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Biochemistry I > Chapter 4 - Tertiary structure > Flashcards

Chapter 4 - Tertiary structure Flashcards

1
Q

The majority of 3D structures are stabilized by ______, but some are stabilized by ______ or coordinated ____ atoms.

A

numerous weak interactions

covalent disulfide bonds

metal

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2
Q

weak interactions

A

Hydrogen bonding

electrostatic interaction

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3
Q

Disulfide bonds are formed when:

A

two nearby cysteine residues are oxidized

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4
Q

____ and ____ are the most
common metal ions in
proteins

A

Zinc

Iron

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5
Q

First protein structure determined

A

Myoglobin

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6
Q

Myoglobin

A

largely α-helical in structure

153 amino acids

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7
Q

4 major classes of structure

A
  1. all alpha helices
  2. all beta sheets
  3. alpha/beta (intermixed)
  4. mixed alpha + beta (separate regions)
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8
Q

Fold types:

A

Four helix bundle fold

Greek key fold

Rossmann fold

TIM barrel fold

FERM domain fold

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9
Q

fold in Heme domain of cytochrome b:

A

Four helix bundle

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10
Q

Four helix bundle provides ______ for the heme group

A

hydrophobic pocket

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11
Q

fold in Bacterial CusF copper binding protein

A

Greek key fold

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12
Q

Fold in bacterial lactate dehydrogenase, with bound

nicotinamide adenine dinucleotide

A

Rossman fold

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13
Q

Rossman fold is found in:

A

Proteins that bind nucleotides

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14
Q

TIM Barrel aka:

A

a/b barrel

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15
Q

TIM barrel found in:

A

A large number of metabolic

enzymes

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16
Q

Fold found in triose phosphate isomerase

A

TIM Barrel

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17
Q

FERM domain fold components:

A

FA: Mostly beta sheets

FB: Only alpha helices

FC: Mostly beta sheets

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18
Q

Quaternary Structure

A

Polypeptide chains organized in

multiple subunit protein complexes

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19
Q

Homodimer

A

Simplest quaternary structure

Contains two identical protein subunits

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20
Q

Heterodimer

A

Contains subunits from different gene products

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21
Q

Quaternary Structures Increase _______

A

Functionality

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22
Q

Quaternary structure provide:

A

structural properties not present in individual properties

a mechanism for regulation of protein function through conformational change

Bring linked functional components into close
proximity

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23
Q

Fibrous Proteins

A

Keratin

Silk

Collagen

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24
Q

Collagen

A

Primarily found in soft tissues that holds bones together and is the major
constituent of tendons and cartilage.

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25
Q

Multi-subunit complexes that are abundant in

nature

A

Fibrous proteins

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26
Q

Spherical proteins that consist of multi-subunit protein complexes

A

Globular proteins

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27
Q

An Example of Globular Proteins

A

Immunoglobulins

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28
Q

Structure and function are dependent on:

A

Folding

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29
Q

The free energy difference between the
native (folded) and denatured (unfolded)
must be:

A

favorable (G < 0)

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30
Q

_____ changes can contribute to the folding

process.

A

Entropy

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31
Q

Chaperone proteins

A

Proteins that facilitate the formation of stable 3D

structures

32
Q

Chaperone fxn:

A

Help newly synthesized proteins fold properly

Rescue mis-folded proteins

Disrupt protein aggregates

33
Q

2 types of chaperone protein:

A

Clamp type (Hsp 70)

Chamber type (GroEL-GroES complex)

34
Q

Chaperones selectively bind to short stretches of_______ that tend to be exposed in ____ but buried in proteins having a ______ conformation

A

hydrophobic amino acids

non-native proteins

native

35
Q

GroEL-GroES has:

A

seven subunits, 97 residues each.

36
Q

Tm = 0.5 (50%)

A

Half of molecules are unfolded

37
Q

Alzheimers caused by aggregation of:

A

small Aβ peptides (β-amyloid) causing neuronal death

38
Q

β-amyloid peptide is released by:

followed by:

A

the cleavage of amyloid precursor protein by β-secretase

cleavage involving γ-secretase

39
Q

_____ is then thought to self associate under certain

circumstances to form _____ called _____ in the brain

A

β-amyloid protein

aggregates

β-amyloid

40
Q

3 protein folding models:

A

Hydrophobic collapse

Framework model

Nucleation model

41
Q

loosely folded tertiary structure

A

molten globule

42
Q

______ is necessary since no amino acid side chains can reversibly bind to oxygen.

A

The Fe2+ -porphyrin

complex

43
Q

Oxygen only binds to the

A

prosthetic group with iron in its reduced state (ferrous state)

44
Q

The Fe2+ -porphyrin complex is called _____ and fxns as a _____

A

heme

prosthetic group

45
Q

Myoglobin and hemoglobin are both ______

A

heme-using oxygen binding proteins

46
Q

Hemoglobin fxn as

A

transport of heme bound O2 from lungs and through out circulatory system

47
Q

Myoglobin fxns as

A

O2 depot stored in muscle tissue

48
Q

Two histidine residues are crucial in for O2 binding in globin proteins:

A

His F7

His F8

49
Q

His F7

A

Distal histidine

Hydrogen bound to O2 which is bound to Fe2

Attached to E helix

50
Q

His F8

A

Proximal histidine

coordinates to Fe2 directly

Attached to F helix

51
Q

Oxygenation alters the _____ of the Fe(II)-heme complex

A

electronic state

52
Q

the color of hemoglobin in venous blood

A

dark purple (de oxygenated)

53
Q

the color of hemoglobin in arterial blood

A

brilliant scarlet (oxygenated)

54
Q

These proteins are responsible for the brown color of old meat and dried blood

A

the Fe(II) becomes oxidized to Fe (III) to form metmyoglobin or methemoglobin

55
Q

Why is an oxygen carrier such as heme important:

A

O2 has poor solubility

O2 has poor diffusion through our skin

56
Q

α1-β1 and α2-β2

A

Have 35 residues that interact

57
Q

α1-β2 and α2-β1

A

Have 19 residues that interact

58
Q

α-β interactions are mostly:

A

Hydrophobic, H bonding and ion pairing

59
Q

In hemoglobin, solvent F channel _____ when O2 is bound

A

Narrows

60
Q

How does channel narrow?

A

α-β complexes shift by 15 degrees in clockwise direction, bring β1-β2 closer together

61
Q

α -β arrangement in hemoglobin

A

α2 β1

β2 α1

62
Q

T state

A

Tense state

O2 unbound

63
Q

R state

A

Relaxed state

O2 is bound

64
Q

In the T state _____ is ~____ out of the _____

Which is called ______ heme

A

Fe

0..6 Angstroms

heme plane

Puckered

65
Q

In R state ___ drags ___ and attached _____

Binding to _____ making heme ____

A

Fe II
His F8
F helix

O2
planar

66
Q

Helix F tilta and translates by:

A

~1 Angstrom

67
Q

____ are released in T-R transition

A

Protons

68
Q

T-R transition requires breakage and reformation of:

A

many non-covalent interactions between adjacent α -β sub-units

69
Q

As O2 binds, the other subunits ______, increasing the likelihood of additional O2 binding.

A

change conformation

70
Q

Information about the O2-binding status of a heme group is _____ transmitted to the other heme groups by: .

A

mechanically

motions of the protein

71
Q

binding of a ligand at one site affects the binding of

another ligand at another site

A

Allosteric effects

72
Q

Two models proposed for allosteric effects:

A

Concerted Model of Allosterism

Sequential Model of Allosterism

73
Q

Concerted Model of Allosterism

A

All the subunits must be in either T or R
form, model does not allow combinations
of T and R state

Binding of ligand increases the population of the R state.

74
Q

Sequential Model of Allosterism

A

Ligand binding progressively induces
conformational changes in the subunits

greatest changes occurring in
those subunits that have bound ligand.

75
Q

Protein folding:

A

G = H - TS

G should be favored (-)

H = (-)

S = (-)

76
Q

Entropy of water molecules

A

H2O forms cages around hydrophobic AA, when they get folded, they are free to move around increasing surrounding entropy

Biochemistry I (13 decks)

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