EXAM 2: review

Question 1

What are the three classes of proteins?

Answer 1

1. globular (blood/fluids)
2. Fibrous (collagen/structural)
3. Membrane (receptors/channels)

Question 2

What is resonance and how does it affect protein folding?

Answer 2

Donation of electrons; more resonance means easier folding.

Question 3

What is a Peptide?

Answer 3

A string of amino acids.

Question 4

What is the importance of ionic state in peptide bond?

Answer 4

They stabilize structures and the electrostatic attractions affect the structure.

Question 5

What is a Protein?

Answer 5

Proteins are polypeptide structures consisting of long chains of amino acids.

Question 6

What is a Zwitterion?

Answer 6

A functional group molecules in which at least one has a negative charge and one has a positive charge.

Question 7

What is an isoelectric Point and how does relative pH affect the protein’s charge?

Answer 7

The pH at which the molecule carries no net charge.

higher pH than IP is positive
lower pH than IP is negative

Question 8

What is Stereochemistry?

Answer 8

The study of the relative spatial arrangement of atoms that form the structure of molecules and their manipulation.

Question 9

What is chiral carbon?

Answer 9

Chiral carbons are carbons that are attached to four different substituents.

Question 10

What does light polarimetry do?

Answer 10

It is used for the analysis of chiral substituents and determines the concentration in solutions by passing light through a sample.

Question 11

What is an enantiomer?

Answer 11

An enantiomer is a pair of molecules that exists in two forms and are mirror images of one another but cannot be super imposed.

Question 12

What is an absolute enantiomer?

Answer 12

The exact 3D arrangement of atoms in a molecule.

Question 13

What is a relative enantiomer?

Answer 13

The described spatial arrangement of a molecule.

Question 14

What is Fischer’s Projection?

Answer 14

The abbreviated structural forms allow one to convey valuable information to a chemist.

Question 15

What is protein folding?

Answer 15

The process in which a protein chain is translated into its native 3D shape.

Question 16

What is the process for identifying R and S enantiomers?

Answer 16

1. assign the priorities for chiral carbons
2. trace priorities from 1 - 4
3. assign R and S as the following

when 4 is in the front
CW is S => CC is R
when 4 is in the back
CW is R => CC is S

Question 17

What are the 4 levels of protein structure?

Answer 17

Primary, Secondary, Tertiary, and Quaternary

Question 18

What are the three local arrangements of Secondary Structures?

Answer 18

Alpha helix, Beta sheets/strings, and Beta coils

Question 19

What forces stabilize protein structures?

Answer 19

1. hydrogen bonds
2. disulfide linkages
3. Van-Der-Waals forces
4. electrostatic forces

Question 20

Where are the R groups in an Alpha Helix?

Answer 20

The R groups are facing outside of the helix.

Question 21

Where are the R groups in a Beta Helix?

Answer 21

The R groups extend above and below the plane of sheet 3.

Question 22

What proteins make a helix?

Answer 22

Methionine, alanine, leucine, glutamine, and lysine.

Question 23

What proteins make beta turns?

Answer 23

Glysine, proline, asparagine, aspartic acid.

Question 24

What is the Ribonuclease Refolding Experiment and what did it imply?

Answer 24

The proteins were broken down and denatured and they eventually reformed.

implied that the sequence of amino acids determines the structure and its folding.

Question 25

What is Levinthal’s Paradox?

Answer 25

The time it would take for protein to fold randomly is in the millions of years; this implies that protein folding is not by chance and is spontaneous.

Question 26

What is the role of Gibb’s free energy in protein folding?

Answer 26

The amino acid sequence of a protein determines the native structure.

The native structure has the lowest Gibb’s, so the delta G will be negative and spontaneous, explaining the Levi- paradox.

Question 27

What are some advantages of quaternary structure?

Answer 27

1. allows multiple functions
2. allows complicated conformational changes
3. conserves resources / up efficiency
4. increased stability
5. assembly of catalytic sites is facilitated

Question 28

What amino acids are in Collagen

Answer 28

ALL OF THEM

mainly: proline, glycine, and hydroxyproline

NOTE: triple helix structure

Question 29

What is a polyclonal antibody?

Answer 29

Antibodies with many different cells that have the affinity for the same antigen with different epitomes.

Question 30

What is a monoclonal antibody?

Answer 30

Antibodies with singular, identical immune cells.

Question 31

What is ELISA?

Answer 31

An assay test is used to detect antibodies and antigens by using fluorescent chemicals that bind to antigens; the concentration is measured by light absorbance.

Question 32

What is Western Blot?

Answer 32

An analytical technique to identify a specific protein in a complex mixture of them; electrophoresis is just the first step.

Question 33

What is SDS-Page?

Answer 33

A test where molecules are put into a mixture and put into wells where the proteins are moved through a medium, sorted by size forming bands by which they can be identified.

Question 34

What is the difference between SDS-Page and size exclusion chromatography?

Answer 34

Size exclusion is used for purification, whereas SDS-Page is used for identification.

Question 35

What is a specific activity assay?

Answer 35

It is a measure of enzyme processivity at a specific substrate concentration; measures enzyme efficiency and purity.

Allows to compare enzymes and tests across different labs.