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MCAT BIochem > Nonenzymatic Protein & Protein Analysis > Flashcards

Nonenzymatic Protein & Protein Analysis 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
What are the three outcomes of antibody binding?
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
26
Opsonization
Marking pathogen for destruction by other wbcs
27
What phagocytizes agglutinated antigen & antibodies?
Macrophages
28
Which domain on antibody binds to the antigen
V domain
29
Which domain on antibody is constant?
C domain
30
What part of the antibody has a variable domain?
The light chain, V domain
31
Electrophoresis
Subject compounds to electric field & move them according to net charge & size
32
What does anions (negatively charged ) move towards?
Anode
33
What do cations (positively charged) move towards
Cathodes
34
Migration velocity equation
v=Ez/f z=net charge on molecule f=frictional coefficient (depends on mass & shape
35
Polyacrylyamide gel
Porous & acts a sieve, allows smaller molecules to move toward anode
36
Native PAGE
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
SDS- PAGE
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
Isoelectric focusing
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
How is concentration usually determined?
UV spec
40
Other concentration determining tests?
Bichoninic acid (BCA) assay, Lowry reagent assay, Bradford protein assay
41
Bradford protein assay
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
When is Bradford protein assay most accurate?
When only one type of protein is in the sample
43
The stationary phase of chromotography is ?
Polar
44
Biosignaling
Cells receive & act on signals
45
Ion channels
Proteins that create specific pathways for charged molcules
46
Facilitated diffusion
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
Ungated channel
No gates & are unregulated
48
Voltage-gated channels
Gate is regulated by the membrane potential change near the channel
49
Ligand-Gated Channels
Binding of a specific substance or ligand to channel causes it to open or close Neurotransmitters
50
Enzyme-linked receptor
Shows catalytic activity in response to ligand binding
51
Membrane-spanning domain
Anchors receptor in cell membrane
52
Ligand-binding domain
Stimulated by the appropriate ligand & induces a conformational change that activates the catalytic domain
53
Example of a second messenger cascade
Receptor tyrosine kinases A monomer dimerizes upon ligand binding & phosphoylates additional cellular enzymes & autophosphorylates the receptor
54
G Protein coupled receptor
Integral membrane proteins involved in signal transduction | Have 7 membrane spanning a-helices
55
Heterotrimeric G protein
Used by G protein coupled receptors to transmit signals to an effector cell
56
Gs G protein
Stimulates adenylate cyclase which increases cAMP
57
Gi G Protein
Inibits adenylate cyclase which decreases cAMP levels
58
Gq G protein
Activates phospholipase C to make DAG & IP3 to open calcium channels in the ER to increase Ca2+ cell levels
59
What subunit stimulates adenylate cycylase?
alpha s
60
What subunit inhibits adenylate cyclase?
alpha i
61
Homogenization
Crushing, grinding, blending tissue of interest into even solutions to isolate proteins or other biomolecules
62
Centrifugation
Isolate proteins from smaller molecules before other isolation techniques
63
What common techniques are used for protein isolation?
Electrophoresis & Chromotography
64
What kind of cell is used in electrophoresis
Electrolytic, nonspontaneous Delta G >0 E<0
65
Chromatography
Uses physical and chemical properties to separate and identify compounds from a complex mixture Fractioning through a porous material
66
When is chromotography preferred?
When large amounts of protein are being separated
67
Stationary phase/ absorbent
Solid, more polar phase
68
Elution
Allowing mobile phase to rune through the stationary phase
69
Retention time
Amount of time a compound spends in the stationary phase
70
Column Chromatography
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
Ion-exchange chromatography
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
Size-Exclusion Chromatography
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
Affinity Chromatography
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
X-ray crystallography
Most common & reliable method | Measures electron density on a high resolution scale
75
What is used to determine protein structure?
X-ray crystallography and NMR spec
76
Why can't amino acids be easily sequenced?
Random nature of hydrolysis would not work, must have sequential digestion with specific cleavage enzymes
77
Edman degradation
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
What can be used to breakdown larger proteins?
Chymotrypsin, trypsin, cyanogen bromide

MCAT BIochem (8 decks)

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