Table of Contents
Fundamentals of Biochemistry
Biochem 380 - Fall 2006
Lecture 004
Outline
- Announcements
- Quiz
- Questions about previous lecture
- Section 2.1: Water is Polar
- Section 2.2: Hydrogen Bonds
- Section 2.3: Water is a Good Solvent
Announcements
- Lecture 3 notes are online
Quiz
- Short Quiz on Chapter 1 (approx 15-20 minutes)
Questions
- Any questions about the quiz?
- Any questions on the material from the previous lecture?
Chapter 2: Homework Problems
- Assigned homework problems for Chapter 2:
- 1, 2, 4, 5, 7, 13, 15
Chapter 2: Water
- In Chapter 2, we'll look at the particular properties of water and some more general chemical interactions
between atoms
- These chemical properties and interactions are important in biochemistry because they help to determine
the structure of biomolecules, such as the folding of proteins into their well-defined 3-dimensional shapes
- We'll also talk about acids, bases and the pH scale
- We'll examine qualitatively and quantitatively how changes in pH affect the charge of ionizable
groups in biomolecules
- Chapter 2 concludes with considering how pH levels can be stabilized in buffered solutions, and
regulated physiologically, in the circulatory systems of mammals
The Properties of Water
- Water has a number of distinct properties that perhaps may explain why it is the environment in which all
life is found
- First, water is a polar molecule, because a separation of charge exists between its atoms
- Second, water has the ability to form hydrogen bonds, between molecules of itself and also with other
molecules
- Finally, because of its polar nature and small size, water is an excellent solvent for many ionic
and polar substances.
Section 2.1: Water is Polar
- A water molecule overall is electrically neutral, but a separation of charge between its atoms causes it
to be polar
- This polar quality is a result of two features:
- its tetrahedral geometry
- its bond polarities
- These combine to produce a net dipole, which is an uneven distribution of equal and opposite charges
Orbital Structure of Water
- Water (H2O) consist of an oxygen atom covalently bonded to two hydrogen atoms. It has a tetrahedral
bond structure that results from 4 sp3 hybridized orbitals
- Oxygen has six electrons that occupy the orbitals. Four of the electrons fill two of the orbitals as
non-bonding electron pairs.
- The remaining two electrons each occupy one of the other two orbitals, where a covalent bond is formed
with a hydrogen atom that provides the second electron
Water has a Net Dipole
- Because the oxygen atom is more electronegative than the hydrogens, it will attract the shared electrons
more strongly to it, producing a dipole along each of its covalent bonds
- Because of the bent bond angle, these two bond dipoles add up to produce a net dipole for the entire
water molecule
Section 2.2: Hydrogen Bonds
- In organic chemistry, we have seen how the tetravalent nature of carbon enables a huge diversity of
stable, covalently-bonded structures in 3D space
- Water has a similar opportunity for forming tetravalent structures through hydrogen bonding.
However, these structures are much weaker than covalent bonds and consequently provide a much more dynamic and 'fluid'
environment. The typical lifetime of a hydrogen bond between two water molecules is around 10 picoseconds
(10-11 s), so they are constantly breaking and reforming
Hydrogen Bonding in Water
- Hydrogen bonds occur between an electronegative atom and a hydrogen that is covalently bonded to another
electronegative atom. For water, both of these electronegative atoms are oxygen.
- The typical distances in a hydrogen bond are shown above. The distance between the hydrogen and its
covalent oxygen (the hydrogen bond donor) is about 1 Angstrom (1 x 10-10 m).
- The typical distance between the hydrogen and the non-bonded oxygen (the hydrogen bond acceptor)
is around 1.8 A (0.18nm or 180 pm). Consequently, the total distance from donor to acceptor atom is about 2.8 A
for a linear hydrogen bond
Hydrogen Bond Energies
- Hydrogen bonds are much weaker than covalent bonds. The energy of a hydrogen bond can range from
around 2 - 20 kJ/mol. In contrast, covalent bonds are commonly around 400 kJ/mol.
- Hydrogen bonds between water molecules have been measured to be 20 kJ/mol, which is on the upper end.
Hydrogen bonds between water and other biomolecules such as proteins and nucleic acids are generally weaker,
towards the low end of around 2 - 7.5 kJ/mol
- The local environment of bonded and non-bonded atoms surrounding the hydrogen bond determine
how strong or weak it will be
- Another factor is orientation. Linear hydrogen bonds are the strongest, and successive bending of
the angle between donor and acceptor atoms will result in a weaker hydrogen bond
Hydrogen Bonding in Ice
- The energy of hydrogen bonds in ice are the strongest, 23 kJ/mol. This is a result of the regular,
symmetrical arrangement of the water molecules in the solid state
- Ice also has the unusual property of being less dense than water, which is the exception compared to
most solids. The reduced density results from the more linear orientations of the bonds, spreading out
the molecules slightly, compared to the liquid state
Section 2.3: Water is a Good Solvent
- A third important property of water is its ability to dissolve other polar compounds and compounds that
can be ionized
- Ionization is the loss or gain of electrons, resulting in a compound having a net charge
- Examples of ionized compounds include proteins, which have a positively-charged amino terminus, a
negatively-charged carboxyl terminus, and many ionized side chains
Interaction between Water and Ions
- A compound such as salt (sodium chloride) is an example of an ionizable compound that dissolves in water
- Although the positively charged sodium atoms (cations) are strongly attracted to the
negatively-charged chlorine atoms (anions), they can also interact with a larger number of polar water
molecules
- The small size of water molecules, compared to other solvents, also contributes to its solvation abilities,
because it allows more water molecules to interact with a given solute molecule
Osmosis
- One consequence of a water-filled cell containing dissolved ions is osmosis
- What is osmosis?
- Osmosis is the flow of solvent from a less concentrated solution to a more concentrated one
- The pressure required to prevent the flow of solvent is called the osmotic pressure
Osmotic Pressure
- Osmosis is a problem that many cells must deal with, because the outer cell membrane is
permeable to water and the interior generally has a higher concentration of solutes than the outside
- The natural consequence is for water to flow into the cell, increasing the pressure and possibly
causing the cell to burst
- Cells have a number of mechanisms for reducing the osmotic pressure, including ion pumps to
reduce the internal concentration of some solutes, and also by combining multiple small solute molecules such as
glucose into fewer, larger ones such as glycogen. This reduces the number of solute molecules available
for interaction with solvent, and consequently, reduces the osmotic pressure.
Questions
Next Lecture: Sections 2.4 - 2.7