Term
|
Definition
| Linear sequence in amino acids |
|
|
Term
| Define secondary structure |
|
Definition
| regular repetitive patterns over short regions of the peptide |
|
|
Term
| What are the two secondary structures |
|
Definition
|
|
Term
| Define tertiary structure |
|
Definition
| Overall folding pattern of the peptide |
|
|
Term
| Define quaternary structure |
|
Definition
| The assembly of several protein molecules to form a larger complex with distinct properties |
|
|
Term
True or False
Amino acids located close to each other have a large effect on protein structure, even if they are far apart in the sequence of amino acids |
|
Definition
|
|
Term
| Individual helical structures in myoglobin are an example of what level of protein folding? |
|
Definition
|
|
Term
| The combination of 8 alpha helical structures to enclose a central cavity (myoglobin) is an example of what kind of protein folding? |
|
Definition
|
|
Term
| The assembly of four globin subunits to form hemoglobin is an example of what type of protein structure? |
|
Definition
|
|
Term
| Peptide bonds between amino acids can be broken via _______ |
|
Definition
|
|
Term
| What classification of enzymes catalyzes the hydrolysis of peptide bonds? |
|
Definition
|
|
Term
| What are the four atomic forms that act as nucleophiles? |
|
Definition
|
|
Term
| What are the 3 ways a nucleophile may 'use' its lone pair of electrons? |
|
Definition
-Hydrogen bond acceptor (by attracting an OH or NH group)
-as a base (if it captures H+)
-As a nucleophile (shares lone pair to form a new bond) |
|
|
Term
| Define nucleophilic displacement |
|
Definition
| When a nucleophile targets an atom causing another group to leave |
|
|
Term
| Describe the stability of the transition state that forms when a nucleophile targets a molecule |
|
Definition
| It is semi-stable (leaving group is still attached) |
|
|
Term
| How can you identify the first amino acid in a sequence? |
|
Definition
| tag it with flurodinitrobenzene which is bright yellow |
|
|
Term
| What method did Fred Sanger develop to identify AA sequence in a protein? |
|
Definition
-tagged the N terminus with fluorodinitrobenzene (Yellow)
-hydrolyzes the peptide bond; N-terminal amino acid is released |
|
|
Term
| Why did Fred Sanger's method prove uneffective? |
|
Definition
| Because all of the amino acids of the peptide continued to be hydrolyzed |
|
|
Term
| Who improved Fred Sanger's method? |
|
Definition
|
|
Term
| How was Edman's method an improvement? |
|
Definition
| The individual removal of N-terminal amino acids can be removed controlled and without hydrolyzing all peptide bonds at once |
|
|
Term
| What is the first step of Edman Degredation? (the coupling step) |
|
Definition
- carried out in a weak base
- um
- N-terminal amino group reacts with phenylisothiocyanate to produce a PTC carbonate |
|
|
Term
| What is the second step of Edman Degredation? (the cyclization step) |
|
Definition
- carried out in an anhydrous acid
- coupled product from step one is attacked and the N-terminal AA is released |
|
|
Term
| What are short segments of a peptide called? |
|
Definition
|
|
Term
| What is selective hydrolysis? |
|
Definition
| When an enzyme cuts peptides at specific points along the chain |
|
|
Term
| What digestive enzyme recognizes & cuts at R and K? |
|
Definition
|
|
Term
| What digestive enzyme recognizes & cuts at W, Y & F? |
|
Definition
|
|
Term
| Where in the targeted amino acid does the digestive enzyme position itself? |
|
Definition
| at the carboxylate group of the targeted AA |
|
|
Term
How many segments will chymotrypsin cut this peptide into?
M I D W E F S G Y P T R A V
A |
|
Definition
|
|
Term
| What chemical reagent cuts amino acids at methionine residues? |
|
Definition
|
|
Term
| Why are single bonded molecules flexible? |
|
Definition
| because of rotation about the bond axis |
|
|
Term
| Chain flexibility arises from bond ______ not bond ________ |
|
Definition
|
|
Term
| What is the difference between a configuration or conformation? |
|
Definition
Conformation: can be changed by rotating bonds (no bonds broken)
Configuration: bonds are broken, not rotated e.g. changing from cis to trans form |
|
|
Term
| How can x ray diffraction be used to determine patterns of molecules? |
|
Definition
-molecules arranged in repetitive patterns will deflect xrays at specific angles creating a consist pattern
-dimensions of the molecular pattern can then calculated based on the known wavelength of the xray |
|
|
Term
| What is the conversion of 1 angstrom to meters? |
|
Definition
|
|
Term
| Who created accurate models of peptide chains? What was his key finding? |
|
Definition
Linus Pauling
peptide bond has double bond character |
|
|
Term
| What does the statement 'peptide bonds have double bond character' mean? |
|
Definition
-peptide bonds have 2 resonance forms, one with a double bond
-acts more like a double than a single
-the peptide bond is rigid, fixed in trans form |
|
|
Term
True or False
When bond rotation is restricted only a few possible structures can be formed? |
|
Definition
|
|
Term
| In a peptide chain, which bonds are fixed and which can rotate freely? |
|
Definition
-alpha amino and alpha carboxylate are fixed
-R group and H on the alpha carbon can rotate |
|
|
Term
True or False
In a helical shape, every alpha-C bond rotates in the same direction |
|
Definition
|
|
Term
| What is the extended shape of a peptide chain? |
|
Definition
| bonds rotate in opposite directions |
|
|
Term
| If there is no regular repeating structure in a peptide chain, what will the resulting shape be? |
|
Definition
|
|
Term
| In extended conformation, if strands run in the same direction what shape will be formed? How do the H bonds bonds connect? |
|
Definition
parallel B sheet
H bonds connect strand to strand |
|
|
Term
| In extended conformation, if strands run in opposite direction what shape will be formed? |
|
Definition
antiparallel B sheet
H bonds align better |
|
|
Term
| Why do bulky/large AAs form extended shapes? |
|
Definition
| Because it allows for maximum space |
|
|
Term
| Which AA's form B sheets? |
|
Definition
Tryp, Tyr, Phe, Val, Ile, Thr, Cys
WYFVITC |
|
|
Term
| Which AA's act as secondary structure breakers? |
|
Definition
GPNDS
Glycine, Proline, Asparagine, Aspartate, Serine |
|
|
Term
| What do secondary structure breakers do? How many are required to have an effect? |
|
Definition
form a turn or flexible loop which changes direction of the peptide
at least 2/4 |
|
|
Term
| If a protein is in its normal 3D structure it is in its _______ state |
|
Definition
|
|
Term
True or false
Denaturation is often irreversible |
|
Definition
|
|
Term
| What is the simplest possible tertiary structure? |
|
Definition
| continuous (all alpha helical or all beta) |
|
|
Term
| What is the major driving force in protein folding? What does this mean? |
|
Definition
hydrophobic effect
-non polar amino acids are kept inside
-polar AAs form outer layer |
|
|
Term
| What does 'good fit' mean in regards to protein structure? |
|
Definition
| Tertiary folding maximizes number of closer contacts |
|
|
Term
| Mostly alpha AAs will form what tertiary structure? |
|
Definition
|
|
Term
| Mostly beta AAs will form what tertiary struture? |
|
Definition
|
|
Term
| What will happen if a B sheet is polar on one side and nonpolar on the other? |
|
Definition
| Will wrap around to enclose the non-polar side |
|
|
Term
| what is a parallel B sheet composed of? |
|
Definition
-mostly non polar AAs
-alternating alpha & beta secondary structures |
|
|
Term
| What forces stabilize the structure of a protein? |
|
Definition
Non-covalent interactions (LDF/van der waals & hydrophobic effect)
H-bonds
Ion exchange (e.g. salt bridges) |
|
|
Term
| When would an disulfude bridge occur in protein folding? What functional groups/atoms are typically involved? |
|
Definition
-if two oppositely charged AAs align
-pairs Cys SH groups react together & bond, releasing water |
|
|
Term
| Where are you most likely to find polar interactions that are essential for maintaining structure? Why? |
|
Definition
| On the inside of the protein rather than on the surface |
|
|
Term
| What effect does urea have on protein folding? |
|
Definition
| weakens the hydrophobic effect so the protein unfolds |
|
|
Term
| What effect does 2-mercaptoethanol have on protein folding? |
|
Definition
| It's a reducing agent, will break disulfide bonds. |
|
|
Term
True or False
A protein that has been exposed to urea can re-fold to its original structure when urea is removed. |
|
Definition
True
Remove urea, allow to refold, then expose the protein to O2 so the disulfide bonds can re-form |
|
|
Term
| What might happen if a protein that was denatured by urea were exposed to O2 before having a chance to refold? |
|
Definition
| The disulfides would pair up randomly so it wouldn't fold properly back to its original structure |
|
|
Term
| What are the characteristics of a parallel beta sheet |
|
Definition
-sections of B amino acids alternating with sections of alpha amino acids
-B segments follow the same direction
-B/A/B fold to form a parallel sheet
-mainly NON POLAR AAs |
|
|
Term
| What are the characteristics of an antiparallel beta sheet? |
|
Definition
-B AA's
-can be polar on one side non polar on the other (AAs would alternate polar/non polar)
-if this is the case the non polar side will be enclosed in the center |
|
|
Term
| If a beta sheet only 3-5 strands long folds back on itself what shape will be formed? |
|
Definition
|
|
Term
| What are the characteristics of a parallel beta sheet? |
|
Definition
-segments of alpha helixes & beta sheets
-beta sheets run in the same direction
-primarily non polar AAs |
|
|
Term
| What are the characteristics of a parallel alpha-beta barrel? |
|
Definition
-segments of alpha helices & B sheets
-B sheets run in the same direction
-alpha helices are all on one side of the B sheets |
|
|
Term
| Who demonstrated that denaturing by urea could be reversed? |
|
Definition
|
|
