chemistry for bio 11. chemistry is relevant to biological concepts all living things are made of...
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Chemistry for Bio 11
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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
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Biochemical reactions
• All living things are collections of a vast number of chemical reactions
• Even the simplest living things contain impossibly complex pathways
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Complex biological molecules
• All living things are made of complex macromolecules
• Chemical principles rule their assembly
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Chemical energy
Photosynthesis creates molecules rich in energy:• 6CO2(g)+ 6H2O(l) + hν C6H12O6(s) + 6O2(g)
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The Chemical Environment
• The physical properties of water determine the fate of life on earth
• pH, salinity and other chemical factors influence
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Basic principles of chemistry
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Atoms
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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= 1Electron: Chg = -1, mass=
~0Mass= p + nCharge = p - e
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LE 2-4a
2
2
2
Protons
Neutrons
Electrons
Helium atom
Massnumber = 4
6
6
6
Protons
Neutrons
Electrons
Carbon atom
Massnumber = 12
Electroncloud
Nucleus
2e–
6e–
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Elements are defined by the number of their protons
• There are 92 naturally occurring elements
• Many others have been synthesized
Atomic number: # protonsAtomic mass: protonsIsotopes- different atoms of
same element, with different # neutrons
Atomic weight: Naturally occurring average of isotopes of a substance
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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
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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
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The number of neutrons in atoms is variable
• Isotopes• Some isotopes are
stable, others are radioactive
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Isotopes of carbon have important applications in biology and archaeology
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Other radioactive isotopes are also important
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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
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Molecules, compounds, chemical reactions, and bonding
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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
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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
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Noble gases have a stable electron structure
• Their outer orbitals have a full complement of electrons
• Noble gases are very unreactive
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In ionic bonding, an atom takes an electron from another atom, forming 2
ions
LE 2-7
Transfer ofelectron
NaSodium atom
ClChlorine atom
Na
Sodium ionCl
Chloride ion
Sodium chloride (NaCl)
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Ions
• Ions- Charged atoms or molecules
• Anion- negative ion• Cation- positive ion• Ionization- reaction
producing ions• Salt- a neutral
compound comprised of ions
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LE 2-7a-2
Na
Sodium ionCl
Chloride ion
Sodium chloride (NaCl)
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LE 2-7b
Na
Cl
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In covalent bonding, pairs of valence electrons are shared, and molecules are formed
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LE 2-17a
2 H2 O2 2 H2O
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LE 2-6b
Nitrogen (N)Atomic number = 7
Oxygen (O)Atomic number = 8
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In neutral molecules, carbon always forms 4 bonds
Structuralformula
Ball-and-stickmodel
Space-fillingmodel
Methane
The 4 single bonds of carbon point to the corners of a tetrahedron.
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LE 3-1b
Ethane Propane
Carbon skeletons vary in length.
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LE 3-1c
Butane Isobutane
Skeletons may be unbranched or branched.
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LE 3-1d
1-Butene 2-Butene
Skeletons may have double bonds, which can vary in location.
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LE 3-1e
Skeletons may be arranged in rings.
Cyclohexane Benzene
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Organic Chemistry
• The chemistry of carbon• Hydrocarbons are the
most basic example– Combustible– Can form rings
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The variety of carbon compounds is limitless
All terrestrial life is based on carbon
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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
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Electronegativity determines properties of covalently bonded
molecules
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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
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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
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Water dissolves many ionic compounds (“like dissolves like”)
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Figure 2.11
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Figure 2.12
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LE 2-13
Hydrogen bond
Ice
Hydrogen bonds are stable
Liquid water
Hydrogen bondsconstantly break and re-form
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pH is a measure of acidity/basicity
• pH = -log [H+] (logarithmic scale)• pH 1 6.9: acid• pH 7.114: 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
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LE 2-15
Acidic solution
OH
H
HH
HOH
H H
H
OH
OH
OH
OH
OH
H
H
H
H
HH
I ncr
ea
sin
gl y
AC
IDI C
(Hi g
he
r c
on
c en
tra
t io
n o
f H
)Neutral solution
OH
OH
OH
OH
OH
OH
H
H
Basic solution
NEUTRALH
pH scale
Lemon juice, gastric juice
Grapefruit juice, soft drink
Tomato juice
Human urine
Pure water
Human blood
Seawater
Milk of magnesia
Household ammonia
Household bleach
Oven cleaner
Incr
ea
sin
gl y
BA
SIC
(Lo
we
r c
on
cen
tra t
i on
of
H )
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Figure 2.16a
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Figure 2.16b