Amino Acids and Protein Chemistry Flashcards
Functions of Globular Proteins
Storage of ions and molecules Transport of ions and molecules Defense against pathogens Muscle contraction Biological Catalysis
Binding of Oxygen does what to Heme?
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.
Oxygen binds pulls what amino acid toward it when in the heme group.
His F8
Positive Cooperativity definition
First binding event increases affinity at remaining sites.
Negative Cooperativity definition
First binding event reduces affinity at remaining sites.
How to recognize positive cooperativity?
Sigmoid binding curves.
When oxygen is bound to the Heme group what state is the heme in?
R-State
What is the Bohr effect?
The increase in O2 transport efficiency between lungs and metabolic tissues that is caused by pH difference.
H+ Promotes release of O2 from hemoglobin.
What type of regulator is 2,3-Bisphosphoglycerate for O2
It is a negative Heterotropic regulator of Hb function.
How does 2,3-BPG regulate Hb function?
It stabilizes the T state (deoxy) of Hb.
What charge does 2,3-BPG have?
It is negatively charged
Where is 2,3-BPG produced?
It is produced from an intermediate in glycolysis.
When does 2,3-BPG increase?
At high altitudes.
15-20% of CO2 is exported in the form of a ______ on the _______ of each of the polypeptide subunits.
Carbamate
Amino terminal residues.
The formation of a carbamate yields what?
And what is the effect of this?
Yields a proton that can contribute to the Bohr effect.
It can form additional salt bridges that stabilize the T state.
Why is CO dangerous?
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+.
CO blocks the function of what?
Myoglobin, hemoglobin, and mitochondrial cytochromes that are involved in oxidative phosphorylation.
Natural defenses against CO poisoning?
Protein pockets decrease affinity.
His E7 sterically hinders CO from binding in its preferred configuration (linear conformation).
What mutation results in sickle cell anemia?
Glu6 -> Val6 in the B chain of Hb.
Methemoglobinemias are caused by what?
Fe3+ in Hb instead of Fe2+ results in a reduced ability to bind and deliver oxygen to tissues (hypoxia).
Newborns are born with only half the normal level of this, and as such are more susceptible to oxidative stress?
NADH - methemooglobin reductas.
Converts Hb Fe3+ to Hb Fe2+
Nonpolar, Aliphatic R groups
Glycine G Alanine A Proline P Valine V Leucine L Isoleucine I Methionine M
Aromatic R groups
Phenylalanine F
Tyrosine Y
Tryptophan W
Polar, uncharged R groups
Serine S Threonine T Cysteine C Asparagine N Glutamine Q
Positively charged R groups
Lysine K
Arginine R
Histidine H
Negatively Charged R groups
Aspartate D
Glutamate E
pI equation
pI = (pK1 + pK2) / 2
What is pI
Isoelectric Point, the point at which the net charge is zero.
- -AA is least soluble in water.
- AA does not migrate in electric field.
What is the pKa of the a-carboxyl group?
2.34
What is the pKa of the a-amino group
9.6
If the pH group is below the pKa, the group will be?
Largely protonated
If the pH group is above the pKa, the group will be?
Largely deprotonated
4 Methods of Column Chromatography
Charge, Size, Specificity, Polarity.
Edman Degradation
Fragmenting proteins into smaller peptides/purification
Successive rounds of N-terminal modification, cleavage, and identification.
Where does Trypsin cleave?
Lys, Arg (C)
Where does cyanogen bormide
Met (C)
Why are some phi and psi combinations more favorable?
They can form favorable H-bonding interactions along the backbone.
Why are some phi and psi combinations less favorable?
Steric Crowding.
What is the phi
Angle around the a-carbon –amide nitrogen bond
circle with line
What is the psi
Angle around the a-carbon – carbonyl carbon bond.
Trident
What does the Ramachandran plot show?
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.
How many residues per turn in an A-helix
3.6 residues
Hydrogen bonds are every ____ between the backbone amides?
n + 4 amino acids.
Where are side chains in an alpha helix?
Pointing out and roughly perpendicular.
What are strong helix formers?
Ala and Leu
What effect does Pro have on an a helix?
It is a helix breaker because the rotation around the N-Ca phi bond is impossible.
What effect does Gly have on a helix?
It is a helix breaker because the tiny R-group supports other conformations.
What is the difference between parallel and anti-parallel B sheets
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)
Common components of beta turns?
Proline (position 2) and Glycine (position 3)
Effect of Proline on a beta turn
Proline can force formation of a B-turn and anti-parallel strands resulting in a type 1 turn.
How to determine secondary structure?
Circular Dichroism measures the molar absorption difference (:delta:E)
Chromophores in the chiral environment produce characteristic signals.
How is tertiary structure stabilized?
Largely by hydrophobic and polar interactions
Disulfide bonds.
How are quaternary structures stabilized?
Same interactions as tertiary.
What is X-ray crystallography and pros and cons
Crystallize the protein
No size limits, well established
Difficult for membrane proteins
Cannot see hydrogen
Nuclear Magnetic Resonance process
Purify the protien Dissolve the protein Collect NMR Data Assign NMR signals Calculate the structure
Globular proteins
Most numerous of cellular proteins
Soluble in aqueous media.
Amphipathic.
Stabilized by hydrogen bonds, ionic interactions, and less often by disulfide bonds.
Collagen
Important connective tissue
Collagen composition
Rich in Gly and pro-rich left handed helix.
Collagen structure
Three collagen chains intertwine into a right-handed superhelical triple helix.
Role of 4-Hydroxyproline in Collagen?
Forces the proline ring into a favorable folding, offers more hydrogen bonds between the three strands.
Lacking vitamin C will cause what effect?
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.
Example of globular protein?
Hemoglobin, myoglobin, and various enzymes.
Example of fibrous protein?
Collagen, elastin, keratin.
