Chapter 2 Chemical Foundations

Question 1

Acid

Answer 1

Any compound that can donate a proton (H1). The carboxyl and phosphate groups are the primary acidic groups in biological macromolecules.

Question 2

adenosine triphosphate (ATP)

Answer 2

A nucleotide that is the most important molecule for capturing and transferring free energy in cells. Hydrolysis of each of the two phosphoanhydride bonds in ATP releases a large amount of free energy that can be used to drive energy-requiring cellular processes. (Figure 2-31)

Question 3

amino acid

Answer 3

An organic compound containing at least one amino group and one carboxyl group. In the amino acids that are the monomers for building proteins, an amino group and carboxyl group are linked to a central carbon atom, the a carbon, to which a variable side chain is attached. (Figures 2-4 and 2-14)

Question 4

amphipathic

Answer 4

Referring to a molecule or structure that has both a hydrophobic and a hydrophilic part.

Question 5

base

Answer 5

Any compound, often containing nitrogen, that can accept a proton (H1) from an acid. Also, commonly used to denote the purines and pyrimidines in DNA and RNA.

Question 6

buffer

Answer 6

A solution of the acid (HA) and base (A2) form of a compound that undergoes little change in pH when small quantities of strong acid or base are added at pH values near the compound’s pKa.

Question 7

catalyst

Answer 7

A substance that increases the rate of a chemical reaction without undergoing a permanent change in its structure. (Figure 3-22)

Question 8

chemical potential energy

Answer 8

The energy stored in the bonds connecting atoms in molecules.

Question 9

covalent bond

Answer 9

Stable chemical force that holds the atoms in molecules together by sharing of one or more pairs of electrons. (Figures 2-2 and 2-6)

Question 10

dipole

Answer 10

A positive charge separated in space from an equal but

opposite negative charge.

Question 11

dissociation constant

Answer 11

equals 1/K

Question 12

disulfide bond

Answer 12

A common covalent linkage between the sulfur atoms on two cysteine residues in different polypeptides or in different parts of the same polypeptide.

Question 13

endergonic

Answer 13

Referring to reactions and processes that have a positive G and thus require an input of free energy in order to proceed; opposite of exergonic.

Question 14

endothermic

Answer 14

Referring to reactions and processes that have a positive change in enthalpy, H, and thus must absorb heat in order to proceed; opposite of exothermic.

Question 15

enthalpy

Answer 15

Heat; in a chemical reaction, the enthalpy of the reactants or products is equal to their total bond energies.

Question 16

entropy

Answer 16

A measure of the degree of disorder or randomness

in a system; the higher the entropy, the greater the disorder.

Question 17

equilibrium constant

Answer 17

Ratio of forward and reverse rate constants for a reaction. For a binding reaction, A 1 B Sd
AB, the association constant (Ka) equals K, and the dissociation constant (Kd) equals 1/K.

Question 18

exergonic

Answer 18

Referring to reactions and processes that have a negative G and thus release free energy as they proceed; opposite ofendergonic.

Question 19

exothermic

Answer 19

Referring to reactions and processes that have a negative change in enthalpy, H, and thus release heat as they proceed; opposite of endothermic.

Question 20

fatty acids

Answer 20

Any long hydrocarbon chain that has a carboxyl group
at one end; a major source of energy during metabolism and a precursor for synthesis of phospholipids, triglycerides, and cholesteryl esters. (Figure 2-21; Table 2-4)

Question 21

free energy change

Answer 21

A measure of the potential energy of a system, which is a function of the enthalpy (H) and entropy (S).

Question 22

hydrogen bond

Answer 22

A noncovalent interaction between an atom (commonly oxygen or nitrogen) carrying a partial negative charge and a hydrogen atom carrying a partial positive charge. Important in stabilizing the conformation of proteins and in formation of base pairs between nucleic acid strands. (Figure 2-8)

Question 23

hydrophilic

Answer 23

Interacting effectively with water.

Question 24

hydrophobic

Answer 24

Not interacting effectively with water; in general, poorly soluble or insoluble in water.

Question 25

hydrophobic effect

Answer 25

The tendency of nonpolar molecules or parts of molecules to associate with each other in aqueous solution so as to minimize their direct interactions with water; commonly called a hydrophobic interaction or bond. (Figure 2-11)

Question 26

monomer

Answer 26

Any small molecule that can be linked chemically | with others of the same type to form a polymer. Examples include amino acids, nucleotides, and monosaccharides.

Question 27

monosaccharide

Answer 27

Any simple sugar with the formula (CH2O)n where n 5 3–7.

Question 28

noncovalent interactions

Answer 28

Any relatively weak chemical interaction that does not involve an intimate sharing of electrons. ( Figures 2-6 and 2-12)

Question 29

nucleoside

Answer 29

A small molecule composed of a purine or pyrimidine base linked to a pentose (either ribose or deoxyribose). (Table 2-3)

Question 30

nucleotide

Answer 30

A nucleoside with one or more phosphate groups linked via an ester bond to the sugar moiety, generally to the 5 carbon atom. DNA and RNA are polymers of nucleotides containing deoxyribose and ribose, respectively. (Figure 2-16 and Table 2-3)

Question 31

oxidation

Answer 31

Loss of electrons from an atom or molecule as occurs | when a hydrogen atom is removed from a molecule or oxygen is added; opposite of reduction.

Question 32

phosphoanhydride bond

Answer 32

A type of high-energy bond formed between two phosphate groups, such as the g and b phosphates and the b and a phosphates in ATP. (Figure 2-31)

Question 33

phosphoglyceride

Answer 33

Amphipathic derivatives of glycerol 3-phosphate that generally consist of two hydrophobic fatty acyl chains esterified to the hydroxyl groups in glycerol and a polar head group attached to the phosphate; the most abundant lipids in biomembranes. (Figures 2-20 and 10-8a)

Question 34

phospholipid

Answer 34

``` The major class of lipids present in biomembranes, including phosphoglycerides and sphingolipids. (Figures 7-8a, b and 2-20) ```

Question 35

polar

Answer 35

Referring to a molecule or structure with a net electric | charge or asymmetric distribution of positive and negative charges. Polar molecules are usually soluble in water.

Question 36

polymer

Answer 36

Any large molecule composed of multiple identical or similar units (monomers) linked by covalent bonds. (Figure 2-13)

Question 37

redox reaction

Answer 37

An oxidation-reduction reaction in which one or more electrons are transferred from one reactant to another.

Question 38

reduction

Answer 38

Gain of electrons by an atom or molecule as occurs | when a hydrogen atom is added to a molecule or oxygen is removed. The opposite of oxidation.

Question 39

saturated

Answer 39

Referring to a compound (e.g., fatty acid) in which all the carbon-carbon bonds are single bonds.

Question 40

Enzymes

Answer 40

proteins with catalytic activity

Question 41

Ribozymes

Answer 41

RNAs that can function as catalysts