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Biochemistry > Chapter 5: 3-D Structure of Proteins > Flashcards

Chapter 5: 3-D Structure of Proteins Flashcards

1
Q

The rigidity of a peptide group can be attributed to..

A

the double bond character

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2
Q

Is a peptide’s carbonyl-nitrogen bond shorter or longer than a regular carbon-nitrogen single bond?

A

shorter

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3
Q

Peptide groups usually assume the….

A

trans conformation

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4
Q

In the trans conformation of a peptide group the alpha carbons are found on the ___________ side of the amide groups

A

opposite

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5
Q

Why is the trans conformation more stable?

A

b/c of the steric interference of the R groups or side chains

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6
Q

The ________ of a peptide are the atoms that participate in peptide bonds while ignoring the side chains.

A

backbone

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7
Q

The torsion angle about the alpha C-N bond is known as

A

Phi (Φ)

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8
Q

The torsion angle about the alpha C-C bond is known as

A

Psi (Ψ)

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9
Q

The angles that Phi and Psi can adopt in a peptide bond can be depicted in a diagram called a…

A

Ramachandran Diagram

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10
Q

The Ramachandran Diagram is about 75% blank, what does this indicate?

A

most conformation of Phi and Psi are conformationally inaccessible

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11
Q

In a Ramachandran Diagram, heavy clustering on the top right-hand side is indicative of…

A

left-handed α helix

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12
Q

In a Ramachandran Diagram, heavy clustering on the bottom left-hand side is indicative of…

A

right-handed α helix

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13
Q

In a Ramachandran Diagram, heavy clustering on the top left-hand side is indicative of…

A

β pleated sheets

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14
Q

On a Ramachandran Diagram antiparallel β pleated sheets are found…

A

on the top left-hand side slightly more to the left

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15
Q

On a Ramachandran Diagram parallel β pleated sheets are found…

A

on the top left-hand side slightly more to the right

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16
Q

Helical structures can be characterized by

A

the # of peptide units (n) and pitch (p)

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17
Q

define pitch

A

the distance the helix rises per turn

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18
Q

right-handed helices have a _______ “n” value

A

positive

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19
Q

left-handed helices have a _______ “n” value

A

negative

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20
Q

What is a helical polypeptide arrangement that has both allowed conformation angles and favorable hydrogen bonds

A

α helix

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21
Q

Linus Pauling discovered the

A

α helix

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22
Q

The α helix is a common secondary structure found in…

A

fibrous & globular proteins

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23
Q

How are right-handed α helices formed?

A

from polypeptides made from L-α-amino acid residues

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24
Q

How are left-handed α helices formed?

A

from polypeptides made from D-α-amino acid residues

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25
Q

In β pleated sheets hydrogen bonding occurs between

A

neighboring chains

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26
Q

What are common structural motifs of proteins

A

β sheets

27
Q

What type of β sheet is less stable? Why?

A
  • parallel
  • b/c they are distorted when compared to antiparallel
28
Q

What were the 2 repetitive structures discussed?

A

β bends
Ω loops

29
Q

β bends normally connect successive strands of

A

antiparallel β sheets

30
Q

What normally occur at protein surfaces

A

β bends & Ω sheets

31
Q

In type II β bends, residue 2 is usually ____ while residue 3 is usually ____.

A

proline
glycine

32
Q

What were the fibrous proteins discussed?

A

keratin & collagen

33
Q

α keratins normally occur in

A

mammals

34
Q

β keratins occur in

A

birds and reptiles

35
Q

acidic polypeptides are composed of

A

type I keratin chains

36
Q

basic polypeptides are composed of

A

type II keratin chains

37
Q

What is a unique characteristic of keratin?

A

it has a heptad pseudorepeat

38
Q

the heptad pseudorepeat has a and d positions that form the

A

hydrophobic strip

39
Q

Keratin is rich in what type of residues?

A

cysteine (Cys)

40
Q

Cysteine residues in keratin form disulfide bonds that cross link

A

adjacent polypeptide chains

makes it resistant to stretching

41
Q

Keratins can be _____ like _____ and _____, or ____ like _____.

A

hard
hair
nails
soft
skin

42
Q

Mutation of the keratin gene leads to

A

Epidermolysis Bullosa

43
Q

Describe Epidermolysis Bullosa

A

rupturing of epithelial cells resulting in skin blistering

44
Q

What protein occurs in multicellular animals, is extracellular, and occurs most abundantly in vertebrates.

A

collagen

45
Q

collagen is organized into….

A

insoluble fibers w/ incredible tensile strength

46
Q

what is a major stress-bearing component of connective tissue

A

collagen

47
Q

Collagen has distinct amino acid composition with high levels of

A

Gly
Pro
Hyp

Hyp- hydroyproline
-OH group @ C3

48
Q

Hydroxylated residues of hydroxyproline result from

A

synthesis by prolyhydroxylase

49
Q

prolyhydroxylase requires ______ for its activity

A

ascorbic acid (vitamin c)

50
Q

What disease results from vitamin c deficiency

A

Scurvy

51
Q

Scurvy results in

A

skin lesions
blood vessel fragility

52
Q

When do collagen residues denature @ 25°C?

A

when they are synthesized w/o Hyp

53
Q

Collagen consists if repeating triplets of Gly-X-Y amino acids where X is ____ and Y is _____

A

proline
hydroxyproline

54
Q

What heritable disorder results from the mutation of Type I collagen

A

Osteogenesis Imperfecta

55
Q

All known amino acid changes within the…..results in abnormalities

A

triple helices region of Type I collagen

56
Q

Examples of globular proteins include

A
  • enzymes
  • transport & receptor proteins
57
Q

globular proteins contain both

A

α and β sheets

58
Q

functions of carbonic anhydrase

A
  • converts CO2 to bicarbonate (HCO3-)
  • maintains acid-base balance
  • helps transport CO2 out of tissues
  • metalloenzyme
59
Q

Metalloenzyme means

A

it requires a metal in its active site for activity

60
Q

What is the metal needed for carbonic anhydrase?

A

zinc ion

61
Q

The zinc ion is held in place by

A

imidazole rings of 3 His residues

62
Q

What does NOSEY stand for

A

Nuclear Overhauser Effect Spectroscopy

63
Q

NOE determines interproton distances through

A

space

Biochemistry (3 decks)

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