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

Chapter 3: Nonenzymatic Protein Function and Protein Analysis Flashcards

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MCAT flashcards
1
Q

A repetitive organization of secondary strucutral elements together sometimes referred to as a ________.

A

motif

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2
Q

____________ has a characteristic trihelical fiber (three left-handed helices woven together to form a secondary right-handed helix) and makes up most of the extracellular matrix of connective tissue.

A

Collagen

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3
Q

________ is another important component of the extracellular matrix of connective tissue. Its primary role is to stretch and then recoil like a spring.

A

Elastin

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4
Q

____________ are intermediate filament proteins found in epithelial cells. Contribute to mechanical integrity of the cell and also function as regulatory proteins. Makes up hair and nails.

A

Keratins

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5
Q

________ is a protein that makes up microfilaments and the thin filaments in myofibrils. Most abundant protein in eukaryotic cells.

A

Actin

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6
Q

What allows motor proteins to travel unidirectionally on actin?

A

They have polarity; has a positive and negative side.

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7
Q

____________ is the protein that makes up microtubules.

A

Tubulin

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8
Q

4 functions

What do microtubules do?

A
  1. provide structure
  2. separate chromosomes in cell cyle
  3. intracellular transport with kinesin and dynein
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9
Q

Does tubulin have polarity?

A

Yes!

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10
Q

What other activity do motor proteins also exhibit? What kind?

A

Enzymatic activity; ATPases

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11
Q

____________ power the conformational change necessary for motor function.

A

ATPases

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12
Q

____________ is the primary motor protein that interacts with actin. It is involved in cellular transport and has a head/neck.

A

Myosin

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13
Q

The movement at the ________ of myosin is responsible for the power stroke of sarcomere contraction.

A

neck

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14
Q

____________ and ____________ are the motor proteins associated with microtubules.

A

Kinesins and dyneins

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15
Q

How many heads do kinesin/dynein have? What are they attached to?

A

2; at least one is attached to tubulin at all times

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16
Q

What role do kinesins play?

A

Align chromosomes during metaphase and depolymerase microtubules during anaphase

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17
Q

What do dyneins do?

A

Sliding movement of cilia and flagella

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18
Q

What do both kinesin and dynein do?

A

Vesicle transport

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19
Q

Which way does kinesin go and which way does dynein go? What is an example of where this occurs?

A

Kinesin goes towrad the positive end of the MT, and dynein goes toward the negative end

occurs when kinesins bring neurotransmitter vesicles to the positive end of axonal microtubules, dynein brings vesicles of waste/recycled neurotransmitter back toward the negative end of the microtubule

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20
Q

____________ ____________ include hemoglobin, calcium-binding proteins, DNA-binding proteins (often transcription factors), and others. These have the role of stabilizing functions and transporting/sequestering molecules by binding to them.

A

Binding proteins

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21
Q

Each binding protein has an ____________ ________ for its molecule of interest.

A

affinity curve

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22
Q

What is unique about the affinity curves of transport proteins?

A

They have varying affinity in different conditions so they can bind or unbind their targets

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23
Q

________ ____________ ____________ are proteins found on the surface of most cells and aid in binding the cell to the extracellular matrix or other cells.

A

cell adhesion molecules (CAMs)

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24
Q

What are the 3 major families of CAMs?

CIS

A
  1. Cadherins
  2. Integrins
  3. Selectins
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25
Q

____________ are a group of glycoproteins that mediate calcium-dependent cell adhesion.

A

Cadherins

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26
Q

Cadherins often hold similar cell types together and have type-specific cadherins. What are some examples?

A

E-cadherin for epithelial cells, N-cadherin for nerve cells

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27
Q

____________ are a group of proteins that all have 2 membrane-spanning chains called α and β. These chains are important in binding to and communicating with the extracellular matrix.

A

Integrins

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28
Q

Integrins also play a role in ____________ ____________ and can greatly impact cellular function by promoting what processes?

A

cellular signaling; cell division, apoptosis, others

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29
Q

____________ bind to carbohydrate molecules that project from other cell surfaces.

A

Selectins

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30
Q

Which CAM forms the weakest bonds?

A

Selectins

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31
Q

Selectins are expressed on which cells?

A

white blood cells, endothelial cells that line blood vessels

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32
Q

Antibodies are also called ________________, and they are proteins produced by ____-cells that function to neutralize targets in the body, like toxins and bacteria, and then recruit other cells to help eliminate the threat.

A

immunoglobulins (Ig); B-cells

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33
Q

What shape are antibody proteins?

A

Y

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34
Q

What are antibodies made up of?

A

2 identical heavy chains and 2 identical light chains

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35
Q

What holds heavy and light chains together?

A

disulfide linkages and noncovalent interactions

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36
Q

Each antibody has an ____________-____________ region at the tips of the Y.

A

antigen-binding region

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37
Q

What is in the antigen-binding region?

A

Specific polypeptide sequences that will bind one, and only one, specific antigenic sequence.

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38
Q

The remaining part of the antibody molecule (aside from the antigen-binding region) is known as the ____________ region.

A

constant

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39
Q

What is the constant region of an antibody responsible for?

A

Recruitment and binding of other cells of the immune system, such as macrophages

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40
Q

What are the targets of antibodies called?

A

Antigens

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41
Q

What 3 things can happen when an antibody binds to an antigen?

A
  1. Antigen is neutralized, making the pathogen or toxin unable to exert its effect on the body
  2. The pathogen is marked for destruction by other white blood cells
  3. The antigen and antibody are clumped together into large insoluble protein complexes that can be phagocytized and digested by macrophages
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42
Q

When antibodies mark pathogens for destruction by WBCs, what is this process called?

A

opsonization

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43
Q

When the antigen and antibody are clumped together into large insoluble protein complexes, this process is called?

A

Agglutinating

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44
Q

____________ is a process in which cells receive and act on signals.

A

biosignaling

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45
Q

________ ____________ are proteins that create specific pathways for charged molecules.

A

Ion channels

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46
Q

____________ ____________, a type of passive transport, is the difficusion of molecules down a concentration gradient through a pore in the membrane created by this transmembrane protein.

A

Facilitated diffiusion

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47
Q

What 3 types of molecules is facilitated diffusion used for?

A

Molecules that are impermeable to the membrane:
1. Large
2. Polar
3. Charged

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48
Q

What are the 3 main types of ion channels?

A
  1. ungated
  2. voltage-gated
  3. ligand-gated
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49
Q

____________- ________ channels are regulated by the membrane potential change near the channel.

A

voltage-gated

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50
Q

________-________ channels open or close due to the binding of a specific substance or ligand to the channel

A

ligand-gated

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51
Q

What parameters that apply to enzyemes are also applicable to transporters like ion channels?

A

Km and vmax

52
Q

____________-________ receptors are membrane receptors that may also display catalytic activity in response to ligand binding.

A

enzyme-linked

53
Q

What are the 3 primary protein domains of enzyme-linked receptors?

A
  1. membrane-spanning domain
  2. ligand-binding domain
  3. catalytic domain
54
Q

The ____________-____________ domain anchors the receptor in the cell membrane.

A

membrane-spanning

55
Q

The ________-________ domain is stimulated by the appropriate ligand and induces a conformation change that activates the ________ domain.

A

ligand-binding; catalytic

56
Q

After the catalytic domain of an enzyme-linked receptor is activated, a ________ ____________ cascade is initiated.

A

second messenger

57
Q

What is an example of enzyme-linked receptor?

A

receptor tyrosine kinase

58
Q

____ ________-________ receptors are a large family of integral membrane proteins involved in signal transduction.

A

G protein-coupled (GPCRs)

59
Q

What characterizes GPCRs?

A

7 membrane-spanning alpha-helices

60
Q

In order for GPCRs to transmit signals to an effector in the cell, they uitilize a ________________ ____ protein.

A

heterotrimeric G

61
Q

G proteins are named for their intracellular link to ____________ ____________.

A

guanine nucleotides (GDP, GTP)

62
Q

The binding of a ligand increases the affinity of a GPCR for what?

A

G protein

63
Q

When a G protein binds to a GPCR, what happens?

A

The GPCR is switched to the active state and affects the intracellular signaling pathway

64
Q

What are the 3 main types of G proteins?

A

Gs, Gi, and Gq

65
Q

What does Gs do?

A

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

G**s** stimulates

66
Q

What does Gi do?

A

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

67
Q

What does Gq do?

A

Activates phospholipase C

Mind your p’s and q’s - Gq activates phospholipase C

68
Q

What does phospholipase C do when it is activated by Gq?

A

It cleaves a phospholipid from the membrane to form PIP2

69
Q

What happens to PIP2?

A

It is cleaved into DAG and IP3

70
Q

What does IP3 do?

A

It opens calcium channels in the endosplasmic reticulum, which increases calcium levels in the cell

71
Q

What are the 3 subunits that comprise the G protein?

A

alpha, beta, and gamma

72
Q

When the ____ subunit of a G protein is inactive, it binds GDP and is in a complex with the beta and gamma subunits.

A

alpha

73
Q

When a ligand binds to the GPCR, the receptor becomes activated and engages what?

A

The corresponding G protein

74
Q

Once GDP is replaced with GTP, the alpha subunit ________________ from the beta and gamma subunits.

A

dissociates

75
Q

An activated alpha subunit can then alter the activity of ____________ ____________.

A

adenylate cyclase

76
Q

Once GTP on an activated alpha subunit is dephosphorylated to GDP, it does what?

A

Rebinds to alpha and gamma subunits and the G protein is inactive

77
Q

Proteins and other biomolecules are isolated by using cell lysis and ________________. Then ____________________ can be used to isolate proteins from much smaller molecules before other isolation techniques must be employed.

A

homogenization, centrifugation

78
Q

________________ is a method of protein separation which works by subjecting compounds to an electric field, which moves them according to their net charge and size.

A

Electrophoresis

79
Q

How does elecrophoresis work?

A

Negatively charged compounds migrate toward the positive anode, and the positively charged compounds migrate toward the negative cathode

80
Q

The velocity of a molecule undergoing electrophoresis is called ________________ ________________.

A

migration velocity

81
Q

Migration velocity is directly proportional to what?

A

Electric field (E) and charge (z)

82
Q

What is migration velocity inversely proportional to?

A

frictional coefficient, f, which dpeends on mass and shape of migrating molecules

83
Q

What is the equation for migration velocity?

A

v = Ez/f

84
Q

What is the standrd medium for protein electrophoresis?

A

polyacrylamide gel

85
Q

A smaller molecules moves (faster/slower?) through gel.

A

faster

86
Q

Polyacrylamide gel electrophoresis (PAGE) is limited by what?

A

The varying mass to charge and mass to size ratios because multiple different proteins may experience the same level of migration

87
Q

What is PAGE most useful for?

A

Comparing the molecular size or the charge of proteins known to be similar in size from other analytic methods like SDS-PAGE or size-exclusion chromatography

88
Q

____________ ____________ ____________-PAGE electrophoresis is a useful tool because it separates proteins on the basis of relative molecular mass alone.

A

sodium dodecyl sulfate

89
Q

What is SDS?

A

A detergent that disrupts all noncvalent interactions. It binds to proteins and creates large chains with net negative charges, which neutralizes a protein’s original charged and denaturing the protein.

90
Q

How does SDS-PAGE work?

A

Since SDS removes charge, the proteins move through the gel and are only affected by E and f, which depends on mass.

91
Q

Proteins can also be separated on the basis of their ________________ ________, which is the pH at which the protein or amino acid is electrically neutral.

A

isoelectric point

92
Q

For most amino acids, the zwitterion form occurs when the amino group is ____________, the carboxyl group is ____________, and any side chain is electrically ____________. What are the exceptions?

A

protonated, deprotonated, neutral

arginine and lysine - they have basic side chains

93
Q

For arginine and lysine, they have side chains with (higher/lower?) pKa values than their amino groups. The zwitterion form occurs when the amino group is ________________, side chain is ____________, and carboxyl group is ____________.

A

higher; deprotonated, protonated, deprotonated

94
Q

____________ ____________ exploits the acidic and basic properties of amino acids by separating on the basis of isoelectric point.

A

isoelectric focusing

95
Q

How does isoelectric focusing work?

read p102

A

proteins are placed in a gel with a pH gradient, where acidic is at positive, basic is at negative, and neutral is in the middle.

An electric field is generated. Proteins that are positively charged will migrate toward the cathode and proteins that are negative will migrate toward the anode (A+, b/c H+ rich).

As the protein reaches the portion of the gel where pH is equal to pI, the protein will become neutral and stop moving.

96
Q

____________ uses physical and chemical properties to separate and identify compounds from a complex mixture.

A

chromatography

97
Q

How does chromatography work?

A

The more similar the compound is to its surroundings, the more it will stick to and move slowly through its surroundings.

98
Q

Chromatography works by placing the sample onto a solid medium called the ________________ ____________ or ____________.

A

stationary phase, adsorbent

99
Q

After placing a sample onto the stationary phase, the ____________ phase is run through the staionary phase, which allows the sample to run through the stationary phase and ____________.

A

mobile; elute

100
Q

The amount of time that a compound spends in the stationary phase is referred to as ____________ ________.

A

retention time

101
Q

Varying retenting times of each compound in the solution results in separation of the components within the stationary phase, or ________________.

A

partitioning

102
Q

In ________ ________________, a column is filled with silica or alumina beads as an adsorbent, and gravity moves the solvent and compounds down the column.

A

column chromatography

103
Q

How does column chromatography work?

A

The less polar a compound, the faster it elutes. Solvent polarity, pH, or salinity can be changed to help elute the protein of interest.

104
Q

In ____-________ chromatography, the beads are coated with charged substances, so they attract/bind compounds that have an opposite charge.

A

ion-exchange

105
Q

What is used to elute charged molecules that have stuck to an ion-exchange column?

A

salt gradient

106
Q

In ________-____________ chromatography, the beads used in the column contain tiny pores of varying sizes.

A

size-exclusion

107
Q

In size-exclusion chromatography, what happens to small compounds?

A

they get stuck in the pores of beads and are slowed down, meanwhile large compounds move around these beads

108
Q

In ____________ chromatography, columns can be customized to bind any protein of interest by creating a column with high affinity for that protein.

A

affinity

109
Q

How is affinity chromatography accomplished?

A

Coating beads with a receptor that binds the protein or a specific antibody to the protein; the protein is retained in the column and then eluted by washing the column with a free receptor (or target or antibody), which competes with the bead-bound receptor to free the protein

110
Q

Protein structure can be determined by what two processes?

A

X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy

111
Q

Before crystallographic analysis, what must be done?

A

The protein must be isolated and crystallized

112
Q

How does crystallography work?

A

It measures electron density on an extremely high-resolution scale and can also be used for nucleic acids. This generates an X-ray diffraction pattern, which has dots that can be interpreted to determine protein structure

113
Q

Amino acids that compose a protein can be determined how?

A

Complete protein hydrolysis and subsequent chromatographic analysis

114
Q

To determine the primary structure of a protein, what must occur?

A

Sequential digestion of the protein with specific cleavage enzymes

115
Q

Small proteins are best analyzed with the ________ ________________, which uses cleavage to sequence proteins of up to 50 to 70 amino acids.

A

Edman degradation

116
Q

Edman degradation works by doing what?

A

Selectively and sequentially removing the N-terminal amino acid of the protein, which can be analyzed via mass spectroscopy

117
Q

For larger proteins, a ____________ ____________ may be used.

A

synthetic

118
Q

In larger proteins, amino acid composition can be done by using a synthetic reagent to digest, which cleaves proteins at specific amino acid residues, which does what?

A

Creates smaller fragments that can then be analyzed by electrophoresis or Edman degradaation

119
Q

Protein activity is generally determined how?

A

by monitoring a known reaction with a given concentration of substrate and comparing it to a standard; activity is correlated with concentration

120
Q

Concentration is determined almost exclusively through ________________

A

spectroscopy

121
Q

Because proteins contain ________ side chains, they can be analyzed with UV spectroscopy without any treatment. This type of analysis is particularly sensitive to sample contaminants.

A

aromatic

122
Q

Proteins can also cause colorimetric changes with specific reactions/ Give examples of assays.

A
  1. bicinchoninic acid (BCA) assay,
  2. Lowry reagent assay
  3. Bradford assay
123
Q

The ____________ protein assay mixes a protein in solution with Coomassie brilliant blue dye.

A

Bradford

124
Q

How does Coomassie work?

A

It gives up protons upon binding to amino acid groups, turning blue in the process. Ionic attractions between dye and protein stabilize the blue form.

Increased protein concentrations correspond to a larger concentration of blue dye!

125
Q

How is concentration determined in Bradford assay?

A

Create a standard curve with known concentration reagent, then determine concentration based on standard.

MCAT Biochemistry (13 decks)

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