1.2.amino acids and proteins

Question 1

List 21 amino acids and categorize them accordingly

Answer 1

1. hydrophobic-form hydrophobic cores, span the membrane, connect via Van der Waals forces
   
   1. GAVLIP
2. aromatic
   
   1. FWY
3. polar uncharge-hydrogen bonding, found in surface to solubalize cell
   
   1. NQ
   2. alcohol
      
      1. ST
4. sulfur
   
   1. MC
   2. sulfur->Selenium
      
      1. SeC- found in antioxidant specific proteins
5. charged- bind with eachother and other charged biomolcules, bind metals to stabalize interactions
   
   1. basic
      
      1. HRK
   2. acid
      
      1. DE

Question 2

What are the requirements for SeC for it to become incorporated into a protein?

Answer 2

Need genetic code and secondary structure in the mRNA to be incorporated into a protein.

Question 3

Define what will happen in the following circumstances

1. pH< < pKa
2. pH>>pKa

Ph=pKa

Answer 3

1. protonated
2. deprotonated
3. group is protonated/deprotonated half way. Zwitterion

Question 4

describe the generation of a disulfide bond. conditions and molecule reaction.

Answer 4

Two cysteine’s form a disulfide bridge under oxidative conditions and generate a cystine. This reaction is responsible for the 3-4 structures.

Question 5

What are some exmples of protein varibility during embryonic development and in tissue specific expression?

Answer 5

tissue specific protein variations are known as isoforms.

hemaglobin types are a great example of isoforms that are important during different stages of development. While an adult produces alphs-beta couples for hemeglobin, embryonic conditions require hemeglobins that are specfic to these enviornments.

notice the foloowing trends:

1. zeta->alpha
2. epsilon->gamma->beta

Question 6

what are the forces involved with the following interactions

1. hydrophobic
2. charged
3. polar

Answer 6

1. van der waals
2. ionic
3. hydrogen

Question 7

Dr.Oz is in the ER and is treating a person with severe chest pain. what tests will he order? how do they work?

Answer 7

CK and troponin blood tests are used to diagnose an MI.

1. CK has two components that are coded by 2 genes. this generates 3 isoforms of the protein
   
   1. brain-ck1
      
      1. bb
   2. cardiac muscle-ck2
      
      1. mb
   3. skeletal muscle-ck3
      
      1. mm
2. blood concentrations are usually really low for mb, but during an MI the heart muscles fracture and CK-2(MB) gets into the blood stream.

Question 8

Patient Z presents with head aches, fatigue and pain in his finger tips. His father and mother are from africa. What could Z have? What evidence can support the decision(6)?

Answer 8

A single point mutation leads to a single AA change can that alters the function of a protein and may lead to disease. A healthy person with normal hemoglobin has a K(Glu)-6. this is an integral part of the hemglobin for ionic interaction/repulsion. Disease may manifest according to the mutation.

1. E->v, [(-)->(neutral)]
   
   1. this mutation generates an extension for the on the beta group and interacts with the pocket found on the alpha group. The Hb tertiary structure stacks together like legos and causes the cell to sickle. Sickle shape causes the RBC to block arteries leading to anoxia and pain.
   2. if he is autosomal recessive the conditions may be severe, but if he is heterozygous for the trait it may be asymptomatic.
2. E->k, (-)->(+)
   
   1. this presents with fatigue and symptoms similar to SC.
   2. Hb coagulates to generate a target shape, but may sickle.
3. diagnosing sickle cell or HbC disease
   
   1. results of electrophoresis
      
      1. healthy adult = one smear closer to anode
      2. SC=will show two smears
         
         1. alpha group->closer to anode
         2. mutant beta group-> lagging behind, due to lack of negative charge.
      3. HbC
         
         1. alpha group->closer to anode
         2. (+) charge beta group repulses anode charge and maintains position
   2. hemolytic anemia
      
      1. the sickled RBCs are being destroyed faster than being replaced
   3. elevated bilirubin
      
      1. heme groups are being introduced to blood stream faster than liver can process.
      2. may present with jaundice
   4. elevated reticulocytes
      
      1. BM is generating more RBC precurors than usual.
   5. dactylitis
      
      1. pain and swelling in hands and feet, due to the end arteries being blocked
   6. splenomeagaly
      
      1. enlarged spleen due to massive increase in RBC degradation
      2. spleen may fail and increase susceptability to infection
   7. both diseases frequent african american population

Question 9

determine the properties of post translational modification.

1. glycosilation
2. glycation
3. lipid addition
4. phosphorylation
5. acetylation
6. ADP-ribosylation
7. proline->hydroxyproline
8. lysine->hydroxylysine
9. glutamate->gammy-carboxyglutamate

Answer 9

1. glycosylation is the postranslational modification of a protein via an enzymatic process.
   
   1. increases solubility
   2. ABO groups
2. glycation is the nonenzymatic process of a sugar moiety being added to a protein. occurs in the blood stream when blood glucose levels are high. hemeglobin becomes glycated (HbA1c)
   
   1. used to asses compliance with diabetic insulin treatment
   2. AGE- advanced glycated end-products
      
      1. when many different products become heavily glycated they may generate problems as they build up in the tissues
3. lipid addition-allows proteins to enter the membrane w/o a transmembrane region(series of proetins thaat are hydrophobic and designed to span or insert in to the cell membrane)
4. phosphorylation-activates enzymes(atp)
5. acetylation- histone modification with an acetyl group changes the charge and loosens the bind of DNA and histones to allow for gene expression
6. ADP-ribosylation-can alter intracellular signaling or protein synthesis.
   
   1. system implemented as a toxin by some bacteria to modify the metabolism of a host
7. hydroxyproline-enzymatically driven, stabalizes triple helix structure of collagen.
8. hydroxylysine-enzymatically driven, serves as a glycosylation and crosslinking site in collagens
9. gamma-carboxyglutamate
   
   1. enzymatically driven
   2. abundant in coagulation proteins
   3. required for coagulation and ca2+ binding proteins

Question 10

explain how changes in a protein sequence through protein engineering can provide better patient managment

Answer 10

beneficial changes in protein structure

1. protein engineering can lead to better treatments of certain diseases
2. example
   
   1. recombinant human insulin (lispro) for treatment of diabetes.
      
      1. exchange position of P28 and K29
      2. leads to
         
         1. less insulin aggregation
         2. better absorption
         3. faster action