The Chemical Context of Life

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The Chemical Context of Life

• AP Biology
• Chapter 2

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Biology is the study of life, so why in the heck
do we have to study chemistry?
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Essential Questions

• How do atoms arrange to make the molecules for
  life?
• What molecules are most important for life?
• How do atoms bond?

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Biochem Vocabulary Review

• Organisms are composed of matter
• anything that takes up space and has mass.
• An element is a substance that cannot be broken
  down into other substances by chemical reactions.
• A compound is a substance consisting of two or
  more elements in a fixed ratio.

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• About 25 of the 92 natural elements are known to
  be essential for life.
• Four elements - carbon (C), oxygen (O), hydrogen
  (H), and nitrogen (N) - make up 96 of living
  matter.
• Most of the remaining 4 of an organisms weight
  consists of phosphorus (P), sulfur (S), calcium
  (Ca), and potassium (K).

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• Trace elements are required by an organism but
  only in minute quantities.
• Some trace elements, like iron (Fe), are required
  by all organisms.

• Other trace elements are required only by some
  species.
• For example, a daily intake of 0.15 milligrams of
  iodine is required for normal activity of the
  human thyroid gland.

Fig. 2.4
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Atomic TheoryWhat do you remember?
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Atomic structure determines the behavior of an
element

• Each element consists of unique atoms.
• An atom is the smallest unit of matter that still
  retains the properties of an element.
• Subatomic particles
• Neutrons
• Protons
• Electrons
• Size, location and charge

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• Each element has a unique number of protons, its
  unique atomic number
• 2He
• Unless otherwise indicated, atoms have equal
  numbers of protons and electrons
• Mass number ? is the sum of the number of protons
  and neutrons in the nucleus of an atom.
• 4He
• isotopes ?2 atoms of the same element that differ
  in the number of neutrons
• In nature, an element occurs as a mixture of
  isotopes
• 99 of carbon atoms have 6 neutrons (12C)
• Most of the other carbon atoms have 7 neutrons
  (13C) while the rarest isotope, with 8 neutrons
  is 14C.
• Some isotopes are stable while others are not

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Radioactive Isotopes

• The nuclei of some isotopes are unstable and
  decay spontaneously, emitting particles and
  energy.
• Ex. 14C
• Radioactive isotopes have many applications in
  biological research.
• To date fossils
• To trace atoms in metabolism.

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Important Little Electrons

• The different states of potential energy that the
  electrons of an atom can have are called energy
  levels or electron shells or orbitals.
• The first shell ? lowest potential energy.
• Outer shells ? more potential energy.
• Electrons can only change their position if they
  absorb or release a quantity of energy

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• The chemical behavior of an atom is determined by
  its electron configuration - the distribution of
  electrons in its electron shells.

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Basic Electron Configuration

• 1st shell ? 2 e-
• 2nd shell ? up to 8 electrons
• 3rd shell ? up to 8 electrons
• The chemical behavior of an atom depends mostly
  on the number of electrons in its outermost
  shell, the valence shell

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Key Points about Valance Electrons

• Atoms with the same number of valence electrons
  have similar chemical behavior.
• An atom with a completed valence shell is
  unreactive.
• Octet rule ? most elements want to have 8
  electrons in their outer energy level
• Atoms with unfilled valence shells will react to
  have a full outer valance
• How?
• Form ions, ion ? an atom that carries a charge
• Lose or gain electrons
• Donate or accept e- ? form ionic bonds
• Share electrons with other atoms

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• Covalent Bond Video

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• A covalent bond is the sharing of a pair of
  valence electrons by two atoms
• molecule ?2 or more atoms held together by
  covalent bonds
• structural formula ? substituting a line for
  each pair of shared electrons, Ex. H-H
• molecular formula ? indicates the number and
  types of atoms present in a single molecule,
  Ex.H2

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Sometimes atoms share more than one pair of
electrons

• double covalent bond ? sharing 2 pairs of valence
  electrons
• triple covalent bond ? sharing 3 pairs of valence
  electrons

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Electronegativity determines the nature of the
bond

• electronegativity ?the attraction of an atom for
  the electrons of a covalent bond
• Strongly electronegative atoms attempt to pull
  the shared electrons toward themselves
• If electrons in a covalent bond are shared
  equally, then this is a nonpolar covalent bond
• The greater the difference in electronegativites
  of 2 atoms in a bond, the more polar the bond

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• If the electrons in a covalent bond are not
  shared equally by the two atoms, then this is a
  polar covalent bond.
• Water example

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• Ionic Bond Video

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Ionic Bonds

• The differences in electronegivitity are so
  unequal that one atom strips an electron
  completely from the other
• Electrons are gained/lost rather than shared

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• Cation? an atom with a positive charge
• Anion ? an atom with a negative charge
• Compounds formed by ionic bonds are ionic
  compounds or salts, like NaCl or table salt.

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Weak chemical bonds play important roles in the
chemistry of life

• Receptors and chemical transmission
• Molecule shape

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Hydrogen bonds

• form when a hydrogen atom that is already
  covalently bonded to a strongly electronegative
  atom is attracted to another strongly
  electronegative atom
• typically nitrogen or oxygen
• polar covalent bond leaves the H atom with a
  partial positive charge and the other atom with a
  partial negative charge

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van der Waals interactions

• Molecules or atoms in close proximity can be
  attracted by these fleeting charge differences,
  creating van der Waals interactions
• While individual bonds (ionic, hydrogen, van der
  Waals) are weak, collectively they have strength

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A molecules biological function is related to
its shape

• Simple molecules have simple shapes
• Ex. Water, methane
• More complex molecules have complex shapes that
  enable them to perform specific biological
  functions
• Ex. Proteins, lipids, carbohydrates and nucleic
  acids

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• Molecules with similar shapes can interact in
  similar ways.
• Ex. morphine, heroin, and other opiate drugs and
  endorphins.

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Chemical reactions make and break chemical bonds

• In chemical reactions chemical bonds are broken
  and reformed, leading to new arrangements of
  atoms.
• The starting molecules in the process are called
  reactants and the end molecules are called
  products.
• In a chemical reaction, all of the atoms in the
  reactants must be accounted for in the products.
• The reactions must be balanced.

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