Biochemistry 3: Nonenzymatic Protein Function and Protein Analysis

Question 1

structural proteins

Answer 1

collagen

elastin

keratins

actin

tubulin

generally fibrous in nature

Question 2

collagen

Answer 2

structural protein

right-handed triple helix

makes up most of the extracellular matrix in connective tissue

provides strength and flexibility

Question 3

elastin

Answer 3

structural protein

often a component of ECM in connective tissue

provides stretch and recoil

Question 4

keratin

Answer 4

structural protein

makes up intermediate filaments in epithelial cells

provides mechanical integrity primary protein in hair and nails

Question 5

actin

Answer 5

structural protein

makes up microfilaments, thin filaments in myofibrils

most abundant protein in eukaryotic cells

polarized with (+) and (-) side to allow direction for motor proteins

Question 6

tubulin

Answer 6

structural protein

makes up microtubules

aid in structure, chromosome separation, intracellular transport

polarized with (+) and (-) side to allow direction for motor proteins

(-) near nucleus while (+) is near cell periphery

Question 7

motor proteins

Answer 7

act as ATPases for conformational change

myosin

kinesin

dynein

Question 8

myosin

Answer 8

motor protein

thick filament in myofibrils, interacting with actin

can be involved in cellular transport

has one head and neck

Question 9

kinesin

Answer 9

motor protein

two heads with one attached to tubulin at all times as it moves

align chromosomes during metaphase, depolymerize microtubules during anaphase transport vesicles towards (+) cell periphery

Question 10

dynein

Answer 10

motor protein

two headed involved in sliding movement of flagella and cilia

transport vesicles towards (-) nucleus

Question 11

binding protein

Answer 11

proteins which bind a specific substrate to sequester it in the body or hold its concentration at a steady state

Question 12

cell adhesion molecules

Answer 12

found on cell surfaces

allow cells to bind to other cells or surfaces

Cadherins, Integrins, Selectins

are often integral membrane proteins

Question 13

Cadherins

Answer 13

cell adhesion molecule

glycoproteins that mediate Ca2+ - dependent cell adhesion

hold similar cells together

Question 14

Integrins

Answer 14

cell adhesion molecule

span two membranes

permit cells to adhere to proteins in the ECM

can have signaling properties, promote division, apoptosis,

Question 15

selectins

Answer 15

weakest cell adhesion molecule

bind to carb molecules that project from other cells

present on WBC and endothelial cells lining blood vessels

Question 16

antibodies

Answer 16

made by B cells used by immune system to target specific antigens

binding of antigens at the antigen-binding region can…

1. neutralize antigen
2. opsonize (mark for destruction)
3. agglutinate (make insoluble)

Question 17

G protein

Answer 17

trimeric protein involved in initiating a second messenger system

ligand binging engages G protein –> GDP replaced with GTP, alpha subunit leaves beta and gamma –> alpha subunit alters activity of adenylate cyclase or phospholipase C —> GTP dephosphorylated to GDP, alpha rebinds

Question 18

Gs

Answer 18

type of alpha G protein which stimulates adenylate cyclase leads to increase in cAMP

Question 19

Gi

Answer 19

type of alpha G protein which inhibits adenylate cyclase leads to decrease in cAMP

Question 20

Galpha

Answer 20

type of alpha G protein that activates phospholipase C

PIP2 -> DAG and IP3

IP3 opens Ca2+ channels in ER leads to increase in Ca2+

Question 21

electrophoresis

Answer 21

use of a gel matrix to observe the migration of proteins in response to an electric field

small, charged proteins migrate faster

Question 22

anode

Answer 22

the positively charged electrode

attracts negatively charged proteins

Question 23

cathode

Answer 23

the negatively charged electrode

attracts positively charged proteins

Question 24

polyacrylamide gel

Answer 24

standard medium for protein electrophoresis

gel is slightly porous, so small proteins pass easily while large proteins are retained

Question 25

native-PAGE

Answer 25

polyacrylamide gel electrophoresis (PAGE) method for analyzing proteins in their **native states** **maintains shape** but **hard for comparison** because mass-to-charge ratio differs

Question 26

SDS-PAGE

Answer 26

sodium dodecyl sulfate method in which proteins are **denatured**, **uncharged**, and separated based on **molecular mass** **comparison of size** is more accurate but functional protein **can't be recaptured** from gel

Question 27

isoelectric focusing

Answer 27

electrophesis method in which proteins are separated by their **isoelectric points** gradient: **acidic gel by the anode** and **basic gel by the cathode** protein migrates towards electrode until it reaches a region where **pH = pI** protein becomes **zwitterion and stops moving**

Question 28

chromatography

Answer 28

method that separates protein mixtures on the basis of their **affinity for a stationary phase or a mobile phase** the more similar a protein is to its surroundings, the slower it will move

Question 29

column chromatography

Answer 29

chromatography that uses **beads of a polar compound** (silica/alumina) **as stationary phas**e and some **nonpolar solvent as mobile phase** size and polarity determines retention time

Question 30

ion-exchange chromatography

Answer 30

chromatography that uses a **charged column with beads (stationary)** to attract proteins of opposite charges and later uses some **saline eluent (mobile)** to bind the charged molecules that were previously captured

Question 31

size-exclusion chromatography

Answer 31

chromatography that uses **tiny beads with pores of varying sizes** to capture **small compounds (stationary)** larger molecules elute first since they aren't trapped

Question 32

affinity chromatography

Answer 32

chromatography in which **beads are coated with a bound receptor/ligand (stationary)** and later an **eluent with a free ligand/receptor** is used to capture the protein of interest

Question 33

X-ray crystallography

Answer 33

analysis that determines **protein structure** by measuring **electron density**

Question 34

NMR

Answer 34

analysis that determines the **presence of functional groups** and **carbon arrangement** of a compound

Question 35

Edman degradation

Answer 35

sequential **protein degradation** that allows for amino acid sequencing simple hydrolysis of proteins **only reveals amino acid composition**