Lecture 1 - Amino Acids Flashcards
How many amino acids are commonly found as constituents of protein? They are mostly what kind of AA? What is the exception?
20
alpha-amino acids
proline (IMINO acid)
What differentiates the 20 amino acids?
R groups aka side chain
What do ALL amino acids have?
alpha carbon attached to hydrogen, amino group (NH3+), R side chain, and carboxyl group
What allows amino acids to be linked together covalently in a peptide chain?
carboxyl group and amino group
What does aliphatic mean?
non-aromatic; can be saturated or unsaturated
What are the amino acids with nonpolar, aliphatic R groups? GAPVIL
glycine (H) alanine (CH3) proline (5 sided ring with CH2) branched: valine leucine isoleucine
GAPVIL
What is the simplest AA?
Glycine (just an H)
What do alanine, valine, leucine, and isoleucine have in common?
their methyl groups make them nonpolar
they cannot H-bond with water (hydrophobic)
found in places in protein not surrounded by water
What is special about proline?
the amino group is within a ring, which makes proline an IMINE
the ring adds steric hindrance, making proline nonpolar
What are the amino acids with polar, uncharged R groups? TAGS
(OH) Serine Threonine (amide - carboxyl + amine) Asparagine Glutamine
called uncharged b/c at physiological pH, R groups do not act as acids or bases
TAGS
What gives free acids their buffering ability?
amino group (H3N+) and carboxyl group (COO-)
what makes an amide?
carboxyl and amine
Why are asparagine and gluatmine polar?
both their carbonyl and amide group can H-bond with water, but they are not ionizable in body pH and they do not behave like buffers
Why are serine and threonine uncharged and yet still polar?
both have OH group that can H-bond with water
they have a proton that can be released, but does not happen in physiological pH
What are the sulfur containing amino acids?
cysteine and methionine
What is special about cysteine?
Sulfhydryl group can be oxidized and form di-sulfide bonds with other oxidized sulhydryls
What is special about methionine?
has thioether (S b/w 2 methyl groups)
therefore it cannot form a disulfide bond
So, methionine is usually the first AA of a chain aka start site for protein translation
What are the amino acids with negatively charged R groups? What can they do?
aspartate and glutamate
(COO-)
negative charge = acidic
these 2 AA at phys pH can donate H+
AA with positively charged R groups? What can they do?
lysine + arginine have +N within R side chains
histidine - can become positively charged due to delocalized electrons in ring
(+N)
positive charge = basic
at phys pH they accept protons
AAs with aromatic R groups? which is nonpolar? Which are more polar?
nonpolar: phenylalanine more polar: tyrosine tryptophan - has largest side chain + N, which makes it more polar by allowing H-bonds formation
aromatic ring - ring structure with conjugated, alternated double bonds
AA stereochemistry
all AA except glycine are stereoisomers (same properties but two different arrangements possible)
AA acid-base
all amino acids can pick up/release H from amino group and from carboxyl group
acidic/basic R groups
What are the post-translational modifications? important for?
structure and function
carbohydrate addition (trafficking + structure) lipid addition (membrane anchors) regulation (phosphorylation, acetylation, ADP-riboxylation) modified AA (oxidization of proline and lysine (found in collagen) & carboxylation of glutamate
All amino acids in protein are in what form?
L form
L-Alanine
What form are sugars found in?
D form
ex: D-Glyceraldehyde
What does pKa = pH mean?
in solution, there are equal amounts of protonated and unprotonated forms of ionizable group
If pKa = 1.82, what happens?
Carboxylate group has equal amts of COO - (conjugate base) and COOH
If pKa = 9.17, what happens?
amino group has equal amts of NH3+ and NH2
