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Biological Chemistry- Samiyah > Protein Structure > Flashcards

Protein Structure Flashcards

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1
Q

What is an oligopeptide

A

3-10 amino acids joined together

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2
Q

What is the primary structure and what does it affect

A

Made up of covalent (peptide) bonds between amino acids

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3
Q

What is the secondary structure

A

Made up of hydrogen bonds between parallel strands in the beta sheet

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4
Q

How can polypeptides adapt the lowest energy conformation possible

A
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5
Q

why is the backbone of a polypeptide rigid

A

Due to restricted rotation around pi bonds (so around the peptide bond rotation can’t occur)
However, rotation can occur around the sigma bonds in an amino acid

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6
Q

What is a beta pleated sheet and its structure

A

Dipole-dipole interactions aka hydrogen bonds

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7
Q

What is an alpha helix

A

Same angles over and over again (regular structure)
R groups all stick out
When H bonds form every 3 residues the dipoles line up

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8
Q

What is the tertiary structure of a protein

A

Formed from hydrophobic effect and van der Waals interactions

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9
Q

Where are residues wit hydrophobic and residues with hydrophilic side chains found and why

A
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10
Q

What is the quaternary structure of a protein

A

2 types- fibrous and globular
Is the interaction of multiple polypeptides

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11
Q

What is a disulphide bond

A
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12
Q

What is a fibrous and globular protein

A
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13
Q

What happens if there’s a small change in polypeptide sequence

A

There would be a big change in protein structure and folding

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14
Q

Where is keratin found in the body

A

Skin
Hair
Nails

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15
Q

What is the structure of keratin

A

2 alpha helices put into bundles

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16
Q

What is an anti parallel beta pleated sheet

A

When the starting point of the row alternates between being the C and N terminus

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17
Q

What are loops and turns and what is the difference

A
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18
Q

What is the role of aromatic amino acids in a protein

A

They make the protein more rigid and stable (stops things from moving around)
This is because the rings are flat and stable
They are found on the inside of a protein (along with the hydrophobic non polar amino acids)

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19
Q

Why can glycine fit in places that other amino acids can’t fit inside a protein

A

It’s side chain is absent locally so can make tight turns while the amino acids maintain its planar shape
It’s side chain is absent because if it was present there would be steric clash
So glycin is always involved in turns (when the polypeptide turns in a protein- turn regions ) since it has no side chain

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20
Q

What is collagen

A

The structural protein in cartilage and bone

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21
Q

What is the distance between each residue in collagen

A

2.9 angstroms

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22
Q

What is the structure of collagen

A

Every third amino acid used is glycine which allows the formation of fibrous proteins
However, this would make the protein flexible

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23
Q

How is the problem of a fibrous protein being flexible due to the presence of glycine every third amino acid overcome

A

Proline is used as it forms a ring with its side chain (since it bonds to the nitrogen in the amino group)
This helps to provide rigidity to counteract the flexibility of glycine
This makes the overall structure of the protein stable

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24
Q

What is a Ramachandran plot

A
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25
Q

What are phi and psi angles

A

They involve 2 amino acids

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26
Q

What is a phi angle

A

Rotation around the bond from the alpha carbon to nitrogen (this bond is called the phi bond)
Is the angle between 2 carbonyl carbon atoms on the 2 separate amino acids

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27
Q

What is the psi angle

A

Rotation around the bond from the alpha carbon to the carbonyl group (this is the psi bond)
The angle between the two nitrogen atoms on the two separate amino acids

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28
Q

What is the omega angle

A

This bond refers to the dihedral angle around the peptide bond (C-N bond) that links two amino acids together. The omega angle is usually either 0° (for cis configuration) or 180° (for trans configuration), with the trans configuration being far more common in proteins.

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29
Q

Label the psi, phi and omega angles and bonds on a diagram

A
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30
Q

What happens when you look down the alpha C-N bond (to measure the phi angle) and what would this look like diagrammatically

A

Nitrogen will be hidden behind the alpha carbon
alpha carbon would be at the front

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31
Q

What happens when you look down the alpha C- carbonyl C bond (to measure the psi angle) and what would this look like diagrammatically

A

The carbonyl carbon would be hidden

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32
Q

What is meant by a staggered conformation

A

All atoms are equally spaced out

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33
Q

What is meant by an eclipsed conformation

A

Carbons are aligned so that the hydrogens line up with eachother
Forms steric hinderance/ steric clash

34
Q

What is the range for dihedral angles . Explain using the clock analogy

A

-180 degrees to + 180 degrees

35
Q

What is the angle is the 2 carbonyl carbons are eclipsed

A

The angle is 0

36
Q

How can rotation occur around a peptide bond

A

Would have to break the bond

37
Q

Explain the Ramachandran plot

A
38
Q

What is the distance between each residue in an alpha helix

A

1.5 angstroms

39
Q

What is the width of an alpha helix

A

5 angstroms

40
Q

What do you see if you look down at the top of an alpha helix

A
41
Q

What is the distance between 2 R groups of an amino acid in a beta strand

A

7 angstroms

42
Q

What are the regular secondary structures

A

Alpha helix
Beta sheet

43
Q

What is a parallel beta sheet

A
44
Q

What is regular secondary structure and what it is regulated by

A

Repeating the same psi and phi bonds over and over

Regulated by:
- ideal peptide geometry
- ideal van der Waals interactions
- ideal H bonds in backbone

45
Q

What charge do acidic amino acids side chains have with the example of aspartate and glutamate

A

They are Negatively charged
So their names ending is -ate

46
Q

What is the ratio of [A-]/[HA] for acidic amino acids

A

The acidic amino acids are aspartic acid and glutamic acid. They have carboxylic acid side chains that can lose a proton , forming an anionic form

47
Q

Show the distribution of electrons/ resonance forms of the carboxyl group when acidic amino acids are missing the hydrogen attached to the oxygen in the carboxyl group

A

All the atoms in the carboxyl group at sp2 hybridised
Grey = pi orbitals
White= sigma orbitals

48
Q

What charge do amino acids with basic side chains have with the example of lysine (plus its name)

A

They are positively charged

49
Q

What are the different resonance forms of arginine and why does it have so many resonance forms

A

Is very basic due to its guanodino group

50
Q

Show the distribution of electrons across the atoms in arginines side chain for this version of arginines resonance form

A

Red arrows= movement. Of electrons
Purple = pi bond = where double bond is

51
Q

Show the distribution of electrons across the atoms in arginines side chain for this version of arginines resonance form

A
52
Q

Show the distribution of electrons across the atoms in arginines side chain for this version of arginines resonance form

A
53
Q

Explain the formation of arginines different resonance forms

A

2 pi orbitals have one electron in them while the other 2 pi orbitals have 2 electrons in them
The two pi orbitals with only one electron in them form a pi bond between them, and this is where the double bond would be in arginines side chain
The an electron from the p orbital with 2 electrons can move to a p orbital that has only one electron in it
Therefore the p orbital that the electron moved from can overlap with the other p orbital with only one electron in it to form the double bond between those atoms
This can happen for all of the p orbitals so the double bond can occur between different atoms depending on where the electron moved from

54
Q

Show the distribution of electrons between the orbitals of the atoms in this version of arginines side chain

A
55
Q

What type of bond can help stabilise quaternary structures

A

Disulphide bonds between cysteine amino acids

56
Q

How do beta sheets come together

A

Due to the hydrophobic effect which puts hydrophobic amino acids on the inside

57
Q

What are the properties of amino acids with amide groups such as ASN and GLN

A

All atoms in the amide group are sp2 hybridised so they all have pz orbitals
These amino acids have resonance forms
The atoms in the amide group have strong dipoles
These amino acids can form 3 hydrogen bonds due to the strong dipoles of the atoms in the amide group
Amides don’t undergo chemical reactions
These amino acids aren’t charged as they don’t protonate/deprotonate

58
Q

What is serine protease Chymotrypsin

A

It’s an enzyme (protease)
They break peptide bonds

59
Q

What are DNA-binding proteins

A

They bind to specific parts of DNA

60
Q

What is a modular protein

A

They are folded into units
They are made of domains. Each domain has its own function and can carry that function out independently

61
Q

What are the two examples of post translational modifications which involve amino acids

A

Reversible reaction with serine to produce phosphoserine
Irreversible reaction which converts glutamic acid to gamma-carboxyglutamic acid

62
Q

Give the post translational modification reaction of serine

A
63
Q

Give the post translational modification of glutamic acid and the function of the product as well as the form that the product is found naturally

A
64
Q

What is this group called

A

Ether

65
Q

What is this group called

A

Thioether

66
Q

Give the reaction between two cysteine side chains and the name of this reaction + the name of the product

A

This is another example of a post translational modification

67
Q

What is the difference between cysteine and cystine

A

Cysteine is in the cytoplasm and doesn’t have disulphide bonds
Cystine is formed when proteins go down the secretory pathway

68
Q

What is protein folding

A

When polypeptide forms secondary or tertiary structure
The folded protein would have native tertiary structure

69
Q

What is a denatured protein and what can it also be called

A

It is an unfolded polypeptide which has no defined structure
It can have many conformation s
Phi and psi angles changes constantly

It is also known as a random coil, which has no native structure

70
Q

How is a loop different to a random coil

A

A loops structure wouldnt change
The polypeptide would always fold the same way as the sequence of amino acids in the polypeptide would be the same, so the loops would stay the same

71
Q

What is denaturation

A

When a protein unfolds

72
Q

What is an oligomeric structure/ quaternary structure

A

2 or more polypeptides to make up the protein

73
Q

What is a subunit in an oligomer

A

Individual polypeptides

74
Q

What does it mean if a protein has one subunit/monomer

A

The protein is monomeric

75
Q

What does it mean if a protein is dimeric

A

It has 2 subunits (2 polypeptide chains)

76
Q

What does it mean if a protein is homo dimer

A

Composed of 2 identical polypeptides
Can be represented by lowercase alpha 2 (show in image)

77
Q

What does it mean if a protein is heterodimer

A

Composed of 2 different polypeptides
Represented by lowercase alpha beta

78
Q

What is meant by a protein being heterotetromer

A

Has 2 of the same polypeptides, 2 different polypeptides
Represented by :

79
Q

What is meant by heterotrimer

A

A protein which has 3 different subunits/polypeptides
Represented by alpha beta gamma

80
Q

What are the two ways to make hetero oligomers

A
81
Q

What are the long range interactions which stabilise protein structures

A

The long-range interactions in protein structure include disulfide bond and many non-bond interactions, such as electrostatic interaction, hydrophobic interaction, van der Waals interaction, and hydrogen bond

82
Q

what are functional sites on proteins

A

Protein functional sites are amino acid residues, or groups of residues, that perform functional roles in proteins. Examples of functional sites include catalytic sites in enzymes, ligand-binding sites for small molecules, metal ions, nucleic acids and other proteins and protein–protein interaction sites.

Biological Chemistry- Samiyah (24 decks)

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