BMS1021: Lecture 2 Role of water in biological systems
Ionisation of water
- Although H₂O is essentially a neutral molecule, it can ionise to release a proton H₂O ⇌ H⁺ + OH⁻ - In water a free proton has only a fleeting existence. It usually will combine with a water to form a hydronium ion. Water accepts the proton to form a hydronium ion H₂O + H⁺ ⇌ H₃O⁺ - Water thus acts both as a proton donor and a proton acceptor. - In pure water, H⁺ (or H₃O⁺ ) and OH⁻ are present in equal concentration (1x10⁻⁷ M at 25ºC)
Effect of pH on activity of molecules
- Enzymes typically work best at or near their optimal pH - Activity is determined by the ionization state of the charged groups of the constituent amino acids, especially those in their active sites - Small changes in pH affect metabolism greatly and can be life threatening - Maintenance of pH achieved by buffering systems
The effect of pH on dissolved molecules
- Many biological molecules contain more than one dissociable protons. Amino acids for example contain at least two. - The charge on such molecules is dependent on pH in a complex manner. - The amino acid alanine has one amino group and one carboxylic acid group. In the fully protonated form (at low pH) it has a charge of +1.0. In the fully dissociated form (high pH) it has a charge of -1.0. At intermediate pH values it has a charge between these extreme values.
How do buffers maintain pH in biological systems?
- Phosphate or Bicarbonate buffer systems maintain intracellular and extracellular fluids respectively at optimal physiological pH - Internal pH of cells is close to 7 - Human blood pH is close to 7.4 (7-7.8) - Level of Carbonic Acid (H₂CO₃) regulated by respiratory rate
SUMMARY
- Water is a polar molecule that is able to form hydrogen bonds and to ionise. - These features give rise to the strong cohesion of water that is manifest both at a macroscopic and a cellular level. - Presence of hydrogen bonds can explain water's high specific heat and heat of vapourisation, as well as the low density of ice. - Non-polar molecules are subject to the "hydrophobic effect" and polar molecules and ions can be dissolved in water. - Ionisation of water and changes in pH of a solution result in changes to charges on dissolved biological molecules. - Buffering systems maintain pH of cells and tissues at optimal levels for metabolic functioning.
Interaction of water and biological macromolecules
- many biological macromolecules are ionic in character - eg. proteins, carbohydrates and nucleic acids - water will dissolve macromolecules, providing they have polar regions on their surface. These are generally readily soluble in water
What are some biologically important hydrogen bonds?
1. Between the hydroxyl group of an alcohol and water. 2. Between the carbonyl group of a ketone and water. 3. Between peptide groups in polypeptides. 4. Between complementary bases of DNA.
What are the four types of noncovalent ("weak") interactions among biomolecules in aqueous solvent?
1. Hydrogen bonds 2. Ionic interactions 3. Hydrophobic interactions 4. Van der Waals interactions
What are the essential and unique properties of the hydrogen bonds that form between water molecules?
1. cohesion 2. high specific heat 3. heat of vapourisation 4. low density of ice 5. water as a solvent
What is a hydrogen bond?
A hydrogen bond is the attractive force between the hydrogen attached to an electronegative atom of one molecule and an electronegative atom of a different molecule. Usually the electronegative atom is oxygen, nitrogen, or fluorine, which has a partial negative charge. The hydrogen then has the partial positive charge.
What is the relevance of water's high specific heat to life on Earth?
A large body of water can absorb and store a huge amount of heat from the sun in the daytime and during summer while warming up only a few degrees. At night and during winter, the gradually cooling water can warm the air. This capability of water serves to moderate air temperatures in coastal areas. It also tends to stabilize ocean temperatures, creating a favorable environment for marine life. Thus, because of its high specific heat, the water that covers most of Earth keeps temperature fluctuations on land and in water within limits that permit life. Also, because organisms are made primarily of water, they are better able to resist changes in their own temperature than if they were made of a liquid with a lower specific heat.
What is an amphipathic molecule?
A molecule with both hydrophobic and hydrophilic regions is termed amphipathic - the fatty acid stearic acid is an example of a hydrophobic alkane-based molecule CH₃ - (CH₂)₁₆ - CO₂H - when the carboxylic acid dissociates, the result is the stearate ion with a polar grouping at one end - a charged carboxylate ion. CH₃ - (CH₂)₁₆ - CO₂‾
What are hydrophobic molecules?
Alkanes and related molecules (non-polar) are termed hydrophobic. They do not readily dissolve in water.
Why is water cohesive?
Although the arrangement of molecules in a sample of liquid water is constantly changing, at any given moment many of the molecules are linked by multiple hydrogen bonds. These linkages make water more structured than most other liquids. Collectively, the hydrogen bonds hold the substance together, a phenomenon called cohesion.
What do amphipathic molecules tend to do in water?
Amphipathic molecules tend to cluster in water
What is the effect of water's high specific heat on change in temperature?
Because of the high specific heat of water relative to other materials, water will change its temperature less than other liquids when it absorbs or loses a given amount of heat.
What are buffers?
Buffers are a mixture of a weak acid and its conjugate base, working best when both are present in equal amounts. They resist changes in pH caused by addition of H⁺ or OH⁻, due to a balancing act between the two dissociation equations
What is the importance of water's heat of vapourisation?
Due to the strength of the hydrogen bond, it takes a lot of energy to break the bonds and allow molecules to escape the liquid. Evaporation, used by many animals and plants to cool themselves, is achieved by using the large amount of heat needed to break the hydrogen bonds between water molecules, to release water as vapour.
What forms strong attractive forces between water molecules, and what is its strength compared to a covalent bond?
Hydrogen bonds are equivalent to about 1/20th of a covalent bond.
What 3-D shape do hydrogen bonds form around the oxygen?
Hydrogen bonds form in a nearly tetrahedral arrangement about the oxygen.
What is a hydrophobic interaction?
Hydrophobic interactions describe the relations between water and hydrophobes (low water-soluble molecules). Hydrophobes are nonpolar molecules and usually have a long chain of carbons that do not interact with water molecules. The mixing of fat and water is a good example of this particular interaction.
Is H₂O polar?
H₂O is polar
What is the importance of water's low density of ice?
Ice forms at the SURFACE of ponds and lakes, allowing life to continue underneath. Because ice floats on water, oceans and lakes do not readily freeze; ice in fact insulates the water from the cold air above. If ice did not float, the antarctic glaciers would extend far under water and melt far more slowly than they do at the ocean surface. Much of the ocean would freeze. Life as we know it could not exist.
Why is ice less dense than liquid water?
Ice hydrogen bonds are stable while the hydrogen bonds of liquid water constantly break and reform. As a result the ice lattice that forms when water freezes forces water molecules further apart than they are in liquid water.
What interactions can be seen in molecules with a localized charge on a particular atom?
Ionic interactions For example, the full negative charge associated with ethoxide, the conjugate base of ethanol, is most commonly accompanied by the positive charge of an alkali metal salt such as the sodium cation (Na+).
What is an ionic interaction?
Ionic interactions involve the attraction of ions or molecules with full permanent charges of opposite signs. For example, sodium fluoride involves the attraction of the positive charge on sodium (Na+) with the negative charge on fluoride (F−). These bonds are harder to break than covalent bonds because there is a strong electrostatic interaction between oppositely charged ions. However, this particular interaction is easily broken upon addition to water, or other highly polar solvents.
What is surface tension?
Related to cohesion is surface tension, a measure of how difficult it is to stretch or break the surface of a liquid. At the interface between water and air is an ordered arrangement of water molecules, hydrogen-bonded to one another and to the water below. This gives water an unusually high surface tension, making it behave as though it were coated with an invisible film.
What does the flickering model of water postulate?
The flickering cluster model of water postulates that 85% of water molecules exist in short lived (~10-12 s) hydrogen-bonded, clusters. These are of variable size, averaging about 25 molecules at room temperature. All the molecules are in rapid flux, with clusters constantly growing, shrinking, breaking apart and reforming.
What is the specific heat of water?
The specific heat of water is 1 calorie per gram and per degree Celsius, abbreviated as 1 cal/g °C.
What is a Van der Waals interaction?
Van der Waals forces are driven by induced electrical interactions between two or more atoms or molecules that are very close to each other. Van der Waals interaction is the weakest of all intermolecular attractions between molecules. However, with a lot of Van der Waals forces interacting between two objects, the interaction can be very strong (i.e. in molecules with high molecular mass). There are two kinds of Van der Waals forces: weak Dispersion Forces and stronger dipole-dipole forces
How does water interact with ionic molecules?
Water dissolves ionic molecules by interacting with ions forming hydration shells e.g. sea water has many different dissolved ions.
How does cohesion contribute to the transport of water and dissolved nutrients against gravity in plants?
Water from the roots reaches the leaves through a network of water-conducting cells. As water evaporates from a leaf, hydrogen bonds cause water molecules leaving the veins to tug on molecules farther down, and the upward pull is transmitted through the water-conducting cells all the way to the roots.
What is the structure of H₂O?
Water has a bent shape. The oxygen region of the molecule has a partial negative charge (δ-), and each hydrogen has a partial positive charge (δ+).
What is the importance of water as a solvent?
Water is the principal SOLVENT for materials within cells. Water thus acts as the medium through which all solute molecules are transported. Because it is polar, water can form hydrogen bonds and dipole-dipole interactions with other molecules. Any molecule which can form a hydrogen bond - either as a hydrogen donor or as a hydrogen acceptor - can form hydrogen bonds with water. Such molecules are hydrophilic (water loving).
Why do water molecules stay close together?
Water molecules stay close to each other as a result of hydrogen bonding.
Why does water have a high specific heat?
Water's high specific heat results from hydrogen bonding. Heat must be absorbed in order to break hydrogen bonds; by the same token, heat is released when hydrogen bonds form. A calorie of heat causes a relatively small change in the temperature of water because much of the heat is used to disrupt hydrogen bonds before the water molecules can begin moving faster. And when the temperature of water drops slightly, many additional hydrogen bonds form, releasing a considerable amount of energy in the form of heat.
How can surface tension be observed>
You can observe the surface tension of water by slightly overfilling a drinking glass; the water will stand above the rim. The spider takes advantage of the surface tension of water to walk across a pond without breaking the surface.