Bio Genetics Review

E. PROTEIN PRIMARY STRUCTURE ELUCIDATION. 1. Determine the primary structure of the protein described below. Write the final sequence using the corresponding three-letter code for each amino acid. Example: M-F-Y-R should be written as Met-Phe-Tyr-Arg Treatment with cyanogen bromide and sequencing yields the following peptide fragments: o D-M o R-A-Y-G-N o L-F-M Chymotrypsin digestion and sequencing yields the following peptide fragments: o G-N D-M-L-F o M-R-A-Y o o

Please, need help with the explanation and diagram. The structure and properties of poly peptides: A) Describe the type of bonding that would occur when three amino acid monomers (include a diagram of the amino acids) form a tripeptide and describe how such bonds could be formed. B) During the period of Chemical Evolution, what is the significance of the structure of the polymer formed? (Include a diagram)

1.Describe in detail how to detect the primary structure of protein. 2.Given a mixture of lysine,histidine and cysteine.The isoelectronic point of the amino acids are as follows: histidine:7.64 lysine:9.74 cysteine:5.02 Show how you will separate the mixture into the pure forms. State and describe any instrument that you will use to separate the components in the mixture.

Solve the peptide problem. 1. Write the structure of tripeptide in which the first amino acid is Trp, the second one is Glu, and the third one is Asp. Mark its N- and C-ends. What is the pl area of the tripeptide (>7)? Explain. What is the charge of the tripeptide placed in a buffer solution with pH 9,2? Explain. How do you think, would the Xanthoprotein reaction be positive in the solution of this peptide? Explain.

3. A. Briefly discuss the four levels of structure in proteins. Knowing that the 3-dimensional shape of a protein is important to its function, discuss on a qualitative basis whether the changes below will likely alter the function of a protein, justifying your answer with why or why not. B. What would happen to a protein's functionality if a serine residue were replaced with threonine? C. What would happen if serine were replaced with leucine? D. What would happen if serine were replaced with cysteine? E. What would happen if aspartic acid were replaced with tryptophan in the part of the protein (an enzyme) that serves as an active site to catalyze a reaction? F. What would happen if aspartic acid were replaced with tryptophan in a non-active site?

1.a.If this molecule was the side chain of an amino acid, in a protein, what tertiary structure stabilizers could be present? b.Make a key and use color to highlight what part of you structure can be stabilized in each manner?

I. Apply your knowledge on the basic structure of amino acids by creating a polypeptide chain that is 4 amino acids long showing its structural formula, II. Why are R groups important in amino acids?

. Pick all that are TRUE regarding analysis of quaternary structures of proteins using polyacrylamide electrophoresis:I. The added β-mercaptoethanol disrupts S--S bonds bridging the polypeptide chains causing the appearance of higher Rf bands compared to the native protein run. II. Heating up any protein before subjecting to SDS-PAGE will always result in the formation of more than one band.III. A good asymmetrical gel layout would be : (Lane 1) MW ladder, (2) native protein, (3) protein + β-ME, (4) protein + HCL, (5) protein + β-ME + HCl.IV. Formation of a single band in the protein + β-ME + HCl run, whose Rf is lower than the native run, could be indicative that the protein is a homodimer.A. I onlyB. I and IIC. II and IIVD. None is true

1.Describe in detail how to determine the primary structure of protein. 2.You have been given a mixture of lysine, histidine and cysteine.The isoelectric point of the amino acids are as follows; histidine 7.64 lysine:9.74 cysteine:5.02 Show how you will separate the mixture into the pure forms. State and describe any instrument that you will use to separate the components in the mixture.

Describe the tertiary level of protein structure and state the type of interactions present.14. With the aid of diagrams, explain the difference between spontaneous and non￾spontaneous enzyme reactions15. Briefly explain how enzymes decrease the activation energy of biochemical reactions.16. What is the difference between a nucleoside and a nucleotide?17. A nucleic acid has 13% of adenine. Determine the composition of guanine, cytosine and thymine.

B- Calculate the missing value of the amino acids listed in the table below. Amino acid phenylalanine pKal pKa2 pl 1.83 9.13 Serine 9.15 5.56 Asparagine 2.02 5.41

ASAP. NOTE: ANSWER ALL THE SUBQUESTIONS TO RECEIVE A LIKE. THANK YOU. CHOOSE THE ANSWER FROM THE FOLLOWING CHOICES: Phosphodiester Bond Glycosidic Bond Ester Bond 1.1. It is the bond present in nucleotides which combines the nitrogenous base and the pentose sugar together. 1.2. It is the bond present in nucleotides which joins the phosphate group and pentose sugar together. 1.3. It is the bond present between nucleotides, combining them together to form DNA and RNA strand.

1. Draw an amino acid. Join it to another amino acid via dehydration synthesis to make a dipeptide. Label all parts of each amino acid and the peptide bond. (See figure 4.3 for inspiration) 2. Now draw two dipeptides one on top and one below it-connect the dipeptides on top to the ones on the bottom with a line to show that they are two strands of the same protein molecule. 3. Connect the two dipeptides via hydrogen bonds (see figure 4.6 for inspiration). Label the hydrogen bonds. Be sure to connect the correct atoms via H-bonds (Many students connect incorrect atoms. Focus on which atoms will have opposite partial charges to form H-bond). You have drawn a secondary structure of proteins known as beta sheets. Focus on the fact that that secondary structure ns between backbone elements like carbonyvl groups and amide groups.

Tt O 8. What are the driving forces that promotes tertiary -3D and quaternary -4D structure formation of proteins. Provide specific examples of the interactions that drive the formation of 3D and 4D structures?

01 Description Please draw the structure of the 19 L-a-amino acids and proline in any form, as you prefer. You may want to use a letter-size sheet or larger, it's up to you. Guiding principle: You want to understand the differences among amino acids. Although you may want to only draw the R-group it's preferable to draw it along with the rest of the molecule (i.e., the Ca, the amino group and the carboxyl group). Here are some examples (your drawings should not limited to the following styles): NH₂ OH Alanine H H O OH Proline lysine alarmy stock płwłos Tryptophan OH COOH | H₂N-C-H CH₂ Phenylalanine arginine

pls answer the following question. -Which amino acids contain the following?a.sulfur/sulfhydryl group b. aromatic group c. imidazole ring d. guanidine group e. indole group -Classify the following proteins according to their biological function: casein, albumin gluten, and myoglobin. -Which levels of protein structure organization are lost during hydrolysis and denaturation? -What is the Beer-Lambert's Law? Why is it relevant to the quantitative analysis of proteins? -What are the other protein components of milk aside from casein?

Select all that apply. The primary structure of a protein: is determined using NMR methods. can be determined as long as the peptide is not broken or denatured. is determined by cleaving the protein into smaller peptides. is its sequence of amino acids. is determined by combining overlapping peptide segments to obtain the sequence of the entire protein.

8. Multiple choice. Which of the following is not a method that can be used to determine the 3° structure of proteins? (2 pts) a) Protein X-ray crystallography b)) Circular dichroism c) Cryogenic electron microscopy d) Protein NMR 9. Multiple choice. Approximately what overall yield can you expect from the solid phase peptide synthesis (SPPS) of a "10-mer" (a 10 amino acid peptide), if the yield from each step is 85%? (2 pts) 23% b) 20% c) 85% d) 71% 10. Multiple choice. Which protein purification method is best for an experiment in which you want to purify a monomeric form of a protein away from a tetrameric form? (2 ptrs) (-His a) Affinity chromatography S b) High pressure liquid chromatography c) lon exchange chrommatography d) Size exclusion chromatography 2. I1. Short answer. What is the Edman degradation experiment useful for? (3 pts) purdinate an for prry structers steps .

A/B: 3. Amino acid residues and peptide bonds (a) Draw the chemical structure of F, S and H joined by peptide bonds and also connected to neighboring residues as found in a protein. (b) Include all charges as expected at physiological pH (pH = 7.5) () Rank these three amino acid residues by hydrophobicity, pKa, and by nucleophilicity (d) For the central amino acid residue, identify the phi and psi dihedral angles by drawing a curved arrow indicating rotation about the chemical bond. (e) What group(s) eclipse each other if Phi = 0 degrees? Words and Pictures. (f) While Phi = 0 is not well tolerated, Psi = 0 is not uncommon, a so-called “allowed" but not most-favored region of the Ramachandran plot. What group(s) eclipse each other if Psi = 0 degrees and why is this less problematic than the situation created by Phi = 0. Words and Pictures H₂N* Pka: 9.13 H₂C с C._hydrophobicity: 1. phenylalanine (most) 2. Serine 3. Histidinelleast) ده H H. HIN OH I CH₂ CHO pka: 1. Serine (nighest) 2.…

Identify. Examine the following four amino acids (A-D): Co0 "H,N- CH "H,N CH "H;N-CH "H,N CH CH2 CH2 CH, CH CH2 CH3 CH, CH2 OH NH," B D What are their names, three-letter abbreviations, and one-letter symbols?

Organic Molecules and Carbohydrates How many covalent bonds are formed by one carbon, and why? When a double covalent bond is formed, how many electrons are being shared? 3. Given a molecule that was drawn incorrectly, indicate which carbon does not have a sufficient number of bonds. 1. 2. Given a molecular formula (such as CH4) identify the molecule as inorganic or organic. 5. Given an organic molecule (molecular or structural formula) indicate whether the molecule is hydrophobic or hydrophilic and why. 6. Given two molecules, identify whether they are isomers of each other and explain why. 7. Explain the importance of functional groups. Be able to identify and name all functional groups. Define and explain the relationship of the following words: macromolecule, monomer, dimer and polymer. 9. Describe the chemical reactions of dehydration synthesis and hydrolysis in terms of what occurs, and what is accomplished. (Which can bond together monomers? Which splits a dimer or polymer into…

b. What is the difference between the 3' and the 5' ends of a nucleotide chain? C. Do the chains run the same way? d. How are the chains connected? e. Which bases bond to each other? f. What kinds of bonds hold the chain together? 3. What are the main differences between RNA and DNA? 4. Distinguish between the structure of pyrimidines and purines. Explain why adenine bonds only to thymine. 5. Name the five nitrogenous bases in the table below, and put an X in the correct column for each base. Then indicate if the base if found in DNA (D), RNA (R), or both (B) hp

age 2 of 9 FI 1. Recognize the following types of biomolecules when given images such as the ones below and on the next page: ● glucose (which is a monosaccharide) HO 0 of 618 words F2 ● ● ● amino acid protein (recall a protein with less than 50 amino acids can also be called a peptide whereas a protein with 50 or more amino acids can also called a polypeptide) steroids polysaccharide ● • triglycerides ● ● phospholipids ● ● DNA RNA CH₂OH H OH H H OH English (United States) 20 F3 $ +: OFF Draw with Add Pen Trackpad 000 % F5 MacBook Air A DNA F6 & ◄◄ F7 * ► 11 F8 Focus F9 R F10 - F11 212

a.Describe the bonds which hold a quaternary protein molecule together. b. Discuss the reasons why glycine and proline are not usually found in an alpha helix of proteins.

Name: Protein Structure 1. Draw the structure of each peptide below at pH 7.0. Using the structure, predict which peptide is more soluble in water at pH 7.0. Explain why using chemical details. RISK PALM

4. Let’s build a polypeptide chain a. Using your arsenal of 4 amino acids, write out the primary structure of an 8 amino acid long polypeptide that you might be called amphipathic and thus allow it to form a micelle in aqueous solution, identify amino acid 1 through 8 as well as the location of the amino and carboxy termini of the polypeptide. b. Explain why this polypeptide would be considered amphipathic and draw what the micelle might look like in water. c. Taking amino acids 3, 4, and 5, draw the molecular structure of this particular stretch of polypeptide chain. Along the backbone linkage of the polypeptide identify the peptide bonds with a PB, the bonds with free rotation FR, and bonds with limited rotation LR.

1. Define proteins 2. Discuss the different properties of proteins 3. Discuss the classification proteins based on the structure of protein 4. Discuss the classification proteins based on composition 5. Discuss the classification proteins based on functions 6. Discuss the solubility of protein in water 7. Discuss the denaturation and renaturation 8. Discuss the protein metabolism 9. Discuss the chemical properties of protein 10. Define amino acids 11. Discuss the non-essential and essential amino acids

1. Is there more than one way to fold a protein, given the conflicting demands of the different "R" groups and the protein existing in a watery environment? 2. Explain what an R group is. 3. Compare the backbone of a polypeptide with that of a nucleic acid. 4. Proteins perform critical functions in all of our cells. Without proteins, life wouldn’t exist. Think of some specific proteins and describe what function they perform.  5. Explain the difference between secondary and tertiary protein structures.

3c) The 3 structure of a protein incorporates any 2 structure the protein has, but results primarily from interactions between amino acid side groups. Name two different amino acids whose side groups could participate in each type of interaction given below under physiological conditions (pH 7.2-7.5). Ionic bonding: Hydrophobic clustering: Hydrogen bonding: