Chapter 2

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Chapter 2 the chemistry of life

• Why is it important to have an understanding of
  chemistry to study anatomy?
• All biological functions can be explained
  chemically
• What are the components of life?
• Matter
• Energy

2
Nature of Matter Atomic Structure

• Nucleusvery small size compared to the entire
  atom, composed of a) protons (p) have a
  positive electrical charge, have some mass, and
  b) neutrons (n0) have no electrical charge,
  have the same mass as a proton.
• Electrons (e-) these orbit the nucleus, they
  have a negative electrical charge which is equal
  and opposite the charge of a proton, they have a
  negligible mass.
• Atoms are usually electrically neutralnumber of
  electrons number of protons.

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Nature of Matter Atomic Structure

• How can we tell one atom from another? What is
  the distinction?
• Atomic Number the number of protons in an atom.
• Atomic Mass (weight) mass of atom, which would
  include of protons of neutrons
• Other Definitions
• Element matter composed of atoms of only one
  kind.
• The number of protons in the nucleus of any given
  atom is always the same AND each element has a
  different number of protons in its nucleus
• Molecules A combination of atoms where electrons
  in the outermost orbital are either transferred
  or shared.
• Compound A molecule that has two or more kinds
  of atoms.
• Chemical Formula C6H12O6

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http//wine1.sb.fsu.edu/chm1045/tables/period/PT_l
arge.jpg
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Earths crust
Human body
other 8
other 7
hydrogen 10
oxygen 50
oxygen 65
silicon26
aluminum 8
carbon 18
calcium 3
iron 5
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Table. 2.2
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Nature of Matter Key Components of the Atom

• Size - nucleus is much smaller than surrounding
  orbital and atoms are really, really tiny.
• Identity of protons determines identity of
  atom. Neutrons only provide additional mass.
• Charge - is determined by comparing the number
  of electrons to number of protons. If they are
  equal, then atom is electrically neutral. If
  they are not, then atom is existing in an ionic
  state.
• Reactivity is determined by the valence
  electrons in the outermost shell. The number of
  valence electrons really does make a difference
  in the way an atom will behave around other
  atoms. Some are stable others are very
  reactive.
• Lowest Energy State all matter (atoms being the
  smallest particles of matter) always seek there
  lowest energy state, so they prefer to be neutral
  and they prefer to have their outermost energy
  shell full!
• Isotopes Most atoms exist in various isotopic
  forms. How can you tell? If number of neutrons
  is different from number of protons, atom is in
  an isotopic state. of neutrons atomic mass
  (weight) atomic number.

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Radioactive Isotopes

• Medical Diagnosis
• Cancer Therapy
• Other Biological Uses
• Radiometric Dating
• Radioactive Labeling

9
Chemical Bonding

• The goal of atoms is to find their lowest energy
  state!
• Types of bonds
• Ionic Bonding one atom loses an electron and
  one gains an electron.
• Covalent Bonding two atoms share a pair of
  electrons, sometimes equally/sometimes unequally.
  
• Single Covalent Bond (one pair of electrons)
• Double Covalent Bond (two pairs)
• Triple Covalent Bond (three pairs)

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e-
e-
e-
Hydrogen
Helium
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
Carbon
Neon
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
e-
Sodium
Argon
unstable, very reactive stable,
unreactive
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Sodium atom (Na)
Chlorine atom (Cl)
e-
electron transfer
e-
Chlorine ion (Cl-)
Ionic Compound (Na Cl-)
Salt crystals
12

• Polar vs. Non-polar Covalent Bonds
• Nonpolar Covalent Bonds
• Neither nucleus exerts more attractive pull on
  shared electrons (equal electronegativity and
  equal sharing, like joint custody).
• Polar Covalent Bonds
• H2O is most common example in the body
• Oxygen has a greater atomic number than hydrogen.
• Oxygens nucleus attracts the shared electrons
  with a greater electronegativity than hydrogen in
  a water molecule.
• Unequal sharing results in polar charges on
  different parts of the molecule.

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H


O
O
H
H



H



O
H
H
O
H



H

H
H
O


H
O


H

H

H


O

O
H
Hydrogen bond
H
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Dissociation and Electrolytes
15
Functional Groups (Handout)

• These are small groups of atoms that when
  attached to larger organic molecules will give
  those molecules predictable properties such as
  hydrophilic (polar) or hydrophobic
  (non-polar)/acid or base.
• Hydroxyl (R-OH) When attached to a hydrocarbon
  chain, it creates an alcohol. This group is
  found all over sugars. Because it contains a
  polar covalent bond, the Hydrogen atom is polar
  positive () and makes that part of the molecule
  hydrophilic and capable of forming H-bonds.
• Carbonyl (gtCO) It contains a polar covalent
  bond and the oxygen is therefore polar negative
  (-) which makes that part of the molecule
  hydrophilic and capable of forming H-bonds.
  There are two types of carbonyl
• 1) Aldehyde when the group is found at the
  end of a chain, and the
• 2) Ketone when the group is found in the
  middle of a chain.

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Functional Groups, Continued

• Carboxyl (R-COOH) This group loses the H off of
  the hydroxyl group which forms both a negative
  charged Oxygen (- ion) and a Hydrogen ion (H) is
  released into solution. This makes the molecule
  to which it is attached an acid. The polar
  charges and the ionic charges cause this part of
  a molecule to be highly hydrophilic.
• Amino (gtNH2) This group tends to pick up H
  ions from the solution and causes the pH to rise.
  Therefore this group makes the molecule a base.
  The group becomes ionically charged () and this
  makes this part of the molecule highly
  hydrophilic.
• Phosphate (R-PO4) This group releases H into
  solution making the molecule to which it is
  attached both acidic and hydrophilic.
• Methyl (R-CH3) The nonpolar covalent bonds in
  this group make the part of the molecule to which
  it is attached hydrophobic.

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ACIDIC
100
0
battery acid
1
10-1
hydrochloric acid
10-2
2
lemon juice, gastric (stomach) juice
10-3
3
cola, beer, wine, vinegar
10-4
4
tomatoes
10-5
5
black coffee
10-6
6
urine
10-7
pure water
NEUTRAL
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human blood
10-8
8
seawater
10-9
9
baking soda
10-10
10
Great Salt Lake
10-11
11
household ammonia
10-12
12
household bleach
10-13
13
oven cleaner
10-14
14
lye
BASIC
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Chemical reactions

• Types of chemical reactions
• Synthesis reactions
• Decomposition reactions
• Exchange reactions single or double replacement
• All metabolic pathways require energy at some
  point! ATP/ADP
• Most biological reactions are reversible as well!

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Fig. 2.20
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Chemical reactions, contd

• Reversible reactions - equilibrium
• In the body, reactants and products tend to react
  with one another back and forth until equilibrium
  is reached - homeostasis
• Reaction Rates what affects rate of rxn?
• Concentration of reactants
• Temperature
• Enzymes (catalyst)

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biochemistry

• Inorganic Molecules Molecules that do not
  contain carbon
• Water inorganic
• High Specific Heat, meaning water resists
  temperature changes which helps in maintaining
  body temperature.
• High Heat of Vaporization Evaporative Cooling
• Effective lubricant surface of the eye
• Necessary reactant in chemical reactions
  digestion
• Universal Solvent works for transport of
  nutrients throughout body

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Biochemistry, contd

• Macromolecules of Life (organic) Molecules that
  contain carbon (Table 2.3 page 31)
• Carbohydrates mono, di and polysaccharides
• Lipids fats, fatty acids, glycerol,
  triaglycerols/triglycerides saturated and
  unsaturated fats
• Proteins amino acids
• Enzymes activation energy
• Nucleic acids DNA, RNA

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Fig. 2.11
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Fig. 2.12
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Fig. 2.13
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Fig. 2.14
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OH
CH3
CH3
CH3
HC
CH3
CH2
CH2
testosterone
CH2
O
CH3
HC
OH
CH3
CH3
CH3
cholesterol
estrogen
HO
HO
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Fig. 2.16a
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Fig. 2.16b
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Fig. 2.19b
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The detailed structure of an animal cells plasma
membrane, in cross section
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Enzyme Action

• Three-Dimensional Shape Important in Biology
• Compounds have very definite spatial
  configurations.
• Shape determines how molecules can bind one
  another, a critical step in many activities.
  This is especially true where enzymes are
  concerned.
• Throughout biology we see a complementarity of
  structure to function. This is easily seen
  throughout all of biology.

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Activation Energy Enzymes