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