Meanwhile, some of the product molecules begin to partici- pate in the reverse reaction, which re-forms the reactants. The ability of a reaction to go “backward” is called

micro- scopic reversibility

e.g., the hormone insulin or adrenalin

ligand

Kd values of _______ are considered to be tight, ___________ modestly tight, and ____________ relatively weak.

Kd values of ∼10−9 M (nanomolar) are considered to be tight, ∼10−6 M (micromolar) modestly tight, and ∼10−3 M (millimolar) relatively weak.

Such a molecule, containing an equal number of positive and negative ions, is called a

Zwitterion

pKa equals

−logKa

the products contain less energy than the reactants.

Exergonic

the products contain more energy than the reac- tants, and energy is absorbed during the reaction.

Endergonic

The useful energy in an ATP molecule is contained in

phosphoanhydride bonds

is used to control cellular systems (e.g., protein synthesis, hormonal signaling)

GTP hydrolysis

Much of the ATP produced in photosynthesis is hydrolyzed to provide energy for the conversion of carbon dioxide to six-carbon sugars, a process called

Carbon fixation

In plants, animals, and nearly all other organisms, the free energy in sugars and other molecules derived from food is released in the processes of

glycolysis and cellular respi- ration.

is the major pathway for generating ATP in all animal cells, all non- photosynthetic plant cells, and many bacterial cells.

Aerobic catabolism of glucose

In oxidation reaction, electrons are often transferred to small electron- carrying molecules, sometimes referred to as

Coenzyme

The most common of these electron carriers are

NAD+ (nicotin- amide adenine dinucleotide), which is reduced to NADH, and FAD (flavin adenine dinucleotide), which is reduced to FADH2 (Figure 2-33).

NAD+ (nicotin- amide adenine dinucleotide), which is reduced to ___________, and FAD (flavin adenine dinucleotide), which is reduced to _____________ _(Figure 2-33).

NADH FADH2. 

The readi- ness with which an atom or a molecule gains an electron is its

reduction potential (E)

standard reduction potential, E′0. A mol- ecule or an ion with a positive E′0 has a higher affinity for electrons than

the H+ ion does under standard conditions.

the linear, unbranched polymer of amino acids composing any protein will fold into only one or a few closely related three-dimensional shapes—called

conformations

To accomplish their diverse missions efficiently, some proteins assemble into large com- plexes, often called

Molecular machines

the entire protein complement of an organism.

Proteome

The principles relating biologi- cal structure and function were initially formulated by the biologists _________ their ideas greatly influenced the school of “organic” architec- ture pioneered in the early twentieth century that is epitomized by the dicta “form follows function”

Johann von Goethe (1749–1832), Ernst Haeckel (1834–1919), and D’Arcy Thompson (1860–1948)

the linear covalent arrangement, or sequence, of the amino acid resi- dues that compose a protein

primary structure

A short chain of amino acids linked by peptide bonds and having a defined sequence is called an

Oligopeptide

are often 200–500 residues long

polypeptides

a polypeptide (or complex of polypeptides) that has a well-defined three- dimensional structure.

Protein

stable spa- tial arrangements of segments of a polypeptide chain held together by hydrogen bonds between backbone amide and carbonyl groups and often involving repeating structural patterns.

Secondary structure

arts of the polypeptide that don’t form these secondary structures but never- theless have a well-defined, stable shape are said to have an

irregular structure

applies to highly flexible parts of a polypeptide chain that have no fixed three- dimensional structure

random coil

the backbone forms a spiral structure in which the carbonyl oxygen atom of each peptide bond is hydrogen-bonded to the amide hydrogen atom of the amino acid four residues farther along the chain in the direction of the C-terminus

α helix

Proteins that differ in mass can be separated on a column of porous beads made from polyacrylamide, dextran (a bacterial polysaccharide), or aga- rose (a seaweed derivative) 

Gel filtration chromatography

proteins are separated on the basis of differ- ences in their charges. This technique makes use of specially modified beads whose surfaces are covered by amino groups or carboxyl groups and thus carry either a positive charge (NH3+) or a negative charge (COO−) at neutral pH. 

Ion-exchange chromatography

ligands or other molecules that bind to the protein of interest are covalently attached to the beads used to form the column. Ligands can be enzyme substrates, inhibitors or their analogs, or other small molecules. In principle, column will retain only those proteins that bind the molecule attached to the beads; the re- maining proteins, regardless of their charges or masses, will pass through the column because they do not bind. 

Affinity chromatography

combines the resolving power of gel electrophoresis with the specific- ity of antibodies. This multistep procedure is commonly used to separate proteins and then identify a specific protein of interest. As shown in Figure 3-41, two different antibodies are used, one that is specific for the protein of interest (primary antibody) and a secondary antibody that binds to the first and is linked to an enzyme or other molecule that permits detection of the first antibody (and thus the protein of interest to which it binds). The enzyme to which the second antibody is attached can either generate a visible colored product or, by a process called chemiluminescence, produce light that can readily be recorded by film or a sensitive detector. 

Immunoblotting/western blotting

exploits the specificity of antibodies to separate a protein of interest from other molecules in a complex mixture—for example, all proteins extracted from a sample of cells or a sample of blood. An antibody to the protein of inter- est is added to a sample, and the antibody is given time to bind to epitopes on the target protein. An agent that binds to the antibody is then added to cause the antibody and its bound target to precipitate out of solution into particles that can be isolated by centrifugation. 

Immunoprecipitation, often abbrevi- ated as IP 

A sensitive method for tracking a protein or other biologi- cal molecule is by detecting the radioactivity emitted from a radiolabel introduced into the molecule. In a radiolabeled molecule, at least one atom is present in a radioactive form, called a 

Radioisotope

exposure of the sample on a two-dimensional detector (photographic emulsion or elec- tronic detector) 

Autoradiography

a cell sample is exposed to a radiola- beled compound that can be incorporated into or otherwise attached to a cellular molecule of interest—the “pulse”— for a brief period. The pulse ends when the unincorporated radiolabeled molecules are washed away and the cells are exposed to a vast excess of the identical, but unlabeled, compound to dilute the radioactivity of any remaining, but unincorporated, radiolabeled compound 

Pulse-chase

The classic method for determining the amino acid sequence of a protein is ________In this procedure, the free amino group of the N-terminal amino acid of a poly- peptide is labeled, and the labeled amino acid is then cleaved from the polypeptide and identified by high-pressure liq- uid chromatography. The polypeptide is left one residue shorter, with a new amino acid at the N-terminus. The cycle is repeated on the ever-shortening polypeptide until all the residues have been identified. 

Edman degradation

the systematic study of the amounts (and changes in the amounts), modifications, interactions, local- ization, and functions of all or subsets of all proteins in bio- logical systems at the whole-organism, tissue, cellular, and subcellular levels. 

Proteomics

Such a lineage of cells origi- nating from one initial primary culture is called a 

Cell strain

A culture of cells with an indefinite life span is considered immortal and is called a 

Cell line

Each normal antibody-producing B lymphocyte in a mammal is capable of producing a single type of antibody that can bind to a particular determinant, or _____ on an antigen mol- ecule 

Epitope

the fusion of a myeloma cell with a normal antibody-producing cell from a rat or mouse spleen yields a hybrid that proliferates into a clone called a 

Hybridoma

having a different number of chromosomes than the parent cell from which they were derived. 

Aneuploid

DNA Polymerases Require a ____ to Initiate Replication 

Primer 

cannot initiate chain synthesis de novo; instead, they require a short, preexisting RNA or DNA strand, called a primer, to begin chain growth 

DNA polymerases

Duplex DNA Is Unwound, and______Are Formed at the DNA Replication Fork 

Daughter strands

this unwinding of the parent DNA strands is performed by enzymes called 

Helices

Once helicases have unwound the parent DNA at an origin, a specialized RNA polymerase called ______ forms a short (∼12-nucleotide) RNA primer complementary to the unwound template strands. The primer, still base-paired to its complementary DNA strand, is then elongated by DNA polymerase α for another 25 nucleotides or so, forming a primer made of RNA at the 5′ end and DNA at the 3′ end. This primer is further extended by DNA polymerase δ, thereby forming a new daughter strand. 

Primase

The DNA region at which all these proteins come to- gether to carry out the synthesis of daughter strands is called the 

Replication fork

A major complication in the operation of a DNA rep- lication fork arises from two properties of DNA: the two strands of the parent DNA duplex are antiparallel, and DNA polymerases (like RNA polymerases) can add nucleotides to the growing daughter strands only in the 5′→3′ direction. Synthesis of one daughter strand, called the______, can proceed continuously from a single RNA primer in the 5′→3′ direction, the same direction as movement of the rep- lication fork (Figure 5-29) 

Leading strand

Each of these primers, base-paired to the template strand, is elongated in the 5′→3′ direction, forming discontinuous segments named 

Okazaki fragments

DNA Replication Occurs _____ from Each Origin

Bidirectionally

_____ Introduce Copying Errors and Also Correct Them 

DNA Polymerases

Proofreading depends on the 3′→5 

Exonuclease activity of some DNA polymerases

In humans, the most common type of point mutation is a change from a

C to a T, which is caused by deamination of 5-methyl C

The predominant mechanism for repairing double-strand breaks in multicellular organisms involves

 rejoining of the nonho- mologous ends of two DNA molecules. 

A variety of DNA lesions that are not repaired by the mechanisms discussed earlier can be repaired by mechanisms in which the damaged DNA sequence is copied from an un- damaged copy of the same or a highly homologous sequence on the homologous chromosome in diploid organisms or the sister chromosome following DNA replication in hap- loid and diploid organisms. These mechanisms involve an exchange of strands between separate DNA molecules and hence are referred to as 

Recombination