EXAM 2: review Flashcards
What are the three classes of proteins?
- globular (blood/fluids)
- Fibrous (collagen/structural)
- Membrane (receptors/channels)
What is resonance and how does it affect protein folding?
Donation of electrons; more resonance means easier folding.
What is a Peptide?
A string of amino acids.
What is the importance of ionic state in peptide bond?
They stabilize structures and the electrostatic attractions affect the structure.
What is a Protein?
Proteins are polypeptide structures consisting of long chains of amino acids.
What is a Zwitterion?
A functional group molecules in which at least one has a negative charge and one has a positive charge.
What is an isoelectric Point and how does relative pH affect the protein’s charge?
The pH at which the molecule carries no net charge.
higher pH than IP is positive
lower pH than IP is negative
What is Stereochemistry?
The study of the relative spatial arrangement of atoms that form the structure of molecules and their manipulation.
What is chiral carbon?
Chiral carbons are carbons that are attached to four different substituents.
What does light polarimetry do?
It is used for the analysis of chiral substituents and determines the concentration in solutions by passing light through a sample.
What is an enantiomer?
An enantiomer is a pair of molecules that exists in two forms and are mirror images of one another but cannot be super imposed.
What is an absolute enantiomer?
The exact 3D arrangement of atoms in a molecule.
What is a relative enantiomer?
The described spatial arrangement of a molecule.
What is Fischer’s Projection?
The abbreviated structural forms allow one to convey valuable information to a chemist.
What is protein folding?
The process in which a protein chain is translated into its native 3D shape.
What is the process for identifying R and S enantiomers?
- assign the priorities for chiral carbons
- trace priorities from 1 - 4
- 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
What are the 4 levels of protein structure?
Primary, Secondary, Tertiary, and Quaternary
What are the three local arrangements of Secondary Structures?
Alpha helix, Beta sheets/strings, and Beta coils
What forces stabilize protein structures?
- hydrogen bonds
- disulfide linkages
- Van-Der-Waals forces
- electrostatic forces
Where are the R groups in an Alpha Helix?
The R groups are facing outside of the helix.
Where are the R groups in a Beta Helix?
The R groups extend above and below the plane of sheet 3.
What proteins make a helix?
Methionine, alanine, leucine, glutamine, and lysine.
What proteins make beta turns?
Glysine, proline, asparagine, aspartic acid.
What is the Ribonuclease Refolding Experiment and what did it imply?
The proteins were broken down and denatured and they eventually reformed.
implied that the sequence of amino acids determines the structure and its folding.
What is Levinthal’s Paradox?
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.
What is the role of Gibb’s free energy in protein folding?
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.
What are some advantages of quaternary structure?
- allows multiple functions
- allows complicated conformational changes
- conserves resources / up efficiency
- increased stability
- assembly of catalytic sites is facilitated
What amino acids are in Collagen
ALL OF THEM
mainly: proline, glycine, and hydroxyproline
NOTE: triple helix structure
What is a polyclonal antibody?
Antibodies with many different cells that have the affinity for the same antigen with different epitomes.
What is a monoclonal antibody?
Antibodies with singular, identical immune cells.
What is ELISA?
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.
What is Western Blot?
An analytical technique to identify a specific protein in a complex mixture of them; electrophoresis is just the first step.
What is SDS-Page?
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.
What is the difference between SDS-Page and size exclusion chromatography?
Size exclusion is used for purification, whereas SDS-Page is used for identification.
What is a specific activity assay?
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.
