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BMSC 200 > Chapter 4: Protein Three-Dimensional Structure > Flashcards

Chapter 4: Protein Three-Dimensional Structure Flashcards

1
Q

What are polypeptides?

A

Amino acids linked by peptide bonds.

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2
Q

What is another name for a peptide bond?

A

An amide bond.

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3
Q

What is an amino acid that is part of a protein called?

A

A residue.

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4
Q

What is the forward reaction in the formation of a peptide chain?

A

A condensation/dehydration reaction.

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5
Q

What type of reaction occurs in the stomach which breaks down peptide bonds?

A

A hydrolysis reaction.

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6
Q

Does a polypeptide chain have directionality? Explain.

A

Yes a polypeptide chain has directionality. The amino terminal end is taken as the beginning of the polypeptide chain. The carboxyl terminal end is the end of the polypeptide chain.

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7
Q

Which way is the primary structure always written?

A

The primary structure is always written from the amino terminal to the carboxyl terminal, or left to right.

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8
Q

How many chiral centres does isoleucine have?

What determines a chiral centre?

A

Ile has two chiral centres. A chiral centre is determined by the presence of 4 different groups attached to a central carbon. Chiral molecules cannot be superimposed (L to D) with each other.

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9
Q

Is glycine a chiral molecule?

A

No. Glycine can be superimposed on itself. Also, there are two hydrogen groups, only giving three distinct side groups.

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10
Q

What does the C-N bond in peptide chains act as?

A

The C-N bond, while a single bond, acts like a double bond.

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11
Q

What are the parts of a polypeptide chain?

A

The polypeptide chain consists of a repeating part called the main chain or backbone and a variable part consisting of the distinctive amino acid side chains.

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12
Q

What kind of bonding does the backbone use? Why?

A

The backbone has hydrogen-bonding potential because of the peptide / amide functional group.

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13
Q

Between oxygen and nitrogen, which is the hydrogen bond donor and which is the acceptor?

A

Acceptor: Oxygen
Donor: Nitrogen (specifically N-H)

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14
Q

How many amino acids do most proteins consist of?

A

50-2000.

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15
Q

What is the mean (average) molecular weight of an amino acid?

A

110 g/mol.

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16
Q

What is the approximate molecular weight of a protein composed of 300 amino acids?

A

33,000.

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17
Q

What is the residue at the amino terminus of the tripeptide Gly-Ala-Asp

A

Glycine.

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18
Q

What kind of bonds can cross-link some proteins in polypeptide chains?

A

Disulfide bonds. Typically found in cysteine molecules as a result of the thiol group at the end of the chain.

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19
Q

What is the resulting unit of two linked cysteine called?

A

Cystine.

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20
Q

Is the peptide bond planar?

A

The peptide bond is essentially planar. Six atoms (Cα, C, O, N, H, and Cα) lie in a plane.

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21
Q

What kind of bond is present in peptide bonds? What happens to the rotation about the bond as a result ?

A

The peptide bond has partial double-bond character because of resonance; thus, rotation about the bond is prohibited.

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22
Q

Does the double bond freely rotate in a polypeptide chain? What happens if you switch the C and H?

A

No. If you switch the C and H, you’ll get the cis configuration.

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23
Q

Is there a charge on the peptide bond?

A

No, it is uncharged.

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24
Q

Which configuration is most common with amino acids? Why are they in this configuration?

A

Trans (more than 99%). Trans = α-carbons on either end of the protein. Most peptide bonds are in the trans configuration so as to minimize steric clashes between neighboring R groups. The cis conformer is rare.

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25
Q

What interactions are present between atoms in the Cis configuration?

A

Van-der Waals forces (repulsion).

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26
Q

About what bond is rotation permitted? Are they rotatable to a fairly large degree?

A

Rotation is permitted about the N–Cα bond [the phi (Φ)bond) and about the Cα- carbonyl bond (the psi (ψ) bond]. Yes, they are rotatable to a fairly large degree.

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27
Q

What do the colours on a Ramachandran

Diagram signify?

A

The yellow parts are the most observed, lighter yellow less so, and white is not observed.

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28
Q

Are all phi and psi values possible without collisions between atoms?

A

No, not all phi and psi values are possible without collisions between atoms.

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29
Q

What is secondary structure? What are some prominent examples?

A

Secondary structure is the three-dimensional structure formed by hydrogen bonds between peptide NH and CO groups of amino acids. The α helix, β sheets, and turns are prominent examples of secondary structure.

30
Q

What is the α helix?

A

The α helix is a tightly coiled rodlike structure, with the R groups bristling out from the axis of the helix.

31
Q

What hand spin do essentially all α helices found in proteins use?

A

Essentially all α helices found in proteins are right-handed.

32
Q

What does screw-sense refer to?

A

Screw sense refers to the direction in which a helical structure rotates with respect to its axis. If viewed down the axis of a helix (N terminus to C terminus), the chain turns in a clockwise direction; it has a right-handed screw sense. If turning is counterclockwise, the screw sense is left-handed.

33
Q

Ribosomes only make what kind of amino acids?

A

L amino acids.

34
Q

What is the distance between O and H on an alpha helix?

A

About 3.6

35
Q

How many different patterns of proteins do we have?

A

About 1200.

36
Q

How are beta sheets formed?

A

Adjacent β strands.

37
Q

How are β sheets different compared to α strands?

A

In contrast to an α helix, the polypeptide in a β strand is fully extended.

38
Q

What is the bond angle between nitrogen and carbon on a β strand?

A

109.5º

39
Q

Are parallel or antiparallel beta sheets more common?

A

Antiparallel is slightly more abundant due to configuration when folding.

40
Q

Why would we never observe stacked alpha strands?

A

Too unstable.

41
Q

Why is proline not present in α helices or perfect beta strands?

A

Proline doesn’t have an H (hydrogen bond breaker) as the ring is integrated into the central body. Because of this, it is not present in alpha helices or perfect beta strands.

42
Q

Where are proteins rich in beta sheets commonly found? Why?

A

Common in membrane proteins. Its barrel shaped, making no open end.

43
Q

Where is α-keratin found? What is it composed of?

A

Found in wool and hair, is composed of two right-handed α helices intertwined to form a left-handed superhelix called a coiled coil. The helices interact with ionic interactions or van der Waals forces.

44
Q

What superfamily does α-keratin belong to? What are some other members of this family?

A

Coiled-coil proteins. Other members include cytoskeleton proteins and muscle proteins.

45
Q

What way does each α-keratin helix twist? What twist do they coil each other with?

A

Two alpha helices (superhelix), both individually right hand twist, coiling each other with left hand twist.

46
Q

What is collagen?

A

Collagen is a structural protein that is a component of skin, bone, tendons, cartilage, and teeth.

47
Q

What does collagen consist of?

A

Collagen consists of three intertwined helical polypeptide chains that form a superhelical cable. The helical polypeptide chains of collagen are not α helices.

48
Q

Where does glycine appear? What sequence is common?

A

Glycine appears at every third residue, and the sequence Gly-Pro-Pro is common.

49
Q

What role does glycine play in collagen?

A

Collagen is stabilized by glycine. In order to create hydrogen bonds, the distance between atoms need to be closer than normal VDW reactions. Glycine is small enough to shorten the space to create hydrogen bonds.

50
Q

How are the helices in collagen stabilized? Why is glycine critical?

A

The helices in collagen are stabilized by hydrogen bonds. The small size of glycine is critical for stabilizing the three intertwined chains interact with one another with hydrogen bonds. The interior of the superhelical cable is crowded, and only glycine can fit in the interior.

51
Q

Which residue is abundant in collagen? Where is it located on the triple helix? Are they hydroxylated or not?

A

Prolines residues are abundant. They are located on the outskirts of the triple helix, and are often hydroxylated.

52
Q

What does the mutation in osteogenesis imperfecta cause?

A

The mutation results in the substitution of another amino acid in place of glycine.

53
Q

What is the role of hydroxyproline in collagen? What is required for its formation?

A

Hydroxyproline stabilizes glycine. Vitamin C is required for its formation, a lack results in scurvy (House MD yoga-girl case [toenail]).

54
Q

What does tertiary structure refer to? What is the result of the level of this structure?

A

Tertiary structure refers to the spatial arrangement of amino acids that are far apart in the primary structure and to the pattern of disulfide bond formation. This level of structure is the result of interactions between the R groups of the peptide chain.

55
Q

Give an example of a globular protein. Are they compact or is there a lot of space?

A

Myoglobin. Globular proteins are very compact. There is little or no empty space in the interior of globular proteins.

56
Q

What kind of amino acids does the inside of globular proteins consist of? What about the outside?

A

Hydrophobic amino acids on the inside. Mainly charged and polar amino acids on the outside.

57
Q

What atom is an essential part of the myoglobin molecule?

A

Iron.

58
Q

What are motifs?

A

Supersecondary structures. Combinations of secondary structure found in many proteins. (configurations of proteins)

59
Q

What are domains?

A

Two or more similar or dissimilar compact structures.

60
Q

What are subunits? What do proteins that have them are said to display?

A

Subunits are multiple polypeptide chains that compose a protein. Said proteins are said to display quaternary structure. Quaternary structure can be as simple as two identical polypeptide chains or as complex as dozens of different polypeptide chains.

61
Q

How do you calculate turn angles in proteins?

A

Take the prefix (di-, tri-, tetra-) and divide 360º using the numerical value. (e.x., tetramer: 90º turn angles).

62
Q

How similar are the amino acid sequences between α and β strands in terms of bonds? Where do α and β strands most differ?

A

Approximately 50% similar. α and β strands are most different in terms of length (α-strands are longer).

63
Q

What experiment did Christian Anfinsen perform? What were the results and what did it show?

A

Christian Anfinsen placed the enzyme ribonuclease (suffix -ase denotes breaking down, in this case hydrolysis), which degrades RNA, in a solution containing urea (urea is able to break the structure of proteins without raising the temperature) and β-mercaptoethanol. Urea destroyed all noncovalent bonds, whereas the β-mercaptoethanol destroyed the disulfide bonds. The ribonuclease was denatured. The enzyme displayed no enzymatic activity and existed only as a random coil. When the urea and β-mercaptoethanol were slowly removed, the enzyme regained its structure and its activity. Ribonuclease was renatured and attained its normal or native state. These results demonstrated that the information required for a polypeptide chain to fold into a functional protein with a defined three-dimensional structure is inherent in the primary structure.

64
Q

What is the typing monkey analogy? What does it have to do with protein folding?

A

The typing monkey analogy says that a monkey would be able to randomly poke at a keyboard and would eventually type a sentence of Shakespeare in a few thousand keystrokes if the correct letters are retained. This process is called cumulative selection. Protein folding also occurs by cumulative selection. Partly correct folding intermediates are retained because they are slightly more stable than unfolded regions.

65
Q

What is the folding tunnel diagram? Where are the notable points?

A

Protein folding is often represented as a folding funnel. The protein has maximum entropy and minimal structure at the top of the funnel. The folded protein exists at the bottom of the funnel.

66
Q

What is odd about intrinsically disordered proteins (IDP’s)?

A

Intrinsically disordered proteins (IDPs) do not have a defined structure under physiological conditions until they interact with other molecules. IDP’s do not have a dominant structure, but are more dynamic.

67
Q

What state do metamorphic proteins live in?

A

Metamorphic proteins exist in an ensemble of structures of approximately equal energies that are in equilibrium.

68
Q

What are amyloidoses? Give an example. What form do they live in? Why is this bad?

A

Amyloidoses are diseases that result from the formation of protein aggregates, called amyloid fibrils or plaques.
Alzheimer disease is an example of an amyloidosis.
The good form is the hydrophobic form, the bad forms are aggregates, which are easy to tip over into the wrong form.

69
Q

What are prions? What states do they live in and which disrupts cell function?

A

Infectious proteins that cause some infectious neurological diseases. Prions exist in two states, one α-helix-rich (PrP) and the other β-sheet-rich (PrPSC).
PrPSC forms aggregates that disrupt cell function.

70
Q

What are the four levels of proteins?

A
  1. Amino acid sequence (peptide bonds)
  2. Backbone interactions (H bonds)(α helix, β sheets)
  3. Distant interactions: polypeptides. (H bonds, VDW forces, disulfide bonds, hydrophobic packing)(cystine)
  4. Quaternary structure: multiple polypeptides (tetramers, dimers, trimers, multimers, monomers)

BMSC 200 (5 decks)

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