Nonenzymatic Protein Function and Protein Analysis

Question 1

collagen

Answer 1

makes up most of the extracellular matrix of connective tissue; has characteristic trihelical fibers (three left handed helices woven together to form a secondary right handed helix); found throughout the body and is important in providing strength and flexibility

Question 2

elastin

Answer 2

primary role is to stretch and then recoil like a spring, which restores the original shape of the tissue; another important component of the extracellular matrix of connective tissue

Question 3

keratin

Answer 3

intermediate filament proteins found in epithelial cells; contribute to mechanical integrity of the cell and function as regulatory proteins; primary protein that makes up hair and nails

Question 4

actin

Answer 4

protein that makes of microfilaments and the thin filaments in myofibrils; most abundant protein in eukaryotic cells; have a positive and negative side, creating polarity and allowing motor proteins to travel unidirectionally along a filament

Question 5

tubulin

Answer 5

makes up microtubules; has polarity - the negative end of a microtubule usually is located adjacent to the nucleus, whereas the positive is usually in the periphery of the cell

Question 6

motor proteins

Answer 6

proteins that are involved in cell motility through interactions with structural proteins; have ATPase activity and include myosin, kinesin, and dyenin

Question 7

ATPase

Answer 7

enzyme that catalyzes hydrolysis of ATP

Question 8

myosin

Answer 8

the primary motor protein that interacts with actin; acts in cellular transport

Question 9

dynein

Answer 9

one of two motor proteins associated with microtubules; they have two heads and at least one remains attached to microtubules; involved in sliding movement of cilia and flagella; brings vesicles toward the negative end of a microtubule

Question 10

binding proteins

Answer 10

proteins that transport or sequester molecules by binding to them; have affinity curves for their molecules of interest

Question 11

cell adhesion molecules

Answer 11

specialized structural proteins that are involved in cell-cell junctions as well as transient cellular interactions; includes cadherins, integrins, and selectins

Question 12

cadherins

Answer 12

calcium-dependent glycoproteins that hold similar cells together

Question 13

integrins

Answer 13

have two membrane-spanning chains and permit cells to adhere to proteins in the extracellular matrix. Some also have signaling capabilities

Question 14

selectins

Answer 14

allow cells to adhere to carbohydrates on the surfaces of other cells and are most commonly used in the immune system

Question 15

Immunoglobulins (antibodies)

Answer 15

a specialized protein molecule produced by lymphocytes for interaction with antigens; consist of two heavy and two light chains that have constant and variable regions; mediators of the immune response

Question 16

antigen-binding region

Answer 16

Portion of an antibody that is specific for a particular antigen; the area of the antibody to which the antigen binds.

Question 17

antigen

Answer 17

A protein that, when introduced in the blood, triggers the production of an antibody

Question 18

opsonization

Answer 18

the marking of a pathogen by an antibody for later destruction

Question 19

agglutination

Answer 19

clumping of particles caused by the binding of antibody to target antigen

Question 20

biosignaling

Answer 20

the process by which cells receive and act on messages

Question 21

ion channels

Answer 21

proteins that form a pore through the membrane in which they are embedded

Question 22

facilitated diffusion

Answer 22

the movement of solute molecules across the cell membrane down their concentration gradient through a transport protein or channel; used for ions or large polar molecules

Question 23

ungated channels

Answer 23

type of ion channel that have no gates and are unregulated; i.e. potassium channels

Question 24

voltage-gated channels

Answer 24

open and close in response to changes in membrane potential

Question 25

ligand-gated channels

Answer 25

open in the presence of a specific binding substance, usually a hormone or neurotransmitter

Question 26

enzyme-linked receptors

Answer 26

a transmembrane protein that displays catalytic activity in response to ligand binding

Question 27

membrane-spanning domain

Answer 27

anchors the receptor in the cell membrane; type of enzyme-linked receptor

Question 28

ligand-binding domain

Answer 28

stimulated by the appropriate ligand and induces a conformational change that activates the catalytic domain; type of enzyme-linked receptor

Question 29

catalytic domain

Answer 29

protein domain in enzyme-linked receptors, activated by a conformational change induced by the ligand-binding domain, causes the initiation of a second messenger cascade

Question 30

second messenger cascade

Answer 30

a multistep process that couples activation of a neurotransmitter receptor to activation of intracellular enzymes

Question 31

G protein-coupled receptors (GPCRs)

Answer 31

a special class of membrane receptors with an associated GTP-binding protein; activation of this involves dissociation and GTP hydrolysis

Question 32

heterotrimeric G protein

Answer 32

it is a G- protein consisting of three subunits (alpha, beta, and gamma). When a hormone binds, a GDP bound to the alpha subunit dissociates and a GTP associates, and the alpha subunit dissociates from the beta and gamma subunits.

Question 33

homogenization

Answer 33

the process of breaking cell membranes and creating a uniform mixture of cell components for further separation; may be accomplished chemically or physically

Question 34

centrifugation

Answer 34

the process of separating components of the basis of their density and resistance to flow by spinning a sample at very high speeds; the highest density materials form a solid pellet and the lowest density materials remain in the supernatant

Question 35

electrophoresis

Answer 35

the process of separating compounds on the basis of size and charge using a porous gel and an electric field

Question 36

migration velocity

Answer 36

velocity at which a compound moves through a gel during electrophoresis

Question 37

polyacrylamide gel

Answer 37

standard medium for protein electrophoresis

Question 38

Polyacrylamide gel electrophoresis (PAGE)

Answer 38

method for analyzing proteins in their native states; compare molecular size or charge of proteins; maintains protein’s shape, but results are difficult to compare because the mass-to-charge ratio differs for each protein

Question 39

Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE)

Answer 39

separates proteins on the basis of relative molecular mass alone; denatures the proteins and masks the native charge so that comparison of size is more accurate, but the functional protein cannot be recaptured from the gel

Question 40

isoelectric point

Answer 40

The pH at which an amino acid is predominantly in zwitterionic form

Question 41

isoelectric focusing

Answer 41

a specialized method of separating proteins by their isoelectric point using electrophoresis; the gel is modified to possess a pH gradient

Question 42

chromatography

Answer 42

the process of separating molecules by their interactions with a stationary phase and a mobile phase; most processes rely on the chemical similarity of molecules, with the exception of size-exclusion

Question 43

stationary phase (adsorbent)

Answer 43

solid medium in chromatography

Question 44

elution

Answer 44

The process of extracting a substance that is bound to another by washing it with a solution; process of passing a liquid or gas through a chromatography column

Question 45

retention time

Answer 45

the amount of time a compound spends in stationary phase

Question 46

partitioning

Answer 46

separation of components within the stationary phase of chromatography

Question 47

column chromatography

Answer 47

Chromatography in which the substances to be separated are introduced onto the top of a column packed with an adsorbent (as silica gel or alumina), pass through the column at different rates that depend on the affinity of each substance for the adsorbent and for the solvent or solvent mixture, and are usually collected in solution as they pass from the column at different times

Question 48

ion exchange chromatography

Answer 48

uses a charged column and a variably saline eluent to separate protein mixtures

Question 49

size exclusion chromatography

Answer 49

relies on porous beads to separate protein mixtures; larger molecules elute first because they are not trapped in the small pores

Question 50

affinity chromatography

Answer 50

separates protein mixtures by using a bound receptor or ligand and an eluent with free ligand or a receptor for the protein of interest

Question 51

X-ray crystallography

Answer 51

a method of determining molecular structure using apparent bond angles and diffraction and refraction of x-rays

Question 52

Nuclear Magnetic Resonance (NMR) Spectroscopy

Answer 52

a method of determining molecular structure that uses the relative position of carbons and hydrogens determined by the relative shielding and spins of electrons observed when molecule is exposed to a magnetic field

Question 53

Edman degradation

Answer 53

a step-wise process for determining the amino acid sequence in an isolated protein

Question 54

UV spectroscopy

Answer 54

a method of determining the concentration of a protein in an isolate by comparison against a protein standard; relied on the presence of aromatic amino acids; it can also be used with nucleic acids and other compounds

Question 55

Bicinchoninic Acid (BCA) Assay

Answer 55

used for quantitation of total protein in a sample. The principle of this method is that proteins can reduce Cu+2 to Cu+1 in an alkaline solution (the biuret reaction) and result in a purple color formation by bicinchoninic acid

Question 56

Lowry reagent assay

Answer 56

uses copper, which bonds with the peptide bonds in proteins under alkaline conditions. This forms a monovalent copper ion which can then react with the Folin reagent, which in turn can be reduced into a blue colored substance. … Thus, the concentration of protein can be determined

Question 57

bradford protein assay

Answer 57

a colorimetric method of determining the concentration of protein in an isolate against a protein standard; relies on a transition between bound and unbound Coomassie Brilliant Blue dye

structural proteins
compose the