CH3: nonenzymaticc protein function and analysis

Question 1

primary structural proteins

Answer 1

collagen, elastin, keratin, actin, and tubules

have highly repetitive secondary structure and supersecondary structure

Question 2

collagen

Answer 2

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

Question 3

elastin

Answer 3

another important component of the extracellular matrix of connective tissue, primary role: to stretch and then recoil like spring, respores original shape of tissue

Question 4

keratins

Answer 4

intermediate filament proteins found in epithelial cells, contribute to the mechanical integrity of the cell and also functions as regulatory proteins. keratin is the primary protein that makes up hair and nails.

Question 5

actin

Answer 5

proton that makes up microfilaments and the thin filament sin myofibrils. most abundant protein in eukaryotic cells. polarity allows motor proteins to travel unidirectionally along an actin filament, like a one way street

Question 6

tubulin

Answer 6

proton that makes up MICROTUBULS (important for providing stucture, chromosome separation, and intracellular transport, like actin, tubules has polarity. neg end is located adjacent tot eh nucleus, positive end is usually in the periphery of the cell

Question 7

motor protines

Answer 7

myosin, kinesics, and dyneins

atlases power the ocnfomaitn change necessary for motor functions

Question 8

myosin

Answer 8

primary motor protein that interacts with actin. thick filament in a myofibril, cellular transport, has a single tea dna dnneck, movement at the neck is responsible fo the power stroke of sarcomere contraction

Question 9

kinesics and dyeins

Answer 9

motor proteins associated with MICROTUBULes. two heads, at least one of thwack remains attached to tubule at all times

important for vesicle transport

Question 10

kinesines

Answer 10

play key roles in aligning chromosomes during metaphase and depolymerizing microtubules during anaphase of mitosis

vesicles toward the positive end of the microtubules

Question 11

dyneins

Answer 11

involved in sliding movement of cilia and flagella

vesicles toward the negative end

Question 12

binding protein

Answer 12

hemoglobin, calcium-binding protein, DNA-binding protein (often transcription factors) and others

Question 13

CAM (cell adhesionmoecules)

Answer 13

proteins found on the surface of most celll and aid in binding the cell to the extracellular matrix or there cells. all are integral membrane proteins

major families: cadherins, interns, and selectins

Question 14

cadherins

Answer 14

group of glycoproteins that mediate calcium dependent cell adhesions, often hold similar cell types together

Question 15

itegrins

Answer 15

group of proteins that all have two membrane spanning chains called alpha and beta, which are very important in binding to an dcommunicating with the extracellular matrix, cellular signaling and can greatly impact cellular function by promoting cell division, apoptosis, etc (clot)

Question 16

selectins

Answer 16

unique- gouré of proteins bc they bind to carbohydrate molecules that project from other cell surfaces, bonds are weaker of the CAMS, white blood cells and endothelial cells (line blood vessels), host defense like integrins

Question 17

immunoglobulins/antibodies

Answer 17

to rid the body of foreign invaders

produced by B cells that functions to neutralize targets in the body such as toxins and bacteria, and then recite other cells to help eliminate the threat. Each B cell produces a single type of antibody with a constant region that is specific to the host and a variable region the tis specific to an antigen, so antibodies are specific to a single antigen

Y shaped protein made up of two identical heavy chains and two identical light chancy, disulfide linkages and non covalent interactions hold heavy and light chains together, antigen binding region at tips of Y

Question 18

when antibodies binding to their targets, called antigens, they can cause of the three outcomes:

Answer 18

neutralizing the antigen, pathogen unable to exert

opsonization: marking th epathogen for destruction by other white blood cells
agglutinating: clumping together the antigen and antibody into large insoluble protein completes that can by phagocytize and digested b macrophages

Question 19

how do cytoskeletal proteins differ from motor proteins

Answer 19

cytoskeletal proteins tend to be fibrous with repeating domains, while motor proteins tend to have ATPase activity and binding heads. both types of protein functioning cellular motility

Question 20

motor proteins are enzymes? t/f?

Answer 20

true, they do have catalytic acivity, but motor FUNCITON is generally considered no enzymatic, bu the ATPase functionality fo motor proteins indicate sthaththse molecules do have catalytic activity

Question 21

what are the three types of cell adhesion molecules and what are their types of adhesion?

Answer 21

cadherin: two cells of the same or similar type using calcium
integrin: one cell to proteins in the extracellular matrix
selection: one cell to carbohydrates, usually on the surface of other cells

Question 22

biosignalling

Answer 22

process in which cells receive and act on signals, proteins participate in diff capacities

Question 23

ion channels

Answer 23

proteins that creat specific pathway for charged molecules, facilitated diffusion (diff of a molecule down a concentration gradient thru a pore int he membrane created by their transmemebrane protein, allows integral proteins to serve as channels)

ungated
voltage gated channels
ligand gated channels

Question 24

undated channels

Answer 24

no gates, unregulated

potassium channels

Question 25

voltage gated channels

Answer 25

the gate is regulated by the membrane potential change near the channel neurons

Question 26

ligand gated channels

Answer 26

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

Question 27

enzyme linked receptors

Answer 27

three primary domains: membrane spanning domain- anchors the receptor in the cell memebrane ligand binding domain- stimulated by the appropriate ligand and induces a conformation change that activates the catalytic domain, which results in the initiation of a second messenger cascade

Question 28

G coupled receptors

Answer 28

large family of integral membrane proteins involved in signal transduction, characterized by their seven membrane spanning alpha helices, receptors differ in specificity

Question 29

heterotrimeric G protin

Answer 29

utilized fo when GPCRS transmit signals to an effector in the cell

Question 30

G proteins

Answer 30

named for they intracellular link to GDP/DTP, the binding of a ligand increases the affinity of the receptor for the G protein The types of G alpha (differ dep on function of receptor): Gs- Stimulates! adntlyate Cyclades, increases cAMP levels Gi- inhibits! adneylate Cyclades- decreasing cAMP levels Gq- activates phohpholipase C, which cleaves a phospholipid form the membrane to form PIP2, cleaved into DAG and IP3 which can open calcium channel sent he ER, increasing calcium levels

Question 31

thee subunits of G protein:

Answer 31

alpha beta and gamma

Question 32

enzyme linked receptors and G protein coupled receptors difference and sims

Answer 32

enzyme linked: autoactivity, enzymatic activity G preteen coupled: two protein complex, dissociation upon activation, trimer same: extracellular domain, transmembrane domain, ligand binding, use second messenger systems

Question 33

which ion channel is always open

Answer 33

ungated!! they're unregulated, remember

Question 34

transport kinetics differ form enzyme kinetics how?

Answer 34

transport kinetics display both Km and max values, the, also can be cooperative, like some binding protiens however, transporters do not have analygous Keq values for reactions because there is no catalysis

Question 35

isoelectric point (pI)

Answer 35

the pH at which the protein or Has is electrically neutral, with an equal numb rod positive and negative charges for individual AA this electrically neutral form is called a zwitterion, in which the amino group pis protonated, the carboxyl group is deprotonated, and any side chain is electrically neutral

Question 36

isoelectric focusing

Answer 36

exploits the acidic and basic properties of Acs by separating on the basis of pI the Gell in this uses a pH gradient, when a protein is in a region with a pH above its pI, it is negatively charged and moves toward the anode. when it pH is below, pos, cathode, when pH=pI migration halts! A+Anode was an Acidic (H+ rich) gel and a (+) chg

Question 37

chromotography

Answer 37

sample is loaded onto a stationary phase/adsorbent, then eluts during the retention time, resulting in the separation of the components within the stationary phase, or partitioning column chromatography: column is filled with silica or alumina beads as an adsorbent and gravity moves the solvent and compounds down the column ion exchange chromoatography: the beads in the column are coated with charged substance, so they attract or bind compounds that have an opp chg size exclusion chromatophraphy: the beads used int ehcolumn contain time pores of varying sizes affinity chromatography: receptor that binds the protein to the protein so that its retained int he column. protein nelutes off of an affinity column by binding free lignad

Question 38

what separations methods can be used to isolate a protein on the basis of isoelectric point?

Answer 38

isoelectric focusing and ion exchange chromatography both separate proteins based on chg, the chg of a protein in any given environment is determined by its pI

Question 39

What are the realtive benefits of native PAGE compared to SDS-PAGE

Answer 39

Native PAGE allows a complete protein to be recovered after analysis, it also more accurately determines the relative globular size of proteins. SDS-PAGE can be used to eliminate conflation from mass to charge ratios

Question 40

two drawbacks of affinity chromatography

Answer 40

the protein of interest may not elute form the column because its affinity is too high or it may be permanently bound tot he free receptor in the eleutent

Question 41

t/f? in size exclusion chromatophy, the largest molecules elute first

Answer 41

ture, the small pores in size exclusion chromatography trap smaller particles, retaining them in the coluumn

Question 42

protein structure can be determined by __ and __

Answer 42

X-ray crystallography and nuclear magnetic resonance spectroscropy

Question 43

Edman degradation

Answer 43

best tool to analyze small proteins, uses cleavage to sequence proteins of up to 50 or 70 AAs selectively and sequentially removes the N Terminal AA of the protein, which can be analyzed via mass spectroscopy for larger fragments, gestation with chrotrypsin, trypsin and cyanogen bromide (synthetic reagent) selectively cleaves them into smaller fragments

Question 44

UV spectroscopy

Answer 44

analyzes concentration or proteins, since they contain aromatic side chains particularly sensitive to sample contaminants proteins also cause colorimetric changes with specific reactions, particularly at the bicinchonic acid (BCA) assay, Lowry reagent assay, and Bradford protein assay

Question 45

Bradford protein assay

Answer 45

mises a protein in solution with Coomassie Brilliant Blue dye, which is protonated and free brown in color prior to mixing with proteins. ionic attractions between the dye and the protein stabilitze blue form of the the dye when it binds to AA groups, so an increased protein conc corresponds to larger conc of blue dye in sol

Question 46

why are proteins analyzed after isolation?

Answer 46

isolation is generally the first step in an analysis. the protein identity must be confirmed by AA analysis or activity, which unknown proteins, classification of their feature sis generally desired.

Question 47

What factors would cause an activity assay to display lower activity that expected after concentration determination

Answer 47

contamination: artificial incr protein level, lower activity that expected enzyme could have been denatured during isolation and analysis

Question 48

t/F?? the Edman degradation proceeds form the carboxyl terminus

Answer 48

FALSE! from the N terminus

Question 49

the pH at which a protein can be obtained through electrophoresis has to have a pI that is: A: the same as the pH B: above the pH C: below the PH

Answer 49

B

Question 50

the SDS in SDS-PAGE

Answer 50

detergent, gester proteins to form mycels with uniform negative charges. bc the protein is sequestered within the micelle, other factors such as charge of the prtein and shape have min roles during separation.

Question 51

tubulin, collagen, elastin, keratin, actin are ...

Answer 51

primary cytoskeletal proteins TEACK

Question 52

myosin, kinesin, and dyneins are...

Answer 52

motor proteins | MKD

Question 53

the most prevalent extracellular proteins are:

Answer 53

keratin, elastin, and collagen ECKstracelluar proteins

Question 54

both enzyme linked receptors and G protein couple receptors use.... while ion channels do not

Answer 54

second messenger systems

Question 55

for a ligand to be present in low quantities yet have a strong action/effect, we expect it to have a ___

Answer 55

second messenger cascade system, which amplify signals becuase enzymes can catalyze a reaction more than once while they are active, and often activate other enzymes

Question 56

Classically, calcium and magnesium are ___

Answer 56

protein bond

Question 57

___ and ___ must exist in their free states to participate in action potentials

Answer 57

Sodium and potassium

Question 58

___ is readily excreted by the kidney, so its not protein bound

Answer 58

chloride

Question 59

___ must be sequestered in both th bloodstream an intracellularly becuase it is used for muscle contraction, exocytosis (of neurotransmitters and other) and many other cellular processes that must be tightly regulated

Answer 59

calcium

Question 60

resting potential is displayed by cells that are....

Answer 60

not actively involved in signal transductions, and are unregulated

Question 61

the basic AAs

Answer 61

arginine, lysine, and histidine

Question 62

acidi AAs

Answer 62

aspartic acid and glutamic acid

Question 63

the overall pI of a protein is determined by the # of ___ ___ _-_-_-_

Answer 63

acid and basic amino acids

Question 64

aromatic AAs

Answer 64

phenylalanine, tyrosine, and tryptophane

Question 65

what property of protein digesting enzymes allows for a sequence not be detained without fully degrading the protein

Answer 65

the selective cleavage of protein soy digestive enzymes allows fragments of diff lengths with known AA endpoints to be created. by cleaving the protein with several diff enzymes, a basic out line of the AA sequence can be created