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Cell Biology > Chapter 4: Protein Structure and Function > Flashcards

Chapter 4: Protein Structure and Function Flashcards

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1
Q

______ are the main building blocks from which cells are assembles, and they constitute most of the cell’s dry mass.

A

Proteins

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2
Q

What are the functions of enzymes?

A

Catalyze covalent bond breakage or formation

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3
Q

What does alcohol dehydrogenase do?

A

Makes the alcohol in wine

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4
Q

What is the function of pepsin?

A

To degrade dietary proteins in the stomach

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5
Q

What is the enzyme that helps convert carbon dioxide into sugars in plants?

A

Ribulose bisphosphate Carboxylase

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6
Q

What does protein kinase do?

A

Adds a phosphate group to a protein molecule

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7
Q

What is the function of structural proteins?

A

To provide mechanical support to cells and tissues

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8
Q

What are some examples of structural proteins?

A
  • collagen and elastin
  • tubulin
  • actin
  • keratin
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9
Q

What is the function of transport proteins?

A

To carry small molecules or ions

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10
Q

What are the names of the motor proteins?

A

Myosin
Kinesin
Dynein

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11
Q

Name the motor protein in skeletal muscle cells provides the motive force for humans to move

A

Myosin

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12
Q

Name the motor protein that interacts with microtubules to move organelles around the cell

A

Kinesin

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13
Q

What does Dynein do?

A

enables eukaryotic cilia and flagella to beat

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14
Q

How is iron stored in the liver?

A

By binding to the small protein ferritin

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15
Q

What are some examples of signal proteins?

A

insulin, it controls glucose levels in the blood.

netrin, attracts axons to specific locations.

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16
Q

Name the function of receptor proteins

A

Detect signals and transmit them to the cell’s response machinery

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17
Q

What does rhodopsin do?

A

detects light in the retina

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18
Q

What are transcription regulators?

A

They are proteins that function by binding to DNA to switch genes on or off

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19
Q

What is an example of a transcription regulator in bacteria

A

The Lac repressor in bacteria silences the genes for the enzymes that degrade the sugar lactose

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20
Q

What are a few examples of special purpose proteins?

A
  • antifreeze proteins found in the arctic and antarctic fishes to protect their blood against freezing
  • monellin, a protein found in an african plant, has an intensely sweet taste
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21
Q

What are the most structurally complex and functionally sophisticated molecules known?

A

PROTEINS

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22
Q

T/F the shape of a protein is specified by its amino acid sequence

A

True

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23
Q

Amino acids are linked together by _______ bonds.

A

peptide

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24
Q

What is the N-terminus?

A

the amino side of a polypeptide chain

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25
Q

What is the C-terminus?

A

The carboxyl side of the amino acid

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26
Q

What is the part of the amino acid that is not involved in forming peptide bonds?

A

side chains

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27
Q

Name the negatively charged amino acids

A 
Aspartic acid (Asp)
Glutamic acid (Glu)
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28
Q

Name the positively charged amino acids

A

Arginine (Arg)
Lysine (Lys)
Histidine (His)

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29
Q

Name the uncharged polar Amino acids

A 
Asparagine (Asn)
Glutamine (Gln)
Serine (Ser)
Threonine (Thr)
Tyrosine (Tyr)
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30
Q

What are the three types of noncovalent bonds that help fold proteins?

A
  • Hydrogen Bonds
  • Electrostatic attractions
  • Van der Waals attractions
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31
Q

What is the fourth weak interaction that determines the shape of proteins?

A

The hydrophobic force

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32
Q

Which side chains tend to cluster in the interior of the folded protein?

A

The nonpolar (hydrophobic) side chains—which belong to amino acids such as phenylalanine, leucine, valine, and tryptophan

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33
Q

Which side chains tend to cluster in the exterior of the folded protein?

A

polar side chains—such as those belonging to arginine, glutamine, and histidine

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34
Q

T/F Proteins form into a conformation of lowest energy

A

True, Proteins will adopt the structure in which free energy is minimized

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35
Q

Define conformation:

A

The final folded structure adopted by any polypeptide chain.

36
Q

The folding process is _______ _______ as it releases heat and increases the disorder of the universe

A

Energetically favorable

37
Q

What is it called when the protein that is formed unfolds?

A

Denaturation

38
Q

What is it called when the denatured protein reforms?

A

Renaturation

39
Q

Can a protein fold back into its formation after denaturation without help?

A

Yes

40
Q

Which proteins assist protein folding in the cell?

A

Chaperone proteins

41
Q

How can single polypeptide chains fold without the risk of forming aggregates in the crowded conditions of the cytoplasm?

A

Isolation chambers

42
Q

What is the size range of proteins?

A

30 amino acids - more than 10,000

43
Q

What are the two most common folding patterns?

A

a helix and b sheet

44
Q

In an a helix a hydrogen bond is made between every ___ amino acid.

A

fourth

45
Q

what is handedness?

A

whether a helix is right or left handed (which way it twists

46
Q

what is a coiled coil?

A

when 2 or 3 a helices will wrap around one another to form a structure

47
Q

T/F B sheets form rigid structures at the core of many proteins

A

True

48
Q

What are the two types of beta sheets?

A

paralell

antiparallel

49
Q

What are the properties of beta sheets?

A

tensile strength,

basis of amyloid structures –> stacked together in long rows like the teeth of a zipper

50
Q

T/F misfolded proteins can form amyloid structures that cause prion diseases

A

True

51
Q

Name the levels of organization of proteins:

A
  1. primary structure
  2. secondary structure.
  3. tertiary structure
  4. quaternary structure
52
Q

What are the serine proteases?

A

a family of protein-cleaving (proteolytic) enzymes that includes the digestive enzymes chymotrypsin, trypsin, and elastase, as well as several proteases involved in blood clotting. When any two of these enzymes are compared, portions of their amino acid sequences are found to be nearly the same.

53
Q

globular proteins:

A

proteins in which the polypeptide chain folds up into a compact shape like a ball with an irregular surface

54
Q

enzymes tend to be ____ proteins

A

globular

55
Q

Fibrous proteins:

A
  • these proteins generally have a relatively simple, elongated three-dimensional structure
  • have roles in the cell that require them to span a large distance
56
Q

Define intermediate filaments:

A

a component of the cytoskeleton that gives cells mechanical strength

57
Q

Fibrous proteins are especially abundant ________ the cell.

A

outside

58
Q

What is the most abundant fibrous extracellular protein?

A

Collagen

59
Q

What is the most common covalent cross links in proteins?

A

Sulfur-sulfur bonds. These disulfide bonds act as an atomic staple to reinforce the proteins most favored conformation.

60
Q

What is a lysozyme?

How does this enzyme relate to covalent cross links?

A

an enzyme in tears, saliva, and other secretions that can disrupt bacterial cell walls—retains its antibacterial activity for a long time because it is stabilized by such disulfide cross-links

61
Q

Why don’t disulfide bonds generally form in the cell cytosol?

A

There is a high concentration of reducing agents that convert these bonds back to cysteine-SH groups. Proteins also rarely require these reinforcements in the calm intracellular environment.

62
Q

T/F all proteins bind to other molecules

A

true

63
Q

Any substance that is bound by a protein is referred to as a _______

A

ligand

64
Q

T/F the binding of a protein to another molecule is highly selective

A

true

65
Q

Define antibodies:

A

immunoglobulin proteins produced by the immune system in response to foreign molecules, especially those on the surface of an invading microorganism.

(y shaped molecules with 2 antigen binding sites)

66
Q

Define antigen:

A

An antibody recognizes its target molecule

67
Q

B lymphocytes (cells) produce ______

A

antibodies

68
Q

what is the complex to which molecules bind?

A

an enzyme-substrate complex

69
Q

What are the 10 enzyme classes?

A
  1. hydrolase
  2. nuclease
  3. protease
  4. ligase
  5. isomerase
  6. polymerase
  7. kinase
  8. phosphatase
  9. oxido-reductase
  10. ATPase
70
Q 
Name the enzyme class for the following function:
General term for enzymes that catalyze a hydrolytic cleavage reaction
A

hydrolase

71
Q 
Name the enzyme class for the following function:
Breaks down nucleic acids by hydrolyzing bonds between nucleotides
A

Nuclease

72
Q 
Name the enzyme class for the following function:
Breaks down proteins by hydrolyzing peptide bonds between amino acids
A

Protease

73
Q 
Name the enzyme class for the following function:
Joins two molecules together; DNA ligase joins two DNA strands together end-to-end
A

Ligase

74
Q 
Name the enzyme class for the following function:
Catalyzes the rearrangement of bonds within a single molecule
A

Isomerase

75
Q 
Name the enzyme class for the following function:
Catalyzes polymerization reactions such as the synthesis of DNA and RNA
A

Polymerase

76
Q 
Name the enzyme class for the following function:
Catalyzes the addition of phosphate groups to molecules. Protein kinases are an important group of kinases that attach phosphate groups to proteins
A

Kinase

77
Q 
Name the enzyme class for the following function:
Catalyzes the hydrolytic removal of a phosphate group from a molecule
A

Phosphotase

78
Q 
Name the enzyme class for the following function:
General name for enzymes that catalyze reactions in which one molecule is oxidized while the other is reduced. Enzymes of this type are often called oxidases, reductases, or dehydrogenases
A

Oxido-reductase

79
Q 
Name the enzyme class for the following function:
Hydrolyzes ATP. Many proteins have an energy-harnessing ATPase activity as part of their function, including motor proteins such as myosin (discussed in Chapter 17) and membrane transport proteins such as the Na+ pump (discussed in Chapter 12)
A

ATPase

80
Q

where does catalysis take place?

A

On the proteins active site (binding site on the surface)

81
Q

T/F Allosteric enzymes have two or more binding sites that influences on another

A

true

82
Q

define allosteric in relation to proteins:

A

a protein can adopt two or more slightly different conformations, and their activity can be regulated by a shift from on to another

83
Q

Reversible ______ ______

A

controls the activity of many types of proteins in eukaryotic cells.

84
Q

phosphorylation is catalyzed by a _____ _____

A

protein kinase

85
Q

dephosphorylation is catalyzed by a _____ ______

A

protein kinase

Cell Biology (11 decks)

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