Nonenzymatic Protein Function and Protein Analysis

Question 1

motif

Answer 1

repetitive organization of secondary structural elements together

Question 2

collagen

Answer 2

has a trihelical fiber; makes up most of the extracellular matrix of connective tissue; strength and flexibility

Question 3

elastin

Answer 3

extracellular matrix of connective tissue; stretches and recoils, restoring shape to cell

Question 4

keratin

Answer 4

intermediate filament proteins found in epithelial cells; contribute to the mechanical integrity of the cell and also function as regulatory proteins; make up hair and nails

Question 5

actin

Answer 5

makes up microfilaments and the thin filaments in myofibrils; most abundant protein in eukaryotic cells; have a + side and a - side, allowing motor proteins to travel unidirectionally along actin filament

Question 6

tubulin

Answer 6

makes up microtubules; provide structure, chromosome separation and intracellular transport; has + and - side

Question 7

myosin

Answer 7

primary motor protein that interacts with actin; can be involved in cellular transport

Question 8

kinesin

Answer 8

align chromosomes; depolarizing microtubules; vesicle transport + end of microtubule

Question 9

dynein

Answer 9

cilia and flagella; vesicle transport towards - end of microtubule

Question 10

binding proteins

Answer 10

transport or sequester molecules by binding them

Question 11

cell adhesion molecules (CAMs)

Answer 11

aid in binding the cell to the extracellular matrix of other cells

Question 12

cadherin

Answer 12

group of glycoproteins that mediate calcium-dependent cell adhesion

Question 13

integrins

Answer 13

group of proteins that all have two membrane-spanning chains called alpha and beta; chains are imporrtant in binding to and communicating with extracellular matrix ; role in cellular signaling and can greatly impact cellular function by promoting cell division, apoptosis and other processes

Question 14

selectins

Answer 14

bind to carbohydrate molecules that project from other cell surfaces

Question 15

antibodies (immunoglobulins)

Answer 15

proteins produced by B-cells that function to neutralize targets in the body and then recruit other cells to help eliminate the threat

Question 16

antigen-binding region

Answer 16

within this region are specific polypeptide sequences that will bind on specific antigen sequence

Question 17

outcomes of antibody binding

Answer 17

• neutralizing the antigen
• marking antigen for destruction by other white blood cells, process known as opsonization
• clumping together (agglutinating) the antigen so it can be phagocytized

Question 18

ion channels

Answer 18

proteins that create specific pathways for charged molecules

Question 19

facilitated diffusion

Answer 19

type of passive transport, diffusion of molecules down a concentration gradient through a pore in the membrane created by transmembrane protein

Question 20

ungated channels

Answer 20

have no gates

Question 21

voltage-gated channels

Answer 21

regulated by membrane potential change near the channel

Question 22

ligand-gated ion channels

Answer 22

binding of a specific substance or ligand to the channel causes it to open or close

Question 23

enzyme-linked receptors

Answer 23

membrane-spanning domain, ligand-binding domain and catalytic domain

Question 24

G protein coupled receptors

Answer 24

seven membrane spanning alpha helices; integral membrane protein involved in signal transduction

Question 25

heterotrimeric G protein

Answer 25

have an intracellular link to guanine nucleotides (GDP and GTP)

Question 26

three main types of G protein

Answer 26

- Gs stimulates adenylate cyclase, increasing cAMP levels - Gi inhibits adenylate cyclase, decreasing cAMP levels - Gq activates phospholipase c, which cleaves a phospholipid from the membrane to form pip2. pip2 is then cleaved into DAG and ip3. ip3 can open calcium channels, increasing calcium levels

Question 27

electrophoresis

Answer 27

subjects compounds to electrical field, which moves them according to their net charge and size

Question 28

migration velocity

Answer 28

``` v=Ez/f v=velocity E=electric field strength z=net charge of molecule f=frictional coefficient ```

Question 29

polyacrylamide gel

Answer 29

standard medium for electrophoresis; smaller particles pass more quickly

Question 30

polyacrylamide gel electrophoresis (PAGE)

Answer 30

method for analyzing proteins in their native states; useful to compare the molecular size or charge of proteins

Question 31

sodium dodecyl sulfate-PAGE (SDS-PAGE)

Answer 31

separates proteins on the basis of relative molecular mass alone; SDS is a detergent that disrupts all non covalent interactions

Question 32

isoelectric focusing

Answer 32

separating proteins based on their isoelectric point; protein stops moving when the gel pH equals its PI

Question 33

chromatography

Answer 33

require homogenized protein to be fractionated through a porous matrix;

Question 34

chromatography process

Answer 34

- place sample on stationary phase or absorbent - run mobile phase through stationary phase - retention time is the amount of time the compound stays in the stationary phase - partitioning is the separation of the compounds based on their varying retention times

Question 35

Column chromatography

Answer 35

a column is filled with silica or alumina beads as an absorbent and gravity moves the solvent and compounds down the column; less polar compounds move more quickly;

Question 36

ion-exchange chromatography

Answer 36

solvent beads are charged so a positive charged column will attract and hold negatively charged compounds and vice versa

Question 37

size-exclusion chromatography

Answer 37

beads in the column have tiny pores of varying sizes; the small compounds go into the holes while the large molecules keep moving

Question 38

affinity chromatography

Answer 38

a column is coated with a substance that binds a particular protein, retaining it

Question 39

ways to determine protein structure

Answer 39

x-ray crystallography and nuclear resonance spectroscopy

Question 40

Edman degradation

Answer 40

uses cleavage to sequence small proteins (50-70aa)

Question 41

UV spectroscopy

Answer 41

analysis to determine concentration of proteins

Question 42

bradford protein assay

Answer 42

mixes a protein with blue dye; dye is protonated and green-brown in color props to mixing with proteins; dye binds to proteins, turns blue; higher protein concentration means more blue