Proprep - Biochemistry - Protein's Three Dimensional Structure - workbook

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Biochemistry Workbook For more information and all the solutions, please go to www.proprep.com For any questions please contact us at 1-818-273-1725 or info@proprep.com © All rights in this workbook reserved to proprep™ 1 Table of Contents Protein's Three Dimensional Structure ............................................................................... 2 Primary Structure ..................................................................................................................... 2 Higher Order Structure ............................................................................................................ 5

Biochemistry Workbook For more information and all the solutions, please go to www.proprep.com For any questions please contact us at 1-818-273-1725 or info@proprep.com © All rights in this workbook reserved to proprep™ 2 Protein's Three Dimensional Structure Primary Structure Questions What is the defining factor that distinguishes proteins, how do they differ chemically? We introduced several Levels of Protein Structure have several levels of complexity. Please mention how many and what each one of them is. Describe how differences in primary structure of proteins are informative. Protein structure is dynamic, explain what this means and its significance. What are the five themes of Protein structure as explained in the lesson? What is a native conformation, a native protein? What forces stabilize the native conformation/s of a polypeptide chain? What is the Solvation layer, a hydration shell and the hydration number? Explain this statement: Hydrogen bonds between groups in proteins form cooperatively. Most of the structural patterns reflect two simple rule, what are these? What can be said about the peptide C-N bond?

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Biochemistry Workbook For more information and all the solutions, please go to www.proprep.com For any questions please contact us at 1-818-273-1725 or info@proprep.com © All rights in this workbook reserved to proprep™ 3 Complete the sentence – fill in the blanks: a. The ______ atoms of the _______ group are in a ________ plane, with the oxygen atom of the carbonyl group and the hydrogen atom of the amide nitrogen _________ to each other. b. The peptide _________ that link amino acid residues in a polypeptide are formed in a __________ reaction between the acidic carboxyl group of one amino acid and the basic amino group of another amino acid. In the context of a peptide, the amide group (CO – NH) is referred to as the _________ ________. What did Linus Pauling and Robert Corey conclude with regard to the peptide bond in the late 1930s?

Biochemistry Workbook For more information and all the solutions, please go to www.proprep.com For any questions please contact us at 1-818-273-1725 or info@proprep.com © All rights in this workbook reserved to proprep™ 4 Answer Key The defining factor that distinguishes proteins is structural. There are 4 levels of protein structure that are commonly defined: a. Covalent bonds linking amino acid residues in a polypeptide chain is its primary structure. b. Secondary structure refers to particularly stable arrangements of amino acid residues giving rise to recurring structural patterns. c. Tertiary structure describes all aspects of the 3-dimensional folding of a polypeptide. d. When a protein has two or more polypeptide subunits, their arrangement in space is referred to as quaternary structure. To view the answer to this exercise, please refer to the appropriate video on site. The covalent backbone of a protein contains hundreds of bonds. The 5 themes of Protein structure are: a. The 3-dimensional structure of a protein is determined by its amino acid sequence b. The function of a protein depends on its structure c. An isolated protein usually exists in one or a small number of stable structural forms d. The most important forces stabilizing the specific structures maintained by a given protein are noncovalent interactions e. Among the huge number of unique protein structures, we recognize some common structural patterns that help organize our understanding of protein architecture The spatial arrangement of atoms in a protein is called its conformation. Proteins in their functional, folded conformations are called native proteins. hydrogen bonds, the hydrophobic effect, and ionic interactions. Solvation layer - it is what forms when water surrounds a hydrophobic molecule; the optimal arrangement of hydrogen bonds results in a highly structured shell. When the solvent is water it is often referred to as a hydration shell or hydration sphere The number of solvent molecules surrounding each unit of solute is called the hydration number of the solute. Formation of one hydrogen bond facilitates the formation of additional hydrogen bonds. 1. Hydrophobic residues are buried in the protein interior, away from water. 2. The number of hydrogen bonds within the protein is maximized. To view the answer to this exercise, please refer to the appropriate video on site. a. 6, peptide group, single, trans. b. bonds, condensation, peptide group. The peptide C-N bonds are unable to rotate freely because of their partial double-bond character.

Biochemistry Workbook For more information and all the solutions, please go to www.proprep.com For any questions please contact us at 1-818-273-1725 or info@proprep.com © All rights in this workbook reserved to proprep™ 5 Higher Order Structure Questions Explain what the term secondary structure refers to in a protein. Which statement is false and why? a. Pauling and Corey were scientists that studied peptides and that predicted the existence of protein secondary structures. b. Common Secondary Structures have characteristic bond angles and amino acid content. c. The α helix and β conformation are the major repeti tive secondary structures in a wide variety of proteins. d. Other repetitive structures exist in some specialized proteins. e. Some Secondary structures can be described by the bond angles φ and ψ at each residue . a. What is the simplest arrangement a polypeptide chain could assume, and what is it specifically called? b. Mention 2 characteristics of this arrangement. Why does the α helix form more readily than many other possible conformations, and approximately what portion of amino acid residues are found in such arrangements? What can be said about the α helix with regard to stereoisomers and L - or D- amino acids? Explain this statement and elaborate, give examples: Amino Acid Sequence affects α Helix Stability . Complete the statements by filling out the blanks: In 1951 Pauling and Corey predicted a __________ type of repetitive structure, the _________, which is a more extended conformation of polypeptide chains. The backbone of the polypeptide in this arrangement is extended into a _______ rather than helical structure. The arrangement of several such ___________segments side by side, all of which are in the ___________ is called the __________, and has pleated appearance.

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Biochemistry Workbook For more information and all the solutions, please go to www.proprep.com For any questions please contact us at 1-818-273-1725 or info@proprep.com © All rights in this workbook reserved to proprep™ 6 Which statement about the β sheet is false? a. Hydrogen bonds are formed between the adjacent segments of polypeptide chains in the β sheet . b. The individual segments that form a β sheet are usually nearby on the polypeptide chain, but can also be distant from each other in the linear sequence of the polypeptide; they may even be segments in different polypeptide chains. c. The R groups of adjacent amino acids protrude from the zigzag structure in opposite directions, creating an alternating pattern. d. The adjacent polypeptide chains in a β sheet are parallel to each other. e. When two or more β sheets are layered close together within a protein, the R groups of the amino acid residues on the touching surfaces must be relatively small. f. None of the above. What is an additional type common β conformation other than the β Sheet and describe this? What is protein tertiary and quaternary structure? a. In considering the higher levels of protein structure covered in this lesson, it is useful to classify proteins into 2 major groups, list these and define them. b. Explain the differences between these 2 types of protein classes. Which statement with regard to protein quaternary structures is false? a. Protein Quaternary Structures Range from Simple Dimers to Large Complexes. b. The quaternary structure of a protein is the association of several protein chains or subunits into a closely packed arrangement. c. Many proteins have multiple polypeptide subunits that are part of their quaternary structure, and these can take on separate but related functions, (such as catalysis and regulation). d. All of the subunits of the multiple polypeptide that makes up the quaternary structure have different primary but the same secondary, and tertiary structure. e. The subunits of the multiple polypeptide are held together by hydrogen bonds and van der Waals forces between nonpolar side chains. What are the 4 classes protein structures are divided into?

Biochemistry Workbook For more information and all the solutions, please go to www.proprep.com For any questions please contact us at 1-818-273-1725 or info@proprep.com © All rights in this workbook reserved to proprep™ 7 Proteins can be organized based on the presence of the various motifs and their arrangements. Which statements in this regard are true: a. The top two levels of organization, class and fold, are purely structural. b. Below the fold level, categorization is based on evolutionary relationships. c. Many examples of recurring domain or motif structures reveal that protein tertiary structure is not as conserved as protein primary sequence. d. The comparison of protein structures can provide information about evolution. e. A, B, C, and D. f. A, B, and C. g. A, B, and D. Define a protein family and a superfamily.

Biochemistry Workbook For more information and all the solutions, please go to www.proprep.com For any questions please contact us at 1-818-273-1725 or info@proprep.com © All rights in this workbook reserved to proprep™ 8 Answer Key The term secondary structure refers to any chosen segment of a polypeptide chain and describes the local spatial arrangement of its main-chain atoms, without regard to its side chains or its relationship to other segments. e - Eve ry type of Secondary structure can be completely described by the bond angles φ and ψ at each residue . a. H elical one, and it is called the α helix . b. To view the answer to this exercise, please refer to the appropriate video on site. Generally, about one-fourth of all amino acid residues in polypeptides are found in α helices, with the exact fraction varying greatly from one protein to the next. To view the answer to this exercise, please refer to the appropriate video on site. To view the answer to this exercise, please refer to the appropriate video on site. Second, β conformation , zigzag, zigzag, β conformation , β sheet . d. β Turns Are Common in Proteins . The overall 3-dimensional arrangement of all atoms in a protein is referred to as the protein’s tertiary structure . The arrangement of these protein subunits in 3-dimensional complexes constitutes quaternary structure. a. Fibrous proteins – these have polypeptide chains arranged in long strands or sheets. Globular proteins - these have polypeptide chains folded into a spherical or globular shape. b. The structures that provide support, shape, and external protection to vertebrates are made of fibrous proteins. Most enzymes and regulatory proteins are globular proteins d. All α , All β , α/β , α & β . g. Proteins with significant primary sequence similarity, and/or with demonstrably similar structure and function, are said to be in the same protein family.

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