Chapter 3 - Exploring proteins and proteomes

Question 1

Proteins can be separated from one another on the basis of

Answer 1

solubility, size, charge, and binding ability.

Question 2

Genomes

Answer 2

The complete DNA base sequences.

Question 3

Proteome

Answer 3

The entire complement of proteins that is or can be expressed by a cell, tissue, or organism.

Question 4

The proteome is much _______ than the genome.

Answer 4

larger

Question 5

The purification process of proteins is an essential first step in

Answer 5

understanding their function.

Question 6

Purification should yield a sample containing

Answer 6

only one type of molecule.

Question 7

Assay

Answer 7

An analytical procedure to detect and quantify cellular process or metabolic reactions.

Question 8

A positive result on the assay indicates

Answer 8

that the protein is present.

Question 9

Specific activity

Answer 9

the ratio of enzyme activity to the amount of protein in the mixture.

Question 10

Ideally, the specific activity will ______ as the purification proceeds.

Answer 10

rise

Question 11

Common protein purification techniques

Answer 11

• salting out
• dialysis
• gel-filtration chromatography
• ion-exchange chromatography
• affinity chromatography
• HPLC

Question 12

Salting out

Answer 12

Most proteins are less soluble at high salt concentrations and can be precipitated out of solution.

Question 13

Dialysis

Answer 13

Separating proteins from small molecules through a semipermeable membrane.

Question 14

In IEC, to force the migration of analytes, mobile phases consist of

Answer 14

buffers, often with increasing ionic strength (e.g. a higher concentration of NaCl).

Question 15

Affinity chromatography is

Answer 15

a separation method based on a specific binding interaction between an immobilized ligand and its binding partner.

Question 16

Transcription factors

Answer 16

proteins that regulate gene expression by binding to specific DNA sequences.

Question 17

What is the absorbance wavelength of a peptide bond?

Answer 17

220 nm.

Question 18

Velocity of a protein in an electric field equation

Answer 18

v = Ez/f

E = electric field strength

z = charge

f = frictional coefficient

Question 19

In gel electrophoresis, small molecules will

Answer 19

move faster through the gel.

Question 20

The isoelectric point (pI) of a protein is the

Answer 20

pH at which its net charge is zero.

Question 21

Isoelectric focusing

Answer 21

A method of separating proteins according to their isoelectric point.

Question 22

SDS-PAGE

Answer 22

sodium dodecyl sulfate - polyacrylamide gel electrophoresis

Question 23

In 2-D electrophoresis, proteins are separated vertically by _______ and horizontally by ________.

Answer 23

mass; isoelectric point

Question 24

sediment coefficient equation

Answer 24

s = m(1 - vp)/f

m = mass

v = partial specific volume

p = density of the medium

f = frictional coefficient

Question 25

Sediment coefficients are usually expressed in

Answer 25

Svedberg units (S)

Question 26

The smaller the S value, the

Answer 26

slower a molecule moves in a centrifugal field.

Question 27

The sedimentation technique for determining mass is

Answer 27

very accurate.

Question 28

Antibody

Answer 28

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

Question 29

Antigen

Answer 29

A foreign substance in the body which results in the production of antibodies.

Question 30

Epitope

Answer 30

The part of the antigen molecule to which the antibody attaches itself.

Question 31

The specificity of the antibody-antigen interaction is a consequence of

Answer 31

the shape complementarity between the two surfaces.

Question 32

Polyclonal antibodies

Answer 32

A heterogeneous mix of antibodies, derived from the immune response of many different B-cells.

Question 33

ELISA stands for

Answer 33

Enzyme-linked immunosorbent assay

Question 34

Indirect ELISA is used to detect

Answer 34

the presence of antibody.

Question 35

Sandwich ELISA is used to detect

Answer 35

the presence of antigen.

Question 36

Fluorescent markers provide a powerful means of

Answer 36

examining proteins in their biological context.

Question 37

Synthetic peptides can serve as antigens to

Answer 37

stimulate the formation of specific antibodies.

Question 38

Synthetic peptides can be used to isolate receptors for

Answer 38

many hormones and other signal molecules.

Question 39

Solid phase peptide synthesis involves

Answer 39

the successive addition of protected amino acid derivatives to a growing peptide chain immobilized on a solid phase.

Question 40

3 components in x-ray crystallographic analysis.

Answer 40

• protein crystal
• source of x-rays
  
  • detector

Question 41

3 basic principles underlying x-ray diffraction

Answer 41

1. Electrons scatter x-rays
2. The scattered waves recombine
3. The way waves recombine depends only on the atomic arrangement

Question 42

NOESY stands for

Answer 42

nuclear Overhauser enhancement spectroscopy