CHEM 351: Biochemistry: Exam #1 pt. 2

What two forms of the amino acids can it exist in?

nonionic and ionic forms

What is the difference between the nonionic and ionic form of amino acids?

The nonionic form does

not occur in significant

amounts in aqueous

solutions.

What is the pI (isoelectric point)?

the pH at which the average net charge on the molecule is zero

What is the isoionic point pI?

the pH of a solution of a compound in which no other solutes are present

Why are pKas so imporant?

The acid-base properties of any protein are dependent solely on the ionizable groups present in the protein

What are peptide bonds?

form by condensation reactions between amino acids

What are polypeptides?

contain multiple, > about 20, amino acids covalently bonded via the peptide bond

What is the general molecular mass of polypeptides?

generally have molecular masses below about 10,000 daltons

What is the general molecular mass of proteins?

proteins generally have molecular masses of above 10,000 daltons

What is the most powerful technique for protein purification?

column chromatography

what does chromatography do?

separates mixtures into their constituent components

what does column chromatography require?

1. something to hold the system

2. matrix serving as stationary phase

3. Mobile phase

4. sample

What does ion exchange chromatography do?

separates based on charge

- everything with positive charge with stick to the beads

What is size exclusion chromatography?

relies on porous beads; larger molecules elute first because they are not trapped in small pores

What is affinity chromatography?

separates based on the ability of your protein to bind a specific ligand

what is HPLC? what are its specific characteristics?

High Performance L. C.

- typically used as qualitative and quanitative(analytically)

-operates under high pressure

- stainless steeling tubing and column used

what is FPLC? what are its specific characteristics?

Fast Protein L. C.

- typically used for preparatory

- does not operate under high pressures

- uses plastic or glass tubing and columns

What is an assay?

a procedure for analyzing the presence, amount, or activity of some molecule within a sample

What is electrophoresis?

the movement of charged particles in a fluid or gel under the influence of an electric field.

How do we sequence peptides?

we use automated procedures that employ the Edman Degradation.

What happens in edman degradation?

Edman Degradation cleaves the N-terminal residue which can then be identified by HPLC

How do we synthesize peptide?

Typically uses solid support beads, called Solid Phase Peptide Synthesis (SPPS).

What does peptide synthesis require?

Requires the use of protecting groups and activating groups.

What were Linus Pauling and Robert Corey findings?

-planar nature of the peptide bond

-alpha helix

-beta structure

- 3,10-helix

All alpha helixes are always ____ handed turns

right handed

What are the interactions that stabilized the helix in a hydrogen bond?

i and i+4 peptide groups are the main interactions that stabilize the helix.

What can affect the stability of the alpha helix?

-Side chains can affect the stability of the helix. The amino acid content.

-Terminating and capping residues can affect the stability of the helix

What are beta strands?

The backbone is extended in a zigzag structure, with the side chain groups extending perpendicular to the plane of the zigzag

What are antiparallel strands?

-strands where the protein molecules are oriented in opposite directions

What are parallel strands?

-strands where the protein molecules are all oriented in the same direction

What is the difference between loops and turns?

loop have no structure and turns are more structure/defined

What are turns?

Turns allow transitions between two α-helices, between α-helices and β-strands or between different strands of a β-sheet

Type 1 beta turns are distinctive because...

proline is typically in the #2 position

Type 2 beta turns are distinctive because...

there is no proline in the #2 position and it usually has glycine in the #3 position

Other than proline, >______% of peptide bonds in proteins are in the trans- configuration

>99.95%

Interactions between secondary structural elements lead to ________ structure

tertiary

What are the two major groups of proteins in terms of tertiary structures?

Fibrous and Globular proteins

What are fibrous proteins?

polypeptide chains arranged in long helices, strands and sheets

What are globular proteins?

polypeptide chains that are folded into a globular or somewhat spherical shape and more compact

What is a beta barrel?

beta-sheet composed of tandem repeats that twists and coils to form a closed toroidal structure in which the first strand is bonded to the last strand (hydrogen bond).