Card Set Information
What are proteins composed of?
COOH and NH3 are both what
Why are there usually 2 forms of a molecule
Bc the C is the chiral center
What are the two forms?
Found in ALL proteins
What is the L (leurotary)-form based on?
The configuration of NH3
How are amino acids classified?
basis of 'D' groups
based on polarity
How many classes of AAs are there and what are they?
Non-polar, Aromatic, Polar, Positive charged (basic), and Negative charged (acidic)
akly side chains (hydrocarbons)
hydrophobic bonding in proteins
aromatic ring structure
dipole but no formal charge (+/-) [h bonding]
freq found on the surface of "soluble" proteins
Full (+) charge on R group
variation on Nitrogen-containing FG
Full (-) on R groups
How many AAs are there
What do non-standard do?
have biochemical roles
What are the biochemical roles and how were they created?
modification of standard AAs
they are metabolic roles
What is Isoelectric point?
pH at which a molecule has a net charge of 0
What is the net charge?
Sum of (+ charges) - (- charges)
What is the pI?
sum of all the pk values/2
pH < pI
net charge will be +
pH > pI
net charge will be -
What are peptides?
Short polymers of AAs
What does partial double bind pressure do?
limits rotation about bond
What is the peptide/protein rotation also limited by?
by steric hindrance (R' groups)
What is the Ramachandran plot?
What are the proteins/peptide ends?
Amino terminal (N terminal)
Carboxyl (C terminal)
Long peptides assume what configurations?
native, active 3D configurations
What does entropy play a role in?
"driving" folding as protein folds
What occurs after the protein folds
more H2O is released from solvation "shell"
greater freedom=^ randomness=^ entropy
Which are weak bonds?
H-bonding, H-phobic, ionic bonding
What about weak bonds
maximized in folded, native structures
What about soluble (aqueous) proteins?
H-phobic AAs more prevalent in interior of protein
H-bonding, ionic bonding
FG in protein interior have to have a bonding partner
What do small proteins often have?
disulfide bonds (covalent) stabilized folded structures
Hierarchal levels of proteins of all proteins
1, 2, 3 are in all proteins
4 is only in some
in covalent structures
location of disulfides
local 3D structures
only part of the protein
How is level 2 defined?
by the set of structures
i AA double helix
polypeptide winds itself around an imaginary axis
How are things stabilized
H bonding among peptide bonds
What can destabilize the helix
incompatible 'R' groups
Which AAs dont perform well in double helix
Gly and Pro
What are B-strands/sheets
linear stretches of AAs that fold back upon one another to forms sheets
How can steric hindrance be reduced
r groups will be perpendicular
alternate position in up/down
short seq of AA
common is about 4 AAs
Where are B turns usually seen
freq seen on the surface of proteins
What do B turns usually contain
small flexible AAs
What are super-secondary structure
common structural patterns that include multiple representations of 2
What are the rules for super-secondary structure of 2
2 seq are usually close together in 1
do NOT form what?
doesn't form knots