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Protein Struction and Function


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What is the change in beta subunit of the hemoglobin residue that causes sickle cell anemia
Glutamic acid to Val, glutamic acid is negative charged and is thus hydrophilic while val is not
Since Val is hydrophobic in the beta subunit of hemoglobin, what happens in this mutation?
They aggregate and form stacks... thus the sickling effect... a thus these blood cells cannot pass through capillaries.
which of the following will Arg NOT form an electrostatic bond with? and Explain
a. Asp
b. Lys
c. Glu
d. Alpha amino group at end of protein
e. Alpha carboxylate group at the end of a protein
f. Phosphorylated amino acids
b. Lys (+)
d. alpha-amino group at the end of the protein (+)

Asp (-)
Glu (-)
alpha-carboxylate at the end of protein (-)
phosphorylated residues (-) (eg., Ser, Thr, Tyr)

Note: phosphorylated residues have a NEGATIVE charge!!!!
How can an uncharged residue,(such as serine threonine, or tyrosine), become charged? and what type of effect will this have on the residue
a. post transitional modification... adding a phosphate group (-)
b. it will be come negatively charged.
1. What are the 3 types of hydrogen bonding that occurs in amino acids?

2. What angle of H-bonding is the strongest between 3 atoms, Bent or straight?
a. backbone: between two peptide backbones
b. bonding between two residues
c. amino acid w/water

2. Straight
Name4 residues that are involved in hydrogen bonding
Ser, theronine, cysteine (S-H) and sometimes tyrosine
Name the 8 Amino Acids that have apolar or hydrophobic side chains.
Met, Ala, Ile, Leu, Val, Pro, Phe, Trp, Glycine
What type of environment is the cytoplasm, reducing or oxidizing?
Where would you be more likely to see a disulfide bridges?
EC, where it is an oxidizing environment.
Which amino acid forms a disulfide bridge and what type of protein is this likely to be?
cysteine... secreted
Where does a soon to be secreted protein go, where oxidation begins?
What is the function of a disulfide bridge?
b. hold together a protein made of two different polypeptide chains
What is an example of a secreted protein with both intra and inter molecular disulfide bridges?
How many residues per alpha helix turn?
What handed helix is formed by an L-amino acid
Right handed
Where does the the hydrogen bond form from the #1 residue and the #2 residue?
What type of protein is Calmodulin and where is it stable
alpha helix... in water
What type of protein is flavodoxin and what is it's structural significance?
Alpha helix... half is hydrophobic and half is hydrophilic
What type of ß-pleated protein has single chains running in the:
a. same direction
b. different direction
a. parallel
b. anti-parallel
Which type of secondary protein structure is composed of discontinous polypeptides?
Why is a ß-sheet pleated?
because the residues alternate (invert)
What are the three supersecondary structures?
a. Helix-loop helix
b. Hairpin ß-motif
c. sheet-helix-sheet
Which of the three supersecondary structures are well represented in DNA binding elements?
What type of ß-pleated sheet will be seen in Hairpin ß-motif?
a. parallel
b. anti-parallel
b. anti-parallel
Describe the sheet-helix-sheet supersecondary structure?
Just like the name says... sheet connected to a helix connect to a sheet
What is a protein domain?
it's a polypeptide chain or part of a polypeptide chain that INDEPENDENTLY FOLDS into a STABLE globular structure... of several supersecondary structures...

Can have an independent function
What do you call the sum of all domains in a protein?
Tertiary structure
How are hydropathy plots used to predict membrane-embedded primary sequences? and Which sign is more hydrophobic (+) or (-)
By the region .....X..... five residues before and after. (+) is more hydrohobic
_ _ _ can solve structure of 50K or 60K in molecular weight, which is a somewhat small protein size
What is used to solve the structures of very large proteins and what is required?
crystallography... crystals
What method is good for predicting secondary structure and features such as hydrophobicity versus hydrophillicity but not good when it comes to predicting the tertiary structures?
Computational methods
What is the quartenary structure?
The 3-D structure of 2 or more polypeptides
What type of receptors have at least one of the following, either a DNA binding domain or a ligand binding domain
Glucocorticoid receptor
What is the pathway for the production of cortisol?
Hypothalamus is stimulated --> CRH --> POMC (pituitary)--> ACTH (in adrenals) --> cortisol (a glucocorticoid)
Does the glucocorticoid receptor interact directly with the nucleus?
No, it interacts with constiuents in the cytoplasm... they both interact with DNA in nucleus
1) How many zinc fingers does the glucocorticoid receptor have?

2) What are their functions?
2, a recognition helix and a dimerization loop
What does the recognition loop of the zinc fingers of the glucocorticoid receptor do?
It interacts with the major groove of DNA... 2 fingers thus adjacent major grooves.
While recognition sequence interacting with the major grooves of DNA are amphiphilic, which residues would you expect to find abutting the DNA, why?
positively charged residues, like Lys and Arg, His (and the N-terminus of an amino acid) because DNA is negatively charged.
What type of protein structure do you find in Myo-D?
What is Myo-D?
A trascription factor
T/F Myo-D is a monomer
false, it's a dimer
What will you get if you insert, via a plasmid, MyoD into a fiberblast?
it will become a muscle cell
What causes the dimerization of MyoD? and why?
a. The lipophilic residues on H1 and H2 helices form a hydrophobic core that stabilizes the dimer.
2. This stabilized geometry allow H1 to recognize DNA
T/F the helix-loop-helix structure of MyoD is like the GC receptor in that it attaches to two successive major grooves.
False, N-terminal basic regions of the two helices are binding to a single major groove
What is p53?
A transcription factor, a tumor supressor protein, which acts to recognize environmental damage, act either repairs or causes apoptosis.
What is the nature of p53 mutations that causes cancer?
defective binding
What are the three domains of p53?
transactivation, binding, and oligomerization domains
How many subunits does the oligomerization domain of the p53 protein contain?
4, two sets of dimers
What holds the oligomerization domain of the p53 protein together?
the interactions of the 4 alpha helices
How do the ß-sheets on the oligomerization domain of the p53 protein interact?
What function does the ß-barrel serve on the oligomerization domain of the p53 binding protein?
It serves as a foundation for which other residues can interact with DNA
What function does the Zn serve in the oligomerization domain of the p53 binding protein?
It stabilizes loops L1 and L2, which are involved in DNA recognition
What would you expect to find in patients that have defective Arg248 in p53?
Arg248 is in the recognition domain of p53.
What is the net effect of a defective in p53?
After DNA damage occurs there is
a)no apoptosis
b)no gene repair
c)no p21 (which inhibit cell cycle).
At the PFK rxn of Glycolysis, state whether the following criteria will increase, decrease, or have no effect on the rate of glycolysis:
1. Loss of the allosteric site for ATP on PFK
2. Loss of the allosteric site for Citrate on PFK
3. Los
1. Loss of the allosteric site for ATP on PFK --> increase in glycolysis rate
2. Loss of the allosteric site for Citrate on PFK --> increase in glycolysis rate
3. Loss of the allosteric site for Fructose-2,6-bisphosphate on PFK --> decrease in glycolysis rate
4. overexpression of PFK: no change in the rate of glycolysis

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