Chapter 4 Vocab

Question 1

mass spectrometry

Answer 1

technique for determining the exact mass of every peptide present in a sample of purified protein or protein mixture.

Question 2

motor protein

Answer 2

Protein such as myosin or kinesin that uses energy derived from ATP hydrolysis to propel itself along a protein filament or polymeric molecule.

Question 3

N-terminus

Answer 3

The end of a polypeptide chain that carries a free alpha-amino group

Question 4

NMR spectroscopy

Answer 4

Technique used for determining the three-dimensional structure of a protein in solution.

Question 5

peptide bond

Answer 5

Chemical bond between the carbonyl group of one amino acid and the amino group of a second amino acid.

Question 6

polypeptide, polypeptide chain

Answer 6

Linear polymer composed of multiple amino acids. Proteins are composed of one or more long polypeptide chains.

Question 7

polypeptide backbone

Answer 7

Repeating sequence of atoms (-N-C-C-) that forms the core of a protein molecule and to which the amino acid side chains are attached.

Question 8

primary structure

Answer 8

The amino acid sequence of a protein.

Question 9

protein

Answer 9

Polymer built from amino acids that provides cells with their shape and structure and performs most of their activities.

Question 10

protein domain

Answer 10

Segment of a polypeptide chain that can fold into a compact stable structure and that usually carries out a specific function.

Question 11

protein family

Answer 11

A group of polypeptides that shares a similar amino acid sequence or three-dimensional structure, reflecting a common evolutionary origin. Individual members often have related but distinct functions, such as kinases that phosphorylate different target proteins.

Question 12

protein kinase

Answer 12

Enzyme that catalyzes the transfer of a phosphate group from ATP to a specific amino acid side chain on a target protein.

Question 13

protein machine

Answer 13

Large assembly of protein molecules that operates as a unit to perform a complex series of biological activities, such as replicating DNA.

Question 14

protein phosphatase

Answer 14

Enzyme that catalyzes the removal of a phosphate group from a protein, often with high specificity for the phosphorylated site.

Question 15

protein phosphorylation

Answer 15

The covalent addition of a phosphate group to a side chain of a protein, catalyzed by a protein kinase; serves as a form of regulation that usually alters the activity or properties of the target protein.

Question 16

quaternary structure

Answer 16

Complete structure formed by multiple, interacting polypeptide chains within a protein molecule.

Question 17

secondary structure

Answer 17

Regular local folding pattern of a polymeric molecule. In proteins, it refers to alpha helices and beta sheets.

Question 18

side chain

Answer 18

Portion of an amino acid not involved in forming peptide bonds; its chemical identity gives each amino acid its unique properties.

Question 19

subunit

Answer 19

A monomer that forms part of a larger molecule, such as an amino acid residue in a protein or a nucleotide residue in a nucleic acid. Can also refer to a complete molecule that forms part of a larger molecule. Many proteins, for example, are composed of multiple polypeptide chains, each of which is called a protein subunit.

Question 20

tertiary structure

Answer 20

Complete three-dimensional structure of a fully folded protein.

Question 21

transition state

Answer 21

Structure that forms transiently during the course of a chemical reaction; in this configuration, a molecule has the highest free energy, and is no longer a substrate, but is not yet a product.

Question 22

X-ray crystallography

Answer 22

Technique used to determine the three-dimensional structure of a protein molecule by analyzing the pattern produced when a beam of X-rays is passed through an ordered array of the protein.

Question 23

active site

Answer 23

region on the surface of an enzyme that binds to a substrate molecule and catalyzes its transformation

Question 24

allosteric

Answer 24

describes a protein that can exist in multiple conformations depending on the binding of a molecule (ligand) at a site other then the catalytic site.

changes from one conformation to another often alter the proteins activity or ligand affinity.

Question 25

a (alpha) helix

Answer 25

a folding pattern thats common in many proteins. a single polypeptide chain twist around its self to form a rigid cylinder stabilized by hydrogen bonds between every fourth amino acid.

Question 26

amino acid sequecne

Answer 26

the order of the amino acids subunits in a protein chain. sometimes called the primary structure of a protein

Question 27

antibody

Answer 27

protein produced by B lymphocytes in response ti a foreign molecule or invading organism. It binds to the foreign molecule or cell extremely tightly thereby inactivating it or marking it for destruction

Question 28

antigen

Answer 28

molecule or fragment of a molecule that is recognized by an antibody

Question 29

B (beta) sheet

Answer 29

folding pattern found in which neighboring regions of the polypeptide chain associate side by side with each other through hydrogen bonds to give a rigid flattened structure.

Question 30

binding site

Answer 30

region on the surface of a protein, typically a cavity or grove, that interacts with another molecule through the formation of non covalent bonds

Question 31

C-terminus (Carboxyl terminus)

Answer 31

the end of a polypeptide chain that carries a free carboxylic group (-COOH)

Question 32

chromatography

Answer 32

a technique used to separate the individual molecules in a complex mixture on the basis of their size, charge,or their ability to bind to a particular chemical group. in common form of the technique, the mixture is run through a column filled with a material that either binds or lets through the desired molecule.

Question 33

coiled-coil

Answer 33

stable rodlke protein structure formed when two or more alpha helices twist around each other

Question 34

conformation

Answer 34

precise 3D shape of a protein or other macromolecule, based on the spatial location of its atoms in relation to one another

Question 35

disulfide bond

Answer 35

covalent cross-link formed between the sulfhydryl groups on two cysteine side chains; often used to reinforce a secreted proteins structure or join two different proteins together

Question 36

electrophoresis

Answer 36

a technique for separating a mixture of proteins or DNA fragments. by placeing them on a polymer gel and subjecting them to an electric field. the molecules migrate through the gel at different speeds depending on their size and net charge

Question 37

enzyme

Answer 37

a protien that catalyzes a special chemical reaction

Question 38

feedback inhibition

Answer 38

a form of metabolic control in which the end product of a chain of enzymatic reactions reduces the activity of an enzyme early in the pathway

Question 39

fibrous protein

Answer 39

a protein with an elongated , rodlike shape, such as collagen or keratin filament

Question 40

globular protein

Answer 40

any protein in which the polypeptide folds into a compact round shape. includes most enzymes

Question 41

GTP- Binding Protein

Answer 41

intracellular signaling protein whose whos activitiy determined by its association with either GTP or GDP. (smoke dat GDP; grandaddy perp) -jeff

Question 42

helix

Answer 42

an elongated structure whose subunits twist in a regular fashion around the central axis, like a spiral staircase

Question 43

intrinsically disordered sequence

Answer 43

a region in a polypeptide chain that lacks a definite structure

Question 44

ligand

Answer 44

general term for a molecule that binds to a specific site on a protein.

Question 45

lysozyme

Answer 45

enzymes that sever the polysaccharide chains that form the cell walls of bacteria. found in many secretions including saliva and tears