids make up lipids 2 types of fatty acids Saturated and unsaturated Saturated have a carbon-carbon SINGLE bond Unsaturated have a carbon-carbon DOUBLE bond

The top is a example of a saturated fatty acid b/c it has single carbon-carbon bonds.
The bottom is a example of a unsaturated fatty acid b/c it has double carbon-carbon bonds. See the black lines? Also notice the difference in structure.

LIPIDS WATER DON’T MIX WITH ______________.
PHOSPHOLIPIDS – MAKE UP ________ ______________. FATS AND OILS THAT _________ ___________. ORGANISMS USE FATS AND OILS WHEN THEY HAVE USED UP ___________________. _________- SOLID AT ROOM TEMPERATURE. _________- LIQUID AT ROOM TEMPERATURE. CELL MEMBRANE STORE ENERGY CARBOHYDRATES FATS Again, lipids do not mix with water. This is because they are nonpolar. In addition many are LESS dense than water Less dense than water means less than 1.0g/ml, but also tells you it will float on water Fats & oils store energy After a organism uses energy from carbohydrates, they will tap into the stored energy from fats and oils What is the difference between fats and oils? Their state of matter at room temperature! Fats are room temp whereas oils are liquid at room temp OILS

ATP MAJOR ___________ ___________ MOLECULE IN CELL. ENERGY CARRYING
ENERGY IN __________________ AND __________ AND _____________________ MUST BE TRANSFERRED TO ATP IN CELL TO BE USED. ENERGY CARRYING CARBOHYDRATES LIPIDS PROTEINS So we talked about how cells use these macromolecules for energy Macromolecules like carbs, lipids, and proteins In order for their energy to be used, a cell must transfer their energy to ATP ATP stands for adenosine triphosphate ATP is a major energy carrying molecule for cells

Nucleic Acids Detailed instructions to build proteins are stored in extremely long carbon-based molecules called nucleic acids Nucleic acids are polymers that are made up of monomers called nucleotides Nucleic acids differ from the other carbon- based molecules The others have a large # of functions Nucleic acids have just 1 function… make proteins DNA stores info for putting amino acids together to make proteins RNA helps to build proteins The instructions to build proteins come from nucleic acids Nucleic acids are very long carbon-based molecules They are made of nucleotides Nucleic acids are the polymer; Nucleotides are the monomer Nucleic acids only serve 1 purpose; whereas other carbon-based molecules have many Their sole calling in existence is to make proteins There are two nucleic acids in particular that help DNA = Deoxyribose nucleic acid RNA = Ribosomal nucleic acid DNA store the info for putting the amino acids together RNA helps to build the proteins

NUCLEIC ACIDS HAVE ALL INFO NEEDED TO MAKE __________. PROTEIN
“_______________” OF LIFE. BUILDING BLOCKS OF _____________. TWO TYPES: ________ AND _______. PROTEIN BLUE PRINT NUCLEOTIDES DNA RNA

Monomer & polymer Each subunit of a complete carbon- based molecule is called a monomer A polymer is a large molecule, or macromolecule, made of many monomers bonded together Monomers of a polymer may be the same (ex. Starches) Or different (proteins) So we have covered this already but it is important to know Each unit of a carbon-based molecule is called a monomer A polymer is made of many monomers together Starch polymers are made from many of the same monomers together Proteins are many difference kinds of monomers bonded together

COMPOUND BUILDING BLOCK (POLYMER) (MONOMER)
PROTEIN AMINO ACID LIPID (FAT) FATTY ACID CARBOHYDRATE SUGARS NUCLEIC ACIDS NUCLEOTIDE So as a review here are the carbon based polymers we have gone over And also here are the monomers or building blocks that make them up

Review What is the role of carbon in living organisms?
What are the four major families of biological macromolecules? What are the functions of each group of biological macromolecules?

Chemical Basis for Life

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