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

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Flashcards in Chapter 3. Non-enzymatic Protein Function and Protein Analysis Deck (84):
1

What are structural proteins?

Proteins that use their shape to support cells. 

2

What type of structures do structural proteins have?

Repeating secondary structures. 

3

What are motifs?

Organized secondary structures

4

What are five types of structural proteins?

  • Collagen
  • Elastin
  • Keratin
  • Actin
  • Tubulin

5

What is the structure of collagen?

Collagen is made up of a 3-stranded helix. 

6

Finish the sentence. 

 

Collagen makes up most of the ____. 

extracellular matrix of connective tissue

7

Elastin is a structural protein. Where is it found?

It is found in the extracellular matrix of connective tissue. 

8

What is the main function of elastin?

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

9

Keratin is a structural protein. Where is it found?

Found as intermediate filament proteins in epithelial cells.

10

Which structural protein makes up hair and nails?

Keratin

11

What are the three primary roles of keratin?

  • Define cell shape.
  • Anchor the nucleus. 
  • Serves as protection. 

12

Finish the sentence. 

 

Actin is a structural protein that makes up ____. 

Microfilaments and thin filaments of myofibrils. 

13

Which structural protein is the most abundant in eukaryotic cells?

Actin

14

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

Actin and Tubulin

15

Which structural protein makes up microtubules?

Tubulin

16

What are the three primary roles of tubulin?

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

17

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. 

toward; away from

18

Motor proteins are said to act as ATPases. Why?

They power the conformational change necessary for motor function. 

19

What are the three types of motor proteins?

  • Myosin
  • Kinesin
  • Dynein

20

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

away; toward

21

What is the structure of myosin?

  • Subunit with a single head and neck. 

22

Fill in the blank. 

 

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

sarcomere

23

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

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

24

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

Sliding movement of cilia and flagella

25

What are binding proteins?

Proteins that transport or sequester molecules by binding to them. 

26

What are cell adhesion molecules (CAMs)?

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

27

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

  • Cadherins 
  • Integrins
  • Selectins

28

What are cadherins?

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

29

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

Cadherins

30

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

Cadherins

31

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

The chains bind and communicate with the extracellular matrix. 

32

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

Integrins

33

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

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

34

What are selectins?

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

35

Selectins are cell adhesion molecules. Where are they expressed?

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

36

How are immunoglobulins/antibodies formed?

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

37

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

Disulfide linkages and noncovalent bonds

38

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

  • 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

What is biosignaling? 

Process in which cells receive and act on signals. 

40

What is facilitated diffusion?

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

41

What are the three types of ion channels?

  • Ungated channel
  • Voltage-gated channel
  • Ligand-gated channel

42

What is an ungated ion channel?

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

43

What is a voltage-gated ion channel?

  • 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

What is a ligand-gated ion channel?

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

45

Enzyme-linked receptors have ____ monomers and ____ domains. 

two; three

46

How do enzyme-linked receptors function?

  • 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

Fill in the blank.

 

G protein-coupled proteins are involved in ____. 

signal transduction

 

*Signal transduction is bringing signals from exterior to interior. 

48

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

  • Increasing cAMP
  • Initiating signals

49

Fill in the blank.

 

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

seven

50

How do G protein-coupled receptors function?

  • 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

What are the three types of G proteins?

  • Gs
  • Gi
  • Gq

52

What is the function of the G protein "Gs"?

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

53

What is the function of the G protein "Gi"?

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

54

What is the function of the G protein "Gq"?

Activates phospholipase C

55

What is the function of Phospholipase C?

  • 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

What is homogenization?

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

57

What is centrifugation?

Isolating proteins from much smaller molecules?

58

What is electrophoresis used for?

It is a method used to separate proteins. 

59

How does electrophoresis work?

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

60

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

positive; negative

61

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?

v= migration velocity

z= net charge of the molecule

E= electrical field strength

f = frictional coefficient

A image thumb
62

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?

Q image thumb

The mass and shape of migrating molecules. 

63

What is the standard medium for protein electrophoresis? 

Polyacrylamide gel 

64

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

Small highly charged molecules

65

What is Native PAGE? 

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

66

What is SDS-PAGE?

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

67

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

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

68

Fill in the blank. 

 

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

E and f

69

What are the three types of electrophoresis?

  • Native-PAGE
  • SDS-PAGE
  • Isoelectric focusing

70

What is isoelectric focusing?

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

71

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

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

72

What is chromatography? 

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

73

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

Retention time

74

What are the four types of chromatography?

  • Column chromatography
  • Ion-exchange chromatography
  • Size-exclusion chromatography
  • Affinity chromatography

75

What is column chromatography?

  • 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

What is ion-exchange chromatography?

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

 

77

What is size-exclusion chromatography? 

  • 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

What is affinity chromatography?

  • 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

Fill in the blanks. 

 

Protein structure can be determined through ____ and ____. 

x-ray crystallography; NMR spectroscopy 

80

What is Edman degradation?

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

81

Fill in the blank. 

 

Crystallography measures ____. 

electron density

82

How is the concentration of a protein determined?

spectroscopy

83

What is the Bradford Protein Assay?

  • 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

Fill in the blank. 

 

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

higher