Proteins By Steele

Question 0

Which AAs are hydrophobic?

Answer 0

Val, Leu, Ile, Met

Question 1

What parts of amino acids determine the structure of the alpha helix?

Answer 1

The H-bonds in the backbone, NOT the R groups.

Question 2

Which AAs have aromatic side chains?

Answer 2

Phe, Tyr, Trp

Question 3

Which AA has a unique functional group important for cell signaling and what is the functional group?

Answer 3

Hydroxyl on Tyrosine, on the aromatic ring

Question 4

Which are the basic AAs?

Answer 4

Lys, Arg, His (Lys and Arg are the classic basic AAs though)

Question 5

Which AA is important in forming higher levels of structure? What level? Why?

Answer 5

Cysteine. It has -SH. can for disulfide bonds for tertiary structure.

Question 6

Which are the polar AAs?

Answer 6

Asp, Gln.

Question 7

Which AAs have -OH group on side chain?

Answer 7

Ser, Thr

Question 8

What makes Serine and Threonine unique?

Answer 8

They have OH group that makes them substrates for enzymes(protein kinases) which bind phosphate groups to the OHs.

Question 9

AA that has cyclic side chain?

Answer 9

Proline. restricts rotation between alpha C and N. thus impacts protein structure.

Question 10

Acidic AAs?

Answer 10

Asp, Glu
(Aspartate, Glutamate. ).
negative charge at neutral pH

Question 11

What is the angle between C(=O) and C(-R) called in a peptide bond?

Answer 11

Psi. ψ

Question 12

What is the angle between C(-R) and N in peptide bond?

Answer 12

phi φ

Question 13

What are the most common phi and psi angles for the alpha helix?

Answer 13

A phi angle that is negative (0 to -180) and psi angle that could be positive or negative (-180 to 180) but more commonly positive. This forms the right handed helix which is most common.

Question 14

What is a beta turn? What are important properties of beta turns?

Answer 14

It turns the chain 180 degrees so as to reverse the direction. They are on surfaces of proteins, sites of immunological recognition, sites of glycosylation, and often predictable from the AA sequence.

Question 15

Side chains play important role in what level of protein structure?

Answer 15

Tertiary

Question 16

What are some examples of protein mid folding diseases?

Answer 16

Alzheimer’s. spongiform encephalopathies like mad cow disease.

Question 17

They cause a chain reaction of misfolding of proteins.n

Answer 17

Prions. They form aggregates called amyloids.

Question 18

Can proteins have covalent linkages between one another? How?

Answer 18

Disulfide bonds.

Question 19

What is the average MW of an AA in a protein?

Answer 19

110 Da.

Question 20

Given the average MW of an amino acid in a protein, about what is the size range of a protein?

Answer 20

20 k Da to 40 k Da. This means there are approx 200 to 400 AAs in the average protein.

Question 21

What are the types of shapes of proteins?

Answer 21

Globular and structural (collagen, keratin… Slabs.)

Question 22

Name the charged AAs which influence charge on proteins.

Answer 22

D E H K R.

Aspartate, glutamate, histidine, lysine, Arginine.

Question 23

How is blood buffering accomplished?

Answer 23

By carbonic acid and bicarbonate.

Question 24

types of glycosylation?

Answer 24

N-linked which attaches to N of Asparagine.

O-linked which attaches to -OH group of Ser or Thr.

Question 25

Example of disease caused by mutation in protein localization.

Answer 25

Caused by mutation in nuclear localization signal in SHOX transcription factor, Léri-Weill dyschondrosteosis is a disorder of bone growth. Affected individuals have short stature due to shortening of the bones of the arms and legs. Just sits in cytoplasm and doesn’t do job.

Question 26

Describe methods of protein isolation.

Answer 26

Chromatography. Diff types.

1. Ion exchange by charge,
2. gel filtration by size,
3. absorption by hydrophobicity,
4. affinity based on interaxn with other molecules
5. Electrophoresis by size charge or both.

Question 27

What is the change that occurs in sickle cell disease?

Answer 27

Change from E to V, from basic positive charged Glutamate to Valine, which changes the hemoglobin molecule to one referred to as HbS. Then the hydrophobic molecules aggregate and precipitate.

Question 28

What are allozymes and isozymes?

Answer 28

Allozymes are forms of a protein that are encoded by diff alleles of same gene. Isozymes are forms of protein encoded by diff genes but that catalyze the same reaction.

Question 29

What is good way to diagnose myocardial infarction?

Answer 29

Creatine kinase 2 (CK2) isozyme, aka MB, which is in cardiac but not skeletal muscle… Is not usually present in bloodstream so if it is it indicates damaged heart tissue.

Also can measure cardiac troponin.

Question 30

What are types of N terminal modification of proteins?

Answer 30

Proteolysis which involves either exo or endo.

α - amino modification which involves acetylation and myrstolation.

Question 31

What are some purposes of acetylation?

Answer 31

Provides stability against random degradation by aminopeptidase activity, and protects amino terminus from non enzymatic glycation by reducing sugars.

Question 32

What’s is HbA1c?

Answer 32

Modified glycated form of hemoglobin which will be glycated by glucose and be higher in concentration if one has diabetes due to the elevated levels of glucose.

Question 33

What removes phosphates and by what process?

Answer 33

Phosphotases by hydrolysis adding water.

Question 34

How are protein kinases regulated?

Answer 34

They have two R and two C subunits. 4 cAMP binds to the R subunits and causes dissociation so that C subunits are catalytically active.

Question 35

What is the role of Velcade?

Answer 35

Velcade (Bortezomib) inhibits protease activity in the proteasome, blocking the degradation of proteins. Myeloma cells are more sensitive to this blockage than normal cells and thus are killed more easily. Thus works against multiple myeloma which tends to have elevated levels of immunoglobulins.

Question 36

What are the forms of hemoglobin?

Answer 36

Deoxy which is taut T, and oxy which is relaxed R.

Question 37

What are effectors of hemoglobin and what do they do?

Answer 37

2,3-BPG is an effector which stabilizes the deoxy form and facilitates release of oxygen in tissues.

There is ONE BPG cavity per hemoglobin.

Question 38

What is K sub M in enzyme catalysis?

Answer 38

Km refers to the substrate concentration at which half the maximum velocity of reaction is achieved,

Question 39

What is the michaelis menton equation?

Answer 39

Vo = V max ( [S] / ( [S] + Km) )

Question 40

What is chymotrypsin?

Answer 40

It is a serine protease that cleaves peptide bonds by its nucleophilic activated serine.

Question 41

Trypsin and thrombin have what amino acid specificities?

Answer 41

Near the substrate site, trypsin has specificity to Arg or Lys oh the carboxyl side while thrombin has specificity to Arg on carboxyl side and Gly on amino side of the hydrolysis site.

Question 42

What are examples of irreversible inhibition?

Answer 42

Penicillin covalently binds transpeptidase and prevents synthesis of bacterial cell walls.

Aspirin modifies active site serine by acetylation in cyclooxygenases and prevents inflammation.

Question 43

Common metal cofactors?

Answer 43

Zinc, Magnesium, Calcium

Question 44

Collagen has repeats of what primary sequence?

Answer 44

Gly-X-Y where X is often Proline and Y is often Hyl which is Hydroxy-lysine,

Question 45

What is the importance of hydroxylated forms of AAs in collagen?

Answer 45

Tensile strength, forms tight helices. Catalyze by enzyme that requires Vit C as cofactor. Typically lysine and Proline are hydroxylated.