Question 3.

Human haemoglobin is a complex protein molecule made up of four poly-peptides joined to an iron-containing haem group. In normal human adult haemoglobin, haemoglobin A, or HbA, two kinds of polypeptides designated as alpha and beta are found. Two identical alpha and two identical beta chains plus the haem group make up each molecule of haemoglobin A. Haemoglobin S, or HbS, is a haemoglobin variant occurring in individuals affected with the heritable disorder sickle cell anaemia. A comparison of the amino acid sequences of the polypeptides in haemoglobins A and S indicates that the alpha chains in the two molecules are identical, but that the beta chains differ in a single interior amino acid.

a.   How many of genes are necessary for the synthesis of haemoglobin S in an adult who is homozygous for the S allele?

b.   Assuming that the gene for the beta chain of HbS arose from the gene for the beta chain of HbA through a single mutation, what general type of mutation was most likely responsible?

c.   The difference between the beta chains of haemoglobin S and A is restricted to the sixth amino acid from the amino (-NH₂) end of the polypeptide. In haemoglobin S, the amino acid at the site is valine and in haemoglobin A it is glutamic acid. From your knowledge of the genetic code (and with reference to the genetic code) what can you deduce about the specific (and simplest) base alteration in the beta polypeptide that would produce the amino acid substitution?

9. What is an anticodon? Where are anticodons located?

10. What type of bond links amino acids together?

11. What is mRNA processing? What are the three steps?

12. What is a gene?

13. What is a point or substitution mutation?

14. What is a frameshift mutation? What are the two types?

15. Why do most mutations have no effect on the organism?

. In what order will the following amino acids elute from a Dowex-50 cation exchange column at pH 3.2: alanine (pI = 6.02); arginine (pI = 10.76); glutamate (pI = 3.22); serine (pI = 5.68); and tryptophan (pI = 5.88)? (Ignore the polarity characteristics of the side-chains). 


Wouldnt the basic ones bind and the acidic one (glu) elute off first??

During the uptake of low-density lipoprotein (LDL) by a liver cell, LDL-receptor protein complexes are internalized by endocytosis. The endosomes then fuse with lysosomes, where protein components of LDL are hydrolyzed to free amino acids, while cholesterol esters are hydrolyzed by a lysosomal acid lipase. The LDL receptor itself is not affected by lysosomal enzymes.

Why is it important that LDL receptors are not degraded by lysosomal enzymes?

4. How has collagen been used in cosmetics and why is it not common in recent years

5. What are the alternative to collagen injections

6. How is collagen used to prepare artificial skin for burn patients

7. Write the structures of two unusual hyroxylated amino acids that are present in collagen and why are they important component of its structure

8. What is scurry and why is it caused?

1. Given the non-template strand of DNA, draw the template strand with the 5' and 3' ends labeled. Draw the RNA molecule with the proper 5' and 3' ends labeled

Non-Template Strand: 3'- AAT GCT CGT AGC TTC GAT CGG ATC GA-5'

2. How many amino acids would the RNA molecule code for?

1. using your knowledge of nutritional physiology and creative thought processes, explain the ramifications to human metabolism and health if the kidneys were lacking the glutaminase enzyme.

4. Phenylketonuria (fen-ul-ke-toe-NU-re-uh), also called PKU, is a rare inherited disorder that causes an amino acid called phenylalanine to build up in your body. PKU is caused by a defect in the gene that helps create the enzyme needed to break down phenylalanine. Without the enzyme necessary to process phenylalanine, a dangerous buildup of this amino acid can develop when a person with PKU eats foods that are high in protein. This can eventually lead to very serious health problems. Thus, people with PKU (babies, children and adults) for the rest of their lives need to follow a diet that limits phenylalanine, which is found mostly in foods that contain protein. PKU is a disease caused by a recessive allele (p). Normal individuals have at least one dominant allele (P). Problem: If two cousins marry, one who is a carrier (heterozygous for PKU), the other with PKU, please predict the probability that they could have children with the following genotype or phenotype: a) With PKU ? b) Carriers ? c) Normal (No PKU; Not Carrier)

USE Python 2.7(screen shot program with output)

the task is: takes in a list of protein sequences as input and finds all the transmembrane domains and returns them in a list for each sequence in the list with given nonpolar regions and returns the lists for those.

1. This code should call two other functions that you write: regionProteinFind takes in a protein sequence and should return a list of 10 amino acid windows, if the sequence is less than 10 amino acids, it should just return that sequence. (initially it should grab amino acids 1-10…the next time it is called it should grab amino acids 2-11…) for each sequence in the list.

testcode:

"protein='MKLVVRPWAGCWWSTLGPRGSLSPLGICPLLMLLWATLR''

the regionProteinFind returns:['MKLVVRPWAG','KLVVRPWAGC','LVVRPWAGCW','VVRPWAGCWW','VRPWAGCWWS','RPWAGCWWST','PWAGCWWSTL','WAGCWWSTLG','AGCWWSTLGP','GCWWSTLGPR',
'CWWSTLGPRG','WWSTLGPRGS','WSTLGPRGSL','STLGPRGSLS','TLGPRGSLSP','LGPRGSLSPL','GPRGSLSPLG','PRGSLSPLGI','RGSLSPLGIC','GSLSPLGICP','SLSPLGICPL','LSPLGICPLL','SPLGICPLLM','PLGICPLLML','LGICPLLMLL','GICPLLMLLW','ICPLLMLLWA','CPLLMLLWAT','PLLMLLWATL','LLMLLWATLR']

2nd testcode;

protein=MP

region protein sequence should return: ['ME']

2. A second function called testForTM , which should calculate and return the decimal fraction of ten amino acid window which are nonpolar for each sequence in the list. the nonpolar regions are (A,V,L,I,P,M,F,W). my code for this is:

def testForTM(AAWindow):
totalNP= 0
nonPolarList=['A', 'V', 'L', 'I', 'P', 'M', 'F', 'W']
for aa in AAWindow:   
if aa in nonPolarList:   
totalNP+=1
return totalNP/10.0 #THIS SHOULD DEVIDE BY len(AAWindow) so it works for sequences less than 10 length like 'MP'

3. The last function,tmSCANNER should call the get protein region and test for TM and Ultimately, as a result the code should be used to scan each protein sequence in the list as input generating list of numbers of non polar for each protein sequence which measures the fraction of nonpolar residues in each 10bp window(it slides 10 amino acids at a time until it is at the last aa window of a protein sequence with any length and give the lists for those. The code should output what is displayed below.

#Test code for TMFinder

input=> listOfProtein=['MKLVVRPWAGCWWSTLGPRGSLSPLGICPLLMLLWATLR', 'MARKCSVPLVMAWLTWTTSRAPLPH', 'MPWPTSITXXXXXXSWSPEWLSSGLRSILGWEQPRVSHKGHSHEWHRRP']

tmValuesList=TMFinder(listOfProtein)

print 'The list of TM values are:', tmValuesList

as a result it should print out this list:

["protein 1:'MKLVVRPWAGCWWSTLGPRGSLSPLGICPLLMLLWATLR'", 'TMValue:[0.7, 0.6, 0.7, 0.7, 0.6, 0.5, 0.6, 0.5, 0.5, 0.4, 0.4, 0.4, 0.4, 0.3, 0.4, 0.5, 0.4, 0.5, 0.4, 0.5, 0.6, 0.7, 0.7, 0.8, 0.8, 0.8, 0.9, 0.8, 0.9, 0.8]',"protein2:'MARKCSVPLVMAWLTWTTSRAPLPH'", 'TMValue:[0.6, 0.6, 0.6, 0.7, 0.8, 0.8, 0.9, 0.8, 0.7, 0.6, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5]',"protein3:'MPWPTSITXXXXXXSWSPEWLSSGLRSILGWEQPRVSHKGHSHEWHRRP'",'TMValue:[0.5, 0.4, 0.3, 0.2, 0.1, 0.1, 0.2, 0.1, 0.2, 0.2, 0.3, 0.4, 0.4, 0.4, 0.4, 0.5, 0.4, 0.4, 0.4, 0.5, 0.4, 0.4, 0.4, 0.4, 0.5, 0.4, 0.5, 0.5, 0.4, 0.3, 0.3, 0.2, 0.2, 0.2, 0.1, 0.2, 0.1, 0.1, 0.1]']

This is time sensitive.Thank you for the help!!!

Theory of enzymes:

True or False:

___ Enzymes catalyze reactions by increasing the reaction free energy

___ Enzyme are remarkable for their substrate specificity.

___ Enzyme can convert light energy into chemical or mechanical energy

___ Catalytic residues in enzymes can include amino acid side chains, RNA bases, and other organic cofactors

___ Michaelis-Menten kinetic theory only applies to enzymes with single substrates

___ Enzymes bind transition-state analogs more tightly than substrates

___ At high substrate concentration, reactions are rare-limited by how rapidly enzymes convert substrates into products

___ K_m=K_D when k_cat>>k_-1

___ k_cat/K_{M is equivalent to a second-order rate constant}

___ Enzymes can use electrostatics to exceed the rate of diffusion (bimolecualr collision of substrate with enzyme's active site)

___ Drugs that bind to an allosteric site on an enzyme cause a decrease in k_cat