BIOC 460, spring 2008
Lecture 1
Introduction, Noncovalent Bonds,
and Properties of Water
Reading: Berg, Tymoczko & Stryer: Chapter 1
problems in textbook: chapter 1, pp. 23-24, #1,2,3,6,7,8,9,
10,11; practice problems at end of Gen Chem Review
Key Concepts in Biochemistry
• Cells -- important structural features; compartments
(plasma membrane, nucleus or nucleoid, cytoplasm,
ribosomes, organelles like mitochondria, chloroplasts,
endoplasmic reticulum and Golgi apparatus
• Chemical unity of living systems
• Transformation of energy and matter from surroundings -> complex, orderly structures
• Biomolecules -- functional groups; condensation reactions
• Proteins -- molecular workhorses of living systems
• Enzymes increase rates of biological reactions to permit life
on a biological timescale.
• Rates of processes exquisitely regulated to maintain
dynamic steady state.
• 3-D structures of biomolecules determine their functions -role of noncovalent interactions in structure and function.
LEC 1, Introduction, Noncovalent Bonds,
and Properties of Water
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BIOC 460, spring 2008
Key Concepts, continued
• Noncovalent interactions: ionic interactions, hydrogen
bonds, van der Waals interactions, hydrophobic
“interactions”
– individually much weaker than covalent bonds
– collectively very strong
– crucial to structures and functions of biomolecules
• Properties of water -- “solvent”/milieu for living systems
• Most biomolecules have functional groups that are weak
acids or bases, whose ionization properties are crucial to
structures and functions of the molecules; pH determines
state of ionization of biomolecular weak acids and bases.
• Buffers (intracellular and extracellular)
Learning Objectives
•
•
•
Review basic structures of cells and organelles -- important
structural features and compartments (nucleus or nucleoid, plasma
membrane, cytoplasm, ribosomes, mitochondria, chloroplasts, and
endoplasmic reticulum).
Review (from posted lecture notes here) functional groups
important in biomolecules, and condensation reactions involving
some of these functional groups.
List and explain the characteristics of 4 types of noncovalent
interactions important in structures and interactions of biomolecules.
Answer the following questions:
1. What is an ionic interaction (charge-charge interaction), and
what other terms are used to describe the same thing?
• How does the distance between two charged groups affect the
energy of their interaction?
• What are the relative values of the dielectric constants for a
nonpolar solvent and a polar solvent?
• How does solvent polarity affect strength of ionic interactions?
• What type of solvent is water?
• Is an ionic interaction stronger in a polar solvent or in a
nonpolar solvent?
LEC 1, Introduction, Noncovalent Bonds,
and Properties of Water
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BIOC 460, spring 2008
Learning Objectives, continued
(Noncovalent interactions, continued)
2. What is a hydrogen bond, what is a hydrogen bond donor, and
what is a hydrogen bond acceptor?
• How does the strength of a hydrogen bond relate to its
directionality?
• Be able to identify chemical groups (and the specific atoms
involved) that can serve as hydrogen bond donors and groups
which can serve as hydrogen bond acceptors. [Do not confuse
a hydrogen bond donor with a proton donor (Bronsted acid).]
3. What are van der Waals interactions?
• How (qualitatively, not an equation) does their strength relate
to the distance between atoms?
• Why are such weak, nonspecific interactions important in
biochemistry?
4. What is the “hydrophobic effect”?
• Explain the idea of ”hydrophobic interactions" and the roles
they play in biological systems. (Roles will become more
apparent as the semester progresses).
Learning Objectives, continued
•
Explain the properties of H2O (its ionization properties, polarity,
hydrogen bonding ability, and solvent properties) that are so
important to its role as the major constituent of living systems.
– Explain: titration curve, buffer, and pKa. Relate the strength of a
weak acid to its pKa.
– Write out the 3 acid dissociation reactions of phosphoric acid, and
write out condensation reactions showing formation of a
phosphomonoester and of a phosphodiester.
– See practice problems at end of Gen Chem Review notes:
http://www.biochem.arizona.edu/classes/bioc460/spring/460web/l
ectures/chem_review/GeneralChemRev460-08.pdf
Explain relationships between (and be able to do calculations
involving these relationships):
1. [H+] and pH
2. Ka (acid dissociation constant) and pKa
3. ratio of [conjugate base]/[conjugate acid] and pH and pKa
4. ratio of [conjugate base/[conjugate acid] and fraction or
percent of a functional group that's in the form of the
conjugate acid or the conjugate base.
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and Properties of Water
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BIOC 460, spring 2008
BRIEF REVIEW OF CELL STRUCTURE
Bacterial Cells
Nelson & Cox, Lehninger Principles
of Biochemistry, 4th ed., Fig.1-6
Eukaryotic Cells
Nelson & Cox, Lehninger Principles
of Biochemistry, 4th ed., Fig.1-7a
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and Properties of Water
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BIOC 460, spring 2008
Eukaryotic Cells
Nelson & Cox, Lehninger Principles
of Biochemistry, 4th ed., Fig.1-7b
Functional Groups in Biomolecules
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and Properties of Water
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BIOC 460, spring 2008
• Functional Groups in Biomolecules
Condensation and Hydrolysis Reactions
1. Esters
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and Properties of Water
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BIOC 460, spring 2008
Condensation and Hydrolysis Reactions
2. Amides
Condensation and Hydrolysis Reactions
3. Anhydrides
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and Properties of Water
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BIOC 460, spring 2008
Chemical Bonds/Interactions in Biomolecules
• Covalent bonds: single, double, (triple)
– 2 atoms share a pair of electrons to fill an orbital on each
atom
– Equal or nearly equal sharing --> nonpolar group or
molecule
• Examples: C–C and C–H bonds (not polar)
– Unequal sharing --> a polar group or molecule
• 1 atom has partial positive charge (δ+)
• other atom has partial negative charge (δ–)
• Example: an O–H bond (polar)
• Interaction energy (bond energy): the energy released
during formation of the bond/interaction (so that much
energy would have to be put in to break the bond).
from Nelson & Cox, Lehninger
Principles of Biochemistry, 4th ed.)
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and Properties of Water
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BIOC 460, spring 2008
Ionic Interactions (charge-charge interactions,
salt bridges): electrostatic attraction or repulsion
between charged groups
Coulomb’s Law:
E = Energy of interaction
q’s = charges
D = dielectric constant (1 for vacuum, ~2 for hexane,
~80 for H2O)
r = distance between charged atoms
k = proportionality constant; value depends on units
desired for expressing energy
Hydrogen Bonds
• Electrostatic
effect of polarity of solvent (D)
• Donor groups
Acceptor groups
–N-H ----->
N: <---–O-H ----->
O: <---• Directional
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and Properties of Water
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BIOC 460, spring 2008
• van der Waals Interactions
– Energy of a van der Waals interaction as 2 atoms
approach one another within about 4-5 Å
– Individually very weak and nonspecific, but sum of many
can be very important in steric (shape) complementarity
Berg et al., Fig. 1.10
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and Properties of Water
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BIOC 460, spring 2008
Hydrophobic "Interactions"
• hydrophobic effect, the "oil drop" effect
• association of nonpolar groups with each other in aqueous
systems
• due to the unfavorable interaction of nonpolar
groups/molecules with water
• Result: "preference" of hydrophobic groups and molecules to
minimize their exposure to water
• misnamed " hydrophobic 'interactions' "
Berg et al.
Fig. 1-12
Properties of Water
• Polarity
– asymmetric charge distribution makes molecule dipolar
(polar)
– O atom δ–, H atom δ+
– strong ionic character to O-H bond
• Hydrogen bonding
– Water molecule bent:
– In how many hydrogen bonds can
1 H2O molecule participate?
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and Properties of Water
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BIOC 460, spring 2008
H2O
H-bonding in ice
Nelson & Cox, Lehninger Principles of
Biochemistry, 4th ed., Fig. 2-2
Solvent Properties of Water
• Excellent solvent for:
– Ions/charged groups
– Neutral polar compounds, e.g. sugars:
highly solvated (H-bonds to solvent HOH)
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and Properties of Water
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BIOC 460, spring 2008
Solvent Properties of Water, continued
• Poor solvent for hydrophobic groups - fatty acid alkyl “tail”
Nelson & Cox, Lehninger
Principles of Biochemistry,
4th ed., Fig. 2-7a
• Fatty acid: example of an amphipathic (amphiphilic) molecule
Ionization Properties of H2O
• Review from general chemistry -- see Gen Chem review
material for details.
– notes posted, covered in review session given at 2
different times, duplicate sessions to permit more
students to attend (4:00-5:00 pm Thurs. and Fri. p.m.,
first week of classes)
– General chemistry is a prerequisite for biochem, and
you need to understand it -- review it on your own and
come to review session.
• General concepts of chemical equilibrium and equilibrium
constants
• Importance of H+ (proton) concentration in cells and in
extracellular media
• State of ionization of weakly acidic groups on biomolecules
important to structure and function
• Titration curves
• Buffers
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and Properties of Water
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BIOC 460, spring 2008
Ionization Properties of H2O - Summary
• H2O and acids in aqueous solution dissociate to yield protons
(H+) (hydrated, forming H3O+ etc.)
• Proton concentrations often expressed on log10 scale as pH:
pH = –log[H+]
• Tendency of Bronsted acid to donate proton to H2O
(dissociate the proton) is described by its equilibrium acid
dissoc. constant Ka, i.e. by its pKa = –log Ka .
pKa = –log Ka
• pKa values measured experimentally by titration curves as
the pH at half equivalence points
• Relationship between pH, pKa, and ratio of conjugate
base/conjugate acid described by the
Henderson-Hasselbalch Equation:
Buffers
• Homeostasis: maintenance of constant conditions in internal environment
• Fluids in living systems -- pH is regulated, almost constant
• pH regulated by buffer systems
– Buffer: aqueous system that resists changes in pH when small
amounts of acid or base are added
– Buffer system: aqueous solution of a weak acid and its conjugate base
– Buffer range of a weak acid: pH values near its pKa, about ±1 pH unit
from pKa (Maxium buffering capacity is at the pKa.)
• Equilibrium acid dissocation reaction (remember Le Chatelier’s Principle, the
“law of mass action”):
HA <==> H+ + A–
– The higher the [H+] (the lower the pH), the more equilib. shifts to left.
– The lower the [H+] (the higher the pH), the more equilib. shifts to right.
– Exact ratio of base/acid (A–/HA) depends on Henderson-Hasselbalch Eq:
– When pH = pKa, [A–] = [HA],
LEC 1, Introduction, Noncovalent Bonds,
and Properties of Water
i.e., [base] = [acid]
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BIOC 460, spring 2008
2 Physiologically Important Buffer Systems
• Intracellular: Phosphate species
– Inorganic phosphate (phosphoric acid)
– Organic phosphates, e.g., phosphomonoesters
• Extracellular (blood plasma of mammals):
carbonic acid / bicarbonate buffer system
pKa~6.1
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and Properties of Water
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BIOC 460, spring 2008
1. Physiologically, how would a mammal deal with
acidosis (blood pH ↓, [H+] ↑) in the short term?
2. Physiologically, how would a mammal deal with
alkalosis (blood pH ↑; [H+] ↓) in the short term?
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and Properties of Water
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