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Biochemistry
Topics
Inorganic chemistry
 Water
 Organic chemistry (macromolecules)

– Carbohydrates
– Lipids
– Proteins
– Nucleic acids
Why are we studying chemistry?

Biology has chemistry at its foundation
2005-2006
SI Unit Prefixes
The Basics
Everything is made of matter
 Matter is made of atoms
 Atoms are made of:

– protons
– neutrons
– electrons

+
0
-
mass of 1
mass of 1
mass <<1
nucleus
nucleus
orbits
Different kinds of atoms = elements
Models of atoms
(c)
2005-2006
Atomic structure determines behavior

The number of protons in an atom
determines the element
– # of protons = atomic number
– this also tells you # of electrons

All atoms of an element have same
chemical properties
– all behave the same
– properties don’t change
All life processes obey the laws of chemistry and
physics. Living organisms are chemical machines.
A.
Inorganic chemistry
1. introduction:
a. elements – about 25 are essential for life
1. 4 elements make up 96% of living matter
~ carbon (C)
~ hydrogen (H)
~ oxygen (O)
~ nitrogen (N)
2. Four elements make up most of the
remaining 4%
~ phosphorus (P) ~ calcium (Ca)
~ sulfur (S)
~ potassium (K)
3. trace – elements needed by living things
in minute quantities (i.e. Fe and I)
4. atoms – electrons determine chemical
properties
2. diatomic atoms: N2, O2, H2, Cl2, F2, I2, Br2
2005-2006
3. Isotopes
Different number of neutrons (heavier);
same chemical properties i.e. C14, O18
 Some are unstable

– nuclear reactions / decay

Split off neutrons &/or protons
– radioactivity
Biological tool
 Biological hazard

a. radioactive dating - C14 ( half-life of 5,730yrs.)
b. tracers – used to identify pathways or
destinations of substances in the body
1. C14 – used in plants to identify C uptake
2. I123 – injected into bloodstream, taken up
by thyroid
3. S35 – used by enzymes
c. saving lives –
1. P238 – used in pacemakers
2. radium or cobalt – cancer treatments
3. PET [Positron-Emission Tomography]
4. molecules: 2 or more atoms
(electrically neutral)
5. compounds: two or more elements in fixed
proportions by mass
6. ions: charged atoms
7. Bonding properties

Effect of electrons
– chemical behavior of
an atom depends on its
electron arrangement
– depends on the
number of electrons in
its outermost shell, the
valence shell
How does this
atom behave?
Bonding properties

Effect of electrons
– chemical behavior of an atom depends on
number of electrons in its outermost shell
How does this atom behave?
How does this atom behave?
Chemical reactivity

Atoms tend to
– Complete a partially filled outer (valence)
electron shell
or
– Empty a partially filled outer (valence)
electron shell
– This tendency drives chemical reactions
bonds: exothermic versus endothermic
a. ionic – electrons transferred
b. covalent – 2 atoms share electrons
1. nonpolar – hydrophobic
2. polar – hydrophilic
c. weak – stabilize shape of large molecules
1. hydrogen
2. van der Waals interactions
(between nonpolar molecules)
3. hydrophobic interactions
(between groups of molecules that a
are insoluble in water)
d. electronegativity differences
0 = nonpolar covalent (sharing)
0.2–1.7 = polar covalent (unequal sharing)
1.7-3.3 = ionic
Ionic bonds
“Let’s go to the video tape!”
(play movie here)
Ionic bonds
Transfer of an electron
 Forms + & - ions

– + = cation
– – = anion

 example:

Weak bond
2005-2006
salt = dissolves
easily in water
Covalent bonds
Two atoms need an electron
 Share a pair of electrons
 Strong bond

– both atoms holding onto the electrons

Forms molecules

example:
– water = takes energy to separate
Double covalent bonds

Two atoms can share more than one
pair of electrons
– double bonds (2 pairs of electrons)
– triple bonds (3 pairs of electrons)

Very strong bonds
Multiple covalent bonds

1 atom can form covalent bonds with
two or more other atoms
– forms larger molecules
– ex. carbon
2005-2006
Reductionist view of biology







Matter is made of atoms
Life requires ~25 chemical elements
Atomic structure determines behavior of an
element
Atoms combine by chemical bonding to form
molecules
Weak chemical bonds play important roles in
chemistry of life
A molecule’s biological function is related to its
shape
Chemical reactions make & break chemical
bonds
pH Scale

In pure water only 1 water molecule in
every 554 million is dissociated.
– very small amount of ions
– [H+] or [OH-] is 10-7M
[H+] [OH-] = 10-14

pH scale is based on this equation
8.
9.
acids, bases, and salts:
a. pH scale
b. acids – increase H+ ions; i.e. HCl
c. bases – accept H+ ions; i.e. NaOH
d. salts – neutral
e. buffers – mix of slightly ionized weak acid
and its weak salt (helps to maintain a neutral
pH)
mixtures:
a. solution – uniformly dispersed, transparent
(salt water)
b. suspensions – solids added to water
(mud, sand)
c. colloidal dispersions – intermediate in size,
don’t separate (foam, smoke)
pH Scale
In neutral solution [H+]
= 10-7  pH = 7
 Values for pH decline
as [H+] increase
 Acids

– adding acid increases
[H+]

Bases
– adding base increases
[OH-]
Water dissociates to form ions

Hydrogen ion (H+) splits off from water to leave a
hydroxide ion (-OH)
H20 ----> H+ + -OH




If concentration of 2 ions is equal,
water is neutral
If [H+] > [-OH], water is acidic
If [-OH] > [H+], water is basic
pH scale = how acidic or basic a solution is
pH & Biology



pH of a neutral solution = 7
Acidic solutions =
pH < 7
Basic solutions =
pH > 7
Most biological fluids have pH 6 – 8
– pH values in human stomach can reach 2

Each pH unit represents a 10-fold difference in
H+ & OH- concentrations.
– small change in pH actually indicates a substantial
change in [H+] & [OH-]
Buffers

Have properties that allow them to act as either an
acid or a base (minimizing changes in pH)
 pH of blood must stay between 7.4 and 7.2. If
brought to 7 cause a coma.
 Without buffers, a very small amount of an acid
(1x10 -6) will cause a large change in pH (a whole
unit)
10. Importance of Water
~ makes up 70-90% of living things
~ all life occurs in water: every cell is bathed in water for rxns
to occur
~ water has unique physical properties b/c of
Its hydrogen bonding
1. stable & polar
2. three forms: ice, solid, gas
3. high heat capacity & retains heat
4. universal solvent
5. cohesion and high surface tension (elastic film)
6. expands when freezes
7. dissociates to form protons H+ and hydroxide ions
OH9. effective buffer against extreme temperature
fluctuations
Stable & Polar

polar covalent bonds (pair of electrons
not shared equally by 2 atoms)
– + & – poles
– Oxygen has a stronger “attraction” for the H
– Oxygen has a higher electronegativity
Polar covalent bonds
2 hydrogens in the water molecule form
an angle
 Water molecule is polar

– oxygen end is –
– hydrogen end is +

Leads to many
interesting properties
of water….
“Let’s go to the video tape!”
(play movie here)
Water molecules form H bonds
with each other
– + attracted to –
– creates a sticky
molecule
“Let’s go to the video tape!”
(play movie here)
2004-2005
Hydrogen bonds
Positive H atom in
1 water molecule is
attracted to negative O
in another
 Can occur wherever an
-OH exists in a larger
molecule
 Weak bonds

Cohesion (think “cuddle”)

H bonding between H2O creates
cohesion
– water is “sticky”
– surface tension
– drinking straw
• can you suck
sugar up a
straw?
2004-2005
Adhesion (think “attach”)

H2O molecules form H bonds with other
substances
– capillary action
– meniscus
– water climbs up fiber
• ex. paper towel
How does H2O get to top of tree?
(transpiration)

Transpiration
“Let’s go to the video tape!”
(play movie here)
Water is the solvent of life

H2O is a good solvent due to its polarity
– polar H2O molecules surround + & – ions
– solvents dissolve solutes creating aqueous
solutions
Hydrophilic

Hydrophilic
– substances have affinity for H2O
– polar or non-polar?
– ionic
Hydrophobic

Hydrophobic
– substances do not have affinity for H2O
– polar or non-polar?
– non-ionic
fat (triglycerol)
The special case of ice
Most (all?) substances are more
dense when they are solid
 But not water…
 Ice floats!

– H bonds form a crystal with
loose structure
2004-2005
Ice floats
Why is “ice floats” important?

Oceans & lakes don’t freeze solid
– if ice sank…
• eventually all ponds, lakes & even ocean would
freeze solid
• during summer, only upper few inches would
thaw
– surface ice insulates water below
• allowing life to survive the winter
– seasonal turnover of lakes
• cycling nutrients
Specific heat

H2O has high specific heat
– due to H bonding

H2O resists changes in temperature
– takes a lot to heat it up
– takes a lot to cool it down

H2O moderates temperatures on Earth
2004-2005
Evaporative cooling

Organisms rely on
heat of vaporization to
remove heat
2004-2005
Punchline
Water is a polar molecule
 The special properties of water make
life on Earth possible
 The chemical behavior of water governs
how organisms function

Any Questions??
11. inorganic compounds:
1. small
2. very reactive
3. ~20,000 different compounds
4. CO2 – 0.033% composition of atmosphere
5. O2 – 20.9% composition of atmosphere
6. N2 – 78.1% composition of atmosphere
B.
Organic chemistry
1. organic compounds:
a. contain C and H
b. CO & CO2 – the only inorganic compound with C
c. carbon has 4 “open” spots
d. strong, stable bond
e. form rings (strongest), helixes, chains (weakest)
f. diverse compound combinations
g. most are insoluble in water
h. react slowly
i. isomers – same atomic content and molecular
formula, but different structural arrangements
Why study Carbon?
All living things are made of cells
 Cells

– ~72% H2O
– ~3% salts (Na, Cl, K…)
– ~25% carbon compounds
–
–
–
–
carbohydrates
lipids
proteins
nucleic acids
Chemistry of Life
Organic chemistry is the study of carbon
compounds
 C atoms are versatile building blocks

– bonding properties
– 4 stable covalent bonds
2003-2004
Complex molecules assembled like TinkerToys
2003-2004
Hydrocarbons

Simplest C molecules = hydrocarbons
– combinations of C & H

Simplest HC molecule = methane
– 1 carbon bound to 4 H atoms
– non-polar
– not soluble in H2O
– hydrophobic
– stable
– very little attraction between molecules
– a gas at room temperature
Hydrocarbons can grow

methane
adding C-C bonds
ethane
– straight line
• ethane
• hexane
– branching
hexane
• isohexane
– ring
• cyclohexane
isohexane
cyclohexane
Diversity of organic molecules
Isomers

Molecules with same molecular formula
but different structures
Structural isomers

Molecules differ in structural arrangement
of atoms: different chemical properties
Geometric isomers
Different spatial arrangements
 1 isomer has anti-tumor activity other
does not

Enantiomer (stereo) isomers

Molecules which are mirror images of
each other
– Behave identically except in a rxn w/other
stereoisomers
– left-handed & right-handed versions
• “L” versions are biologically active
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
– sometimes with
tragic results…
Form affects function

Thalidomide
– prescribed to pregnant women in 50’s & 60’s
– reduced morning sickness, but…
– stereoisomer caused severe birth defects
Diversity of molecules

Substitute other atoms or groups
around the C
– ethane vs. ethanol
•
•
•
•
H replaced by an hydroxyl group (–OH)
nonpolar vs. polar
gas vs. liquid
biological effects!
ethane
ethanol
Functional Groups
Functional groups

Components of organic molecules that
are involved in chemical reactions
– give organic molecules distinctive
properties
– ex: male & female hormones…
Viva la difference!

Basic structure of male & female hormones is
identical
– identical C skeleton
– attachment of different functional groups
– interact with different targets in the body
2003-2004
Types of functional groups

6 functional groups most important to
chemistry of life:
– hydroxyl
– carbonyl
– carboxyl

amino
 sulfhydryl
 phosphate

Affect reactivity
– hydrophilic
– increase solubility in water
2. functional groups:
determine solubility, reactivity, and other traits
phosphate
Hydroxyl

–OH
– organic compounds with OH = alcohols
– names typically end in -ol
• ethanol
Carbonyl

C=O
– O double bonded to C
• if C=O at end molecule = aldelhyde
• if C=O in middle of molecule = ketone
Carboxyl

–COOH
– C double bonded to O & single bonded to
OH group
• compounds with COOH = acids
– fatty acids
– amino acids
2003-2004
Amino

-NH2
– N attached to 2 H
• compounds with NH2 = amines
– amnio acids
• NH2 acts as base
– ammonia picks up H+ from solution
Sulfhydryl

–SH
– S bonded to H
• compounds with SH = thiols
• SH groups stabilize the structure of proteins
Phosphate

–PO4
– P bound to 4 O
• connects to C through an O
• PO4 are anions with 2 negative charges
• function of PO4 is to transfer energy between
organic molecules (ATP)