Chemistry of Life

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Chemistry of Life

• Honors Biology

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Students Will Be Able To

• Distinguish between atoms, elements, isotopes,
  and compounds.
• Determine protons, neutrons, electrons, charge,
  and atomic mass of an atom.
• Distinguish between ionic, covalent, and hydrogen
  bonds.

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Life depends on chemistry

• Millions of chemical reactions occur in living
  organisms every day. Organisms rely on chemical
  reactions in order to function. Food must be
  broken down, gases must be exchanged, molecules
  must be built.

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Ch. 2-1 Matter

• Everything in the universe is made of Matter.
• Matter is anything that has mass and takes up
  space.
• Mass is the quantity of matter an object has.
• Weight is the amount of gravity pulling on a
  mass.
• Chemical changes in matter are essential to all
  life processes

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Atoms

• An atom is the basic unit of matter.
• An atom is made
• of three parts
• Protons
• Electrons
• Neutrons

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Atomic Particles
Charge Location Mass
Proton 1 amu (atomic mass unit)
Neutron 1 amu (atomic mass unit)
Electron 0
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Parts of an Atom

• The nucleus is the center of the atom
• Contains 2 particles protons and neutrons
• Contains all the mass of the atom

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Parts of an Atom

• Electron shells contain electrons, high energy
  particles that orbit the atoms nucleus.
• First energy shell (or orbital)
• can hold 2 electrons
• All other shells
• can hold 8 electrons

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Elements

• Atoms come in more than 100 different kinds or
  species, called elements.
• Pure substance that cannot be broken down
  chemically into simpler kinds of matter.
• Elements are arranged on the periodic table a
  chart which provides info about the elements
• Each element has its own unique symbol

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The World of Elements
What do you think might be special about these
highlighted elements?
H
C
O
N
P
S
Na
Mg
K
Ca
Different kinds of atoms elements
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Reading the Periodic Table

• Atomic Number
• Tells you the number of protons
• Individual for each element
• of protons also of electrons why?
• Mass Number
• Tells you the mass of the atom
• Number of protons and neutrons
• Why not electrons, too?

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Isotopes

• The number of protons in an element never
  changes, however the neutrons can change
• Isotopes atoms of the same element with a
  different number of neutrons
• have a different mass

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Ions

• The number of electrons can also vary
• Ions atoms of the same element with a different
  number of electrons
• have a charge - why?

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Compound

• Made of two or more elements joined by a chemical
  bond
• Formed by chemical reactions

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Chemical Bonds

• All molecules (including biological ones) are
  held together by chemical bonds between atoms
• Formed by interactions among electrons in
  outermost shells in attempt to fill the outermost
  shell
• 3 Major Types of Chemical Bonds
• -Ionic Bonds
• -Covalent Bonds
• -Hydrogen Bonds

Well come back to these later
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Covalent Bonds

• Forms when two atoms share one or two pairs of
  electrons
• Forms a molecule, a covalently-bonded compound

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To Form a Covalent Bond
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Ionic Bonds

• Electrons are transferred from one atom to
  another.
• Elements become ions and have opposite charges (
  and -).
• Elements are attracted to each other because of
  opposite charges.

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To Form Ionic Bonds
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Ch. 2-4 Energy
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Students Will Be Able To

• Identify reactants, products, and activation
  energy in a chemical reaction.
• Distinguish between exothermic and endothermic
  reactions.

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Flow of energy through life

• Life is built on chemical reactions
• transforming energy from one form to another

organic molecules ? ATP organic molecules
sun
organic molecules ? ATP organic molecules
solar energy ? ATP organic molecules
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Energy

• Energy is the ability to do work or cause change
• Energy cannot be created nor destroyed, only
  transferred or converted to another form
• Free Energy is the energy available to do work.

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Chemical Reactions

• Chemical reaction process in which chemical
  bonds are made or broken, changing one set of
  chemicals into a different set of chemicals
• Reactants elements or compounds that enter into
  a reaction
• Products elements or compounds that are
  produced during a reaction
• ? yields or reacts to form (never use )

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Energy in Reactions

• Energy is either absorbed or released during all
  chemical reactions.
• Reactions that release energy do so as heat light
  or sound and often occur spontaneously.
  (exothermic or exergonic)
• ie. 2H2 O2 ? 2H2O
• Reactions that absorb energy will not occur
  without a source of energy. (endothermic or
  endergonic)
• ie. 2H2O ? 2H2 O2
• Activation energy energy needed to get a
  reaction started

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Activation Energy

• Catalysts are substances that lower the
  activation energy and make it easier to start a
  reaction, without being a part of the reaction
  themselves
• Enzymes are biological catalysts, protein-based
  ones made by living things.

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Enzymes

• Some reactions are too slow or require too much
  energy to happen on their own.
• Enzymes proteins that speed up chemical
  reactions
• Enzymes work by lowering the activation energy of
  the reaction.
• More on them later!

Activation energy without enzyme
Activation energy with enzyme
Course of Reaction
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Ch. 2-2 Water
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Students Will Be Able To

• Explain how four major chemical properties of
  water make it especially important to living
  things.
• Locate acids, bases, and neutral solutions on the
  pH scale, and explain the function of a buffer.

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Water
Why are we studying water?

• All life occurs in water
• inside outside the cell

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Water

• H2O 2 Hydrogen atoms 1 Oxygen atom
• Has many unique properties that make it one of
  the most important compounds in living things
• Covers ¾ of the Earths surface
• Makes up 70-95 of cells

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Polarity

• Oxygen atom 8 protons
• Hydrogen atom only 1 proton
• Oxygen has a stronger pull on the electrons
  and shares unevenly.
• Because of the uneven sharing, oxygen becomes
  PARTIALLY negative and hydrogen becomes
  PARTIALLY positive
• Uneven sharing makes the molecule polar

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Hydrogen Bonding

• Because water molecules are polar they are
  attracted to each other, positive end to
  negative end
• This attraction holds the molecules together,
  called a hydrogen bond
• H-bonds weak, broken and formed easily

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Elixir of Life

• Special properties of water
• 1. cohesion adhesion
• surface tension, capillary action
• 2. good solvent
• many molecules dissolve in H2O
• hydrophilic vs. hydrophobic
• 3. lower density as a solid
• ice floats!
• 4. Temperature moderation

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1. Cohesion Adhesion

• Cohesion
• H bonding between H2O molecules
• water is sticky
• surface tension
• drinking straw
• Adhesion
• H bonding between H2O other substances
• capillary action
• meniscus
• water climbs uppaper towel

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How does H2O get to top of trees?

• Transpiration is built on cohesion adhesion

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2. Water is the solvent of life

• Polarity makes H2O a good solvent
• polar H2O molecules surround ions
• solvents dissolve solutes creating solutions

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Describing Solutions

• Water is called the UNIVERSAL SOLVENT
• Solution a mixture in which one or more
  substances are uniformly distributed into another
  substance
• Example Kool-aid
• Solute the substance being dissolved in the
  solution
• Example Kool-aid mix
• Solvent the substance doing the dissolving
• Example water

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What dissolves in water?

• Hydrophilic
• substances have attraction to H2O
• polar

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What doesnt dissolve in water?

• Hydrophobic
• substances that dont have an attraction to H2O
• non-polar

fat (triglycerol)
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3. The special case of ice

• Most (all?) substances are more dense when they
  are solid, but
• not water
• Ice floats!
• H bonds form a crystal

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Why is ice floats important?

• Oceans lakes dont freeze solid
• surface ice insulates water below
• allowing life to survive the winter
• if ice sank
• ponds, lakes even oceans would freeze solid
• in summer, only upper few inches would thaw
• seasonal turnover of lakes
• sinking cold H2O cycles nutrients in autumn

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4. Temperature Moderation

• H2O resists changes in temperature
• takes a lot of energy to heat it up
• takes a lot of energy to cool it down
• H2O moderates temperatures on Earth

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5. Heat of vaporization
Evaporative cooling

• Organisms rely on heat of vaporization to remove
  body heat

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Ionization of water pH

• Water ionizes
• H splits off from H2O, leaving OH
• if H -OH, water is neutral
• if H gt -OH, water is acidic
• if H lt -OH, water is basic
• pH scale
• how acid or basic solution is
• 1 ? 7 ? 14

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Equation for Dissociation of Water

• 2H2O ? H3O OH-

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Think of pH as Water Balance
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Hydrochloric Acid dissociates in water to
Hydrogen ions and Chloride ions. Water is no
longer balanced Lots of extra Hydrogen ions!
Thats an acid!
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Sodium Hydroxide (lye, common in oven cleaners)
dissociates in water to form sodium ions (Na)
and hydroxide ions (OH-) Water is no longer
balanced Lots of extra Hydroxide ions! Thats a
base!
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pH Scale

• The pH scale is a measure of how acidic or basic
  something is
• Ranges from 0-14
• pH 7 neutral (pure water)
• pH lt 7 acid (tomatoes, lemons)
• pH gt 7 base (soaps, cleaners)

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Acids Bases

• Further from pH 7 stronger acid or base
• Acids
• Solutions where hydronium ions (H) gt hydroxides
  (OH-)
• Can be highly corrosive (acid rain)
• Have a pH below 7
• Bases
• Solutions where hydroxide ions (OH-) gt hydronium
  ions (H)
• Can be corrosive
• Have a pH above 7

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Buffers cellular regulation

• pH of most cells must be kept 7 Homeostasis!
• pH affects shape of molecules
• shape of molecules affect function
• So pH affects cellular function
• Control pH by buffers
• Molecules that help maintain a constant pH
• donate H when H falls
• absorb H when H rises

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Ch. 2-3 Biochemistry

• Honors Biology

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Students Will Be Able To

• Identify carbon as the most important atomic
  element to the chemistry of living things is
  carbon, and explain why. Identify other
  important elements are hydrogen, oxygen,
  nitrogen, potassium, and sulfur.
• Distinguish between condensation reactions,
  dehydration synthesis reactions, and hydrolysis
  reactions.

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• What are we made of?
• Why do we have to eat?

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Elements of Life

• 96 of living organisms is made of
• carbon (C)
• oxygen (O)
• hydrogen (H)
• nitrogen (N)

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The Chemistry of Carbon

• Living organisms are made of carbon based
  molecules known as organic molecules.
• Why is life based on carbon? It is abundant, and
  versatile
• Carbon can bond with up to 4 other atoms at once.
• Carbon can form single, double or triple bonds.
• Carbon bonds easily with other carbon atoms to
  form the backbone of large organic molecules.
• Carbon can bond with many different
  elements such as H, O,
  P, S, N.

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Macromolecules

• Most molecules in cells are so large they are
  macromolecules or giant molecules made from
  thousands of smaller molecules
• Polymerization large molecules are made from
  joining smaller ones together
• Monomers small building blocks
• Polymers long chains of monomers

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Building large molecules of life

• Chain together smaller molecules
• building block molecules monomers
• Big molecules built from little molecules
• polymers

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Building large organic molecules

• Small molecules building blocks monomers
• Bond them together polymers

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Making Polymers

• Monomers link to form polymers in a kind of
  condensation reaction called
• dehydration synthesis
• One water molecule comes out each time two
  monomers form a bond.
• Monomer Monomer ? Polymer Water

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Example of synthesis
amino acids
protein

• Proteins are synthesized by bonding amino acids

• amino acids monomers
• protein polymer

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How to take large molecules apart (digestion)

• Hydrolysis
• Chemical reaction that breaks polymers back down
  into monomers
• getting raw materials
• for synthesis growth
• making energy (ATP)
• for synthesis, growth everyday functions

Energy
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Breaking Down Polymers

• Water is added to break a bond between monomers.
• Exergonic reaction (energy comes out)
• Polymer Water ? Monomer Monomer

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Example of digestion
Energy
Energy
Energy
Energy
Energy
Energy
starch
glucose
Energy

• Starch is digested to glucose

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Energy Currency

• Life processes require energy
• Adenosine Triphosphate (ATP) is a molecule that
  contains LOTS of energy
• When P is removed,
• energy is released
• and can be used by
• the cell.