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Flashcards in Chapter 3 Terms Deck (37):
1

The functional representation of the genome; signifies a more complex level of information content, encompassing the types, functions, and interactions of proteins within its biological environment.

Proteome

2

A test which indicates the presence of a protein.

Assay

3

Enzyme activity in a mixture / Total protein concentration;
Should increase during purification.

Specific activity

4

Is what gets formed by disrupting the cell membrane.

Homogenate

5

The effect where most proteins are less soluble at high salt concentrations.

Salting out

6

Proteins can be purified from small molecules such as salt by this method through a semipermeable membrane. The protein mixture is placed inside the semipermeable bag, which is then submerged in a buffer solution that is devoid of the small molecules to be separated away. Molecules having dimensions greater than the pore diameter are retained inside the bag, where as smaller molecules and ions capable of passing through diffuse down their concentration gradient.

Dialysis

7

A method of purification on the basis of size; the sample is applied to the top of a column consisting of porous beads made of an insoluble but highly hydrated polymer. Large molecules flow more rapidly through this column and emerge first because a smaller volume is accessible to them.

Gel-filtration chromatography

8

Purification method on the basis of charge. Positively charged groups will bind to the anionic beads (Cation exchange). Oppositely, negatively charged groups will bind to the cationic beads. The beads can then be eluted off (Anion exchange).

Ion-exchange chromatography

9

Purification method; This technique takes advantage of the high affinity of many proteins for specific chemical groups.

Affinity chromatography

10

A purification method; the column materials are much more finely divided and, as a consequence, possess more interaction sites and thus greater resolving power. Because the column is made of finer material, pressure must be applied to the column to obtain adequate flow rates. The net result is both high resolution and rapid separation.

High-pressure liquid chromatography (HPLC)

11

Movement of a molecule with a net charge in an electric field.

Gel electrophoresis

12

The pH at which a protein's net charge is zero.

Isoelectric point

13

The method of separating proteins according to their isoelectric point.

Isoelectric focusing

14

A high resolution separation that combines isoelectric focusing with SDS-PAGE.

2-dimensional electrophoresis

15

Is equal to 10^-13 s. The smaller the value, the more slowly a molecule moves in a centrifugal field.

Sedimentation coefficient (Svedberg unit, S)

16

Sequentially removes one amino acid at a time from the amino end of a peptide.

Edman degradation

17

Reacts with the uncharged terminal amino group of a peptide to form a phenylthiocarbamoyl derivative. Is used in the Edman degredation process.

Phenyl isothiocyanate

18

These can be used to establish the order of peptides in a cleaved protein.

Overlap peptide

19

A protein synthesized by an animal in response to the presence of a foreign substance.

Antibody

20

A foreign substance recognized by an antibody.

Antigen

21

A specific group or cluster of amino acids on the target molecule an antibody will bind to.

Antigenic determinant (epitope)

22

Heterogeneous mixtures of antibodies, each specific for one of the various epitopes on an antigen.

Polyclonal antibody

23

All identical, produced by clones of a single antibody-producing cell. They recognize one specific epitope.

Monoclonal antibody

24

Indirect: used to detect the presence of antibody and is the basis of the test for HIV infection.
Sandwich: used to detect the presence of antigen.

Enzyme-linked immunosorbent assay (ELISA)

25

An immunoassay technique that can detect very small quantities of a protein of interest in a cell or in body fluid. This technique is also very useful in monitoring protein purification and in the cloning of genes.

Western blotting

26

Used to reveal the location of a protein of interest.

Fluorescence microscopy

27

A naturally fluorescent protein isolated from the jellyfish Aequorea victoria that is used as a fluorescent marker.

Green fluorescent protein (GFP)

28

The analyte is evaporated to dryness in the presence of a volatile aromatic compound (the matrix) that can adsorb light at specific wavelengths. Some of the anaylate eventually gets converted to the gas phase, and subsequent gaseous collisions enable the intermolecular transfer of charge, ionizing the analyte.

Matrix-assisted laser desorption/ionization (MALDI)

29

Charged droplets of analyate are sent through a chamber where they come out as ionized.

Electrospray ionization (ESI)

30

Ions are accelerated through an elongated chamber-given 2 ions of identical charge, the smaller ion will require less time to traverse through the chamber.
-measures the mass of ion by seeing how long (t) it will take for it to traverse the chamber.

Time-of-flight (TOF) mass analyzer

31

The utilization of 2 mass analyzers. Precursor ions from a first mass analyzer can be broken into smaller peptide chains by bombardment with atoms of an inert gas, yielding product ions.

Tandem mass spectrometry

32

Protect & deprotect COOH and NH groups to synthetically react amino acids together.

Solid-phase method

33

Developed to determine protein structure in atomic detail. The 3 components are: a protein crystal, a source of x-rays, and a detector.

X-ray crystallography

34

A mathematical relation applied to electron diffractions to determine amplitudes and calculated phases of every observed reflection.

Fourier transform

35

A 3-D graphic representation of where the electrons are most densely localized and is used to determine the positions of the atoms in the crystallized molecule.

Electron-density map

36

Is used to reveal the atomic structure of macromolecules in solution, provided that highly concentration solutions can be obtained. This technique depends on the fact that certain atomic nuclei are intrinsically magnetic.

Nuclear magnetic resonance (NMR) spectroscopy

37

The resonant frequency of a nucleus relative to a standard. Often the position and number are diagnostic of the structure of a molecule.

Chemical shift