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M.Phil. Preparatory Flashcards > Proteins2 > Flashcards

Proteins2 Flashcards

1
Q

What bond is not rotatable in protein?

A

Peptide C-N bond

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2
Q

What types of bonds are rotatable in protein?

A

Calpha-C and N-C

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3
Q

What symbols represent the Calpha-C and N-C bond rotations?

A

Psi and phi

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4
Q

What are the axis of Ramachandran plot?

A

Psi vs Phi plot

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5
Q

What represents rotatability and non rotatability in Ramachandran plot?

A

White area of the Rama plot indicates no rotation whereas the variable blue regions indicate various degrees of rotation possibilities

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6
Q

What is a dihedral angle in protein?

A

The psi and phi bonds

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7
Q

The atoms associated with peptide bond are?

A

Coplanar

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8
Q

What are the torsion angles in protein structure?

A

Phi, Psi, and omega

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9
Q

When does a regular secondary structure takes place?

A

When the dihedral angles(Phi and Psi remain the same)

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10
Q

How much is 1 angstrom?

A

0.1nm

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11
Q

In the alpha helix structure where are the R groups located?

A

Protrude outside

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12
Q

What is the length of one helical repeat?

A

About 5.4 A

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13
Q

How much amino acid residues are in one helical turn?

A

3.6

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14
Q

What type of alpha helix is more common?

A

Right handed

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15
Q

What is the reason for the high stability of alpha helix protein secondary structure?

A

Intrinsic hydrogen bonding

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16
Q

What are the 5 types of constraints for alpha helix formation?

A
  1. Intrinsic propensity of amino acid
  2. Interaction between R groups (3-4 residues apart)
  3. Bulkiness of R groups
  4. Presence of proline or Glycine
  5. Interaction between amino acids at the terminal of the helix and the inherent dipolarity
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17
Q

What is the Beta conformation?

A

Extended zigzag structure

18
Q

How are the R groups of the Beta conformation arranged?

A

Away from the zigzag pattern

19
Q

What is the difference between hydrogen bonding of parallel and antiparallel beta sheets?

A

Hydrogen bonding in parallel beta sheets is in line whereas in anti parallel it’s distorted

20
Q

What connects the two segments of anti parallel beta sheet?

A

Beta turns

21
Q

What are commonly found in beta turns but not in beta alpha helix?

A

Proline and glycine

22
Q

What is the least common version of the sheeted protein?

A

Gamma sheet

23
Q

What is circular dichorism?

A

A technique used to access secondary structure of proteins?

24
Q

How does circular dichroism works?

A

Asymmetry in a protein gives differences in absorption of left or right handed polarized light. CD is the measurement of this difference.

25
Q

What’s the difference between secondary and tertiary structures?

A

Secondary structure refers to only the arrangement of amino acids whereas tertiary structure refers to all arrangements of atoms in a protein.

26
Q

What are the two groups in which proteins are divided?

A

Fibrous and Globular protein

27
Q

What are some examples of fibrous proteins?

A

Alpha keratin, silk fiber and collagen

28
Q

What is the structure of alpha keratin?

A

Made of alpha helix structure cross-linked by disulfide linkage

29
Q

What is the composition of silk fiber?

A

Beta conformation

30
Q

What is the structure of collagen?

A

Collagen triple helix

31
Q

What are some examples of motifs?

A

Beta barrels and beta-alpha-beta loops

32
Q

What’s a motif?

A

Super-secondary structure or fold

33
Q

What’s a domain?

A

A polypeptide segment with its own function

34
Q

What is proteostasis?

A

Maintenance of the protein active site

35
Q

What are the two common types of chaperones?

A

Hsp70 and chaperonins

36
Q

What is the structure of hemoglobin?

A

Four Heme groups with four protein subunits namely alpha and beta, protoporphyrin

37
Q

What are some examples of protein tertiary structure?

A

Alpha keratin, collagen, and silk fibrin, myoglobin etc.

38
Q

What are some examples of protein quaternary structure?

A

Hemoglobin, protein transporters, and polymerases etc.

39
Q

Homo and hetero are two terminologies associated with what type of protein structure?

A

Quaternary structure

40
Q

What is the composition of myoglobin?

A

Made of a single polypeptide chain of 153 amino acids

41
Q

What is an important difference between tertiary and quaternary protein structure?

A

Tertiary is usually made of one type of polypeptide and quaternary multiple

M.Phil. Preparatory Flashcards (22 decks)

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