only question b complete Search on google for images of proteins and DNA, in particular those showing their atomicstructures. Write captions on the images you select, one for a protein and one for DNA, and a briefdescription to introduce these figures. (Familiarizing yourselves with structures of proteins andDNA will help you work out the following problems.)(a) Draw the complete linear structure of a small peptide sequence GAKD.(b) At pH=7.0, how many net charges does this peptide carry?A TATA box often occurs upstream of a gene in DNA. Draw the linear strand of a TATA sequence,showing base and sugar rings, as well as the phosphate groups.

Peptides are composed of twenty standard amino acids. The twenty standard amino acids differ from…

Answered: (a) Draw the complete linear structure…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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What kind of information is stored in protein three-dimensional structure. Why 3D structure prediction is important? In detail discuss the major factors involved in 3D protein structure prediction and evaluation computationally.
Before high performance liquid chromatography (HPLC) methods were devised for the separation and analysis of small peptides, electrophoresis on a paper support was frequently used. Separation was affected on the basis of the charge on a peptide at different pH values. a. What is the charge of the primary structure of proteins at pH = 2.0, 4.0, 6.0 and 11.0 of the following proteins. Draw their structures and predict their net charge. i.) Lys- Gly- Ala- Glyii.) Lys- Gly-Ala-Gluiii.) His- Gly- Ala- Gluiv.) Glu- Gly- Ala -Gluv.) Gln-Gly-Ala-Lys b.) Calculate the pI of the following primary structure of protein c.) the migration toward the cathode, the negative pole; A for the migration toward the anode,the positive pole; and O if the peptide remains stationary.
Proteins are composed of both polar (hydrophilic) and nonpolar (hydrophobic) amino acids. Assume you are starting with fresh homogenized/pasteurized cow's milk. A major protein in the milk is a whey protein known as alpha-lactalbumin (in a tertiary structure). If this protein is denatured (for example by the introduction of heat, acid, or other means), discuss how and why scientifically it could end up becoming an effective emulsifier in a product containing olive oil and red wine vinegar.
The amino acid sequence of three peptide fragments are shown below. Peptide 1: QAMGRAGDLKYLGLHSV Peptide 2: ALMALFMVMALVLVSVLFIA Peptide 3: MVEDLLKQIARYLISE (a) Circle all of the charged residues in peptide 1 (assume pH =7.0). Box all of the aromatic residues in peptide 2. Underline all of the nonpolar residues in peptide 3. (b) Determine the net charge of the predominant form of each of the peptides at pH 4.5 and pH 11.5. Assume the ionizable groups have the pKa values listen in Table 2.1 of your text. (c) Which of these peptides would be most likely to be found as an alpha helix in a soluble (cytoplasmic) protein? Which would be most likely to be found as an alpha helix in a transmembrane protein? Which would be least likely to form an alpha helix of any kind?
What type of information is contained in the three-dimensional structure of proteins? What is the significance of 3D structure prediction? Discuss in depth the key aspects involved in 3D protein structure prediction and computational assessment.
Discuss and compare the potential contributions for tertiary structure in a protein for the side chain of histidine at each of the following pH values: pH 3, pH 7 and pH 10. (pKa of R group = 6.5). Mathematically describe (show work) and use a full paragraph when discussing each pH (reminder: grammar and spelling will be graded.
Consider the sequences (i-iv) that represent sections of a protein. ) -АЕEAAAAMAАAАMAAY ii) -KVIVVVTVVTVVVKVV- iii) -GPPGPPGPPGPPGPPGPP- iv) -WYFWYFWYFVVFFFVV- Which of the following statements is likely to be true? O Sequence (iv) is likely to have an alpha-helix structure. O Sequence (i) is likely to have an alpha-helix structure and sequences (i) and (iv) are most likely to have beta- sheet structures O Sequence (ii) is ikely to be a metal-binding domain. O Sequence (i) is likely to have a beta-sheet structure and sequences (ii) and (iv) are most likely to have alpha- helix structures O Sequence (ii) is most likely have a beta sheet structure with a hairpin turn.
You have a peptide that has the following amino acid sequence: GPMG Draw the structure of the polypeptide's most protonated form, and its charge. Then draw the structures of the increasingly deprotonated forms, along with their charges. Use the information from these structures to calculate the pl (isoelectric point) of the peptide using the pKa values provided in the table below. Write the pl as x.yz, for example, 7.62 or 3.09. Group Terminal a carboxyl group Aspartic acid Glutamic acid Histidine Terminal a-amino group Cysteine Lysine Tyrosine Arginine Acid EM 2-0" + H -N H H N-H H N-H T Base 1 1. تر H -5 H H O™ N-H Typical pK, 3.1 4.1 6.0 8.0 8.3 10.8 10.9 12.5
Before high performance liquid chromatography (HPLC) methods were devised for the separation and analysis of small peptides, electrophoresis on a paper support was frequently used. Separation was affected on the basis of the charge on a peptide at different pH values. a. Calculate the pI (isoelectric point) of the following primary structures of the following protein i.) Lys- Gly- Ala- Glyii.) Lys- Gly-Ala-Gluiii.) His- Gly- Ala- Gluiv.) Glu- Gly- Ala -Gluv.) Gln-Gly-Ala-Lys b.) the migration toward the cathode, the negative pole; A for the migration toward the anode, the positive pole; and O if the peptide remains stationary.
A researcher isolates a new protein and finds that it contains 0.755% serine by weight upon amino acid analysis. The molecular mass of serine is 105 g.mol-¹. What is the minimum molecular mass for the protein assuming only one Ser residue per protein molecule? mmin = The researcher estimates the molecular mass of the protein using gel electrophoresis. From this estimated molecular mass, the researcher concludes the protein contains 3 Ser residues. What is the estimated molecular mass of the protein as shown by gel electrophoresis? g.mol-¹ mest = g.mol-1
Provide the number of polypeptide chains present andthe number of amino acid residues in each chain. for https://www.rcsb.org/structure/6j20 Provide the molecular weight of the protein orprotein complex and the total number of atoms. (All of this information can be found in the PDBpage.) Create a figure (available in the PDB page) that shows the topology of your protein, i.e.the secondary structures adopted by different regions of the protein (alpha helix, beta strand).Make sure to also provide a figure legend that helps interpret the figure and appropriate figurecaption that briefly explains the figure.
The following is an assignment question I wrote and then submitted to the AI chatbot – ChatGPT: a poly glutamic acid peptide can form an alpha helix at pH 2.4 but not at pH 7.5, why? Here is the response the AI gave me: “Poly glutamic acid is a peptide composed of multiple units of the amino acid glutamic acid. At low pH, such as pH 2.4, the glutamic acid residues in the peptide are protonated and carry a positive charge. At high pH, such as pH 7.5, the glutamic acid residues are deprotonated and carry a negative charge. The formation of an alpha helix in a peptide is primarily driven by hydrogen bonding between the amide groups of the peptide backbone. At low pH, the positive charges on the glutamic acid residues can interact with the negative charges on the backbone amide groups, stabilizing the helix conformation. However, at high pH, the negative charges on the glutamic acid residues repel the negative charges on the backbone amide groups, destabilizing the alpha helix…

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(a) Draw the complete linear structure of a small peptide sequence GAKD. (b) At pH=7.0, how many net charges does this peptide carry?