Biochemistry Review I - Computational & Systems … · Biochemistry Review I BBSI @ Pitt 2004....

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Biochemistry Review I Biochemistry Review I BBSI @ Pitt 2004 BBSI @ Pitt 2004 Rajan Munshi Center for Computational Biology and Bioinformatics University of Pittsburgh School of Medicine May 25, 2004

Transcript of Biochemistry Review I - Computational & Systems … · Biochemistry Review I BBSI @ Pitt 2004....

Biochemistry Review IBiochemistry Review I

BBSI @ Pitt 2004BBSI @ Pitt 2004

Rajan Munshi

Center for Computational Biology and BioinformaticsUniversity of Pittsburgh School of Medicine

May 25, 2004

Amino Acids

Building blocks of proteins20 amino acidsLinear chain of amino acids form a peptide/proteinα−carbon = central carbonα−carbon = chiral carbon, i.e. mirror images: L and D isomersOnly L isomers are found in proteinsGeneral structure of an amino acid:

(R = side chain)

Amino Acids (contd.)

R group variesTherefore, can be classified based on the R groupGlycine: simplest amino acid, side chain R = HUnique because α carbon is achiral

H

CαH2N COOH

H

Glycine, Gly, G

Amino Acids: Structures

blue = R (side chain)

orange area = non-polar, hydrophobicneutral (uncharged)

green area = polar, hydrophillic,neutral (uncharged)

magenta area = polar, hydrophillic,acidic (negatively charged)

light blue area = polar, hydrophillic,basic (positively charged)

Amino Acids: ClassificationNon-polar, hydrophobic,neutral (uncharged)Alanine, Ala, AValine, Val, VLeucine, Leu, LIsoleucine, Ile, IProline, Pro, PMethionine, Met, MPhenylalanine, Phe, FTryptophan, Trp, W

Polar, hydrophillic,neutral (uncharged)Glycine, Gly, GSerine, Ser, SThreonine, Thr, TCysteine, Cys, CAsparagine, Asn, NGlutamine, Gln, QTyrosine, Tyr, Y

Polar, hydrophillic,basic (positively charged)Lysine, Lys, KArginine, Arg, RHistidine, His, H

Polar, hydrophillic,Acidic (negatively charged)Aspartic acid, Asp, DGlutamic acid, Glu, E

Peptide Bond Formation

Condensation reactionBetween –NH2 of n residue and –COOH of n+1 residueLoss of 1 water moleculeRigid, inflexible

Peptides/Proteins

Linear arrangement of n amino acid residues linked by peptide bondsn < 25, generally termed a peptiden > 25, generally termed a proteinPeptides have

R1

CαH2N C

H

CαN COOH

HO

R2

n

directionality, i.e. N terminal C terminal

N terminal

C terminal

Peptide bond

Hierarchy of Protein Structure

Four levels of hierarchyPrimary, secondary, tertiary, quarternary

Primary structure: Linear sequence of amino acidse.g: MSNKLVLVLNCGSSSLKFAV …e.g: MCNTPTYCDLGKAAKDVFNK …

Secondary Structure: Local conformation of the polypeptidebackboneα-helix, β-strand (sheets), turns, other

Secondary Structure: α-helix

Most abundant; ~35% of residues in a proteinRepetitive secondary structure3.6 residues per turn; pitch (rise per turn) = 5.4 ÅC′=O of i forms H bonds with NH of residue i+4Intra-strand H bondingC′=0 groups are parallel to the axis; side chains point away from the axisAll NH and C′O are H-bonded, except first NH and last C′OHence, polar ends; present at surfacesAmphipathic

α-helix (contd.)

C terminal

N terminal

α−helix Variations

Chain is more loosely or tightly coiled310-helix: very tightly packedπ−helix: very loosely packedBoth are rarely occuring structuresOccur only at the ends or as singleturns

Hemoglobin (PDB 1A3N)

Ribbon Diagram Cylinder Diagram

β−sheetsOther major structural elementBasic unit is a β-strandUsually 5-10 residuesCan be parallel or anti-parallel based on the relative directions ofinteracting β-strands“Pleated” appearanceUnlike α-helices:Are formed with different parts of the sequenceH-bonding is inter-strand (opposed to intra-strand)Side chains from adjacent residues are on opposite sides of the sheetand do not interact with one anotherLike α-helices:Repeating secondary structure (2 residues per turn)Can be amphipathic

Parallel β−sheets

The aligned amino acids in the β-strand all run in the same biochemicaldirection, N-terminal to C-terminal

Anti-parallel β−sheets

The amino acids in successive strands have alternating directions, N-terminalto C-terminal

Nucleoplasmin (PDB 1K5J)

Ribbon Diagram

Amino Acid Preferences

α-helix formingThe amino acid side chain should cover and protect the backbone H-bonds inthe core of the helixAla, Leu, Met, Glu, Arg, Lys: good helix formersPro, Gly, Tyr, Ser: very poor helix formers

β-strand formingAmino acids with large bulky side chains prefer to form β-sheet structuresTyr, Trp, Ile, Val, Thr, Cys, Phe

Secondary structure disruptorsGly: side chain too smallPro: side chain linked to α-N, has no N-H to H-bond; rigid structure due to ringAsp, Asn, Ser: H-bonding side chains compete directly with backbone H-bonds

Turns/Loops

Third "classical" secondary structureReverses the direction of the polypeptide chain Located primarily on protein surface; contain polar and charged residuesThree types: I, II, III

Phosphofructokinase (PDB 4PFK)

Ribbon Diagram Cylinder Diagram

The Torsional Angles: φ and ψ

Each amino acid in a peptide has two degrees of backbone freedomThese are defined by the φ and ψ anglesφ = angle between Cα―Nψ = angle between Cα―C

The Ramachandran Plot

Plot of allowable φ and ψ anglesφ and ψ refer to rotations of two rigidpeptide units around Cα

Most combinations produce stericcollisionsDisallowed regions generally involvesteric hindrance between side chainCβ methylene group and main chainatoms

The Ramachandran Plot (contd.)

Theoreticallypossible;

energeticallyunstable

π-helix

310-helix

Anti-parallelβ-sheet

Parallelβ-sheet

White: sterically disallowed(except Gly)

Red: no steric clashesYellow: “allowable” steric

clashes

“Super-secondary” Structure

Primary structureSecondary structure“Super-secondary” structureAlso called domainsSpatial organization of secondary structures into a functional regionExample: catalytic domain of protein kinase; binding pocket of a ligand

N-terminal

3D Structure of a Protein Kinase Domain phosphate

binding loop

catalyticloop

C-terminal

Quarternary Structure

Spatial organization of subunits to form a functional proteinExample: Hemoglobin2 α chains, 2 β chainsEach chain binds heme (Fe)Forms an α2-β2 tetramer

Putting it all together

Secondary Structureα-helix, β-sheets, turns/loops

Super-secondary StructureHeme-binding pocket/domain (His)

Primary Structure… KAAWGKVGAHA …

Tertiary Structurea single chain (α, β)

Tertiary Structurea single chain (α, β)

Additional Reading

General informationBiochemistry, 5th ed., Berg, Tymoczko, StryerBiochemistry, 3rd ed., Voet and VoetDetailed informationProteins, 2nd ed., CreightonIntroduction to Protein Structure, 2nd ed., Branden and ToozeInternetImages from the Protein Data Bank (PDB): www.rcsb.org/pdbNumerous wesbites (Google protein secondary structure)