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MCAT > Nonenzymatic protein function and protein analysis > Flashcards

Nonenzymatic protein function and protein analysis Flashcards

1
Q

Motif

A

Repetitive organization of secondary structural elements

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2
Q

Collagen

A
  • Extracellular of connective tissue
  • trihelical fiber
  • strength and fiber
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3
Q

Elastin

A

-Extracellular of connective tissue

Stretch and recoil like a spring

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4
Q

Keratin

A
  • Intermediate filaments in epithelial cells
  • mechanical integrity of cells
  • regulatory proteins
  • hair and nails
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5
Q

Actin

A
  • Subunit of microfilaments

- Have + and - ends which allow for unidirectional travel for motor proteins

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6
Q

Tubulin

A
  • Subunit of microtubules
  • Intracellular transport with kinesin and dynesin
    • end is near nucleus and + end is near periphery of cell
  • also involved in structure and chromosome seperation
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7
Q

Myosin

A

Interacts with actin in myofibrils, has one head and one neck

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8
Q

Kinesin and dyneins have how many heads?

A

2 of which one is atleast attached to tubulin

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9
Q

Kinesins

A
  • move to + end
  • align chromosomes in metaphase and depolymerizing microtubules during anaphase of mitosis
  • In neurons, bring besicles to synaptic terminal
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10
Q

Dyneins

A
  • move to - end

- in neurons bring waste or recycled nuerotransmitters to soma (retrograde transport)

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11
Q

Binding proteins

A

Bind to a specific substrate, either to sequester it in body or hold it at steady concentrations

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12
Q

Cadherins

A
  • Glycoproteins that are calcium dependent
  • hold similar tissues together
  • specific tissues have specific cadherins
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13
Q

Integrins

A
  • Bind and communicate with extracellular matrix
  • have a role in cell signaling, cell division, apoptosis, and other processes
  • have 2 membrane-spanning chains alpha and beta
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14
Q

Selectins

A
  • Bind to carbohydrate molecules outside of other cells
  • Found on white blood cells and endothelial cells of blood vessels
  • Host defense, inflammation, white blood cell migration
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15
Q

Antibodies

A

Immunoglobins (Ig) made by B cells

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16
Q

Shape and structure of anitbodies

A

Y shaped with two heavy and two light chains held together by disulfide and noncovalent bonds

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17
Q

Antigen-binding site

A

At tips of “Y”, specific polypeptide sequence that binds to one antigenic sequence

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18
Q

Constant region

A

Recruits and binds immune cells eg macrophages

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19
Q

Antibodies neutralize antigen –> effect?

A

Antigens unable to exert effect on body

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20
Q

Opsonization

A

Antibodies mark antigen for destruction by white blood cells

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21
Q

Agglutinating

A

Antibodies clump antigen and antibody into insoluble complex to be phagocytosed and digested by macrophages

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22
Q

Facilitated diffusion

A

Passive transport where diffusion is down a gradient through a pore created by transmembrane protein

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23
Q

Are ungated channels regulated?

A

No

24
Q

Voltage-gated channels

A

Gated by membrane potential near channel

25
Q

Ligand gated channels

A
  • Binding of specific substance/ligand can open or close channels
  • Can use Michealis-Menten and Lineweaver Burke plots for this as well
26
Q

G protein coupled receptors

A

Heterotrimeric G protein. A ligand binds to a receptor and that receptor binds to G protein to activate it

27
Q

Gs

A

Stimulates adenylate cyclase to increase cAMP

28
Q

Gi

A

Inhibits adenylate cyclase to decreases cAMP

29
Q

Gq

A

Activates phospholipase C to increase intercellular Ca2+ concentration

30
Q

Phospholipase C

A

It cleaves a phospholipid to form PIP2 which is then cleaved to DAG and IP3. IP3 opens up calcium channels in ER

31
Q

IP3

A

Opens up calcium channels in ER

32
Q

Inactive GPCR

A

Has α, β,γ subunits together and α is bound to GDP

33
Q

What happens to GPCR when a ligand binds to a receptor that binds to GPCR?

A

GDP is replaced with GTP and α subunit dissociates. α subunit alters activity of adenylyl cyclase.

34
Q

How is the GCPR signal cascade turned off?

A

GTP is hydrolyzed to GDP and the α subunit binds to beta and gamma subunits to make G protein inactive.

35
Q

Electrophoresis

A

Subject molecules to electric field and move them accordingly to net charge and size

36
Q

Polyacrylamide gel

A

It is a slightly pourous mixture. Larger and electrically neutral move slower than smaller and charged.

37
Q

Native PAGE

A
  • Analyze proteins in native charge
  • can compare similar size molecules based on size or charge
  • Stain
38
Q

What happens to protein if you stain the native PAGE?

A

It denatures and cannot be recovered.

39
Q

SDS-PAGE

A
  • Seperates by molecular mass
  • SDS (detergent) disrupts noncovalent interactions and surrounds proteins with negative charge
  • Stain to visualize bands afterwards
40
Q

Isoelectric focusing

A

A mixture of proteins is placed in a gel with pH graident and then electric field placed. Positively charged proteins move to cathode and negative charged proteins move to anode. They will stop at their pI and become neutral.

41
Q

Dalton

A

g/mol

42
Q

Chromatography

A
  1. Place sample on stationary phase/adsorbent
  2. Run mobile phase for sample to run through stationary phase or elute
  3. Components with high affinity for stationary move slower
43
Q

Retention time

A

Time spent in stationary phase

44
Q

Column chromatography

A

Adsorbent is polar silica or alumina beads. Size and polarity determine speed. Each fraction’s solvent can be evaporated to keep compound of interest.

45
Q

Ion-exchange chromatography

A

Beads have charged substances and they bind to attractive charges. You elute with salt gradient.

46
Q

Size-exclusion chromatography

A

Beads are porous which capture smaller molecules and slow them down. Larger molecules move faster.

47
Q

Nickel has high affinity for ?

A

Histidine tags

48
Q

Affinity chromatography

A

Beads are coated with a receptor. Eluent can be free receptor but it will be harder to seperate protein from eluent later on. It can also have varying pH pr salinity level to disrupt protein-bead interactions.

49
Q

X-ray crystallography

A

Protein is isolated, crystallized, and measured for electron density. Patterns are interpreted for structure

50
Q

Hydrolysis to study protein structure

A

Can tell you about amino acid composition but nothing about sequence

51
Q

Edman degradation

A

Sequential digestion of proteins (50-70 AA). It selectively and sequentially removes the N-terminal AA, which can be analyzed via mass spectroscopy

52
Q

Can you find location of disulfide bonds through electrophoresis?

A

No, because they are broken down.

53
Q

How do you determine protein activity?

A

Looking at how it affects a known reaction, often accompanied by color change

54
Q

How can you analyze aromatic amino acids?

A

UV spectroscopy

55
Q

Bradford Protein Assay

A

It is initially green-brown and is protonated. It gives up protons to amino acids in proteins and turns blue. If there is more than one protein, this test is not accurate.

MCAT (18 decks)

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