Amino Acids Flashcards
Describe hydroxylation
Proline + Hydroxyl = Hydroxyproline. Need Vitamin C to do this. So if you have scurvy you have collagen problems (its rich in Pro-OH)
Describe carboxylation
Carboxyl + Glutamate = Carboxyglutamate. Need Vitamin K to do this. Vit. K deficiency –> clotting problems because carboxyglutamate is rich in clotting factors.
Describe glycosylation
O linked – added to Ser or Thr.
N linked – added to Asparagine.
Sugar helps AA become more soluble. Also helps in cell-cell comm via glycoproteins. Failure means Congenital Disorder of Glycosylation (CDG)
Describe acetylation & methylation
Occurs on Lys & Arg (mostly on histones). Neutralizes charge interactions
Describe [de]phosphorylation
OH –> PO4 on Ser, Thr, Tyr. Needed in signal transduction
Describe ubiquitination
76 AA protein added to Lys residues. Signals degradation
What 3 covalent bonds are found in peptides?
Peptide: between C & N (partial double bond, no twist)
Ca-N = phi angle
Ca-C = psi angle
Both allow twisting; some angles preferred depending on R groups
Proteins with a similar ______ have a similar ______ and, consequently, a similar ________.
sequence; structure; function (sequence determines structure)
Hydrogen bonding typically occurs where in a peptide?
NH—O=C on peptide backbone, but also among AAs where there are free H (donors) and OH (acceptors)
What are the features of two secondary structures?
a-helix: H bond between CO & NH. Turn every 3.6 residues. Fits well into DNA major groove
B-sheet: sidechains alternate up & down, can be parallel or anti-parallel
What are the two major types of tertiary strucutre?
Fibrous: long and lots of one type of 2-structure; insoluble; structural
Globular: mix, does diverse functions
What 2 AAs facilitate the formation of turns & loops?
Proline & glycine.
Define Kd
Literally, dissociation constant. It’s a measure of binding strength. Kd = conc. of ligand where 50% is bound. Smaller # = tighter binding
How is binding specificity achieved?
Lock & Key AND/OR induced fit (key difference: enzyme is induced fit)
Why is hemoglobin a good O2 transporter?
It has 4 subunits and 4 hemes. It starts in T state, but when an O2 binds, it makes it easier for more O2 to bind (positive cooperativity) –> R state. It binds O2 in higher pH (lungs) and releases in lower pH (tissue). Without it, the Fe in heme itself would just get oxidized.
What 3 things can denature a protein?
Heat, pH, chemicals (like guanidinium, urea)
What fundamental conclusion can be drawn from the RNase A experiment?
The fact that RNase A folded back to its correct confirmation on its own shows that all the information necessary for folding is in the primary AA sequence.
What are the 2 classes of chaperones?
- Hsp: bind hydrophobic areas to prevent aggregation
2. GroEL: bind hydrophobic residue and inserts the peptide into a cavity so it can fold properly
Why are Protein Disulfide Isomerase (PDI) and Protein Prolyl Isomerase (PPI) sometimes necessary for folding?
PDI: Swaps S-S for S-H; fixes mispaired cysteine residues
PPI: swaps cis/trans proline; necessary for making some folds/turns
What diseases can be attributed to protein misfolding?
Alzheimer’s, CF, Parkinson’s, prior, amyloidosis
What’s the difference between a normal and bad prion protein?
Normal: rich in a-helix
Bad: rich in B-sheet
What are 2 methods to determine a protein’s sequence?
Edman degradation & mass spec (MS also used to determine a protein’s mass)
