biochemistry

Biochemistry

Teacher: Nan QiDivision of biochemistry

School of Basic Medical ScienceAnhui Meidcal University

Email: [email protected]

CHAPTER 1 Molecules in cells and water

• What is biochemistry about?

• The importance of water

What is biochemistry about?

Learning Objectives– Describe the nature of biochemistry

What is biochemistry about?

• Biochemistry is the study of the molecular events that correspond to the phenomenon of life.

• Biochemistry is concerned with the relationship between the structure and the function of the molecules that occur in living systems.

Cells: Universal Building Blocks • Living organisms

are made of cells• Simplest living

organisms are single-celled

• Larger organisms consists many cells with different functions

• Not all the cells are the same

Molecules in Cells

• Cells contain a great variety of molecules, ranging from enormous polymers containing millions of atoms to small building block and fuel molecules with fewer than 100 atoms.

• The most abundant molecules in cells: water.

The importance of water

Learning Objectives– Describe the unique physical properties of water

– Describe the influence of water in weak intermolecular forces such as hydrogen bonds, electrostatic forces and hydrophobic interactions

– Give examples of biochemical reactions in which water is (a) a reactant and (b) a product


Water accounts for about 60% of the body weight of an adult:

• About 63% of body water is within cells

• 37% is extracellular fluid

• About one-quarter of extra cellular fluid is blood plasma.


• Deviations of more than 1% or 2% from the normal water content of the body have adverse effects on our well-being and performance.

• Water influences the behavior of all other molecules of biochemical interest.

• All biochemical processes occur in, or in contact with, aqueous solution.

Physical properties of water

• The molecular formula for water, H2O, does not reveal what an unusual substance water is.

• Water influences the behavior of all other molecules of biochemical interest.

• All biochemical processes occur in, or in contact with, aqueous solution.

• The molecular formula for water, H2O

• The molecule contains an oxygen atom making covalent bonds with each of two hydrogen atoms.

• The molecule is highly polar.

Physical properties of water

Physical properties of water • Water molecules

act as electrostatic dipoles; they attract each other strongly and form clusters.

• The clusters formed by water molecules are temporary; molecules are continually leaving one cluster and joining another.

Physical properties of water • Cluster of water

molecules held together by hydrogen bonds.

• Polar interactions and hydrogen bonds make water a liquid.

Hydrogen bonds • A hydrogen bond is

the sharing of two electrons on an oxygen or nitrogen atom with a hydrogen atom carried on another atom, usually oxygen or nitrogen (but not carbon).

Hydrogen bonds • The hydrogen bond

is weaker and longer than a covalent bond. The hydrogen bond is about 0.28 nm long compared with a covalent bond length of 0.15 nm.

Hydrogen bonds

• Many molecules of biochemical interest are capable of forming hydrogen bonds.

• Bonds are formed both within and between molecules, but most hydrogen bonds are formed in competition with the bonds that could be formed with water.

• Water thus provide a medium in which hydrogen bonds can be rapidly formed and broken.

Solvent and ionising properties of water

• As a consequence of its polar nature, water has a high dielectric constant.

• This means that it reduces the electrostatic forces between any charged particles it surrounds.

• Water is thus an excellent solvent for ionic materials.


NaCl(s) <=>Na+ + Cl-• Sodium and chloride ions in

a salt crystal attract each other so strongly that the crystal is a highly stable structure in air or in most solvents.

• In the presence of water, the ions become hydrated and attractive forces between the ions are greatly reduced.

• The hydrated ions can readily separate and enter solution.


• An acid is a molecule that can dissociate to form a hydrogen ion, H+, and a base.

• Water can promote the dissociation of hydrogen ions from acid in two ways:


• Water acts an acceptor for the hydrogen ion, which should really be represented not as H+ but as H3O+, and even the H3O+ is hydrated.

• If the base is negatively charged, water reduces the attractive force between the base and the departing positively charged hydrogen ion.


For example, the dissociation of acetic acid, a typical weak acid, is promoted in water, where the H+ produced can be made more stable by hydration (H3O+).


• Hydrogen ions are about 100 times more mobile than any other ions in aqueous solutions since water provides a special tunnelling mechanism for their movement.

• The positive charge representing the hydrogen atom can move through clusters of water molecules with minimal movement of any atoms.


pH = -log[H+]

• The concentration of hydrogen ions, [H+], influences many biochemical processes and is controlled in living cells and the fluid surrounding them.

• It is always quoted in biochemistry as pH.


• Most molecules of biochemical interest have one or more chemical groupings that can act as acids or bases, groups that can donate or accept a hydrogen ion.

• Since dissociation of acids and binding of hydrogen ions by bases are rapid equilibrium processes, the charge on many biochemical molecules varies with the pH of the medium.

Water and non-polar molecules

• Molecules that are not polar are generally insoluble in water.

• Water molecules cling to each other, excluding the non-polar molecules, which remain clustered together as solids or immiscible liquids.

Amphipathic molecules and hydrophobic interactions

• Many biochemical molecules, long-chain fatty acids and their ions are examples, cannot be classified as simply polar or non-polar.

• One part of a molecule may be polar and interact readily with water, and is said to be hydrophilic or ‘water-loving’, whereas another part is non-polar and is excluded from water, being hydrophobic or ‘water-hating’.


Water has a powerful influence on such molecules and organisms them into biochemically important structures such as:

• membranes

• folded globular proteins

• the DNA double helix


• In these structure, hydrophobic parts of molecules associate with other hydrophobic parts to form a core from which water is excluded.

• The surface of the structure is composed of the hydrophilic parts of the molecules.

• The surrounding water molecules stabilise the structure.

Water as a reactant

• Biochemical reactions often involve water molecules as a reactant or product.

• Many reactions in metabolism involve the addition or elimination of a water molecule.

Water as a reactant

• The polymerisation of building block molecules to make macromolecules such as proteins or nucleic acids involves the elimination of a water molecule and the formation of a covalent bond between the building blocks.

• Breakdown of the macromolecules, as in digestion, is by hydrolysis, the cleavage of the bond between the building blocks with the introduction of a molecule of water.

Education

biochemistry