Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BCMB > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

Why are peptide bonds unable to rotate?

A

Peptide bonds have partial double bond character due to resonance stabilization, which gives them a rigid planar geometry.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Why are most peptide bonds found in the trans configuration?

A

to avoid steric clashing between R groups

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Alpha Helix

A

In an alpha helix, hydrogen bonds form between N-H and C=O groups in the same peptide chain. The peptide backbone forms a circular helical structure, making the peptide chain more compact. (most favored because it allows for maximum hydrogen bonding while minimizing steric clashing)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Beta Sheet

A

More extended than alpha helix and is made up of multiple strands with hydrogen bonds forming between the peptide N-H and C=O bonds.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Antiparallel vs Parallel Beta Sheet

A

In antiparallel strands, the N and C terminus are pointed in opposite directions, and in parallel strands, they are pointed in the same direction.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Why do beta sheets require two strands?

A

In beta sheets, hydrogen bonds form between strands, and in alpha helices, they form between groups in the same chain.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Phi and Psi angles

A

A Phi angle is the angle between peptide and alpha carbon. Psi angles are between alpha carbon and peptide carbonyl carbon.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Ramachandran Plot

A

A representation of all the dihedral angles (phi and psi) from a protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Why are only certain combinations of phi and psi angles allowed?

A

Most angles are not permitted due to steric clashing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Alpha Helix Angles

A

The phi angles are from -60 to -120, and the psi angles are at -60. (lower left quadrant of the plot)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Beta Sheet Angles

A

The phi angles are from -60 to -120, and the psi angles are from +180 to +120. (upper left quadrant of plot)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Glycine

A

Glycine is not entropically favored in alpha helices or beta sheets because it is small and flexible. These extreme angles favor reverse turns.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Proline

A

Because the side chain is linked to alpha nitrogen, there is no N-H available for hydrogen bonding. The angles are also restricted.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Which amino acids are not favored in alpha helices or beta sheets?

A

glycine, proline, aspartate, asparagine, serine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Reverse Turn

A

Occur between secondary structural elements when the polypeptide chain reverses direction and are essential for protein folding

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Reverse Loop

A

Similar to turn but with more amino acids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What amino acids are likely to be found in turns?

A

proline and glycine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

In aqueous media, the dielectric constant is 80 in aqueous media and 5 inside a cell membrane bilayer. Why do peptides that are disordered in aqueous media form alpha helices in membranes?

A

The force of hydrogen bonds are guided by Coulomb’s Law. The strength of interactions between charges is inversely proportional to the dielectric constant of the media, so the interactions are much stronger in hydrophobic media.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Which amino acids prefer beta sheet?

A

amino acids containing large bulky side chains or bulkier (sulfur) atom on beta carbon; beta branched carbon in R group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Which secondary structure is the default?

A

alpha helix

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Tertiary Structure of Myoglobin

A

Myoglobin contains eight alpha helices folded into compact globular shape.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Why is heme located inside myoglobin?

A

Heme is hydrophobic and clusters with other hydrophobic amino acid R groups in the center

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Amphipathic

A

Has both hydrophobic and hydrophilic character; myoglobin contains hydrophilic amino acids on the surface exposed to solvent and hydrophobic amino acids that cluster away from water

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Christian Anfinsen

A

Performed experiment that demonstrated that primary sequence determines secondary and tertiary structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Urea

A

disrupts non-covalent interactions leading to protein denaturation (chaotropic reagent)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Beta- Mercaptoethanol

A

breaks disulfide bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Ribonuclease

A

Monomeric polypeptide that degrades RNA; contains eight cysteine groups that form four specific disulfide linkages

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What happened when both reagents were removed?

A

The ribonuclease returned to 100% activity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What happened when only the Beta-ME was removed?

A

The ribonuclease only had 1% activity and many disulfide pairings because there the protein was denatured

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

How did he restore complete functioning?

A

He removed urea and added trace amounts of Beta-ME

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

Why is ribonuclease treated with B-ME more susceptible to heat denaturation?

A

Only non-covalent interactions remain, which are not as strong as covalent bonds.

32
Q

Sickle Cell Anemia is caused when an aspartate is replaced by a valine. Why does this cause hemoglobin to aggregate?

A

Hemoglobin folds in a way that hydrophilic amino acids face the aqueous media. When aspartate is replaced with valine, this amino acid no longer favors exposure to aqueous media. The protein aggregates so that valine is excluded from water, leading to precipitation.

33
Q

Free Energy of Protein Folding

A

Protein folding occurs spontaneously, so the free energy value is negative. Nonpolar amino acids cluster within the hydrophobic core, and release of clathrate water from the side chains increases entropy of the system. A series of non-covalent interactions further stabilize the tertiary structure, decreasing the enthalpy.

34
Q

Cyrus Levinthal’s Paradox

A

The theoretical amount of time it would take a protein to fold from a random structure to the native state (1.45x10^46 sec)

35
Q

Nuclear Condensation Model

A

Proteins fold into several stable intermediates before they reach their native state

36
Q

Molten Globule

A

Hydrophobic effect causes protein to collapse into molten globule similar to the native state. This allows for the rapid formation of more non-covalent interactions that lead to the final conformation.

37
Q

How does the nuclear condensation model avoid Levinthal’s paradox?

A

The protein folding is not completely random, so the number of conformations is restricted, and the favored structures are retained.

38
Q

Why does the funnel narrow?

A

As the protein folds, the favored structures are retained, and the number of possible conformations decreases.

39
Q

Quaternary Structure

A

Multiple polypeptide chains join together.

40
Q

Secondary Structure

A

The three dimensional arrangement of a polypeptide into alpha helices and beta sheets.

41
Q

Why does hemoglobin dissociate into monomers when urea is added?

A

Urea disrupts non-covalent bonds, which stabilize tertiary and quaternary structure. Heme interaction with the hydrophobic core will also be disrupted, so the heme will be released.

42
Q

Domain

A

Functional three dimensional units that are folded separately (beads on a string)

43
Q

Homolog

A

Descended from a common ancestor

44
Q

Paralog

A

Homologs present in one species that may have different functions

45
Q

Ortholog

A

Homologs present in different species that have similar ancestors

46
Q

Gap

A

Inserting gaps into sequences compensates for insertions and deletions.

47
Q

Sequence Shuffling

A

One sequence is shuffled and then realigned with other sequence to calculate new alignment score. If randomly shuffled sequence is significantly different, then original alignment is not due to chance.

48
Q

Evolutionary Tree

A

Shows evolutionary relationships using DNA sequences

49
Q

How identical do sequences have to be to establish common ancestry?

A

at least 25%

50
Q

What is the most important factor in determining ancestry?

A

three dimensional structure

51
Q

What results would be obtained if mRNA and DNA were randomly shuffled?

A

You are more likely to have random agreement between mRNA and DNA compared to amino acids because there are only four bases.

52
Q

What defines the length of branches in an evolutionary tree?

A

The number of amino acid differences between the sequences

53
Q

How do we approximate the time of evolutionary events?

A

Fossil studies

54
Q

Heme

A

Heme is a protoporphyrin ring with a central iron atom. It is bound to myoglobin by the proximal histidine.

55
Q

Proximal Histidine

A

Provides a fifth N atom that binds iron. (oxygen binds at the sixth site)

56
Q

Distal Histidine

A

Forms hydrogen bond with the oxygen bound to the heme.

57
Q

Why are hemoglobin and myoglobin less susceptible to oxidation of iron and CO poisoning than free heme?

A

The distal histidine stabilizes oxymyoglobin in a bent conformation, whereas CO prefers a straight conformation.

58
Q

Why is the oxidation of heme undesirable for myoglobin and hemoglobin function?

A

When heme is oxidized to form metmyoglobin, it does not bind oxygen, so oxygen carrying capacity is lost. Also, superoxide can be damaging to many biological materials.

59
Q

R State

A

Relatively high affinity for oxygen (relaxed)

60
Q

T State

A

Relatively low affinity for oxygen (tense)

61
Q

How does heme structure differ in R and T states?

A

The T states keeps heme out of the plane of the protoporphyrin ring, and the R state brings the iron into the plane.

62
Q

What forces stabilize the T state?

A

A network of inter- and intra-subunit linkages at the amino and carboxy termini of alpha and beta chains

63
Q

Bohr Effect

A

Hydrogen ions and carbon dioxide (allosteric effectors) promote the release of oxygen. Lowering the p releases more oxygen.

64
Q

Why is hemoglobin a more effective oxygen transporter?

A

It uses cooperative binding, which allows hemoglobin to release more oxygen where it is needed.

65
Q

Concerted Model

A

All molecules are either in the T or R state, with T state being favored with no oxygen binding and R state with oxygen binding.

66
Q

How do 2,3-BPG and carbon dioxide bind to hemoglobin and influence oxygen binding?

A

2,3-BPG binds to the central cavity of deoxyhemoglobin that is only present in the T state, where it interacts with three positively charged groups on the beta chain. Carbon dioxide results in a drop in pH, increasing the number of H+. The side chains are protonated, and salt bridges form to stabilize the T state. Carbon dioxide also reacts with terminal amino groups to form negatively charged carbamate groups that form salt bridges.

67
Q

How does the oxygen saturation curve and Hill plot of myoglobin differ from that of hemoglobin?

A

Myoglobin is hyperbolic, while hemoglobin is sigmoidal.

68
Q

P50

A

Half saturation of the binding sites

69
Q

Y

A

The fractional of possible binding sites that contain myoglobin/hemoglobin

70
Q

Hyperbolic vs. Sigmoidal Binding

A

In hyperbolic binding, the oxygen is bound more tightly compared to sigmoidal binding, which is cooperative.

71
Q

Allosteric Protein

A

Binding at one site influences conformation of other sites

72
Q

Ligand

A

An ion or molecule attached to a metal atom by coordinate bonding (e.g. oxygen binding to heme

73
Q

Hill Coefficient

A

Measures the cooperative interaction among the binding sites in a protein

74
Q

Positive Cooperativity

A

Binding of a ligand increases the affinity at other sites of

75
Q

Negative Cooperativity

A

Binding of a ligand decreases the affinity at other sites making it harder for other molecules to bind

BCMB (1 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions