Protein Structure
What direction are proteins named?
N terminus to C terminus
How many Common Amino Acids are there?
20
Amino Acid chains are held together with what kind of bond?
Peptide Bonds
Beta Turns contain how many Amino Acids?
4 Amino Acids
A molecule with a small pKa would be?
Very Acidic
What is an Amphipathic Helix?
A Helix with mostly hydrophobic residues on one side and hydrophilic residues on the other.
What are Amino Acids made of?
Amine group, Carboxylic Acid, Variable R group
What do the phi and psi bond angles refer to?
Bond rotations in a peptide bond. Phi bond angles correlate to the N-alphaC bond. Psi bond angles correlate to the C-alphaC bond.
What protein technique is used to separate proteins by size or remove salts?
Dialysis
What are Buffers?
Conjugate Acid-Base pair that resists pH changes (generally 1 pH unit from their pKa)
What are the main types of Tertiary Protein Structures?
Fibrous Proteins, Globular Proteins, Membrane Proteins, and Intrinsically Disordered Proteins
What are the Acidic Amino Acids?
Glutamic Acid/Glutamate, Aspartic Acid/Aspartate
What interactions Stabilize an Alpha Helix?
Interactions 3 or 4 residues away. Salt-bridges, pi-pi stacking, hydrophobic and hydrophilic interactions
In Gel Electrophoresis the proteins that travel the farthest are?
Smallest Proteins
When is an Amino Acid a Zwitterion?
When an Amino Acid has a positively charged Amine group, a negatively charged Carboxylic Acid group, and a neutral R group.
What is the difference between a Homodimer and a Heterodimer? What are their similarities?
What makes Cysteine unique?
It can make disulfide bonds with other Cysteines.
What bonds hold Beta Strands together to form a Beta Sheet?
Hydrogen bonding of the peptide backbone.
What kind of peptide synthesis joins smaller pieces together to make a larger protein?
Native Chemical Ligation
When an Amino Acid is at a pH above its pKa what happens to it?
It becomes deprotonated, or loses its H+
What kinds of proteins provide structure with varying amounts of flexibility, has repeating secondary structural elements and are generally insoluble in water?
Fibrous Proteins like collagen, keratin and fibroin
What Amino Acids make up this peptide? AQLDRWT
Alanine, Glutamine, Leucine, Aspartic Acid, Arginine, Tryptophan, Tyrosine
In Anion Exchange Chromatography which proteins exit first and why?
Cations (basic) proteins. The column is lined with cations so all the anions (acidic) will stick to it slowing them down.
Which proteins have complex folding, a hydrophobic core, and often have multiple domains?
Globular Proteins
To find the pI of a small peptide with 2 acidic residues and one neutral you would?
Average the 2 most acidic residues.