Proteins ccc 21_08_2012 modified

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• Modified lecture presentations will also be posted after the lecture; and may include additional materials, including problem sets any . Lecture 1 CCC - Proteins........ 1

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Transcript of Proteins ccc 21_08_2012 modified

Page 1: Proteins ccc 21_08_2012 modified

• Modified lecture presentations will also be posted after the lecture; and may include additional materials, including problem sets any .

Lecture 1 CCC -Proteins........

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Proteins: Make up about 15% of the cellHave many functions in the cellEnzymesStructuralTransportMotorStorageSignalingReceptorsGene regulationSpecial functions

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DNA : Sequence of Nucleic AcidsTCATCCACACGCTGAATGGCGCCAAGCTCTCGGCCGACACCGAGGTGGTTTGCGGAGCCCCTTCAATCTACCTTGATTTTGCCCGCCAGAAGCTTGATGCAAAGATTGGAGTTGCAGCACAAAACTGTTACAACGTACCGAAGGGTGCTTTCACAGGAGAGATCAGCCCAGCAATGATCAAAGATATTGGAGCTGCATGGGTGATCCTGGGCCACTCAGAGCGGAGGCATGTTTTTGGAGAGTCTGATGAGTTGATTGGGCAGAAGGTGGCTCATGCTCMTGCTGAAGGC

Transcription and translation (DNAProtein)

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Primary structure = order of amino acids in the protein chain

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Anatomy of an amino acid

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Non-polar (Hydrophobic) a.a

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Polar, non-charged amino acids

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Negatively-charged amino acids

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Positively-charged amino acids

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Charged/polar R-groups generally map to surfaces on soluble

proteins

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Peptide Bonds

- -carboxyl of one amino acid is joined to -amino of a second amino acid (with removal of water)

- only -carboxyl and -amino groups are used, not R-group carboxyl or amino groups

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peptide bond formation

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The peptide bond is planar

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Peptide bonds is planar and quite rigid.

Therefore the polypeptide chain has rotational freedom only about

bonds formed by alpha carbons.These bonds have been termed as Phi (alpha C – N) and

Psi angle (alpha C-C').However the rotational freedom about these abgles is limited

by steric hindrance between the side chains of the residues and the

peptide bachbone.

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Primary sequence reveals important clues about a protein

DnaG E. coli ...EPNRLLVVEGYMDVVAL...DnaG S. typ ...EPQRLLVVEGYMDVVAL...DnaG B. subt ...KQERAVLFEGFADVYTA...gp4 T3 ...GGKKIVVTEGEIDMLTV...gp4 T7 ...GGKKIVVTEGEIDALTV...

: *: :: * * : :

small hydrophobiclarge hydrophobicpolarpositive chargenegative charge

• Evolution conserves amino acids that are important to protein structure and function across species. Sequence comparison of multiple “homologs” of a particular protein reveals highly conserved regions that are important for function.

• Clusters of conserved residues are called “motifs” -- motifs carry out a particular function or form a particular structure that is important for the conserved protein.

motif

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Secondary structure = local folding of residues into regular patterns or local conformation of the polypetide chain

independent of the rest of the protein

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Alpha helix and Beta sheets were actually predicted by Linus Pauling, Robert Corey and H R Branson in 1951.

Alpha helix and Beta sheets are the regular secondary structures.

-helix can be coiled in two directions, Left or right . Almost all helices Observed in proteins are Right Handed, as steric hinderance limit the ability of left handed helices to form.

Among the right handed helices the -helix is most prevalent.

-helix= 3.6 resideus per turn of the backbone coil.

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The -helix• In the -helix, the carbonyl oxygen of residue “i” forms a hydrogen bond with the amide of residue “i+4”.

• Although each hydrogen bond is relatively weak in isolation, the sum of the hydrogen bonds in a helix makes it quite stable.

• The propensity of a peptide for forming an -helix also depends on its sequence.

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The H bonding patterns of different helical secondary structures. The -helix Bonding occurs between the carbonyl oxygen of each residue and the amide proton of the residue 4 residue ahead in the helix. The 310 helix = the carbonyl oxygen of each residue and the amide proton of the residue 3 residue ahead, forming a more narrow and elongated helix.Pi helix= ith and i+5 forming a wider helix.The 27 ribbon is not a regular secondary structure.

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The -sheet • In a -sheet, carbonyl oxygens and amides form hydrogen bonds.

• These secondary structures can be either antiparallel (as shown) or parallel and need not be planar (as shown) but can be twisted.

• The propensity of a peptide for forming -sheet also depends on its sequence.

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Tertiary structure = global folding of a protein chain

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Tertiary structures are quite varied

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Quaternary structure = Higher-order assembly of proteins

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Example of tertiary and quaternary structure - PriB homodimer

Example is PriB replication protein solved at UW: Lopper, Holton, and Keck (2004) Structure 12, 1967-75. 26

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Examples of other quaternary structures

Tetramer Hexamer Filament

SSB DNA helicase Recombinase Allows coordinated Allows coordinated DNA binding Allows complete DNA binding and ATP hydrolysis coverage of an

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Classes of proteinsFunctional definition:Enzymes: Accelerate biochemical reactions

Structural: Form biological structures

Transport: Carry biochemically important substances

Defense: Protect the body from foreign invaders

Structural definition:Globular: Complex folds, irregularly shaped tertiary structures

Fibrous: Extended, simple folds -- generally structural proteins

Cellular localization definition:Membrane: In direct physical contact with a membrane; generally

water insoluble.

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Levels of OrganizationPrimary structureAmino acid sequence of the proteinSecondary structureH bonds in the peptide chain backbone

• -helix and -sheets

Tertiary structureNon-covalent interactions between the R groups within the proteinQuanternary structureInteraction between 2 polypeptide chains

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Domains

A domain is a basic structural unit of a protein structure – distinct from those that make up the conformationsPart of protein that can fold into a stable structure independentlyDifferent domains can impart different functions to proteinsProteins can have one to many domains depending on protein size

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Proteins other facts...

Non-covalent bonds can form interactions

between individual polypeptide chains

Binding site – where proteins interact with one another

Subunit – each polypeptide chain of large protein

Dimer – protein made of 2 subunits

• Can be same subunit or different subunits

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Single subunit proteins

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Different Subunit Proteins

Hemoglobin2 globin subunits2 globin subunits

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MotifFold DomainBiochemical classification of proteins : Globular, Membranous, Fibrous

Structural Classification: Beyond the scop of CCC

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