Chapter 2 Chemical Foundations Flashcards
Acid
Any compound that can donate a proton (H1). The carboxyl and phosphate groups are the primary acidic groups in biological macromolecules.
adenosine triphosphate (ATP)
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)
amino acid
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)
amphipathic
Referring to a molecule or structure that has both a hydrophobic and a hydrophilic part.
base
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.
buffer
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.
catalyst
A substance that increases the rate of a chemical reaction without undergoing a permanent change in its structure. (Figure 3-22)
chemical potential energy
The energy stored in the bonds connecting atoms in molecules.
covalent bond
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)
dipole
A positive charge separated in space from an equal but
opposite negative charge.
dissociation constant
equals 1/K
disulfide bond
A common covalent linkage between the sulfur atoms on two cysteine residues in different polypeptides or in different parts of the same polypeptide.
endergonic
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.
endothermic
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.
enthalpy
Heat; in a chemical reaction, the enthalpy of the reactants or products is equal to their total bond energies.
entropy
A measure of the degree of disorder or randomness
in a system; the higher the entropy, the greater the disorder.
equilibrium constant
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.
exergonic
Referring to reactions and processes that have a negative G and thus release free energy as they proceed; opposite ofendergonic.
exothermic
Referring to reactions and processes that have a negative change in enthalpy, H, and thus release heat as they proceed; opposite of endothermic.
fatty acids
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)
free energy change
A measure of the potential energy of a system, which is a function of the enthalpy (H) and entropy (S).
hydrogen bond
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)
hydrophilic
Interacting effectively with water.
hydrophobic
Not interacting effectively with water; in general, poorly soluble or insoluble in water.
hydrophobic effect
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)
monomer
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.
monosaccharide
Any simple sugar with the formula (CH2O)n where n 5 3–7.
noncovalent interactions
Any relatively weak chemical interaction that does not involve an intimate sharing of electrons. ( Figures 2-6 and 2-12)
nucleoside
A small molecule composed of a purine or pyrimidine base linked to a pentose (either ribose or deoxyribose). (Table 2-3)
nucleotide
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)
oxidation
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.
phosphoanhydride bond
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)
phosphoglyceride
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)
phospholipid
The major class of lipids present in biomembranes, including phosphoglycerides and sphingolipids. (Figures 7-8a, b and 2-20)
polar
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.
polymer
Any large molecule composed of multiple identical or similar units (monomers) linked by covalent bonds. (Figure 2-13)
redox reaction
An oxidation-reduction reaction in which one or more electrons are transferred from one reactant to another.
reduction
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.
saturated
Referring to a compound (e.g., fatty acid) in which all the carbon-carbon bonds are single bonds.
Enzymes
proteins with catalytic activity
Ribozymes
RNAs that can function as catalysts
