Unit II- Protein Building Blocks

Question 1

Why study proteins

Answer 1

• everything in your body is either protein or is made by them
• proteins catalyze or control every process in the cell
• when something goes wrong in the body, a protein is always to blame (genetic disease-caused by defective proteins, infectious disease- dependent on a few key proteins)
• proteins are targets of nearly all drugs

IF YOU WANT TO UNDERSTAND THE MECHANISMS OF DISEASE AND THEIR TREATMENTS, LOOK TO PROTEINS

Question 2

Protein function depends on:

Answer 2

polymer length and amino acid composition

-These factors specify the unique 3D structure that dictates function

Question 3

HIV protease

Answer 3

• a drug to target the protein protease, one of three enzymes in HIV
• HIV encoded proteins mutate rapidly
• the amino acid sequence in constantly changing

Question 4

Alzheimer disease

Answer 4

• extensive deposits of misfolded protein in the brain
• associated with cell death and loss of brain fucntion
• main component 42 residue fragment from the APP (Alzheimer presursor protein
• APP cleaved at wrong place
• makes sticky peptide just from two extra amino acids

Question 5

Unstable protein structure

Answer 5

-proteins are not rocks, they are quite unstable (Change of G= 0-10 kcal/mol)

• they constantly unfold and refold
• up to 40% contain reguons of intrinsic disorder
• many diseases are caused by improper folding or degredation

Question 6

Phi/Psi dihedral angles

Answer 6

• each amino acid in a polypeptide has a (phi/psi) dihedral angle combination
• determines the twists and turns that the chain takes in the final 3D structure
• residues in alpha helices have their own, and beta sheets have their own different ones
• Alpha helix- close to zero, scrunched polypeptide
• Beta sheets close to 180, almost fully extended

Question 7

Phi

Answer 7

atom 1= carbonyl carbon of previous residue
atom 2- nitrogen of residue i
atom 3= alpha carbon of residue i
atom 4= carbonyl carbon of residue i

Question 8

Ramachandran plot of allowed angles

Answer 8

• only a small fraction of phi/psi values are allowed. All of the backbone conformations must lie in the gray area
• the limited amount of phi/psi space allows only certain structures to form. Alpha helices and beta sheets, the two main secondary structural elements, are found in these grey areas
• the shapes of these plots arise simply from the way atoms are connected (bond lengths, bond angles, and hard-sphere repulsions)
• glycine has only a hydrogen for a side chain (very small). Therefore, it experiences fewer repulsions than the other amino acids, as indicated by large grey areas on the right plot. Regions of the polypeptide chain containing Gly will tend to be more flexible

Question 9

Properties of amino acid side chains

Answer 9

1) Hydrophobic (nonpolar)
2) Hydrophilic (polar)
- charged
- polar but uncharged

3) Unique (Pro, Gly, Cys)

• much of protein structure can be understood by the binary code of polar on the outside, nonpolar on the inside
• function in many instances biols down to a few amino acids
• amino acid substitutions are common. Their effects on structure/function/folding can be insignficant or dramatic

Question 10

pKa’s of select amino acids

Answer 10

• Asp (4.0)
  -Glu (4.0)
  -His (6.5)
  -Cys (8.5)
  Lys (10.0)
  Arg (12.0)
  Carboxyl terminus (4.0)
  Amino terminus (8.0)

Question 11

Hydrophobic side chains

Answer 11

• poorly soluble in water
• aliphatic residues Ala, Val, Leu, Ile, Pro) are the most hydrophobic of the amino acids
• side chains chemically inert
• found mostly inside proteins
• the aromatic amino acids are slightly less hydrophobic than the aliphatic ones
• of the amino acids Phe is the most hydrophobic
• Tyr and Trp contain hydrophilic OH and NH groups, respectively making them amphipatheic (part hydrophobic part hydrophilic)
• Pro is unique in that the side chain loops back and forms a covalent bone to the backbone nitrogen, making it the imino acid. X-Pro peptide bones are frequently cis

Question 12

pKa and ionization

Answer 12

• pKa is the acid dissociation constant: high pKa = binds H+ tightly, Low pKa=binds H+ weakly
• think of group as being protonated/deprotonated rather than positively/negatively charged
• pKa is the pH at which half the ionizing groups are protonated, half are deprotonated
• pHpKa: low bulk H+ concentration draws off H+

Question 13

Polar charged side chains

Answer 13

• the pKa of a group is the pH at which 50% of the molecules are ionized and 50% are non-ionized. Below the pKa the group takes up H+ from solution; above it the pKa it releases a proton into solution
• Asp and Glu are the acidic residues because their carboxylic acid functional groups and are negatively charged
• the basic amino acids (Lys, Arg) have a strong affinity for H+ and becomes positively charged
• charged groups are chemically reactive
• they promote breakage and formation of chemical bonds by donating or abstracting H+ from atoms of substrate molecules

Question 14

Changing pKa values in microenvironment

Answer 14

-protein structure is used to alter the charge environment around the critical residue, making it much different than it would be in simple aqueous solution

1) Asp normally wants to give up its proton at physiological pH
2) If Asp is near a positively charged amino acid Asp really wants to give up its H+. Need to add more H+ to water to force it back on. pKa decreases
3) If Asp is near a negatively charged amino acid. Asp wants to keep its H+ more than usual. Don’t have to add as much H+ to force it back on. pKa increases
4) Next to uncharged greasy blob, the pKa increases

Question 15

Polar uncharged side chains

Answer 15

• polar because of the presence of electronegative atoms (O,N,S)
• these have strong electron withdrawing effect which pills negative charge from atoms they are bonded to
• almost never ionized

Question 16

Unique side chains : Glycine

Answer 16

• the only amino acid without a carbon atom without a carbon atom side chain
• since the proton side chain is much smaller and less bulky than a carbon side chain, there are many more phi-psi angles available to Gly
• the polypeptide backbone has much more flexibility where glycine is present compared to any other amino acid
• side chain chemically inactive

Question 17

Unique side chains: Cysteine

Answer 17

-contains a thiol group which can oxidize with another Cys to form a disulfide bridge
-primary way to cross links are introduced into proteins
-

Question 18

Unique side chains: Proline

Answer 18

• cis peptide bonds with the amino acid preceding it
• favors kinds, turns
• no H-bond donor on peptide bond

Question 19

Covalent properties of polypeptides

Answer 19

• Polypeptide backbone
• properties are dominated by the peptide bond
• simple bonding and steric considerations encourage formation of certain types of structures
• peptide groups are necessary for 3D structure, but not sufficient

Amino acid side chains:

• gives proteins their individuality
• chemical interactions and shape of side chains determine structure

Question 20

Four forces of protein folding

Answer 20

1) Electrostatic interactions
2) Hydrogen bonding
3) Van der Waal’s interactions
4) Hydrophobic effect

Question 21

Electrostatic interactions

Answer 21

• follow Coulomb’s law, where the attractive force is proportional to the product of the charges divided by the distance between them squared and the dielectric constant
• operate over fairly long distances
• salt bridges are the strongest
• charged are all on the surface
• buried charges are rare and always there for a reason

Question 22

Fo proton channel

Answer 22

• buried charge is the Fo ring of the ATP synthase
• the Fo proton translocation channel is formed by a ring of helical subunits that sits in the membrane and rotates
• the helices are composed entirely of nonpolar residues with the exception of single Glu per subunit
• the proton binds the Glu and rides it like a merry-go-round
• Glu and Pro are essential for proton transport

Question 23

Dipole interactions

Answer 23

• weaker than salt bridge
• a molecule having partial positive and partial negative charges, without possessing a formal net charge
• the most common dipole in a protein is the peptide bond
• 2 charges separated by distance
• dipole arises from difference in electronegativeity no net charge on molcule

Dipole moment = excess charge x separation

Question 24

Hydrogen bonding

Answer 24

• special case of electrostatic interaction
• results in an excess positive charge on the hydrogen and an excess negative charge on the heavy atom
• 2 electronegative atoms compete for same H+
• oxygen, nitrogen, sulfur in biomolecules

-in proteins all donors are bonded to acceptors and vice versa

Question 25

Proteins are special polymers

Answer 25

• a polypeptide will spontaneously loop back and forth on itself to form a roughly globular, highly compact 3D structure
• each sequence folds to exactly one structure
• the only thing that makes the proteins different are the length of polypetide chain and the order of amino acids

Question 26

Carbons of amino acids

Answer 26

• central carbon, alpha carbon
• central carbon i chiral but only L enationmer is synthesized and incorporated into proteins
• beta is the first of of the side chain

Question 27

Peptide bond is planar and trans

Answer 27

• peptide bonds formed by the 19 amino acids other than proline are found in the trans conformationg >99% time
• planarity reduces bond rotations

Question 28

Planarity reduces bond rotations

Answer 28

• partial double bond character prevents rotation about the CO-NH bond, resulting in only two rotatable bonds per amino acid residue
• phi and psi are dihedral angles, which are defined by the following four bonded atoms:

phi: 1-carboynl carbon of previous residue (i-1)
2- nitrogen of residue i
3- alpha carbon of residue i
4- carbonyl carbon of residue i

psi: 1- nitrogen of residue i
2- alpha carbon of residue i
3- carbonyl carbon of residue i
4- nitrogen of next residue (i+1)

Question 29

Dihedral angle

Answer 29

is Phi and Psi angles between N-Calpha and Calpha-C that have a certain range of allowable values and take into account 3D structure (10-20%)