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MCAT BIochem > Nonenzymatic Protein & Protein Analysis > Flashcards

Nonenzymatic Protein & Protein Analysis Flashcards

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MCAT flashcards
1
Q

What is the common structure of many structural proteins?

A

Highly repetitive motifs of secondary structure & a supersecondary structure-fibrous nature

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2
Q

Motif

A

A repetitive organization of secondary structural elements together

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3
Q

Collagen

A

Trihelical fiber- three left-handed helices woven together to form a secondary right-handed helix
Makes up most of the extracellular matrix of connective tissue
Strength & flexibility

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4
Q

Elastin

A

Stretch & recoil importance

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5
Q

Keratin

A

Intermediate filaments in epithelial cells

Hair & nails

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6
Q

Actin

A

Makes up microfilaments and thin filaments in myofibrils

Have polarity so motor proteins can move down them unidirectionally

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7
Q

What protein is the most abundant in the body?

A

Actin

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8
Q

Tubulin

A

Makes up microtubules-structure, choromosome separation & intracellular transport with kinesin & dyein
Polarity- (+) toward the periphery of the cell

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9
Q

Motor proteins

A

Act as ATPases that power conformational change necessary for motor function
Transient interactions with actin or microtubules

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10
Q

What are examples of motor proteins

A

Myosin

Kinesins & Dyeins

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11
Q

Kinesin & dyneins

A

Associated with microtubules

Have two heads and at least one remains attached to tubulin at all times

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12
Q

Kinesin

A

Aligns chromosomes during metaphase and depolymerization of microtubules during anaphase

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13
Q

Dyneins

A

Involved in sliding movement of cilia & flagella

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14
Q

Different in vesicle transport of kinesin & dynein

A

Kinesin- bring vesicles toward positive end

Dynein-Toward negative end

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15
Q

Examples of binding proteins

A

Hemoglobin, calcium-binding proteins, DNA-binding proteins

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16
Q

Cell adhesion molecules (CAMs)

A

Proteins on the surface of most cells and aid in binding the cell to the extracellular matrix or other cells

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17
Q

What kind of proteins are CAMs?

A

Integral membrane proteins

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18
Q

Cadherins

A

Group of glycoproteins that mediate calcium-dependent cell adhesion
Hold similar types of cells together

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19
Q

Integrins

A

Have alpha and Beta membrane spanning chains
Important to binding to & communicating with the extracellular matrix
Cell signaling

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20
Q

Selectins

A

Bind to carbohydrate molecules that project from other cell surfaces
Expressed on white blood cells & endothelial cells lining blood vessels- important in defense

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21
Q

Antibody/Immunoglobulin (Ig) are produced by?

A

B-cells that function to neutralize targets in the body like toxins & bacteria & recruit other cells to help

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22
Q

How many chains do antibodies/immunoglobulins have?

A

Two heavy chains and two light chains

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23
Q

What are targets of antibodies?

A

Antigens

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24
Q

What is the constant region of the antibody involved in/?

A

Recruitment & binding of other cells like macrophages

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25
Q

What are the three outcomes of antibody binding?

A
  1. )Antigen neutralization
  2. )Opsonization- marking pathogen for destruction by other wbcs
  3. ) Agglutination- clump together antigen & antibody into large insoluble protein complexes that can be digested by macrophages
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26
Q

Opsonization

A

Marking pathogen for destruction by other wbcs

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27
Q

What phagocytizes agglutinated antigen & antibodies?

A

Macrophages

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28
Q

Which domain on antibody binds to the antigen

A

V domain

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29
Q

Which domain on antibody is constant?

A

C domain

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30
Q

What part of the antibody has a variable domain?

A

The light chain, V domain

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31
Q

Electrophoresis

A

Subject compounds to electric field & move them according to net charge & size

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32
Q

What does anions (negatively charged ) move towards?

A

Anode

33
Q

What do cations (positively charged) move towards

A

Cathodes

34
Q

Migration velocity equation

A

v=Ez/f

z=net charge on molecule
f=frictional coefficient (depends on mass & shape

35
Q

Polyacrylyamide gel

A

Porous & acts a sieve, allows smaller molecules to move toward anode

36
Q

Native PAGE

A

Polyacrylamide gel electrophoresis
Useful to compare molecular size or charge of proteins known to be similar in size from other analytic methods like SDS-page or size-exclusion chromatography
Limited by varying mass-to-charge & mass-to-side ratios

37
Q

SDS- PAGE

A

Sodium dodecyl sulfate(SDS)
Separates proteins on basis of mass alone
SDS disrupts all non-covalent interactions & denature them
Only affected by E & f

38
Q

Isoelectric focusing

A

Proteins separated by isoelectric point (pI)
When protein has equal number of positive & negative charges- zwitterion
Proteins in a gel with a pH gradient
When pH moves to point where pH=pI, it stops moving

39
Q

How is concentration usually determined?

A

UV spec

40
Q

Other concentration determining tests?

A

Bichoninic acid (BCA) assay, Lowry reagent assay, Bradford protein assay

41
Q

Bradford protein assay

A

Mixes protein in solution with Coomassie Bradford Blue dye-dye gives up protons to ionizable groups of the protein turning the protein blue
More blue=more protein
Absorbance measured

42
Q

When is Bradford protein assay most accurate?

A

When only one type of protein is in the sample

43
Q

The stationary phase of chromotography is ?

A

Polar

44
Q

Biosignaling

A

Cells receive & act on signals

45
Q

Ion channels

A

Proteins that create specific pathways for charged molcules

46
Q

Facilitated diffusion

A

A type of passive transport that is diffusion of molecules down a concentration gradient through a pore in the membrane created by a transmembrane protein
For molecules impermeable (large, polar or charged)

47
Q

Ungated channel

A

No gates & are unregulated

48
Q

Voltage-gated channels

A

Gate is regulated by the membrane potential change near the channel

49
Q

Ligand-Gated Channels

A

Binding of a specific substance or ligand to channel causes it to open or close
Neurotransmitters

50
Q

Enzyme-linked receptor

A

Shows catalytic activity in response to ligand binding

51
Q

Membrane-spanning domain

A

Anchors receptor in cell membrane

52
Q

Ligand-binding domain

A

Stimulated by the appropriate ligand & induces a conformational change that activates the catalytic domain

53
Q

Example of a second messenger cascade

A

Receptor tyrosine kinases
A monomer dimerizes upon ligand binding & phosphoylates additional cellular enzymes & autophosphorylates the receptor

54
Q

G Protein coupled receptor

A

Integral membrane proteins involved in signal transduction

Have 7 membrane spanning a-helices

55
Q

Heterotrimeric G protein

A

Used by G protein coupled receptors to transmit signals to an effector cell

56
Q

Gs G protein

A

Stimulates adenylate cyclase which increases cAMP

57
Q

Gi G Protein

A

Inibits adenylate cyclase which decreases cAMP levels

58
Q

Gq G protein

A

Activates phospholipase C to make DAG & IP3 to open calcium channels in the ER to increase Ca2+ cell levels

59
Q

What subunit stimulates adenylate cycylase?

A

alpha s

60
Q

What subunit inhibits adenylate cyclase?

A

alpha i

61
Q

Homogenization

A

Crushing, grinding, blending tissue of interest into even solutions to isolate proteins or other biomolecules

62
Q

Centrifugation

A

Isolate proteins from smaller molecules before other isolation techniques

63
Q

What common techniques are used for protein isolation?

A

Electrophoresis & Chromotography

64
Q

What kind of cell is used in electrophoresis

A

Electrolytic, nonspontaneous
Delta G >0
E<0

65
Q

Chromatography

A

Uses physical and chemical properties to separate and identify compounds from a complex mixture
Fractioning through a porous material

66
Q

When is chromotography preferred?

A

When large amounts of protein are being separated

67
Q

Stationary phase/ absorbent

A

Solid, more polar phase

68
Q

Elution

A

Allowing mobile phase to rune through the stationary phase

69
Q

Retention time

A

Amount of time a compound spends in the stationary phase

70
Q

Column Chromatography

A

Column is filled with silica or alumina beads as absorbent and gravity moves solvent and compounds down the column
Size and polarity play roles in elution

71
Q

Ion-exchange chromatography

A

Beads in the column are coated with charged substances so they attract or bind compounds with opposite charge
Salt gradient is used to elute charged molecules stuck to the column

72
Q

Size-Exclusion Chromatography

A

Beads in column contain tiny pores of varying sizes that allow small compounds to enter beads & slow them down
Large compounds move faster & drain out

73
Q

Affinity Chromatography

A

Column with a high affinity for a certain protein
Using a receptor protein or specific antibody so protein stays in column
Can be difficult to separate elutant binding molecule out of the recovered substance

74
Q

X-ray crystallography

A

Most common & reliable method

Measures electron density on a high resolution scale

75
Q

What is used to determine protein structure?

A

X-ray crystallography and NMR spec

76
Q

Why can’t amino acids be easily sequenced?

A

Random nature of hydrolysis would not work, must have sequential digestion with specific cleavage enzymes

77
Q

Edman degradation

A

Selectively and sequentially removes the N-terminal amino acids of a proteins that are small (50-70 amino acids) and analyzes them with mass spec

78
Q

What can be used to breakdown larger proteins?

A

Chymotrypsin, trypsin, cyanogen bromide

MCAT BIochem (8 decks)

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