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BIOCH 200 > Protein Structure and Function > Flashcards

Protein Structure and Function Flashcards

1
Q

What do Proteins Do?

A 
Structure
Movement
Catalysis
Communication
Transport
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2
Q

What is a Zwitterion?

A

A molecule with a neutral overall charge with both positive and negative charges

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3
Q

Draw a Generic Amino Acid at pH 7

A

See Cheat Sheet

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4
Q

Charge of Generic Amino Acid at pH=1

A

Positive

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5
Q

Charge of Generic Amino Acid at pH=14

A

Negative

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6
Q

Draw a Generic Amino Acid at pH 1

A

See Cheat Sheet

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7
Q

Draw a Generic Amino Acid at pH 14

A

See Cheat Sheet

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8
Q

Hydrophobic Amino Acids

A 
Ala
Val
Leu
Ile
Phe
Trp
Met
Pro
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9
Q

Polar Amino Acids

A 
Gly
Ser
Thr
Tyr
Cys
Asn
Gln
His
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10
Q

Charged Amino Acids

A

Asp (-)
Glu (-)
Lys (+)
Arg (+)

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11
Q

Alanine

A

Smallest chiral amino acid

Aliphatic

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12
Q

Draw Alanine

A

See Cheat Sheet

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13
Q

Valine

A

Aliphatic

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14
Q

Draw Valine

A

See Cheat Sheet

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15
Q

Leucine

A

Aliphatic

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16
Q

Draw Leucine

A

See Cheat Sheet

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17
Q

Isoleucine

A

Isomer of leucine

Aliphatic

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18
Q

Draw Isoleucine

A

See Cheat Sheet

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19
Q

Phenylalanine

A

Aromatic

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20
Q

Draw Phenylalanine

A

See Cheat Sheet

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21
Q

Tryptophan

A

Aromatic
Heterocyclic
Bulky
H donor

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22
Q

Draw Tryptophan

A

See Cheat Sheet

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23
Q

Methionine

A

Honourary aliphatic

Thioether

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24
Q

Draw Methionine

A

See Cheat Sheet

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25
Q

Proline

A

Aliphatic

Cyclic Structure

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26
Q

Draw Proline

A

See Cheat Sheet

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27
Q

Glycine

A

Achiral
Weakly polar
Very small
Flexible

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28
Q

Draw Glycine

A

See Cheat Sheet

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29
Q

Serine

A

Hydroxyl Group

H donor

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30
Q

Draw Serine

A

See Cheat Sheet

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31
Q

Threonine

A

Hydroxyl group
H donor
Can be phosphorylated

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32
Q

Draw Threonine

A

See Cheat Sheet

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33
Q

Tyrosine

A 
Aromatic
Hydroxyl group
H donor
Hydrophobic interactions
Can be phosphorylated
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34
Q

Draw Tyrosine

A

See Cheat Sheet

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35
Q

Cysteine

A

Thiol group
Forms disulphide bonds with Cys
pKa=6.5

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36
Q

Draw Cysteine

A

See Cheat Sheet

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37
Q

Asparagine

A

Amide group

H donor and H acceptor

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38
Q

Draw Asparagine

A

See Cheat Sheet

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39
Q

Glutamine

A

Carbamide group

H donor and H acceptor

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40
Q

Draw Glutamine

A

See Cheat Sheet

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41
Q

Histidine

A

Aromatic
Acid or base at pH=7
Proton donor/acceptor
pKa=6

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42
Q

Draw Histidine

A

See Cheat Sheet

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43
Q

Aspartate

A 
(-) charge
Acidic
H acceptor
Polar
pKa=4
44
Q

Draw Aspartate

A

See Cheat Sheet

45
Q

Glutamate

A 
(-) charge
Acidic
Polar
H acceptor
pKa=4
46
Q

Draw Glutamate

A

See Cheat Sheet

47
Q

Lysine

A 
(+) charge
Basic
H donor
Polar
pKa=10
48
Q

Draw Lysine

A

See Cheat Sheet

49
Q

Arginine

A 
(+) charge
Basic
Guanido group
Polar
H donor
pKa=12.5
50
Q

Where are Polar Side Chains Found?

A

On protein surfaces

  • interacts with water
  • polar, uncharged amino acids
51
Q

Where are Nonpolar Side Chains Found?

A

In the protein core

-minimizes interaction with water

52
Q

Sense of Direction In Peptides

A

N-terminus to C-terminus

53
Q

What is Primary Structure?

A

The sequence of amino acids in a polypeptide

Peptide bonds join each amino acid to the next

54
Q

What are Amino Acids Called in Polypeptides?

A

Residues because of the removal of water

55
Q

Properties of Primary Structure

A

Rigid and planar = partial double bond character stabilizes bond - no rotation around C-N bond
Electrons in peptide bonds are somewhat delocalized, generating two resonance forms
Functional groups in peptide bonds are potential H-bond acceptors or donors

56
Q

Polypeptide Backbone

A

The polymerization between amino and carboxylic groups attached to the alpha carbon of each amino acid

57
Q

Primary Structure

A

Amino acid sequence

58
Q

Secondary Structure

A

Alpha-helix and Beta-sheets

59
Q

Tertiary Structure

A

3D structure

60
Q

Quaternary Structure

A

A complex of protein molecules

61
Q

Why are folding conformations limited?

A

Steric clash - high energy and unfavourable
Must minimize any steric conflict
Must maximize H-bonds in structures

62
Q

Alpha-helix Structure

A

Carbonyl oxygen of each residue forms an H-bond with the backbone -NH group
Core composed of backbone - no side chains
Complete H-bond satisfaction
Handedness doesn’t change with orientation
Residues 3-4 apart in the primary structure are close in the secondary structure

63
Q

Beta-sheet Structure

A

Multiple beta-strands are arranged side by side
Strands are joined by loops or other structures
Can be parallel or antiparallel

64
Q

Stabilizing Forces in Secondary Structure

A 
Alpha-helix = H-bonds between backbone CO and NH groups in same helices
Beta-sheet = H-bonds between backbone CO and NH groups of neighbouring strands
65
Q

Irregular Secondary Structure

A

Helices and sheets are regular secondary structure
-the backbone has the same configuration for every amino acid
Elements of regular secondary structure are linked by irregular ones
NOT DISORDERED

66
Q

Tertiary Structure Characteristics

A

Arrangement of atoms in a single polypeptide
-arrangement of secondary structure in relation to each other
-positions of amino acid side chains
-prosthetic groups
Can be fibrous or globular

67
Q

Fibrous Proteins

A

Insoluble in aqueous environments
Long protein filaments
Structural or connective proteins

68
Q

Globular Proteins

A

Soluble in aqueous solutions

Fold into compact structures with nonpolar cores and polar surfaces

69
Q

Hydrophobic Interactions in Globular Proteins

A

Hydrophobic side chains = interior of globular protein
Hydrophilic side chains = surface of globular protein
Irregular structure on the surface of globular proteins =interact with solvent

70
Q

Stabilization of Tertiary Structure

A

Hydrophobic effect
H-bonding
Ion pairs (salt bridges)
Disulphide bridges

71
Q

Hydrophobic effect in Tertiary Structure

A

The shape of globular proteins depends on relative positions of hydrophobic amino acids in the proteins primary structure
Driving force via which soluble proteins adopt and maintain their tertiary structure

72
Q

H-bonding in Tertiary Structure

A

Weak forces between closely positioned polar side chains = fine-tunes and stabilize secondary and tertiary structure
Also forms between backbone groups and side chains

73
Q

Ion pairs in Tertiary Structure

A

Electrostatic interactions between closely positioned formal charged groups
Charges will depend on the pH of the environment

74
Q

Disulphide bonds in Tertiary Structure

A

Covalent bonds between closely positioned cysteines
Forms stabilizing cross-units for extracellular proteins
NOT found in quaternary structure

75
Q

Domain

A

Polypeptide segment that has folded into a single structural subunit with a hydrophobic core

76
Q

Motif

A

A short region of a polypeptide with a recognizable 3D shape

77
Q

Prosthetic Group

A

The non-peptide component that is permanently incorporated into a protein

78
Q

Apoprotein

A

Protein without characteristic prosthetic group

79
Q

Holoprotein

A

Apoprotein combined with its prosthetic group

80
Q

Structure of Heme

A

Circular and planar
The porphyrin ring contains a Fe2+ ion coordinated between the four N atoms
Two substituents at the bottom of the ring are polar charged propionyl groups - the rest are non-polar aliphatic

81
Q

Function of Myoglobin

A

Facilitates O2 diffusion through muscle tissue
Acts as a local reserve of O2 during intense exercise
Stores O2 in aquatic animals

82
Q

Structure of Myoglobin

A 
Single polypeptide
8 helices and irregular structure 
Heme prosthetic group 
Hydrophobic pocket between helix E and F
Polyphyrin ring held in place by hydrophobic interactions and by a coordination bond between Fe2+ and a proximal histidine
83
Q

Function of Proximal Histidine

A

Binds heme into the heme-binding pocket and prevents oxidation of the iron atom

84
Q

Function of Distal Histidine

A

Increases O2 binding affinity
Lowers affinity for other molecules
Increases specificity for O2

85
Q

Oxygen Binding to Myoglobin

A

Hyperbolic Plot
Reversible
When pO2=Kd: [Mb]=[MbO2]

86
Q

Function of Hemoglobin

A

O2 transport from lungs to tissues

Reversibly binds/releases O2

87
Q

Structure of Hemoglobin

A

4 polypeptide chains
2 helices and 2 sheets
1 heme/polypeptide - binds 4 O2/Hb

88
Q

Oxygen Binding to Hemoglobin

A

O2 at the 6th coordination position of a Fe2+ ion in a heme ring
His F8 (proximal) and His E7 (distal) don’t change position
Sigmoidal binding curve
-cooperative binding affinity
-reflects a change in binding affinity

89
Q

Tense State

A

Low affinity for O2
Deoxy Hb
Larger central cavity

90
Q

Relaxed State

A

High affinity for O2
Oxy Hb
Smaller central cavity

91
Q

Allosteric Effectors

A

Compounds which, upon binding, alter affinity at other binding sites

92
Q

Homoallosteric

A

The binding of the effector affects further binding of the same compound

93
Q

Example of Homoallosteric Activator

A

O2 is a homoallosteric activator of Hb

94
Q

Heteroallosteric

A

The binding of the effector affects further binding of a different compound

95
Q

Example of Heteroallosteric Inhibitors

A

BPG and H+ are heteroallosteric inhibitors for O2

96
Q

Allosteric Activators

A

Increases binding affinity

97
Q

Allosteric Inhibitors

A

Decreases binding affinity

98
Q

Events in O2 binding to Hb

A

T state = no O2 bound

  • O2 binds to a subunit
  • Fe2+ moves into plane of heme
  • His F8 moves with iron
  • Helix F moves
  • Subunit interface changes
  • Subunit interface changes affects other subunits
  • Helix F/His F8/Fe2+ movement
  • O2 binding site becomes high affinity
  • O2 binds more readily to other binding sites
99
Q

What Happens When BPG Binds to Deoxyhemoglobin

A

BPG is essential for the formation of the T state
BPG binds to the central cavity of deoxyhemoglobin
The (-) charges on BPG interact with the (+) charged groups on the protein that are directed into the central cavity
The central cavity in oxyhemoglobin is too small to accommodate BPG

100
Q

Hydrogen Ions and Hb

A

Protons lower pH
Lowering pH leads to protonation of side chains and functional groups
Groups associated with BPG binding become protonated
-enhance BPG binding
-reduce O2 binding
Bohr Effect

101
Q

Lungs and Hb

A

Lungs have high ppO2 and high pH

-R state is favoured = O2 binding

102
Q

Tissues and Hb

A

Respiring tissues have low pH and low ppO2

-T state is favoured = oxygen is released

103
Q

Conservative Substitution

A

An amino acid is replaced by another amino acid with similar properties

104
Q

Critical Substitution

A

An amino acid is replaced by another amino acid with different properties

  • sickle cell anemia = disastrous genetic disease
  • fetal hemoglobin = physiologically significant adaptation
105
Q

Sickle Cell

A

In Hb, a small hydrophobic surface patch is expelled between the E and F helices during the transition from R to T
Hydrophobic Val binds and causes the Hb molecules to aggregate

106
Q

Fetal Hemoglobin

A

2 alpha and 2 gamma subunits
-gamma subunit is homologous with the beta subunits
Sub of His 143 with serine
-His 143 is involved in binding BPG
-decreased BPG affinity, increased O2 affinity

BIOCH 200 (9 decks)

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