Amino Acids and Protein Chemistry

Question 1

Functions of Globular Proteins

Answer 1

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

Question 2

Binding of Oxygen does what to Heme?

Answer 2

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.

Question 3

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

Answer 3

His F8

Question 4

Positive Cooperativity definition

Answer 4

First binding event increases affinity at remaining sites.

Question 5

Negative Cooperativity definition

Answer 5

First binding event reduces affinity at remaining sites.

Question 6

How to recognize positive cooperativity?

Answer 6

Sigmoid binding curves.

Question 7

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

Answer 7

R-State

Question 8

What is the Bohr effect?

Answer 8

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

H+ Promotes release of O2 from hemoglobin.

Question 9

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

Answer 9

It is a negative Heterotropic regulator of Hb function.

Question 10

How does 2,3-BPG regulate Hb function?

Answer 10

It stabilizes the T state (deoxy) of Hb.

Question 11

What charge does 2,3-BPG have?

Answer 11

It is negatively charged

Question 12

Where is 2,3-BPG produced?

Answer 12

It is produced from an intermediate in glycolysis.

Question 13

When does 2,3-BPG increase?

Answer 13

At high altitudes.

Question 14

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

Answer 14

Carbamate

Amino terminal residues.

Question 15

The formation of a carbamate yields what?

And what is the effect of this?

Answer 15

Yields a proton that can contribute to the Bohr effect.

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

Question 16

Why is CO dangerous?

Answer 16

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+.

Question 17

CO blocks the function of what?

Answer 17

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

Question 18

Natural defenses against CO poisoning?

Answer 18

Protein pockets decrease affinity.

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

Question 19

What mutation results in sickle cell anemia?

Answer 19

Glu6 -> Val6 in the B chain of Hb.

Question 20

Methemoglobinemias are caused by what?

Answer 20

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

Question 21

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

Answer 21

NADH - methemooglobin reductas.

Converts Hb Fe3+ to Hb Fe2+

Question 22

Nonpolar, Aliphatic R groups

Answer 22

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

Question 23

Aromatic R groups

Answer 23

Phenylalanine F
Tyrosine Y
Tryptophan W

Question 24

Polar, uncharged R groups

Answer 24

Serine S
Threonine T
Cysteine C
Asparagine N
Glutamine Q

Question 25

Positively charged R groups

Answer 25

Lysine K Arginine R Histidine H

Question 26

Negatively Charged R groups

Answer 26

Aspartate D | Glutamate E

Question 27

pI equation

Answer 27

pI = (pK1 + pK2) / 2

Question 28

What is pI

Answer 28

Isoelectric Point, the point at which the net charge is zero. - -AA is least soluble in water. - - AA does not migrate in electric field.

Question 29

What is the pKa of the a-carboxyl group?

Answer 29

2.34

Question 30

What is the pKa of the a-amino group

Answer 30

9.6

Question 31

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

Answer 31

Largely protonated

Question 32

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

Answer 32

Largely deprotonated

Question 33

4 Methods of Column Chromatography

Answer 33

Charge, Size, Specificity, Polarity.

Question 34

Edman Degradation

Answer 34

Fragmenting proteins into smaller peptides/purification | Successive rounds of N-terminal modification, cleavage, and identification.

Question 35

Where does Trypsin cleave?

Answer 35

Lys, Arg (C)

Question 36

Where does cyanogen bormide

Answer 36

Met (C)

Question 37

Why are some phi and psi combinations more favorable?

Answer 37

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

Question 38

Why are some phi and psi combinations less favorable?

Answer 38

Steric Crowding.

Question 39

What is the phi

Answer 39

Angle around the a-carbon --amide nitrogen bond circle with line

Question 40

What is the psi

Answer 40

Angle around the a-carbon -- carbonyl carbon bond. | Trident

Question 41

What does the Ramachandran plot show?

Answer 41

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.

Question 42

How many residues per turn in an A-helix

Answer 42

3.6 residues

Question 43

Hydrogen bonds are every ____ between the backbone amides?

Answer 43

n + 4 amino acids.

Question 44

Where are side chains in an alpha helix?

Answer 44

Pointing out and roughly perpendicular.

Question 45

What are strong helix formers?

Answer 45

Ala and Leu

Question 46

What effect does Pro have on an a helix?

Answer 46

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

Question 47

What effect does Gly have on a helix?

Answer 47

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

Question 48

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

Answer 48

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)

Question 49

Common components of beta turns?

Answer 49

Proline (position 2) and Glycine (position 3)

Question 50

Effect of Proline on a beta turn

Answer 50

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

Question 51

How to determine secondary structure?

Answer 51

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

Question 52

How is tertiary structure stabilized?

Answer 52

Largely by hydrophobic and polar interactions | Disulfide bonds.

Question 53

How are quaternary structures stabilized?

Answer 53

Same interactions as tertiary.

Question 54

What is X-ray crystallography and pros and cons

Answer 54

Crystallize the protein No size limits, well established Difficult for membrane proteins Cannot see hydrogen

Question 55

Nuclear Magnetic Resonance process

Answer 55

``` Purify the protien Dissolve the protein Collect NMR Data Assign NMR signals Calculate the structure ```

Question 56

Globular proteins

Answer 56

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

Question 57

Collagen

Answer 57

Important connective tissue

Question 58

Collagen composition

Answer 58

Rich in Gly and pro-rich left handed helix.

Question 59

Collagen structure

Answer 59

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

Question 60

Role of 4-Hydroxyproline in Collagen?

Answer 60

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

Question 61

Lacking vitamin C will cause what effect?

Answer 61

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.

Question 62

Example of globular protein?

Answer 62

Hemoglobin, myoglobin, and various enzymes.

Question 63

Example of fibrous protein?

Answer 63

Collagen, elastin, keratin.