The Chemical Basis of Life

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The Chemical Basis of Life

• Atoms and Molecules
• Chapter 2

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• Student Link to
• Solomon Textbook 8th Edition

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In the beginning...
Big Bang 15 bya After 300,000 years, 3000º C
photons
protons
neutrons
electrons
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The Chemical Basis of Life

• What is Matter?
• Matter is composed of Elements
• Elements are composed of Atoms
• Atoms are composed of protons, neutrons
  electrons

Matter any substance that takes up space
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Elements

• Elements are substances that cannot be broken
  down into simpler substances by chemical
  reactions (i.e., non-nuclear reactions)
• Chemical symbols
• Carbon
• Hydrogen
• Oxygen
• Nitrogen
• Other elements are important too but are present
  in small quantities

Na Sodium (Natrium)
96 of the mass of most organisms
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Atoms

• Atoms are the smallest forms of matter that
  retain the chemical characteristics of a given
  element
• Atoms have a nucleus , which
• Contains protons (p)
• May contain neutrons (n)
• Clouds of electrons (e) surround the nucleus

Nucleus protons neutrons
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Protons, Electrons, Neutrons

• Protons have 1 charge and have a mass of 1.000
  atomic unit (AU)
• Neutrons have no charge but have a mass of 1.005
  AU
• Electrons have a -1 charge and a mass of 1/1800
  AU

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Atomic Number Atomic Mass

• The number of protons is called the atomic number
  
• The atomic number defines the element if the
  number of protons changes, the element changes
• The number of protons the number of neutrons
  the atomic weight (mass)
• In an uncharged atom, the number of protons
  equals the number of electrons

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The Chemical Basis of Life

• Atomic number protons in an elements nucleus
  (written on the top-left)
• 1H 8O
• a chart in which elements are arranged in order
  by their atomic number is the Periodic Table of
  Elements

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Atomic Mass

• The mass of an atom is so small that it cannot be
  measured in grams or ounces
• amu atomic mass unit dalton
• 1 amu the mass of one proton
• Atomic Mass protons neutrons
• the mass of electrons is ignored because it is
  sooooooooo small

168O
(Atomic Mass is written on bottom-left)
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The Atom

• protons Atomic number
• neutrons Atomic mass - protons
• electrons protons in an uncharged atom
• neutrons protons in a stable atom, all
  others are isotopes

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Isotopes

• Atoms that vary in Atomic mass are called
  isotopes
• Isotopes vary in the number of neutrons

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Isotopes

• Isotopes have the same protons and electrons
• differs from its element in the
• neutrons it has

1H
1H
2
3
deuterium
tritium
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Radioisotopes

• unstable isotopes that emit radioactivity when
  they decay
• autoradiography a technique that detects the
  decay of radioisotopes

1H
3
tritium
6C
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Carbon
15P
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Phosphorus
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Autoradiography

• dating fossils
• tracing biochemical pathways
• sequencing DNA
• medical research
• blood
• urine
• thyroid

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Electrons

• Move in orbitals and shells corresponding to
  energy levels
• The energy levels of the electrons are called
  shells. Shells can have one or more orbitals
  within them.
• each shell contains at least one orbital and a
  minimum of 2 electrons (e)
• shells are depicted as electron clouds

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Electrons and Orbitals
Bohr Model
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Electrons

• Electrons fill orbitals and shells in a
  determined pattern
• 2-8-8-10
• 2n2 where n1st, 2nd, or 3rd shell
• The Lewis electron dot structure shows how
  electrons occupy a shell or orbital

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Electrons and Energy

• The energy levels of the electrons are called
  shells. Shells can have one or more orbitals
  within them. The outermost shell is the valence
  shell
• The farther away the electron is from the
  nucleus, the greater its potential energy.

Lower energy
Higher energy
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Valence Electrons

• Participate in chemical reactions
• When the valence shell is full, the element is
  stable and does not react with other elements
• When the valence shell is incomplete, the element
  is reactive
• It wants to donate, receive, or share electrons
  with other elements

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Valence Electrons
Valence Electrons are found in the valence
shell and participate in chemical reactions
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The Periodic Table

• Elements are grouped and described in the
  Periodic Table
• Columns refer to the number of valence electrons
  (electrons in the outermost shell).

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The Periodic Table

• Column I elements have only one electron in their
  valence shell.
• These elements easily give up that electron.
• In columns II and III, elements have 2 or 3
  electron(s), respectively, in their outer shells
  and are electropositive they tend to give away
  those electrons to other atoms.

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The Periodic Table

• Elements in columns V, VI, VII need 3, 2, or 1
  electron(s), respectively, to fill their outer
  shells
• They are electronegative they pull electrons
  from other elements.
• Electronegative electron greedy

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Combinations of Atoms Molecules

• Atoms react only when they come very close.
• Atoms may stick together and form molecules,
  which are combinations of atoms.
• molecules are formed from more than one element
  (i.e., from different atoms or the same atoms)

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Atoms form Molecules
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Atoms are Joined by Chemical Bonds

• Chemical bonds are forces of attraction
• Each bond has a particular energy bond energy
• Types of chemical bonds
• ionic
• covalent
• hydrogen

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Ions

• Ions are elements that have an electrical charge
• An atom becomes an ion (charged) when it either
  gains or loses electrons
• When an atom has 1,2, or 3 e- in its outermost
  shell, it will tend to lose those electrons and
  become charged
• charged ions are called cations

1H
-
1H


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Ions

• An atom becomes an ion (charged) when it either
  gains or loses electrons
• Atoms with 5,6, or 7 e- in their outermost shell
  will tend to gain electrons and become charged
• charged ions are called anions

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Ionic Bonds

• In ionic bonds, electrons are donated or received
  between atoms
• An electronegative atom steals an electron from
  another atom to fill its valence shell and
  becomes negatively charged.
• An electropositive atom gives away its electrons
  and becomes positively charged

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Ionic Bonds

• formed by the gain or loss of electrons
• are held together by attraction

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11 protons
17 protons
and
11 electrons Sodium (Na)
17 electrons Chlorine C


10 electrons Sodium ion
18 electrons Chlorine ion
Sodium chloride (NaCl)
Na
Cl
Cl
Na
Na
Cl
Na
Arrangement of atoms in a crystal of salt
Fig. 2. 09
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Ionic compounds easily dissociate in water

• NaCl falls apart into ions when placed in water
• Salt dissolves in water

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Electrolytes
Cations and Anions are also called Electrolytes
Gatorade Thirst Quencher contains a blend of
lab-tested electrolytes sodium, potassium and
chloride to replenish the minerals athletes
lose through sweat during exercise and
competition.
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Biologically Important Cations
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Biologically Important Anions
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Acids

• are compounds that dissociate in water to yield a
  H an anion

The acidity of a solution is dependant on the
concentration of H The more H , the more
acidic a solution is
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Bases

• are compounds that dissociate in water to yield
  a hydroxide ion OH- a cation

A base makes a solution alkaline and is
proportional to the concentration of hydroxide
ions
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Salts

• ionize in water to form a cation and an anion

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Covalent Bonds

• are formed by two atoms sharing electrons
• in this way each atom has a filled valence shell
• Ex water

CH4
H2O
NH3
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(a) Single covalent bond formation
H
H

Hydrogen (H)
Hydrogen (H)
Molecular hydrogen (H2)
or
H
H
(b) Double covalent bond formation
O
O
O
O
Oxygen (O)
Oxygen (O)
Molecular hydrogen (O2) (double bond is formed)
or
O
O
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Covalent bonds between different atoms
Oxygen part

Hydrogen parts
Partial negative charge at oxygen end of molecule
Partial positive charge at hydrogen end
of molecule

Hydrogen (H)
Oxygen (O)
Hydrogen (H)
Formation of polar covalent bonds
Water Molecule H2O
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Thinking About Covalent Bonds

• The Lewis structure uses dots to indicate the
  number of electrons in the valence shells of
  atoms
• In contrast, a structural model uses a line to
  represent the shared pair of electrons

methane
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Covalent Bonds can be polar or nonpolar
When electrons are shared evenly, a nonpolar
covalent bond is formed

• Polar covalent bonds are formed when electrons
  are not shared equally among atoms

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Polar Covalent Bonds

• Electronegative atoms are electron greedy atoms
• These atoms tend to form polar covalent bonds and
  take on a slightly negative charge ?-
• oxygen
• nitrogen
• phophorous

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Polar Covalent Bonds

• When electropositive atoms form polar covalent
  bonds they take on a slightly positive charge ?
• Hydrogen

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Polar covalent bonds in the water molecule
Oxygen part

Hydrogen parts
Partial negative charge at oxygen end of molecule
Partial positive charge at hydrogen end
of molecule

Hydrogen (H)
Oxygen (O)
Hydrogen (H)
Formation of polar covalent bonds
Water Molecule H2O
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Polar covalent bonds in a molecule of ammonia
?-
Partial negative charge at nitrogen end of
molecule
?
?
?
Partial charge at the hydrogen end of molecule
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Covalent Bonds
Polar
Non-Polar
Atoms have partial charges (d)
Electrically neutral no charges
Can form hydrogen bonds
Do not form hydrogen bonds
Hydrophilic
Hydrophobic
Hydrophobic Interactions
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Hydrogen Bonds are weak attractions

• Form between electronegative atoms atoms of one
  molecule with the electropositive atoms of
  another molecule (usually Hydrogen)
• Water forms hydrogen bonds with other water
  molecules

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Electronegative atoms
H


O
H
N
H
Hydrogen bond
H
H
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H
H
O
O

Hydrogen bonds between water molecules

H


O
O

H
H
O
O


O
O
H
H

H
H
H
O
O
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Water forms hydrogen bonds with ions
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Properties of Water

• Water is essential to Life
• a large component of all living organisms
• 70 in humans
• 70 of planet earth is water
• source of oxygen in the air we breathe
• (through photosynthesis)

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Properties of Water

• unique chemical and physical properties
• excellent solvent
• facilitates chemical reactions
• Hydrophilic substances are drawn to water
• Hydrophobic substances resist water

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Water is Sticky

• Water is sticky because of H bonding
• Cohesive sticks to itself
• Adhesive sticks to other things
• Meniscus
• Creeps into small polar spaces (moves up fine
  capillaries because it sticks to glass, which is
  charged)

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Properties of Water

• Hydrogen bonding makes water cohesive and
  adhesive
• Cohesive
• water sticks to water
• Adhesive
• water adheres to other substances

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Three forms of Water
Gas
Liquid
steam
water
Solid
Ice
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100 C
212 F
(a) Steam becoming water vapor (gas)
50 C
(b) Water (liquid)
0 C
32 F
(c) Ice (solid)
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Reactions of Ions in Water Acids, Bases, Salts

• Water molecules have a slight tendency to ionize

H OH-
HOH
H OH- 10 -7
water is neutral
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Acids

• are compounds that dissociate in water to yield a
  H an anion

The acidity of a solution is dependant on the
concentration of H The more H , the more
acidic a solution is
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Bases

• are compounds that dissociate in water to yield
  a hydroxide ion OH- a cation

A base makes a solution alkaline and is
proportional to the concentration of hydroxide
ions
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pH
a measure of acidity
pH - log H
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pH is Very Important

• Cell function is greatly dependent on pH
• Normal physiological pH is usually close to pH
  7.4
• Physiological pH is implicated in
• Reaction rates
• Organization of membranes
• Organization of the cytoskeleton
• Enzyme conformation and catalytic properties
• Minor deviations from physiological pH can be
  very devastating to biochemical reactions (and
  therefore, to life processes)

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Buffers minimize changes in pH

• important biological solutions!
• pH must remain in a certain range for cells,
  blood, and other bodily fluids to function
  properly
• a buffer resists changes in pH when an acid or
  base is added

pH 7.4
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Buffers minimize changes in pH

• CO2 (in the blood)
• a common buffering system in vertebrates