Transcript AP Biology - Pasadena High School

UNIT 1
BIOCHEMISTRY
Part 1
Hillis Textbook Chapter 2
Chemistry of Life
AP Biology
2007-2008
 Living and nonliving matter is composed of
atoms.
Octet rule—atoms with at least
two electron shells form stable
molecules so they have eight
electrons in their outermost
shells. Valence electrons are the
outermost electrons.
Like charges repel; different charges attract.
Most atoms are neutral because the number of electrons equals the number of protons.
The number of protons identifies an element.
•Number of protons = atomic number
•Atomic Mass or Weight= total number of protons and neutrons
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Element—pure substance that contains only
one kind of atom
 Living things are mostly composed of 6
elements:
Carbon (C)
Hydrogen (H)
Nitrogen (N)
Oxygen (O) Phosphorus (P) Sulfur (S)
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Behavior of electrons determines whether a chemical bond will
form and what shape the bond will have.
Atoms with unfilled
outer shells tend to
undergo chemical
reactions to fill their
outer shells.
They can attain
stability by sharing
electrons with other
atoms or by losing
or gaining
electrons.
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The atoms are then
bonded together
into molecules.
A chemical bond is an attractive force that links atoms together
to form molecules. There are several kinds of chemical bonds.
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IONIC BONDS
 Ions are charged particle that
form when an atom gains or
loses one or more electrons.

Cations—positively
charged ions

Anions—negatively
charged ions
 Ionic bonds result from the
electrical attraction between
ions with opposite charges.

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The resulting molecules are
called salts.
 Ionic attractions are weak, so salts
dissolve easily in water.
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COVALENT BONDS
 Covalent bonds form when



two atoms share pairs of
electrons.
The atoms attain stability by
having full outer shells.
Each atom contributes one
member of the electron pair.
Carbon atoms have four
electrons in the outer shell—
they can form covalent bonds
with four other atoms.
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Properties of molecules are influenced by
characteristics of the covalent bonds:
Orientation—length, angle, and direction of bonds between
any two elements are always the same.
Example: Methane always forms a tetrahedron.
Strength and stability—covalent bonds are very
strong; it takes a lot of energy to break them.
Multiple bonds
Single—sharing 1 pair of electrons
C H
Double—sharing 2 pairs of electrons
Triple—sharing 3 pairs of electrons
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C C
N N
HYDROGEN BONDS
 Attraction between the δ– end of one molecule and the


δ+ hydrogen end of another molecule forms hydrogen
bonds.
They form between water molecules.
They are important in the structure of DNA and
proteins.
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WATER!
 Water molecules form multiple hydrogen bonds with
each other—this contributes to high heat capacity.
A lot of heat is required to
raise the temperature of water—
the
heat energy breaks the
hydrogen bonds.
In organisms, presence of
water shields them from
fluctuations in environmental
temperature.
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Water has a high heat of vaporization—a lot of heat is
required to change water from liquid to gaseous state.
Thus, evaporation has a cooling effect on the
environment.
• Sweating cools the body—as sweat evaporates from
the skin, it transforms some of the adjacent body heat.
Hydrogen bonds also give water cohesive strength, or
cohesion—water molecules resist coming apart when
placed under tension.
• This permits narrow columns of water to move from
roots to leaves of plants.
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 Any polar molecule can interact with any other polar


molecule through hydrogen bonds. WATER IS POLAR!
Hydrophilic (“water-loving”)—in aqueous solutions, polar
molecules become separated and surrounded by water
molecules
Nonpolar molecules are called hydrophobic (“waterhating”); the interactions between them are hydrophobic
interactions.
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Why study Carbon?
 All of life is built on carbon
 Cells
~72% H2O
;)
 ~25% carbon compounds

 carbohydrates
 lipids
 proteins
 nucleic acids

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~3% salts
 Na, Cl, K…
Chemistry of Life
 Organic chemistry is the study of
carbon compounds
 C atoms are versatile building blocks
bonding properties
 4 stable covalent bonds

H
H
C
H
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H
Hydrocarbons
 Combinations of C & H

non-polar
 not soluble in H2O
 hydrophobic
stable
 very little attraction
between molecules

 a gas at room temperature
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methane
(simplest HC)
Hydrocarbons can grow
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Isomers
 Molecules with same molecular formula
but different structures (shapes)
different chemical properties
 different biological functions

6 carbons
6 carbons
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6 carbons
Form affects function
 Structural differences create important
functional significance

amino acid alanine
 L-alanine used in proteins
 but not D-alanine

medicines
 L-version active
 but not D-version

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sometimes with
tragic results…
stereoisomers
Form affects function
 Thalidomide
prescribed to pregnant women in 50s & 60s
 reduced morning sickness, but…
 stereoisomer caused severe birth defects

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Diversity of molecules
 Substitute other atoms or groups
around the carbon

ethane vs. ethanol
 H replaced by an hydroxyl group (–OH)
 nonpolar vs. polar
 gas vs. liquid
 biological effects!
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ethane (C2H6)
ethanol (C2H5OH)
Functional groups
 Parts of organic molecules that are
involved in chemical reactions

give organic molecules distinctive
properties
hydroxyl
 carbonyl
 carboxyl

amino
 sulfhydryl
 phosphate

 Affect reactivity
makes hydrocarbons hydrophilic
 increase solubility in water

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Viva la difference!
 Basic structure of male & female
hormones is identical



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identical carbon skeleton
attachment of different functional groups
interact with different targets in the body
 different effects
Hydroxyl
 –OH
organic compounds with OH = alcohols
 names typically end in -ol

 ethanol
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Carbonyl
 C=O

O double bonded to C
 if C=O at end molecule = aldehyde
 if C=O in middle of molecule = ketone
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Carboxyl
 –COOH

C double bonded to O & single bonded
to OH group
 compounds with COOH = acids
 fatty acids
 amino acids
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Amino
 -NH2

N attached to 2 H
 compounds with NH2 = amines
 amino acids
 NH2 acts as base
 ammonia picks up H+ from solution
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Sulfhydryl
 –SH

S bonded to H
 compounds with SH = thiols
 SH groups stabilize the structure of proteins
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Phosphate
 –PO4

P bound to 4 O
 connects to C through an O
 lots of O = lots of negative charge
 highly reactive
 transfers energy between organic molecules
 ATP, GTP, etc.
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