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Flashcards in Amino Acids and Protein Structure Deck (113):
1

What are the two main functional roles of proteins in humans?

1.) Dynamic functions -ex: globular proteins (spherical) 2.)Structural proteins -ex: fibrous proteins (elongated)

2

The vast majority of types of protein

-small in abundance

-Spherical

Globular proteins

3

Small in number of types

-large in abundance

-Elongated

Fibrous (structural) proteins

4

What are three transport proteins?

1.) hemoglobin 2.) transferrin 3.) ion translocating ATPases

5

What are three types of gene expression proteins?

1.) Histones 2.) Polymerase 3.) Transcription factors

6

What are two proteins that function in the catalysis of Chemical Transformation?

1.) Glucose-6-phosphate dehydrogenase

2.) Pyruvate Kinase

-both are enzymes

7

Single base substitutions in DNA can cause disease by

Altering protein structure and function

8

What is the central dogma of molecular biology?

DNA ---> RNA ---> Protein

9

Sickle Cell disease is caused by a

Glutimate 6 is substituted with Valine

10

Amino acids can undergo post translational modifications to give far more than 20 types. What are some of the post translational modifications a.a.'s can undergo?

Methylation, formylation, adenylation, etc

11

Amino acids exist as zwitterions, meaning they are

Overall neutral, but have charges

12

What is the pKa of the amino group of an a.a.?

pKa = 9

13

What is the pKa of the carboxyl group of the a.a.?

pKa = 2

14

When pH = pKa, the ratio of protonated to deprotonated amino acid is?

[protonated] = [deprotonated]

15

Proteins are made up exclusively of

L-aminos

16

Generally toxic, but can exist in cell walls

D-aminos

17

To tell configuration, orient amino so you are looking down the H-C bond. For L-aminos, the R group should be

To the right of the COO-

18

What is the driving force in protein folding?

The Hydrophobic effect

19

The surface of a protein is not exclusively

Polar -will be a mixture of polar and nonpolar

20

The interior of a protein is almost exclusively

Hydrophobic side chains

21

A globular group of 100 to 300 amino acids

Domain

22

Out of the 100-300 a.a.'s making up a domain, how many are used for catalysis?

Typically less than a dozen.

-The rest serve structural purposes

23

The sulfur in Methionine is

Inert

24

The only achiral amino acid is

Glycine

25

Provides rigidity and stability to protein

-Only amino acid that occasionlly exists in the cis conformation (15%)

Proline

26

Proline is classified as an

imino acid

27

Aromatic a.a.'s can be on cell surface because of the enhanced stability resulting from

Aromaticity

28

In order to form, a hydrogen bond requires

1.) The right distance (3 Angstroms)

2.) The right geometry

29

The 6 neutral polar amino acids are perfect for

Post translational modifications

30

What three aminos are easily phosphorylated?

-readily reversible

Serine, Threonine, and Tyrosine

31

Add phosphate groups

Kinases

32

Remove phosphate groups

Phosphatases

33

Adding sugar to an amino acid

-creates hydrophilic surface of protein

-a great solubilizer

Glycosylation

34

What are the two types of glycosylation?

1.) O-linked (serine and threonine)
2.) N-linked (Aparagine)

35

Do not occur within cytoplasmic proteins because the cellular environment is highly reducing

-only occurs in oxidizing environments

Disulfide bonds

36

Disulfide bonds are not a driving force in

Protein folding

37

Disulfide bonds readily occur in

Extracellular proteins or domains

38

The inside of cells are reducing environments due to reducing agents such as

Glutathione

39

Has the only side chain that will cross-link protein chains together without the addition of post translational modifications

Cysteine

40

Contains 6 cysteines and three disulfide bonds

-2 interchain

-1 intrachain

Insulin

41

What is the pKa of the side chains of Glutamate and Aspartate?

pKa = 4

42

Great for the surface of a protein because they carry a -1 charge

Aspartate and Glutamate

43

What happens to the pKa of Asp and Glu's side chains if it is unfavorable to deprotinate them?

-i.e. in the hydrophobic interior or if the two negative charges would be too close together

The pKa increases

-shows that pKa's are actually variable

44

The pKa of glutimate increases when it is directly next to an

Aspartate

45

Which amino acid plays a role in metabolism as a nitrogen donor?

Glutamate

46

Why is Glutamate used to incorporate nitrogen into a molecule withing the cell?

Because ammonia is too toxic to be the donor

47

What is the functional group of the Histidine side chain?

imidazole

48

What is the functional group on the side chain of Lysine?

Amine

49

What is the Functional group on the side chain of Arginine?

Guanidinium

50

What aminos are always positively charged at physiological pH?

Lysine and Arginine

51

Amino with the only side chain whose pKa is close to physiological pH. Thus its protonation state varies in the physiological pH range

Histidine

52

A great way to regulate something by pH

-rare but a very important a.a.

Histidine

53

Occasionally involved in helping to scaffold the protein

Arginine (Arg, R)

54

Lysine's and Arginine's tend to pair with

Aspartate (Asp, D) and Glutamate (Glu, E)

55

Important for pH dependent regulation

Histidine's

56

For an amino acid titration curve, the isoelectric point (IpH) is the

plateau between the two equivalence points

57

When looking at peptides, the biochemical unit is described as being made up of

a single amino acid

58

When looking at peptides, the structural unit is described as

The unit ranging from one alpha carbon to the next

59

What type of reaction is the peptide bond formation?

Dehydration

60

What are the characteristics of the peptide bond?

It is Rigid, Planar, and Polar

-has partial double bond character

61

Refers to the two alpha carbons of a structural unit being on opposite corners of the plane

trans configuration

62

15% of prolines are in the

cis configuration

63

Why is the trans configuration preffered in peptides?

cis configurations lead to steric hindrance

64

Specify the path of the polypeptide backbone

phi and psi angles

65

How many sets of phi and psi angles can repeat without steric collisions?

Two

66

The result of the fact that only two sets of φψ angles can be repeated without steric collisions is

The generation of the repetitive secondary structures:

1.) alpha helix (coiled chain)

2.) beta strand (extended chain)

67

Defined by covalent bonds including disulfide bridges

Primary structure

68

Defined by H-bonds

-alpha helix, beta sheet

Secondary Structure

69

The alpha helix is an example of a

Coiled coil

70

All of the carbonyls of an alpha helix point in the

Same direction

-give a net dipole

71

In an alpha helix, what is the charge of the

1.) C-terminus

2.) N-terminus

1.) negatively charged

2.) Positively charged

72

Help to minimize the polarity of an alpha helix

H-bonds within the backbone

73

In an alpha helix, every carbonyl oxygen and amine nitrogen are involved in an H bond. Where the nth atom binds to the

n+4th atom

74

What are the dimensions of an alpha helix

3.6 residues/turn

5.4 Å / turn

1.5 Å rise / residue

75

What are the three types of helices?

1.) hydrophobic

2.) Amphipathic

-one side of helix is hydrophobic and the other is polar

3.) Polar

76

What are the three perpendicular directions of the beta sheet?

1.) directions of strands (polypeptide chain) 2.) H-bonds between strands 3.) Side chains above and below the plane of the sheet

77

Beta strands are connected with one another to form beta sheets by

H-bonds between strands

78

What are the dimensions of a beta sheet

~3.5 Å / residue

79

Cover twice the distance of an alpha helix

beta strand

80

What are the two types of beta sheets

Parallel and anti-parallel

81

Made up of alpha-beta motifs, where the beta sheets are connected by alpha helices

-this burries them in the interior

Parallel Sheet

82

What is the polarity and location of the Parallel beta sheet?

Hydrophobic and burried in the protein interior

83

What is the polarity and location of the anti-parallel beta sheet?

Amphipathic and exposed on the surface of the protein

84

Point alternatively above and below the plane of the beta sheet

Side chains

85

Non-repetitive secondary structures

-usually located at the proteins surface

-50% of residues in globular proteins

Turns and Loops

86

Turns and loops often serve as

Binding surfaces and active sites

87

What are the most common secondary motifs in proteins?

1.) helix-loop-helix 2.) Greek key 3.) beta-alpha-beta

88

A very stable secondary fold

-direction of arrow points to C-Terminus

Greek Key

89

How can we connect two beta strands that lie parallel to one another?

With an alpha helix (beta-alpha-beta motif)

90

What forces stabilize proteins?

1.) Hydrophobic interactrions

2.) van der Waals Interactions

3.) Hydrogen Bonds

4.) Ionic Interactions

5.) Disulfide Bridges

91

What is an example of an ionic interaction that could help stabilize a protein?

Lysine interacting with an Arginine

92

The energy difference between a proteins folded and unfolded state is very

Small -

they are susceptible to denaturation

93

In order to function, proteins need to be

Dynamic (able to move)

94

Structural/functional units of 100-300 amino acids

-Typically globular units

-10-30 kDa

-often contiguous in primary structure

Domains

95

Carries iron in a heme

-it's helices are packed anti-parallel to one another

Cytochrome b562

96

Hard to classify as either hydrophobic or hydrophilic

Glycene's

97

A popular example of the perpendicular packing of helices -1st protein structure to be successfully determined

Myoglobin

98

Made up of anti-parallel beta sheets which fold to create a hydrophobic interior and a hydrophilic surface

-it gets its name from its continuous wrapping sequence

Up-down beta barrel

99

Carries vitamin A around the body because vitamin A is completely insoluble in water

Retinol (an up-down beta barrel)

100

What is the difference between a transmembrane up-down barrel and a cellular up-down barrel?

The transmembrane barrel will be hydrophobic on the outside and hydrophilic on the inside

101

Found in the lense of your eye

-an example of a stable protein, it is not synthesized, so if you lose it, you go blind

γ-Crystallin

102

y-Crystallin is an example of a

Greek key barrel

103

Get's rid of oxygen radicals in the body

Superoxide dismutase

104

What is the most common fold in the human body?

-a parallel beta barrel in the center

-layer of protective Amphipathic alpha helices on the outside

-goes beta-alpha-beta-alpha

α/β Singly Wound Barrel

105

In the α/β Singly Wound Barrel the helices are

Amphipathic, outside is polar, inside is non polar

106

Don't really form barrels

-Stay as flat/twisted sheets with alpha Helices on either side

Doubly Wound α/β

107

What is this structure?

Q image thumb

Up-Down β Barrel

108

What is the difference between these two Up-Down β Barrels?

Q image thumb

Retinol is cellular, Phosphorin is transmembrane

109

Which motif is represented here?

Q image thumb

Greek Key Barrel

110

Which structural motif is represented here?

Q image thumb

anti-parallel beta barrel

111

Which structural motif is represented here?

Q image thumb

α/β Singly Wound Barrel

112

Which structural motif is represented here?

Q image thumb

α/β Singly Wound Barrel

113

Which structural motif is represented here?

Q image thumb

Doubly Wound α/β 

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