What is the naturally occuring configuration for amino acids?
L amino acids are naturally occurring
L = left
LA, DC
What is the naturally occurring configuration for sugars?
D-carbohydrates are the naturally occuring form
D = right
LA, DC
What group is always at the top for a Fischer projection?
The most oxidized group (Carboxylic acid)
Polymerization reactions are typically ___directional and ____?
Polymerization reactions are typically uni-directional and highly specific
Strecker Synthesis
Non-stereoselective synthesis of an amino acid from an Aldehyde
Aldehyde attached to the R-group you want to end with
Gabriel-Malonic Ester Synthesis
Nonstereoselective synthesis of an amino acid from n-phalthimidomalonic ester
Alkyl halide with R-group you want to end with
What are the differences between strong and weak acids?
Strong acids dissociate completely
Ka > 1
Pka < 0
Weak acids don’t dissociate completely
Ka < 1
Pka > 0
When the pH > Pka
Compound is deprotonated
Same when pH > pI
(pKa of carboxylic acid = 2, pKa of amine = 10)
Through what mechanism does a peptide bond form?
Peptide bonds = amides
Forms through an addition-elimination mechanism
Is non-spontaneous and must be enzyme catalyzed
Peptide Bond Characteristics
Due to resonance, peptide bond qcquires
- Partial bond character
- Planar
- Cannot rotate
- Amide H is slightly acidic
What is the difference between peptide bond hydrolysis in vitro and in vivo?
Peptide bond hydrolysis is extremely slow and normally doesn’t occur
- In vitro* - strong acids, high temperatures, and long reaction time may result in complete hydrolysis of all peptide bonds
- In vivo* - proteases result in partial hydrolysis of peptides, catalyzing hydrolysis of specific peptide bonds
What is the repeating peptide backbone?
N-CalphaCcarbonyl
What are the bond forces that govern tertiary structure?
- Hydrogen bonds
- S-S bonds
- Van der Waals Interactions (Hydrophobic forces)
- Ionic Bonds (Salt bridges)
Quaternary structure are governed by the same forces as tertiary structure
Example of tertiary structure - myoglobin
Example of quaternary structure - hemoglobin, DNA polymerase
What is denaturation?
Disruption of a proteins 3D structure without breaking peptide bonds
Affects secondary, tertiary, and quaternary only
Can occur at high temperatures, pH, changes in [salt], addition of urea
Denaturation causes the protein to lose function; Removal of the denaturing agent sometimes allows for renaturation of the protein
Is an aldose a ketose or an aldehyde?
Aldose = aldehyde
Ketose = Ketone
Alpha vs Beta anomers
Alpha anomer = axial
Beta anomer = equatorial
When a cyclic sugar is a hemiacetal..
It is in equilibrium
Mutarotation occurs (constantly changes between open and closed form)
It is a reducing sugar (is oxidized)
When a cyclic sugar is an acetal
The sugar is NOT in equilibrium
Mutatrotation does NOT occur
It is a non-reducing sugar
What does the Benedict’s Test identify?
It identifies a reducing sugar (is oxidized) via a redox reaction
If a precipitate is present = positive test, indication a reducing sugar is present
If there is a hemiacetal, there is a reducing sugar
How would you name a glysodic linkage?
- Indicate the anomeric form of the leftmost sugar (alpha or beta)
- Indicate the two carbons connected by the bridging oxygen
What is the mneumonic for waves?
Raging Martians Invaded Venus Using X-ray Guns
- Increasing frequency
What is a chelate?
A metal atom in a cyclic structure
They are Lewis Bases
What is a Lewis Base
An electron pair donor
- Donates electrons in a coordinate bond
- Nucleophiles
What is a Bronsted Base?
Accepts a Hydrogen atom
