Download document 877442

Introduction to Protein
JL LO & HC Lee
2000 June-July
Gene & Protein
• One gene, one protein
• ..\talks\protein_3.ps
• Genotype & phenotype
• ..\talks\protein_4.ps
What do proteins do?
• Everything
• Structural and Functional
• Structural
– blood, muscle, bone, etc.
• Functional
– metabolic, neural, reproduction
Aberrant gene > malfunction protein > disease
The Genetic Code I
• 20 amino acids are coded by groups
of three bases (triplets or CODONS)
• Bases are: C, T, U (instead of A), G
– 4x4x4 = 64
• 3 are stop codons
• 61 code amino acids (with
degeneracy)
The Genetic Code II
The Genetic Code III
The Amino Acids
• Single and 3-letter Codes
•
•
•
•
•
•
•
•
•
•
Aspartic Acid
Phenylanine
Alanine
Cys
Histidine
Lysine
Methionine
Proline
Arginine
Threonine
Tryptophan
Y
Asp
Phe
Ala
C
His
Lys
Met
Pro
Arg
Thr
Trp
D
F
A
Glutamic Acid
Glu
Glycine
Gly
Cysteine
E
G
H
K
M
P
R
T
W
Isoleucine
Leucine
Asparagine
Glutamine
Serine
Valine
Tyrosine
I
L
N
Q
S
V
Tyr
Ile
Leu
Asn
Gln
Ser
Val
Alanine
Grey carbon
White hydrogen
Alpha carbon
Amine group
Carboxylic
acid group
Side chain
Blue –
nitrogen
Red –
oxygen
The CORN Law
alpha
Carbon
cabOxylic
acid group
side chain
(R)
amiNe group
Peptide Synthesis
Two AminoAcids = 2 x (CORN) – >
Dipeptide + Water
–CO2 +
(NCR)
NH3+ –(CRO)
= (N – C – R) – C=O
| peptide bond
H – N – (C – R – O) + H2O
Polypeptide – chain of peptides
Classification of
Amino Acid Side Chains
Hydrophobic-Aliphatic
•
•
•
•
•
Ala(A)
Val(V)
Leu(L)
Ile (I)
Mostly are bifurcated except Ala
Hydrophobic-aromatic
•
•
•
•
Phe(F)
Tyr(Y)
Trp(W)
Non-polar
Neutral-polar side chains
•
•
•
•
•
•
•
Ser(S)
Thr(T)
Cys(C)
Met(M)
Asn(N)
Gln(Q)
Possess hydroxyl group
Acidic amino acids
•
•
•
•
•
Asp(D)
Glu(E)
Strongly polar nature
Catalytic
Metal ion binding ability
Basic amino acids
•
•
•
•
His(H)
Lys(K)
Arg(R)
Frequently occurring in enzyme
Conformationally important
•
•
•
•
Gly(G)
Pro(P)
G has no side chain
P is the most rigid one
Peptide Geometry
Peptide Torsion Angles
•
•
•
•
Three main chain torsion angle
ψ N - Calpha bond
Ψ C – Calpha bond
ω C – N bond
3D structure of
peptide
determined if all
angles given
Protein Conformation
..\talks\protein_6.ps ..\talks\protein_7.ps
Alpha-helices
..\..\proteins\1AEP_apolipophorin_III_1.gif
Beta-sheets & coils
..\..\proteins\1FSC_fasciculin_1.gif
1IBA.pdb
Structure of Alpha-Helix
Properties of the Alpha-Helix
•
•
•
•
A pitch of 5.4 A
Have 3.6 amino acids residues per turn
3.6/5.4=1.5 --- a rise per residue
Have negative Ψandψangles
Distortion of Alpha-Helix
• Buries against the other 2nd structure
• Solvent
• 310-helix
Structure of Beta Sheet
• Negative ψand Positive Ψ
• Axial distance—3.5 A
• Pitch – 7A
Parallel & Anti-parallel Sheets
More Examples
• ..\..\proteins\1AVH_annexin_V_1.gif
• ..\..\proteins\1ERB_pl_retinol_bp_1.gif
• ..\..\proteins\1ADN_DNA_Repair_1.gif
Tertiary Structure
• ..\talks\protein_8.ps
• More cartoons of Proteins
• Go to-files
THE END