Nonenzymatic Protein Function and Protein Analysis

Question 1

motif

Answer 1

a repetitive organization of secondary structural elements together

Question 2

collagen

Answer 2

characteristic trihelical fiber , makes up most of the extracellular matrix of connective tissue, provides strength and flexibility

Question 3

elastin

Answer 3

component of the extracellular matrix of connective tissue, stretches and recoils

Question 4

keratins

Answer 4

intermediate proteins in epithelial cells, in hair and nails

Question 5

actin

Answer 5

protein that makes up microfilaments and thin filaments in myofibrils

Question 6

tubulin

Answer 6

makes up microtubules, microtubules are important for providing structure, chromosomes separation in mitosis and meiosis, and intracellular transport with kinesin and dynein

Question 7

motor proteins

Answer 7

display enzymatic activity, acting as ATPases that power the conformation al change necessary for motor function

Question 8

myosin

Answer 8

primary motor function that interacts with actin

Question 9

kinesin and dyneins

Answer 9

motor proteins associated with microtubules

Question 10

binding proteins

Answer 10

hemoglobin, transcription factors

Question 11

cell adhesion molecules (CAM)

Answer 11

proteins found on the surface of most cell sand aid in binding, the cell to the extracellular matrix or other cells

different families: cadherins, integrins, and selectins

Question 12

cadherins

Answer 12

glycoproteins that mediate calcium dependent cell adhesion

Question 13

integrins

Answer 13

a group of proteins that all have two membrane-spanning chains called alpha and beta; play a role in cell signaling

Question 14

selectins

Answer 14

bind to carbohydrate molecules that project from other cell surfaces

Question 15

immunoglobulins

Answer 15

also known as antibodies, proteins produced by B cells that function to neutralize targets in the body, such as toxins and bacteria and then recruit other cells to help with the threat

Question 16

each antibody has a ?

Answer 16

antigen-biding region, at the tip of the Y

Question 17

What are the targets for antibodies?

Answer 17

antigens (pathogens)

Question 18

What are the three outcomes of antibodies binding to an antigen?

Answer 18

1. neutralizing the antigen, making the pathogen or toxin unable to exert its effect on the body
2. marking the pathogen for destruction by other white blood cells immediately; this marking is called opsonization
3. clumping together (agglutinating) the antigen and antibody into large insoluble protein complexes that can be phagocytized and digested by macrophages

Question 19

Opsonization

Answer 19

marking the pathogen for destruction by other white blood cells immediately

Question 20

Agglutinating

Answer 20

clumping together, the antigen and antibody into large insoluble protein complexes that can be phagocytized and digested by macrophages

Question 21

Ion channels

Answer 21

proteins that create specific pathways for charged molecules

Question 22

facilitated diffusion

Answer 22

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

ex. ungated, voltage-gated, and ligand-gated

Question 23

ungated channels

Answer 23

have no gates and are therefore unregulated, ex. potassium channels

Question 24

voltage-gated channels

Answer 24

gate is regulated by the membrane potential change near the channel, ex. voltage-gated non-specific sodium-potassium channels are found in the cells of the sinoatrial node of the heart

Question 25

ligand-gated channels

Answer 25

binding of a specific substance or ligand to the channel causes it to open or close…the inhibitory neurotransmitter GABA binds to a chloride channel and opens it

Question 26

Km

Answer 26

refers to the solute concentration at which the transporter is functioning at half of its maximum activity

Question 27

membrane-spanning domain?

Answer 27

anchors the receptor in the cell membrane

Question 28

ligand-binding domain?

Answer 28

stimulated by the appropriate ligand and induces a conformational change that activates the catalytic domain–> often results in the initiation of a second messenger cascade

Question 29

G Protein Coupled Receptors

Answer 29

integral membrane proteins involved in signal transduction, utilize a heterotrimeric G protein (GDP and GTP)
3 types
1. G_s stimulates adenylate cyclase, increases levels of cAMP in the cell
2. G_i inhibits adenylate cyclase, which decreases levels of cAMP in the cell
3. G_q 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 in the endoplasmic reticulum, increasing calcium levels in the cell

Question 30

GPCR - what separates away from GPCR protein?

Answer 30

alpha subunit can dissociate from alpha, beta, and gamma joined together in GPCR .

Question 31

homogenization

Answer 31

crushing, grinding, or blending the tissue of interest into an evenly mixed solution

(centrifugation can then isolate proteins from much smaller molecules before other isolation techniques must be employed)

Question 32

electrophoresis

Answer 32

subjects compounds to an electric field, moves them according to their net charge and size

uses polyacrylamide gel—> standard medium for protein electrophoresis

Question 33

Polyacrylamide gel electrophoresis (Native PAGE)

Answer 33

maintains the protein’s shape, but results are difficult to compare because the mass-to-charge ratio differs for each protein

Question 34

SDS-PAGE

Answer 34

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 35

Isoelectric focusing

Answer 35

separates proteins by their isoelectric point (pI); the protein migrates toward an electrode until it reaches a region of the gel where pH=pI of the protein

Question 36

chromatography

Answer 36

separates protein mixtures on the basis of the their affinity for a stationary phase or a mobile phase

Question 37

column chromatography

Answer 37

uses beads of a polar compound, like silica or alumina (stationary phase), with a nonpolar solvent (mobile phase)

Question 38

ion-exchange chromatography

Answer 38

uses a charged column and a variable saline eluent

Question 39

size-exclusion chromatography

Answer 39

relies on porous beads, larger molecules elute first because they are not trapped in the small pores

Question 40

affinity chromatography

Answer 40

uses a bound receptor or ligand and an eluent with free ligand or a receptor for the protein of interest

Question 41

X-ray crystallography

Answer 41

protein structure can be determined by this after the protein is isolated (NMR can also be used)

Question 42

Edman degradation

Answer 42

a technique that allows sequential degradation for amino acid sequencing

Question 43

Bradford protein assay

Answer 43

uses a color change from brown-green to blue, most common way to test for a protein

could also use BCA assay or Lowry reagent assay