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Biochemistry Module 3

updated Exam

(Short response) A. Define the primary level of protein structure. B) How do scientists communicate the primary sequence? - answer ✅✅The primary level is the order of amino acids covalently bonded together, including disulfide bonds, in a polypeptide chain. The primary sequence is written, for proteins, from N to C terminal using the one-letter or three- letter abbreviations. (short response) One protein has a stable structure known as a"helix-turn-helix" arrangement. What is the term that describes these stable collections of protein structure and where do they fit in protein structure levels? - answer ✅✅The helix-turn-helix structure is a

motif. Motifs are particularly stable arrangements of secondary structure, including the connections between them. Motifs are found in a variety of proteins from across all organisms. They are between true secondary and tertiary structures. (short response) Staphylokinase is said to be a dimer. A) What is a dimer? B) Structurally, a dimer describes what level of protein organization? - answer ✅✅A) This enzyme has two independent polypeptide chains interacting non-covalently. In this case, they are identical chains. B) It is describing the quaternary structure, which has two or more independent polypeptide chains that associate with one another to form a quaternary structure. All of the 20 standard amino acids contain an R-group that is attached to the: A) α carbon B) Carboxyl group

C) Amino group D) β carbon E) None of the above - answer ✅✅A An enzyme requires Cr+3 for catalysis. When the enzyme contains the Cr3+ it called a/an _________. - answer ✅✅Holoenzyme An organic molecule that is necessary for an enzyme's function is called a: - answer ✅✅Coenzyme Consider the following protein structure. A) Is the protein globular or fibrous? Explain your response in at least one complete sentence giving at least one (1) piece of evidence in your response. B) Identify at least two (2) types of secondary structure present in the following protein. - answer ✅✅A) Globular proteins are ball-like in

shape, while fibrous proteins are extended. Note the long strands of alpha-helices. B) Point out the two types of secondary structure shown here in this protein (as indicated in the module). Define the term "active site." - answer ✅✅The active site is the spot on the enzyme where catalysis takes place. This area is often small when compared to the overall size of the protein. In fact, about 10 amino acids make up the active site. Formally, when there are 100 or more amino acids are covalently linked together that is called a _________. - answer ✅✅Protein How many classes of enzymes are recognized by the IUBMB? - answer ✅✅ 6

In an alpha helix, the R groups on the amino acid residues: - answer ✅✅Are found on the outside of the helix spiral Motifs are classified primarily by their: - answer ✅✅Content and arrangement of the secondary structure Roughly how many amino acids are there in one turn of an alpha helix? - answer ✅✅3. The ES stands for: - answer ✅✅Enzyme- substrate The formation of a peptide bond between two amino acids is an example of a(n) _____ reaction. - answer ✅✅Condensation The order of amino acids in a protein is written _________. - answer ✅✅N to C-terminus

The overall three-dimensional shape of a single folded polypeptide is ________ structure. - answer ✅✅Tertiary The peptide Ala-Glu-Gly-Ala-Leu has ______. - answer ✅✅Four peptide bonds The secondary structure shown below is an example of a(n): - answer ✅✅Antiparallel beta sheet True or False: An inhibitor that binds at the active site is a coenzyme. - answer ✅✅False True or False: The amino acids lysine and arginine both contain sulfur atoms. - answer ✅✅False True or False: The following secondary structure shown below is an example of a beta- turn. - answer ✅✅False

True or False: The name of the molecule that binds to an enzyme is called the ligand. - answer ✅✅False True or False. The side chain of histidine is bonded to the backbone nitrogen atom. - answer ✅✅False What unit is used by biochemists to indicate the mass of a protein? - answer ✅✅Da When a substrate has just started its conversion to a new molecule, it is said to be in the ________. - answer ✅✅Transition state Which amino acids both have an R group (side chain) with an - OH functional group? - answer ✅✅Ser and Thr

Which of the following correctly matches the amino acid with its one letter abbreviation? - answer ✅✅Glutamic acid, E Which of the following describes induced fit? - answer ✅✅Substrate binding induces a conformation change in the enzyme Which of the following would change the rate of an enzyme-catalyzed reaction? - answer ✅✅pH, concentration, and temperature