The Chemistry of Life

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The Chemistry of Life

• Unit III
• Chapter 2

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Atoms

• The study of chemistry begins with the basic unit
  of matter, the atom
• Very small (1 million atoms 1cm)
• Atoms are made up of subatomic particles called
  protons, neutrons, and electrons
• Protons are charged
• Neutrons are neutral
• Electrons are charged
• Together, protons and neutrons make up the
  nucleus of an atom (at the center of the atom)
• Electrons are in constant motion in the space
  surrounding the nucleus (much smaller than
  protons neutrons)

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Elements

• A chemical element is a pure substance that
  consists entirely of one type of atom
• Represented by 1 or 2 letter symbols such as C,
  H, Na
• The number of protons in an atom of an element is
  the elements atomic number
• Example Carbons atomic is 6, meaning that an
  atom of carbon has 6 protons and 6 electrons

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Chemical Compounds

• In nature, most elements are found combined with
  other elements in compounds.
• A chemical compound is a substance formed by the
  chemical combination of two or more elements in
  definite proportions
• Chemical formulas are used to show what elements
  make up a compound
• Example H2O, NaCl

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Isotopes

• Atoms of an element can have different numbers of
  neutrons
• These atoms of the same element that differ in
  the number of neutrons they contain are known as
  isotopes
• The sum of the protons and neutrons in the
  nucleus of an atom is called its mass number
• Because they have the same number of electrons,
  all isotopes of an element have the same chemical
  properties

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Radioactive Isotopes

• Some isotopes are radioactive, meaning that their
  nuclei are unstable and break down at a constant
  rate over time
• Can be dangerous but useful
• Geologists can determine ages of fossils by
  analyzing the isotopes found in them
• Radioactive isotopes can be used to treat cancers

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Ions different of electrons

• Elements with more or less electrons than their
  atomic number
• Cl - Chlorine with one extra electron
• Na Sodium with one less electron

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Atomic Structure

• Protons/neutrons nucleus
• Electrons will fill energy levels in specific
  pattern
• 1st level 2 e- (max)
• 2nd level 8 e- (max)
• 3rd level 8 e- (max)
• 4th level 18 e- (max)
• See board for example atomic structure of
  potassium

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• Parts of the Atom
• Using the Periodic Table, determine the number of
  protons (p), neutrons (n0), and electrons (e-)
  in the proper energy levels. Draw a model of the
  atom showing the electrons in the proper energy
  levels.
• H
• C
• Na
• O
• Cl

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Fig. 2-9
Valence Electrons determine bonding ability
Helium 2He
Hydrogen 1H
Atomic number
2
He
4.00
Atomic mass
Element symbol
First shell
Electron- distribution diagram
Lithium 3Li
Beryllium 4Be
Boron 5B
Nitrogen 7N
Fluorine 9F
Neon 10Ne
Carbon 6C
Oxygen 8O
Second shell
Sodium 11Na
Aluminum 13Al
Silicon 14Si
Chlorine 17Cl
Argon 18Ar
Magnesium 12Mg
Phosphorus 15P
Sulfur 16S
Third shell
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The Octet Rule

• Atoms will share or steal electrons in order to
  reach stable valence energy level
• How do we know? Noble Gases
• Helium, Argon, Neon, Radon will NOT bond with any
  other elements
• of electrons for each?

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The AtomTry these
2

• Which elements do these atomic structures
  represent?
• How many more electrons needed to be stable?

1
3
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Chemical bondsForming a compound/molecule

• Bond to join together atoms using electron
  energy/force
• Atoms are most stable when their valence e- cloud
  is full
• Elements can share electrons to fill their
  valence e- cloud
• This causes stability

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The AtomElectron clouds

• EXAMPLE Carbon has 6 electrons
• They are arranged as
• 2 in the first energy level has 4 in the second
  energy level
• How many electrons does carbon need to be stable?
• How many bonds can it make?

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Main Types of Bonds by strengths

• 1. VanDer Waals Forces - weakest
• 2. Hydrogen Bonds
• 3. Ionic Bonds
• 4. Covalent Bonds

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Covalent Bonds
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1. Covalent bonds
EXAMPLE ?Oxygen alone only has 6 e- in its outer
level ?If it shares 2 more it would have 8 in its
outer level and be stable ?co share
Figure 6.6
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Ionic Bonds
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2. Ionic bonds

• When atoms give or take electrons not sharing
• The atoms with extra (or less) e- are now not
  neutral ION bond forms

Figure 6.7
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Water

• Water is 2 Hydrogen 1 Oxygen? H20
• Water is POLAR, meaning that it
• has an unequal distribution of
• charges polar covalent bonds
• Water is the Universal
  Solvent it dissolves other polar
  substances (sugars, some
  proteins) and ionic compounds (NaCl)

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Properties of Water

• Water is sticky
• It is held together by
• Hydrogen Bonds (force
• between H of 1 atom
• and O of another atom)
• Water is Cohesive (attracted to itself).
• Water is Adhesive (attracted to other things).
• Leads to Surface Tension

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Ice floats!BUT other frozen chemicals (benzene)
will sink
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Capillary Action

• Cohesion and Adhesion allow water to travel
  upwards against gravity called Capillary Action

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Covalent bonding

• Ex CH4
• Draw each of the 5 atoms in the formula with the
  correct number and location of protons, neutrons
  and electrons show how bonding occurs by
  indicating which electrons are shared between the
  atoms

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Covalent Bonds Dogs of equal strength

• Bone Electron
• Covalent bonds - two or more dogs with equal
  attraction to bones
• Dogs (atoms) are identical, then the dogs share
  the pairs of available bones evenly
• Since one dog does not have more of the bone than
  the other dog, the charge is evenly distributed
  among both dogs
• The molecule is not "polar" meaning one side does
  not have more charge than the other.

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Ionic Bonding

• HCl
• Draw each atom in the chemical formula showing
  the correct number of neutrons, protons and
  electrons show how bonding occurs by circling
  the electrons that are lost gained

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Ionic Bonds One big greedy thief dog!

• One big greedy dog steeling other dog's bone
• Bone represents the e- that is up for grabs
• then when the big dog gains an e- he becomes
  negatively charged
• the little dog who lost the e- becomes positively
  charged
• The two ions (that's where the name ionic comes
  from) are attracted strongly to each other as a
  result of the opposite charges.

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Mixtures

• Physical combination of 2 or more elements or
  compounds with no chemical combinations
• 2 types
• Solutions
• Suspensions

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Solutions Suspensions

• Solution type of mixture where components are
  uniformly distributed (like sugar water)
• Solute what is being dissolved (sugar)
• Solvent the thing that is doing the dissolving
  (water)
• Suspension mixture where some components do not
  dissolve/ remain suspended (muddy lake water)

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Acids, Bases, pH

• The pH Scale is used to determine the acidity and
  basicity of substances
• pH Scale ranges from 0 to 14

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pH a measurement of hydrogen ions
Acids forms hydrogen (H) ions in water
(H3O) Taste sour Bases forms hydroxide (OH-)
ions in water also called alkaline Taste
bitter slippery
Figure 2.10
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pH Scale
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The pH Scale

• pH scale to indicate the concentration of H ions
  in solution
• Ranges from 0 to 14
• At a pH of 7, the concentration of H ions and
  OH- ions is equal (pure water has a pH of 7)
• pH below 7 are called acidic because they have
  more H ions than OH- ions (the lower the pH, the
  greater the acidity)
• pH above 7 are called basic because they have
  more OH- ions than H ions (the higher the pH,
  the more basic the solution)

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Acid and Base Strength

• The concentration of the acid/base does not
  determine how strong it is
• EX a REALLY concentrated acid can be WEAK
  harmless
• Acid and Base STRENGTH is based on how many H
  are given up (acids) or attracted to (bases) OH-
• Water cant equalize strong acids/bases
• Neutralization reaction acid base ? water
  salt (pH 7)
• NaOH (strong base) HCl (strong acid) ? NaCl
  (salt) H2O (water)

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Acids in Biology

• Affect the rate of enzymes
• Digestion
• Prevent infection
• Damage tissues
• Present in urine
• What will H ions seek out?

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Bases in Biology

• Emulsify fats
• bile release from gall bladder and liver in
  digestion
• Medicines
• Toxins
• Severe burns/tissue damage
• What would OH- ions seek out?

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Blood Buffers

• H and CO2 build up during exercise acidic pH
  of blood
• Blood should be at pH 7.4
• Why is pH important?
• It effects enzyme function and protein structure
• Carbonic Acid Buffer in blood keeps pH in range
• Causes quicker respiration

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Measuring pH

• There are several INDICATORS to measure pH
• pH paper
• litmus paper
• pH meter

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What Life is Made Of

• Living things are composed of
• SULFUR
• PHOSPHORUS
• OXYGEN
• NITROGEN
• CARBON
• HYDROGEN
• REMEMBER SPONCH

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Macromolecules

• Many of the molecules in living cells are so
  large that they are known as macromolecules
• Formed by a process called polymerization (making
  large compounds by joining smaller compounds
  together)
• Smaller unit known as monomer join together to
  form polymers
• Four groups of organic compounds found in living
  things are
• Carbohydrates
• Lipids
• Nucleic acids
• proteins

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Carbohydrates

• Carbohydrates are compounds made up of carbon,
  hydrogen, and oxygen atoms
• Usually found in a ratio of 121
• Living things use carbohydrates as their main
  source of energy
• Plants and some animals also use carbohydrates
  for structural purposes
• The breakdown of sugars, such as glucose,
  supplies immediate energy for all cell activities
• Extra sugar is stored by living things as starch
  (composed of glucose)

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Lipids

• Lipids are a group of molecules that are
  generally not soluble (do not dissolve) in water
• They are made mostly from carbon and hydrogen
  atoms
• Common categories include fats, oils, steroids,
  and waxes
• Lipids can be used to store energy and some
  lipids are important parts of biological
  membranes and waterproof coverings
• Lipids are also used to cushion and insulate the
  body
• Lipids are formed when a glycerol molecule
  combines with 3 fatty acids
• If each carbon atom in a lipids fatty acid chain
  is joined to another carbon atom by a single
  bond, the lipid is said to be saturated
• If there is at least one carbon-carbon double
  bond in a fatty acid, the fatty acid is said to
  be unsaturated

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Nucleic Acids

• Nucleic acids are macromolecules containing
  hydrogen, oxygen, nitrogen, carbon, and
  phosphorus
• They are polymers assembled from individual
  monomers called nucleotides
• Nucleotides consist of 3 parts a 5-carbon
  sugar, a phosphate group, and a nitrogenous base
• Nucleic acids store and transmit hereditary
  (genetic) information
• There are 2 kinds of nucleic acids
• RNA (ribonucleic acid)
• DNA (deoxyribonucleic acid)

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Proteins

• Proteins are macromolecules that contain nitrogen
  as well as carbon, hydrogen, and oxygen
• They are polymers of molecules called amino acids
• Amino acids are compounds with an amino group
  (-NH2) on one end and a carboxyl group (-COOH) on
  the other end
• Each protein has a specific role
• Some control the rate of reactions and regulate
  cell processes
• Others transport substances into or out of cells
  or help to fight disease
• Others are used to build and repair body tissues
  such as muscles

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Chemical Reactions

• Everything that happens in an organism its
  growth, its interaction with the environment, its
  reproduction, and even its movement is based on
  chemical reactions
• A chemical reaction is a process that changes one
  set of chemicals into another set of chemicals
• Can occur slowly or very quickly
• The elements that enter into a chemical reaction
  are known as reactants
• The elements or compounds produced by a chemical
  reaction are known as products
• Chemical reactions always involve the breaking of
  bonds in reactants and the formation of new bonds
  in products

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Energy in Reactions

• Energy is released or absorbed whenever chemical
  bonds form or are broken
• Therefore, all chemical reactions involve changes
  in energy
• Some chemical reactions release energy and some
  absorb energy
• Chemical reactions that release energy often
  occur spontaneously
• Chemical reactions that absorb energy will not
  occur without a source of energy

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Activation Energy

• Even chemical reactions that release energy do
  not always occur spontaneously
• Chemists call the energy that is needed to get a
  reaction started the activation energy
• Activation energy is a factor in whether the
  overall chemical reaction releases energy or
  absorbs energy

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Enzymes

• Some chemical reactions that make life possible
  are too slow or have activation energies that are
  too high to make them practical for living tissue
• These chemical reactions are made possible by
  catalysts
• A catalysts is a substance that speeds up the
  rate of a chemical reaction
• Catalysts work by lowering the activation energy
  needed to make the reaction occur

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Enzymes

• Enzymes are proteins that act as biological
  catalysts
• Cells use enzymes to speed up chemical reactions
  that take place in cells
• Enzymes act by lowering the activation energies
• Enzymes are very specific, generally catalyzing
  only one chemical reaction

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Enzyme Action

• For a chemical reaction to take place, the
  reactants must collide with enough energy so that
  existing bonds will be broken and new bonds will
  be formed
• Enzymes speed up chemical reactions by providing
  a site where reactants can be brought together to
  react
• Such a site reduces the energy needed for the
  reaction by placing the reactants in a position
  favorable for the reaction to occur
• The reactants of enzyme-catalyzed reactions are
  known as substrates
• Enzymes can be affected by changes in pH, changes
  in temperature and can be turned on or off at
  critical stages in the life of a cell