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MCAT Biochemistry > Chapter 3. Non-enzymatic Protein Function and Protein Analysis > Flashcards

Chapter 3. Non-enzymatic Protein Function and Protein Analysis Flashcards

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MCAT flashcards
1
Q

What are structural proteins?

A

Proteins that use their shape to support cells.

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2
Q

What type of structures do structural proteins have?

A

Repeating secondary structures.

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3
Q

What are motifs?

A

Organized secondary structures

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4
Q

What are five types of structural proteins?

A
  • Collagen
  • Elastin
  • Keratin
  • Actin
  • Tubulin
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5
Q

What is the structure of collagen?

A

Collagen is made up of a 3-stranded helix.

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6
Q

Finish the sentence.

Collagen makes up most of the ____.

A

extracellular matrix of connective tissue

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7
Q

Elastin is a structural protein. Where is it found?

A

It is found in the extracellular matrix of connective tissue.

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8
Q

What is the main function of elastin?

A
  • It can stretch and recoil.
    • Restores the shape of tissue.
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9
Q

Keratin is a structural protein. Where is it found?

A

Found as intermediate filament proteins in epithelial cells.

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10
Q

Which structural protein makes up hair and nails?

A

Keratin

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11
Q

What are the three primary roles of keratin?

A
  • Define cell shape.
  • Anchor the nucleus.
  • Serves as protection.
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12
Q

Finish the sentence.

Actin is a structural protein that makes up ____.

A

Microfilaments and thin filaments of myofibrils.

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13
Q

Which structural protein is the most abundant in eukaryotic cells?

A

Actin

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14
Q

Which two structural proteins have polarity, which allows movement of motor proteins?

A

Actin and Tubulin

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15
Q

Which structural protein makes up microtubules?

A

Tubulin

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16
Q

What are the three primary roles of tubulin?

A
  • Provide structure for the cell.
  • Chromosome separation for mitosis and meiosis.
  • Intracellular transport with kinesin and dynein.
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17
Q

Actin and tubulin are both structural proteins that have polarity, which allows for motor proteins to move. The negative end is ___ the nucleus, while the positive end is ____ the nucleus.

A

toward; away from

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18
Q

Motor proteins are said to act as ATPases. Why?

A

They power the conformational change necessary for motor function.

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19
Q

What are the three types of motor proteins?

A
  • Myosin
  • Kinesin
  • Dynein
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20
Q

Kinesin and dynein are both motor proteins associated with tubulin. Kinesin moves ____ the nucleus, while dynein moves ____ the nucleus.

A

away; toward

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21
Q

What is the structure of myosin?

A
  • Subunit with a single head and neck.
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22
Q

Fill in the blank.

Myosin is a motor protein that has a single head and neck. Movement of the neck is responsible for ____ contraction.

A

sarcomere

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23
Q

Kinesin is a motor protein associated with tubulin. What is its primary function?

A
  • Aligning chromosomes during metaphase.
  • Depolymerizing (breaking apart) microtubules during anaphase of mitosis.
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24
Q

Dynein is a motor protein associated with tubulin. What is its primary function?

A

Sliding movement of cilia and flagella

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25
Q

What are binding proteins?

A

Proteins that transport or sequester molecules by binding to them.

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26
Q

What are cell adhesion molecules (CAMs)?

A
  • Proteins found on the surface of most cells.
  • Aid in binding the cell to the extracellular matrix or other cells.
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27
Q

What are the three types of cell adhesion molecules (CAMs)?

A
  • Cadherins
  • Integrins
  • Selectins
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28
Q

What are cadherins?

A
  • Cell adhesion molecule.
  • Group of glycoproteins that mediate calcium-dependent cell adhesion.
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29
Q

Which type of cell adhesion molecule is involved in forming intercellular junctions?

A

Cadherins

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30
Q

Which type of cell adhesion molecule holds similar cell types together?

A

Cadherins

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31
Q

Integrins are a type of cell adhesion molecule that has two membrane-spanning chains: alpha and beta. What is the function of these chains?

A

The chains bind and communicate with the extracellular matrix.

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32
Q

Which type of cell adhesion molecule promotes cell division or apoptosis?

A

Integrins

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33
Q

What is extravasation and which two cell adhesion molecules perform this function?

A
  • Extravasation: Regulation of how the neutrophil leaves the bloodstream and enters surrounding tissue.
  • Regulated by selectins and integrins.
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34
Q

What are selectins?

A

Cell adhesion molecules that bind to carbohydrate molecules that project from other cell surfaces.

35
Q

Selectins are cell adhesion molecules. Where are they expressed?

A

White blood cells and the endothelial cells that line blood vessels.

36
Q

How are immunoglobulins/antibodies formed?

A

By B-cells that function to neutralize targets in the body.

37
Q

How are the light and heavy chains held together in immunoglobulins/antibodies?

A

Disulfide linkages and noncovalent bonds

38
Q

What are three outcomes when an antibody binds to an antigen?

A
  • Neutralizing the antigen
  • Opsonization
    • Marking the pathogen for destruction
  • Agglutinating
    • Clumping together into large insoluble protein complexes that can be phagocytized and digested by macrophages.
39
Q

What is biosignaling?

A

Process in which cells receive and act on signals.

40
Q

What is facilitated diffusion?

A

The diffusion of molecules down a concentration gradient through a pore in the membrane.

41
Q

What are the three types of ion channels?

A
  • Ungated channel
  • Voltage-gated channel
  • Ligand-gated channel
42
Q

What is an ungated ion channel?

A
  • Are always open.
  • Specific ions can diffuse across the membrane whenever it wants.
43
Q

What is a voltage-gated ion channel?

A
  • Regulated by the membrane potential change.
  • Membrane depolymerization causes a protein conformational change that allows them to quickly open and close as the voltage changes.
44
Q

What is a ligand-gated ion channel?

A
  • Binding of a specific substrate or ligand to the channel causes it to open or close.
  • Usually binds to a hormone or neurotransmitter.
45
Q

Enzyme-linked receptors have ____ monomers and ____ domains.

A

two; three

46
Q

How do enzyme-linked receptors function?

A
  • Membrane-spanning domain: Anchors the receptor in the cell membrane.
  • Ligand binding domain: Induces a conformational change that activates the catalytic domain.
  • Often results in the initiation of a second messenger cascade.
47
Q

Fill in the blank.

G protein-coupled proteins are involved in ____.

A

signal transduction

*Signal transduction is bringing signals from exterior to interior.

48
Q

What are the two functions of G protein-coupled receptors?

A
  • Increasing cAMP
  • Initiating signals
49
Q

Fill in the blank.

G protein-coupled receptors have ____ membrane-spanning alpha helices.

A

seven

50
Q

How do G protein-coupled receptors function?

A
  • When the ligand binds to the G-protein, there is a conformational change that causes the subunit to release GDP and bind to GTP.
  • Alpha subunit and GTP bind to adenylate cyclase (AC).
  • GTP releases a pyrophosphate and becomes GDP, which activates AC.
  • ATP is converted to cAMP and diphosphate.
  • This initiates a signaling cascade.
  • Alpha subunit brings back GDP to the seven membrane-spanning alpha helices.
51
Q

What are the three types of G proteins?

A
  • Gs
  • Gi
  • Gq
52
Q

What is the function of the G protein “Gs”?

A

Stimulates AC (adenylate cyclase), which increases cAMP production.

53
Q

What is the function of the G protein “Gi”?

A

Inhibits AC (adenylate cyclase), which decreases cAMP production.

54
Q

What is the function of the G protein “Gq”?

A

Activates phospholipase C

55
Q

What is the function of Phospholipase C?

A
  • Phospholipase C cleaves a phospholipid from the membrane to form PIP2.
  • PIP2 is cleaved to form DAG and IP3 .
  • IP3 can open calcium channels in the ER, which increases calcium in the cell.
56
Q

What is homogenization?

A

Crushing, grinding, or blending the tissue of interest into an evenly mixed solution.

57
Q

What is centrifugation?

A

Isolating proteins from much smaller molecules?

58
Q

What is electrophoresis used for?

A

It is a method used to separate proteins.

59
Q

How does electrophoresis work?

A

A compound is subjected to an electrical field, which moves it according to its net charge and size.

60
Q

In electrophoresis, the anode is the ____ end and the cathode is the ____ end.

A

positive; negative

61
Q

Electrophoresis is a method used to separate proteins by subjecting them to an electrical field. What is the equation used to figure out the migration velocity of a compound?

A

v= migration velocity

z= net charge of the molecule

E= electrical field strength

f = frictional coefficient

62
Q

Shown is the formula used to figure out the migration velocity of a compound during electrophoresis. The variable “f” is the frictional coefficient. What does it depend on?

A

The mass and shape of migrating molecules.

63
Q

What is the standard medium for protein electrophoresis?

A

Polyacrylamide gel

64
Q

In electrophoresis, which type of molecules will move fast through the matrix?

A

Small highly charged molecules

65
Q

What is Native PAGE?

A
  • Analyzes proteins in their native state.
  • Compares the molecular size or charge of the protein.
66
Q

What is SDS-PAGE?

A
  • Separates proteins on the basis of relative molecular mass.
  • Disrupts all noncovalent interactions.
67
Q

SDS-PAGE disrupts all noncovalent interactions. How does it do this?

A
  • Binds to proteins and creates large chains with net negative charges.
    • Neutralizes the protein’s original charge and denatures the protein.
68
Q

Fill in the blank.

In SDS-PAGE, which variable(s) effect v, the migration velocity?

A

E and f

69
Q

What are the three types of electrophoresis?

A
  • Native-PAGE
  • SDS-PAGE
  • Isoelectric focusing
70
Q

What is isoelectric focusing?

A

Electrophoresis technique that separates proteins based on their isoelectric point (pI).

71
Q

In isoelectric focusing, what happens when the protein reaches the portion of the gel where the pH is equal to the protein’s pI?

A

The protein takes on a neutral charge and will stop moving.

72
Q

What is chromatography?

A

A technique that separates a protein mixture on the basis of their affinity for a stationary phase or a mobile phase.

73
Q

In chromatography, what is the amount of time called that a compound spends in the stationary phase?

A

Retention time

74
Q

What are the four types of chromatography?

A
  • Column chromatography
  • Ion-exchange chromatography
  • Size-exclusion chromatography
  • Affinity chromatography
75
Q

What is column chromatography?

A
  • Uses beads of a polar compound (stationary phase) with a nonpolar solvent (mobile phase).
    • The less polar the compound, the shorter the retention time.
76
Q

What is ion-exchange chromatography?

A

Beads in the column are coated with charged substances, so they attract/bind compounds that have an opposite charge.

77
Q

What is size-exclusion chromatography?

A
  • Beads used in the column contain pores, which allow small compounds to enter the beads.
  • Large compounds cannot fit into the pores, so they will move around them and travel through the column faster.
78
Q

What is affinity chromatography?

A
  • Bind any protein of interest by creating a column with high affinity for that protein.
  • Coating beads with a receptor that binds the protein or a specific antibody for the protein.
79
Q

Fill in the blanks.

Protein structure can be determined through ____ and ____.

A

x-ray crystallography; NMR spectroscopy

80
Q

What is Edman degradation?

A
  • Determines the primary structure (amino acid sequence) of a protein in an isolated protein.
  • Removes the N-terminus amino acid of the protein.
81
Q

Fill in the blank.

Crystallography measures ____.

A

electron density

82
Q

How is the concentration of a protein determined?

A

spectroscopy

83
Q

What is the Bradford Protein Assay?

A
  • Mixes a protein in solution with blue dye.
  • The dye is protonated and green-brown in color prior to mixing with proteins.
  • The dye gives up protons upon binding to amino acid groups, turning blue in the process.
84
Q

Fill in the blank.

In the Bradford Protein Assay, the higher the protein concentration the ____ the concentration of blue dye in the solution.

A

higher

MCAT Biochemistry (3 decks)

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