Bk 2 Ch 1 Proteins

Question 1

Ligand

Answer 1

Molecule or ion that binds to a protein at a specific binding site. Different proteins bind to a vast range of ligands, ranging from small ions, through small molecules to proteins or DNA. This binding is highly specific, such that a given protein will bind only one particular ion or molecule or one of a number of chemically and structurally similar molecules.

Question 2

Polypeptide

Answer 2

A sequence of amino acids joined together in a linear chain.

Question 3

Primary structure

Answer 3

The linear order of amino acids in a polypeptide or protein, commonly referred to as the amino acid sequence.

Question 4

Secondary structure

Answer 4

Term used to describe a limited number of regular stable three-dimensional arrangements of a polypeptide of which the two most common forms are α helix and β pleated sheet. A protein may contain numerous elements of secondary structure and different parts of the chain can adopt different secondary structures.

Question 5

Tertiary structure

Answer 5

Term used to describe the arrangement of secondary structures in a folded polypeptide.

Question 6

Subunit

Answer 6

A single polypeptide component of a multimeric protein (a protein composed of more than one polypeptide). The arrangement of subunits in a multimeric protein is referred to as quaternary structure.

Question 7

Multimeric

Answer 7

Term used to describe a protein that contains more than one polypeptide chain (subunit). When a multimeric protein contains subunits of only one type, they are referred to as homomeric; where the subunits are of different types, the protein is described as heteromeric. In some cases a prefix that indicates the number of subunits is included, for example a trimeric protein contains three subunits and would be described as homotrimeric if all three subunits were the same and heterotrimeric if they are all different.

Question 8

Quarternary structure

Answer 8

The highest level of organisation of protein structure; refers to the arrangement of the subunits in a multimeric protein.

Question 9

Peptide bond

Answer 9

The covalent C–N bond formed between the two amino acids when a chemical reaction occurs between the amino group of one amino acid and the carboxyl group of another.

Question 10

Peptide group

Answer 10

The CO–NH group that links Cα atoms of neighbouring amino acid residues in a polypeptide.

Question 11

Residue

Answer 11

In the context of the polypeptide chain, a single amino acid unit; short stretches of amino acid residues linked together are called peptides, and longer chains are polypeptides.

Question 12

Steric interference

Answer 12

When two atoms are brought close together such that their electron clouds overlap, repulsive forces act to drive the atoms apart. This effect is known as steric interference (or steric hindrance) and it influences the conformations that a molecule can adopt.

Question 13

Conformation

Answer 13

Term used to describe the structural arrangement and shape of a folded protein.

Question 14

Random coils

Answer 14

Irregularly structured stretches of polypeptide that link regions of α-helical or β sheet structures. While coil conformations are highly varied between proteins, they nonetheless have a very consistent conformation in any particular protein.

Question 15

Cofactors

Answer 15

Non-protein molecules (e.g. metal ions such as Mg2+ and K+, or coenzymes such as NAD) that associate with and are essential for the function of particular proteins. Where the association with the protein is permanent, such cofactors are referred to as prosthetic groups (e.g. haem which associates with haemoglobin).

Question 16

Homomeric

Answer 16

Term used to describe a protein that consists of two or more identical subunits (the Greek homo prefix meaning ‘the same’, the opposite of hetero).

Question 17

Heteromeric

Answer 17

Term used to describe a protein that consists of two or more non-identical subunits (the Greek hetero prefix meaning ‘other’, the opposite of homo).

Eg haemoglobin is heteromeric, having 2 each of 2 different subunits

Question 18

Chaperones

Answer 18

A type of protein that facilitates the correct folding of polypeptides; can also help to recover and refold misfolded polypeptides.

Question 19

Domain

Answer 19

An independently folded, globular unit of a protein, comprising regions of secondary structure and the loop regions between them. Many proteins are made up of several domains, each with a distinct function and often encoded by distinct exons. (Book 2, Chapter 1)

Question 20

Disulphide bonds

Answer 20

A covalent bond that forms on oxidation of (i.e. loss of hydrogen from) the reactive —SH groups of two cysteine residues in adjacent polypeptides or different regions of the same strand. Disulfide bonds secure the conformation of the folded polypeptide and quaternary structure, making the protein more stable.

Question 21

Proteases

Answer 21

Proteolytic (i.e. protein-digesting) enzymes that catalyse the cleavage of protein peptide bonds.

Question 22

Proteasome

Answer 22

A large complex of proteins found in eukaryotic cells; the site where most cellular proteins are degraded into peptides and amino acids. Proteins to be degraded by proteasomes are identified by covalent attachment to the protein ubiquitin.

Question 23

Post-translational modification

Answer 23

Changes occurring to proteins after they have been translated; may involve covalent modifications such as glycosylation and lipidation or proteolytic cleavage.

Question 24

Glycosylation

Answer 24

A type of post-translational protein modification where sugar residues are added to proteins to produce glycoproteins.

Covalently attached by reacting with the NH2 or OH groups of particular amino acid sidechains to form a glycoprotein.

May offer some protection against proteases by restricting access to the protein component.

Question 25

Glycoprotein

Answer 25

A protein with one or more covalently attached carbohydrate groups (usually short sugar chains). Addition of such groups to proteins, termed glycosylation, is a form of post-translational modification.

Many are incorporated into the cell membrane and have important roles in intercellular and interactions. Others are secreted by the cell and function outside it.

Question 26

Lipidation

Answer 26

The covalent attachment of one or more lipid groups to a protein.

Question 27

Zymogens

Answer 27

Secreted proteins that remain inactive until the required extracellular activation has taken place. Examples include digestive enzymes, whose secretion as zymogens ensures that the cells secreting them are not damaged by digestion in the process.

Question 28

Proteolysis

Answer 28

Breakdown of peptide into amino acids

Question 29

Substrate

Answer 29

The chemical upon which an enzyme acts is known as the substrate. The substrate binds to a binding site on the enzyme and is chemically transformed to form a product or products.

Question 30

Active site

Answer 30

Specific binding site on an enzyme where the substrate binds to form an enzyme–substrate complex and where the enzyme catalyses the transformation of the substrate into product(s).

Question 31

Lock and key hypothesis

Answer 31

The complementary fitting together of the substrate and active site of an enzyme, with the active site being the ‘lock’, into which the substrate or ‘key’ fits very precisely.

Question 32

Michaelis -menten kinetics

Answer 32

A model of enzyme kinetics that describes the relationship between the substrate concentration and the initial rate of an enzyme-catalysed reaction. Because it is only concerned with initial rates of reaction, Michaelis–Menten kinetics assume that the reduction in the concentration of substrate and the accumulation of product do not significantly affect the rate of reaction.

Question 33

Specific activity

Answer 33

When a given enzyme is assayed, specific activity is, by convention, expressed relative to the amount of protein (in mg, which can be measured chemically) that is contained in the preparation. Specific activity of an enzyme preparation is therefore defined as micromoles of substrate converted into product per minute per mg protein
(i.e. μmol min-1 mg-1).

Question 34

KM (Michaelis constant)

Answer 34

For an enzyme catalysed reaction, KM is defined as the substrate concentration that gives half the maximum initial reaction velocity (vmax), rate, so that KM is the value of [S] at ½ vmax. A low value indicates high affinity of the enzyme for the substrate.

Question 35

Denaturation

Answer 35

Disruption of the non-covalent interactions that hold proteins in their native conformation, which results in a usually irreversible drop in activity. In this state, the protein is said to be denatured.

Question 36

relative molecular mass (Mr)

Answer 36

The relative molecular mass (Mr) of a molecule is the ratio of the mass of that molecule to 1/12 the mass of an atom of carbon-12. This value can be calculated as the sum of the relative atomic masses of all the atoms that the molecule contains (where the relative atomic mass of an atom is the ratio of its mass to 1/12 the mass of an atom of carbon-12). Being a relative measure, Mr has no units (it is ‘dimensionless’). Note, however, that relative molecular mass is numerically equivalent to molecular mass which is given in units of Daltons (Da) or kilodaltons (kDa, equivalent to 1000 Da) and, in the case of proteins, it has become more common to indicate protein size in this way.

Question 37

Competitive inhibitors

Answer 37

Molecules that can bind to the active site of an enzyme and block access of the substrate, i.e. they compete with the substrate for binding to the active site.

Question 38

Non-– Competitive inhibitors

Answer 38

Enzyme inhibitors that do not prevent the substrate from binding but compromise the ability of the enzyme to catalyse the reaction. On binding to a site on the enzyme that is not the active site; non-competitive inhibitors alter the conformation of the active site in such a way that the enzyme cannot catalyse the reaction as efficiently as it would do otherwise.

Question 39

Allosteric regulation

Answer 39

Mechanism by which the function of a protein is regulated by binding a specific ligand. The ligand, known as an allosteric effector, can be an activator or an inhibitor and binds to the protein at the allosteric site (from the Greek allos, meaning ‘other’ and steros, meaning ‘shape’). Binding of the effector causes the protein to change shape and thereby modifies its activity, usually by affecting its ability to interact with another ligand at another binding site, or, in the case of an enzyme, affecting its catalytic activity.

Question 40

Reversible covalent modification

Answer 40

Reversible addition of a small chemical group (e.g. phosphate, acetyl) to the side-chain of a particular amino acid residue in a protein. Such modifications are an important means of regulating protein function and the most common modification is phosphorylation.

Question 41

Phosphorylation

Answer 41

The chemical addition of a phosphate group. In proteins, phosphorylation of the –OH group in the side chains of serine, threonine and tyrosine residues is catalysed by enzymes known as protein kinases; such phosphorylation is a particularly important reversible covalent modification of proteins.

Question 42

Site - directed mutagenesis (SDM)

Answer 42

A technique for examining the role of individual amino acid residues in proteins. It involves the use of recombinant DNA techniques to selectively replace the residue of interest with a different amino acid with critically different properties; the resulting protein can then be tested functionally. SDM is most commonly used in the study of enzymes or to identify key residues in protein–protein interactions.

Question 43

Conserved domains

Answer 43

Regions within proteins where there are homologous amino acid sequences between species, which are evolutionarily conserved.

Question 44

Homologous

Answer 44

Relating to structures or molecules that have the same evolutionary origin and reflect common descent.

Question 45

Chiral

Answer 45

Asymmetric in such a way that the structure and its mirror image are not superimposable