Cell and Molecular Biology- Chapter 2

The Chemistry of the Cell

• Five principles important to cell biology

– Characteristics of carbon

– Characteristics of water

– Selectively permeable membranes

– Synthesis by polymerization of small molecules

– Self-assembly

2.1 The Importance of Carbon

• Organic chemistry is the study of carbon-containing compounds.

• Biological chemistry (biochemistry) is the study of the chemistry of living systems.

• The carbon atom (C) is the most important atom in

biological molecules.

• Specific bonding properties of carbon account for the characteristics of carbon-containing compounds.

Bonding Properties of the Carbon Atom

• The carbon atom has a valence of 4, so it can form four chemical bonds with other atoms.

• Carbon atoms are most likely to form covalent bonds with

other carbon atoms and with oxygen (O), hydrogen (H),

nitrogen (N), and sulfur (S).

• Covalent bonds—the sharing of a pair of electrons

between two atoms

Biological Compounds

• These normally contain carbon, hydrogen, and one or

more atoms of oxygen, as well as nitrogen, phosphorus, or

sulfur.

• These (O, N, P, S) are usually part of functional groups,

common arrangements of atoms that confer specific

chemical properties on a molecule.

Functional Groups

• Important functional groups include

– Carboxyl and phosphate groups (negatively charged)

– Amino groups (positively charged)

– Hydroxyl, sulfhydroxyl, carbonyl, and aldehyde groups

(uncharged, but polar)

Some Common Functional Groups Found in Biological Molecules

Bond Polarity

• In polar bonds, electrons are not shared equally between

two atoms.

• Polar bonds result from a high electronegativity (affinity for

electrons) of oxygen and sulfur compared to carbon and

hydrogen.

• Polar bonds have high water solubility compared to C—C

or C—H bonds, in which electrons are shared equally.

2.2 The Importance of Water

• Water has an indispensable role as the universal solvent in biological systems.

• It is the single most abundant component of cells and organisms.

• About 75–85% of a cell by weight is water.

• Water is indispensable for life.

Transport of Water

• Must have transport of water in and out of cells as well as

between cells

• Osmosis—the process of water moving across cellular

membranes based on the concentration of solutes present

• Aquaporin (AQ P)—a specialized channel protein that

allows for water to move more quickly than via osmosis

Polarity of Water

• The most critical attribute of water is its polarity, which

accounts for water’s:

– Cohesiveness

– Temperature-stabilizing capacity

– Solvent properties

Water Molecules Are Polar

• Unequal distribution of electrons gives water its polarity.

• The water molecule is bent rather than linear.

• The oxygen atom at one end of the molecule is highly

electronegative, drawing the electrons toward it.

• This results in a partial negative charge at this end of the

molecule, and a partial positive charge around the

hydrogen atoms.

Hydrogen Bonds and Cohesiveness

• Water is characterized by an extensive network of

hydrogen-bonded molecules, which make it cohesive.

• The combined effect of many hydrogen bonds accounts

for water’s high

– Surface tension

– Boiling point

– Specific heat

– Heat of vaporization

Surface Tension of Water

• Is the result of the collective strength of vast numbers of hydrogen bonds

• Allows insects to walk along the surface of water without breaking the surface

• Allows water to move upward through conducting tissues of some plants

Water Has a High Temperature-Stabilizing Capacity

• High specific heat gives water its temperature-stabilizing capacity.

• Specific heat—the amount of heat a substance must

absorb to raise its temperature 1ºC

• The specific heat of water is 1.0 calorie per gram, which is much higher than most liquids.

Temperature-Stabilizing Capacity

• Heat that would raise the temperature of other liquids is first used to break numerous hydrogen bonds in water.

• Water therefore changes temperature relatively slowly, protecting living systems from extreme temperature changes.

• Without this characteristic of water, energy released in cell metabolism would cause overheating and death.

Heat of Vaporization

• Heat of vaporization is the amount of energy required to convert 1 gram of liquid into vapor.

• This value is high for water because of the many hydrogen bonds that must be broken.

• The high heat of vaporization makes water an excellent coolant.

Water Is an Excellent Solvent

• A solvent is a fluid in which another substance, the

solute, can dissolve.

• Because of its polarity, water is able to dissolve a large variety of substances.

• Many of the molecules in cells are also polar and so can form hydrogen bonds or ionic bonds with water.

Solutes

• Solutes that have an affinity for water and dissolve in it easily are called hydrophilic (“water-loving”).

• Many small molecules—sugars, organic acids, some

amino acids—are hydrophilic.

• Molecules not easily soluble in water—such as lipids and proteins in membranes—are called hydrophobic (“water-fearing”).

NaCl in Water

• A salt, such as NaCl, exists as a lattice of Na+ cations (positively charged) and Cl− anions (negatively charged).

• For a salt to dissolve in a liquid, the attraction of anions and cations in the salt must be overcome.

• In water, anions and cations take part in electrostatic

interactions with the water molecules, causing the ions to separate.

• The polar water molecules form spheres of hydration around the ions, decreasing their chances of reassociation.

The Solubilization of Sodium Chloride

2.3 The Importance of Selectively Permeable Membranes

• Cells need a physical barrier between their contents and the outside environment.

• Such a barrier should be:

– Impermeable to much of the cell contents

– Not completely impermeable, allowing some materials into and out of the cell

– Insoluble in water to maintain the integrity of the barrier

– Permeable to water to allow flow of water in and out of the cell

Membranes Surround Cells

• The cellular membrane is a hydrophobic permeability barrier.

• It consists of phospholipids, glycolipids, and membrane proteins.

• The membranes of most organisms also contain sterols —cholesterol (animals), ergosterols (fungi), or phytosterols (plants).

Membrane Lipids Are Amphipathic

• Membrane lipids are amphipathic; they have both

hydrophobic and hydrophilic regions.

• Amphipathic phospholipids have a polar head; the polarity is due to a negatively charged phosphate group linked to a positively charged group.

• They also have two nonpolar hydrocarbon tails.

The Solubilization of Sodium Chloride

The Solubilization of Sodium Chloride

The Amphipathic Nature of Membranen Phosolipids

A Membrane Is a Lipid Bilayer with Proteins Embedded in It

• In water, amphipathic molecules undergo hydrophobic interactions.

• The polar heads of membrane phospholipids face outward toward the aqueous environment.

• The hydrophobic tails are oriented inward.

• The resulting structure is the lipid bilayer.

Lipid Bilayers Are Selectively Permeable

• Because of the hydrophobic interior, a lipid bilayer is

readily permeable to nonpolar molecules.

• However, it is quite impermeable to most polar molecules and highly impermeable to all ions.

• Cellular constituents are mostly polar or charged and are prevented from entering or leaving the cell.

• However, very small molecules diffuse.

Permeability of Membranes of Various Classes of Solutes

Ions Must Be Transported

• Even the smallest ions are unable to diffuse across a

membrane.

• This is due to both the charge on the ion and the

surrounding hydration shell.

• Ions must be transported across a membrane by

specialized transport proteins.