Chapter 4- Proteins

Question 1

folded structure of a protein is stabilized by multiple ___ ___ between different parts of the polypeptide chain

Answer 1

noncovalent interactions

Question 2

hydrogen bonds between neighboring regions of polypeptide backbone give rise to regular folding patterns known as __ helices and __ sheets

Answer 2

alpha, beta

Question 3

when a protein catalyzes the formation of breakage of a specific covalent bond in a ligand the protein is known as an

Answer 3

enzyme

Question 4

an enzyme can be turned on or off by ___ that bind to a distinct regulatory site to stabilize either the active or inactive conformation

Answer 4

ligands

Question 5

Many thousands of proteins in a typical eukaryotic cell are regulated by cycles of _____ and _____

Answer 5

phosphorylation and dephosphorylation

Question 6

____ ___ produce directed movement in eukaryotic cells through conformational changes linked to the hydrolysis of ATP to ADP

Answer 6

motor proteins

Question 7

molecule or fragment of molecule recognized by an antibody

Answer 7

antigen

Question 8

end of polypeptide chain that carries a free carboxyl group

Answer 8

c-terminus

Question 9

stable, rodlike structure formed when two or more alpha helices twist around each other

Answer 9

coiled coil

Question 10

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

Answer 10

fibrous protein

Question 11

any protein in which the polypeptide chain folds into a compact, rounded shape (most enzymes)

Answer 11

globular protein

Question 12

region in a polypeptide that lacks a definite structure

Answer 12

intrinsically disordered sequence

Question 13

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

Answer 13

protein kinase

Question 14

large assembly of protein molecules that operates as a unit to perform a complex series of biological activities, like replicating DNA

Answer 14

protein machine

Question 15

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

Answer 15

protein phosphatase

Question 16

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

Answer 16

quaternary structure

Question 17

alpha helices and beta sheets are known as ____ structures

Answer 17

secondary

Question 18

the complete 3D structure of a fully folded protein is known as the ___ structure

Answer 18

tertiary

Question 19

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

Answer 19

active site

Question 20

Describes a protein that can exist in multiple conformations depending on the binding of a molecule (ligand) at a site other than the catalytic site; changes from one conformation to another often alter the protein’s activity or ligand affinity.

Answer 20

allosteric

Question 21

The order of the amino acid subunits in a protein chain. Sometimes called the primary structure of a protein.

Answer 21

amino acid sequence

Question 22

Protein produced by B lymphocytes in response to a foreign molecule or invading organism. Binds to the foreign molecule or cell extremely tightly, thereby inactivating it or marking it for destruction.

Answer 22

antibody

Question 23

Region on the surface of a protein, typically a cavity or groove, that interacts with another molecule (a ligand) through the formation of multiple noncovalent bonds.

Answer 23

binding site

Question 24

Molecule that steers proteins along productive folding pathways, helping them to fold correctly and preventing them from forming aggregates inside the cell.

Answer 24

chaperone protein

Question 25

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 a 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.

Answer 25

chromatography

Question 26

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

Answer 26

disulfide bond

Question 27

Technique for separating a mixture of proteins or DNA fragments by placing 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.

Answer 27

electrophoresis

Question 28

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.

Answer 28

feedback inhibition

Question 29

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

Answer 29

helix

Question 30

Enzyme that severs the polysaccharide chains that form the cell walls of bacteria; found in many secretions including saliva and tears.

Answer 30

lysozyme

Question 31

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

Answer 31

motor protein

Question 32

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

Answer 32

peptide bond

Question 33

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.

Answer 33

polypeptide backbone

Question 34

The amino acid sequence of a protein.

Answer 34

primary structure

Question 35

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

Answer 35

protein domain

Question 36

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.

Answer 36

protein phosphorylation

Question 37

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

Answer 37

side chain

Question 38

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.

Answer 38

transition state

Question 39

Folding pattern, common in many proteins, in which a single polypeptide chain twists around itself to form a rigid cylinder stabilized by hydrogen bonds between every fourth amino acid.

Answer 39

alpha helice

Question 40

Describes two similar structures arranged in opposite orientations, such as the two strands of a DNA double helix.

Answer 40

antiparallel

Question 41

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

Answer 41

beta sheet

Question 42

To cause a dramatic change in the structure of a macromolecule by exposing it to extreme conditions, such as high heat or harsh chemicals. Usually results in the loss of biological function.

Answer 42

denature

Question 43

A molecule composed of two structurally similar subunits.

Answer 43

dimer

Question 44

Small discrete region of a structure; in a protein, a segment that folds into a compact and stable structure. In a membrane, a region of the bilayer with a characteristic lipid and protein composition.

Answer 44

domain

Question 45

Selective affinity of one molecule for another that permits the two to bind or react, even in the presence of a vast excess of unrelated molecular species.

Answer 45

specificity

Question 46

Chemical group containing sulfur and hydrogen found in the amino acid cysteine and other molecules. Two can join together to produce a disulfide bond.

Answer 46

sulfihydryl group