Portage Learning Chem 210 - FINAL exam

Portage Learning Chem 210 - Module 3 exam True or False: The amino acids serine and threonine both contain sulfur atoms. FALSE True or False: The following secondary structure shown below is an example of a beta- turn. FALSE True or False. The side chain of phenylalanine is bonded to the backbone nitrogen atom. FALSE True or False: The name of the molecule that binds to an enzyme is called the holoenzyme. FALSE True or False: An inhibitor that binds at the active site is a coenzyme. FALSE Which amino acids differ by only one atom? Ser and Thr Leu and Ile Ala and Ser Asp and Asn Ser and Cys SER AND CYS The formation of a peptide bond between two amino acids is an example of a(n) reaction. Cleavage Condensation Group transfer Isomerization Double-bond breaking CONDENSATION The peptide Ala-Glu-Gly-Ala-Leu has . A disulfide bond Five peptide bonds Four peptide bonds A proline residue No C-terminal FOUR PEPTIDE BOND Formally, when there are 100 or more amino acids are covalently linked together that is called a . Polypeptide Oligopeptide Peptide Protein Polyprotein PROTEIN What unit is used by biochemists to indicate the mass of a protein? kDa kBa Mol/g g/mol kg kDa 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) carbon E) None of the above A) a carbon Which of the following correctly matches the amino acid with its one letter abbreviation? Glutamic acid, E Isoleucine, S Lysine, L Phenylalanine, P Arginine, A GLUTAMIC ACID, E The order of amino acids in a protein is written . 3’ to 5’ 5’ to 3’ N to C-terminus C to N-terminus Smallest to largest amino acid by weight N TO C-TERMINUS Question 14 3 / 3 pts Roughly how many amino acids are there in one turn of an alpha helix? 1 2.8 3.6 4.2 10 3.6 In an alpha helix, the R groups on the amino acid residues: Alternate between the inside and outside of the helix Cause only left-handed helices to form Generate the hydrogen bonds that form the helix Stack within the interior of the helix Are found on the outside of the helix spiral ARE FOUND ON THE OUTSIDE OF THE HELIX SPIRAL Motifs are classified primarily by their: Amino acid sequence Evolutionary relationships Content and arrangement of the secondary structure Content and arrangement of the tertiary structure Subunit content and arrangement CONTENT AND ARRANGEMENT OF THE SECONDARY STRUCTURE The secondary structure shown below is an example of a(n): Parallel beta sheet Antiparallel beta sheet alpha helix beta-turn alpha-turn ANTIPARALLEL BETA SHEET The overall three-dimensional shape of a single folded polypeptide is structure. Primary Secondary Tertiary Quaternary Motif TERTIARY How many classes of enzymes are recognized by the IUBMB? 3 4 5 6 7 6 Question 20 3 / 3 pts An enzyme requires Cr+3 for catalysis. When the enzyme contains the Cr3+ it called a/an . Holoenzyme Apoenzyme Fully ready molecule Inhibitor Competitive inhibitor HOLOENZYME As a substrate reacts to become a product, it goes through the , which is a high potential energy state. Conversion State Stable mode Unstable mode Conversion Mode Transition state TRANSITION STATE Which of the following would change the rate of an enzyme-catalyzed reaction? amino acids, concentration, and temperature pH, concentration, and temperature pH, polarity, and concentration polarity, concentration, and temperature pH, polarity, and temperature PH, CONCENTRATION AND TEMPERATURE Which of the following describes induced fit? Substrate binding induces a conformation change in the enzyme When a substrate binds to an enzyme, the enzyme induces loss of water The substrate bends and twists before it binds to the enzyme Enzyme specificity is induced in the enzyme-substrate The enzyme-substrate binding increases the temperature SUBSTRATE BINDING INDUCES A CONFORMATION CHANGE IN THE ENZYME The ES stands for: Enzyme-specificity Enzyme-substrate Energy-specificity Energy-substance Both B and D ENZYME-SUBSTRATE Any molecule or ion that is necessary for an enzyme’s function is called a: Cofactor Coreactant Coproduct Bienzyme Both B and C COFACTOR 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. 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). Question 27 5 / 5 pts (short response) Hemoglobin is said to be a tetramer. A) What is a tetramer? B) Structurally, a tetramer describes what level of protein organization? Your Answer: A. A tetramer is a protein that has four subunits. Two of the subunits are called alpha subunits while the other two are called beta subunits. B. A tetramer describes the quaternary structure A) Simply it means that hemoglobin has four subunits or four independent polypeptide chains interacting non-covalently. Each protein molecule is composed of two copies each of two different subunits a and b. We say that hemoglobin is a tetramer because it has four polypeptide 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. Question 28 5 / 5 pts (short response) There are collections of protein structure that fit between true secondary and true tertiary structure. What is the name of the collections of protein structure? Explain this type of structure. Motifs occupy a position between secondary and tertiary. 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. Question 29 5 / 5 pts (Short response) A. Define the primary level of protein structure. B) How do scientists communicate the primary sequence? 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. Question 30 5 / 5 pts Define the term “active site.” Your Answer: The active site, made up of about 10 amino acids, is the place on an enzyme where catalysis happens. It is usually small compared to the overall protein. 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.