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Introductory Biochemistry > Protein Structure > Flashcards

Protein Structure Flashcards

1
Q

What is configuration?

A

Structure that can only be changed by breaking and reforming bonds. Ex. cis or trans, L or D

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2
Q

What is conformation?

A

Structure that can be changed by rotating around bonds

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3
Q

What is the primary structure of a protein?

A

The amino acid sequence linked by covalent peptide bonds

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4
Q

How can a mutation in the amino acid sequence affect the final shape of the protein?

A

The sequence of the protein determines its shape and function. A mutation will affect the amino acid produced, which changes the side chain, which changes the interactions and then the folding of the protein

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5
Q

Even in a polypeptide with a long string of amino acids, the chain only has one amino group and one carboxyl group. Why?

A

Only the first amino acid in the chain has the amino group left, and the last amino acid will have the carboxyl group left. For every other amino acid in the chain the amino and carboxyl are part of peptide bonds and are now amides

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6
Q

What are the characteristics of peptide bonds?

A

Planar and rigid. They are partial double bonds from delocalization of the lone pair on the nitrogen and can’t be rotated. Trans orientation

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7
Q

What is the secondary structure?

A

Local conformation of the backbone atoms, not the amino acid side chains

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8
Q

What are the two regular secondary structures?

A

Alpha-helices and beta-sheets

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9
Q

What are the two irregular secondary structures?

A

Loops and turns

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10
Q

How is backbone folding limited?

A
  1. Properties of the peptide bond
  2. Steric hindrance between side chains and backbone
  3. Proline
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11
Q

Can the amide in the backbone of the polypeptide participate in hydrogen bonding?

A

Yes, it can accept and donate one

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12
Q

Which bonds in polypeptide backbone can rotate?

A

The single bonds between the alpha carbon and the nitrogen, or the alpha carbon and the carbonyl

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13
Q

Why is formation of alpha helices and beta sheets so favourable?

A

All the backbone NH and CO are engaged in hydrogen bonding. Only conformations that don’t create steric congestion can form

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14
Q

Why does proline restrict the folding of the backbone of the polypeptide?

A

One single bond that normally is able to rotate can’t

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15
Q

How many polypeptide chains are involved in the formation of an alpha helix?

A

1 chain, coiled into a right handed helix

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16
Q

Which direction do the peptide bonds point in an alpha helix?

A

All in the same direction

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17
Q

In an alpha helix, which residues will hydrogen bond to each other?

A

i and i+4

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18
Q

Where are the side chains found in an alpha helix? Which ones are very close to each other?

A

On the outside. i and i+3, i+4 are very close to each other

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19
Q

What sort of structure can make an alpha helix amphipathic? Where are they found?

A

Coiled coils. Many helices come together into that structure and the hydrophobic portions interact. Found in transcription factors, keratin, cytoskeletal proteins and others

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20
Q

How many polypeptide chains form a beta sheet?

A

Multiple. Can also be one that made a loop and is coming back

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21
Q

What holds the strands together in a beta sheet?

A

Hydrogen bonding between the NH and CO in neighbouring strands

22
Q

What is an antiparallel beta sheet?

A

The strands are running in opposite directions

23
Q

What is a parallel beta sheet?

A

The strands are running in the same direction

24
Q

Which two amino acid side chains are close to each other in a beta sheet?

A

i and i+2, every second amino acid will be on the same side of the sheet

25
What will stabilize alpha helices and beta sheets?
Ionic interactions between side chains and pH changes that cause that
26
What will destabilize alpha helices and beta sheets?
Charge repulsion and pH changes that cause that
27
Where are irregular secondary structures commonly found? What do they hydrogen bond with?
On the surface of the protein. They hydrogen bond with the water
28
What amino acids are common in irregular secondary structures?
Glycine and Proline
29
Why have irregular secondary structures if the regular structures are much more stable?
The irregular structures are required to connect the regular structures together
30
What is the tertiary structure?
The 3D spatial arrangement pf all atoms in the protein
31
What parts of the polypeptide participate in the tertiary structure?
The backbone, amino acid side chains, and prosthetic groups
32
What is a prosthetic group?
A non-amino acid group tightly attached to a protein that provides greater chemical functionality
33
What stabilizes the tertiary structure of a protein?
Hydrogen bonds, electrostatic interactions, hydrophobicity, and disulfide bridges
34
How do hydrogen bonds help stabilize the tertiary structure?
They hydrogen bond to each other and the surrounding water. Anything not hydrogen bonding destabilizes the structure
35
What drives protein folding?
Hydrophobic groups aggregating in the middle of the protein and increasing the entropy of the solution
36
How does the entropy change when a protein folds?
Unfolded proteins have high entropy which decreases when folded. The solution also has a higher entropy when the protein folds
37
What is the most stable conformation of a protein called?
Native conformation
38
What are 6 things that will denature a protein?
Heat, pH changes, urea, guanidine HCl, organic solvents, detergents
39
How does heat denature a protein? What non-covalent bonds get disrupted?
It makes the atoms have a lot more energy, so they start moving around faster. Hydrogen bonds get disrupted?
40
How do organic solvents denature a protein? What non-covalent bonds get disrupted?
They make the environment less polar, which disrupts the hydrophobic effect
41
How does urea denature a protein? What non-covalent bonds get disrupted?
It is very polar, which makes the water more ordered and removes the driving effect of protein folding. Disrupts hydrophobic interactions
42
How do pH changes denature a protein? What non-covalent bonds get disrupted?
pH affects the ionization state of amino acid side chains, which disrupts ionic interactions. Leads to electrostatic repulsions and loss of salt bridges and hydrogen bonds
43
How do detergents denature a protein? What non-covalent bonds get disrupted?
They form a micelle-like structure around the hydrophobic portions of proteins and disrupt the hydrophobicity
44
How does guanidine HCl denature a protein? What non-covalent bonds get disrupted?
Same as urea. Makes the solution very polar and disrupts hydrophobicity
45
What will disrupt disulfide bonds?
Reducing agents like BME
46
How did we find out that the primary structure dictates the tertiary structure of a protein?
An experiment done by Christian Anfinsen. Denatured Ribonuclease A, then renatured it and it put itself back together based on the primary structure
47
What are molecular chaperones?
Proteins that assist in the folding of other proteins
48
How do chaperones work?
They bind to hydrophobic portions of the polypeptide chain to stop them from aggregating incorrectly
49
What are chaperonins?
Large protein complexes that put unfolded proteins inside and won't let them out until they are correctly folded
50
Why is it important that some parts of proteins stay flexible and unfolded?
Some functions require that, and required for binding to other stuff
51
What are amyloidogenic proteins?
Proteins that can misfold into beta sheets instead of alpha helices like they are supposed to be and cause disease
52
What is the quaternary structure?
The arrangement of subunits in a multiprotein complex

Introductory Biochemistry (16 decks)

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