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BMR 601 > Amino Acids and Protein Chemistry > Flashcards

Amino Acids and Protein Chemistry Flashcards

1
Q

Functions of Globular Proteins

A 
Storage of ions and molecules
Transport of ions and molecules
Defense against pathogens
Muscle contraction
Biological Catalysis
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2
Q

Binding of Oxygen does what to Heme?

A

Pulls heme closer to the porphyrin ring. This pulls the histidine and distorts the shape of the a-helix.
Increases Oxygen binding affinity on remaining heme sites.

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3
Q

Oxygen binds pulls what amino acid toward it when in the heme group.

A

His F8

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4
Q

Positive Cooperativity definition

A

First binding event increases affinity at remaining sites.

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5
Q

Negative Cooperativity definition

A

First binding event reduces affinity at remaining sites.

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6
Q

How to recognize positive cooperativity?

A

Sigmoid binding curves.

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7
Q

When oxygen is bound to the Heme group what state is the heme in?

A

R-State

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8
Q

What is the Bohr effect?

A

The increase in O2 transport efficiency between lungs and metabolic tissues that is caused by pH difference.

H+ Promotes release of O2 from hemoglobin.

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9
Q

What type of regulator is 2,3-Bisphosphoglycerate for O2

A

It is a negative Heterotropic regulator of Hb function.

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10
Q

How does 2,3-BPG regulate Hb function?

A

It stabilizes the T state (deoxy) of Hb.

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11
Q

What charge does 2,3-BPG have?

A

It is negatively charged

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12
Q

Where is 2,3-BPG produced?

A

It is produced from an intermediate in glycolysis.

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13
Q

When does 2,3-BPG increase?

A

At high altitudes.

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14
Q

15-20% of CO2 is exported in the form of a ______ on the _______ of each of the polypeptide subunits.

A

Carbamate

Amino terminal residues.

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15
Q

The formation of a carbamate yields what?

And what is the effect of this?

A

Yields a proton that can contribute to the Bohr effect.

It can form additional salt bridges that stabilize the T state.

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16
Q

Why is CO dangerous?

A

CO has a similar size in shape to O2 (can fit the same binding site).

CO binds over 20,000 times better than O2 due to the Carbon donating a lone pair to the Fe2+.

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17
Q

CO blocks the function of what?

A

Myoglobin, hemoglobin, and mitochondrial cytochromes that are involved in oxidative phosphorylation.

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18
Q

Natural defenses against CO poisoning?

A

Protein pockets decrease affinity.

His E7 sterically hinders CO from binding in its preferred configuration (linear conformation).

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19
Q

What mutation results in sickle cell anemia?

A

Glu6 -> Val6 in the B chain of Hb.

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20
Q

Methemoglobinemias are caused by what?

A

Fe3+ in Hb instead of Fe2+ results in a reduced ability to bind and deliver oxygen to tissues (hypoxia).

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21
Q

Newborns are born with only half the normal level of this, and as such are more susceptible to oxidative stress?

A

NADH - methemooglobin reductas.

Converts Hb Fe3+ to Hb Fe2+

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22
Q

Nonpolar, Aliphatic R groups

A 
Glycine G
Alanine A
Proline P
Valine V
Leucine L
Isoleucine I 
Methionine M
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23
Q

Aromatic R groups

A

Phenylalanine F
Tyrosine Y
Tryptophan W

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24
Q

Polar, uncharged R groups

A 
Serine S
Threonine T
Cysteine C
Asparagine N
Glutamine Q
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25
Q

Positively charged R groups

A

Lysine K
Arginine R
Histidine H

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26
Q

Negatively Charged R groups

A

Aspartate D

Glutamate E

27
Q

pI equation

A

pI = (pK1 + pK2) / 2

28
Q

What is pI

A

Isoelectric Point, the point at which the net charge is zero.

  • -AA is least soluble in water.
    • AA does not migrate in electric field.
29
Q

What is the pKa of the a-carboxyl group?

A

2.34

30
Q

What is the pKa of the a-amino group

A

9.6

31
Q

If the pH group is below the pKa, the group will be?

A

Largely protonated

32
Q

If the pH group is above the pKa, the group will be?

A

Largely deprotonated

33
Q

4 Methods of Column Chromatography

A

Charge, Size, Specificity, Polarity.

34
Q

Edman Degradation

A

Fragmenting proteins into smaller peptides/purification

Successive rounds of N-terminal modification, cleavage, and identification.

35
Q

Where does Trypsin cleave?

A

Lys, Arg (C)

36
Q

Where does cyanogen bormide

A

Met (C)

37
Q

Why are some phi and psi combinations more favorable?

A

They can form favorable H-bonding interactions along the backbone.

38
Q

Why are some phi and psi combinations less favorable?

A

Steric Crowding.

39
Q

What is the phi

A

Angle around the a-carbon –amide nitrogen bond

circle with line

40
Q

What is the psi

A

Angle around the a-carbon – carbonyl carbon bond.

Trident

41
Q

What does the Ramachandran plot show?

A

It shows the distribution of Phi and Psi dihedral angles that are found in a protein.
This reveals:
Common secondary structures
Regions with unusual backbone.

42
Q

How many residues per turn in an A-helix

A

3.6 residues

43
Q

Hydrogen bonds are every ____ between the backbone amides?

A

n + 4 amino acids.

44
Q

Where are side chains in an alpha helix?

A

Pointing out and roughly perpendicular.

45
Q

What are strong helix formers?

A

Ala and Leu

46
Q

What effect does Pro have on an a helix?

A

It is a helix breaker because the rotation around the N-Ca phi bond is impossible.

47
Q

What effect does Gly have on a helix?

A

It is a helix breaker because the tiny R-group supports other conformations.

48
Q

What is the difference between parallel and anti-parallel B sheets

A

Parallel: H-bonded strands run in the same direction
–Bent H-Bonds
Antiparallel: H-bonded strands run in the opposite directions.
– Linear H-bonds (stronger)

49
Q

Common components of beta turns?

A

Proline (position 2) and Glycine (position 3)

50
Q

Effect of Proline on a beta turn

A

Proline can force formation of a B-turn and anti-parallel strands resulting in a type 1 turn.

51
Q

How to determine secondary structure?

A

Circular Dichroism measures the molar absorption difference (:delta:E)
Chromophores in the chiral environment produce characteristic signals.

52
Q

How is tertiary structure stabilized?

A

Largely by hydrophobic and polar interactions

Disulfide bonds.

53
Q

How are quaternary structures stabilized?

A

Same interactions as tertiary.

54
Q

What is X-ray crystallography and pros and cons

A

Crystallize the protein
No size limits, well established

Difficult for membrane proteins
Cannot see hydrogen

55
Q

Nuclear Magnetic Resonance process

A 
Purify the protien
Dissolve the protein
Collect NMR Data
Assign NMR signals
Calculate the structure
56
Q

Globular proteins

A

Most numerous of cellular proteins
Soluble in aqueous media.
Amphipathic.
Stabilized by hydrogen bonds, ionic interactions, and less often by disulfide bonds.

57
Q

Collagen

A

Important connective tissue

58
Q

Collagen composition

A

Rich in Gly and pro-rich left handed helix.

59
Q

Collagen structure

A

Three collagen chains intertwine into a right-handed superhelical triple helix.

60
Q

Role of 4-Hydroxyproline in Collagen?

A

Forces the proline ring into a favorable folding, offers more hydrogen bonds between the three strands.

61
Q

Lacking vitamin C will cause what effect?

A

Postranslational processsing of collagen will not be able to occur so collagen formation and wound healing will be limited.
Vit - C is vital for crosslinking.

62
Q

Example of globular protein?

A

Hemoglobin, myoglobin, and various enzymes.

63
Q

Example of fibrous protein?

A

Collagen, elastin, keratin.

BMR 601 (19 decks)

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