amino acids Flashcards
Central dogma
DNA-> mRNA -> Protein
Native Structure, where are polar and non polar amino acids
Proteins spontaneously fold into 3D structure (lowest free energy state), Apolar (hydrophobic) amino acids are usually on the inside, polar (hydrophilic) amino acids are on the outside
Parts of an amino acid
All amino acids have a carboxyl group (COOH), amino group (NH3+), a hydrogen, and an R group surrounded by an alpha carbon.
When the alpha carbon is surrounded completely by different groups (all of them except glycine), its said to be chiral and optically active. Chiral amino acids exist as L and D enantiomers, but in nature all of them exist in the L confirmation
Hydrophobic amino acids
G-Gly, A-Ala, V-Val, L-Leu, I-Ile, M-Met, P-Pro
Gly (only H)
Ala (CH3)
Met (has an S) starts peptide
Pro (a ring)
Aliphatic Amino Acids: 280 nm absorbance
Y-Tyr (tyrosine kinases phosphorylate it–cancer drugs), F-Phe, W-Trp
Hydrophilic (polar) amino acids, NON-charged
S, Ser (also phos by TKs) T, Thr (also phos by TKs) C, Cys has an S group N, Asn Q, Gln
Honorary member:
Met- bc polar nature of S
Hydrophilic (polar) amino acids, CHARGED
(+) positive basic beaches
K-Lys, R-Arg, H-His
(-) negative acids
D-Asp, E-Glu
Honorary Members:
Tyr, Cys
pKa values
Charged groups have pKa values. pKa is the pH at which the group is 50% protonated and 50% unprotonated
at pH values lower than the pKa there will be more than 50% that are portonated
at pH values higher than the pKa there will be more unprotonated
ratio can be calculated by HH equation: pH= pKa + log (A)/(HA)
when pH is one unit higher than the pka the A/HA ratio is 10
Isoelectric point (pI)
an intermediate pH that the peptide or protein has a net charge of zero
buffer zones
when the pH is close to the pKa, the pH of the solution is stabilized (near the pKa values of ionizable groups
* physiological advantage
Sulfur containing amino acids
Met and Cys,
Met is always the first AA in a peptide.
The thiol or sulfhydryl group of cysteine will make a disulfide bridge (usually outside of cell
limitations of conformational states possible for peptides
Resonance of the amide bond creates a semi double bond charachter that makes it planar
they are usually in trans conformation so R groups dont clash
Protein folding forces
Hydrophobic interactions (apolar on the inside, polar on the outside)
Folding begins with local interactions for 2ndry structure, Tertiary structure continues with hydrophobic interaction
Correct and inncorrect conformations happen until the correct one is reached,
the correct conformation is thermodynamically stable, this is the biologically active one
Secondary structure
alpha helix and beta sheets
Right- handed alpha helix: 3.6 residues per turn, stabilized by H-bonds, H-bonds are parallel to the and R groups are jutting out (minimizing steric clash), if there is a bunch of steric clash, itll destabilize the helix, alpha helix is considered “amphipathic” b/c the face is polar and the inside core is a polar.
Beta pleated sheets: stabilization by H bonds that are planar with the sheet, and R groups are above and below the sheet, there are usually a lot more sheets in the hydrophobic core of proteins. Parallel sheets have the peptides going in the same direction (N-C, N-C) and antiparallel have peptides going in opposite directions (N-C, C-N) you can have a mix of both and have a stable.
Antiparallel beta sheets that are of the same peptide, need reverse turns, hairpin turns, B-turns
Secondary structure solves the problem of peptide bond polar nature into hydrophobic core
Proline usually isnt in helix or sheet but at the end of secondary structure
Tertiary structure is done by
hydrophobic interactions
Metamorphic proteins
multiple free enerygy states,so the protein has two different shapes with two different functions
