Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

MCAT: Biochemistry > Chapter 3: Nonenzymatic Protein Function and Protein Analysis > Flashcards

Chapter 3: Nonenzymatic Protein Function and Protein Analysis Flashcards

You may prefer our related Brainscape-certified flashcards:
MCAT flashcards
1
Q

What do structural proteins compose?

A

The cytoskeleton, anchoring proteins, and much of the extracellular matrix

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What are the 5 most common structural proteins?

A
  • Collagen
  • Elastin
  • Keratin
  • Actin
  • Tubulin
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Structural proteins are generally _____ by nature

A

fibrous

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What gives structural proteins their fibrous nature?

A

Highly repetitive secondary structure and supersecondary structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is supersecondary structure? What is it sometimes known as?

A
  • Motif

- Repetitive organization of secondary structural elements together

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What is the structure of collagen?

A

Three a-helices woven together to form a secondary helix

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

_______ and _____ make up most of the extracellular matrix of connective tissue

A

Collagen and elastin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is the primary role of elastin?

A

To stretch and then recoil like a spring, which restores the original shape of the tissue

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

In which cells are keratins found?

A

Epithelial cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

____ is the primary protein that makes up hair and nails

A

Keratin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is the primary role of keratin?

A
  • Contributes to the mechanical integrity of the cell

- Functions as regulatory proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is the most abundant protein in eukaryotic cells?

A

Actin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Which protein makes up microfilaments and thin filaments in myofibrils?

A

Actin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Actin has a + and a - side; this polarity allows for what?

A

Allows motor proteins to travel unidirectionally along an actin filament

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Which protein makes up microtubules?

A

Tubulin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Which two structural proteins have polarity?

A

Actin and tubulin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What is the characteristic of motor proteins that allow them to move?

A

Have one or more heads capable of force generation through a conformational change

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

How do motor proteins have catalytic activity? What does that power?

A

Acting as ATPases to power movement

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Name the most common applications of motor proteins.

A
  • Muscle contraction
  • Vesicle movement within cells
  • Cell motility
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What are the three common examples of motor proteins?

A
  • Myosin
  • Kinesin
  • Dynein
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Motor proteins have transient interactions with either _____ or _____

A

actin or microtubules

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What is the primary motor protein that interacts with actin?

A

Myosin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Which protein is the thick filament in a myofibril?

A

Myosin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What is responsible for the power stroke of sarcomere contraction?

A

Movement at the neck of myosin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What is myosin also involved in, apart from muscle contraction?

A

Cellular transport

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Which two motor proteins are associated with microtubules?

A

Kinesins and dyneins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

How many heads and necks does myosin have?

A
  • One head

- One neck

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

How many heads and necks do kinesins and dyneins have?

A
  • Two heads, at least one remains attached to tubulin at all times
  • 0 necks
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

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

A

Kinesins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

____ are involved in the sliding movement of cilia and flagella.

A

Dyneins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

Kinesins bring vesicles toward the _____ end of the microtubule, and dyneins bring vesicles toward the ____ end.

A

Kinesins: +
Dyneins: -

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

What is the role of binding proteins?

A

Bind a specific substrate, either to sequester it in the body or hold its concentration at steady state

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

The oxyhemoglobin dissociation curve is an example of what?

A

A binding protein’s affinity curve for its molecule of interest

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Give examples of binding proteins.

A

Hemoglobin, calcium-binding proteins, DNA-binding proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Where are cell adhesion molecules (CAMs) found?

A

Proteins found on the surface of most cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What is the primary role of CAMs?

A

Aid in the binding of the cell to the extracellular matrix or other cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

What kind of membrane proteins are CAMs?

A

Integral membrane proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

What are the three major families of CAMs?

A
  • Cadherins
  • Integrins
  • Selectins
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

Cadherins are a group of ______ that mediate ____-dependent cell adhesion.

A
  • glycoproteins

- calcium

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

______ often hold similar cell types together.

A

Cadherins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

______ are a group of proteins that all have two membrane-spanning chains called _ and _.

A
  • Integrins

- a and B

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

What is the major role of integrins?

A
  • Permit cells to adhere to proteins in the extracellular matrix
  • Some also have signalling capabilities
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

Selectins are unique because they bind _________ molecules that project from other cell surfaces.

A

carbohydrates

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

Which bonds are the weakest formed by the CAMs?

A

Selectins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

Where are selectins expressed?

A

White blood cells and endothelial cells that line blood vessels

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

What is the major role of selectins?

A

Host defense, including inflammation and white blood cell migration (immune system)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

What is the most common type of protein found in the immune system?

A

Antibody

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

What are antibodies also called?

A

Immunoglobulins (Ig)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

What are antibodies produced by?

A

B-cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

What is the structure of antibodies?

A
  • Y-shaped proteins
  • 2 identical heavy chains
  • 2 identical light chains
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

What hold the heavy and light chains in antibodies together?

A

Disulfide linkages and noncovalent interactions

52
Q

Where is the antigen-binding region on an antibody? What does it bind to?

A
  • At the tips of the “Y”

- Polypeptide sequences will bind to ONE specific antigenic sequence

53
Q

What are the two main regions on the antibody?

A
  • Antigen-binding region

- Constant region

54
Q

What is the role of the constant region in an antibody?

A

Involved in recruitment and binding of other cells of the immune system (ex: macrophages)

55
Q

What are the targets of antibodies called?

A

Antigens

56
Q

When antibodies bind to their antigens, what are the three possible outcomes?

A

1) Neutralizing the antigen, making the pathogen or toxin unable to exert its effect on the body
2) Opsonization
3) Agglutinating

57
Q

What is opsonization?

A

Marking the pathogen for destruction by other white blood cells immediately

58
Q

What is agglutinating?

A

Clumping together the antigen and the antibody into large insoluble protein complexes that can be phagocytized and digested by macrophages

59
Q

Which two proteins function in cellular motility?

A

Cytoskeletal (structural) and motor proteins

60
Q

Are motor proteins enzymes?

A

Yes, they can be
Motor function is generally considered nonenzymatic, but the ATPase functionality of motor proteins indicates that these molecules do have catalytic activity

61
Q

What could permit a binding protein involved in sequestration to have a low affinity for its substrate and still have a high percentage of substrate bound?

A

If the binding protein is present in sufficiently high quantities relative to the substrate, nearly all the substrate will be bound despite a low affinity

62
Q

Which CAM does this description correspond to: two cells of the same or similar type using calcium

A

Cadherin

63
Q

Which CAM does this description correspond to: one cell to proteins in the extracellular matrix

A

Integrin

64
Q

Which CAM does this description correspond to: one cell to carbohydrates, usually on the surface of other cells

A

Selectin

65
Q

Define biosignaling.

A

Process in which cells receive and act on signals

66
Q

Acting as extracellular ligands, transporters for facilitate diffusion, receptor proteins, and second messengers are example of what process?

A

Biosignaling

67
Q

Can biosignaling have functions in both substrate binding and enzymatic activity?

A

Yes

68
Q

What are ion channels?

A

Proteins that create specific pathways for charged molecules

69
Q

What is facilitated diffusion?

A
  • Type of passive transport
  • Diffusion of molecules down a concentration gradient through a pore in the membrane created by integral membrane proteins, which serve as channels for these substrates
70
Q

What kind of substrates pass through facilitated diffusion?

A
  • Molecules that are impermeable to the membrane
  • Large, polar, or charged
  • Avoid the hydrophobic FA tails of the phospholipid bilayer
71
Q

Name the three types of ion channels.

A

1) Ungated
2) Voltage-gated
3) Ligand-gated

72
Q

What are ungated ion channels?

A
  • Always open

- Net efflux through these channels unless substrate is at equilibrium

73
Q

What are voltage-gated channels?

A
  • Open within a range of membrane potentials

- ex: membrane depolarization in neurons allows voltage-gated channels to open

74
Q

How are ligand-gated channels opened?

A

Open in the presence of a specific binding substance

75
Q

What kind of substances can open a ligand-gated channel?

A

Hormone or neurotransmitter

76
Q

In terms of kinetics of transport, what is Km?

A

Solute concentration at which the transporter is functioning at half of its maximum activity

77
Q

How do enzyme-linked receptors participate in cell signalling?

A

Through extracellular ligand binding and initiation of second messenger cascades

78
Q

What are the three primary domains of enzyme-linked receptors?

A
  • Membrane-spanning domain
  • Ligand-binding domain
  • Catalytic domain
79
Q

What does the membrane-spanning domain do in enzyme-linked receptors?

A

Anchors the receptor in the cell membrane

80
Q

What does the ligand-binding domain stimulated by in enzyme-linked receptors? What does it induce?

A
  • Stimulated by the appropriate ligand

- Induces a conformational change that activates the catalytic domain

81
Q

When the catalytic domain of an enzyme-linked receptor is activated, what does this result in?

A

Second messenger cascade

82
Q

What are G protein-coupled receptors (GPCRs)?

A
  • Large family of integral membrane proteins, involved in signal transduction
  • Have a membrane-bound protein associated with a trimeric G protein
83
Q

How are GPCRs characterized?

A

By their seven membrane-spanning a-helices

84
Q

How do GPCRs differ?

A

In specificity of the ligand-binding area found on the extracellular surface of the cell

85
Q

In order for GCPRs to transmit signals to an effector in the cell, what do they utilize?

A

Heterotrimeric G protein

86
Q

Explain the trimeric G protein cycle.

A
  • Ligand binding engages the G protein
  • GDP is replaced with GTP; the a subunit dissociates from the B and g subunits
  • The activated a subunit alters the activity of adenylate cyclase or phospholipase C
  • GTP is dephosphorylated to GDP; the a subunit rebinds to the B and g subunits
87
Q

What are the three main types of G proteins?

A
  • Gs
  • Gi
  • Gq
88
Q

What is the role of Gs?

A

Stimulates adenylate cyclase, which increases levels of cAMP in the cell

89
Q

What is the role of Gi?

A

Inhibits adenylate cyclase, which decreases levels of cAMP in the cell

90
Q

What is the role of Gq?

A
  • Activates phospholipase C, which cleaves a phospholipid from the membrane to from PIP2
  • PIP2 is then cleaved into GAD and IP3
  • IP3 can open calcium channels in the endoplasmic reticulum, increasing calcium levels in the cell
91
Q

What are the similarities between enzyme-linked receptors and G protein-coupled receptors?

A
  • Extracellular domain
  • Transmembrane domain
  • Ligand binding
92
Q

What are the differences between enzyme-linked receptors and G protein-coupled receptors?

A
  • Enzyme-linked receptors: autoactivity, enzymatic activity
  • G protein-coupled receptors: two-protein complex, dissociation upon activation
  • Trimer
93
Q

How do transport kinetics differ from enzyme kinetics?

A
  • Transport kinetics display both Km and vmax values
  • They can also be cooperative, like some binding proteins
  • Transporters do not have analogous Keq values for reactions because there is no catalysis
94
Q

How are proteins and other biomolecules isolated from body tissues or cell cultures?

A

By cell lysis and homogenization (crushing, grinding, or blending the tissue of interest into an evenly mixed solution)

95
Q

How does electrophoresis work? What does it separate on the basis of?

A
  • Subjecting compounds to an electric field

- Moves them according to their net charge and size

96
Q

What is the velocity of migration equation for electrophoresis?

A

v = Ez/f
where E is the electric field strength
z is the net charge on the molecule
and f is the frictional coefficient

97
Q

What is the standard medium for protein electrophoresis?

A

Polyacrylamide gel

98
Q

Which compounds move faster in electrophoresis? Which compounds move slower?

A

Faster: small, highly charged, or placed in a large electric field
Slower: bigger, more convoluted, or electrically neutral

99
Q

What is the advantage and disadvantage of PAGE electrophoresis?

A
  • Maintains the proteins shape

- Results are difficult to compare because the mass-to-charge ratio differs for each protein

100
Q

What is the advantage and disadvantage of SDS-PAGE electrophoresis?

A
  • Denatures the protein and masks the native charge so that comparison of SIZE is more accurate
  • Functional protein cannot be recaptured
101
Q

What is PAGE useful for?

A

Compare the size or the charge of proteins KNOWN to be similar in size from other analytical methods

102
Q

What does SDS do to proteins? What is the only variable affecting their velocity?

A
  • Denatures them, and creates large chains with net negative charges
  • Frictional coefficient, which is only affected by mass
103
Q

What is pI?

A

The pH at which the protein or amino acid is electrically neutral, with an equal number of positive and negative charges

104
Q

What is isoelectric focusing?

A
  • Protein placed in a gel with a pH gradient (acidic +, neutral, basic -)
105
Q

In isoelectric focusing, where do positively charged proteins migrate? Where do negatively charged proteins migrate?

A

Positive: cathode (-)
Negative: anode (+)
* A+ : Anode has acidic (H+ rich) gel and a (+) charge

106
Q

How do chromatography techniques separate protein mixtures?

A

On the basis of their affinity for a stationary or a mobile phase

107
Q

Which chromatography technique is not about the affinity of a substance for the mobile and stationary phases?

A

Size-exclusion chromatography

108
Q

The amount of time a compound spends in the stationary phase is referred to as what?

A

Retention time

109
Q

What is the stationary phase in column chromatography? What is the mobile phase?

A

Stationary: beads of a polar compound (silica or alumina)
Mobile: nonpolar solvent

110
Q

Column chromatography separates on the basis of what?

A

Size and polarity

111
Q

What is ion-exchange chromatography?

A

Uses a charged column and a variably saline eluent. The column will bind opposite charged compounds

112
Q

What is size-exclusion chromatography?

A

Relies on porous beads; larger molecules elute first because they are not trapped in the small pores

113
Q

What is affinity chromatography?

A

Uses a bound receptor or ligand and an eluent with free ligand or a receptor for the protein of interest

114
Q

What are the two potential drawbacks of affinity chromatography?

A

1) Protein of interest may not elute from the column because its affinity is too high
2) Can be permanently bound to the free receptor in the eluent

115
Q

Protein structure is primarily determined through ____________ after the protein is isolated, though ____ can also be used

A
  • X-ray crystallography - 75%

- Nuclear Magnetic Resonance (NMR) - 25%

116
Q

How does X-ray crystallography work?

A
  • Protein must be isolated and crystallized
  • Measures electron density
  • X-ray diffraction pattern is generated; the dots can be interpreted to determine the protein’s structure
117
Q

How can amino acid composition be determined?

A

By simple hydrolysis and subsequent chromatographic analysis

118
Q

How can amino acid sequencing be determined?

A

Sequential degradation, such as the Edman degradation

119
Q

How can amino acid composition be determined for larger proteins?

A

Digestion with a synthetic reagent (ex: chymotrypsin) creates smaller fragments which can then be analyzed by electrophoresis

120
Q

How is protein activity determined?

A

Monitoring a known reaction with a given concentration of substrate and comparing it to a standard, often accompanied by a colour change

121
Q

How can protein concentration be determined?

A
  • Almost exclusively through spectroscopy (UV spectroscopy - aromatic side chains)
  • Colorimetric changes
122
Q

Which protein concentration method is the most common? Name other methods.

A
  • Bradford protein assay

- Lowry reagent assay, BCA assay

123
Q

What is the colour change in the Bradford protein assay? Which colour is associated with deprotonation and protonation?

A 
Brown-green (protonation)
to Blue (deprotonation)
124
Q

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

A
  • Contamination of the sample with detergent or SDS could yield an artificially increased protein level
  • Enzyme could have been denatured during isolation and analysis
125
Q

T or F: The Edman degradation proceeds from the carboxyl terminus

A

False. The Edman degradation proceeds from the amino terminus

MCAT: Biochemistry (12 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions