Lecture 3 Flashcards
(32 cards)
Positively Charged AAs, and protonation at pH = 7
Lysine (Lys, K): R protonated at neutral pH; R’s pKa is high
Arginine (Arg, R): R protonated at neutral pH; R’s pKa is high
Histidine (His, H): R NOT protonated at neutral pH
Negatively Charged AAs, and protonation at neutral pH
Aspartate (Asp, D): R has low pKa; deprotonated at neutral pH
Glutamate (Glu, E): R has low pKa; deprotonated at neutral pH
Configuration vs conformation
configuration
-switch configs by breaking and reforming cov bond(s)
conformation
- switch configs by without breaking cov bonds
- esp: rotation about single bond
stereoisomers
differ only in spatial arrangement of atoms
- cis/trans
- enantiomers (nonsuperimposable mirror images)
proteins contain nearly all of which enantiomer (L or D?
L
-determination based on glyceraldehyde(–>alanine)
Trick to tell if L or D AA
alpha carbon in center. line up is R group. Line (wedge) out of page is H, carboxyl and amino groups are the left and right dashes. If spells Corn in clockwise arch, it’s an L- amino acid
Why must most AAs be same chirality (all L or all D)?
Can’t make uniform structures with mixture.
Peptide bond
creates amide
H
-C - N -
ll
O
This section is planar because of resonance.
Note C is carbonyl C, not alpha carbon (although it’s attached to an alpha C)
pI (notes say don’t need to know)
Looks like it’s pH at equiv point on titration curve
Merrifield Method for protein synthesis
- Attachment to resin (beads)
- carboxyl terminal attached to resin - Removal of protecting group
- Fmoc protects amino group
- remove by flushing with mild org base - Activation of next amino acid
- carbonyl activated with DCC (like opposite of protecting group) - Peptide bond formation
- amino of AA1 attacks activated carbonyl of AA2 - Removal of polypeptide from resin
- HF cleaves ester between peptide and resin
Direction of protein synthesis
in cells: amino to carbonyl terminus
Merrifield: carbonyl to amino terminus
Convention for naming peptide sequences
N-terminus to C-terminus
Protein vs Peptide
Protein: Mr > 10,000
Peptide: Mr< 10,000
Note: Mr means molecular weight
Avg weight of AA in protein
110
absolute configuration
config of four diff substituent groups around asymmetric carbon, in relation to D- and L- glyceraldehyde (corn=L)
amphipathic
containing both polar and nonpolar domains
phospholipids in cell membrane
amphoteric
capable of donating or accepting protons and therefore of being acid or base (noun form ampholyte)
makes me think of HA- form of a diprotic acid
conjugated protein
protein containing one or more prosthetic groups
prosthetic group
metal ion or orgainc compound (other than AA) covalently bound to a protein
essential to protein’s activity
isoelectric pH (pI)
the pH at which a solute has no net electric charge and thus does not move in an electric field
lipoprotein
lipid-protein aggregate that carries water-insoluble lipids in blood
-just the protein is called apolipoprotein
metalloprotein
protein with a metal ion as prosthetic group
metalloprotein
protein with a metal ion as prosthetic group
oligomeric protein
multisubunit protein having two or more polypeptide chains
