As part of development of a new test for detection of misuse of human erythropoietin (EPO) by world athletes, Sydney researchers have studied the signals arising from native and administered EPO within 2D gels of urine samples. “The amino acid sequence of endogenous human erythropoietin (EPO) and (rEPO) is identical and consist of 165 amino acids, with three N-glycosylation sites and one O-glycosylation site. This gives an apparent molecular weight of 34 kDa by SDS-PAGE of which approximately 40% by weight is sugar content. Different micro-heterogeneity in glycosylation profiles (in particular, the number of sialic acid residues attached and the length of the sugar chains) between EPO and rEPO gives each form of the protein a different series of isoelectric points (pI) and a small change in molecular mass. The experimentally determined pI ranges are approximately 3.7–4.7 and 4.4–5.1 for EPO and rEPO, respectively. …. Analysis of unknown urine samples was carried out by two-dimensional electrophoresis. Total separated urinary proteins were visualized on the gel with SYPRO Ruby (Molecular Probes, USA) per the manufacturer’s instruction. After cutting the protein spots, the protein was digested by adding trypsin dissolved in 50 mM ammonium bicarbonate and incubated at 30o C overnight. The peptide solution was desalted, concentrated and spotted onto a MALDI plate alpha-cyano-4-hydroxy-cinnamic acid dissolved in 70% (v/v) acetonitrile and 0.1% (v/v) trifluoroacetic acid. MALDI-TOF MS was performed with an Axima CFR instrument (Shimadzu Kratos, UK), equipped with N2 laser (337 nm, 10 Hz repetition rate).”

Identification of other abundant urinary proteins pH range 3-7 is given below :

Tamm Horsfall glycoprotein (THP) – with mass (Da) 69715 and pI 5.05

Alpha-1-antichymotrypsin (AC)   - with mass (Da) 47651 and pI 5.3

Alpha-2-thiol proteinase inhibitor (PI) - with mass (Da)   71946 and pI 6.3

Alpha-2-HS-glycoprotein precursor (HSGP) - with mass (Da) 39325 and pI 5.4

Questions.

(a) Suggest the actual types of amino acid sidechains subject to glycosylation in EPO.

(b) Different rEPO products are currently available.

(i) Why might these products differ from one another in sugar content and structure?

(ii) Give two reasons why this chemical difference affects the 2D gel behaviour of the isoforms present

(c) Why are the protein components shown above have such a high precision of mass accuracy?

Note:

Please give explicit and comprehensive explanation .

4. Amino acids are weak polyprotic acids. There they will readily form ________ systems which control the pH of a system.

a) Give an example of a biological system within the human body that is buffered.
b) What is the pH of a glutamic acid solution if the alpha carboxyl group is 1⁄4 dissociated?

c) Lysine is an amino acid with a basic side chain. Often, basic side chains accept protons and are thus positively charged. What could you do to generate a lysine that was not positively charged?

1- All of the following are types of modifications that can result in an active, functional protein EXCEPT:

a. Covalent disulfide bonds between cysteine amino acids

b. Cleavage of proteins

c. Glycosylation

d. Addition of lipids to the N- or C-terminus

e. Amyloidosis

2- All of the following are reversible protein modifications EXCEPT:

a. Proteolysis

b. Phosphorylation

c. Acetylation

d. Methylation

e. Ubiquitination

3- How can protein-protein interactions regulate enzymes?

a. These interactions change the pH of the local environment, causing enzymes to be less efficient

b. These interactions change the conformation of the enzyme, which may inactivate the enzyme

c. These interactions change the enzyme’s amino acid sequence, which may enhance enzyme activity

d. These interactions prevent translation of the enzyme’s mRNA, leading to lower levels of the enzyme

e. These interactions send enzymes out of the cell, so that they can no longer catalyze cellular processes

4. how do crebs cycle and glycolysis communicate?

a. who is the molecule in crebs cycle that influences the glycolysis pathway?

b. who is the enzyme that is relevant to that in crebs cycle?

c. to which enzyme in glycolysis pathway will the molecule in question a attach?

d. how does this bond affect the activity of the enzyme from b in glycolysis pathway?

1. Synthesis of amino acids are homeostatically regulated such that an overproduction of a particular amino acid is prevented. Explain how this works in the trp operon of E.coli at

a) the level of the enzyme pathway and b) the level of gene regulation.

2. What is the role of a repressor of gene expression for lactose consuming bacteria? (Assume absence of glucose.)

3. Cells control their level of all proteins by regulating both synthesis and degradation. Describe the role of ubiquitination and the proteasome in regulating the level of cellular proteins.

please help me, thank you

An aminoacyl-tRNA exhibits which one of the following characteristics?

Concerning generation of ATP from glucose during glycolysis which of the following statements is not correct?

Insulin results in phosphorylation of acetyl-coA carboxylase, which stimulate fatty acid synthesis?

True

False

Which of the following statement(s) is or are correct?

Which of the following would be observed in a person who is resting after an overnight fast?

List major cofactors of metabolic enzymes discussed in this course, point out their precursors, describe their roles in metabolic reactions, and provide one reaction for each cofactor participates as an example of a general pattern. It does not have to be all the metabolic pathways listed but please be at least 3 or 4. The metabolic pathways are

1). Krebs cycle

02). Oxidative phosphorylation

03). Glycolysis and lactate formation

04). Glycogen synthesis & breakdown

05). Gluconeogenesis

06). Beta oxidation of fatty acids

07). Pentose phosphate pathway

08). Biosynthesis of fatty acids & phospholipids

09). Biosynthesis of cholesterol & cholesterol dynamics

10). Biosynthesis of amino acids & one carbon units

11). Biosynthesis of nitrogenous molecules

12). Disposal of nitrogenous molecules & urea cycle

1.How do D -amino acids differ from L-amino acids? What biological roles are played by peptides that contain D -amino acids?

2.Which amino acid is technically not an amino acid? Which amino acid contains no chiral carbon atoms?

3.For each of the following, name an amino acid in which the R group contains it: a hydroxyl group, a sulfur atom, a second chiral carbon atom, an amino group, an amide group, an acid group, an aromatic ring, and a branched side chain.

4.Identify the polar amino acids, the aromatic amino acids, and the sulfur-containing amino acids, given a peptide with the following amino acid sequence:

Glu-thr-val-asp-ile-ser-ala

Practical electronics strongly favors binary representations for encoding information (two-state; 0 or 1). In DNA, biology uses a quaternary representation of four different nucleobases (four-state; cytosine [C], guanine [G], adenine [A] or thymine [T]) to code for the amino acids with which all the proteins in our bodies are constructed. All proteins are long chemical chains assembled from 20 different types of amino acids.

a) What is the minimum number of nucleobase “digits” required to code for the 20 different amino acids? (Groups of nucleotides, each coding for a single amino acid in a protein chain, are called “codons” by biologists.) (Hint: How many four-state "digits" are needed to represent 20 unique things?)

b) A binary representation is used to store the human genome on a digital computer. How many bits are required to represent each nucleotide in the genetic code? (Note: There is one nucleobase in a nucleotide)

c) The DNA in a human genome consists of about 3 billion (3,000,000,000) nucleotides (base pairs). How many bits are required to store this information in a binary format?

d) The memory in a computer is usually organized in groups of 8 bits, called “Bytes.” How many bytes of memory are required to store your genome in a digital computer?

choose the correct answer

1)

The Second Law of Thermodynamics simply states that

Group of answer choices

disorder (or entropy) in the universe is continually increasing.

energy can be recycled through the universe.

energy can be created but not destroyed.

energy cannot be created or destroyed, just changed from one form to another.

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2)

The non-protein components that aid in enzyme functioning are called

Group of answer choices

macromolecules

cofactors

reactants

substrates

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3)

Enzymes are very specific in their choices of substrates because each different enzyme has an active site that

Group of answer choices

has a certain unique amino acid to fit each substrate.

depends on unusual amino acids not common in proteins.

is shaped to fit a certain substrate molecule.

passes electrons from one part of the substrate to another.

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4)