Chapter 3; Amino Acids (New) Flashcards
What are the common features of all amino acids?
- All contain an alpha amino group and alpha carboxyl group
- All are L isomers in proteins
- contain an alpha carbon
- Are dipolar (zwitterion) at a neutral pH
________ are the building blocks of proteins & have 20 different variation
Amino acids
What are some roles of proteins?
Proteins are the workhorses of the cell where they storage and transport, support the shape of cells, help mechanical movement, factors/regulate different hormones, recptors, etc
What are the 4 levels to protein structure?
- Primary structure
- Secondary structure
- Tertiary structure
- Quaternary structure
Are amino acids chiral or achiral?
Chiral
Proteins are formed from what type of isomer of amino acids L or D?
L amino acids
What amino acids is achiral?
Glycine since it has a hydrogen atom as its side chain
What amino acids have chiral carbons in their side chain?
Threonine & Isoleucine
When the alpha amino group is on the left what stereoisomer is the amino acid?
L (& if it was on the right it would b D)
Nonpolar (alipathetic & aromatic) amino acids like to do what?
They are hydrophobic & bury away from water
Polar uncharged amino acids like to do what?
They are hydrogen bond donors & acceptors & interact with water
Polar charged amino acids like to do what?
They are cationic & anionic groups at neutral pH
What are the two amino acids that contain sulfur?
Cysteine & methionine
Name all the aliphatic amino acids?
- Glycine
- Alanine
- Leucine
- Valine
- Isoleucine
Name all the aromatic amino acids
- Methionine
- Proline
- Phenylalanine
- Tryptophan
What aromatic amino acids can absorb UV light?
- Tyrosine (280 +nm)
- Tryptophan (280 +nm)
- Phenylalanine (270nm)
What are the polar uncharged amino acids?
- Serine
- Threonine
- Asparagine
- Glutamine
- Tyrosine
- Cysteine
Which of the polar uncharged amino acids has a hydroxyl side chain? (make a strong nucleophile)
- Serine
- Threonine
- Tyrosine
Which of the polar uncharged amino acids has a amide side chain?
- Glutamine
- Asparagine
Cysteine side chains can be cross-linked if oxidized to form a _______ bridge that stabilize the 3D structure
Disulfide bridge
What amino acids are polar charged
- Lysine
- Argine
- Histidine
- Aspartic acid
- Glutamic acid
Within the charge polar amino acids which are the basic (+) charge?
- Histidine
- Lysine
- Arginine
Within the charge polar amino acids which are the acidic (-) charge?
- Aspartate
- Glutamate
What are the ionizable amino acid groups?
- C-terminus
- N-terminus
- Glu
- His
- Cys
- Tyr
- Lys
- Arg
Delocalized electron density (resonance) stabilizes __________
(protonated form of glutamate side chain) & stabilizes __________
(arginine side chain)
carboxylate, guanidium ion
If the pH below the pKa, then the _________ form of the group dominates
protonated (acid)
If the pH is above the pKa, the ___________ form of the group dominates
Deprotonated
Zwitterionic form can act as what?
Acid or base
pH = pI when what?
Between 2 pKa values when the net charge is zero
__________ amino acids have ionizable side chains
Polar charge
In a titration curve if an amino acid has an ionizable R group how many stage will it have on the titration curve?
3 (pKa 1, pKa 2, pKar)
How would you calculate the partial charge on an amino acid at a particular pH?
Use the henderson hasselbatch equatin (pH = pKa + log [A]/[HA]) & then solve it for [A]/[HA] & [HA] charge will be its value / its value + 1 & [A] fraction charge will be 1- charge of HA & to calculate its pI its is pKa 2 + pKr)
________ bonds form between amino acids
Peptide bonds
What type of reaction occurs to form a peptide bond?
Condensation reaction where the O atom is lost on the alpha carboxyl group & two hydrogen atoms are lost from the alpha amino group on the other amino acid that its connecting to
What is the Primary structure of a protein?
Its the linear sequence of amino acids in a polypeptide
What is an oligopeptide?
Has 3 - 10 or 20 amino acids
What is a polypeptide?
Has many amino acids up to 1000s
Polypeptide chains are read & numbered in what order?
From the N- terminus to the C-terminus
Peptide formation eliminates ________ alpha carboxyl & alpha amino groups of free amino acids
Ionizable
What are the rules for naming peptides?
Name from N-terminus to C- terminus & at the end replace the end with yl (ex. ala-tyr-asp-gly) (instead of glu)
Isopeptide bonds
Form between side chains carboxyl or amino groups and alpha-amino or carboxyl group through disulfide bridge
At certain pH values these ionizable side chains groups will be able to exchange hydrogen atoms & that will allow them to form ______ bonds
Ionic bonds
What are the protein purification techniques?
- Dialysis
- Salting out
- Gel fraction chromatography
- Ion exchange chromatography
- Affinity chromatography
- Gel electrophoresis
- Isoelectric focusing
- 2D electrophoresis
What is dialysis
Separates proteins from small molecules & ions
What is salting out?
Using salt concentration to cause precipitation of proteins (if it doesn’t precipitate means the salt concentration too low for the protein & need to be higher)
What is Gel fraction chromatography?
Separates proteins based on size (it contains a tube with beads & the proteins move thru the beads & the proteins thar largest move faster & the smaller ones get trapped in the beads)
What is ion exchange chromatogrpahy?
Separates proteins based on charge (if the column is an anion column then positively charge proteins will move faster & negatively charge will move slower & vis versa if its a cation column)
What is an affinity chromatography?
Separates proteins based on their affinity for a certain molecule
Gel electrophoresis
Separates proteins based on size
Isoelectric focusing
Separates based on their isoelectric point
2D electrophoresis
Combines isoelectric focusing & gel electrophoresis
Specific activity
Used to determine the purity of the sample (enzyme activity/ concentration)
What is the difference between gel electrophoresis & gel chromatography
In gel electrophoresis all proteins move along in it but in gel chromatography small proteins get trapped in the beads
_________ allows us to purify a mixture of proteins that contain nonproteins. Substances where small molecules move outwards through the insoluble membrane but the large proteins can’t
Dialysis
What are the conditions used to determine the pI of an amino acid?
- If the side chain is not ionizable then the pI is the average of the pKa values of the terminal alpha amino & alpha carboxyl group
- If the side chain is ionizable & acidic then the pI is the average of the pKa value of the terminal alpha carboxyl group & the side chain
- If the side chain is ionizable & basic the pI is the average of the pKa values of the terminal alpha-amino group & the side chain
- For all other ionizable groups, we must determine the middle pKa value & average it with the terminal alpha carboxyl group
How do you calculate the pI of a protein?
- Estimate the pH at which the net charge on the proteins will be zero
- Find the average of the two pKa values directly above & directly below the estimate
