Chapter 2 The Chemical Context of Life

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Chapter 2The Chemical Context of Life

• The three subatomic particles and their
  significance.
• The types of bonds, how they form, and their
  relative strengths

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Overview

• Living organisms and the world they live in are
  subject to the basic laws of physics and
  chemistry.
• Biology is a multidisciplinary science, drawing
  on insights from other sciences.
• Life can be organized into a hierarchy of
  structural levels.
• At each successive level, additional emergent
  properties appear.

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The Basics

• Everything is made of matter
• Matter is made of atoms
• Matter is anything that takes up space and has
  mass.
• Atoms are made of
• protons mass of 1 nucleus
• neutrons 0 mass of 1 nucleus
• electrons - mass ltlt1 orbits
• Different kinds of atoms elements

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The World of Elements
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• An element is a pure substance that cannot be
  broken down into other substances by chemical
  reactions.
• There are 92 naturally occurring elements.
• Each element has a unique symbol, usually the
  first one or two letters of the name. Some of the
  symbols are derived from Latin or German names.

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• A compound is a pure substance consisting of two
  or more elements in a fixed ratio.
• Table salt (sodium chloride or NaCl) is a
  compound with equal numbers of atoms of the
  elements chlorine and sodium.

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Models of atoms
Atoms have volume and mass. Mass of one proton
or one neutron atomic mass unit (amu) or 1
dalton, or 1.7 1024 grams. Mass of one
electron 9 1028usually ignored
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Atomic structure determines behavior

• The number of protons in an atom determines the
  element
• of protons atomic number
• this also tells you of electrons, if neutral
• of neutrons atomic mass- atomic
• All atoms of an element have same chemical
  properties
• all behave the same
• properties dont change

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Life requires 25 chemical elements

• About 25 elements are essential for life
• Four elements make up 96 of living matter
• carbon (C) hydrogen (H)
• oxygen (O) nitrogen (N)
• Four elements make up most of remaining 4
• phosphorus (P) calcium (Ca)
• sulfur (S) potassium (K)

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Isotopes
Isotopes forms of an element with different
numbers of neutrons, thus different mass
numbers Example 12C has 6 neutrons 13C has 7
neutrons 14C has 8 neutrons
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Radioactive Isotopes

• Spontaneously give off particles and energy
• Alpha, beta, gamma radiation

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Bonding properties

• Effect of electrons
• chemical behavior of an atom depends on its
  electron arrangement
• depends on the number of electrons in its
  outermost shell, the valence shell

How does this atom behave?
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The Energy Levels of Electrons

• Energy
• Is defined as the capacity to cause change
• Potential energy
• Is the energy that matter possesses because of
  its location or structure

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Bonding properties

• Effect of electrons
• chemical behavior of an atom depends on number of
  electrons in its outermost shell

How does this atom behave?
How does this atom behave?
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Elements their valence shells

• Elements in the same row have the same number of
  shells

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Elements their valence shells

• Elements in the same column have the same valence
  similar chemical properties

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Elements their valence shells

• Moving from left to right, each element has a
  sequential addition of electrons (and protons)

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Chemical reactivity

• Atoms tend to
• Complete a partially filled outer (valence)
  electron shell
• or
• Empty a partially filled outer (valence)
  electron shell
• This tendency drives chemical reactions

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Electron Configuration and Chemical Properties

• Orbitals occur in series called electron shells
  or energy levels.
• First shell one orbitals orbital
• Second shell one s and three p orbitals (holds
  eight electrons)
• Third shell one s and three p orbitals (holds
  eight electrons)
• Fourth Fifth Shells d orbitals added (10 more
  electrons)
• Seventh Eighth Shells f orbitals added (16
  more electrons)

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Ionic bonds
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Ionic bonds
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• Transfer of an electron
• Forms - ions
• cation
• anion
• Weak bond

• example
• salt dissolves easily in water

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Covalent bonds
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• Two atoms need an electron
• Share a pair of electrons
• Strong bond
• both atoms holding onto the electrons
• Forms molecules
• example
• water takes energy to separate

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Double covalent bonds

• Two atoms can share more than one pair of
  electrons
• double bonds (2 pairs of electrons)
• triple bonds (3 pairs of electrons)
• Very strong bonds

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Multiple covalent bonds

• 1 atom can form covalent bonds with two or more
  other atoms
• forms larger molecules
• ex. carbon

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Hydrogen bonds

• Positive H atom in 1 water molecule is attracted
  to negative O in another
• Can occur wherever an -OH exists in a larger
  molecule
• Weak bonds

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Polar covalent bonds

• Pair of electrons not shared equally by 2 atoms
• Water O H

• oxygen has stronger attraction for the shared
  electrons than hydrogen
• oxygen has higher electronegativity

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Polar covalent bonds

• 2 hydrogens in the water molecule form an angle
• Water molecule is polar
• oxygen end is
• hydrogen end is
• Leads to many interesting properties of water.

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Van der Waals Interactions

• Van der Waals interactions
• Occur when transiently positive and negative
  regions of molecules attract each other

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Strong and weak chemical bonds
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Structure and Function run from large scale body
systems through molecules and atoms.Structure
and function are what Enzymes are all about
Figure 2.17
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Chemical reactions make and break chemical bonds

• Chemical reactions
• Convert reactants to products

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Life is the result of Chemical Reactions

• Photosynthesis
• Is an example of a chemical reaction

Figure 2.18
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Chemical Equilibrium

• Chemical equilibrium
• Is reached when the forward and reverse reaction
  rates are equal

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Reductionist view of biology

• Matter is made of atoms
• Life requires 25 chemical elements
• Atomic structure determines behavior of an
  element
• Atoms combine by chemical bonding to form
  molecules
• Weak chemical bonds play important roles in
  chemistry of life
• A molecules biological function is related to
  its shape
• Chemical reactions make break chemical bonds