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

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

1

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

2

DNA : Sequence of Nucleic AcidsTCATCCACACGCTGAATGGCGCCAAGCTCTCGGCCGACACCGAGGTGGTTTGCGGAGCCCCTTCAATCTACCTTGATTTTGCCCGCCAGAAGCTTGATGCAAAGATTGGAGTTGCAGCACAAAACTGTTACAACGTACCGAAGGGTGCTTTCACAGGAGAGATCAGCCCAGCAATGATCAAAGATATTGGAGCTGCATGGGTGATCCTGGGCCACTCAGAGCGGAGGCATGTTTTTGGAGAGTCTGATGAGTTGATTGGGCAGAAGGTGGCTCATGCTCMTGCTGAAGGC

Transcription and translation (DNAProtein)

3

Primary structure = order of amino acids in the protein chain

4

Anatomy of an amino acid

5

Non-polar (Hydrophobic) a.a

6

Polar, non-charged amino acids

7

Negatively-charged amino acids

8

Positively-charged amino acids

9

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

proteins

10

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

11

peptide bond formation

12

13

The peptide bond is planar

14

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.

15

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

16

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

independent of the rest of the protein

17

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.

18

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.

19

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.

. 20

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.

21

22

Tertiary structure = global folding of a protein chain

23

Tertiary structures are quite varied

24

Quaternary structure = Higher-order assembly of proteins

25

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

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

extended molecule27

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.

Soluble: Water soluble; can be anywhere in the cell.28

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

29

30

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

31

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

32

Single subunit proteins

33

Different Subunit Proteins

Hemoglobin2 globin subunits2 globin subunits

34

MotifFold DomainBiochemical classification of proteins : Globular, Membranous, Fibrous

Structural Classification: Beyond the scop of CCC

35