What is alpha-amino acid?
its the molecule with amino group, carboxylate (COO-) with side chain (R) and H
How many chiral amino acids are there? Which one is the exception?
19/20 except Glycine (gly, G)
Entiomer
The stereoisomer that has non-superimposable mirror image
(D and L are enantiomer)
What is zwitterion? What is the example of this?
The dipolar molecules (positive and negative charge at the same time)
Amino Acid under physiological pH=7.4 (deprotonated COO- and protonated NH3+)
What is the amphoteric molecule?
the molecule that can act as acid and base (Histidine, H)
What is AA of 20 AAs that has constrained conformation angle?
Proline (Pro, P) due to the ring structure
What is AA of 20 AAs that has most free conformation angle?
Glycine (Gly, G) due to small size
What is special about HIstidine?
It can act as base or Acid based on the external pH
(pH < pKa: acid (+) charge ) and (pH>pKa: base - neutral charge)
What is important about primary structure?
It determines the chemical and physical properties of protein (protein's conformation and folding process)
How many possible sequences for n -residues?
20n possible sequences
Peptide
Protein
< 40 residues and doesn't have distinct 3D structure (linked many amino acids)
>40 residues
Characteristics of Peptide Bond?
Have limitations on rotation
Have resonance at double bond C=O
Dalton (D)
1 residue equal to (D)?
g/mol
110D
Beside peptides, proteins also have?
metal ions or organic molecules as cofactos
alpha-helix
# of residues per turn? length/ turn?
one polypeptide strand in helix formation
3.6 residues and spans 5.4 Å/turn
How is alpha-helix structure held?
by the backbone of hydrogen bonds between C=O bond at n residue and N-H bond of n+4 residue
What are the conditions that don't favor the alpha-helix formation?
Proline (helix breaker)
Glycine (too many conformations)
bulky or large/ branched side chain (I, Y, Trp)
Interactions between two same charges side chains
Where is the position of R-groups in alpha-helix conformation?
they extend outward from helix
What force hold together the beta-sheet?
the H-bonds backbone (C=O and NH)
Where does R-groups locate in beta-sheet?
above and below the sheet
Which one is more stable than? antiparallel or parallel?
antiparallel because it has smaller # of strands and thus less distorted bonds than in parallel (higher # of strands)
What technique can be used to determine 3D structure of protein?
X-ray crystallography
Tertiary structure
the folding 2nd structure of polypeptides and the "absolute configuration" of side chains (R)
What does 3D structure of protein have?
hydrophobic core and hydrophilic surface
What stabilize that 3D protein structure?
hydrophobic effect
hydrogen bonds
salt bridge
disulfide bonds
inorganic ions crosslink
salt bridge
disulfide bond
inorganic ion crosslink
ionics bonds btw acid and base
covalent bond
Zn (2+) interactions with R-group
polypeptide loops
irregular 2nd structures
the hairpin turn that connect secondary structures of beta-sheets or alpha-helix
backbone conformation is not defined
WHat solven can use to denature protein?
salt, urea
Can protein has more than one conformation?
Yes, depend on pH of cellular, charged state of other side chains
pKa of C-terminus
Asp
Glu
His
Cys
N-terminus
Tyr
Lys
Arg
3.5
3.9
4.1
6.0
8.4
9.0
10.5
10.5
12.5
