MMBIO 240 CH 2 Evans – Flashcards
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| Describe an amino acid |
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| They have a central carbon atom attached to an amino (-NH2) group, a carboxyl (-COOH) group a hydrogen atom, and a side chain (R) |
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| What are the basic side chain groups? |
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| Arg, Lys, His |
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| What are the acidic side chain R groups |
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| Asp, Glu |
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| What are the polar, uncharged side chain groups? (hydrophillic) |
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| Asn, Gln, Ser, Thr, Tyr, Cys |
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| What are the nonpolar side chain groups (hydrophobic) |
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| Gly, Ala, Ile, Leu, Val, Phe, Trp, Met, Pro |
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| What is a peptide bond? |
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| Peptide bond are amide bonds between amino acids that link the carboxyl group of one amino acid with the amino group of the next amino acid |
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| How is a peptide bond drawn? |
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| With the amino (N) terminus to the left and the carboxyl (C) terminus to the right |
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| Ion exchange chromatography does what? |
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| Separates proteins by electrostatic interactions (charge) |
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| Reverse phase chromatography does what |
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| separates proteins by hydrophobic interactions |
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| Gel Filtration does what |
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| separates proteins by size |
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| Protein Electrophoresis does what |
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| separates proteins by size and can be used to visualize protein purity. |
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| Edman degradation does what |
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| removes one amino acid from the N-terminus end of a protein. |
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| What are the four types of weak non-covalent bonds from strongest toe weakest? |
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| Ionic, hydrogen, van der Waals interactions, and hydrophobic interactions |
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| Ionic bonds are? |
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| Interactions between positively and negatively charged ionic groups. |
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| Hydrogen bonds are? |
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| Interactions between a partially negative electronegative atom and a partially positive hydrogen atom |
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| Only ___ and ___ participate in hydrogen bonds with hydrogen. |
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| O and N |
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| Van der Waals interactions are? |
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| Weak electrostatic interactions between two polar groups , a polar group and a nonpolar group, or two nonpolar groups. |
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| Hydrophobic interactions do what? |
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| They cluster nonpolar amino acids together |
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| What is an Alpha Helix? |
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| A right handed helix with one helical turn per 3.6 amino acids and is stabilized by hydrogen bonding between residues. |
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| Which amino acids are least likely to be found in alpha helices, as are runs or negatively charged residues |
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| Proline or Lysine |
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| What does beta conformation mean |
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| polypeptides are almost fully extended and can line up to form nearly flat beat-sheets in which C=O and N-H groups on adjacent chains interact through hydrogen bonds. |
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| What connect alpha helices and are usually located on protein surface? |
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| Loops and turns? |
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| Why is xray crystallography useful? |
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| it can be used to determine the three dimensional structure of proteins by allowing the interatomic distances in a protein to be measured through xray diffraction. |
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| Nuclear magnetic resonance spectroscopy is used for? |
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| It can be used to determine the three dimensional structure of smaller proteins. The advantage of this method is that proteins can be studied in solution and do not have to be crystallized |
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| T or false... The primary structure is sufficient to determine the tertiary structure. |
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| true |
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| What are the three kinds of membrane proteins |
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| integral membrane proteins, peripheral membrane proteins, and lipoproteins |
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| True or false- the rotation of the carboxyl group and the amino groups of an amino acid are not constrained? |
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| False- they are constrained |
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| What is the bond between the amino group and the alpha carbon of an amino acid called |
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| the phi bond. |
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| What is the average molecular weight of an amino acid |
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| 110 daltons |
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| Native state |
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| (of a protein) is its operative or functional form |
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| Nuclear magnetic resonance spectroscopy |
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| is the technique that exploits the magnetic properties of certain nuclei. Various electromagnetic pulses are applied to nuclei which absorb the energy and radiate the energy back out at specific resonance frequencies dependent upon the strength of the magnetic field and other factors |
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| Beta-turn |
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| a turn is an element of secondary structure in proteins where the polipeptide chain reverses its overall direction -a peptide conformation characterized by hydrogen bonds for which the donor and acceptor residues are separate by three residues |
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| Oligopeptide |
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| consist of between 2 and 20 amino acids. (includes dipeptides, tripeptides, tetrapeptides, etc.) a peptide containing a relatively small number of amino acids |
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| Beta-strand |
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| refers to a single continuous stretch of amino acids adopting an extended conformation and involved in backbone hydrogen bonds to at least one other strand |
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| Peptide |
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| are short polymers of amino acids linked by peptide bonds. They have the same chemical structure as proteins, but are shorter in length. The shortest are dipeptides. Have an amino end and a carboxyl end. |
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| Column chromatography |
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| is a method used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms. |
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| Peptide bonds |
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| is a covalent chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule thereby releasing a molecule of water. |
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| Denatured state |
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| A process in which proteins or nucleic acids lose their tertiary structure by application of some external stress or compound such as a strong acid or base, a concentrated inorganic salt, an organic solvent, or heat. |
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| Peripheral membrane protein |
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| are proteins that adhere only temporarily to the biological membrane with which they are associated. These molecules attach to integral membrane proteins, or penetrate the peripheral regions of the lipid bilayer. |
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| Fluid mosaic model |
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| (S.J. Singer and Garth Nicolson) the biological membranes can be considered as a two-dimensional liquid where al lipid and protein molecules diffuse more or less easily. |
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| Pleated sheets |
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| also called the ? sheet, is the second form of regular secondary structure in proteins consisting of beta strands connected laterally by five or more hydrogen bonds, forming a generally twisted, pleated sheet (the most common form of regular secondary structure in proteins is the alpha helix). |
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| Gel filtration |
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| when an aqueous solution is used to transport the sample through the column. The main application of gel filtration is the fractionation of proteins and other water-soluble polymers. |
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| Polypeptide |
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| is a single linear chain of amino acids. |
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| High-performance liquid chromatography (HPLC) |
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| is a technique that can separate a mixture of compounds and is used to identify, quantify and purify the individual components of the mixture. |
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| Primary structure |
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| is the exact specification of its atomic composition and the chemical bonds connecting those atoms.- the linear sequence of amino acids covalently linked by peptide bonds to form a single polypeptide change. (the precise sequence of monomeric units) |
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| Hydrogen bond |
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| a chemical bond consisting of a hydrogen atom between two electronegative atoms (ex. Oxygen or nitrogen) with one side be a covalent bond and the other being an ionic bond. |
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| Quaternary structure |
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| is the arrangement of multiple folded protein or coiling protein molecules in a multi-subunit complex. |
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| Random conformation |
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| is a polymer conformation where the monomer subunits are oriented randomly while still being bonded to adjacent units. From the idea that in the absence of specific, stabilizing interactions, a polymer will “sample” all possible conformations randomly. |
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| Hydrophobicity |
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| is the physical property of a molecule that is repelled from a mass of water. |
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| Hydrophobicity |
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| is the physical property of a molecule that is repelled from a mass of water. |
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| Renaturation |
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| the reconstruction of the original form of a protein or nucleic acid following denaturation |
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| Integral membrane protein |
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| is a protein molecule (or assembly of proteins) that is permanently attached to the biological membrane. Such proteins can be separated from the biological membranes only using detergents, nonpolar solvents, or sometimes denaturing agents. |
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| Residue |
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| this refers to a specific monomer within the polymeric chain of a polysaccharide, protein or nucleic acid. For example, one might say, “the protein consists of 118 amino acid residues” |
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| Ion exchange chromatography |
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| is a technique that uses ion exchange to separate compounds, anions and cations according to their electrical properties |
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| Ionic bond |
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| a chemical bond in which one atom loses an electron to form a positive ion and the other atom gains an electron to form a negative ion. |
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| Secondary structure |
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| is the general three-dimensional form of local segments of biopoymers such as proteins and nucleic acids. Does not however describe specific atomic positions in 3-D space. |
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| Secondary structure |
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| is the general three-dimensional form of local segments of biopoymers such as proteins and nucleic acids. Does not however describe specific atomic positions in 3-D space. |
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| Isoelectric ph |
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| is the pH at which a particular molecule or surface carries no net electrical charge. |
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| Side chain |
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| is a chemical group that is attached to a core part of the molecule called main chain or backbone |
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| Ligand |
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| is an ion or molecule that binds to a central metal atom to form a coordination complex. The bonding between metal and ligand generally involves formal donation of one or more of the ligand’s electron pairs. |
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| Tertiary structure |
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| is the three-dimensional structure, as defined by the atomic coordinates. |
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| Lipid bilayer |
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| is a thin membrane made of two layers of lipid molecules. These membranes are flat sheets that typically have a hydrophobic interior, and two hydrophilic surfaces. |
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| Van der Waals interaction |
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| is the attractive or repulsive force between molecules (or between parts of the same molecule) other than those due to covalent bonds or to the electrostatic force. |
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| x-ray crystallography |
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| a technique in which the patterns formed by the diffraction of X-rays on passing through a crystalline substance yield information on the lattice structure of the crystal, and the molecular structure of the substance. |
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| What are two known alpha helices breakers? |
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| Proline and Glycine |
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| True or false. Alpha helices are stabilized by hydrophobic interactions |
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| False |
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| What stabilizes an alpha helix? |
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| -intramolecular hydrogen bonds -minimizing unfavorable R-group interactions |
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| True or false. Boiling temperatures are not usually sufficient to break peptide bonds |
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| True |
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| What type of amino acids would probably be positioned near the surface in a globular protein |
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| hydrophillic |
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| In secondary structure of proteins hydrogen bonds occur where? |
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| in the backbone |
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| In the tertiary structure of proteins, hydrogen bonds occur where? |
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| Between the R groups |
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| A peptide bond is formed by the reaction of the alpha-carbonyl group of one amino acid with____ |
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| the alpha amino group of a second amino acid |
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| Which chromatography technique uses the weak attractive interaction between nonpolar amino acid side chains and nonpolar groups attached to polysaccharide beads to retard protein migration> |
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| Reverse Phase |
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| ____ interactions result from weak electrostatic interactions between two polar groups, a polar group and a nonpolar group, or two nonpolar groups. |
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| Van der Waals |
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| The local folding pattern within a segment of a polypeptide chain containing neighboring residues is called its ___ |
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| secondary structure |
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| Proteins with just one polypeptide chain have primary, secondary, and ____ structures. |
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| tertiary |
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| The hydrophobic effect is a result of the ___. |
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| tendency of water to form ordered structures around nonpolar molecules |
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| Proline tends to not participate in alpha helices because ____ |
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| its side chain is rigid and does not fit easily |
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| Alpha helices and beta sheets are both stabilized by___ |
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| hydrogen bonds |
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| True or False- Primary sequence is sufficient for accurate protein folding |
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| True. This is the conclusion of the Afinsen experiment |
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| The three dimensional relationship of the different polypeptide chains in a multi-subunit protein or protein complex is |
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| the quaternary structure |
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| Common folding pattern in proteins n which a linear sequence of amino acids folds into a right handed coil stabilized by internal hydrogen bonding between backbone atoms is |
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| alpha helix |
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| The amino acid sequence of a protein is... |
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| primary structure |
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| A region on the surface of a protein that can interact with another molecule through noncovalent bonding is called the... |
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| binding site |
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| Complex three dimensional form of a folded protein is called the |
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| tertiary structure |
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| The chain of repeating carbon and nitrogen atoms, linked by peptide bonds, in a protein is called |
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| polypeptide backbone |
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| Common structural motif in proteins in which different sections of the polypeptide chain run alongside each other and are joined together by hydrogen bonding between atoms of the polypeptide backbone. |
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| ? sheet |
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| Portion of a protein that has a tertiary structure of its own. |
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| Protein domain |
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| Regular local folding patterns in a protein including alpha helix and ? sheet |
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| secondary structure |
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| True or False- A protein is at a near entropy minimum (point of lowest disorder, or greatest order) when it is completely stretched out like a string and when it is properly folded up. |
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| True. |
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| Each strand in a ? sheet is a helix with two amino acids per turn. |
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| True |
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| Loops of polypeptide that protrude from the surface of a protein often form the binding sites for other molecules. |
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| True |
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