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Biochemistry > Nonenzymatic Protein Function and Protein Analysis > Flashcards

Nonenzymatic Protein Function and Protein Analysis Flashcards

1
Q

Primary Structural Proteins of the Body

A 
Collagen
Elastin
Keratin
Actin
Tubulin
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2
Q

Motif

A

repetitive organization of secondary protein structural elements together

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3
Q

Collagen

A

three left handed helices woven in fiber

makes up extracellular matrix of connective tissue

strength and flexibility

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4
Q

Elastin

A

extracellular matrix of connective tissue

stretch and recoil like spring to regain original shape of tissue

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5
Q

Keratins

A

intermediate filament proteins in epithelial cells

mechanical integrity and regulatory proteins

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6
Q

Actin

A

microfilaments and thin filaments in myofibrils

most abundant protein in EK cells

polarity to have motor proteins move along actin filament

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7
Q

Tubulin

A

makes up microtubules which provide structure, intracelluar transport and chromosomal seperation

has polarity like actin : + towards periphery of cell and - towards the nucleus

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8
Q

Motor proteins display ____ acting as ____ that power the conformational change necessary for motor function. Have transient interactions with either ____ or _____

A

enzymatic activity

ATPases

actin

microtubules

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9
Q

Myosin

A

primary motor protein interacting with actin

thick filament in myofibril

cellular transport

neck causes power stroke

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10
Q

Kinesins/Dynesins

A

motor proteins with microtubules

two heads where one is attahced to tubule at all times

align chromosomes at metaphase and depolymerize microtubules during anaphase

Dyenins slide the movement of cilia and flagella

Kinesisns bring vesicles toward positive end of microtubule

Dyenins bring vesicles toward the negative end

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11
Q

Binding Proteins

A

transport/sequester molecules by binding to them

hemoglobin, calcium binding proteins, DNA binding proteins

has affinity curve for molecule of interest

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12
Q

Cell Adhesion Molecules (CAMS)

A

proteins found on the surface of most cells that aid in binding the cell to ECm or other cells

integral proteins

Cadherins, Integrins, Selectins

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13
Q

Cadherins

A

glycoproteins that conduct calcium dependent cell adhesion

hold similar type cells together

ither cells have type specific cadherins E for epithelial and N for nerve

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14
Q

Integrins

A

proteins with two membran spanning chains of alpha and beta

bind and communicate with ECM

cellular signaling and cell division and apoptosis

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15
Q

Selectins

A

bind to carbohydratte molecules from the surface

weakest bonds formed by CAMs

expressed on white blood cells and endothelial cells of blood vessls

host defense

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16
Q

Antibodies/Immunoglobulins

A

proteins made by B cells to neutralize targets in the body like toxins/bacteria and recruit other cells to destroy them

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17
Q

___ hold the heavy and light side chains of antibodies togehter

A

disulfide linakges

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18
Q

Antigen binding Region

A

Tips of the Y that bind to a specigic antigenic sequence

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19
Q

Constant Region

A

part of antibody thT RECRUITS AND BINDS CELLS OF IMMUNE SYSTEM LIKE MACROPHAGES

20
Q

Three Outcomes of Antigen Binding

A

1) Neutralizing Antigen
2) Making pathogen for destruction by other blood cells immediately (Opsonization)
3) Agglutinating antigen and antibody into insoluble complex to phagocitize

21
Q

Biosignaling

A

process in whcih cells receive and act on signals

EC ligands, transporters for facilitated diffusion, receptor proteins, second messengers

22
Q

Facilitated Diffusion

A

passive transport

diffusion down a gradient through pore in transmembrane

allow molecules to avoid the fatty chains of membrane

23
Q

Ungated Channels

A

unregulated

no gates

potassium channels

net efflux of ions unless at eq

24
Q

Voltage-Gated Channels

A

gate is regulated by membrane potential

neruons with sodium channels

depolarization causes a change to let them open

non specific Na/K channels in sinoatrial node of heart as pacemaker current

25
Q

Ligand-Gated Channels

A

binding to a specific substance or ligand to cause channel to open or close

neurotransmitters

Km and vmax of enzymes apply here too

26
Q

Enzyme Linked Receptors

A

three primary protein domains

membrane spanning - anchors receptor

ligand binding - stimulated by ligand yo induce change

catlyitc activateed by ligand binding domain changing

leads to second messenger cascafe

27
Q

G Protein Coupled Receptors

A

family of integral membrane proteins involved in signal transduction

characterized by 7 alpha helices

receptors differ in specificity of the ligand binding area on extracellular surface

28
Q

Heterotrimeric G Protein

A

g proteins for GPCR with intracellular link GDP/GTP

29
Q

Three Types G Protein

A

Gs - stimulate adenylate cyclase to increase cAMP

Gi - inhibit adenylate cyclase to decrease cAMP
Gq - activates phospholipase C to leave phospholipid from PIP 2 to cleave from DAG and IP3 which then opens calcium channels

30
Q

alpha beta and gamma subunits of G protein

A

alpha binds to GDP and is complex with B and gamma

when ligand binds to G protein, receptor is activasted and engages corresponding G protein

GDp replaced with GTP and alpha dissociate from beta and gamma

alpha alters adenylate cyclase activity

alpha s activates

alpha i enzyme is inhibited

once GTP on alpha is dephosphorylated alpha will go back to B and hgamma and inactivate the protein

31
Q

Centrifugation

A

isolate proteins from smaller molecules before other isolation techniques

32
Q

Electrophoresis

A

moves protein according to net charge and size

velocity is migration velocity

v = Ez/ f

E = e;ectroc field strength
f = frictional coefficient
z = net charge
33
Q

Poly acrylamide Gel

A

used in electrophoresis

small go fast, large go slow

34
Q

Native PAGE

A

mass to charge and mass to size ratios

molecular size and charge of proteins

35
Q

SDS-PAGE

A

sodium dodecyyl sulfate

proteins seperated on mass

SDS disrupts non covalent interactions and negative charges

only E affects velocity

36
Q

Isoelectric Focusing

A

seperation by isoelectric point pI

pH when protein is neutal

for individual amino acids this is zwitterion phase

37
Q

Chromatography

A

fractioned through a porous matrix

seperated by chemical and physical properties

38
Q

Stationary Phase Adsorbant

A

sasmple on solid medium

mobile phase for sample to elute out of

39
Q

Column Chromatography

A

size and polarity have to role with how quickly compound goes

less polar, the faster it goes

pH, salinity, polarity

40
Q

Ion Exchange CHromatography

A

charged beads

attract/bind opposin charge

after all compounds are gone, salt is used to compete with charged protein to elute it out

41
Q

Szie Exclusion Chromatography

A

beads have pores allowing small compounds to elute out slowly and large ones to elute out faster

different MW are key here

42
Q

Affinity Chromatography

A

coating stationary beads with item that has affinity for target like nickel for histags, antibodies, enzyme substrate,

target is then washed off using elutant that competes for affinity of target letting it elute out

eluent can also be certain pH or salinity to rid of ligand interaction on beads

43
Q

X Ray Crystallography

A

protein is isolated and crystalized

measures electron density and generates a pattern of dots to determine structure

44
Q

Nuclear Magnetic Resonance

A

protein structure

45
Q

Edman Degradation

A

small protein analysis of AMINO ACIDS

CLEAVAGE TO SEQ PROTEINS OF 50-70

protein hydrolysis

removes N terminal amino acid one at a time

46
Q

Chymotrypsin, TrypsinCyanogen Bromide

A

selectively cleaves proteins at specific amino acid residues to create smaller fragment for Edman/Gel electrophoresis

positions cannot be determines as disulfide/salt bridges are broken

47
Q

Bradford Protein Assay

A

mixes protein in solution with coomassie blue dye

dye gives protons to ionizable groups in protein to turn blue

increase protein concentrations have larger concentration of blue dye

standard curve created measuring absorbance and then unknown

only one protein is effective

Biochemistry (5 decks)

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