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biochemistry > chapter 12 lipids and membranes > Flashcards

chapter 12 lipids and membranes Flashcards

1
Q

Lipids are a very diverse set of molecules related how?

A

By their hydrophobic properties

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2
Q

What are the hydrophobic properties of lipids?

A
  • not appreciably soluble in water
  • soluble in organc solvents
  • waxy, greasy or oily compounds in plants and animals.
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3
Q

Are lipids soluble in water?

A

Not appreciably soluble

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4
Q

Are lipids soluble in chloroform (CHCl3)?

A

yes because its an organic solvent

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5
Q

Are lipids soluble in methanol (CH3OH)?

A

yes because it is an organic solvent

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6
Q

How is lipid formation different than other biomolecules

A

Lipids form large aggregates, but not polymers like other biomolecules.

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7
Q

What are function of lipids?

A

Functions are diverse:

  • Storage of energy
  • Structure of cell membranes
  • Signaling and other biological activities
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8
Q

What are the two main categories of classifying lipids?

A

1) Saponifiable

2) Non-saponifiable

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9
Q

What are Saponifiable?

A

Ester-containing compounds

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10
Q

What are non-saponifiable?

A

Does NOT contain an ester group and are NOT capable of being hydrolyzed

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11
Q

Steroids are an example what type of lipid?

A

Non-saponifiable thus not able to be hydrolyzed

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12
Q

Eicosanoids are an example of what type of lipids?

A

Non-saponifiable thus not hydrolyzed

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13
Q

Sphingolipids are an example of what type of lipid?

A

Saponifiable meaning it contains an ester containing compounds

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14
Q

Glycerophospholipids are an example of what type of lipid?

A

Saponifiable; meaning it contains an ester containing compounds

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15
Q

Triacylglycerides are an example of what type of lipid?

A

Saponifiable; meaning it contains ester containing compounds

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16
Q

What are fatty acids?

A

carboxylic acids with long-chain hydrocarbon side groups

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17
Q

/\/\/\/\/\/\/\/\/\/\/\/\/COOH

is an example of what type of lipid?

A

fatty acid (non polar tail and polar head)

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18
Q

Is the polar head of a fatty acid soluble? if so under what conditions?

A

yes at physiological pH (7.4)

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19
Q

If a fatty acid has a polar head of COOH and is in water at physiological pH (7.4) what dominates?

A

carboxylate ion (COO-) dominates

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20
Q

What are the common characteristics of fatty acids?

A
  • tails are usually straight
  • most range from 10-20 carbons
  • Usually even # carbons
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21
Q

Are fatty acids saturated, unsaturated or polysaturated?

A

all of the above

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22
Q

Most unsaturated fatty acids have hat type of configuration?

A

almost always cis-isomers

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23
Q

Common name: Lauric acid has a systemic name of what?

A

dodecanoic acid

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24
Q

Dodecanoic acid is also called what?

A

Lauric acid

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25
Q

What is the structure of Dodecanoic acid (Lauric acid)?

A

CH3(CH2)10COOH

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26
Q

What is the melting point of Dodecanoic acid (Lauric acid)?

A

44.2 degrees C

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27
Q

What is the systemic name of Myristic acid?

A

Tetradecanoic acid

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28
Q

Tetradecanoic acid is also called what?

A

Myristric acid

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29
Q

What is the structure of Tetradecanoic acid (Myristic acid)?

A

CH3(CH2)12COOH

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30
Q

What is the melting point of Tetradecanoic acid (Myristic acid)?

A

53.9 degrees C

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31
Q

What is the systemic name for Palmitic acid?

A

Hexadecanoic acid

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32
Q

What is the common name for Hexadecanoic acid?

A

Palmitic acid

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33
Q

What is the structure of Hexadecanoic acid (Palmitic acid)?

A

CH3(CH2)14COOH

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34
Q

What is the melting point of Hexadecanoic acid (palmitic acid)

A

63.1 degrees C

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35
Q

What is systemic name for Stearic acid?

A

Octadecanoic acid

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36
Q

What is the common name for Octadecanoic acid?

A

Stearic acid

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37
Q

What is the structure for Octadecanoic acid (Steric acid)?

A

CH3(CH2)16COOH

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38
Q

What is the melting point of Octadecanoic acid (Steric acid)?

A

69.6 degrees C

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39
Q

What is the systemic name for Palmitoleic acid?

A

9-Hexadecanoic acid

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40
Q

What is the common name for 9-Hexadecanoic acid?

A

Palmitoleic acid

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41
Q

What type of lipid is Hexadecanoic acid (Palmitic acid)?

A

Fatty acid

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42
Q

What type of lipid is Dodecanoic acid (Lauric acid)?

A

Fatty acid

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43
Q

What type of lipid is Tetradecanoic acid (Myristic acid)?

A

Fatty acid

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44
Q

What type of lipid is Octadecanoic acid (Steric acid)?

A

Fatty acid

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45
Q

What is the structure of 9-Hexadecanoic acid (Palmitoleic acid)?

A

CH3(CH2)CH=CH(CH2)7COOH

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46
Q

What is the melting point of 9-Hexadecanoic acid (Palmitoleic acid)?

A

-0.5 degrees C

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47
Q

What is the systemic name for Oleic acid

A

9-Octadecanoic acid

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48
Q

What is the common name for 9-Octadecanoic acid

A

Oleic acid

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49
Q

What is the structure of 9-Octadecanoic acid (oleic acid)?

A

CH3(CH2)CH=CH(CH2)COOH

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50
Q

What is the melting point of 9-Octadecanoic acid (oleic acid)?

A

12 degrees C

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51
Q

Is Hexadecanoic acid (Palmitic acid) a saturated or unsaturated fatty acid?

A

saturated acid

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52
Q

Is type of lipid is Dodecanoic acid (Lauric acid) a saturated or unsaturated fatty acid?

A

Saturated acid

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53
Q

Is Tetradecanoic acid (Myristic acid) a saturated or unsaturated fatty acid?

A

saturated

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54
Q

Is Octadecanoic acid (Steric acid) a saturated or unsaturated fatty acid?

A

Saturated

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55
Q

Is 9-Octadecanoic acid (oleic acid) a saturated or unsaturated fatty acid?

A

unsaturated fatty acid in cis

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56
Q

Is 9-Hexadecanoic acid (Palmitoleic acid) a saturated or unsaturated fatty acid?

A

Unsaturated fatty acid in cis

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57
Q

what is the systemic name for Linoleic acid?

A

9, 12 Octadecadienoic acid

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58
Q

What is the common name for 9, 12 Octadecadienoic acid?

A

Linoleic acid

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59
Q

Is 9, 12 Octadecadienoic acid (Linoleic acid) a saturated or unaturated fatty acid?

A

unsaturated fatty acid in cis

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60
Q

What is the structure of 9, 12 Octadecadienoic acid (Linoleic acid)?

A

CH3(CH2)4(CH=CHCH2)2(CH2)6COOH

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61
Q

What is the melting point of 9, 12 Octadecadienoic acid (Linoleic acid)?

A

-5 degrees C

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62
Q

What is the systemic name for alpha-Linolenic acid?

A

9, 12, 15 Octadecatrienoic acid

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63
Q

What is the common name for 9, 12, 15 Octadecatrienoic acid?

A

alpha-Linolenic acid

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64
Q

What is the structure of 9, 12, 15 Octadecatrienoic acid (alpha-Linolenic acid)?

A

CH3CH2(CH=CHCH2)3(CH2)6COOH

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65
Q

What is the melting point of 9, 12, 15 Octadecatrienoic acid (alpha-Linolenic acid)?

A

-11 degrees C

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66
Q

Is 9, 12, 15 Octadecatrienoic acid (alpha-Linolenic acid) a saturated or unsaturated fatty acid?

A

Unsaturated fatty acid in cis

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67
Q

How many double bonds does a saturated fatty acid?

A

No double bonds

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68
Q

What type of fatty acids has double bonds?

A

unsaturated fatty acids

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69
Q

How are unsaturated fatty acid biosynthesized in eukaryotes?

A

Biosynthesized in eukaryotes from corresponding saturated fatty acids by an aerobic process.

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70
Q

Linoleic acid and linolenic acid is found where?

A

plants and fish oils

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71
Q

Linoleic acid and linolenic acid are necessary for what?

A

regulating blood pressure, clotting, lipid levels, immune response, and inflammation response

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72
Q

Triglycerides from animals are _____ at room temperature and called what?

A

Triglycerides from animals are solid at room temperature and called fats

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73
Q

Triglycerides from plants and fish are _____ at room temperature and called _____

A

Triglycerides from plants and fish are liquids at room temperature and called oils.

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74
Q

Phospholipases disrupts what?

A

disrupts membranes

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75
Q

Bees and snake venom makes a lot of what?

A

Phospholipase A2

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76
Q

Sphingomyelin is what type of lipid?

A

sphingolipids

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77
Q

Sphingomyelin has what two components?

A

1) phosphocholine head group

2) Palmitate residue

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78
Q

Sphingomyelin makes up 10-20% of what?

A

Plasma membrane

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79
Q

Sphingomyelin is the primary component of what?

A

myelin sheath

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80
Q

Springosine’s N-acyl fatty acid derivative is called what?

A

ceramides

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81
Q

sphingolipids are derviatives of what?

A

C18 amino alcohols sphingosine, dihydrosphingosine and their C16, C17 C19 and C20 homologs.

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82
Q

Ceramides occur only in small amounts in ______ but form the parent compound of the more abundant ______

A

Ceramides occur only in small amounts in plants and animal tissues but form the parent compounds of more abundant sphingolipids.

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83
Q

What is the most common sphingolipids?

A

Sphingomyelins

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84
Q

Sphingomyelins contain what?Thus are considered sphingophospholipids.

A

bear a ceramide bearing either a phosphocholine or a phosphoethanolamine moiety.

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85
Q

the myelin sheath of nerve cells is rich in what?

A

sphingomyelin

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86
Q

What is the simplest sphingolipid?

A

Cerebrosides or AKA glucosphingolipids

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87
Q

Cerebrosides are also called what?

A

glucosphingolipids

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88
Q

Cerebrosides are what?

A

Ceramides with head groups consisting of a single sugar residue

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89
Q

Galactocerebrosides have a head group of what?

A

Beta-D-galactose

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90
Q

Galactocerbosides are most prevalent where?

A

neuronal cell membranes

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91
Q

cerebrosides lack what group?

A

phosphate group

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92
Q

Glucocerebrosides have what type of head?

A

Beta-D-glucose

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93
Q

Glucocerbrosides occur where?

A

In the membranes of other tissues.

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94
Q

What group does phospholipids have cerbrosides lack? Making cebrosides what?

A

phosphate group making cerebrosides the most frequent nonionic compounds.

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95
Q

The galactose residue of some galactocerebrasides are _____ at what position to form ionic compounds called what?

A

are sulfated at C3 position to form ionic compounds called sulfatides.

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96
Q

More complex sphingoglycolipids have what?

A

unbranched oligosaccharides head groups of up to four sugar residues

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97
Q

What are the three types of sphingolipids

A

1) sphingomyelin
2) Cerebrosides
3) Gangliosides

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98
Q

What is the most complex group of sphingolipids?

A

Gangliosides

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99
Q

Gangliosides have what types of significance?

A

physiological and medical

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100
Q

Gangliosides are the primary components of what?

A

cell surface membranes

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101
Q

Gangliosides constitute a significant fraction of ____ lipids?

A

brain lipids (6%)

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102
Q

Gangliosides act as what for toxins?

A

receptors

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103
Q

What is the structure of Gangliosides?

A

ceramide oligosaccharides that include atleast one sialic acid residue (N-acetylneuraminic acid and its derivatives).

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104
Q

How does complex carbohydrate head groups of gangliosides act?

A

Their complex carbohydrate head groups, which extend beyond the surfaces of cell membranes, act as specific receptors for certain pituitary glycoprotein hormones that regulate a number of physiological functions.

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105
Q

Disorders of ganglioside break down are responsible for what type of hereditary disesease? which are characterized how?

A

Sphingolipid storage diseases such as Tay-Sachs disease which are characterized by an invariably fatal neurological deterioration.

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106
Q

GM1 Gangliosides include?

A
  • > D-Galactose
  • > N-Acetyl-D-galactosamine
  • > D-Galactose
  • > D-Glucose
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107
Q

GM2 gangliosides include?

A
  • > N-Acetyl-D-galactosamine
  • > D-Galactose
  • > D-Glucose
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108
Q

GM3 gangliosides

A
  • > D-Galactose

- > D-Glucose

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109
Q

Gangliosides are specific determinants of cell-cell recognition so they have inportant role in what?

A

growth and differentiation of tissues as well as in carcinogens (cancer generation).

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110
Q

What is the most common steroid in animals?

A

Cholesterol

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111
Q

What is the metabolic precursor to steroid hormones?

A

cholesterol

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112
Q

Steroids are derivatives of what?

A

cyclopentanoperhydrophenanthrene

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113
Q

Cholesterol is classified as what? why?

A

sterol because of its C3-OH group and its branched aliphatic side chain of 8 to 10 carbon atoms at C17.

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114
Q

Cholesterol is a major component of what? Present at what mol %.

A

animal plasma membranes which typically is present at 30-40 mol%

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115
Q

Cholesterol is present in lesser amount than 30-40 mol% in the membranes or what?

A

membranes of animal sub-cellular organelles.

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116
Q

What gives cholesterol its weak amphiphilic character?

A

Its polar OH group

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117
Q

What gives cholesterol its rigidity which is greater than other membrane lipids?

A

its fused ring system.

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118
Q

Cholesterol is abundant is _____ in which ~70% is esterified to what?

A

abundant in blood plasma lipoproteins where ~ 70% of it is esterified to long-chain fatty acids to form cholesteryl esters.

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119
Q

steroid hormaones regualte what?

A

a great variety of physiological functions including sexual development and carbohydrate metabolism.

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120
Q

plants contain little cholesterol but rather their most common sterol membrane components are what?

A

stigmasterol and Beta-sitosterol.

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121
Q

How does cholesterol differ fro, stigmasterol and Beta-sitosterol?

A

differ only in their aliphatic side chain.

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122
Q

Yeast and fungi have the sterol _____ which has what structure?

A

erosterol which has a C7 to C8 double bond.

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123
Q

Prokaryotes except for mycoplasmas contain what sterol?

A

little if any sterol

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124
Q

Gluccorticoids are what?

A

sterois used for biomolecule metabolism that deal with inflammation and stress

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125
Q

Mineralocorticoids are what?

A

steroids that deal with kidney osmosis (salt/water balance)

126
Q

Androgens and estrogens are what?

A

steroids that deal with sexual development and function

127
Q

Vitamin D is what?

A

a steroid hormone

128
Q

What are the actions of Eicosinoids?

A
  • blood pressure
  • Coagulation
  • pain
  • fever
129
Q

What are liposomes?

A

closed. self-sealing, solvent-filled vesicles

130
Q

The fluidity of lipid bilayer is ____ dependent and a function of ______ composition?

A

temperature dependent and a function of membrane composition (chain length and unsaturated)

131
Q

Biological membranes are composed of what?

A

phospholipods, cholosterol and proteins

132
Q

Phospholipids are made up of?

A

phosphoglycerides and sphingolipids

133
Q

what are membrane associated proteins?

A
  • integral
  • lipid linked
  • peripheral
134
Q

The protein/lipid ration in nerve cells is

A

0.23

135
Q

The protein/lipid ration in protein rich membrane is

A

3.2

136
Q

what is sonication?

A

agitation by ultrasonic vibrations

137
Q

what are liposomes?

A

phospholipids suspeneded in water that are sonicated transforming them from lipid bilayer to a liposome.

138
Q

what forms lipid bilayers and liposomes?

A

glycerolphospholipids

139
Q

What is the structure of oil on water?

A

a monomolecular layer on the surface of water form in which the polar heads of the amphiphilic oil molecules are immersed in the water and their hydrophobic tails extend into the air.

140
Q

What is oils effect on water?

A

calming effect because it largely reduced water’s surface tension due to oil’s weak intermolecular cohesion character of hydrocarbons rather than the strong interactions of water. Only calms smaller waves does not affect larger swells

141
Q

In aqueous solutions amphiphilic molecules like soaps and detergents form what?

A

micelles (globular aggregates whose hydrocarbons are not in contact with water).

142
Q

What does the micelles arrangement accomplish?

A

eliminate unfavorable contact between water and the hydrophobic tails of the amphiphiles yet permits the solvation of polar head groups.

143
Q

How is micelle formation a cooperative process?

A

An assembly of just a few amphiphiles will not shield its tails from contact with water.

144
Q

When do dilute aqueous solutions of amphiphiles form micelles?

A

When their concentration surpasses a certain critical micelle concentration (cmc).

145
Q

what is the value of critical micelle concentrations needed to form a micelle?

A

depends on the identity of the amphiphile and solution conditions. For relatively small single tail this value is around ~1mM while for biological lipids with two large hydrophobic tails this value is generally less than 10^-6 M.

146
Q

what type of micelles do single-tailed amphiphiles such as soap anions form?

A

spheroidal or ellipsoidal micelles because of their conical shapes (their hydrated head group are wider than their tails).

147
Q

Why do most amphilphiles that form a micelle have a narrow range of the number of amphilphiles?

A

Too few would expose the hydrophobic core while too many would give the micelle an energetically unfavorable hollow center filled with water. The large micelle could flatten out to eliminate hollow center but the resulting decrease of curvature at the flattened surfaces would also generate empty space filled with water.

148
Q

What types of lipids form lipid bilayers and liposomes?

A

Glycerophospholipids and sphingolipids

149
Q

What are the difference between the molecules that make up bilayers/liposomes an micelles?

A

Micelles are single tailed while liposome/bilayers have 2 tails

150
Q

Why are the amphiphiles more orless cylindrical in shape than micelles?

A

Because of the 2 hydrocarbon tails of glycerophospholipids and sphingolipids; the steric requirements of packing such molecules together yeilds a large disk like micelles that are extended biomolecular leaflets.

151
Q

Lipid bilayers are extremely impermeable to what?

A

ionic and polar substance

152
Q

How does lipid bilayer permeability of ionic and polar substances change? which suggest what?

A

the permeability of such substances increase with their solubilities in nonpolar solvents; which suggest that to penetrate a lipid bilayer a solute molecule must shed its hydration shell and become solvated the bilayer’s hydrocarbon core.

153
Q

Why are polar molecules so impermeable to mipid bilayers?

A

to penetrate a lipid bilayer a solute molecule must shed its hydration shell and become solvated the bilayer’s hydrocarbon core. This process is highly unfavorable for polar molecules.

154
Q

Lipid bilayers are appreciably permeable to what? why?

A

water despite its polarity its small molecular size makes it significantly soluble in the hydrocarbon core of lipid bilayers and therefore able to permeate them.

155
Q

Liposomes are promising vehicles for what? why?

A

delivering therapeutic agents, such as drugs, enzymes and genes s(for gene therapy) to particular tissues because their impermeability to many substances.

156
Q

How are liposomes absorbed by many cells?

A

through fusion with their plasma membranes.

157
Q

What type of lipsosome-delivered drugs are used currently?

A

some anti cancer agents and antibiotics

158
Q

How are lipid molecules transferred across a bilayer?

A

transverse diffusion/ flip flop (which is a rare event)

Or lateral diffussion

159
Q

what is transverse diffusion/flip flop and why is it such a rare event?

A

one way to transfer lipid molecules across a bilayer; flip flop requires the polar head groups of the lipid to pass through the hydrocarbon cor e of the bilayer. The half time of a flip flop event are minimally several days.

160
Q

the bilayer is a ____ dimensional fluid which the hydrocarbon chains undergo what?

A

a 2 dimensional fluid which the hydrocarbons undergo rapid fluxional (continously changing) motion involving rotations about their C-C bonds.

161
Q

The lateral diffusion rate of lipids molecules is quantitatively determined from what?

A

rate of fluorescence recovery after photobleaching(FRAP) as well as magnetic resonance measurements.

162
Q

Molecular dynamic simulations of lipid bilayers indicate that their lipid tails are what?

A

highly conformationally mobile due to rotation about their C-C bonds.

163
Q

How is the viscosity of lipid tails different at different parts of the tail?

A

The viscosity of these tails sharply increases closer to the lipid head groups because of their lateral mobilities are more constrained by interactions with the more rigid head groups.

164
Q

The methyl ends of the tails from the opposite leaflet of the bilayer frequently do what instead of forming entirely separate layers? why?

A

are frequently interdigitated; particularly in biological membranes because their various lipids have different lengths and/or kinked due to the presence of double bonds.

165
Q

In lipid bilayers is all the water on top of the lipid bilayer (polar heads)?

A

No; water molecules commonly penetrate well below the level of the head group and glycerol residues.

166
Q

A lipid bilayer typically consists of what?

A
  • ~30 A thick hydrocarbon core
  • core bounded on both sides by ~15 A thick interface regions containing rapidly fluctuating glmoerations of head groups, water, glycerol, carbonyl and methylene groups
167
Q

When a lipid bilayer cools below a characteristic transition temperature what happens?

A

It undergoes a phase change termed as order-disorder transition in which it becomes a gel-like solid; loses fluidity and hydrocarbons in chain become fully extended and packed in a hexagonal array as in crystalline paraffins.

168
Q

What is the tansition temperature of a bilayer?

A

vaires but typically in the range of 10-40 degrees C; increases with chain length and degree of saturation of its component fatty acid residues

169
Q

what is the melting temperature of a bilayer?

A

vaires; increases with chain length and degree of saturation of its component fatty acid residues.

170
Q

Cholesterol does what to membrane fluidity?

A

decreases membrane fluidity near the membrane surface.

171
Q

Why does cholesterol affect membrane fluidity the way it does?

A

decreases membrane fluidity at membrane surface because cholesterol’s rigid steroid ring system interferes with the motions of the fatty acid tails causing them to be more ordered.

172
Q

Does cholesterol spread through all the way through a lipid bilayer? what is this effect?

A

No it does not extend as far into a membrane as most lipids; It thus acts as a spacer that facilitates the increased mobility of fatty acids near the methyl ends.

173
Q

How does cholesterol affect membrane temperature range of order-disorder transition? Why?

A

Broadens it and in high concentrations completely abolishes it; because cholesterol inhibits crystallization (cooperative aggregation into ordered arrays) of fatty acids by fitting between them.

174
Q

Cholesterol acts as _____

A

membrane plasticizer

175
Q

The transition temperatures of mammalian membranes are well below what?

A

body temperature and hence all have fluid character

176
Q

Why is fluidity of biological membranes important?

A

allows embedded proteins to interact

177
Q

Bacteria and poikilothermic (cold-blooded) animals such as fish do what to their fatty acid compositions of membrane lipids? How?

A

modify thheir fatty acid compositions of membrane lipids with ambient temperature via lipid biosynthesis and degradation to maintain membrane fluidity.

178
Q

Most membranes are atleast ____ proteins except _____.

A

half proteins except for myelin membrane which is only 18% protein.

179
Q

Membrane proteins are operationally classified according to what?

A

How tightly they are associated with membranes

1) Integral or intrinsic proteins
2) Peripheral or extrinsic proteins

180
Q

Integral proteins are what?

A

tightly bound to membranes by hydrophobic forces and can only be separated by treatment with agents that disrupt membranes

181
Q

How can Integral proteins be separated from the membrane?

A

treatment with agents that disrupts membranes such as detergents, organic solvents, chaotropic agents (ions that disrupt water structure).

182
Q

What is Sodium dodecyl sulfate (SDS)?

A

a detergent used to disrupt membranes

183
Q

What is polyoxyethylenelauryl ether?

A

a detergent used to disrupt membranes

184
Q

What is polyoxyethylene-p-isooctylphenyl ether>

A

A detergent used to disrupt membranes.

185
Q

What is butanol an example of?

A

water-miscible organic solvent used to disrupt membranes

186
Q

What is glycerol an example of?

A

water-miscible organic solvent used to disrupt membranes

187
Q

What are peripheral or extrinsic proteins?

A

proteins that bind to the surface of membrane by binding to the lipid head group or its integral proteins through electrostatic or hydrogen binding interactions.

188
Q

Membrane free peripheral proteins behave how?

A

as water-soluble globular proteins and can be purified as such

189
Q

How are peripheral or extrinsic proteins dissociated from membranes?

A

By mild procedures that leave the membrane intact such as exposure to high ionic salt solutions (such as 1M NaCl), metal chealating agents or pH changes.

190
Q

Treating a membrane with 1 M NaCl does what?

A

causes its peripheral proteins to dissociate but leaves the membrane intact.

191
Q

Integral proteins are ______ orientated amphiphiles?

A

asymmetrically orientated

192
Q

The location of integral proteins on a membrane may be determined how?

A

through surface labeling, a technique employing agents that react with proteins but cannot penetrate membranes.

193
Q

An integral protein on the outer surface of an intact cell membrane binds _____

A

antibodies elicited against it

194
Q

An internal protein on the membrane’s inner surface can bind antibodies if what?

A

only if the membrane has been ruptured.

195
Q

some integral proteins are exposed to a specific surface of a membrane whereas others known as _____ do what?

A

transmembrane proteins span the membrane

196
Q

How many proteins are known to be completely buried in a membrane?

A

None all have some exposure to the aqueous environment.

197
Q

what does it mean that the integral protein is asymmetrical?

A

a particular membrane is invariably located on only one particular face of a membrane or in the case of a transmembrane protein, orientated in only one direction with respect to the membrane; Thus the oligosaccharides are located only one one side of teh integral protein exposed.

198
Q

Integral proteins are amphiphilic how?

A

the proteins segments immersed in a membrane’s nonpolar interior have predominately hydrophobic surface residues whereas those portions that extend into the aqueous environment are by and large sheathed with polar residues.

199
Q

The transmembrane domain as is common in many integral proteins forma what?

A

alpha helix

200
Q

Is glycine polar or nonpolar?

A

nonpolar

201
Q

Is alanine polar or nonpolar?

A

nonpolar

202
Q

Is valine polar or nonpolar?

A

nonpolar

203
Q

Is Leucine polar or nonpolar?

A

nonpolar

204
Q

Is Isoleucine polar or nonpolar?

A

nonpolar

205
Q

Is Methionine polar or nonpolar?

A

nonpolar

206
Q

Is proline polar or nonpolar?

A

nonpolar

207
Q

Is phenylalanine polar or nonpolar?

A

nonpolar

208
Q

Is Tryptophan polar or nonpolar?

A

nonpolar

209
Q

G is

A

Glycine

210
Q

A is

A

alanine

211
Q

V is

A

valine

212
Q

L is

A

Leucine

213
Q

I is

A

Isoleucine

214
Q

M is

A

Methionine

215
Q

P is

A

proline

216
Q

F is

A

phenylanine

217
Q

W is

A

Tryptophan

218
Q

In many integral proteins the hydrophobic segments does what?

A

anchors the active region of the protein to the membrane.

219
Q

Trypsin does what to membrane bound enzyme cytochrome b5?

A

cleaves the membrane-bound enzyme cytochrome b5 into a polar, enzymatically active ~85 residue N-terminal fragment and an ~50 residue C-terminal fragment that remains embedded in the membrane.

220
Q

How can you predict the position of transmembrane helix

A

It is going to be the largest peak; more than 85 kJ*mol-1 of free energy.

221
Q

The asymmetric orientation of integral proteins in the membrane is maintained how?

A

by their infinitesimal flipflop rates (even slower than those of lipids) which results from the greater sizes of the membrane protein “head groups” in comparison to those of lipids

222
Q

Are transmembrane proteins purely noonpolar

A

no has polar and non polar regions

223
Q

what type of protein is a transporter protein

A

Integral protein

224
Q

Bacteriorhodopsin (BR) is from where?

A

from the halophilic (salt loving) bacterium Halobacterium salinarium that inhabits salty place like the Dead sea.

225
Q

Bacteriorhodopsin contains how many hydrophobic helical rods?

A

7 hydrophobic helical rods

226
Q

Bacteriohodopsin is a _______ residue protein that does what?

A

247 residue protein is a light-driven proton pump; it generates a proton concentration gradient across the membrane that power the synthesis of ATP.

227
Q

Bacteriorhodopsin’s light-absorbing element, ______, is covalently bound to what?

A

light-absorbing element, retinal, is covalently bound to its Lys 216

228
Q

Retinal is a _____ which is responsible for bacteriorhodopsin membrane’s ______ color and is also the light sensitive element of what?

A

Retinal is a chromophore (light-absorbing group) which is responsible for the membrane’s purple color and is the light sensitive element of vision

229
Q

Under low O2 conditions bacteriorhodopsin develops what?

A

wide patches of purple membrane whose protein component is bacteriohodopsin (BR)

230
Q

The purple membrane of bacteriohodopsin is _____% protein and ____% lipid

A

75% protein and 25% lipids

231
Q

A membrane’s bacteriohodopsin (BR) molecules are arranged how?

A

IN a highly ordered 2-D array (a 2-D crystal)

232
Q

Bacteriohodopsin forms what type of trimer?

A

homotrimer

233
Q

Each of the 7 hydrophobic alpha helical rods of Bacteriohodopsin consist of what?

A

of approximately 25-residue alpha helical rods that each span the lipid bilayer in directions almost perpendicular to the bilayer plane.

234
Q

Bacteriohodopsin is _____ topic

A

polytopic (multispanning); span the lipid bilayer

235
Q

The ~20 A spaces between the protein molecules in the purple membrane are occupied by what?

A

the lipid bilayer

236
Q

Adjacent alpha helices which are largely _____ in character are connected ______

A

hydrophobic in character; connected in head-to-tail fashion by short polypeptide loops.

237
Q

What type of residue will be found in the exterior of integral membrane?

A

uncharged polar

238
Q

Serine is?

A

uncharged polar

239
Q

Threonine is?

A

uncharged polar

240
Q

Asparagine is?

A

uncharged polar

241
Q

Glutamine is?

A

uncharged polar

242
Q

Tyrosine is?

A

uncharged polar

243
Q

Cysteine is?

A

uncharged polar

244
Q

S is

A

Ser

245
Q

T is

A

Threonine

246
Q

N is

A

Asparagine

247
Q

Q is

A

Glutamine

248
Q

Y is

A

Tyrosine

249
Q

C is

A

Cysteine

250
Q

Where are the charged residues of the Alpha helices of bacteriorhodopsin located? Is this the same as other membrane pumps and channels?

A

protein charged residues near the surface of the membrane in contact with aqueous solvent. The internal charge residues line the center of the helix bundle of each monomer as to form a hydrophilic channel that facilitates the passage of protons; similar structure to other membrane pumps and channels.

251
Q

The primary photochemical process of photosynthesis in purple photosynthetic bacteria is mediated what?

A

mediated by the photosynthetic reaction center (PRC), a transmembrane (TM) protein, four other chromophores and a nonheme Fe(II) ion.

252
Q

A transmembrane (TM) protein consists of what?

A

atleast three nonidentical ~300 residue subunits that collectively bind four chlorophyll molecules

253
Q

The transmembrane portions of most TM proteins consist of what?

A

bundles of one to >20 helices, most of which are closely perpendicular to the membrane although some may be obliquely orientated and/or not fully transverse the membrane,

254
Q

The outer membranes of gram negative bacteria contain what?

A

contain embedded channel-forming proteins called porins

255
Q

The porins or gram negative bacteria are usually what?

A

trimers of identical 30- to 50- kD subunits that permit the passage of solutes of less than ~600D

256
Q

porins are located where?

A

in outer membranes of gram negative bacteria as well as in eukaryotes’s mitochondria membrane and chloroplast membranes.

257
Q

what is an indicator that mitochondria and chloroplast come from bacteria?

A

They contain porin

258
Q

Rhodobacter is an example of what?

A

porin

259
Q

OmpF and PhoE is an example of what?

A

E. coli porin

260
Q

porin forms what?

A

channels

261
Q

Each monomer of the porin homotrimeric protein predominately consists of what?

A

16-stranded antiparallel Beta-barrel which forms a solvent-accessible pore

262
Q

In the OmpF and phoE porin, the N- and C- termini associate how?

A

via a salt bridge in the 16th Beta-strand thereby forming a pseudocyclic structure.

263
Q

the side chains of OmpF and phoE porin at the membrane-exposured surface are _____ forming what?

A

nonpolar forming a hydrophobic band encircling the trimer.

264
Q

The side chains of OmpF and phoE porin atthe solvent-exposed surface of the protein, including the lining of walls for the aqueous channel are _____

A

polar

265
Q

TM proteins are ____ proteins?

A

Integral proteins

266
Q

Fatty acid amide hydrolase (FAAH) is what?

A

an enzyme that is an integral protein that binds to the cytoplasmic leaflet of the plasmic membrane.

267
Q

How is FAAH like cytochrome b5?

A

monotopic; an integral protein that binds to cytoplasmic leaflet of the plasma membrane.

268
Q

How does integral proteins structure differ from that of water soluble proteins.

A

Their organizations are opposite of each other

269
Q

What is the structure of integral proteins?

A

Their membrane-exposed residues are more hydrophobic on average than their interior residues that have average hydrophobicities and packing densities comparable to those of water-soluble proteins.

270
Q

For integral proteins What residues are at the C and N terminus?

A

hydrophilic segments (only a few) most of the outer region is still hydrophobic

271
Q

Integral and water-soluble proteins are are both stabilized by what?

A

the exclusion of their interior residues from the surrounding solvent, although in the case of integral proteins the solvent is the lipid bilayer

272
Q

What strengthens transmembrane proteins hydrogen bonds?

A

the low polarity and anhydrous environments

273
Q

In TM proteins the portions of the transmembrane secondary structural elementary (helices in BR and PRC and beta strands in the porins) that contact the bilayer’s hydrocarbon core consists mainly of?

A

nonpolar residues Ala, Ile, Leu, Val, Phe

274
Q

In TM proteins the portions of the transmembrane secondary structural elementary (helices in BR and PRC and beta strands in the porins) that penetrate the bilayer’s interface region, are enriched with?

A

Trp, and Tyr. Hence TM proteins’s hydrophobic transmembrane bands are bordered by rings of Trp and Tyr side chains that delineate the water-bilayer interface.

275
Q

The side chains of Tm proteins are orientated such that the polar portions (N and O atoms) extend _____ called? while ______ side chains located near the interface tend to be similar orientated.

A

extend into the polar region of the membrane called snorkeling; Lys and Arg located near the interface tend to be similar orientated.

276
Q

Phe, Leu, and Ile side chains in TM proteins tend to do what?

A

point inward toward the membrane core called antisnorkeling.

277
Q

G-Protein Coupled Receptors (GPCRs) are what?

A

very large superfamily of genes all encoding proteins containing 7 trans-membrane (7TM) helixes with little homology between family.

278
Q

G-Protein Coupled Receptors (GPCRs) are unique in eukaryotes these receptors are the major sensors involved in _______

A

transducing stimuli from outside the cell to inside the cell.

279
Q

ligands vary in size from ___ to ____

A

from very small olfactory molecules to multi-protein complexes

280
Q

G-proteins are what type of species?

A

trimeric species consisting of three subunit: Galph, GBeta and Glambda

281
Q

Galpha are _____ binding proteins that are what ?

A

GDP/GTP binding proteins are farnesylated at their C termini and thus associated with the intracellular membrane

282
Q

These Galpha proteins possess intrinsic GTP-ase activity, and cycle between?

A

an inactive GDP-bound form and an active GTP- bound form.

283
Q

Gbeta and G lambda are _____ species

A

dimeric

284
Q

there are _____ different genes for distinct Gbeta?

A

7

285
Q

There are ____ different genes for Glambda

A

12

286
Q

Exocytosis

A

Release of vesicle contents outside of cell.

287
Q

Endocytosis

A

Vesicles form around something outside cell,

Bringing it inside cell.

288
Q

Vesicles are coded with what?

A

proteins

289
Q

post translationally translocated secretory proteins have signal sequences that are only _______

A

only mildly hydrophobic

290
Q

where are secretory proteins synthezied?

A

cytoplasm atleast partially some cannot be translocated until after fully synthezied in the cytoplasm

291
Q

co and post translation is mediated by

A

translocon which a passive pore but noes not have free energy that drives translocation

292
Q

in cotranslation translocation is mediated by

A

ribosomially mediated extension of polypeptide

293
Q

the rough RER contains ______ channels?

A

ion conducting channels

294
Q

what happens to ion conducting channels when RER is treated with puromycin? what does this suggest?

A

increases; puromycin is an antibiotic that causes ribosome to prematurely release growinf polypeptides suggesting the channels are usually pluged by the presence of polypeptides.

295
Q

the ion channels in RER are callled?

A

translocons

296
Q

translocons are?

A

ion conducting channels that enclose aqueous pores that completely span the ER membrane

297
Q

shortly after polypeptide synthesis is completed the partially processed proteins are transported to ______. where what happens?

A

golgi apparatus where further post-translational processing mostly glycosylation.

298
Q

the Golgi stack has two faces which are

A

cis golgi network snc trans golgi network

299
Q

the cis Golgi stack face is what?

A

is opposite ER and is port through which proteins enter the Golgi apparatus

300
Q

The trans Gogi face is what?

A

processed proteins exit to final destination

301
Q

anterograde transport

A

one form of transportation; cis to trans where cargo within membrane vesicles that bud off one compartment and fuse with another

302
Q

cisterinal progression or maturation?

A

proteins carried as passenger of Golgi compartment that transit Golgi stack, cis eventually becomes tran cisternae. mediated by retorograde transport.

303
Q

what are coated vesicles used for?

A

vehicle transport of proteins between RER, Golgi, and finalndestination

304
Q

coated vesicles buds off _____ and fuses to ____

A

buds off from membrane of origin and later fuses to its target membrane.

305
Q

carbohydrate moieties of TM glycoproteins and GPI anchors of GPI anchors of GPI linked proteins occur

A

only on external surface of plasma membrane

306
Q

clathrin is an example of what?

A

coated vessicle

307
Q

clathrin does wbat

A

transport TM, GPI linked and secreted proteins from the Golgi to plasma membrane.

308
Q

COPI carries

A

retro and antertlgrade transport of proteins between Golgi compartments and returns escaped ER protein from Golgi to ER

309
Q

COPII

A

transports from ER to Golgi

310
Q

Clathrin shape?

A

polyhedral cage

biochemistry (6 decks)

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