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BIOCH 200 > Protein Structure > Flashcards

Protein Structure Flashcards

1
Q

In all cases, how is a protein’s function determined?

A

By its structure.

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2
Q

What is a zwitterion?

A

A neutral ion with an equal number of positive and negative charges.

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3
Q

What is pKA?

A

The strength of the weak acid; as pKA becomes smaller, the conjugate strong acid becomes stronger (more likely to be present in a solution).

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4
Q

What happens when pKA is less than pH

A

The base form of the ion is more present in a solution. The molecule will be deprotonated.

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5
Q

What happens when pKA>pH?

A

The acid form of the ion is more present in a solution.

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6
Q

What is the pKA of COO-?

A

pKA = 2

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7
Q

What is the pKA of NH3+?

A

pKA = 9.5

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8
Q

Why are amino acids chiral? Which amino acid is the exception? Why is it important that amino acids are chiral?

A
  1. They are chiral because the alpha carbon always has 4 different substituents.
  2. Glycine is achiral.
  3. Amino acids occur in L- and D- conformations based on their chirality (enantiomers). While L-isomers are present in living organisms and are the most common isomer, D- conformations are present in pharmacological substances and have vastly different functions from their L-type conformers.
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9
Q

Which amino acids are nonpolar?

A 
[A] Alanine
[V] Valine
[L] Leucine
[F] Phenylalanine
[W] Tryptophan
[P] Proline
[I] Isoleucine
[M] Methionine
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10
Q

Which amino acids are polar uncharged?

A 
[G] Glycine
[S] Serine
[T] Threonine
[C] Cysteine
[N] Asparagine
[Q] Glutamine
[Y] Tyrosine
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11
Q

Which amino acids are polar charged?

A 
[D] Aspartate
[E] Glutamate
[K] Lysine
[R] Arginine
[H] Histidine
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12
Q

What is the pKA of cysteine?

A

8.5

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13
Q

What is unique about cysteine?

A

It is able to form disulphide bonds with other cysteine molecules in oxidizing environments.

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14
Q

What is the pKA of Tyrosine?

A

10.5

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15
Q

What is the pKA of Histidine?

A

6

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16
Q

What is the pKA of Aspartate?

A

4

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17
Q

What is the pKA of Glutamate?

A

4

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18
Q

What is the pKA of Lysine?

A

10

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19
Q

What is the pKA of Arginine?

A

12.5

20
Q

Where are polar side chains typically found within a protein? Why?

A

On the surface; these groups can interact with water.

21
Q

Where are nonpolar side chains typically found within a protein? Why? What is the exception?

A

In the core to minimize interaction with water. Alanine is the exception.

22
Q

How are peptide bonds formed?

A

Peptide bonds are formed when two hydrogens from the N-terminus are accepted by an oxygen atom at the C-terminus. The result is an amide bond at the expense of a water molecule.

23
Q

What are peptides/oligopeptides?

A

A general term for a larger number of amino acids that are generally synthetically synthesized.

24
Q

What is a polypeptide?

A

A long chain of amino acids that is usually produced naturally.

25
Q

What is a protein?

A

A large polypeptide or group of polypeptides with a biological function.

26
Q

What is the primary structure of a protein? What interactions are present?

A

The basic sequence of amino acids in a polypeptide. Peptide/amide bonds between amino acids.

27
Q

What is the secondary structure of a protein? What interactions are present?

A

The local folding of the polypeptide backbone driven by hydrogen bonding between carbonyl and amino groups.

28
Q

What are the two most regular patterns of secondary structure in a protein?

A

Alpha-helix and Beta-sheet.

29
Q

How many residues downstream can carbonyl and amino groups interact in an alpha-helix?

A

4 residues downstream.

30
Q

What forces stabilize beta-sheets?

A

Hydrogen bonds between backbone CO and NH groups of neighbouring strands.

31
Q

What forces stabilize alpha-helices?

A

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

32
Q

What is an irregular structure?

A

Polypeptide loops of varying sizes that link together regular secondary structures.

33
Q

What is the tertiary structure of a protein? What interactions are present?

A

The arrangement of all atoms in a single polypeptide; the arrangement of secondary structures in relation to one another.

The structure is determined by non-covalent interactions between amino acid R-groups, as well as interactions with prosthetic groups. In some cases, salt bridges form between ionizable amino acid chains.

34
Q

What are the two classifications of tertiary structures?

A

Fibrous and Globular.

35
Q

What are fibrous proteins?

A

Insoluble in aqueous, long-filament proteins that contain limited residues with many repeats. Their primary function is structure or connectivity.

36
Q

What are globular proteins?

A

Soluble in aqueous solutions, folded into compact structures with nonpolar cores and polar surfaces.

37
Q

How is the hydrophobic effect relative in protein folding?

A

The hydrophobic effect drives soluble globular proteins to maintain a tertiary structure in which their hydrophobic cores remain compacted in the internalized structure.

38
Q

What are salt bridges?

A

Ionic interactions that form between closely-positioned charged amino acids that stabilize secondary and tertiary structure.

39
Q

What is a domain?

A

A polypeptide segment that has folded into a single structural unit with a hydrophobic core. There may be more than one present in a protein.

40
Q

What is a motif?

A

A short region of polypeptide with a recognizable 3D shape (Zinc fingers).

41
Q

What is a prosthetic group?

A

A non-peptide component in a protein that is permanently incorporated.

42
Q

What is the function of a prosthetic group?

A

To provide structure and function in different proteins.

43
Q

How are globular proteins stabilized? Are they easily denatured?

A
  1. Weak noncovalent forces.

2. Easily denatured.

44
Q

What can disrupt a disulphide bond?

A

Reducing agents (DTT)

45
Q

What is the quaternary structure of a protein?

A

The association of multiple polypeptides, stabilized by same forces as in tertiary.

BIOCH 200 (7 decks)

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