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BIOCH 200 > Protein Structure and Fonction > Flashcards

Protein Structure and Fonction Flashcards

1
Q

What do Proteins do?

A

They are involved in movement, catalysis, communication and transport

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2
Q

How do proteins do all of their tasks

A

The essence of a protein’s function is in its interaction with other molecules

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3
Q

What force stabilizes the shape of the protein

A

Non-covalent interactions

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4
Q

What is a Zwitterion

A

A neutral (overall) ion with a positive and negative charges. It occurs when the pH is between ~2-9.5

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5
Q

What is pKa?

A

Reflection of the strength of an acid

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6
Q

What happens when we are at a pH > pKa

A

Then the [A-] > [HA]

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7
Q

What happens when we are at a pH < pKa

A

Then the [A-] < [HA]

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8
Q

What happens to the charge of the amino acids when the pH is at 1?

A

Overall positive

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9
Q

What happens to the charge of the amino aids when the pH is at 11

A

Overall negative

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10
Q

Are amino acids chiral molecules

A

Amino acids are chiral molecules

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11
Q

What is a chiral molecule

A

A chiral molecule cannot be superimposed on its mirror image. The property of being asymmetric

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12
Q

What are amino acids

A

20 incorporated into proteins. Classified by overall chemical properties of their side chains. They are nonpolar (hydrophobic), polar (uncharged), or charged (very polar).

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13
Q

What are the particularities of nonpolar amino acid side chains

A

Lack reactive functional groups. Have mainly hydrocarbon side chains

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14
Q

What are the nonpolar amino acid side chains

A

Alanine, Valine, Phenylalanine, Tryptophan, Leucine, Isoleucine, Methionine and Proline

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15
Q

What is the side chain of Alanine

A

CH3

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16
Q

What is the description of Alanine

A

Aliphatic R group (Methyl; Carbons and Hydrogens are not aromatic). Hydrophobic R group. Participates in hydrophobic interactions. Smallest chiral amino acid

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17
Q

What is the side chain of Valine

A

CH3-CH-CH3

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18
Q

What is the three letter format of Alanine

A

Ala

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19
Q

What is the three letter format of Valine

A

Val

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20
Q

What is the description of Valine

A

Aliphatic R group; Branched Carbon in the side chain. Highly hydrophobic R group.

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21
Q

What the side chain of Leucine

A

CH2-CH-CH3

-CH3

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22
Q

What is the three letter format of Leucine

A

Leu

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23
Q

What is the description of Leucine

A

Aliphatic R group; Branched. Highly hydrophobic R group. Participates in hydrophobic interactions

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24
Q

What is the side chain of Isoleucine

A

-H
C-CH2-CH3
-CH3

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25
Q

What is the the three letter format of Isoleucine

A

Ile

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26
Q

What is the description of Isoleucine

A

Aliphatic R group. Highly hydrophobic R group. Participates in hydrophobic interactions

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27
Q

What is the side chain of Phenylalanine

A

CH2-Benzene ring

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28
Q

What is the three letter format of Phenylalanine

A

Phe

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29
Q

What is the description of Phenylalanine

A

Aromatic R group. Highly hydrophobic R group. It is the highest hydrophobic R group of all amino acids. Participates in hydrophobic interactions

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30
Q

What is the side chain of Tryptophan

A

CH2 - NH pentene ring - benzene ring

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31
Q

What is the three letter formation of Tryptophan

A

Trp

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32
Q

What is the description of Tryptophan

A

Aromatic R group -heterocyclic. Mostly hydrophobic because it is bulky. Participates in hydrophobic interactions. Forms hydrogen bonds as a donor.

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33
Q

What is the side chain of Methionine

A

CH2-CH2-S-CH3

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34
Q

What is the three letter format of Methionine

A

Met

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35
Q

What is the description of Methionine

A

Aliphatic R group (it could be deemed honorary). Hydrophobic. Participates in hydrophobic interactions. Sulfur containing side group (thioether)

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36
Q

What is the side chain of proline

A

-CH2-CH2-CH2-

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37
Q

What is the three letter format of Proline

A

Pro

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38
Q

What is the description of Proline

A

Aliphatic side chain with distinctive cyclic structure. Secondary amino group. Hydrophobic but often found on protein surface because it has unique structural characteristics.

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39
Q

What are the particularities of polar amino acid side chains

A

Polar. Reactive due to presence of functional groups. Polar amino acids have side chains that contain an electronegative atom. Not all R groups have ionizable R group

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40
Q

What are the polar amino acids

A

Serine, Threonine, Tyrosine, Cysteine, Asparagine, Glutamine, Histidine and Glycine

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41
Q

What is the side chain of Glycine

A

H

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42
Q

What is the three letter format of Glycine

A

Gly

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43
Q

What is a description of Glycine

A

Achiral. Weakly polar. Small so it is flexible.

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44
Q

What is the side chain of Serine

A

CH2-OH

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45
Q

What is the three letter format of Serine

A

Ser

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46
Q

What is the description of Serine

A

Polar, uncharged. Contains hydroxyl group. Forms hydrogen bonds as an acceptor and donor; but it is typically a donor. Can be modified through phosphorylation

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47
Q

What is the side chain of Threonine

A

-OH
C-CH3
-H

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48
Q

What is the three letter format of Threonine

A

Thr

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49
Q

What is a description of Threonine

A

Polar, uncharged. Contains a hydroxyl. group, forms hydrogen bonds as an acceptor and donor but it is typically a donor. Can be phosphorylated

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50
Q

What is the side chain of Tyrosine

A

CH2-Benzene ring-OH

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51
Q

What is the three letter format of Tyrosine

A

Tyr

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52
Q

What is the pKa of Tyrosine

A

10.5

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53
Q

What is the description of Tyrosine

A

Weakly polar, uncharged. Aromatic R group, phenol and can participate in hydrophobic interactions. Contains hydroxyl group. Forms hydrogen bonds as an acceptor and donor; typically it is a donor

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54
Q

What is the side chain of Cysteine

A

CH2-SH

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55
Q

What is the three letter format of Cysteine

A

Cys

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56
Q

What is the pKa of Cysteine

A

8.5

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57
Q

What is the description of Cysteine

A

Polar, uncharged. Sulfur-containing side chain (thiol group - SH). Can form hydrogen bonds as a donor. Can form a thiolate anion (S-). Forms disulfide bonds with another Cysteine

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58
Q

How does Cystine form

A

Thiols in neighbouring cysteine resides can undergo oxidation to form a disulfide bond

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59
Q

What is Cystine

A

-NH3(+)(on the last CH)
(-)OOC-CH-CH2-S-S-CH2-CH-COO(-)
-NH3(+) (on the first CH)

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60
Q

What is the side chain of Asparagine

A

=O
CH2-C
-H2N

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61
Q

What is the three letter format of Asparagine

A

Asn

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62
Q

What is the description of Asparagine

A

Amide-containing side chain. Carboxamide functional group. Polar, uncharged. Forms hydrogen bonds as donor and acceptor. Nitrogen acts as donor and Oxygen acts as acceptor

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63
Q

What is the side chain of Glutamine

A

=O
CH2-CH2-C
-H2N

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64
Q

What is the three letter format of Glutamine

A

Gln

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65
Q

What is the description of Glutamine

A

Amide-containing side chain. Carboxamide functional group. Polar, uncharged. Forms hydrogen bonds. Nitrogen acts a donor and Oxygen acts as an acceptor

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66
Q

What is the side chain of Histidine

A

CH2-Heterocyclic (N and HN) pentene ring

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67
Q

What is the three letter format of Histidine

A

His

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68
Q

What is the pKa of Histidine

A

6.0. Side chain can be acidic or basic at neutral pH. Base form is predominant when pH is at or above 7.0. Acid form is predominant when pH is below 6.0

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69
Q

What is the description of Histidine

A

Polar, charged/uncharged. Histidine resides important in many enzyme catalyzed reactions. Proton donor (acid) / acceptor (base). Hydrogen bonding capability - proton donor or acceptor

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70
Q

What is the side chain of Aspartate

A

CH2-COO(-)

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71
Q

What is the three letter format of Aspartate

A

Asp

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72
Q

What is the pKa of Aspartate

A

4.0. Negatively charged R group at pH 7. Second carboxyl group. “Acidic” amino acid

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73
Q

What is the description of Aspartate

A

“Acidic” amino acid. Very polar. Forms hydrogen bonds, hydrogen bond acceptor. At pH 1 called aspartic acid.

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74
Q

Why does Aspartate change to Aspartic acid at pH 1

A

Contains a neutral functional group the COO(-) becomes COOH

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75
Q

What is the three letter format of Glutamate

A

Glu

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76
Q

What are the charged amino acids

A

Aspartate, Glutamate, Lysine, and Arginine

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77
Q

What are the negatively charged charged amino acids

A

Aspartate and Glutamate

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78
Q

What are the positively charged charged amino acids

A

Lysine and Arginine

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79
Q

What is the pKa of Glutamate

A

4.0. Negatively charged R group at pH 7. Second carboxyl group. “Acidic” amino acids.

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80
Q

What is the description of Glutamate

A

Very polar. Forms hydrogen bonds, Hydrogen bond acceptor. At pH 1 called glutamic acid

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81
Q

Why does Glutamate become Glutamic acid at pH 1

A

Contains a neutral functional group the COO(-) becomes COOH

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82
Q

What is the side chain of Lysine

A

CH2-CH2-CH2-CH2-NH3(+)

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83
Q

What is the three letter format of Lysine

A

Lys

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84
Q

What is the pKa of Lysine

A

10.0. Positively charged side group at pH 7. “Basic” amino acid

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85
Q

What is a description of Lysine

A

“Basic” amino acid. Side group contains an amino, so the total group contains 2 primary amino groups. Forms hydrogen bonds. It is a hydrogen bond donor and at pH 14 would be allow it to act as a hydrogen bond acceptor. Very polar

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86
Q

What is the side chain of Arginine

A

=NH2(+)
CH2-CH2-CH2-NH-C
-H2N

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87
Q

What is the three letter format of Arginine

A

Arg

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88
Q

What is the pKa of Arginine

A

12.5. Positively charged side group at pH 7. Guanido group. “Basic” amino acid. Never deprotonate under physiological conditions

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89
Q

What is a guanido group

A

Three nitrogen that are attached to a carbon

90
Q

What is a description of Arginine

A

“Basic” amino acid. Never deprotonate under physiological conditions. Very polar. Forms hydrogen bonds as a donor and 5 are in the side chain.

91
Q

What are the exceptions of the amino acids that don’t use the first three letters of their names

A

Asparagine (Asn), Glutamine (Gln), Isoleucine (Ile), and Tryptophan (Trp)

92
Q

Where are polar side chains found

A

They are on in proteins on the surface because it can interact with water. It includes polar uncharged and polar charged amino acids

93
Q

Where are the non-polar side chains found

A

Non-polar side chains are usually found buried in the protein core. Minimizes interactions with water (hydrophobic effect)

94
Q

How do name when many amino acids joined together

A

Two peptides: dipeptide
Three peptides: tripeptide
Four peptides: tetrapeptide
etc.

95
Q

What is a peptide/oligopeptide

A

General term for a larger number of amino acids, often refers to synthetic peptides (<40 residues)

96
Q

What is a polypeptide

A

Produced by a translational process. Long chain of amino acids usually produced naturally.

97
Q

What is a protein

A

Large polypeptide (or >1 polypeptide) with a biological function

98
Q

What is a dipeptide

A

When you have Ser.Ala it is not equivalent to Ala.Ser. Sense of direction is important in distinguishing different molecules/and ulitmately sequencing. Direction is Nitrogen to Carbon by convention

99
Q

What is a tetrapeptide

A

Only the terminal amino and carboxylate groups in a peptide retain their charge. The others are eliminated by the formation of peptide bonds. Side chains retain their charge (if they have one)

100
Q

What is the backbone of a tetrapeptide

A

All non-sidechain R group atoms (Nitrogen-Carbon-Carbon-etc.)

101
Q

What is the primary structure of proteins

A

The sequence of amino acids in a polypeptide is the “primary structure.” Covalent peptide bonds join each amino acid to the next. Every protein or polypeptide has a unique sequence

102
Q

What are the characteristics of peptide bonds

A

They are rigid and planar

103
Q

What are properties of peptide bonds

A

The electrons in peptide bonds are somewhat delocalized generating two resonance forms. Peptide bonds therefore exhibit double-bond character with no rotation around the C-N bond. The functional groups in peptide bonds are potential Hydrogen bond acceptors or donors

104
Q

What happens because the peptide bonds are rigid and planar

A

The backbone of a polypeptide includes the Alpha carbon atoms and those involved in peptide bonds

105
Q

What occurs in the folding conformations in proteins

A

Folding conformations are limited because two oxygens take the same space they minimize steric conflicts.

106
Q

What are the hydrogen bonds in polypeptide backbones

A

The chemical groups found in peptide bonds are highly polar. Carbonyl groups are hydrogen bond acceptors. NH groups are hydrogen bond acceptors. They maximize their hydrogen bonding capabilities.

107
Q

What are some secondary structures of proteins

A

Local folding of the polypeptide backbone. Allows for hydrogen bonding of the groups in the polypeptide backbone (C=O, N-H). “Regular” secondary structures occur when every amino acid in a segment of the polypeptide adopts the same geometry. A few regular patterns occur: alpha-helix and beta-sheet which both minimize steric conflicts and maximize hydrogen bonds

108
Q

What occurs in an alpha-helix

A

The carbonyl oxygen of each residue forms a hydrogen bond with the backbone -NH group four resides downstream (C1…N5, C2…N6, etc). Complete hydrogen potential satisfied for backbone. Except for amino acid residues at either end all the backbone CO and NH groups are hydrogen bonded to one another in the helix. There is a right-handed twist.

109
Q

What happens to the side chains in an alpha-helix

A

Helix is SOLID with atoms in the polypeptide backbone in Van der Waals contact with one another in the center. Amino acids project outwards residues 3-4 apart in the primary structure are close in the secondary structure

110
Q

What are parallel and anti-parallel Beta-sheets

A

Multiple beta-strands are arranged side by side. Strands a joined by loops or other structures. Parallel strands appear to join diagonally and anti-parallel join vertically

111
Q

How are beta-sheets drawn

A

They are often drawn as arrows. The arrows are shown pointing from the nitrogen-terminal to the carbon-terminal end.

112
Q

How are anti-parallel sheets drawn

A

It flows from one arrow to other to form an easy zig-zag

113
Q

How are parallel sheets drawn

A

The strands overlap because the arrows will be point the same direction.

114
Q

Where are side chains located on a beta-sheet

A

Side chains are located above and below the plane of the sheet; they are alternating

115
Q

What forces stabilize alpha-helices

A

Hydrogen bonds between the backbone CO and NH groups in the same helices

116
Q

What forces stabilize beta-helices

A

Hydrogen bonds between CO and NH groups of neighbouring strands

117
Q

What makes an irregular secondary structure

A

Distinct elements of regular secondary structure are linked together by polypeptide loops of various sizes ranging from simple hairpins to longer loops. These structures are irregular.

118
Q

What is the tertiary structure of a protein

A

Arrangement of all atoms in a single polypeptide. Arrangement of secondary structure in relation to one another. Positions of amino acid side chains. Prosthetic groups (heme, FAD, etc.)

119
Q

What are the two morphologies of tertiary protein structures

A

Fibrous (elongated) and Globular (compact)

120
Q

What are fibrous proteins

A

Practically insoluble into aqueous solutions. Form long protein filaments - limited resides with repeats. Usually structural or connective proteins.

121
Q

What are globular proteins

A

Practically soluble in aqueous solutions. Fold into compact structures with nonpolar cores and polar surfaces.

122
Q

What structures do fibrous proteins adopt

A

Fibrous proteins (like collagen) tend to adopt linear extended structures

123
Q

How variable is the structure of globular proteins

A

The tertiary structure in globular proteins is highly variable

124
Q

Where are hydrophobic side chains found in a globular protein

A

Hydrophobic side chains are most likely to be found in the interior of a globular protein

125
Q

Where are hydrophilic side chains found in a globular protein

A

Hydrophilic side chains are most likely to be found on the surface of a globular protein

126
Q

Where are loops located in a globular protein

A

Loops tend to be located on the surface

127
Q

Where are irregular structures located in a globular protein

A

Irregular structures are on the surface

128
Q

Where are the regular structures located in a globular protein

A

Regular structures are in the core

129
Q

What impacts the shape of the globular proteins

A

The shape of globular proteins depend of the relative positions of hydrophobic amino acids in the proteins primary structures

130
Q

How does the hydrophobic effect have an impact on globular proteins

A

The hydrophobic effect is the “driving force” via which soluble globular proteins adopt and maintain their tertiary structure

131
Q

What is Ion Pairs (“Salt Bridges”)

A

Electrostatic interactions between closely positioned formal charged groups. Like hydrogen bonds, these helps to “fine tune” and stabilize secondary and tertiary structures

132
Q

What are the positive charges in ion pairs

A

N-terminus, Lys, Arg and His

133
Q

What are the negative charges in ion pairs

A

C-terminus, Asp, Glu, Tyr and Cys

134
Q

What can impact the charges of ion pairs

A

Charges will depend on pH of the environment

135
Q

What is Disulfide bonds/bridges

A

Covalent bonds between closely positioned cysteines. These form stabilizing crosslinks for extracellular proteins (or proteins in the lumen)

136
Q

What happens in the cytosol of Disulfide bonds/bridges

A

In the cytosol, cysteines do not oxidize to cystine as it is a reducing environment

137
Q

What are the two main parts of protein structure

A

Domain and Motif

138
Q

What is the domain of protein structure

A

A polypeptide segment that has folded into a single structural unit with a hydrophobic core. Proteins may contain more than one domain

139
Q

What is the motif of protein structure

A

A short region of polypeptide with a recognizable 3D shape. Zinc fingers. May be found in many contexts

140
Q

What are some examples of protein domains

A

Pyruvate kinase and Cow gamma crystalline

141
Q

How many protein domains are in pyruvate kinase

A

It is composed of a single polypeptide chain, which can be divided into 3 domains

142
Q

How many protein domains are in cow gamma cystalline

A

Contains two domains one polypeptide

143
Q

What are some motifs in protein structure

A

Helix-loop-helix, Coiled coil, Helix bundle, Beta-alpha-beta unit, hairpin, beta-meander, greek key and beta sandwich

144
Q

What are zinc fingers

A

An example of a structural motif including a prosthetic group.

145
Q

What are prosthetic groups

A

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

146
Q

What are some examples of prosthetic groups

A

Zinc fingers and functional groups such as heme in hemoglobin

147
Q

How are globular proteins impacted by outside forces

A

Globular proteins are stabilized by weak noncovalent forces and easily unfolded or “denatured” by heat, changes in pH, salt and detergents.

148
Q

What can disrupt Disulfide bonds

A

Reducing agents (DTT) can disrupt disulfide bridges

149
Q

What are quaternary structures

A

Proteins composed of more than one polypeptide chain. Each polypeptide chain is called a subunit.

150
Q

How are quaternary structures named

A

Named by number and types of subunits.
2 subunits: Dimer
3 subunits: Trimer
etc.

151
Q

What is the name of identical subunits in quaternary structures

A

Homodimer

152
Q

What is the name of non-identical subunits in quaternary structures

A

Heterodimer

153
Q

How are quaternary structures stabilized

A

They are stabilized by hydrophobic interactions and hydrogen bonds, ion pairs “fine-tune)

154
Q

How is the function of a protein determined

A

The function of a protein is determined absolutely by its structure.

155
Q

What is the name of the subunit of Myoglobin

A

Monomer with no quaternary structure

156
Q

What is the name of the subunit of Hemoglobin

A

Oligomer with a quaternary structure

157
Q

What is the role of Hemoglobin

A

Hemoglobin red blood cells binds O2 in the lungs and releases it in the tissues

158
Q

What is the role of Myoglobin

A

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

159
Q

What is the role for both Hemoglobin and Myoglobin

A

Both bind oxygen reversibly but bind it with different affinities and under different conditions

160
Q

What is the structure of Myoglobin

A

Polar propionyl groups. Porphyrin ring held in place by hydrophobic interactions AND by coordination bond between Fe2+ and a histidine which is called the proximal histidine

161
Q

What does the proximal histidine do

A
  1. Binds heme into heme-binding pocket

2. Prevents oxidation of iron atom

162
Q

What is the structure of heme

A

Heme is circular and planar. In heme, the porphyrin ring contains an Fe2+ ion coordinated between the four Nitrogen atoms. The two substituents at the bottom of the ring are polar (uncharged) propionyl groups whereas the rest are non-polar aliphatic groups

163
Q

Where does Fe2+ ion position in Heme

A

5th coordination position

164
Q

Where does O2 atom position in Heme

A

6th coordination position

165
Q

What is the oxygen binding site in myoglobin

A

Binding sites are designed precisely to optimize binding specificity and affinity

166
Q

How much stronger is the free Heme carbon monoxide affinity than O2

A

Free Heme Carbon monoxide affinity is ~2500 times higher than O2

167
Q

How much stronger is Myoglobin / Hemoglobin carbon monoxide affinity than O2

A

Myoglobin / Hemoglobin carbon monoxide ~250 times higher than 02.

168
Q

What are the two types of globin with within the tetramer of Hemoglobin

A

2 alpha subunits (alpha-globin) and 2 beta subunits (beta-globin)

169
Q

What is the tertiary structure of beta-globin, alpha-globin and myoglobin

A

All 3 polypeptides comprise 8 alpha-helices with a heme binding pocket between helices E and F (plus irregular structures).

170
Q

How much of the primary structure is approximately identical

A

20-25% identical

171
Q

What are homologous proteins/polypeptides

A

They share an ancestral heritage

172
Q

What is the composition of hemoglobin (Hb)

A

4 polypeptide chains, 2 alpha-globin chains, 2 beta-globin chains and 1 heme/polypeptide - binds 4 O2/Hb

173
Q

What is the composition of Myoglobin

A

1 polypeptide chain, 1 heme - binds 1 O2/Mb

174
Q

What are conservative substitutions

A

Relatively minor effects on structure/function. Examples are: Leu and Ile, and Thr and Ser

175
Q

What are critical substitutions

A

Change structure and function depending on location. Examples are: polar to nonpolar, Ser and Val, and Phe and Lys

176
Q

How does the alpha-subunit and beta-subunit of hemoglobin binds O2 in the same manner as myoglobin

A

Oxygen at the 6th coordination position of an Fe2+ ion in a heme ring

177
Q

What are the critical resides that are invariant

A

Several critical residues in/near the oxygen binding are invariant (do not change) among the three polypeptides: -His F8, and - His E7

178
Q

What does a hyperbolic curve indicate

A

Hyperbolic curve is indicative of constant affinity

179
Q

What is an example of a hyperbolic curve

A

Myoglobin

180
Q

What is a sigmoidal curve

A

A sigmoidal curve is diagnostic of cooperative binding affinity

181
Q

What is an example of sigmoidal curve

A

Hemoglobin

182
Q

What is the function of Myoglobin and Hemoglobin

A

Reversibly bind/release O2

183
Q

What is the function of Myoglobin that is different than Hemoglobin

A

O2 transport within tissue

184
Q

What is the function of Hemoglobin that is different than Myoglobin

A

O2 transport from lungs to tissues

185
Q

What is the point of the sigmoidal binding curve

A

Cooperative process (positive cooperativity), necessary for efficient O2 delivery, and reflects change in binding affinity; change in tertiary structure and quaternary structure of hemoglobin

186
Q

How does Hb change its affinity for O2?

A

Two Distinct Structures of Hemoglobin, T state or R state

187
Q

What does T state look like

A

In the T state, in deoxyhemoglobin, a His residue on the beta subunit fits between a Thr and a Pro residue in the alpha-subunit

188
Q

What does R state look like

A

In the R state, upon oxygenation, the hemoglobin changes shape and the His residue is now located between two Thr residues on the alpha subunit

189
Q

What is the O2 affinity to T state

A

Low affinity for O2

190
Q

What is the O2 affinity to R state

A

High affinity for O2

191
Q

Does T state or R state have deoxy hemoglobin

A

T state

192
Q

Does T state or R state have oxy hemoglobin

A

R state

193
Q

What size is the central cavity of T state

A

Larger central cavity

194
Q

What size is the central cavity of R state

A

Smaller central cavity

195
Q

What does Allostery mean

A

“Other” “Space”

196
Q

What are allosteric effectors

A

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

197
Q

What is Homoallosteric

A

Binding of the effector affects further binding of the same compounds

198
Q

What is Heteroallosteric

A

Binding of the effect affects further binding of the different compound

199
Q

What are activators in allostery

A

Increase binding affinity they are positive effectors

200
Q

What are inhibitors in allostery

A

Decrease binding affinity they are negative effectors

201
Q

What is the Action of Allosteric Effectors

A

Equilibrium between T and R is being affected by the binding of X. The binding of a ligand/substrate at one site on a macromolecule affects the affinity of other sites for the SAME ligand.

202
Q

What are the conformational changes in oxygen binding to hemoglobin

A

The iron moves into plane of heme (when they are changing from T state to R state). The proximal histidine moves with the iron atoms

203
Q

What are the events in O2 binding to Hemoglobin

A

T-state (no O2 bound). O2 binds to a subunit.. Fe2+ moves into plane of heme. Histidine F8 moves with iron. Helix F moves, Subunit interface changes. Subunit interface change affects other subunits. Helix F/His F8/Fe2+ movement. Oxygen binding site becomes high affinity (R). Oxygen binds more readily to other binding sites

204
Q

What kind of allosteric effect does O2 have

A

O2 is a homoallosteric activator

205
Q

What kind of allosteric effect does BPG have

A

BPG is a heteroallosteric inihibiter (for O2)

206
Q

What is BPG

A

2,3-bisphophoglycerate

207
Q

What kind of allosteric effect does H+ have

A

H+ is a heteroallosteric inhibitor (for 02)

208
Q

What does BPG and H+ do in the T state

A

BPG and H+ stabilize T state they are both part of the ‘Bohr effect’.

209
Q

How is BPG essential to the T state of Hemoglobin

A

Small and highly negative. Negative Allosteric Effector of O2 binding

210
Q

How does BPG bind to Deoxyhemoglobin

A

BPG binds in the central cavity of the deoxyhemoglobin (T state). The negative charges on the BPG interaction with positively charged groups on the protein that are directed into the central cavity. 4 His, 2 Lys, 2 N-terminal residues The central cavity in oxyhemoglobin (R state) is too small to accommodate BPG.

211
Q

What is the result of metabolism generating protons

A

It lowers pH
Examples:
ATP + H2O → ADP + Pi + H (+)
CO2 + H2O → HCO3 (-) + H (+)

212
Q

What does lowering pH lead do to side chains and functional groups

A

Lowering pH leads to protonation of side chains and functional groups
Examples:
His + H (+) → His (+)
NH2 + H (+) → NH3 (+)

213
Q

What does the Bohr Effect do

A

pH dependence of O2 binding. As we lower the pH oxygen affinity decreases. As we raise the pH oxygen affinity increases

214
Q

In the lungs and in the tissues how does Hemoglobin exist

A

In the lungs and in the tissues, any given molecule of Hb can exist in either the T state or the R state. The lungs have a high pp O2 and a relatively high pH. The R state is thus favoured, and when oxygen binds it triggers the switch to the R form. Actively respiring tissues have a relatively low pH and a low pp O2. The T state is favoured, and oxygen is released.

215
Q

What affects the proportion of molecules

A

Their proportion of molecules that are in either form (the position of the equilibrium) depends on the presence of BPG, on the [H+] ions, and on the pp O2. The proportion of molecules that are in either form (high or low affinity) determines how much oxygen is bound or released.

216
Q

How do sickled red blood cells come to be

A

B-chain Glu6 is replace with Val. (Polar charged amino acid change with to a nonpolar amino acid) Critical substitution

217
Q

What are the effects of the sickle mutation

A

In Hb there is a small hydrophobic surface patch which is exposed between the E and F helices during the transition from R to T form. The hydrophobic Val binds here, causing the Hb molecules to aggregate into long polymers/fibres.

218
Q

What is Fetal Hemoglobin

A

2 alpha and 2 gamma subunits. (Gamma subunit replaces the Beta subunit.) Gamma subunit is the adult beta subunit. (Homologous (73% identical to Beta subunit). Substitution of His143 with serine) His143 is one of the His residues that is involved in binding BPG. (Decreased BPG affinity. Increased O2 affinity)

219
Q

What are the roles of HisF8 (proximal histidine)

A

Attachment of heme. Prevent oxidation of Fe2+

220
Q

What is the roles of HisE7 (distal histidine)

A

Assist O2 binding. Decreases affinity of CO

221
Q

What do the 4 Histidine in the central cavity and subunit interface do

A

4 His in the central cavity and the subunit interface are part of the “Bohr effect.”

BIOCH 200 (8 decks)

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