Chemical basis of life part 2 Disulfide bridges Often form between 2 cysteins In a polypeptide backbone Or in separate polypeptides

polar or nonpolar characters (of side chains) Polar hydrophilic Associate with surrounding water On the outside Make the protein soluble Enzymes, into nonpolar interior atabolic acti!ity

"onpolar hydrophobic #ightly packed together $ri!ing force in protein folding ontribute to o!erall stability in an a%ueous medium

Posttranslational Modification Amino acids may arise from posttranslational modification &P#Ms' (a!e altered side chains

an generate dramatic changes in the #hree dimensional structure )e!el of acti!ity )ocalization in the cell

Interaction with other molecules )ifespan of the cell

A change in a single phosphate group could determine whether a cell would be normal or cancerous P#Ms allow a single polypeptide to e*ist as a number of distinct biological molecules Proteins: Levels of Organization Primar !tructure

Amino acid chain 2+ amino acids 2+n possible amino acid combinations n, - of amino acids in a chain

.ased on information from the genome #he specific se%uence determines the functional /d shape0 confirmation Any changes or mutations could render it non1functional !ic"le cell anemia

Protein se#uence errors $egree of change allowable depends on degree by which the shape or function is disturbed !e#uencing 2rederick 3anger $etermined the first amino acid se%uence .eef insulin A!ailability, small size

$efinable structure "ot repeating or regular &like carbs' !econdar !tructure onformation /d arrangement of atoms

"o longer flat or one dimensional like the amino acid chain Linus Pauling and $obert Core Polypeptide chains e*ist in preferred conformations %lpha heli& .ackbone on the inside in the form of a helical twisting spiral .ackbone inside 3ide chains outward 3tabilized by hydrogen bonds 4 ray diffraction 5eratin in hair Myoglobin (emoglobin Ma*imize hydrogen bonds between other amino acids

'eta pleated sheet 3egments of the polypeptide are side by side .ackbone is in a pleated or folded configuration Many hydrogen bonds &perpendicular to a*is of polypeptide chain and pro6ect across one part of the chain to another' (ighly e*tended1 can resist tensile forces

3egments of the polypeptide side by side .ackbone in a pleated or folded configuration Many hydrogen bonds (ighly e*tended can resist tensile forces

3ilk 3pider silk 7 times stronger than steel fiber of the same weight

!econdar structures other than alpha heli& or bate sheet (inges, turns, loops, finger1like e*tensions Often the most fle*ible parts 3ites of greatest biological acti!ity ribonuclease

(ertiar

structure

3tabilized by co!alent bonds between the different side chains

an gi!e rise to unlimited possibility in structures

8se 4 ray crystallography rystal of the protein bombarded by 4 rays

9adiation scattered Analyzed by a radiation sensiti!e plate or detector omple* math to deri!e the structure

Disordered regions Occupy many different positions 9oles in !ital cellular processes .inding to $"A or other proteins May undergo a physical transformation, then ha!e a defined, folded structure

)ibrous or *lobular Proteins 2ibrous Elongated Most structural proteins :lobular ompact Most proteins in the cell ollagens, elastins of connecti!e tissue 5eratins of hair, skin, silk

M oglobin :lobular

 #ertiary structure 3tores o*ygen in muscles O*ygen bound to an iron atom at the center of the heme group M oglobin ;ohn 5endrew1 <=7> 4 ray diffraction patterns

ompact

2olded upon itself omple*

"o regularity or symmetry 2urther analysis (eme group within a pocket of hydrophibic side chains promotes o*ygen binding without loss of electrons in iron

Mainly non1co!alent bonds Mainly non1co!alent bonds !an der ?aals forces Ionic bond (ydrogen bond

Protein domains $istinct modules that fold independently (a!e specific functions 3pecific binding

$omains 3aid to ha!e e!ol!ed from the fusion of genes

?ere once separate molecules an see similar domains on different proteins

e+& Phospholipase C ,uclear magnetic resonance "uclear magnetic resonance &"M9' Monitor dynamic changes or mo!ements in the protein Easily affected by energy shifts from the en!ironment an also determine rotations in the protein structure

8nlike * ray crystallography apable of internal mo!ements

%cet lcholinesterase

Conformational change Predictable mo!ements in a protein triggered by the binding of a specific molecule .acterial proteins :roE3 and :ro E) Myosin -uarternar .inding with actin structure onformational change in e!ery acti!ity

More than one chain or subunit May be linked by co!alent bonds but are held together by non1co!alent bonds (omodimer1 2 identical units (eterodimer1 non identical Multisubunit protein: haemoglobin arries o*ygen in blood cell

 2 alpha globins, 2 beta globins Each bind to a single molecule of O2 (etero tetramer Ma* Perutz Each globulin tertiary structure O*ygen binding with mo!ement of bound iron atom closer to the heme group Pulls alpha heli* inwards )eads to other changes in shape

Protein protein interactions Multiprotein comple* Pyru!ate dehydrogenase of E. coli @+ polypeptide chains1 / different enzymes Affect glycolysis and the # A cycle Product of one enzyme channeled directly to the ne*t enzyme

Multiprotein comple* $ifferent proteins with different functions become associated

Pyru!ate dehydrogenase of E. coli @+ polypeptide chains / different enzymes Affect glycolysis and the # A cycle Product of one enzyme channeled directly to the ne*t enzyme

Multiprotein comple&es "ot necessarily stable (ighly dynamic Interacting proteins often ha!e complementary surfaces 3(/ domain of PI/5 enzyme

3(/ domain of PI/5 enzyme .inds to proline rich peptides 2orms hydrophobic pockets

Multiprotein comple&es 9egulated by modifications affects its ability to bind to another protein

$"A synthesis, A#P formation, 9"A processing interacting proteins

.east 2 h brid assa

(.2/)

#o test for protein interaction :enes for 2 proteins introduced into the same yeast cell If the yeast cells are positi!e for a reporter protein interacted

,et0or" of protein protein interactons (.2/ assa )

Protein folding hristian Anfinsen

9ibonuclease A

break disulfide bonds with a reducing agent mercaptoethanol

Molecule had to be unfolded0 denatured first $etergents, organic sol!ents, radiation, heat, urea, guanidine chloride )ost enzymatic acti!ity "o longer folded, no longer functional 9egained when chemicals were remo!ed 2olded back

9ibonuclease capable of self assembly Amino acid se%uence contained all the info for the /d configuration

#ertiary structure is most thermodynamically stable )ess energy

2 possible routes of folding Mutations can alter 1d structure Protein misfolding reutzfeldt1 ;akob disease AlzheimerAs disease

Molecular chaperones (elp unfolded or misfolded proteins reach proper /d conformation 3electi!ely bind to short stretches of hydrophobic amino acids Other functions import of proteins into organelles pre!ention and re!ersal of protein aggregation

/sp23 famil

 Pre!ent partially formed &nacent' polypeptides from binding to other cytosolic proteins Pre!ent aggregation which could lead to misfolding

3ynthesis1 released by chaperones into the cytoplasm1 fold to nati!e state May in!ol!e chaperonins Chaperonin ylindrical protein comple*es with chambers where newly synthesized polypeptides can fold without interference from other macromolecules in the cell #9i

,ucleic %cids "ucleotides $eo*yribonucleic acid &$"A' 9ibonucleic acid &9"A' / ma6or parts phosphate group nitrogenous base purine Adenine :uanine pyrimidine ytosine

#hymine 8racil &only 9"A' .onds phosphodiester bond

 phosphate and sugar hydrogen bond nucleotide bases glycosidic bond 3ugar and base Other structures ,ucleoside sugar and base "ucleotide nucleoside and phosphate Directionalit

!econdar structures

.acterial r9"A $ouble stranded 2olds inwards

!iroid r9"A double stranded helical

$ibosomal $,% 3tructural scaffolds for synthesized proteins to attach 9ibozymes 9"As with catalytic roles

(ammerhead ribozyme Able to clea!e its own 9"A

 Other terms "ucleoside monophosphate "ucleoside diphosphate "ucleoside triphosphate &egB A#P, :#P' #hese are useful in bioenergetics