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]
What is Isoelectric point (pI)?
- pH at which the net charge on a molecule is zero
- Diprotic amino acids:
- Average of pK1 and pK2 (balance btwn NH3+ and COO-)
- Triprotic: Average of pK values bounding species with net 0 charge
- Diprotic amino acids:
pH > pI =
pH < pI =
pH > pI = excess OH- = deprotonates = NEG (COO– and NH2)
pH < pI = excess of H+ = protonated = Pos (COOH and NH3+)
Define Diprotic:
Two titratable groups
- Have 2 buffering regions, each centered around the pKa of the carboxylic group (pK1) or the amino group (pk2)
Eg: Glycine:
pk1 = 2.34
pk2 = 9.78
pI = (2.34+9.78) / 2 = 6.06 (where [COO-] = [NH3+]
Acid/base property of Histidine?
Histidine is a weak acid
How to calculate the fraction of the side chain that is protonated under a certain pH?
Use His (pKR = 6.04): what fraction of side chain is protonated at pH 7?
Ratios converted to fractions:
See image
What are the titratable groups in amino acids?
- Glu, Asp, C-Terminus
- Lys, N-terminus
- His
- Arg
- Cys
- Tyr
- How does environment impact the pka values for functional groups?
- Presence of ____-groups
- example:
- Presence of other charged groups
- Nearby Neg charges will _____ pka
- Nearby Pos charges will ______ pka
- ex:
- Presence of ____-groups
- How does environment impact the pka values for functional groups?
- Presence of electron withdrawing-groups
- example: Example: pKa of alpha amino group DROPS because of alpha carboxyl (becomes stronger acid - more deprotonated in water)
- presence of e- - withdrawing groups DECREASES pka
- Presence of -groups
- Nearby Neg charges will often raise a pka value
- Nearby Pos charges will often lower pka value
- ex: pKa of alpha-carboxylate drops because of alpha-amino group
- Presence of electron withdrawing-groups
The pKR of selenocysteine is 5.43. What effect will this have on the pI of Sec relative to that of Cys? Assume pK1 and pK2 are unchanged.
A.Decrease
B.Stay the same
C.Increase
D.Impossible to predict
The pKR of selenocysteine is 5.43. What effect will this have on the pI of Sec relative to that of Cys? Assume pK1 and pK2 are unchanged.
A. Decrease
B. Stay the same
C. Increase
D. Impossible to predict
Draw the structure of the tripeptide YEG.
How would you determine pI on the tripeptide YEG?
See image
Identify and describe shared structural features of the common amino acids.
Each amino acid has the same fundamental structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom.
Identify the 20 common amino acids by name, 3-letter code and 1-letter code.
- Non-polar
- G
- A
- V
- L
- I
- M
- P
- F
- W
- Uncharged Polar
- S
- T
- N
- Q
- Y
- C
- Charged Polar
- K
- R
- H
- D
- E
- Non-polar
- G - Gly - Glycine
- A - Ala - Alanine
- V - Val - Valine
- L - Leu - Leucine
- I - Ile - Isoleucine
- M - Met - Methionine
- P - Pro - Proline
- F - Phe - Phenylalanine
- W - Trp - Tryptophan
- Uncharged Polar
- S - Ser - Serine
- T - Thr - Threonine
- N - Asn - Asparagine
- Q - Gln - Glutamine
- Y - Tyr - Tyrosine
- C - Cys - Cysteine
- Charged Polar
- K - Lys - Lysine (basic (pos))
- R - Arg - Arginine (basic (pos))
- H - His - Histidine (Basic aromatic)
- D - Asp - Aspartic Acid ( Acidic - NEG)
- E - Glu - Glutamic Acid (Acidic - Neg)
PENDING:
Classify and describe the 20 common amino acids by the chemical and physical properties of their R-groups, including polarity, aromaticity, charge, hydrogen-bonding ability, size and shape.
pending
NEEDS ANSWERED
- Describe the special properties of Tyr, Trp, Cys, His and Pro.
- Proline Pro P
- Cyclic
- only amino acid where the side chain is connected to the protein backbone twice, forming a five-membered nitrogen-containing ring
- Tyr Tyrosine
- it is capable of donating both an electron and a proton in enzymatic reactions. As a result, a Tyr is found in the active sites of a number of enzymes such as galactose oxidases, ribonucleotide reductase, and cytochrome c oxidase (CcO)
- Trp W
- It is the largest of all twenty amino acids
- side chain is indole, which is aromatic with a binuclear ring structure, whereas those of Phe, Tyr, and His are single-ring aromatics
- Cys
- Cysteine contains a reactive sulph-hydryl group.
- Therefore, two cysteine residues may form a cystine (disulfide link) between various parts of the same protein or between two separate polypeptide chains
- His
- histidine can act as both an acid and a base, both donating and accepting protons. These properties are exploited in different ways in proteins
NEEDS ANSWERED:
- Draw the 20 common amino acids as single amino acids or as part of a peptide at different pH values.
pending
NEEDS ANSWERED
- Refer to atoms in amino acids based on both Greek letters and numbers.
pending
NEEDS ANSWERED
- Define the term “buffer” and describe how a buffer system resists changes in pH.
pending
NEEDS ANSWERED
- Explain why biological buffer systems are necessary.
PENDING
NEEDS ANSWERED
- Use the Henderson-Hasselbalch equation to calculate pKa, pH and buffer proportions.
PENDING
NEEDS ANSWERED
- Know the approximate pKa values for a-amino, a-carboxylate groups and common side chains.
PENDING
NEEDS ANSWERED
- Explain how free amino acids are polyprotic acids with characteristic titration curves.
PENDING
NEEDS ANSWERED
- Sketch titration curves for amino acids and identify: buffer zones, pKa values for all ionizable groups, equivalance points, isoelectric points.
PENDING
NEEDS ANSWERED
- Draw the different protonated states for the 20 common amino acids, using the Henderson-Hasselbalch equation to calculate ratios of the different forms.
PENDING
NEEDS ANSWERED
- Identify the predominant ionic species present at each stage of a titration.
PENDING
NEEDS ANSWERED
- Describe how chemical environment may alter pKa
PENDING
NEEDS ANSWERED
- Calculate the pI for amino acids with 2 or 3 ionizable groups.
PENDING
NEEDS ANSWERED
- Distinguish between common and uncommon amino acids.
pendin
needs answered
- Given an uncommon amino acid, describe it in terms of pI, functional groups, general properites and relationship to common amino acids.
pending
NEEDS ANSWERED
- List different roles for uncommon amino acids.
pending
NEEDS ANSWERED
List mechanisms by which uncommon amino acids may appear in a polypeptide chain.
pending
