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MMBIO 240 CH 2 Evans
Chapter 2
96
Microbiology
Undergraduate 1
01/26/2011

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Term
Affinity chromatography
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
Alpha- helix
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
Amino acid
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
Describe an amino acid
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
Arg, Lys, His
Term
What are the acidic side chain R groups
Definition
Asp, Glu
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
What is a peptide bond?
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
Gel Filtration does what
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
Ionic bonds are?
Definition
Interactions between positively and negatively charged ionic groups.
Term
Hydrogen bonds are?
Definition
Interactions between a partially negative electronegative atom and a partially positive hydrogen atom
Term
Only ___ and ___ participate in hydrogen bonds with hydrogen.
Definition
O and N
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
What is an Alpha Helix?
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
Proline or Lysine
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
Loops and turns?
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
true
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
the phi bond.
Term
What is the average molecular weight of an amino acid
Definition
110 daltons
Term
Native state
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
Beta-turn
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
Oligopeptide
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
Beta-strand
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
Peptide
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
Column chromatography
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
Peptide bonds
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
Denatured state
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
Fluid mosaic model
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
Pleated sheets
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
Gel filtration
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
Polypeptide
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
Primary structure
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
Hydrogen bond
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
Quaternary structure
Definition
is the arrangement of multiple folded protein or coiling protein molecules in a multi-subunit complex.
Term
Random conformation
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
Hydrophobicity
Definition
is the physical property of a molecule that is repelled from a mass of water.
Term
Hydrophobicity
Definition
is the physical property of a molecule that is repelled from a mass of water.
Term
Renaturation
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
Residue
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
Ionic bond
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
Secondary structure
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
Secondary structure
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
Isoelectric ph
Definition
is the pH at which a particular molecule or surface carries no net electrical charge.
Term
Side chain
Definition
is a chemical group that is attached to a core part of the molecule called main chain or backbone
Term
Ligand
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
Tertiary structure
Definition
is the three-dimensional structure, as defined by the atomic coordinates.
Term
Lipid bilayer
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
x-ray crystallography
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
Proline and Glycine
Term
True or false. Alpha helices are stabilized by hydrophobic interactions
Definition
False
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
True
Term
What type of amino acids would probably be positioned near the surface in a globular protein
Definition
hydrophillic
Term
In secondary structure of proteins hydrogen bonds occur where?
Definition
in the backbone
Term
In the tertiary structure of proteins, hydrogen bonds occur where?
Definition
Between the R groups
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
Reverse Phase
Term
____ interactions result from weak electrostatic interactions between two polar groups, a polar group and a nonpolar group, or two nonpolar groups.
Definition
Van der Waals
Term
The local folding pattern within a segment of a polypeptide chain containing neighboring residues is called its ___
Definition
secondary structure
Term
Proteins with just one polypeptide chain have primary, secondary, and ____ structures.
Definition
tertiary
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
hydrogen bonds
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
the quaternary structure
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
alpha helix
Term
The amino acid sequence of a protein is...
Definition
primary structure
Term
A region on the surface of a protein that can interact with another molecule through noncovalent bonding is called the...
Definition
binding site
Term
Complex three dimensional form of a folded protein is called the
Definition
tertiary structure
Term
The chain of repeating carbon and nitrogen atoms, linked by peptide bonds, in a protein is called
Definition
polypeptide backbone
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
ß sheet
Term
Portion of a protein that has a tertiary structure of its own.
Definition
Protein domain
Term
Regular local folding patterns in a protein including alpha helix and ß sheet
Definition
secondary structure
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
True.
Term
Each strand in a ß sheet is a helix with two amino acids per turn.
Definition
True
Term
Loops of polypeptide that protrude from the surface of a protein often form the binding sites for other molecules.
Definition
True
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