in determining the structure of a fully folded protein?involving the amino acid side chains of the polypeptide. Which has the largest effect5.hydrogen bondingionic interactionsa)b)c)d)hydrophobic interactionsvan der Waals interactionsnone of the aboveThe misfolded, insoluble, and aggregated proteins characteristic of Alzheimer'sdisease and Parkinson's disease are known as:zymogensb)c)d)e)open quaternary structure proteinsprotein domainsamyloid depositsmolecular chaperones6.

The tertiary structure of the protein is the three-dimensional conformation of the protein. It is…

Answered: involving the amino acid side chains of…

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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Amino acid structure and composition: Assuming physiological pH conditions, draw the peptide backbone of a protein composed of four amino acids. The protein is a) overall positively charged b) capable of forming disulfide bond with another protein c) has two amino acid that can participate in hydrogen bond formation d) one peptide bond in cis conformation you must show the complete name, single letter abbreviation and structure of each amino acid. Make sure to highlight the peptide bond that is in cis conformation
A researcher performed an SDS-PAGE experiment (with 2- mercaptoethanol) on a mixture containing 3 peptides: (1) NAKQLEPDEYRTSC (2) EQCNLKGATCPSASWSGTQ (3) SCKRKA Note that I've bolded positively charged residues and underlined negatively charged residues In which of the gels below are the bands properly labeled? A |(1) (3) |(3) |(2) |(1) |(2) |(2) |(1) |(1) |(3) (+) (3) |(1) (2) |(3) |(2)
Polypeptide Handout Amino acids are linked together to form a peptide bond through an aminidation reaction. The-COO group of one amino acid reacts with the -NH3+ of another amino acid. When two are more amino acids are linked together a peptide is formed. Draw the Following Polypeptides: a) Gly-Ser-Met-Lys b) Lys-Pro-Val-His c) Trp-Thr-Leu-lle d) Cys-Met-Phe-Glu e) G-L-A-R-E f) G-L-A-D g) F-H-E-D h) K-E-M-S
Currently, aspartic acid is forming an ionic interaction with arginine in a protein. Part a) If arginine is replaced with glutamic acid, would the ionic interaction have its stability increased, decreased, or have no effect on the ionic interaction? Part b) If arginine is replaced with Lysine, would the ionic interaction have its stability increased, decreased, or have no effect on the ionic interaction? Part c) If arginine is replaced with isoleucine, would the ionic interaction have its stability increased, decreased, or have no effect on the ionic interaction?
Rationalize the following observations.(a) Serine is the amino acid residue that can be replaced with theleast effect on protein structure and function.(b) Replacement of tryptophan causes the greatest effect on protein structure and function.(c) Replacements such as Lys -> Arg and Leu -> Ile usually havevery little effect on protein structure and function.
Which of the following statements are False? (i) Parallel b-sheets characteristically distribute hydrophobic side chains on both sides of the sheet, and antiparallel B-sheets are usually arranged with all their hydrophobic residues on one side of the sheet. (ii) Planarity of the peptide bond means that no rotation occurs about the N-Ca bond while rotation is allowed about the C(O)-N and Ca-C(O) bonds. (iii) Silk fibers consist of fibroin proteins consisting of alternating A and G or S residues. (iv) If an aspartic acid residue were present in the interior of a globular protein, it would most likely be deprotonated and thus negatively charged.
9. A) Please write down the names of the following protein folds. A B C B) Which one(s) is made of more than one polypeptide? D E 000 C) Give an example of a protein containing the motif in C and explain how the structure of this motif facilitates function. 10. What is Levinthal's paradox? Describe the paradox and explain the conclusion to which it led.
An oligopeptide has the following amino acid sequence: NH2-Ala-Glu–Leu–Trp–Tyr-Ser–Gly–Lys–Leu-Ala–Arg-Ala-Phe-Ile-Pro–Gly-COOH a) Estimate the net electric charge of the molecule at pH 8.0 and pH 11.0. b) If the above peptide is passed through a cation exchange chromatographic column (that is, the matrix of the column has negative charges) stabilized at pH 8.0, would you expect it to be retained on the column? c) Indicates the number of fragments, and the sequence of each of them, that would be obtained when treating the peptide in question with: i) trypsin, ii) chymotrypsin.
The major difference between a protein molecule in its native state and inits denatured state lies in the number of conformations available. To a firstapproximation, the native, folded state can be thought to have one conformation. The unfolded state can be estimated to have three possible orientations about each bond between residues.(a) For a protein of 100 residues, estimate the entropy change per moleupon denaturation.(b) What must be the enthalpy change accompanying denaturation to allow the protein to be half-denatured at 50 °C?(c) Will the fraction denatured increase or decrease with increasingtemperature?
The major difference between a protein molecule in its native state and in its denatured state lies in the number of conformations available. To a first ap- proximation, the native, folded state can be thought to have one conforma- tion. The unfolded state can be estimated to have three possible orientations about cach bond between residues. (a) For a protein of 100 residues, estimate the entropy change per mole upon denaturation. (b) What must be the enthalpy change accompanying denaturation to allow the protein to be half-denatured at 50 °C? (c) Will the fraction denatured increase or decrease with increasing temperature?
In each of the following pairs of amino acids, identify which amino acid would be more soluble in water: (a) Ala, Leu; (b) Tyr, Phe; (c) Ser, Ala; (d) Trp, His
13) Like beans, eggs would be most likely to be deficient in at least one essential amino acid. True or False 14) There are hydrophilic interactions between the following R groups in the tertiary structure of a protein. True or False -CH2 CO- and -CH2CH2CH2CH2NH3+ 15) In digestion, proteins are broken down into amino acids in a hydrolysis reaction. True or False 16) The ionized form of all ami o acids at physiological pH (7.4) has a net charge of zero. True or False

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