KHAN Unit 1: Biomolecules Flashcards
nonpolar, hydrophobic amino acids
glaciers in Alaska valiantly locate isolated prowlers
- Glycine = G, Gly
- H - Alanine = A, Ala
- methyl group - Valine = V, Val
- CH, 2 methyls - Leucine = L, Leu
- CH2, CH, 2 methyls - Isoleucine = I, Ille
- methyl jumps to first carbon - Proline = P, Pro
- ring - Methionine = M, Met
- CH2, S, CH3
aromatic amino acids
the aroma of fine pine and yellow timber are worth the tryp
- Phenylalanine = F, Phe
- benzene - Tyrosine = Y, Tyr
- benz + OH - Tryptophan = W, Trp
- 2 rings
Polar, uncharged amino acids
alcohol is a serious treat
1. Serine = S, Ser
- CH2, OH
2. Threonine = T, Thr
- CH, CH3, OH
3. Cysteine = C, Cys
- CH2, SH
4. Asparagine = N, Asn
- CH2, C=O, H2N
5. Glutamine = Q, Gln
- Add carbon
Charged amino acids
basically, his lost kid always returned
1. Histidine = H, His
- 5 ring, 2 N
2. Lysine = K, Lys
- 4 CH2, NH3+
3. Arginine = R, Arg
- 3 CH2, NH, C - NH2 x 2
as peter digested the glue, his stomach became acidic
4. Aspartate = D, Asp
- CH2, COO-
5. Glutamate = E, Glu
- glue another carbon on
How does a peptide bond form?
dehydration rxn: carboxyl group of AA reacts with amino group, releasing water
What are the post-translational modifications that affect protein function?
- Phosphorylation: p groups to ser, threonine, tyr; signaling
- Glycosylation: carbohydrate groups; folding
- Acetylation and methylation: lysine in histones; loose DNA packing vs. dense DNA packing
- Ubiquination: lysine; degredation
Summarize protein folding.
- primary: peptide bonds between amino acids
- secondary: H-bonding between backbone; a-helix or B-sheet
- tertiary: interaction between R groups = H bonding, ionic bonding, dipole-dipole, LDF, hydrophobic interaction; disulfide bonds = covalent linkages between cysteines
- quaternary: multiple polypeptide chains = subunits come together
What is the hydrophobic effect?
hydrophobic residues aggregate inside the protein, expelling water, increasing the entropy of the system
What guides protein folding?
molecular chaperones: bind to nascent polypeptides, preventing improper interactions
chaperonins: large, cylindrical complexes that provide a protected environment for protein folding
What determines is something is protonated/deprotonated? What is the isoelectric point?
pKa>pH = protonated
pKa<pH = deprotonated
pKa1 + pKa2 / 2 = pI
- NEUTRAL
- acid: average 2 more acidic pKas (lower)
- base: oppposite (higher)
higher pI = more basic
lower pI = more acidic
What is isoelectric focusing?
separate molecules based on their pI
travels along gel until it hits the pH = pI where it has no net charge
low pH, most proteins have + charge
at high pH, most proteins have - charge
What is protein electrophoresis?
Native PAGE separates proteins based on their size and charge
- affected by mutations and changes in charge
SDS-PAGE denatures proteins and coats them in negative charge so they are separated by weight
- is not affected by mutations
Describe the SDS-PAGE Technique.
- prepare the gel
- mix protein sample with SDS to denature + uniform negative charge, a reducing agent to break disulfide bonds, tracking dye, and then heat it
- load samples into wells
- electrophoresis: gel filled with buffer, E field applied, smaller proteins move faster towards anode (+ electrode)
What do the blotting techniques detect?
western: proteins
southern: DNA
northern: RNA
Describe the steps of Western Blotting.
- protein separated by SDS-PAGE based on weight
- proteins transferred from gel to a membrane
- membrane incubated with a primary antibody specific to the target protein; unbound are washed away; incubated with secondary antibody that is conjugated to enzyme that binds to primary antibody
- substrate to enzyme is added, causing color change
**measure levels of specific protein
