Term
|
Definition
is a method of separating biochemical mixtures and based on a highly specific biological interaction such as that between antigen and antibody, enzyme and substrate, or receptor and ligand. |
|
|
Term
Molecular exclusion chromatography |
|
Definition
is a chromatographic method in which molecules in a solution are separated by their molecular weight? |
|
|
Term
|
Definition
a common motif in the secondary structure of proteins, the alpha helix, is a right handed coiled or spiral conformation, in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier. |
|
|
Term
|
Definition
are molecules containing an amine group, a carboxylic acid group and a side chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen and nitrogen. |
|
|
Term
|
Definition
They have a central carbon atom attached to an amino (-NH2) group, a carboxyl (-COOH) group a hydrogen atom, and a side chain (R) |
|
|
Term
What are the basic side chain groups? |
|
Definition
|
|
Term
What are the acidic side chain R groups |
|
Definition
|
|
Term
What are the polar, uncharged side chain groups? (hydrophillic) |
|
Definition
Asn, Gln, Ser, Thr, Tyr, Cys |
|
|
Term
What are the nonpolar side chain groups (hydrophobic) |
|
Definition
Gly, Ala, Ile, Leu, Val, Phe, Trp, Met, Pro |
|
|
Term
|
Definition
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 |
|
|
Term
How is a peptide bond drawn? |
|
Definition
With the amino (N) terminus to the left and the carboxyl (C) terminus to the right |
|
|
Term
Ion exchange chromatography does what? |
|
Definition
Separates proteins by electrostatic interactions (charge) |
|
|
Term
Reverse phase chromatography does what |
|
Definition
separates proteins by hydrophobic interactions |
|
|
Term
|
Definition
separates proteins by size |
|
|
Term
Protein Electrophoresis does what |
|
Definition
separates proteins by size and can be used to visualize protein purity. |
|
|
Term
Edman degradation does what |
|
Definition
removes one amino acid from the N-terminus end of a protein. |
|
|
Term
What are the four types of weak non-covalent bonds from strongest toe weakest? |
|
Definition
Ionic, hydrogen, van der Waals interactions, and hydrophobic interactions |
|
|
Term
|
Definition
Interactions between positively and negatively charged ionic groups. |
|
|
Term
|
Definition
Interactions between a partially negative electronegative atom and a partially positive hydrogen atom |
|
|
Term
Only ___ and ___ participate in hydrogen bonds with hydrogen. |
|
Definition
|
|
Term
Van der Waals interactions are? |
|
Definition
Weak electrostatic interactions between two polar groups , a polar group and a nonpolar group, or two nonpolar groups. |
|
|
Term
Hydrophobic interactions do what? |
|
Definition
They cluster nonpolar amino acids together |
|
|
Term
|
Definition
A right handed helix with one helical turn per 3.6 amino acids and is stabilized by hydrogen bonding between residues. |
|
|
Term
Which amino acids are least likely to be found in alpha helices, as are runs or negatively charged residues |
|
Definition
|
|
Term
What does beta conformation mean |
|
Definition
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. |
|
|
Term
What connect alpha helices and are usually located on protein surface? |
|
Definition
|
|
Term
Why is xray crystallography useful? |
|
Definition
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. |
|
|
Term
Nuclear magnetic resonance spectroscopy is used for? |
|
Definition
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 |
|
|
Term
T or false... The primary structure is sufficient to determine the tertiary structure. |
|
Definition
|
|
Term
What are the three kinds of membrane proteins |
|
Definition
integral membrane proteins, peripheral membrane proteins, and lipoproteins |
|
|
Term
True or false- the rotation of the carboxyl group and the amino groups of an amino acid are not constrained? |
|
Definition
False- they are constrained |
|
|
Term
What is the bond between the amino group and the alpha carbon of an amino acid called |
|
Definition
|
|
Term
What is the average molecular weight of an amino acid |
|
Definition
|
|
Term
|
Definition
(of a protein) is its operative or functional form |
|
|
Term
Nuclear magnetic resonance spectroscopy |
|
Definition
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 |
|
|
Term
|
Definition
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 |
|
|
Term
|
Definition
consist of between 2 and 20 amino acids. (includes dipeptides, tripeptides, tetrapeptides, etc.) a peptide containing a relatively small number of amino acids |
|
|
Term
|
Definition
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 |
|
|
Term
|
Definition
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. |
|
|
Term
|
Definition
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. |
|
|
Term
|
Definition
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. |
|
|
Term
|
Definition
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. |
|
|
Term
Peripheral membrane protein |
|
Definition
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. |
|
|
Term
|
Definition
(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. |
|
|
Term
|
Definition
also called the ß 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). |
|
|
Term
|
Definition
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. |
|
|
Term
|
Definition
is a single linear chain of amino acids. |
|
|
Term
High-performance liquid chromatography (HPLC) |
|
Definition
is a technique that can separate a mixture of compounds and is used to identify, quantify and purify the individual components of the mixture. |
|
|
Term
|
Definition
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) |
|
|
Term
|
Definition
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. |
|
|
Term
|
Definition
is the arrangement of multiple folded protein or coiling protein molecules in a multi-subunit complex. |
|
|
Term
|
Definition
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. |
|
|
Term
|
Definition
is the physical property of a molecule that is repelled from a mass of water. |
|
|
Term
|
Definition
is the physical property of a molecule that is repelled from a mass of water. |
|
|
Term
|
Definition
the reconstruction of the original form of a protein or nucleic acid following denaturation |
|
|
Term
Integral membrane protein |
|
Definition
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. |
|
|
Term
|
Definition
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” |
|
|
Term
Ion exchange chromatography |
|
Definition
is a technique that uses ion exchange to separate compounds, anions and cations according to their electrical properties |
|
|
Term
|
Definition
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. |
|
|
Term
|
Definition
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. |
|
|
Term
|
Definition
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. |
|
|
Term
|
Definition
is the pH at which a particular molecule or surface carries no net electrical charge. |
|
|
Term
|
Definition
is a chemical group that is attached to a core part of the molecule called main chain or backbone |
|
|
Term
|
Definition
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. |
|
|
Term
|
Definition
is the three-dimensional structure, as defined by the atomic coordinates. |
|
|
Term
|
Definition
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. |
|
|
Term
Van der Waals interaction |
|
Definition
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. |
|
|
Term
|
Definition
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. |
|
|
Term
What are two known alpha helices breakers? |
|
Definition
|
|
Term
True or false. Alpha helices are stabilized by hydrophobic interactions |
|
Definition
|
|
Term
What stabilizes an alpha helix? |
|
Definition
-intramolecular hydrogen bonds -minimizing unfavorable R-group interactions |
|
|
Term
True or false. Boiling temperatures are not usually sufficient to break peptide bonds |
|
Definition
|
|
Term
What type of amino acids would probably be positioned near the surface in a globular protein |
|
Definition
|
|
Term
In secondary structure of proteins hydrogen bonds occur where? |
|
Definition
|
|
Term
In the tertiary structure of proteins, hydrogen bonds occur where? |
|
Definition
|
|
Term
A peptide bond is formed by the reaction of the alpha-carbonyl group of one amino acid with____ |
|
Definition
the alpha amino group of a second amino acid |
|
|
Term
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> |
|
Definition
|
|
Term
____ interactions result from weak electrostatic interactions between two polar groups, a polar group and a nonpolar group, or two nonpolar groups. |
|
Definition
|
|
Term
The local folding pattern within a segment of a polypeptide chain containing neighboring residues is called its ___ |
|
Definition
|
|
Term
Proteins with just one polypeptide chain have primary, secondary, and ____ structures. |
|
Definition
|
|
Term
The hydrophobic effect is a result of the ___. |
|
Definition
tendency of water to form ordered structures around nonpolar molecules |
|
|
Term
Proline tends to not participate in alpha helices because ____ |
|
Definition
its side chain is rigid and does not fit easily |
|
|
Term
Alpha helices and beta sheets are both stabilized by___ |
|
Definition
|
|
Term
True or False- Primary sequence is sufficient for accurate protein folding |
|
Definition
True. This is the conclusion of the Afinsen experiment |
|
|
Term
The three dimensional relationship of the different polypeptide chains in a multi-subunit protein or protein complex is |
|
Definition
|
|
Term
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 |
|
Definition
|
|
Term
The amino acid sequence of a protein is... |
|
Definition
|
|
Term
A region on the surface of a protein that can interact with another molecule through noncovalent bonding is called the... |
|
Definition
|
|
Term
Complex three dimensional form of a folded protein is called the |
|
Definition
|
|
Term
The chain of repeating carbon and nitrogen atoms, linked by peptide bonds, in a protein is called |
|
Definition
|
|
Term
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. |
|
Definition
|
|
Term
Portion of a protein that has a tertiary structure of its own. |
|
Definition
|
|
Term
Regular local folding patterns in a protein including alpha helix and ß sheet |
|
Definition
|
|
Term
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. |
|
Definition
|
|
Term
Each strand in a ß sheet is a helix with two amino acids per turn. |
|
Definition
|
|
Term
Loops of polypeptide that protrude from the surface of a protein often form the binding sites for other molecules. |
|
Definition
|
|