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Biochemistry > Chapter 4: The 3D structure of proteins > Flashcards

Chapter 4: The 3D structure of proteins Flashcards

1
Q

The most important forces stabilizing the specific structure maintained by a given protein are _________________

A

noncovalent & hydrophobic effect

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2
Q

Conformation

A

is the spatial arrangement of atoms in a protein

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3
Q

Native protein

A

Proteins in any of their functional folded conformations

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4
Q

A protein’s conformation is stabilized by ____________

A

Weak interactions

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5
Q

The term stability in context to protein structure can be defined as the ________

A

Tendency to maintain a native conformation

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6
Q

The chemical interactions that stabilizes the native conformation are ________

A

Disulfide (covalent) bonds & weak (noncovalent) interactions & forces such as hydrogen bonds, the hydrophobic effect & ionic interactions

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7
Q

Protein biological function depends on _______

A

Its 3D structure & are dynamic & marginally stable

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8
Q

The ________ has the lowest energy with the maximum number of weak interactions

A

Native 3D Structure

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9
Q

The proteins conformation that is most stable (lowest free energy) is the one with the maximum number of ____________

A

Weak interactions

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10
Q

The ________ predominates in weak interactions stabilizing a protein

A

hydrophobic effect

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11
Q

Hydrophobic effect(predominant stabilizing force)

A

Cluster nonpolar groups from a hydrophobic core reducing highly ordered water shells

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12
Q

What are the forces in proteins?

A
  1. Hydrophobic effect (predominates stabilizing force)
  2. Hydrogen bonds between protein hydrogen bond donor & acceptors
  3. London dispersion weak interactions between atoms
  4. Electrostatic interactions (between charged groups)
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13
Q

Hydrophobic residues are largely buried in the protein’s ____________

A

Interior

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14
Q

The peptide bond is _____ & ______

A

Rigid & Polar

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15
Q

Protein structure are partially dictated by _____ properties

A

Peptide bond

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16
Q

Peptide group

A

Contains 6 atoms that occupy the same plane due to the peptide bond double bond characteristic

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17
Q

Partial double bond characteristic restricts conformation in either the ____ or ____ configurations

A

Trans or cis

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18
Q

Phi angle (circle with line across)

A

Is between the amino group & alpha carbon

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19
Q

Psi angle (look like a y)

A

Is between the carbonyl group & alpha carbon

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20
Q

Steric hinderance from backbone & R group size/shape limit a peptide conformation which is why ____ conformation is favored

A

Trans

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21
Q

Ramachandran plots

A

Shows the distribution of phi & psi angle

22
Q

Peptide bond ___________ allows for an observed range of angle in proteins structure

A

flexibility (Gly- less restricted & pro more restricted)

23
Q

Secondary structure

A

Refers to any chosen segment of a polypeptide chain & describes the local spatial arrangement off its main chain atoms

24
Q

What are the two regular secondary arrangement common in most proteins structures?

A
  1. Alpha helix- hydrogen bonding between nearby residues
  2. Beta sheets-hydrogen bonds between adjacent peptide segments that may not be nearby
25
Q

Irregular arrangement of the polypeptide chain is called

A

Random coil

26
Q

________ alpha helix is the common form in most proteins

A

Right handed

27
Q

A right handed twist has _____ residues per turn (5.4A) & hydrogen bonds roughly parallel to the helix & optimal distance between N & O is 0.28nm

A

36

28
Q

10A = how many nm?

A

1nm

29
Q

The C=O groups point towards the _______

A

C -terminal

30
Q

Negatively charged residues are positioned near _____ helix dipole

A

positive

31
Q

Side chains spiral outward from heli axis where the helix are diameter is ______(when no side chains) & _____ (with side chains) & fits into major grooves of dsDNA

A

4-5A, 10-12A

32
Q

The average length of an alpha helix is ____ amino acids per helix

A

12

33
Q

The most form an alpha helix consisting of a D-amino acid is ________

A

Left hand alpha helix

34
Q

Interaction between ______ side chains can stabilize & destabilize the alpha helical structure

A

Amino acid

35
Q

Amino acids usually stabilize an alpha helix if it has the prefer helical ____ & _____ angles

A

Phi & psi (small & hydrophobic (ala, leu))

36
Q

Amino acids are usually disrupted if they are too _____ or inflexible (gly,pro) or highly charged (arg, lys)

A

flexible

37
Q

A constraint on the formation of the alpha helix is the presence of ____ or _____ since they have the least prodivity to form alpha helices

A

Pro or Gly

38
Q

________ destabilize an alpha helix because in proline the nitrogen atom is part of the rigid ring & rotation about the N-Calpha bond is not possible & the nitrogen atom of a pro residue in a peptide linkage has no substituent hydrogen to participate in hydrogen bonds with other residues

A

Proline

39
Q

______ & ____ aren’t found in alpha helix

A

Gly & pro

40
Q

_______aren’t in alpha helix because its two flexible & polymers of glycine tend to form a coiled structure different from alpha helix

A

Glycine

41
Q

The other factor that affects the stability of an alpha helix is the identity of the amino acid near the end of the alpha helix where negative charged amino are found near the _________ & positive charge amino acids found near __________

A

Amino terminus, Carboxyl terminus

42
Q

What are the five constraints that affect the stability of an alpha helix?

A
  1. The intrinsic propensity of an amino acid to form an alpha helix
  2. The interactions between R groups (ones spaced 3-4 residues apart)
  3. The bulkiness of the adjacent R group
  4. The occurrence of Pro & Gly
  5. Interactions between amino acid residues at the ends of the helical segment & electric dipole inherent to the alpha helix
43
Q

The beta conformation organizes polypeptides chains into _______

A

Sheets

44
Q

___________ diagram shows how amino acids sequences influence helix properties

A

Helical wheel

45
Q

________ alpha helix are from sperm whales myoglobin

A

Amphipathic

46
Q

___________ are extended peptide chains & have hydrogen bonding between backbone

A

Beta sheets

47
Q

A _________ is an arrangement of several beta segments side by side

A

beta sheet

48
Q

What are the two possible beta sheet arrangement?

A
  1. Antiparallel beta sheet
  2. Parallel beta sheet
49
Q

In the anti-parallel beta sheet the strands are in the _______ directions & have straight H bonds (0.35nm (3.5A) per residue))

A

Opposite

50
Q

In parallel beta sheets the strands are in the _______ directions distorted hydrogen bonds & lower stability (0.33nm (3.3A) per residue)

A

Same

Biochemistry (26 decks)

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