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Biochemistry > Lecture 2: Protein Structure > Flashcards

Lecture 2: Protein Structure Flashcards

1
Q

What are the (4) Main Fxs of Proteins

A

Catalysis. Transport. Structure. Motion

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2
Q

How do you name Amino Acids?

A

Begin at the Alpha-Carbon down to the R-Group

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3
Q

True or False

The Alpha Carbon in Amino Acids always has a chiral carbon?

A

True

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4
Q

All AA except which one have an (A) acidic carboxyl group (B) Basic Amino Group (C) Alpha Hydrogen) connected to the carbon

A

Proline

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5
Q

Name the Aromatic AA?

A

Tyrosine- Tryptophan- Phenylalanine

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6
Q

FX. of Aromatic AA

A

Absorb UV light at 270-180 nm

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7
Q

Name the Non-polar, aliphatic AA

A

(Glyanna and Alanna went pro but vaguely lets Isolesha Methionate)
Glycine- Alanin-Proline-Valine-Leucine-Isoleucine-Methionine

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8
Q

Fx. of Non-polar, aliphatic AA

A

Side chains are hydrophobic

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9
Q

Name polar, uncharged AA

A

(Three cysters seriously asparged glutamine_

Threonine-Cysteine- Serine- Asparganine-Glutamine

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10
Q

Fx polar, uncharged AA

A

side chains can form H+ bonds; cysteine forms disulfide bonds

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11
Q

Name positively charged AA

A

(HIs arm was Lysed)

Histidine Arginine Lysine

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12
Q

Fx. positively charged

A

Serve as proton donors/acceptors

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13
Q

Name negatively charged AA

A

(Georgeate -GA)

Glutamate Aspartate

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14
Q

What is twitter-ionic?

A

Dipole ion with spatially separated (+)/(-) charges

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15
Q

What are covalently linked AA

A

Peptides

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16
Q

General Term for fx. non0AA component

A

Cofactor

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17
Q

Used to designate an organic cofactor

A

Coenzyme

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18
Q

Covalently attached cofactors

A

Prosthetic Groups

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19
Q

True or False; there is no cost in conformational energy for a native fold

A

False; there IS a cost of conformational energy

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20
Q

True or False; Electrostatic Interactions- salt-bridges stabilize the protein

A

True

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21
Q

True or False; Interaction of N-H/C–O of the peptide bond leads to local regular structures such as Alpha-Helixes/Beta-Sheets

A

True

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22
Q

True of False; Protein Structure is partially dictated by the properties of the peptide bond

A

True

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23
Q

True or False; Resonance causes peptide bonds to be rigid/planar

A

True

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24
Q

Psi bond refers to which bond in AA?

A

Bond bt. alpha & carbonyl Carbon

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25
Q

Phi bond refers to which bond in AA?

A

Bond bt. alpha & amide Nitrogen

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26
Q

Intermolecular Interactions are responsible for what secondary structures

A

H-Bonding; carbonyl-amide of Amino Acid Groups

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27
Q

Will you find proline residues on a secondary structure?

If so, where

A

Yes; Beta-Sheets

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28
Q

What is an alpha helix?

A

Stabilized by H+ bonds between nearby residues

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29
Q

What is a beta sheet?

A

Stabilized by H+ bonds between adjacent segments that may not be nearby in primary sequence

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30
Q

What is random coil?

A

Irregular arrangement of the polypeptide chain

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31
Q

What is the secondary structure

A

Spatial arrangement of he polypeptide chain

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32
Q

What is the Ramachandran Plot?

A

Distribution of psi/phi dihedral angels in a protein (tendency of AA to interact)

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33
Q

What favors/disfavors interactions of AA in configuration?

A

Prohibit- Steric Hinderance & Repulsive Forces

Promote- H-Bonding & Attractive forces bt. atoms

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34
Q

In collagen, what makes up the right hand, superhelical triple helices?

A

3 left handed chains intertwined into “SUPER DUPER” right-handed triple helix.

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35
Q

Folding of a peptide to its native form is favorable or unfavorable?

A

unfavorable

36
Q

What is the 3rd AA in B- sequence

A

Glycine

37
Q

True or False

Alpha Helix; Backbons is NOT compact

A

False, it is very compact

38
Q

True or False

Alpha Helix; the inner diameter is too small for anything to fit “inside”

A

True

39
Q

True or False; Alanine & Leucine are strong helix formers

A

True

40
Q

True or False; Proline acts as a helix breaker because the rotation around N-C alpha bond is impossible

A

True

41
Q

True or False; Glycine as as a helix breaker because the tiny R-group supports other conformations

A

True

42
Q

True or false; Beta Sheets; Backbone is more extended with psi dihedral between 90-180 degrees?

A

True

43
Q

True or False; H-bonded strands run in opposite direction

A

False; parallel run in the same direction

44
Q

What is the 2nd AA in B turn sequence?

A

proline

45
Q

What is the tertiary structure?

A

Spatial arrangement of atoms in a polypeptide chain or protein

46
Q

What are the (2) major classes of proteins

A

Fibrous Proteins/Globular Proteins

47
Q

What are Fibrous Proteins?

A

Insoluble; made from single secondary structure

48
Q

What are Globular Proteins

A

Water-soluble globular proteins; lipid-soluble membraneous proteins

49
Q

Which collagen is the strongest and has the greatest tensile strength?

A

right-handed superhelical triple helix (Super-Duper)

50
Q

True or False; Collagen is NOT a constituent of connective tissue

A

False; Collagen is a constituent of connective tissue

51
Q

What makes up a collagen fibril?

A

Many triple-helixes

52
Q

What shape do globular proteins have?

A

Spherical

53
Q

Are Globular Proteins water soluble or insoluble?

A

water soluble

54
Q

What causes quaternary structure?

A

formed by spontaneous assembly of individual polypeptides into a fx. cluster.

55
Q

You extract a protein from a lipid bilayer of a cancel cell. What category of protein is this?

A

Globular Protein

56
Q

What is the basic building block of collagen protein Alpha-Helix?

A

Threonine

57
Q

True or False; Proteins function depends on its 3-D structure?

A

True

58
Q

What is denaturation

A

Loss of structural integrity/loss

59
Q

What are a few ways proteins can be denature?

A

pH extremes, temperature, organic solvents, chaotropic events

60
Q

How many Cystein residues and disulfide bonds does Ribonuclease have?

A

8 Cys residues/ 4 disulfide bonds

61
Q

If urea and 2-meracaptoethanol are removed, what does the protein do?

A

Spontaneously refold; correct disulfide bonds are reformed

62
Q

What is one way enzymes speed up reactions?

A

Lower activation energy/coupling to a fast one

63
Q

What is the underlying determinant of a tertiary structure?

A

Primary Structure Sequence

64
Q

Keratin is made up of which proteins?

A

Alpha-Helices

65
Q

Protein structure is determined by which sequence and what does it dictate?

A

Primary; dictates function of the protein

66
Q

What drives the formation of a peptide’s secondary structure?

A

side chain interactions

67
Q

What is the second turn in a Beta sheets?

A

Proline (I have to PEE!)

68
Q

How many AA are required to complete a B-turn in a B-sheet?

A

4

69
Q

All of the following are considered “weak” interactions in proteins, except:

A) hydrogen bonds. 
B) hydrophobic interactions. 
C) ionic bonds. 
D) peptide bonds. 
E) van der Waals forces.
A

D

70
Q

The most important contribution to the stability of a protein’s conformation appears to be the:

A) entropy increase from the decrease in ordered water molecules forming a solvent shell around it.
B) maximum entropy increase from ionic interactions between the ionized amino acids in a protein.
C) sum of free energies of formation of many weak interactions among the hundreds of amino acids in a protein.
D) sum of free energies of formation of many weak interactions between its polar amino acids and surrounding water.
E) stabilizing effect of hydrogen bonding between the carbonyl group of one peptide bond and the amino group of another.

A

A

71
Q

In an aqueous solution, protein conformation is determined by two major factors. One is the formation of the maximum number of hydrogen bonds. The other is the:

A) formation of the maximum number of hydrophilic interactions.
B) maximization of ionic interactions.
C) minimization of entropy by the formation of a water solvent shell around the protein.
D) placement of hydrophobic amino acid residues within the interior of the protein.
E) placement of polar amino acid residues around the exterior of the protein.

A

D

72
Q

Pauling and Corey’s studies of the peptide bond showed that:
A) at pH 7, many different peptide bond conformations are equally probable.
B) peptide bonds are essentially planar, with no rotation about the C—N axis.
C) peptide bonds in proteins are unusual, and unlike those in small model compounds.
D) peptide bond structure is extraordinarily complex.
E) primary structure of all proteins is similar, although the secondary and tertiary structure may differ greatly.

A

B

73
Q

In the diagram below, the plane drawn behind the peptide bond indicates the:
A) absence of rotation around the C—N bond because of its partial double-bond character.
B) plane of rotation around the Cα—N bond.
C) region of steric hindrance determined by the large C=O group.
D) region of the peptide bond that contributes to a Ramachandran plot.
E) theoretical space between -180 and +180 degrees that can be occupied by the φ and ψ angles in the peptide bond.

A

A

74
Q 
Which of the following best represents the backbone arrangement of two peptide bonds? 
A) Cα—N—Cα—C—Cα—N—Cα—C 
B) Cα—N—C—C—N—Cα 
C) C—N—Cα—Cα—C—N 
D) Cα—C—N—Cα—C—N 
E) Cα—Cα—C—N—Cα—Cα—C
A

D

75
Q 
Which of the following pairs of bonds within a peptide backbone show free rotation around both bonds? 
A) Cα—C and N—Cα 
B) C=O and N—C 
C) C=O and N—Cα 
D) N—C and Cα—C 
E) N—Cα and N—C
A

A

76
Q

Roughly how many amino acids are there in one turn of an α helix?

A) 1 
B) 2.8
C) 3.6 
D) 4.2 
E) 10
A

C

77
Q

In the α helix the hydrogen bonds:

F) are roughly parallel to the axis of the helix.
G) are roughly perpendicular to the axis of the helix.
H) occur mainly between electronegative atoms of the R groups.
I) occur only between some of the amino acids of the helix.
J) occur only near the amino and carboxyl termini of the helix.

A

F

78
Q

In an α helix, the R groups on the amino acid residues:

A) alternate between the outside and the inside of the helix.
B) are found on the outside of the helix spiral.
C) cause only right-handed helices to form.
D) generate the hydrogen bonds that form the helix.
E) stack within the interior of the helix.

A

B

79
Q

Thr and/or Leu residues tend to disrupt an α helix when they occur next to each other in a protein because:

A) an amino acids like Thr is highly hydrophobic.
B) covalent interactions may occur between the Thr side chains.
C) electrostatic repulsion occurs between the Thr side chains.
D) steric hindrance occurs between the bulky Thr side chains.
E) the R group of Thr can form a hydrogen bond.

A

D

80
Q

A D-amino acid would interrupt an α helix made of L-amino acids. Another naturally occurring hindrance to the formation of an α helix is the presence of:
A) a negatively charged Arg residue.
B) a nonpolar residue near the carboxyl terminus.
C) a positively charged Lys residue.
D) a Pro residue.
E) two Ala residues side by side.

A

D

81
Q

An α helix would be destabilized most by:
A) an electric dipole spanning several peptide bonds throughout the α helix.
B) interactions between neighboring Asp and Arg residues.
C) interactions between two adjacent hydrophobic Val residues.
D) the presence of an Arg residue near the carboxyl terminus of the α helix.
E) the presence of two Lys residues near the amino terminus of the α helix.

A

E

82
Q

The major reason that antiparallel β-stranded protein structures are more stable than parallel β-stranded structures is that the latter:
A) are in a slightly less extended configuration than antiparallel strands.
B) do not have as many disulfide crosslinks between adjacent strands.
C) do not stack in sheets as well as antiparallel strands.
D) have fewer lateral hydrogen bonds than antiparallel strands.
E) have weaker hydrogen bonds laterally between adjacent strands

A

E

83
Q 
Amino acid residues commonly found in the middle of β turn are: 
A) Ala and Gly. 
B) hydrophobic. 
C) Pro and Gly. 
D) those with ionized R-groups. 
E) two Cys.
A

C

84
Q 
A sequence of amino acids in a certain protein is found to be -Ser-Gly-Pro-Gly-. The sequence is most probably part of a(n): 
A) antiparallel β sheet. 
B) parallel β sheet. 
C) α helix. 
D) α sheet. 
E) β turn.
A

E

85
Q

The three-dimensional conformation of a protein may be strongly influenced by amino acid residues that are very far apart in sequence. This relationship is in contrast to secondary structure, where the amino acid residues are:
A) always side by side.
B) generally near each other in sequence.
C) invariably restricted to about 7 of the 20 standard amino acids.
D) often on different polypeptide strands.
E) usually near the polypeptide chain’s amino terminus or carboxyl terminus.

A

B

Biochemistry (12 decks)

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