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Biomolecules > Midterm 2 > Flashcards

Midterm 2 Flashcards

1
Q

What is the primary structure of proteins?

A

The sequence of amino acids that are covalently linked via peptide bonds.

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2
Q

What is the secondary structure of proteins? What stabilizes it?

A

The local spatial arrangement of the polypeptide backbone to give rise the alpha helices and beta pleated sheets via hydrogen bonds.

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3
Q

What is the tertiary structure of proteins? What stabilizes it?

A

The unique 3D conformation of a protein including the entire polypeptide (side chains) via hydrophobic interaction (non polar chains don’t like H2O while polar ones are exposed to it), electrostatic interactions (charges and dipoles), hydrogen bonds, and covalent bonds (disulfide bridges).

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4
Q

What is the quaternary structure of proteins? What stabilizes it?

A

The assembly of two or more polypeptide chains to form a larger supramolecular complex via hydrophobic interaction (non polar chains don’t like H2O while polar ones are exposed to it), electrostatic interactions (charges and dipoles), hydrogen bonds, and covalent bonds (disulfide bridges).

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5
Q

How are multi-subunit (quaternary) proteins connected?

A

Non-covalently associated via backbones.

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6
Q

Oligomer

A

2 or more identical subunits (protomers).

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7
Q

Why do multi-subunit proteins occur?

A
  1. Less chance of error if you synthesize in smaller units then join together afterwards
  2. Swapping subunits in and out give more freedom, allowing damage to be restored efficiently
  3. The interactions regulate the biological function
  4. More subunits mean more complex functionalities
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8
Q

Why can’t a peptide bond rotate?

A

Due to the resonance of a double bond character reducing the bonds and giving a rigid, planar structure.

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9
Q

What is a trans formation of a peptide bond?

A

Both alpha carbons are on the different sides of the peptide bond (psi = 180 degrees).

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10
Q

What is the cis formation of a peptide bond?

A

Both alpha carbons are on the same side of the peptide bond (psi = 0 degrees).

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11
Q

Why is the cis conformation less stable and energetically unfavorable compared to the trans conformation?

A

Due to steric interference of the amino acid groups of these alpha carbons existing close to one another.

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12
Q

Why is steric interference reduced in P (proline) residues?

A

90% of them follow the trans formation whereas the other 10% form a cis peptide bond

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13
Q

What is the phi bond?

A

Alpha C – N

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14
Q

What is the psi bond?

A

Alpha C – C

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15
Q

What are the angles when the peptide backbone is fully extended?

A

Phi = psi = 180 degrees

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16
Q

What do ramachandran plots show?

A

The allowed conformations (black or blue) of a polypeptide and sterically forbidden ones (white or beige). Also shows the extreme limits of unfavourable atomic contacts (green or spots of black).

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17
Q

Why is there asymmetry in ramachandran plots?

A

Due to the chirality of amino acids.

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18
Q

Why does G have the greatest range of phi and psi angle in the ramachandran plots?

A

Least amount of steric hindrance by its R group.

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19
Q

Why does P have a limited range of phi values? What are they?

A

Due to its cyclic side chain to a range of -35 to -85 degrees.

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20
Q

What do amino acids with unbranched side chains have similar ramachandran plots to?

A

Alanine

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21
Q

What happens to branched amino acids in ramachandran plots?

A

Those like V, I, and T have a more limited range than A.

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22
Q

What is an alpha helix?

A

A right handed coil when viewed from the N terminal that has a repeating unit of a single turn of helix every 5.4 A.

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23
Q

How do backbones interact in the alpha helix?

A

H bonds form between the amide group (donor) and carbonyl group (acceptor due to two lone pairs).

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24
Q

What does each turn of an alpha helix include?

A

3.6 amino acids with the R groups pointed outside and downwards.

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25
Q

How does the core exist in an alpha helix?

A

Tightly packed due to van der waals forces.

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26
Q

What does the dipole in an alpha helix depend on?

A

The longer the helix, the greater the dipole due to the H bond arrangement allowing a free NH group and COOH group.

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27
Q

How many H bonds hold one turn of an alpha helix?

A

3-4 H bonds

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28
Q

When do H bonds occur in an alpha helix?

A

Every fourth nitrogen group from a carbonyl.

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29
Q

What is an L amino acid?

A

When H is pointed backwards, from COOH - R group - NH2 (CORN) is counterclockwise.

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30
Q

What is a D amino acid?

A

When H is pointed backwards from COOH - R group - NH2 (CORN) is clockwise.

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31
Q

How must D and L amino acids occur in a helices?

A

Either all L or all D amino acids since one substitution will disrupt the polypeptide.

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32
Q

What is a left handed helix?

A

Left hand can curl fingers in the direction of the coil and point thumb up

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33
Q

What is a right handed helix?

A

The right hand can curl fingers in the direction of the coil and point thumb up.

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34
Q

What does the formation of a helix depend on?

A

Sequence dependent, thus a long block of D + E or K + R can destabilize the helix due to repulsion between like charges OR steric bulk/shape like C, T, S, N. Stabilizing occurs between maximum hydrophobic and hydrophilic interactions.

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35
Q

Where do side chains of amino acids residues interact in an alpha helix?

A

3 to 4 amino acids apart

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36
Q

Why is proline bad for an alpha helix?

A

Too rigid so no N-H group to participate in an H bond.

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37
Q

Why is glycine bad for an alpha helix?

A

Too flexible where polyglycine coils differently.

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38
Q

What are beta pleated sheets formed by?

A

H bonding between amide and carbonyl groups of neighboring polypeptide chains.

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39
Q

Antiparallel beta pleated sheet

A

Neighbouring chains run in opposite directions giving straight H bonds.

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40
Q

Why are H bonds in antiparallel beta pleated sheets stronger than those in parallel ones?

A

Due to being more linear = stronger

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41
Q

Parallel beta pleated sheet

A

Neighbouring chains run in the same direction with bent H bonds between strands.

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42
Q

What are the phi and psi angles of a beta pleated sheet? WHY?

A

-180, and 180 degrees do to being flat and fully extended.

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43
Q

What is the repeat distance in antiparallel beta pleated sheets? Parallel?

A

7 A versus 5.6 A (tighter angles).

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44
Q

How do beta pleated sheets look?

A

A zig zag pattern that follows a right handed twist.

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45
Q

What is a beta turn?

A

Occurs between antiparallel strands where it’s a hairpin loop.

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46
Q

What is a crossover?

A

Common between parallel strands.

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47
Q

How do the beta bends differ?

A

Based on a 180 degrees flip of the amid bond between residues 2 and 3.

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48
Q

Type 3 beta bend

A

3rd residue is glycine where it residues steric clash.

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49
Q

Where does the H bond occur in beta bends?

A

Between residue 1 and 4

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50
Q

Where are proline residues found?

A

In beta bends at residue 2 based as cis isomers as they form a natural turn in the direction of the peptide.

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51
Q

How does the newly synthesized protein folds?

A

To yield the thermodynamically most stable protein with the lowest G.

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52
Q

Conformation

A

Spatial arrangement of an atom within a protein that can be altered by rotation about a single bond.

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53
Q

Native conformation

A

Protein in its functional folded conformation

54
Q

What can tertiary structures contain?

A

Combinations of secondary structural elements: supersecondary structures:
- 2 parallel strands of beta sheets connected by an alpha helix
- a beta hairpin formed from a series of antiparallel beta sheets
- folded beta where antiparallel strands are connected by a beta hairpin and the ones in the same line by an alpha helix.

55
Q

What are domains?

A

Regions in tertiary structures that contain one subunit (globular clusters).

56
Q

Where do non-polar residues exist in polypeptides?

A

In the interior due to hydrophobic nature.

57
Q

Where do charged polar residues exist?

A

In the surface of a protein due to hydrophilic.

58
Q

Where do uncharged polar residues exist?

A

The protein surface and the interior as well (H bonded to other groups).

59
Q

What does hemoglobin consist of?

A

2 alpha helices and 2 beta subunits where two aB dimers (protomers) form that then associate.

60
Q

Multimeric

A

Composed of 2 or more polymers

61
Q

What are extreme examples of quaternary structures?

A

The human polio virus has 60 subunits whereas the tobacco mosaic virus has 2130 identical subunits.

62
Q

How does the bond distance in antiparallel versus parallel beta sheets compare?

A

Shorter in antiparallel ones.

63
Q

What is protein stability?

A

The tendency to maintain a native conformation.

64
Q

What is a native conformation?

A

A folded protein.

65
Q

What interactions does a folded (native) protein have?

A
  1. Intramolecular H bonds between amino acids
  2. Other non-covalent interactions
  3. Covalent bonds –> disulfide bonds formed between cysteine residues
  4. Release of ordered H20
  5. Electrostatic interactions –> van der waal forces where it works best when side chains are folded in close proximity
  6. Ion-pair interactions –> salt bridges formed by interactions between 2 amino acid side chains of opposite charges (constrained in protein with a low entropy)
  7. Metal ligand bonds –> bond to metal ions that stabilize the internal structure
66
Q

What does a protein unfold?

A

Flexibility to allow the protein to breathe so that it can bind to and release substrates.

67
Q

Does renaturation always happen?

A

Folding back can occur SOMETIMES

68
Q

How does rotation in an unfolded protein compare to a native one?

A

More rotation freedom

69
Q

What H bonds occur in unfolded proteins?

A

Ordered H bonds between water and the polar amino acids

70
Q

How does a protein denature?

A

Heating which causes conformational changes, and detergents which interfere with hydrophobic bonds.

71
Q

What is the main forces of folding?

A
  1. Hydrophobic interactions between non polar amino acid residues
  2. Entropy
  3. Lone H bonding or charged group in the interior can be destabilizing –> form in pairs and co-operate
72
Q

Where are hydrophobic residues in a protein?

A

In the interior

73
Q

What happens to the number of hydrogen bonds in a folded protein?

A

Always maximized.

74
Q

Folding funnel

A

Relationship between free energy and entropy

75
Q

What does each ridge of the folding funnel represent?

A

A molten globule, which is the intermediate state between the unfolded and native state.

76
Q

How does entropy and free energy compare in unfolded proteins versus folded ones?

A

Unfolded ones have a higher free energy and entropy than folded ones.

77
Q

What amino acids are in alpha helices?

A

Ala, glu, leu, and met.

78
Q

What amino acids are found in beta sheets?

A

Val, thr, his, tyr, and ile.

79
Q

How do we discover protein structure?

A

Use X-ray crystallography to form a direct reconstruction from crystals (higher resolution = more clear amino acid depiction).

80
Q

What is used to discover non-crystalline protein structure?

A

Small angle x-ray scattering (used for more water-soluble ones).

81
Q

What is the purpose of myoglobin?

A

To store and release O2 into muscles.

82
Q

Which protein structure exists within myoglobin?

A

Alpha helices.

83
Q

How many O2 binding sites does myoglobin have?

A

1 and it’s reversible.

84
Q

Why does O2 need a transporter?

A

It has a low solubility in water thus diffusion past tissue of a few mm is very ineffective, thus not receiving energy to make ATP.

85
Q

What is a prosthetic group?

A

A non-protein group that bind to a protein group either covalently or non-covalently to aid in a function.

86
Q

How is the heme prosthetic group in myoglobin bound?

A

Via non-covalent bonds, where the heme forms a non-covalent bond to the myoglobin via the iron centre itself with his residue.

87
Q

What is the purpose of the Fe 2+ in myoglobin?

A

Part of the heme group where O2 will bind.

88
Q

Why can’t there just be a free Fe 2+?

A

It will become a highly reactive species that will cause damage to the cell.

89
Q

What encases the Fe 2+ in myoglobin?

A

A ring of 4N that are then composed of 4 pyral rings of CH groups.

90
Q

What happens if the O2 binds to the His residue in myoglobin?

A

Creates highly reactive radical species that would undergo reactions that can cause destruction of a protein.

91
Q

How is the heme prosthetic group binded into the protein myoglobin?

A

Wedged into a hydrophobic pocket between 3 alpha helices, since the faces of the heme are non-polar.

92
Q

What creates the hydrophobic effect in myoglobin?

A

Val and phe create the hydrophobic pocket.

93
Q

How does the myoglobin O2 binding curve look?

A

Like a hyperbola (is logarithmic).

94
Q

What does it mean when K = pO2?

A

Half the binding sites are occupied, thus Y O2 = 0.5.

95
Q

What is p50 (or K)?

A

The O2 pressure at which Mb is 50% saturated.

96
Q

What is p50 in myoglobin?

A

2.8 torr

97
Q

What does a lower p50 and K mean?

A

Greater affinity of the protein to its ligand.

98
Q

What can the equation for myoglobin binding curve be applied to?

A

To proteins with one binding site and those with multiple bindings sites for the same substrate that act independently of each other.

99
Q

What does Hb consist of?

A

2 alpha helices and 2 B subunits that interact via 35 amino acid residues.

100
Q

What is similar and different for Hb and Mb in terms of protein structure?

A

Almost identical tertiary structure while different primary structures.

101
Q

What kind of protein is a Mb?

A

Monomeric protein.

102
Q

What protein is a Hb?

A

Tetrameric (4 subunits).

103
Q

How do the protomer interact in Hb?

A

The strong faces bind first through H bonds and ionic interactions via 35 amino acid residues to give two aB dimers. Each weak side of the subunits binds to a protomer via hydrophobic interactions of 19 amino acid residues.

104
Q

What binding of O2 does Mb have?

A

Non-cooperative binding where there is a single binding side or independent binding sites on one protein.

105
Q

What binding does Hb have of O2?

A

Cooperative binding where one O2 that binds either favors or unfavours the next O2 binding to the subunit (dependent).

106
Q

How does Hb undergo a conformational change via binding of O2?

A

Oxygenation causes the subunits to slide past one another and 1 protomer rotates the other by 15 degrees.

107
Q

What is the T form of Hb?

A

Deoxyg Hb

108
Q

What is the R form of Hb?

A

Oxy Hb

109
Q

How does the T form change to the R form?

A

Exposure of deoxygenated crystals to O2 causes them to shatter.

110
Q

Why is Hb an allosteric protein?

A

A ligand that binds to Hb at one site can alter the binding of a ligand at another site.

111
Q

Homotropic

A

When all the ligands bonding are the same.

112
Q

Heterotropic

A

When all the ligands bonding are different (regulatory molecule).

113
Q

What is the Hill constant?

A

A measure of the cooperativity between bindingsites.

114
Q

What happens is n=1?

A

Ligand binding is non-cooperative.

115
Q

What happens if n > 1?

A

Ligand binding enhances the affinity of another ligand binding site.

116
Q

What happens if n < 1?

A

Ligand bonding reduces the affinity at another site.

117
Q

What is the maximum number of n?

A

The total number of binding sites.
ex. in Hb it is 4

118
Q

What does a higher p50 or pO2 mean?

A

Lower affinity for a ligand.

119
Q

How does the binding sites of O2 in Hb communicate?

A
  1. O2 causes the Fe2+ to move into the plane of the porphyrin
  2. Movement of the Fe2+ and the flattening of the porphyrin forces the helix F to shift, pulling the his residues with it
  3. H bond changes at a1-B2 interface during T-R where the T state it’s asp and tyr, whereas this bond is broken and replaced with asn and asp
  4. This reduces the number of salt-pair interactions at their C-terminals (tear apart some ionic interactions)
120
Q

Explain the Bohr effect in O2 transport.

A

Decreasing the pH lowers the affinity of Hb to O2. This is because lower pH favours protonation, thereby stabilizing the T state and lowering affinity for O2. When the pH increases, there is a greater tendency to deprotonate since the R state are not in ion-pairs, thus the Hb will give up more protons, allowing more O2 to bind.

121
Q

What are pKas are increases in the unbinding of O2?

A

N-terminal a-subunit and C-terminal His of B-subunit interact to form an ion bridge.

122
Q

Why does a higher pH mean greater affinity of O2?

A

This is because the H+ originally bound to the Hb is releases to form bicarbonate, allowing O2 to bind to the free Hb.

123
Q

How does CO2 control binding of O2 to Hb?

A

By reacting with N-terminal amino groups to form carbamates that bind to the T-state of Hb (more CO2 = this form), stabilizing it to form more salt bridges and ion pairs. The release of H+ upon carbamate formation promotes the O2 release.

124
Q

What is BPG?

A

A heterotropic allosteric modulator that binds to the central cavity of Hb.

125
Q

When does BPG bind to Hb?

A

During T-state, as it will form H bonds and ion pairs with the N terminal groups of each B-subunit.

126
Q

Why doesn’t BPG bind to Hb in the R state?

A

The cavity is too narrow and both B-subunits are too far apart.

127
Q

What does an increase in BPG mean?

A

A lower oxygen curve, thus more O2 can be released into muscles.

128
Q

What is the long term adaptation for high altitude?

A

An increase in number of urethra sites and the amount of Hb per erythrocyte (RBC).

129
Q

What is the short term adaptation for high altitude?

A

Doubling of BPG content, so that we have a lower affinity of O2 and can releases the lower concentrations of pO2 easily into the muscles.

130
Q

What is the mutation in sickle-cell anemia?

A

A single amino acid change for a caline that removes the negative charges and creates a site for more hydrophobic interactions.

131
Q

Why can sickle-cell anemia protect against malaria?

A

In early stages, the parasites decreases the pH favouring deoxy-Hb, thus more sickly occurs and an increases in the clearance of infected RBCs. In the later stages, the sickling stops parasites from infecting.

Biomolecules (2 decks)

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