question

Affinity chromatography

answer

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.

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Molecular exclusion chromatography

answer

is a chromatographic method in which molecules in a solution are separated by their molecular weight?

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Alpha- helix

answer

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.

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Amino acid

answer

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.

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Describe an amino acid

answer

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?

answer

Arg, Lys, His

question

What are the acidic side chain R groups

answer

Asp, Glu

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What are the polar, uncharged side chain groups? (hydrophillic)

answer

Asn, Gln, Ser, Thr, Tyr, Cys

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What are the nonpolar side chain groups (hydrophobic)

answer

Gly, Ala, Ile, Leu, Val, Phe, Trp, Met, Pro

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What is a peptide bond?

answer

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?

answer

With the amino (N) terminus to the left and the carboxyl (C) terminus to the right

question

Ion exchange chromatography does what?

answer

Separates proteins by electrostatic interactions (charge)

question

Reverse phase chromatography does what

answer

separates proteins by hydrophobic interactions

question

Gel Filtration does what

answer

separates proteins by size

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Protein Electrophoresis does what

answer

separates proteins by size and can be used to visualize protein purity.

question

Edman degradation does what

answer

removes one amino acid from the N-terminus end of a protein.

question

What are the four types of weak non-covalent bonds from strongest toe weakest?

answer

Ionic, hydrogen, van der Waals interactions, and hydrophobic interactions

question

Ionic bonds are?

answer

Interactions between positively and negatively charged ionic groups.

question

Hydrogen bonds are?

answer

Interactions between a partially negative electronegative atom and a partially positive hydrogen atom

question

Only ___ and ___ participate in hydrogen bonds with hydrogen.

answer

O and N

question

Van der Waals interactions are?

answer

Weak electrostatic interactions between two polar groups , a polar group and a nonpolar group, or two nonpolar groups.

question

Hydrophobic interactions do what?

answer

They cluster nonpolar amino acids together

question

What is an Alpha Helix?

answer

A right handed helix with one helical turn per 3.6 amino acids and is stabilized by hydrogen bonding between residues.

question

Which amino acids are least likely to be found in alpha helices, as are runs or negatively charged residues

answer

Proline or Lysine

question

What does beta conformation mean

answer

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?

answer

Loops and turns?

question

Why is xray crystallography useful?

answer

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.

question

Nuclear magnetic resonance spectroscopy is used for?

answer

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.

answer

true

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What are the three kinds of membrane proteins

answer

integral membrane proteins, peripheral membrane proteins, and lipoproteins

question

True or false- the rotation of the carboxyl group and the amino groups of an amino acid are not constrained?

answer

False- they are constrained

question

What is the bond between the amino group and the alpha carbon of an amino acid called

answer

the phi bond.

question

What is the average molecular weight of an amino acid

answer

110 daltons

question

Native state

answer

(of a protein) is its operative or functional form

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Nuclear magnetic resonance spectroscopy

answer

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

question

Beta-turn

answer

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

answer

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

answer

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

answer

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.

question

Column chromatography

answer

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.

question

Peptide bonds

answer

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.

question

Denatured state

answer

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.

question

Peripheral membrane protein

answer

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.

question

Fluid mosaic model

answer

(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.

question

Pleated sheets

answer

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).

question

Gel filtration

answer

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.

question

Polypeptide

answer

is a single linear chain of amino acids.

question

High-performance liquid chromatography (HPLC)

answer

is a technique that can separate a mixture of compounds and is used to identify, quantify and purify the individual components of the mixture.

question

Primary structure

answer

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)

question

Hydrogen bond

answer

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.

question

Quaternary structure

answer

is the arrangement of multiple folded protein or coiling protein molecules in a multi-subunit complex.

question

Random conformation

answer

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.

question

Hydrophobicity

answer

is the physical property of a molecule that is repelled from a mass of water.

question

Hydrophobicity

answer

is the physical property of a molecule that is repelled from a mass of water.

question

Renaturation

answer

the reconstruction of the original form of a protein or nucleic acid following denaturation

question

Integral membrane protein

answer

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.

question

Residue

answer

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”

question

Ion exchange chromatography

answer

is a technique that uses ion exchange to separate compounds, anions and cations according to their electrical properties

question

Ionic bond

answer

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.

question

Secondary structure

answer

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.

question

Secondary structure

answer

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.

question

Isoelectric ph

answer

is the pH at which a particular molecule or surface carries no net electrical charge.

question

Side chain

answer

is a chemical group that is attached to a core part of the molecule called main chain or backbone

question

Ligand

answer

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.

question

Tertiary structure

answer

is the three-dimensional structure, as defined by the atomic coordinates.

question

Lipid bilayer

answer

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.

question

Van der Waals interaction

answer

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.

question

x-ray crystallography

answer

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.

question

What are two known alpha helices breakers?

answer

Proline and Glycine

question

True or false. Alpha helices are stabilized by hydrophobic interactions

answer

False

question

What stabilizes an alpha helix?

answer

-intramolecular hydrogen bonds
-minimizing unfavorable R-group interactions

question

True or false. Boiling temperatures are not usually sufficient to break peptide bonds

answer

True

question

What type of amino acids would probably be positioned near the surface in a globular protein

answer

hydrophillic

question

In secondary structure of proteins hydrogen bonds occur where?

answer

in the backbone

question

In the tertiary structure of proteins, hydrogen bonds occur where?

answer

Between the R groups

question

A peptide bond is formed by the reaction of the alpha-carbonyl group of one amino acid with____

answer

the alpha amino group of a second amino acid

question

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>

answer

Reverse Phase

question

____ interactions result from weak electrostatic interactions between two polar groups, a polar group and a nonpolar group, or two nonpolar groups.

answer

Van der Waals

question

The local folding pattern within a segment of a polypeptide chain containing neighboring residues is called its ___

answer

secondary structure

question

Proteins with just one polypeptide chain have primary, secondary, and ____ structures.

answer

tertiary

question

The hydrophobic effect is a result of the ___.

answer

tendency of water to form ordered structures around nonpolar molecules

question

Proline tends to not participate in alpha helices because ____

answer

its side chain is rigid and does not fit easily

question

Alpha helices and beta sheets are both stabilized by___

answer

hydrogen bonds

question

True or False- Primary sequence is sufficient for accurate protein folding

answer

True. This is the conclusion of the Afinsen experiment

question

The three dimensional relationship of the different polypeptide chains in a multi-subunit protein or protein complex is

answer

the quaternary structure

question

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

answer

alpha helix

question

The amino acid sequence of a protein is...

answer

primary structure

question

A region on the surface of a protein that can interact with another molecule through noncovalent bonding is called the...

answer

binding site

question

Complex three dimensional form of a folded protein is called the

answer

tertiary structure

question

The chain of repeating carbon and nitrogen atoms, linked by peptide bonds, in a protein is called

answer

polypeptide backbone

question

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.

answer

? sheet

question

Portion of a protein that has a tertiary structure of its own.

answer

Protein domain

question

Regular local folding patterns in a protein including alpha helix and ? sheet

answer

secondary structure

question

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.

answer

True.

question

Each strand in a ? sheet is a helix with two amino acids per turn.

answer

True

question

Loops of polypeptide that protrude from the surface of a protein often form the binding sites for other molecules.

answer

True

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