1. Amino Acids Flashcards
Which is the amino terminus of the following dipeptide: alanylvaline
Alanine is the amino terminus (meaning that the amino group -NH3 is available for forming new peptide bonds)
Naming convention of peptides (e.g. dipeptides)
We write the from NH3+ (amino terminus) –> to the COO- group (carboxy terminus)
What is the impact of Proline in alpha helices?
Proline disrupts alpha-helices due to being large and bulky
What is the impact of Proline in beta sheets?
Proline allows for kinking in the chain and is GOOD for forming beta-sheets
What is another name for Aspartate? (synonymous for MCAT)
Aspartic Acid
*Why can Tyrosine be found both inside and outside?
Due to the benzene ring and -OH (hydroxy) group
What is the general structure of an α-amino acid?
- central (α) carbon
- carboxyl group
- α-Amino group
- R-group
- α-Hydrogen
What type of amino acids are proteinogenic amino acids?
- All proteinogenic AAs are α-amino acids
- “α” describes the amino group’s position
- Some biologically active amino acids are not α
Types of amino acids
Alpha α
Beta
Gamma
Are enantiomers possible for α-amino acids?
Proteinogenic amino acids are L-isomers
L ≠ S in all cases, so we can’t base it just on that
All but cysteine and glycine are S enantiomers
What is the fisher layout of L-amino acids?
W/ amino group on the left
What are the amino acid exceptions to L=S?
- L-Cysteine (is an R configuration - clockwise)
- Glycine is ACHIRAL (w/o D or L designation)
S configuration is (clockwise/counterclockwise)
S configuration is COUNTERCLOCKWISE; and most proteinogenic amino acids are S configuration
*Cysteine is the exception and is R configuration
Basic amino acids
- Lysine - Lys, K
- Histidine - His, H
- Arginine - Arg, R
BASIC bitches Lyk Halloween & dress up like pirates, Arg!
Acidic AAs
Aspartate = Aspartic acid
Glutamate = Glutamic acid
Polar amino acids
- Asparagine
- Glutamine
- Serine
- Threonine
- Cysteine
Ganster CATS survive polar weather
Non-polar amino acids
- Glycine
- Alanine
- Leucine
- Isoleucine
- Methionine
- Valine
- Proline
Vivid MAGILP - non-polar
Aromatic AAs
- Phenylalanine
- Tryptophan
- Tyrosine
What are peptides?
Linear chain of amino acids or residues (residues = amino acids)
Oligopeptides vs. Polypeptides
Oligopeptides: 2-20 residues
Polypeptides: longer chains of residues
What is a peptide bond?
a specialized amide bond between the COOH and NH2 groups on adjacent amino acid residues
What allows for the resonance in the peptide bond?
Delocalizable electrons → allow for resonance
C-N has partial double bond character
Rotation around the C-N amide backbone is restricted
What can break down peptide bonds?
Peptides can be broken into single amino acids for digestion by hydrolytic enzymes, or strong acids and heat
(reverse of condensation)
What are titrations?
In essence, limiting reactant problems
- Mechanism: one reagent is limiting (analyte), the other is excess (titrant)
- We add what we have in excess of until we just barely consume all of the limiting reactant- the “endpoint” of the titration
- We use wither color indicator or an electrode to monitor when it reaches the endpoint
What is monoprotic acid-base titration?
- determines # of equivalents of titrant
- pH is monitored to determine equivalence point (EP)
- EP is found at steepest slope on titration curve
- EP is where the Equivalents of Acid and Base are equal
What is the equivalence point?
The point at which Equivalents of acid and equivalents of base are equal; found at steepest slope on titration curve
*Map out polyvalent/polyprotic acid-base titration; where does the Isoelectric point occur?
Isoelectric point
pI is the pH at which a particular molecule carries no net electrical charge in the statistical mean
pI (isoelectric point) occurs halfway between the 2 closest 1/2 EPs (aka pKas)
How to calculate the isoelectric point?
pI (isoelectric point) is calculated by averaging the two closest pKa’s
Zwitterion
An amino acid at it’s isoelectric point (meaning net neutral charge)
How do you calculate Histidine’s isoelectric point?
The pKas are 2, 6, 9
So you average pH 6 and 9 ⇒ pH=7.5
Half equivalence points (other name, where on graph)
Equal concentrations of adjacent forms; pKa’s
Found at plateaus of the curve
Equivalence points
When there is a dominant form;
the verticals of the curve
General pIs of acidic amino acids? Basic amino acids?
Acidic amino acids have pI’s around pH ~3
Basic amino acids have pIs around pH ~10
What factors cause denaturation of proteins?
- high temperatures
- high salt concentrations
- detergents
- adding urea (high concentration)
Which amino acid has a side chain that can become ionized in cells?
Histidine has ionizable side chain; its imidazole ring has a nitrogen atom that can be protonated
What are reasons for conjugating proteins?
Conjugated proteins can have lipid or carbohydrate “tags” added to them
- to direct their delivery to a particular organelle
- to direct their delivery to the cell membrane
- to add a cofactor needed for their activity
If carbon backbones are close together (forming triple helix), what type of amino acid helps reduce steric hindrance to make this possible?
Glycine has smallest side chain; reduces steric hindrance
Aliphatic vs. Aromatic
Aromatic : describe a cyclic (ring-shaped), planar (flat) molecule with a ring of resonance bonds that exhibits more stability than other geometric or connective arrangements with the same set of atoms
Aliphatic: can be a ring structure, but NOT aromatic
