The Chemical Basis of Life

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The Chemical Basis of Life

• Atoms and Molecules
• Chapter 2

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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

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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

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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 Atomic Number IS the number of protons
• The Atomic Number defines the element, if the
  number of protons changes, the element changes
• The Atomic Weight (Mass) the number of protons
  the number of neutrons
• In an uncharged atom, the number of protons
  equals the number of electrons

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Periodic Table of Elements

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

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Fig. 2.5
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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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Summary of the Atom

• protons Atomic number
• neutrons Atomic mass - protons
• electrons protons in an uncharged atom

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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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Radioisotopes

• unstable atoms 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 is used for

• Dating fossils
• Medical research and diagnostics
• Thyroid a PET scan is shown on the left.
  Radioactive Iodine is used to view the thyroid
  gland
• Digestive system

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Electrons

• Move in orbitals and shells
• 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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Fig. 2.3
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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 energy levels of the electrons are called
  shells. Shells can have one or more orbitals
  within them.
• The outermost shell is the valence shell

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Shells and Orbitals
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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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Electrons and 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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Electrons and 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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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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Table 2.3
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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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Atoms are Joined by Chemical Bonds

• 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)
• Types of chemical bonds
• ionic
• covalent
• hydrogen

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Ionic Bonds

• The definition of an ionic bond
• Electrons are
• Donated
• Received
• Gained
• Lost
• Transferred

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Ionic Bonds

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

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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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Fig. 2.16
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Acids

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

Acid H 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
• Are compounds that accepts protons (H)

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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pH
a measure of acidity
pH - log H
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pH is Very Important

• Many cellular functions are greatly dependent on
  pH
• Normal physiological pH is usually close to pH
  7.4
• Physiological pH is implicated in
• The rates of chemical reactions
• 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
FYI

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

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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
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Covalent Bonds can be polar or nonpolar

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

When electrons are shared evenly, a nonpolar
covalent bond is formed
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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
• phosphorous

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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
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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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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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Hydrogen bonds between water molecules
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Water forms hydrogen bonds with ions
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Properties of 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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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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Fig. 2.20g
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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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• Hydrophobic substances resist water
• Hydrophobic substances are made of atoms that are
  held together by non-polar covalent bonds

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Three Forms of Water
Gas
steam
Liquid
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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pH
a measure of acidity
pH - log H