The Chemistry of Life

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The Chemistry of Life

• Chapter 2, U401PP

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• The obvious question- why study chemistry in this
  class?
• The obvious answer chemistry is the foundation
  of life
• However, I would like you to think about
  chemistry a little differently

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Two examples

• In the largest study of chemical exposure ever
  conducted on human beings, the U.S. Center for
  Disease Control and Prevention reported (2005)
  that most American children and adults were
  carrying in their bodies dozens of pesticides and
  toxic compounds used in consumer products, many
  of them linked to potential health threats.
• Looked at 2400 people, most comprehensive report
  of its kind
• Steep declines in secondhand smoke exposure and
  lead
• More than 100 other substances were found
• We have fouled our own nest
• (A measurable amount of a chemical in the body
  does not necessarily mean there is a pending
  health risk however many of the chemicals are
  not well understood)
• 11 of the 12 compound used in the manufacture of
  nail polish, beauty products, and soft plastics
  was higher in children than adults
• Children are more exposed, dont metabolize the
  chemicals well, or?
• 1 in 18 women of childbearing age had mercury
  levels that exceeded the EPA level of safety for
  a fetus

Scientific questions???
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Two examples

• Bryan Fry, University of Melbourne, catches the
  highly venomous island taipan (9 foot long
  Australian snake), among others to study the
  evolution of venom
• Reconstructing the history will lead to medical
  breakthroughs (for 35 years, scientists have been
  turning snake venoms into drugs)
• For example, venoms that slow the heart may be
  useful to treat congestive heart failure
• Once venom molecules enter a snakes prey, the
  specific molecular shapes lock particular
  receptors on the surface of cells or onto
  specific proteins floating in the bloodstream.
  Some plug channels that paralyze muscles, some
  trigger immune system failure. Some loosen blood
  vessel walls, leading to shock and bleeding.
• Traditional thinking was that venomous and
  nonvenomous snakes evolved independently. He has
  shown that different lineages of venomous snakes
  are related to nonvenomous ones- most of the
  snakes we think as nonvenomous (e.g., garter
  snake) actually produce venom
• Sequenced all of the genes active in snake venom
  glands
• Venom only evolved once in snakes
• Snakes with venom no longer had to rely on
  constriction or physically subduing prey
• Constructed evolutionary trees of 24 venom genes,
  searching on-line databases for their closest
  relatives. (sound familiar? ?)
• Venom genes did not evolve from saliva proteins
  as was previously thought

Scientific questions???
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Elements and Compounds

• Organisms are composed of matter, whichis
  anything that takes up space and hasmass

• Matter is made up of elements, substancesthat
  cannot be broken down to other substances by
  chemical reactions

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• A compound
• Is a substance consisting of two or more elements
  combined in a fixed ratio
• Has characteristics different from those of its
  elements

Figure 2.2
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Essential Elements of Life

• Essential elements
• Include carbon, hydrogen, oxygen, and nitrogen
• Make up 96 of living matter

Shhh! Dont tell chemists, but biologists
really arent interested in most of the periodic
table
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• Concept 2.2 An elements propertiesdepend on
  the structure of its atoms

• Each element
• Consists of a certain kind of atom that is
  different from those of other elements
• An atom
• Is the smallest unit of matter that still retains
  the properties of an element

Elements then are different (chemically) because
of their number and arrangement of subatomic
components
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Elements then are different (chemically) because
of their number and arrangement of subatomic
components (specifically electrons)
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Nice, but
It is important to know that electron
configuration gives the atom certain chemical
properties
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Subatomic Particles

• Atoms of each element
• Are composed of even smaller parts called
  subatomic particles

• Relevant subatomic particles include
• Neutrons, which have no electrical charge
• Protons, which are positively charged
• Electrons, which are negatively charged

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• Simplified models of an atom

• Protons and neutrons
• Are found in the atomic nucleus
• Electrons
• Surround the nucleus in a cloud

Figure 2.4
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Atomic Number and Atomic Mass

• Atoms of the various elements
• Differ in their number of subatomic particles

• The atomic number of an element
• Is the number of protons
• Is unique to each element

• The mass number of an element
• Is the sum of protons plus neutrons in the
  nucleus of an atom
• Is an approximation of the atomic mass of an atom

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Isotopes

• Atoms of a given element
• May occur in different forms

• Isotopes of a given element
• Differ in the number of neutrons in the atomic
  nucleus
• Have the same number of protons

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• Many isotopes are unstable
• The nucleus of the atom begins to break up
  releases energy
• Some are more unstable than others and give off
  harmful amounts of energy
• Radiation (at particular energies) can damage
  living cells, cause mutations
• Cells that are most mitotically active suffer
  first (e.g., hair loss in radiation therapy)
• Isotopes are used for internal imaging and
  radioactive dating

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Figure 2.5
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Ions- unequal charge

• Cations
• More protons than electrons ( charge)
• Anions
• More electrons than protons (- charge)

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The Energy Levels of Electrons

• An atoms electrons
• Vary in the amount of energy they possess

• 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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• The electrons of an atom
• Differ in the amounts of potential energy they
  possess

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• Energy levels
• Are represented by electron shells

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• The periodic table of the elements
• Shows the electron distribution for all the
  elements

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• Valence electrons
• Are those in the outermost, or valence shell
• Determine the chemical behavior of an atom
• Atomic nuclei dont come close enough to each
  other in nature to interact
• Atoms are mostly empty space
• Electron interaction between atoms allows them to
  chemically interact (or not)

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Electron Orbitals

• An orbital
• Is the three-dimensional space where an electron
  is found 90 of the time

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• Each electron shell
• Consists of a specific number of orbitals

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• Concept 2.3 The formation and function of
  molecules depend on chemical bonding between
  atoms (now, biologists are really interested ?)

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Covalent Bonds

• A covalent bond
• Is the sharing of a pair of valence electrons

What kind of self-respecting atom would SHARE
electrons?

• NUMBER and ARRANGEMENT of electrons!
• become more stable
• no net charge
• satisfies octet rule (in essence, the shared
  electrons orbit both atomic nuclei)
• no free electrons (by locking up electrons,
  there are no electrons left to react with other
  atoms

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• Formation of a covalent bond

Figure 2.10
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• A molecule
• Consists of two or more atoms held together by
  covalent bonds
• A single bond
• Is the sharing of one pair of valence electrons
• A double bond
• Is the sharing of two pairs of valence electrons

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• Single and double covalent bonds

(a)
(b)
A line represents a covalent bond
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• Covalent bonding in compounds

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Are covalent bonds strong or weak?
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• Electronegativity
• Is the attraction of a particular kind of atom
  for the electrons in a covalent bond
• The more electronegative an atom
• The more strongly it pulls shared electrons
  toward itself

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• In a nonpolar covalent bond
• The atoms have similar electronegativities
• Share the electron equally

• In a polar covalent bond
• The atoms have differing electronegativities
• Share the electrons unequally

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Ionic Bonds

• In some cases, atoms strip electrons away from
  their bonding partners

• Electron transfer between two atoms creates ions
• Ions
• Are atoms with more or fewer electrons than
  usual
• Are charged atoms

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• An ionic bond
• Is an attraction between anions and cations

What kind of self-respecting atom would lose or
want to gain electrons?
Figure 2.13
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• Ionic compounds
• Are often called salts, which may form crystals

Will it easily dissolve in water?
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Weak Chemical Bonds

• Several types of weak chemical bonds are
  important in living systems

• Weak chemical bonds
• Reinforce the shapes of large molecules
• Help molecules adhere to each other

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Hydrogen Bonds

• A hydrogen bond
• Forms when a hydrogen atom covalently bonded to
  one electronegative atom is also attracted to
  another electronegative atom

?
?
?
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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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Molecular Shape and Function

• The precise shape of a molecule
• Is usually very important to its function in the
  living cell
• Is determined by the positions of its atoms
  valence orbitals

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• In a covalent bond
• The s and p orbitals may hybridize, creating
  specific molecular shapes

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• Molecular shape
• Determines how biological molecules recognize and
  respond to one another with specificity

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• Concept 2.4 Chemical reactions make and break
  chemical bonds

• A Chemical reaction
• Is the making and breaking of chemical bonds
• Leads to changes in the composition of matter

• Chemical reactions
• Convert reactants to products

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• Photosynthesis
• Is an example of a chemical reaction

Figure 2.18