Biochemistry

Front 1

ligand:

Back 1

small molecule or macromolecule that recognizes and binds to a specific site on a macromolecule. (2-1)

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motif:

Back 2

characteristic sequence or structure that in the case of a structural motif may comprise a whole domain or protein but usually consists of a small local arrangement of secondary structure elements which then coalesce to form domains. Sequence motifs, which are recognizable amino-acid sequences found in different proteins, usually indicate biochemical function. Structural motifs are less commonly associated with specific biochemical functions. (1-16)

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hydrolysis:

Back 3

I breaking a covalent bond by addition of a molecule of water. (1-3)

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hydrophobic effect:

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the tendency of nonpolar groups in water to self-associate and thereby minimize their contact surface area with the polar solvent. (1 -9)

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induced fit:

Back 5

originally, the change in the structure of an enzyme induced by binding of the substrate, that brings the catalytic groups into proper alignment. Now generalized to the idea that specific ligands can induce the protein conformation that results in optimal binding interactions. (1-22, 2-2)

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native state:

Back 6

the stably folded and functional form of a biological macromolecule. (1-9)

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van der Waals interaction:

Back 7

a weak attractive force between two atoms or groups of atoms, arising from the fluctuations in electron distribution around the nuclei. Van der Waals forces are stronger between less electronegative atoms such as those found in hydrophobic groups. (1-4)

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activation energy:

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the energy required to bring a species in a chemical reaction from the ground state to a state of higher free energy, in which It can transform spontaneously to another low-energy species. (2-6)

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activation-energy barrier:

Back 9

the higher-energy region between two consecutive chemical species in a reaction. (2-6)

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active site:

Back 10

asymmetric pocket on or near the surface of a macromolecule that promotes chemical catalysis when the appropriate ligand (substrate) binds. (2-1)

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alpha helix:

Back 11

a coiled conformation, resembling a right-handed spiral staircase, for a stretch of consecutive amino acids in which the backbone –N-H group of every residue n donates a hydrogen bond to the C=0 group of every residue n+4. (1-5)

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antiparallel beta sheet:

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a beta sheet, often formed from contiguous regions of the polypeptide chain, in which each strand runs in the opposite direction from its immediate neighbors. (1-7)

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beta sandwich:

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a structure formed of two antiparallel beta sheets packed face to face. (1 -17)

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beta sheet:

Back 14

a secondary structure element formed by backbone hydrogen bonding between segments of extended polypeptide chain. (1 -5)

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codon:

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three consecutive nucleotides in a strand of DNA or RNA that represent either a particular amino acid or a signal to stop translating the transcript of the gene. The formula for translating the codons is given by the genetic code. (1-2)

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coenzyme:

Back 16

a cofactor that is an organic or organometallic molecule and that assists catalysis. (2-13)

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cofactor:

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a small, non-protein molecule or ion that is bound in the functional site of a protein and assists in ligand binding or catalysis or both. Some cofactors are bound covalently, others are not. (1 -13, 2-13)

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coiled coil:

Back 18

a protein or a region of a protein formed by a dimerization interaction between two alpha helices in which hydrophobic side chains on one face of each helix interdigitate with those on the other. (1-19)

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competitive inhibitor:

Back 19

a species that competes with substrate for binding to the active site of an enzyme and thus inhibits catalytic activity. (3-0)

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cooperative binding:

Back 20

interaction between two sites on a protein such that the binding of a ligand to the first one affects the properties—usually binding or catalytic—of the second one. (3-4)

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cooperativity:

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interaction between two sites on a protein such that something that happens to the first one affects the properties of the second one. (3-4)

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domain:

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a compact unit of protein structure that is usually capable of folding stably as an independent entity in solution. Domains do not need to comprise a contiguous segment of peptide chain, although this is often the case. (1-14)

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enthalpy:

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a form of energy, equivalent to work, that can be released or absorbed as heat at constant pressure. (1-12)

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entropy:

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a measure of the disorder or randomness in a molecule or system. (1-12)

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exon:

Back 25

coding segment of a gene. The coding DNA of many eukaryotic genes is interrupted by segments of non-coding DNA (Introns). (1-2)

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G protein:

Back 26

a member of a large class of proteins with GTPase activity that act as molecular switches in many different cellular pathways, controlling processes such as sensory perception, intracellular transport, protein synthesis and cell growth and differentiation. They undergo a large conformational change when a bound GTP is hydrolyzed to GDP. (3-6)

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GTPase-activating protein (GAP):

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a protein that accelerates the intrinsic GTPase activity of switch GTPases. (3-7)

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Heterotetramer:

Back 28

an assembly of four subunits of more than one kind of polypeptide chain. (1-19)

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Hexamer:

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an assembly of six identical or different subunits. In a protein the subunits are individual folded polypeptide chains. (1-19)

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Homotrimer:

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an assembly of three identical subunits: in a protein, these are individual folded polypeptide chains. (1-19)

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Hydrogen bond:

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a noncovalent interaction between the donor atom, which is bound to a positively polarized hydrogen atom, and the acceptor atom, which is negatively polarized. Though not covalent, the hydrogen bond holds the donor and acceptor atom close together. (1-4)

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Intron:

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an intervening sequence in a gene that does not correspond to any portion of the final protein sequence and is spliced out of the RNA transcript ire translation. (1-2)

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Ligand-binding site:

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site on the surface of a protein at which another molecule binds. (2-1)

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Lipid anchor:

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lipid attached to a protein that inserts into a membrane, thereby anchoring the protein to the bilayer. (3-2)

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Methylation:

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modification, usually of a nitrogen or oxygen atom of an amino-acid side chain, by addition of a methyl group. Some bases on DNA and RNA can also be methylated. (3-20)

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Monomer:

Back 36

a single subunit: in a protein, this is a folded peptide chain. (1-19)

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Interaction domain:

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a protein that recognizes another protein, usually via a specific recognition motif. (3-1)

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Mixed beta sheet:

Back 38

beta sheet containing both parallel and antiparallel strands. (1-17)

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Monomer:

Back 39

a single subunit: in a protein, this is a folded peptide chain. (1-19)

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Myristoylation:

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irreversible attachment of a myristoyl group to a protein via an amide linkage. (3-19)

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N-acetylation:

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covalent addition of an acetyl group from acetyl-CoA to a nitrogen atom at either the amino-terminus of a polypeptide chain or in a lysine side-chain. The reaction is catalyzed by M-acetyltransferase. (1-13, 3-20)

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Native state:

Back 42

the stably folded and functional form of a biological macromolecule. (1-9)

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Nitrosylation:

Back 43

modification of the –SH group of a cysteine residue by addition of nitric oxide produced by nitric oxide synthase. (3-20)

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Nucleotide:

Back 44

the basic repeating unit of a nucleic acid polymer. It consists of a base (A, U [in RNA, T in DNA], G or C), a sugar (ribose in RNA, deoxyribose in DNA) and a phosphate group. (1-2)

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Oligomer:

Back 45

an assembly of more than one subunit: in a protein, the subunits are individual folded polypeptide chains, (1-19)

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peptide bond:

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another name for amide bond, a chemical bond formed when a carboxylic acid condenses with an amino group with the expulsion of a water molecule. The term peptide bond is used only when both groups come from amino acids. (1-3)

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Phosphorylation:

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covalent addition of a phosphate group, usually to one or more amino-acids side chains on a protein, Catalyzed by protein kinases.

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Pka values:

Back 48

Strictly defined as the negative logarithm of the equilibrium constant for the acid-base equation. For ranges of pka between 0 and 14, it can be thought of as the ph of an aqueous solution at which a proton donating group is half protonated and half deprotonated. Pka is a measure of the proton affinity of a group: the lower the Pka, the more weakly the proton is held. (2-12)

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Primary structure:

Back 49

the amino-acid sequence of a polypeptide chain. (1-2)

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Protein kinase:

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enzyme that transfers a phosphate group from ATP to the OH group of serines, threonines and tyrosines of target proteins. Kinases that phosphorylate carboxylates and histidines also occur as part of two-component system in prokaryotes, fungi and plants, but not in animals.

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Quaternary structure:

Back 51

the subunit of a protein.

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Salt bridge:

Back 52

a hydrogen bond in which both donor and acceptor atoms are fully charged. The bonding energy of a salt bridge is significantly higher than that of a hydrogen bond in which only one participating atom is fully charged or in which both are partially charged. (1-4)

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Switch I region:

Back 53

a conserved sequence motif in GTPase- and ATPase-based nucleotide switch proteins that, with the switch II region, binds the terminal gamma-phosphate in the triphosphate form of the bound nucleotide and undergoes a marked conformational change when the nucleotide is hydrolyzed. (3-6)

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Switch II region:

Back 54

a conserved sequence motif in GTPase- and ATPase-based nucleotide switch proteins that, with the switch I region, binds the terminal gamma-phosphate in the triphosphate form of the bound nucleotide and undergoes a marked conformational change when the nucleotide is hydrolyzed.

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tertiary structure:

Back 55

the folded conformation of a protein, formed by the condensation of the various secondary elements, stabilized by a large number of weak interactions.

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Tetramer:

Back 56

an assembly of four identical or different subunits. (1-19)

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Trimer:

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an assembly of three identical or different subunits. (1-19)

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Transition state:

Back 58

the species of highest free energy either in a reaction or a step of a reaction; the highest region on the activation-energy barrier. (2-6)