Bio 340 - Chapter 2: Cell Chemistry and Bioenergetics

Carbon skeletons

carbon has a unique role in the cell because of its ability to form strong covalent bonds with other carbon atoms (e.g. chains, branched trees, rings)

Covalent bonds

forms when two atoms come very close together and share one or more of their outer-shell electrons. Each atom forms a fixed number of covalent bonds in a defined spatial arrangement

Single covalent bonds

two electrons shared per bond

Double covalent bonds

four electrons shared per bond

Atoms joined by two or more covalent bonds cannot ___

rotate freely around the bond axis

The precise spatial arrangement of covalent bonds influences the ___ and ___

three-dimensional structure, chemistry of molecules

Weak noncovalent chemical bonds

have less than 1/20 the strength of a strong covalent bond. They are less strong enough to provide tight binding only when may of them are formed simultaneously

Hydrogen bonds

because they are polarized, two adjacent H2O molecules can form a noncovalent linkage known as a hydrogen bond. Hydrogen bonds have only about 1/20 the strength of a covalent bond. Hydrogen bonds are strongest when the three atoms lie in a straight line.

Hydrophilic molecules

substances that dissolve readily in water. They include ions and polar molecules that attract water molecules through electrical charge effects. Water molecules surround each ion or polar molecule and carry it into solution

Hydrophobic molecules

substances that contain a preponderance of nonpolar bonds are usually insoluble in water. Water molecules are not attracted to such hydrophobic molecules and so have little tendency to surround them and bring them into solution

Electrostatic attractions

occur both between fully charged groups (ionic bond) and between partially charged groups on polar molecules. The force of attraction between the two partial charges, ∂+ and ∂-, falls off rapidly as the distance between the charges increases

In the absence of water, ___ are very strong. They are responsible for the strength of such minerals as marble and agate and for crystal formation in common table salt

ionic bonds

Electrostatic attractions in water

charged groups are shielded by their interactions with water molecules. Electrostatic attractions are therefore quite weak in water

Hydrophobic forces

water forces hydrophobic groups together in order to minimize their disruptive effects on the water network formed by the hydrogen bonds between water molecules. Hydrophobic groups held together in this way are sometimes said to be held together by “hydrophobic bonds,” even though the attraction is actually caused by a repulsion from water

Acids

substances that release hydrogen ions (protons) into solution

Many of the acids important in the cell are not completely dissociated, and they are therefore ___

weak acids

Bases

substances that reduce the number of hydrogen ions in solution

Many bases found in cells are partially associated with H+ ions and are termed ___

weak bases

Cells contain four major families of ___

small organic molecules

Monosaccharides

have the general formula (CH2O)n, where n can be 3, 4, 5, ,6, 7, or 8, and have two or more hydroxyl groups. They contain either an aldehyde group (R-CH=O) and are called aldoses or a ketone group and are called ketoses

Sugar derivatives

the hydroxyl groups of a simple monosaccharide, such as glucose, can be replaced by other groups

Disaccharides

the carbon that carries the aldehyde or the ketone can react with any hydroxyl group on a second sugar molecule to form a disaccharide

Oligosaccharides and polysaccharides

large linear and branched molecules can be made from simple repeating sugar subunits. Short chains are called oligosaccharides, and long chains are called polysaccharides

Nucleotides

consists of a nitrogen-containing base, a five-carbon sugar, and one or more phosphate groups

Nucleic acid bases

nitrogen-containing ring compounds, either pyrimidines or purines

Phosphates

are normally the C5 hydroxyl of the ribose or deoxyribose sugar (designated 5’). The phosphate makes a nucleotide negatively charged

Nucleic acid sugars

each numbered carbon on the sugar of a nucleotide is followed by a prime mark. ß-D-ribose used in ribonucleic acid (RNA). ß-D-2-deoxyribose used in deoxyribonucleic acid (DNA)

To form nucleic acid polymers, nucleotides are joined together by ___ between the 5’ and 3’ carbon atoms of adjacent sugar rings

phosphodiester bonds

Nucleoside di- and triphosphates carry a chemical energy in their easily hydrolyzed ___

phosphoanhydride bonds

Nucleotides and their derivatives combine with other groups to form ___

coenzymes

Nucleotides and their derivatives are used as small intracellular ___ in the cell

signaling molecules

Fatty acids

have a carboxyl group at one end and a long hydrocarbon tail at the other. Some have one or more double bonds in their hydrocarbon tail and are said to be unsaturated. Fatty acids with no double bonds are saturated

Fatty acids are stored in cells as an energy reserve (fats and oils) through an ester linkage to glycerol to form ___

triacylglycerols

If free, the carboxyl group of a fatty acid will be ___. But more often it is linked to other groups to form either ___ or ___

ionized, esters, amides

Phospholipids

two of the -OH groups in glycerol are linked to fatty acids, while the third -OH group is linked to phosphoric acid. The phosphate, which carries a negative charge, is further linked to one of a variety of small polar group

Fatty acids have a hydrophilic head and a hydrophobic tail. In water, they can form either a ___ or small, spherical ___

surface film, micelles

Two other common types of lipids are steroids and polyisoprenoids. Both are made form ___ unites

isoprene

Steroids

have a common multiple-ring structure

Glycolipids

Like phospholipids, these compounds are composed of a hydrophobic region, containing two long hydrocarbon tails, and a polar region, which contains one or more sugars. Unlike phospholipids, there is no phosphate

The free-energy change for a reaction, ∆G, determines whether it can ___

occur spontaneously

Cells need to carry out energetically ___ as well as energetically ___ reactions to survive

favorable (spontaneous), unfavorable

Enzymes do not affect ___, and only lower activation energy during a reaction

free energy

Cells obtain energy by the ___ of ___. Some of that energy is used to make ATP

oxidation, organic molecules (food molecules, internal macromolecules)

Cells use ___ to make macromolecules for structure and function of cells and tissues

ATP

Both exergonic (catabolic) and endergonic (anabolic) reactions have an ___ to overcome

initial activation energy

Energetically favorable reaction

the free energy of Y is greater than the free energy of X. Therefore, ∆G < 0, and the disorder of the universe increases during the reaction Y —> X

Energetically unfavorable reaction

if the reaction X —> Y occurred, ∆G would be > 0, and the universe would become more ordered. This reaction can occur only if it is coupled to a second, energetically favorable reaction

The formation of an activated carrier is coupled to an ___

energetically unfavorable reaction

___ is the most widely used activated carrier molecule

ATP

Energy stored in ATP is often harness to join two molecules together and to drive ___

anabolic reactions

In the ___, ATP transfers a phosphate to A-OH to produce a ___

activation step, high-energy intermediate

In the ___, the activated intermediate reacts with B-H to form the produce A-B, a reaction accompanied by the release of ___

condensation step, inorganic phosphate

Molecules are 3 dimensional via their ___ and ___

folding, interactions

Molecular interactions are also driven by ___

Gibbs free energy concept

Molecules will interact, bind, and fold to reach their lowest state of ___

free energy