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BMS > Amino Acids and Protein Structure > Flashcards

Amino Acids and Protein Structure Flashcards

1
Q

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

A

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

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2
Q

The vast majority of types of protein

  • small in abundance
  • Spherical
A

Globular proteins

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3
Q

Small in number of types

  • large in abundance
  • Elongated
A

Fibrous (structural) proteins

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4
Q

What are three transport proteins?

A

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

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5
Q

What are three types of gene expression proteins?

A

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

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6
Q

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

A
  1. ) Glucose-6-phosphate dehydrogenase
  2. ) Pyruvate Kinase
    - both are enzymes
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7
Q

Single base substitutions in DNA can cause disease by

A

Altering protein structure and function

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8
Q

What is the central dogma of molecular biology?

A

DNA —> RNA —> Protein

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9
Q

Sickle Cell disease is caused by a

A

Glutimate 6 is substituted with Valine

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10
Q

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?

A

Methylation, formylation, adenylation, etc

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11
Q

Amino acids exist as zwitterions, meaning they are

A

Overall neutral, but have charges

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12
Q

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

A

pKa = 9

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13
Q

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

A

pKa = 2

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14
Q

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

A

[protonated] = [deprotonated]

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15
Q

Proteins are made up exclusively of

A

L-aminos

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16
Q

Generally toxic, but can exist in cell walls

A

D-aminos

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17
Q

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

A

To the right of the COO-

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18
Q

What is the driving force in protein folding?

A

The Hydrophobic effect

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19
Q

The surface of a protein is not exclusively

A

Polar -will be a mixture of polar and nonpolar

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20
Q

The interior of a protein is almost exclusively

A

Hydrophobic side chains

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21
Q

A globular group of 100 to 300 amino acids

A

Domain

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22
Q

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

A

Typically less than a dozen.

-The rest serve structural purposes

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23
Q

The sulfur in Methionine is

A

Inert

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24
Q

The only achiral amino acid is

A

Glycine

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25
Q

Provides rigidity and stability to protein

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

A

Proline

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26
Q

Proline is classified as an

A

imino acid

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27
Q

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

A

Aromaticity

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28
Q

In order to form, a hydrogen bond requires

A
  1. ) The right distance (3 Angstroms)
  2. ) The right geometry
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29
Q

The 6 neutral polar amino acids are perfect for

A

Post translational modifications

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30
Q

What three aminos are easily phosphorylated?

-readily reversible

A

Serine, Threonine, and Tyrosine

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31
Q

Add phosphate groups

A

Kinases

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32
Q

Remove phosphate groups

A

Phosphatases

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33
Q

Adding sugar to an amino acid

  • creates hydrophilic surface of protein
  • a great solubilizer
A

Glycosylation

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34
Q

What are the two types of glycosylation?

A
  1. ) O-linked (serine and threonine)
  2. ) N-linked (Aparagine)
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35
Q

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

-only occurs in oxidizing environments

A

Disulfide bonds

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36
Q

Disulfide bonds are not a driving force in

A

Protein folding

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37
Q

Disulfide bonds readily occur in

A

Extracellular proteins or domains

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38
Q

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

A

Glutathione

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39
Q

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

A

Cysteine

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40
Q

Contains 6 cysteines and three disulfide bonds

  • 2 interchain
  • 1 intrachain
A

Insulin

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41
Q

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

A

pKa = 4

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42
Q

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

A

Aspartate and Glutamate

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43
Q

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

A

The pKa increases

-shows that pKa’s are actually variable

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44
Q

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

A

Aspartate

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45
Q

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

A

Glutamate

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46
Q

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

A

Because ammonia is too toxic to be the donor

47
Q

What is the functional group of the Histidine side chain?

A

imidazole

48
Q

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

A

Amine

49
Q

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

A

Guanidinium

50
Q

What aminos are always positively charged at physiological pH?

A

Lysine and Arginine

51
Q

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

A

Histidine

52
Q

A great way to regulate something by pH

-rare but a very important a.a.

A

Histidine

53
Q

Occasionally involved in helping to scaffold the protein

A

Arginine (Arg, R)

54
Q

Lysine’s and Arginine’s tend to pair with

A

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

55
Q

Important for pH dependent regulation

A

Histidine’s

56
Q

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

A

plateau between the two equivalence points

57
Q

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

A

a single amino acid

58
Q

When looking at peptides, the structural unit is described as

A

The unit ranging from one alpha carbon to the next

59
Q

What type of reaction is the peptide bond formation?

A

Dehydration

60
Q

What are the characteristics of the peptide bond?

A

It is Rigid, Planar, and Polar

-has partial double bond character

61
Q

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

A

trans configuration

62
Q

15% of prolines are in the

A

cis configuration

63
Q

Why is the trans configuration preffered in peptides?

A

cis configurations lead to steric hindrance

64
Q

Specify the path of the polypeptide backbone

A

phi and psi angles

65
Q

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

A

Two

66
Q

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

A

The generation of the repetitive secondary structures:

  1. ) alpha helix (coiled chain)
  2. ) beta strand (extended chain)
67
Q

Defined by covalent bonds including disulfide bridges

A

Primary structure

68
Q

Defined by H-bonds

-alpha helix, beta sheet

A

Secondary Structure

69
Q

The alpha helix is an example of a

A

Coiled coil

70
Q

All of the carbonyls of an alpha helix point in the

A

Same direction

-give a net dipole

71
Q

In an alpha helix, what is the charge of the

  1. ) C-terminus
  2. ) N-terminus
A
  1. ) negatively charged
  2. ) Positively charged
72
Q

Help to minimize the polarity of an alpha helix

A

H-bonds within the backbone

73
Q

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

A

n+4th atom

74
Q

What are the dimensions of an alpha helix

A
  1. 6 residues/turn
  2. 4 Å / turn
  3. 5 Å rise / residue
75
Q

What are the three types of helices?

A
  1. ) hydrophobic
  2. ) Amphipathic
    - one side of helix is hydrophobic and the other is polar
  3. ) Polar
76
Q

What are the three perpendicular directions of the beta sheet?

A

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

77
Q

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

A

H-bonds between strands

78
Q

What are the dimensions of a beta sheet

A

~3.5 Å / residue

79
Q

Cover twice the distance of an alpha helix

A

beta strand

80
Q

What are the two types of beta sheets

A

Parallel and anti-parallel

81
Q

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

-this burries them in the interior

A

Parallel Sheet

82
Q

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

A

Hydrophobic and burried in the protein interior

83
Q

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

A

Amphipathic and exposed on the surface of the protein

84
Q

Point alternatively above and below the plane of the beta sheet

A

Side chains

85
Q

Non-repetitive secondary structures

  • usually located at the proteins surface
  • 50% of residues in globular proteins
A

Turns and Loops

86
Q

Turns and loops often serve as

A

Binding surfaces and active sites

87
Q

What are the most common secondary motifs in proteins?

A

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

88
Q

A very stable secondary fold

-direction of arrow points to C-Terminus

A

Greek Key

89
Q

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

A

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

90
Q

What forces stabilize proteins?

A
  1. ) Hydrophobic interactrions
  2. ) van der Waals Interactions
  3. ) Hydrogen Bonds
  4. ) Ionic Interactions
  5. ) Disulfide Bridges
91
Q

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

A

Lysine interacting with an Arginine

92
Q

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

A

Small -

they are susceptible to denaturation

93
Q

In order to function, proteins need to be

A

Dynamic (able to move)

94
Q

Structural/functional units of 100-300 amino acids

  • Typically globular units
  • 10-30 kDa
  • often contiguous in primary structure
A

Domains

95
Q

Carries iron in a heme

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

A

Cytochrome b562

96
Q

Hard to classify as either hydrophobic or hydrophilic

A

Glycene’s

97
Q

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

A

Myoglobin

98
Q

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

A

Up-down beta barrel

99
Q

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

A

Retinol (an up-down beta barrel)

100
Q

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

A

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

101
Q

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

A

γ-Crystallin

102
Q

y-Crystallin is an example of a

A

Greek key barrel

103
Q

Get’s rid of oxygen radicals in the body

A

Superoxide dismutase

104
Q

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
A

α/β Singly Wound Barrel

105
Q

In the α/β Singly Wound Barrel the helices are

A

Amphipathic, outside is polar, inside is non polar

106
Q

Don’t really form barrels

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

A

Doubly Wound α/β

107
Q

What is this structure?

A

Up-Down β Barrel

108
Q

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

A

Retinol is cellular, Phosphorin is transmembrane

109
Q

Which motif is represented here?

A

Greek Key Barrel

110
Q

Which structural motif is represented here?

A

anti-parallel beta barrel

111
Q

Which structural motif is represented here?

A

α/β Singly Wound Barrel

112
Q

Which structural motif is represented here?

A

α/β Singly Wound Barrel

113
Q

Which structural motif is represented here?

A

Doubly Wound α/β

BMS (62 decks)

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