Download Chemistry for Bio 11

Chemistry for Bio 11
Chemistry is relevant to Biological
Concepts
• All Living things are made of matter
• The interactions of matter are described by
chemical principles
• Biolgists are interested in:
– Biochemical reactions
– Complex biological molecules
– Chemical energy
– The chemical environment
Biochemical reactions
• All living things are
collections of a vast
number of chemical
reactions
• Even the simplest living
things contain
impossibly complex
pathways
Complex biological molecules
• All living things are
made of complex
macromolecules
• Chemical principles
rule their assembly
Chemical energy
Photosynthesis creates molecules rich in energy:
• 6CO2(g)+ 6H2O(l) + hν  C6H12O6(s) + 6O2(g)
The Chemical Environment
• The physical properties
of water determine the
fate of life on earth
• pH, salinity and other
chemical factors
influence
Basic principles of chemistry
Atoms
Atoms are the smallest individual unit
of matter
• Atoms are comprised of
protons, neutrons and
electrons
Proton: Charge= +1,
Mass= 1
Neutron: Chg= 0, mass= 1
Electron: Chg = -1, mass=
~0
Mass= p + n
Charge = p - e
LE 2-4a
Electron
cloud
6e–
2e–
Nucleus
2
Protons
2
Neutrons
2
Electrons
Helium atom
Mass
number = 4
6
Protons
6
Neutrons
6
Electrons
Carbon atom
Mass
number = 12
Elements are defined by the number
of their protons
• There are 92 naturally
occurring elements
• Many others have been
synthesized
Atomic number: # protons
Atomic mass: protons
Isotopes- different atoms of
same element, with
different # neutrons
Atomic weight: Naturally
occurring average of
isotopes of a substance
96% of human tissue is comprised of 6
elements
• Carbon, Hydrogen,
Nitrogen, Oxygen,
Phosphorous, Sulfur
(CHNOPS)
• 25 elements serve
known functions in the
body, incl. Ca, K, Na, Cl,
Mg, Fe
Atomic structure
• Protons and electrons in
the nucleus
• Electrons orbit around
• Bohr atom- classic
model featuring
electrons in “planetary”
orbitals
• Each orbit holds a
determined number of
electrons (first holds
two, 2nd and 3rd hold
eight
The number of neutrons in atoms
is variable
• Isotopes
• Some isotopes are
stable, others are
radioactive
Isotopes of carbon have important
applications in biology and archaeology
Other radioactive isotopes are also
important
Electron cloud model
• Currently accepted
model of atomic
structure
• 90% probability cloud
• Mostly empty space
• Unfilled orbitals found
in unstable, reactive
elements
• Therefore, orbitals
influence bonding
Molecules, compounds, chemical
reactions, and bonding
Elements combine in chemical
reactions to form compounds
• Molecules- 2 or more atoms combined in a specific way
• Compounds- different elements in a molecule, in exact,
whole-number ratios, joined by a chemical bond
• 2 major means of intramolecular chemical bonding:
Covalent (incl. polar and nonpolar) and Ionic
Atoms are stable when their outer
shells are filled with electrons
•
•
•
•
Shell 1: Holds 2 electrons
Shell 2: Holds 8
Shell 3: Holds 8
Hydrogen- 1p, 1e, seeks a
second electron in its
outermost shell
• Carbon seeks 4
• The electrons in the
outermost shell are called
valence electrons
Noble gases have a stable electron
structure
• Their outer orbitals
have a full complement
of electrons
• Noble gases are very
unreactive
LE 2-7
In ionic bonding, an atom takes an
electron from another atom, forming 2
ions
Transfer of
electron
Na+
Sodium ion
Na
Sodium atom
Cl
Chlorine atom
ClChloride ion
Sodium chloride (NaCl)
Ions
• Ions- Charged atoms or
molecules
• Anion- negative ion
• Cation- positive ion
• Ionization- reaction
producing ions
• Salt- a neutral
compound comprised
of ions
LE 2-7a-2
Na+
Sodium ion
ClChloride ion
Sodium chloride (NaCl)
LE 2-7b
Na+
Cl-
In covalent bonding, pairs of valence electrons
are shared, and molecules are formed
LE 2-17a
+
2 H2
+
O2
2 H2O
LE 2-6b
Nitrogen (N)
Atomic number = 7
Oxygen (O)
Atomic number = 8
In neutral molecules, carbon always
forms 4 bonds
Structural
formula
Ball-and-stick
model
Space-filling
model
Methane
The 4 single bonds of carbon point to the corners of a tetrahedron.
LE 3-1b
Ethane
Propane
Carbon skeletons vary in length.
LE 3-1c
Butane
Isobutane
Skeletons may be unbranched or branched.
LE 3-1d
1-Butene
2-Butene
Skeletons may have double bonds, which can vary in location.
LE 3-1e
Cyclohexane
Benzene
Skeletons may be arranged in rings.
Organic Chemistry
• The chemistry of carbon
• Hydrocarbons are the
most basic example
– Combustible
– Can form rings
The variety of carbon compounds is
limitless
All terrestrial life is based on carbon
Covalent bonds hold together the
macromolecules of life
• Living things create
macromolecular products for
structure:
• 6CO2(g)+ 6H2O(l) + hν  C6H12O6(s)
+ 6O2(g)
• Macromolecules as reactants are
broken down for energy:
C6H12O6(s) + 6O2(g)  6CO2(g)+ 6H2O(l)
All the reactions of a living thing are
called its metabolism
Electronegativity determines properties
of covalently bonded molecules
Electronegativity = “electron
greediness”
• Atoms in covalently bonded
molecules do not always
share electrons equally
• This creates polar molecules
• Polar regions of water
molecules interact to form
hydrogen bonds
• Hydrogen bonds:
weak/temporary
intermolecular forces
Hydrogen bonding in water determine
many of water’s unique properties
• H-bonds can form a
lattice (ice)
• H-bonds require much
energy to break
• H-bonds give water
surface tension
Hydrogen bond
Water dissolves many ionic
compounds (“like dissolves like”)
Figure 2.11
Figure 2.12
LE 2-13
Hydrogen bond
Ice
Liquid water
Hydrogen bonds are stable
Hydrogen bonds
constantly break and re-form
pH is a measure of acidity/basicity
•
•
•
•
•
•
pH = -log [H+] (logarithmic scale)
pH 1 6.9: acid
pH 7.114: base
pH 7 neutral
Acids donate [H+] to water
Bases remove [H+] from water (or donate [OH-]
to water)
• Proteins are very sensitive to small changes in
pH
LE 2-15
pH scale
H+
H+
H+
-
H+ OH
+
OH- H
H+
Lemon juice, gastric juice
H+
H+
Grapefruit juice, soft drink
Acidic solution
Tomato juice
Human urine
OH-
OH-
-
H+
H+ OH
OH OHH+
H+
H+
Neutral solution
NEUTRAL
[H+[
-
Pure water
Human blood
Seawater
Milk of magnesia
OHOHOH-
Household ammonia
OH-
H+
H+
OH-
Household bleach
OHOven cleaner
Basic solution
Figure 2.16a
Figure 2.16b