Chapter 6 Chemistry in Biology

Chapter 6.1 Atoms, Elements, and Compounds Matter – anything that occupies space and has a mass.

Atoms, Elements, & Compounds Atoms – the simplest particles of en element; the building block of all matter

Structure of Atoms

Structure of Atoms Protons Positively (+) charged particles + Have mass (1 amu = 1 atomic mass unit) Located in the nucleus + Neutrons Neutral particles (No charge) Have mass (1 amu) Also located in the nucleus n Electrons Negatively (-) charged particles Mass is negligible (1/1840 amu) Remain in constant motion in orbitals/shell

Structure of Atoms Electrons constantly move around the atom’s nucleus in energy levels. These energy levels are sometimes referred to as shells or orbitals. The electrons (-) are attracted to the protons (+). Atoms contain an equal number of protons and electrons so the overall charge is ZERO

Elements Elements are substances that cannot be broken down chemically into simpler kinds of matter.

Elements in Living Things Hydrogen (H) Carbon (C) Oxygen (O) Nitrogen (N) Calcium (Ca) Magnesium (Mg) Sodium (Na) Potassium (K) Phosphorus (P)

C The Periodic Table 6 12.011 Atomic Number Chemical Symbol Atomic Mass

Biology Class Notes - October 3, 2006 The Periodic Table The number of protons in an atom is called the atomic number. In an atom, the number of positive protons is balanced by an equal number of negative electrons. net electrical charge equals zero The model to the left represents an atom of which element? How many electrons must be in the electron shells? = neutron = proton

Biology Class Notes - October 3, 2006 Atomically Speaking… The Periodic Table The mass number of an atom is equal to the total number of protons and neutrons of the atom. What is the mass number of our carbon atom? = neutron = proton

Practice 19 39 20 What is the atomic number of potassium? What is the mass number of potassium? How many protons does potassium contain? How many neutrons does potassium contain? (Mass number – Atomic Number = Neutrons) How many electron does potassium contain? 19 39 20

Drawing an Atomic Model Find the element’s ATOMIC NUMBER. This determines the number of protons and electrons. Find the MASS NUMBER. Subtract the atomic number from the mass number to determine the number of neutrons. How many protons, electrons, and neutrons are found in an oxygen atom?

Drawing an Atomic Model Draw the PROTONS and NEUTRONS in the nucleus of the atom. Place the electrons in the correct shell: Draw the first shell around the nucleus and place TWO electrons in the first shell. Draw the next shell and place up to EIGHT electrons in the second shell If electrons remain, draw the third shell and place up to EIGHTEEN electrons in the third shell Draw the model for an oxygen atom.

Oxygen Example Atomic Number is 8 Mass Number is 16 Protons - 8 Electrons - 8 Mass Number is 16 Neutrons – 8 (16-8 = 8) 8 P 8 N

Atomic Models Draw the following atoms in you notebook: Fluorine Magnesium Aluminum

Bill Nye Atoms Part 1 - http://www.youtube.com/watch?v=zbc85dv3ouk

Isotopes Isotopes are atoms of the same element that have different numbers of neutrons. Isotopes will have different mass numbers (isotopes have the same atomic number) Isotopes react the same chemically = neutron = proton These two atoms are both carbon atoms. But the atom on the left has 6 neutrons while the atom on the right has 7 neutrons. Because of this, these two atoms are said to be isotopes of one another.

Radioactive Isotopes Sometimes having too many neutrons can make the nucleus of an atom unstable. Unstable nuclei decay, or break apart. Particles (usually neutrons) and energy in the form of radiation are released. This radiation can be used to calculate the age of an object or it can be used in medical treatments such as radiation therapy.

Compounds Elements combine to form more complex structures called compounds Compounds are represented by their chemical formula H2O CO2 C6H12O6 NaCl (subscripts show how many atoms of each element are in the compound)

Compounds Each compound has a specific ratio of elements Physically and chemically different from the elements that make up the compounds Cannot be broken down into smaller elements by physical means (may be broken down chemically) Held together by chemical bonds

Chemical Bonds Compounds form because most atoms are not stable in their natural state. A partially-filled outermost energy level is not as stable as an energy level that is completely filled with the maximum number of electrons it can hold. Is this carbon atom stable? = neutron = proton = electron

Chemical Bonds Atoms become more stable by losing electrons or attracting electrons from other atoms This results in the formation of chemical bonds

(electrons are shared) Two Ways to Bond Covalent Bonds (electrons are shared) Ionic Bonds (attraction of a charged atom)

Chemical Bonds Covalent Bond Ionic Bond A chemical bond that forms when electrons are SHARED Example: water An atom can gain or lose an electron to make a stable energy level. This atom is called an ion and is now charged. An ionic bond is electrical attraction between two oppositely charged atoms. Example: sodium chloride

Covalent Bonds

Ionic Bond

Covalent Bonding Examples Hydrogen and Chlorine

Covalent Bonding Examples Carbon and Hydrogen Nitrogen and hydrogen

Ionic Bonding Examples Magnesium and Oxygen

Ionic Bonding Examples Sodium and Oxygen

Ionic Bonding Examples Calcium chloride

Chapter 6.2 Chemical Reactions http://www.youtube.com/watch?v=PlwuxpMh8nk&feature=related (until 3:45/8:00)

Chemical Reactions 4 Fe + 3 O2 2 Fe2O3 Process by which atoms or groups of atoms in substances reorganize into different substances Involve the breaking and reforming of chemical bonds. For example – 4 Fe + 3 O2 2 Fe2O3

Physical Change vs. Chemical Change Physical change affects appearance, not composition. You have the same substance before and after the physical change. A chemical change affects composition. You have a different substance after the chemical change. How do you know a chemical change has occurred? Clues: Production of heat or light Formation of a solid, liquid, or gas

Chemical Equations C6H12O6 + 6O2  6H2O + 6CO2 Scientists often use chemical equations to show what is happening during a chemical change. C6H12O6 + 6O2  6H2O + 6CO2 The substances on the left side of the arrow are called the reactants. They are reacting and are forming the substances on the right side, the products.

Reactants and Products Chemical Equation: C6H12O6 + O2 CO2 + H20 (Glucose and oxygen react to form carbon dioxide and water) Reactants (starting substances): C6H12O6 + O2 Products (substances formed): CO2 + H20

Balanced Equation According to the principle of conservation of mass, matter cannot be created or destroyed So the number and types of atoms on each side of the equation must be balanced. (or the number of atoms of each element on the reactant side must equal the number of atoms of the same element on the product side) http://www.youtube.com/watch?v=_B735turDoM For example: 2 H2O2 2 H20 + O2 C6H12O6 + 6 O2 6 CO2 + 6 H20

How to Balance an Equation Step 1: Count the number of atoms of each element on both the product and reactant side. You can create a chart to help you. Step 2: Determine which atoms are not balanced. Element Reactant Side Product Side O C

How to Balance an Equation Step 3: Balance one atom at a time, using coefficients. Start with atoms that appear only once in the reactants and only once in the products. Usually leave Hydrogen atoms followed by Oxygen atoms until last. Step 4: After you believe that you have successfully balanced the equation, repeat Step 1, to be certain that mass conservation has been achieved. Note: DO NOT Change subscripts in a molecular formula (i.e., 2 NaCl Na2Cl2 )

Balanced Equation H2O2 H2 + O2 Na + Cl2 NaCl Zn + HCL ZnCl2 + H2 Fe + Cl2 FeCl2

Energy of Reactions Activation Energy – minimum amount of energy needed to start a chemical reaction; energy needed for reactants to form products

Energy of Reactions Endothermic Exothermic Energy-Absorbing Reaction Energy-Releasing Reaction Products Activation energy Activation energy Reactants Endothermic Exothermic

Enzyme Tutorials Activation Energy and Enzymes - Overview – http://www.sumanasinc.com/webcontent/animations/content/enzymes/enzymes.html Overview – http://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter2/animation__how_enzymes_work.html Sucrose Example - http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__enzyme_action_and_the_hydrolysis_of_sucrose.html http://www.northland.cc.mn.us/biology/Biology1111/animations/enzyme.html http://www.phschool.com/science/biology_place/labbench/lab2/temp.html http://bcs.whfreeman.com/thelifewire/content/chp06/0602001.html

Enzymes Most chemical reactions proceed slowly since the activation energy is high A catalyst is a substance that lowers the activation energy needed to start a chemical reaction Enzymes are biological catalysts; enzymes are proteins

Enzymes http://www.sumanasinc.com/webcontent/animations/content/enzymes/enzymes.html

How Enzymes Work Reactants, called substrates, bind to specific enzymes; the site where enzymes bind is called the active site Once the substrate binds to the active site, it changes shape and forms the enzyme-substrate complex The substrates react to form new products; the enzyme-substrate complex helps to break and form bonds

Example of Enzyme Reaction http://blog.poolcenter.com/print.asp?articleid=6072

Another View of Enzymes

Enzymes Many factors can affect enzyme activity such as: pH Temperature Concentration of substrates

Chapter 6.3 Water & Solutions

Water’s Polarity Water molecules are formed by covalent bonds between 2 hydrogens and 1 oxygen atom Since the electrons are more strongly attracted to the oxygen, the electrons spend more time near the oxygen nucleus The unequal distribution of electrons gives oxygen a slight negative charge Molecules with an unequal distribution of charges are polar molecules – they have oppositely charged regions Slight Negative Charge Slight Positive Charge

Water’s Polarity and Hydrogen Bonds The two water molecules are brought together, their polar ends attract each other This attraction between water molecules is called hydrogen bonding It is a weak bond between the hydrogen of one atom and the oxygen of another A water molecule can hydrogen bond with four other water molecules

Hydrogen Bonding in Water http://commons.wikimedia.org/wiki/File:3D_model_hydrogen_bonds_in_water.jpg

Properties of Water Physical property – properties that describe a substance without changing the identity of the substance. Physical change – change that does not result in the production of a new substance, only the appearance of the substance Chemical property – properties that describe how a substance changes into a completely different substance Chemical change – change that results in the production of another substance

Water is COHESIVE and ADHESIVE Properties of Water Water is COHESIVE and ADHESIVE Because of hydrogen bonding, Water is attracted to other water molecules – this is called COHESION Water is attracted to other surfaces – this is called ADHESION

Cohesion How many paper clips were added before the cup overflowed? What did the water on the surface of the cup look like just before it overflowed?

Surface Tension Tendency of water molecules on the edges of a water droplet to attract inward toward other water molecules thus producing a “skin” Predict / Results What will happen to pepper grains that are sprinkled on a cup of water? What will happen to the grains when soap is added to the water?

Cohesion Causes Surface Tension

Adhesion

Adhesion (Capillary Action) http://discovermagazine.com/2003/mar/featscienceof http://www.sciencebuddies.org/science-fair-projects/project_ideas/PlantBio_p033.shtml

Temperature Moderation Temperature is a measure of heat which is a form of energy Water can absorb large amounts of energy as heat for its molecular size Water has the highest specific heat of any common substance. Specific heat is the heat required to raise the temperature of one gram of a substance one degree Celsius.

Effects of a High Specific Heat Water can absorb/release a large quantity of heat without a large change in temperature Moderates coastal climates Reduces dramatic day-night temperature fluctuations

Evaporative Cooling As water evaporates, the surface of the water that remains behind cools. Principle behind sweating to maintain body temperature in land animals

Density of Ice Angle of hydrogen bonds causes ice crystals to have lots of open space Open space leads to low density As a result, ice floats! Ponds & lakes freeze from top to bottom. Ice insulates deeper water from colder air. Ice crystal Liquid water

Water Expands When It Freezes Properties of Water Water Expands When It Freezes Because of hydrogen bonding, water molecules separate when freezing and water becomes less dense Extremely important for marine organisms

Solid Water (Ice) Liquid Water http://cc.oulu.fi/~nmrwww/comp_res4.html

Mixtures Two or more substances which are combined so that each substance keeps its own chemical identity. Water combines to form many types of mixtures Mixtures can be classified as Homogeneous – a combination of substances that is uniform throughout or Heterogeneous – a combination of substances that are physically distinct from one another

Mixtures Mixtures can be classified as Homogeneous – a combination of substances that is uniform throughout or Heterogeneous – a combination of substances that are physically distinct from one another

Homogenous Mixtures Solution – A mixture in which one substance (the solute) is dissolved completely into another substance (the solvent) so that the two cannot be distinguished Water is the universal solvent Examples: Salt in water Powdered drink mix in water Saliva

Water is the UNIVERSAL SOLVENT Properties of Water Water is the UNIVERSAL SOLVENT Because water is polar, it can dissolve many substances For example, NaCl http://www.mhhe.com/physsci/chemistry/essentialchemistry/flash/molvie1.swf http://www.youtube.com/watch?v=CLHP4r0E7hg&feature=related

http://www.visionlearning.com/library/module_viewer.php?mid=57

Homogenous Mixtures Same uniform appearance Same composition throughout Examples Sugar water Salt water Water and vinegar Air in the atmosphere

Homogeneous Mixture Solutions are a homogeneous mixture There are two components of solution: Solvent – a substance in which another substance is dissolved Solute – the substance that is dissolved

Heterogeneous Mixtures Suspension – heterogeneous mixture that contains fine solids or liquids that will settle out spontaneously Example: sand in water Colloid – heterogeneous mixture containing particles larger than solutes, but small enough to not settle out spontaneously Examples: blood, fog, smoke, butter, paint, ink

Heterogeneous Mixture Visibly different substances Components remain distinct Examples – Vinegar and oil Salad (lettuce, vegetables, croutons, etc.) Sand and water

Acids and Bases WATER H2O ACIDS BASES Substances that release H+ ions when dissolved in water WATER H2O Substances that release OH- ions when dissolved in water ACIDS BASES

pH Scale H2O H+ + OH- pH scale – measurement system used to indicate the concentration of H+ ions in a solution pH scale ranges from 0-14 pH 7 is neutral and the concentration of H+ ions and OH- ions is equal Acids – any compound that forms H+ ions in solution; contain pH values less than 7 (the lower the pH values, the higher the acidity) Bases – a compound that produces hydroxide ions (OH-) in solution; contain lower concentrations of H+ ions than water and have pH value greater than 7 Buffers weak acids or bases that can react with strong acid or bases to prevent sudden changes in pH For example, to buffer a strong acid, you would add a weak base

The Building Blocks of Life Chapter 6.4 The Building Blocks of Life

Organic Chemistry Organic compounds are those containing CARBON Life forms are carbon-based and therefore considered organic

Organic Chemistry Carbon has FOUR electrons in its outermost shell Therefore, carbon can form up to FOUR covalent bonds with other atoms

Macromolecules CARBOHYDRATES LIPIDS PROTEINS NUCLEIC ACIDS Macromolecules – large molecules that form from joining smaller molecules together The smaller molecules are called monomer The larger molecules are called polymers Four biologically important macromolecules: CARBOHYDRATES LIPIDS PROTEINS NUCLEIC ACIDS

Macromolecules Monomer – smaller molecule Polymer – larger molecule formed by joining together smaller molecules

Biological Macromolecules Group Function Carbohydrates Store Energy Provide structural support (cell wall) Lipids - Store energy - Provide cellular barriers Proteins - Transport substances - Speed up reactions Provide structural support Make hormones Nucleic Acids Store and communicate genetic information

Carbohydrates Chemical Composition Made of Carbon, Hydrogen , and Oxygen Ratio of 1:2:1 (# of C atoms: # of H atoms: # of O atoms) Or (CH2O)2 Functions in Living Things ENERGY! Structural support (cellulose in plant cell walls or chitin in animal shells) Structure Monomers may be small carbohydrates like glucose or sucrose. These monomers are called monosaccharide The monomers join to form large polymer called polysaccharides Examples Sucrose – table sugar Cellulose – support of plant cell walls Chitin – rigid support for animal shells (ex. lobster)

Carbohydrates Polymer Monosaccharaides linked together to form larger molecules 2 linked together in a chain are called disaccharides 3 or more are called polysaccharides (starches) Monomer - 3 – 7 CH2O molecules linked in a ring structure are a simple sugar or monosaccharide

Lipids Chemical Composition Made of Carbon, Hydrogen, and Oxygen Higher ratio of Hydrogen to Carbon Functions in Living Things ENERGY storage Provide barriers for cell (cell membranes) Protective layers Structure Composed of several fatty acids attached to glycerol Examples Fats Waxes – protective coating on leaves Oils Biological steroids

Lipids Lipids have fatty acid tails that are made of carbon and hydrogen by single or double covalent bonds Single Bond = Saturated Fat Double Bond = Unsaturated Fat More than one double bond is called a polyunsaturated fat

Proteins Chemical Composition Composed of Carbon, Hydrogen, Oxygen, Nitrogen, and sometimes Sulfur Functions in Living Things Transport substances Speed up chemical reactions Hormones Structural support Structure Monomers of proteins are amino acids The monomers, amino acids, join to form long chains of proteins Examples Enzymes – speed up chemical reactions

Proteins Monomer is the amino acid Polymer is the Protein – several amino acids are joined together by covalent bonds called a peptide bond

Nucleic Acids Chemical Composition Composed of Carbon, Hydrogen, Oxygen, Nitrogen, and Phosphorus Functions in Living Things Store genetic information Structure Smaller monomers, called nucleotides, join together to form long polymers, DNA and RNA Examples DNA – stores genetic information RNA – copies and transmit genetic information; help to make proteins

Nucleic Acids Monomer is the nucleotide Polymer is the nucleic acid Nucleotide with 3 phosphate group is ATP 6 major nucleotides Polymer is the nucleic acid DNA and RNA