Definitions

Question 1

Zwitter ions

Answer 1

Dipolar ion is a hybrid molecule containing positive and negative ionic groups
Proton moves from carboxyl group to amino group

Question 2

Achiral

Answer 2

Are superimposable on their mirror images

Question 3

Chiral

Answer 3

Are not superimposable over their mirror images

Question 4

Stereoisomers

Answer 4

Molecules that differ only in 3D configuration; also optical isomers

Question 5

Proteinogenic amino acids

Answer 5

Biosynthetically incorporated into protein chains by ribosomes

Question 6

Non-proteinogenic amino acids

Answer 6

Amino acids of polypeptides incorporated and chemically modified by non-ribosomal polypeptide synthesis and amino acid derivatives such as GABA, L-DOPA, and important metabolites

Question 7

Aliphatic

Answer 7

Lacks benzene ring

Question 8

Group 1

Answer 8

Non-polar: hydrophobic

Proline has an aliphatic cyclic structure => imino acid

Question 9

Group 2

Answer 9

Polar neutral amino acids

Polar side chains that are electrically neutral at neutral ph

Question 10

Group 3

Answer 10

Because of the presence of the carboxylate, the side chain of each amino acid is negatively charged at neutral ph

Question 11

Group 4

Answer 11

Basic amino acids

Basic side chains that are positively charged at or near neutral ph

Question 12

pI

Answer 12

Isoelectric pH at which positive and negative charges are the same
Isoelectric charge - molecules have no not charge

Question 13

Electrophoresis

Answer 13

Separation of polar compounds based on their mobility through a solid support. The separation depends on difference in the charge (pI) and molecular mass of the molecules
Zwitterions will not be mobile during electrophoresis

Question 14

Native conformations

Answer 14

3D shapes of proteins with specific biological activities

Question 15

Random coil

Answer 15

Large segment of protein with no specific structure

• NOT a denature protein
• a functional native conformation of the specific protein

Question 16

Primary structure

Answer 16

The order in which the amino acids in a protein are linked by peptide bonds

Question 17

Secondary structure

Answer 17

The arrangement in space of the backbone atoms in a polypeptide chain
-hydrogen bonding between the amide and the carbonyl groups of the peptide backbone
-the conformations of the side chains of the AA are not part of the secondary structure
a-helix, B- pleated sheet

Question 18

Tertiary structure

Answer 18

An arrangement in space of all the atoms in a protein, including those in the side chains and prosthetic groups (atom groups other than AA)

Question 19

Supersecondary structures and domains

Answer 19

BaB-motif
Helix turn helix
B-Meander
Greek key motif

Question 20

Electrostatic bonds

Answer 20

Exist between positively and negatively charged side chains

Question 21

Hydrophobic bonds

Answer 21

Exist between aromatic and aliphatic side chains

Question 22

Sequence similarity

Answer 22

a measure of matches
between two aligned sequences (from 0 to 100%)

Question 23

Homology

Answer 23

immeasurable conclusion that two sequences are so similar that they very likely evolved from the same common ancestor (25-30%)

Question 24

Orthology

Answer 24

means homology supported by a evidence that the proteins still retain the same function.

Question 25

X-Ray Crystallography

Answer 25

The protein structure is predicted by the diffraction pattern produced by exposure of a protein crystal to X rays. Only highly purified proteins can be crystalized. There is a big problem to obtain structures of fibrous and membrane bound proteins by this method

Question 26

X-Ray Crystallography problem

Answer 26

For one crystal, several diffraction patterns are produced under different angles. Then a Fourier series mathematical analysis is used to identify spatial positions of all atoms in the crystal. Then other computational programs are used to predict existence of covalent and noncovalent bonds between atoms

Question 27

NMR Spectroscopy

Answer 27

Another technique that supplements the results of X-ray diffraction has come into wide use recently. It is a form of 2D nuclear magnetic resonance (NMR) spectroscopy
Like X-ray diffraction, this method uses a Fourier series to analyse the resulted spectra and predict the distribution of hydrogen atoms in the structure. One way in which 2-D NMR differs from X-ray diffraction is that it uses protein samples in aqueous solution rather than crystals. This environment is closer to that of proteins in cells, and thus it is one of the main advantages of the method.
The best result is obtained when NMR and X-Ray crystallography supplement each other.

Question 28

Proteolytic activation

Answer 28

Regulates enzyme catalytic activity

A different regulatory motif is used to irreversibly convert an inactive enzyme (zymogens) to an active one.