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BioChem > Ch. 6 > Flashcards

Ch. 6 Flashcards

1
Q

Angle between Nitrogen and alpha Carbon

A

Phi (Φ)

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2
Q

Angle between alpha carbon and carbonyl carbon

A

Psi (Ψ)

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3
Q

What is the shaded area of a Ramachandran plot

A

most favorable Φ and Ψ angles

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4
Q

What are the 3 secondary structures

A

α-helix, β-sheets, and turns and cross overs

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5
Q

How are α-helices stabilized

A

Backbone stabilized by H-bonds spaced 4 residues apart

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6
Q

Residues per turn in an α-helix

A

3.6

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7
Q

Most common orientation of α-helices in nature

A

right handed (Φ=-60, Ψ=-50)

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8
Q

What effect do side chains have in an α-helix

A

Determines solubility in water

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9
Q

What amino acids can be considered helix breakers

A

Proline and Glycine

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10
Q

How are β-sheets stabilized

A

Backbone is stabilized by H-bonding between separate β-strands

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11
Q

What are β-strands composed of

A

tight α-helix with 2 residues per turn

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12
Q

Orientation of R groups in β-strands

A

180 apart

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13
Q

3 types of β-sheets

A

parallel (N-terminals start at same sport), anti-parallel, and mixed (both parallel and anti-parallel)

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14
Q

3 ways to change direction

A

Proline, β-turn, and cross over

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15
Q

What conformation around the peptide bond allows proline to have a natural turn

A

cis conformation

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16
Q

How to form β-turn

A

H-bond between carbonyl oxygen of a residue with the amide proton of another residue 3 AA away

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17
Q

Favored AAs in β-turns

A

Glycine (less sterics) and Proline (natural curve)

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18
Q

What is a cross over

A

short α-helical segment that connects β-strands

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19
Q

Two types of Fibrous proteins

A

keratin (hair and nails) and collagen (skin, bones, tendons, blood vessels)

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20
Q

Structure of the initial monomer in keratin

A

central right handed α-helix (rod domain)

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21
Q

two initial keratin monomers form a dimer called

A

left handed coiled coil

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22
Q

Why do coiled coils form

A

red domain is composed of heptad repeats that create a non-polar strip on the outside of the helix (hydrophobic effect)

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23
Q

Two coiled coils associate to form?

A

protofilament

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24
Q

Two protofilaments associate to from?

A

right handed protofibril

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25
Q

4 protofibrils form?

A

keratin filament

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26
Q

Why do protofilaments and protfibrils form

A

H-bonding or disulfide bonds

27
Q

Structural difference between hair and nails

A

relative amounts of H-bonds (flexible) and disulfide bonds (rigid)

28
Q

Structure of initial collagen monomer

A

left handed α-helix with 3.3 residues per turn

29
Q

AA composition of collagen

A

High in Glycine and Proline

30
Q

What amino acids are formed after the protein is formed

A

4-hydroxy proline, 3-hydroxy proline, and 5-hydroxy lysine

31
Q

Enzyme that forms hydroxy proline

A

prolyl hydroxylase

32
Q

Enzyme that forms hydroxy lysine

A

lysyl hyroxylase

33
Q

Effect of hydroxylating proline and lysine

A

increases H-bonding

34
Q

Key molecule in formation of hydroxy proline

A

Vitamin C

35
Q

3 collagen monomers associate to form?

A

right handed triple helix (tropocollagen)

36
Q

AA pattern found in collagen

A

Gly-X-Y
X=proline
Y=hydroxyproline

37
Q

Location of glycine in tropocollagen

A

buried in interior b/c of glycines low sterics

38
Q

What holds tropocollagen together

A

H-bonding in the hydroxy proline backbone

39
Q

tropocollagen forms?

A

collagen fibers

40
Q

What holds collagen fibers together

A

covalent crosslinks

41
Q

Lysine can be oxidized to what

A

aldehyde form (allysine)

42
Q

Lysine and allysine crosslink?

A

imine (schiff base)

43
Q

allysine and allysine crosslink?

A

aldol condensation

44
Q

Disrupting cross links does what to collagen

A

destabilizes collagen

45
Q

Why does a vitamin C deficiency (scurvy) cause a diseased state

A

Hydroxy proline can not be made without vitamin C, disrupting the structure of collagen

46
Q

Tertiary structures form the most stable structure through?

A

covalent and non-covalent interactions

47
Q

Globular protein themes

A

α-helices and β-sheets in core
cavities filled with hydrophobic side chains
water stabilized the surface

48
Q

What are protein domains

A

distinct tertiary regions connected by a flexible backbone

49
Q

Levinthals paradox in relation to protein folding

A

protein folding is not random

50
Q

What does mean that protein folding is all or nothing

A

remains folded until Tm then rapidly unfolds

51
Q

Folding themes

A
  1. secondary structures fold first
  2. hydrophobic collapse
  3. long-range interactions
52
Q

Intermediate folded shape?

A

molten globules

53
Q

what does it mean that proteins are marginally stable

A

they have flexibility and motion

54
Q

Why is protein folding represented as a funnel

A

each step leads to an intermediate lower in energy making each step easier than the last

55
Q

What are molecular chaperones

A

proteins that help other proteins fold

56
Q

Example of molecular chaperone

A

heat shock proteins (HSP-90)

57
Q

Effects of Misfolding

A

loss of function and can lead to aggregation

58
Q

Examples of misfolding

A

sickle cell, alzheimers, and cancer

59
Q

What is an IUP

A

intrinsically unstructured protein

60
Q

What AAs are found in IUPs

A

polar AAs and proline

61
Q

Function of IUPs

A

can bind ligands and can increase surface area

62
Q

Advantages of quaternary structure

A

Stability
Genetic economy
Bring catalytic sites together
Cooperativity

63
Q

Example of Cooperativity in quaternary structures

A

ligand binding at one subunit can trigger a conformational change in another

64
Q

What is Allostery

A

information transfer across long distances in a protein

BioChem (5 decks)

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