1. Amino Acids Flashcards
Slide 1
What are the common structural features of amino acids?
- R-group (side chain)
- Alpha carbon (C connected to COO(-/H)
- Amino group (NH3+)
What are the alpha and beta carbons?
______ is the only standard amino acid without a Beta carbon
_____ and _____ have branched Beta-Carbons
_____ has a branched gamma-Carbon
Alpha is the Carbon connected to the Carboxylic acid carbon (carbon Number 1)
Beta is the carbon connected to alpha in the R group
Glycine is the only standard amino acid without a Beta carbon
Valine and isoleucine have branched Beta-Carbons
Leucine has a branched gamma-Carbon
Nine amino acids with Non-polar side chains?
- Glycine Gly G
- Alanine Ala A
- Valine Val V
- Leucine Leu L
- Isoleucine Ile I
- Methionine Met M
- Proline Pro P
- Phenylalanine Phe F
- Tryptophan Trp W
Six Amino Acids with Uncharged Polar Side Chains
- Serine Ser S
- Threonine Thr T
- Asparagine Asn N
- Glutamine Gln Q
- Tyrosine Tyr Y
- Cysteine Cys C
Five Amino Acids with charged polar side chains?
- Lysine Lys K (Basic/Positive)
- Arginine Arg R (Basic/pos)
- Histidine His H (Basic / POS - Aromatic)
- Aspartic Acid Asp D (Acidic / NEG)
- Glutamic Acid Glu E (Acidic / NEG)
Masses of amino acids (and proteins) are typically given in units of ______
1 ___ = ____
Masses of amino acids (and proteins) are typically given in units of Daltons (Da)
1 dalton = 1/12 the mass of 12C =1g/mol
What is the mass difference between a Free amino acid and an amino acid residue?
The free amino acid will be 18Da heavier than the same amino acid as a residue
eg: Glycine = 75Da as a Free AA and 57Da as a residue
(The mass of H2O = 18Da - lost during bonding)
What are the one letter codes for:
- Cysteine
- Histidine
- Isoleucine
- Leucine
- Methionine
- Serine
- Valine
- Alanine
- Glycine
- Proline
- Threonine
- Arginine
- Phelyalanine
- Tyrosine
- Tryptophan
- Aspartic acid
- Glutamic acid
- Asparagine
- Glutamine
- Lysine
What are the one letter codes for:
- Cysteine - C
- Histidine - H
- Isoleucine - I
- Leucine - L
- Methionine - M
- Serine - S
- Valine - V
- Alanine - A
- Glycine - G
- Proline - P
- Threonine - T
- Arginine - R
- Phelyalanine - F
- Tyrosine - Y
- Tryptophan - W
- Aspartic acid - D
- Glutamic acid - E
- Asparagine - N
- Glutamine - Q
- Lysine - K
Features of the imidazole ring of histidine:
- _____
- _____
- _____
- _____
Features of the imidazole ring of histidine:
- aromatic
- weak base (pKR around 6.0)
- Protonated forms distribute the positive charge between the two nitrogen atoms
- Two tautomers exist for the neutral form
Aromatic groups in which two amino acids are of particular use in spectroscopy? Why?
Tyr and Trp (tyrosine and tryptophan) - both absorb strongly in ultraviolet wavelengths (~280nm) which allows for spectroscopic studies of protein preparations (and distinction from nucleic acid preparations)
Absorption peak reflects proportion of protein
Page 16
How is a disulfide bond formed between cysteines?
- Two molecules of cysteine are oxidized to form a disulfide bridge
- In oxidizing conditions (extracellular/lumen - exterior membrane associated/secreted proteins) cysteine is oxidized to cystine (Non polar; disulfide bond “covalent cross link”
- In reducing conditions (cytosol) - Cysteine maintained as free thiol
What is Selenocysteine?
How might it be incorporated into proteins?
Sec, U
Uncommon amino acid - structure similar to Cysteine but Selenium replaces the Sulfur
Derived from serine - incorporated as part of protein synthesis in some organisms (bacteria for eg)
________ is often used in laboratory protein synthesis to replace methionine
Functionally equivalent to methionine but provides useful spectroscopic characteristics
Selenium replaces sulfur
Selenomethionine is often used in laboratory protein synthesis to replace methionine
Functionally equivalent to methionine but provides useful spectroscopic characteristics
Selenium replaces sulfur
SLIDE 17
_______has been found inserted into polypeptides of certain organisms, the side chain is formed from two lysine chains. The ring Nitrogen is weakly basic
SLIDE 17
Pyrrolysine (Pyl, O) has been found inserted into polypeptides of certain organisms, the side chain is formed from two lysine chains. The ring Nitrogen is weakly basic
Denaturing a protein is destruction of:
Tertiary structure
Define the pKa of a functional group?
- The pKa of a functional group is the pH at which the conjugate acid and base concentrations are equal
- pH < pKa the acid form dominates ( [A] < [HA] )
- pH > pKa the Base form dominates ( [A] > [HA] )
A = base
HA = conjugate acid
What is the Henderson-Hasselbalch Eq’n?
Describes:
Relates:
pH = pKa + log ( [A] / [HA] )
Describes the shape of the titration curve for all weak acids
Relates pH, pKa and buffer concentration
Equation to calculate Ka?
Ka = ( [H+] [A-] ) / [HA]
Equation for pKa and pH
HA ⇠⇢ H+ + A- OR H- + A+
pKa = pH - log ( [A] / [HA] )
pH = pKa + log [A-]/[HA]