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biochem > CH3: nonenzymaticc protein function and analysis > Flashcards

CH3: nonenzymaticc protein function and analysis Flashcards

1
Q

primary structural proteins

A

collagen, elastin, keratin, actin, and tubules

have highly repetitive secondary structure and supersecondary structure

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2
Q

collagen

A

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

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3
Q

elastin

A

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

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4
Q

keratins

A

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.

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5
Q

actin

A

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

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6
Q

tubulin

A

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

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7
Q

motor protines

A

myosin, kinesics, and dyneins

atlases power the ocnfomaitn change necessary for motor functions

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8
Q

myosin

A

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

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9
Q

kinesics and dyeins

A

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

important for vesicle transport

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10
Q

kinesines

A

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

vesicles toward the positive end of the microtubules

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11
Q

dyneins

A

involved in sliding movement of cilia and flagella

vesicles toward the negative end

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12
Q

binding protein

A

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

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13
Q

CAM (cell adhesionmoecules)

A

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

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14
Q

cadherins

A

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

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15
Q

itegrins

A

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)

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16
Q

selectins

A

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

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17
Q

immunoglobulins/antibodies

A

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

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18
Q

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

A

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

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19
Q

how do cytoskeletal proteins differ from motor proteins

A

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

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20
Q

motor proteins are enzymes? t/f?

A

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

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21
Q

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

A

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

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22
Q

biosignalling

A

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

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23
Q

ion channels

A

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

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24
Q

undated channels

A

no gates, unregulated

potassium channels

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25
Q

voltage gated channels

A

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

neurons

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26
Q

ligand gated channels

A

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

neurotransmitters

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27
Q

enzyme linked receptors

A

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

28
Q

G coupled receptors

A

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

29
Q

heterotrimeric G protin

A

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

30
Q

G proteins

A

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

31
Q

thee subunits of G protein:

A

alpha beta and gamma

32
Q

enzyme linked receptors and G protein coupled receptors difference and sims

A

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

33
Q

which ion channel is always open

A

ungated!! they’re unregulated, remember

34
Q

transport kinetics differ form enzyme kinetics how?

A

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

35
Q

isoelectric point (pI)

A

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

36
Q

isoelectric focusing

A

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

37
Q

chromotography

A

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

38
Q

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

A

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

39
Q

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

A

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

40
Q

two drawbacks of affinity chromatography

A

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

41
Q

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

A

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

42
Q

protein structure can be determined by __ and __

A

X-ray crystallography and nuclear magnetic resonance spectroscropy

43
Q

Edman degradation

A

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

44
Q

UV spectroscopy

A

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

45
Q

Bradford protein assay

A

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

46
Q

why are proteins analyzed after isolation?

A

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.

47
Q

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

A

contamination: artificial incr protein level, lower activity that expected

enzyme could have been denatured during isolation and analysis

48
Q

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

A

FALSE! from the N terminus

49
Q

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

A

B

50
Q

the SDS in SDS-PAGE

A

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.

51
Q

tubulin, collagen, elastin, keratin, actin are …

A

primary cytoskeletal proteins

TEACK

52
Q

myosin, kinesin, and dyneins are…

A

motor proteins

MKD

53
Q

the most prevalent extracellular proteins are:

A

keratin, elastin, and collagen

ECKstracelluar proteins

54
Q

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

A

second messenger systems

55
Q

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

A

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

56
Q

Classically, calcium and magnesium are ___

A

protein bond

57
Q

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

A

Sodium and potassium

58
Q

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

A

chloride

59
Q

___ 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

A

calcium

60
Q

resting potential is displayed by cells that are….

A

not actively involved in signal transductions, and are unregulated

61
Q

the basic AAs

A

arginine, lysine, and histidine

62
Q

acidi AAs

A

aspartic acid and glutamic acid

63
Q

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

A

acid and basic amino acids

64
Q

aromatic AAs

A

phenylalanine, tyrosine, and tryptophane

65
Q

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

A

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

biochem (3 decks)

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