BIO CHEM PROTEINS

Secondary linkages

(Hydrogen bonds)

Synthesis and processing of collagen

- 2 important enzyme mediated process- hydroxylation and cross linking - collagen is an extracellularly matrix protein- poly peptide chains have to be secreted - ribosomes are site for protein synthesis located on RER - teriatary stuctures cause disulfide linakages and it has 3 polypeptide chains which is quantanry structure as well - amino acids that undergo hydroxylation- proline and lysine - glycosylation resides are OH lys (must first hydroxylize then it becomes a substrate for glycosylation) -

A host of disease are associated with improperly folded proteins, including

- Alzheimer's disease - Parkinson's disease -Huntington diseas -transmissible spongiform encephalopathies (prion disease) Beta conformation accumulation

Secondary

Will make hydrogen bonds with the primary structure, every 4th peptide there is a hydrogen bonds. When folded it can interact with other things. Alpha helices and beta sheets

Energy from food

You need proteins to grow! In third world countries you get these diseases from lack of protein (skin and bone disease, stunted growth and muscle wasting) - stage 1- break down macromolcules in to monomeric units amino acids - amino acids are oxidized to generate energy (stage 2 and 3 ) - protiens are digested in the stomach - digestion starts when you are cooking - place where you see digestion is the stomach (pepsin) (HCL stomach acid)

CCK will tell pancreases to secrete

Zygomin and make them into active enzymes

The native fold has a

a large number of favorable interactions within the protein

dimers

a molecule or molecular complex consisting of two identical molecules linked together.

Edman degradation

a stepwise process for determining the amino acid sequence in an isolated protein (N terminus )

Hydroxylation

addition of a hydroxyl group

Primary

amino acid sequence- read from N terminus- proline to valine - linked togther by peptide bonds - can have disulfide bonds

chaperone

helps protein folding

Zymogen

inactive form of an enzyme

Keratin

keratin alpha helix—> Two chain alpha helices —> protofilament—> protofibril—> intermediate filament—> cells - alpha helices - disulfide bonds

tetramers

molecules consisting of four subunits

Insulin is a

peptide hormone 2 poly peptides - disulfide linakages (covalent linakages) tertiary structures In notch Chains - preproinsulin (signal sequence and C peptide inactive form) - goes to ER reason for signal sequence where the disulfide linakages are introduced. Pro insulin - no longer signal sequence - Golgi to get rid of C peptide now we have a funtional insulin molecule

4 levels of protein structure

primary, secondary, tertiary, quaternary

Know this

Endmans reacgeant- introducing sequencing techniques Model for protein chemistry Came to highlight proteins sequences And now have lots of proteins

Trypsinogen activation

Enterropeptidase and trypsin

Collagen II

Fibril - cartilage, discs, virtreous body

Collegen III

Fibril Blood vessels, skin, muscle

Collage I

Fibril - skin, bone , tendon, blood vessels, cornea - most abundant in body long shelve life

Collagen is

Fibrous - triple helix - 3 polypeptide chains - secondary structural element - super helices - as they are secretes they are left handed helices when 3 come together they are then right handed helices - tensile strength and fibrous

Fibrous are important

For structual support

Fibrous proteins

Form structure to function - fibrous proteins provide support for cell and tissue - collagen and alpha keratin are examples of fibrous proteins having just primary and secondary stuctures - have alpha and Beta conformations - alpha are tough insoluble protective Iike hair nails etc - beta are soft and flexible like silk can be formed into prions bad - collagen triple helix - high tensile without the stretch - collegen bone etc,

Desaturation is brought about by

HCL

Pepsinogen activation

HCL (pepsin)

There is a cost in blank blank of folding the proteins into a specific native fold

Conformational entropy (requires energy) - very energy expensive , primary, secondary, tertiary forms pick up where they left off nad build on each other in folding or else it would take a long time

Collagen is an important constituent of

Connective tissue, tendons, cartilage, bones, cornea of the eye

Intrinsically disordered proteins

Contain protein segments that lack definable structure Composed of amino acids whose higher concentration forces less-defined structure Lys, Arg, Glu, and Pro Disordered regions can conform to many different proteins, facilitating interaction with numerous different partner proteins

Proteins can be denatured by

Heat or cold - pH extreme - detergents - reducing agents :DTT and mercatioethanol - disrupt disulfide bond -chaotic Agnes : urea and guanidium hydrochloride - disrupts H bonds, denatures secondary stuctures

Hydroxylation involves

Inside cell - hydroxylation (enzyme important iron and ascorbate ) proline and lysine - Metallic enzymes need vitamins C as well - vitamin C acts as a redundant - ascorbate is vitamin C -

Hydrogen Bonds

Inteaction of N-H and C=O of the peptide bond leads to local regular structures such as alpha helices and beta sheets

Reducing agents

Introduce more sulfur hydrol groups which curls the hair then oxidize it taking away hydrogens this stabilzed it

Quantanry structure

Is formed by the assembly of individual polypeptides into a large funtional cluster - subunit is the basic unit of quantnary structure; non-covalent interactions stabilize subunits

quantanary structure

Is many tertiary put togther- many poly peptide chains with interactions - subunits- hemoglobin is an example - one subunits is a tertiary structure.

Pepsin is the enzyme in the stomach that begins the breakdown of proteins. This enzyme continues the breakdown of proteins in the small intestine.

It forms oilogo peptides not complete yet

Each collagen chain is a

Left handed helix called alpha chain Tripeptide sequence : GLY-X-pro or GLY- X-4HYP

Denaturing

Loosing the folded structure and loosing the activity

Trypsin specific targets

Lys and Arginie

The bond between N and alpha carbon carboxyl carbon consists the

Poly peptide back bone

Quantnary structure cont.

Polypepride chains are interacting non covalent - disulfide bridges as well- teritary structure (subunits)

Helix stability

Sequence effects this for exmaple charges amino acids can form electrostatic interaction - proline will be a helix destabilized cause its bulk R group - steric hinderance - glycine it can interact with other molecules its very small - can fit into any small crevice and distort the geometry - not all polypeptide sequences adopt alpha structures - small hydrophobic resides such as alanine and leucine are strong helix formers

Primary structure

Sequence of amino acids- peptide or amide bonds

The carbonyl oxygen has a partial negative charge and the amine nitrogen has a partial positive change this

Sets us a small dipole

Beta sheets

Stabilized by hydrogen bonds between adjacent segments that may not be nearby

The alpha Helix

Stabilzed by broken bonds between nearby residues

Salivary amalyse (ptyalin)

Starts digestion

The triple helix has higher tensile strength than a

Steal wire of equal cross section- many triple helices assemble into a collagen fibril

Pepsin source

Stomach

Pepisin made by

Stomach adn it is inactive till activated by HCL then break down the amide linakages

Structure of keratin

Strong, rope-like structures interwined alpha helices. Major component of external protective layers in mammals. - 2 coils frmos a protofilament - alpha helices - disulfide bonds

Beta sheet structure

The planarian of the peptide bond and tetrahedral geometry of the alpha carbon create a pleased sheet like structure - valine isoleucine tryosine cysteine and tryptophan common

MRNA is synthesized in the nucleus

Then head to RER - post translation modifications hydroxylation adn glycosylation

Unlike most organic polymers, protein molecules adopt a specific

three-dimensional conformation- this structure is able to fulfill a specific biological funtion

Secondary Structurs

- How are they arranged main bonds are hydrogen bonds - Secondary structure refers to a local spatial arrangement of the poly peptide backbone - two regular arrangements are common The alpha helix and beta sheets - adding a level of complexity to stabilize structure

Alpha- synnuceliom

- alpha conforms usually but beta confoartions aggregate and form Lewy bodies this causes Parkinson's disease - dopamine producing cells are degenerated- in the neuron we run into problems - look at dopamine levels- to tell if they have this disease - one line of treatment is to give them dopa to make dopamine

Affect brain and nervous tissue

- bovine spongiform encephalopathy - Kuru - Creutzfeldt- Jacob disease

Tertiary seen in

- globular and fibrous proteins Globular - contain tertiary stuctures usually more dynamic involves in defense mechanisms antibodies and enzymes - usually membrane bound or cytosolic can be both insoluble and soluble. Dynamic roles , usually intra cellular ex. Hemoglobin myoglobin enzymes Fibrous- increased to contain only one type secondary structure - insoluble involved in structural ridigidy - collagen ex. - bone- rigidity for bones mineral will grow and gives hard toughness of bone. Structural roles. Usually extracellularly ex. Keratin, elastin, collagens

Alpha helix arrangement

- intrachain hydrogen bond - side chains of amino aicds extend outwards - imaginary axis with poly peptide backbones - helical manner - hydrogen bonds - 3.6 amino acids per turn of the helix

Secondary structure

- local arrangement of the poly peptide bone- Alpha helix easiest imaginary axis where they will be arranged on right handed helix. Stabilized by hydrogen bonds cause they are very easy to break and very easy to form. Polypeptide chain is folded into a helix. Nearby residues. - Beta sheet- poly peptide chain is spread out, but with hydrogen bond contacts its like a sheet stabilized between adjacent segments that may not be nearly by. R groups are pointed out words

Collagen

- long lived proteins (existing ) high shelf life - more stable in terms of resistance and undergoes many changes with aging - left handed helix (3 coils 3 polypeptide chains) - total orientation is a right handed super helix's - X is an amino acid - two amino acids predominantly found in collagen (glycerine, proline) - proline is rigidity - opposite intertwining makes this possible proline is a steric big molecule

Elctrostatic interactions

- long range strong interactions between permanent ally charges groups - salt bridges, esp. buried in the hydrophobic enviroment strongly stabilize the protein

Parkinson's disease

- many genes contribute - major protein : alpha-synuclein - intrinsically disordered protein, abundant in the brain - can form insoluble aggregates termed Lewy bodies - increase in the percent of beta conformations

Prion protein, Prp is a Brain protein with unknown funtion

- mice lacking PrP display normal phenotype - prion diseases - Proteinaceous infectious only

alpha keratin structure

- most humans and mammals - alpha helices - secondary stuctures (helices)

How can proteins fold so fast?

- proteins fold to the lowest - energy fold in the microsecond to second time scales. How can they find the right fold so fast? - each fold takes small part of a second - helices form through hydrogen bonds then tertiary structure maybe it is not ideal when you begin at the top you have many diffrent conformations at the top you want to stabilze the folded intermediates - once it has tried secondary it will stabilze it - then it will go to tertiary state - bottom of funnel finds perfect native fold. (Molten globule intermediate) once it gets comtoable with one configation it goes to the next

Protein tertiary structures

- refers to the overall spatial arrangement of atoms in a protein - stabilzed by numerous weak interactions between amino acid side chains - largely hydrophobic and polar interactions can be stabilzed by disulfide bonds - interacting amino aicds are not nessarly next to each other in the primary structure - two major classes - fibrous and globular (water or lipid soluble)

Disordered proteins

- regions of disordered - ends usually - collegen before complete we had disorganized parts - reason for disorganization it will help in facilities numerous interactions with numerous binding partners - allows lots of interactions with different proteins - stabilze molecules as well can interacts with diffrent pathways

Beta sheet arrangement

- spread out extended out stretched out - either all one direction - or in zigzag manner - parallels or antiparallel - hydrogen bonds between - polypeptide chains almost fully extend - sheets are more than 1 polypeptide chains - trans

Inside cells

- synthesis of pro-alpha-chains on ribosome -ER to facilitate secretion - hydroxylation of selected pro and lys resides - catalyzed by pro and lys hydroxylases - glycosylation of selected OH-lys resides - enzymes catalyzed process - triple helix formation of pro - collagen molecule - spontaneous process, no enzyme is needed - secreation of pro-collagen molecule

Structure of insulin

- they needed a technique to find its structure - it has two peptides A and B with disulfide bridges between modules and chains - not active when produced needs a protylictic processing have to fold and undergo protylictic processing. Post translational modifications. - preproinsulin has a signal sequence as N terminus and C terminus has C peptide. - signal sequence will have information where it needs to go or destination site - signal sequences sends it to the endoplasmic reticulum additions of disulfide bridges from ER Pro insulin now - c peptide is responsible for some info on further modifications - lost signal sequence but still has C site so its proinsulins it lost the n terminus - in endoplasmic reticulum oxidizes and disulfide bridges form - goes back to Golgi C peptide is removed and we have a shorted peptide and devoid of C peptide becomes C peptide

The resonance causes the peptide bonds

- to be less reactive compared to esters, for example - to be quite ridge and nearly planar - to exhibit a large dipole movement in the favored Trans config.

Misfolded protein from water soluble PrP to insoluble prion form

- universally fatal - infectious

Desmosine

-3 of the allysyl side chains plus one altered lysyl side chain for this cross link -this produces an extensively interconnected rubbery network that can stretch and ben in any direction when stressed, therefor giving elastic tissue its elasticity

A proteins funtion depends on its

3D structure

Myoglobin structure

8 helices - teritary structure - 70% in helices form

Glycosylation

Addition of a carbohydrate group to a molecule.

Mode of infection

Aggregates of misfolded prions serve as a nucleus for mantra formation of healthy prion protein (mad cow or bovine spongiform encephalopathy) PrP(prion protein) bad protein

Silk fibroin

All betta sheets - proteins natural occurring - easier to build

Primary Structure tells us

Amino acid sequence.

Nurological diseases such as Alzheimer's, Parkinson's, Huntington and creutzfeldt-Jacobs diseases result in the deposition of protein aggregates called

Amyloid fibrils or plaques - these diseases are called (amyloidoses)

Chemoytipsin target

Aromatic and bulky AA

Type III and V collagen and genetic disease

Ehlers- Danlos syndrome - fragil skin and blood vessels (type III aroma rupteu) and hyper molbile joints (type V) Type V - ehlers danlos syndromes- normal life usually - easily extent there skin hyper extension in joints and skin Type III- leathal

Motifs

Assembly of secondary structal elements - common in globular proteins - all alpha helix - all beta sheets - both Motifs can be found as reoccurring structures in numerous proteins - proteins are made of diffrent motifs folded together - ex. Alpha betta barrel - alpha betta loop

Tertiary

Assmembly of alpha helices and beta sheets many, more complex organization-

Secondary molecules and types

Between peptide bonds, alpha helix beta sheets and beta turn

Teritiary molecules and types

Between r groups of molecules have secondary structure such as motifs folds and domains

Quantnary molceus and types

Between subunits mostly r groups types are dimers tetramers and others

Native state

Catalytically acitve

Type II collagen genetic disease

Chondriodysplasias - abnormal cartilage, bone and joint deformities - more prevalent in birds

Outside cells

Cleavage of extension peptides - can also take place just before secreation- catalyzed by procollagen peptidases - assembly into microfibril - spontaous process - cross link fromatino- catalyzed by copper containing enzyme called Lysyl oxidase -assembly into mature collagen fibril - spontaous - aggregation of collagen fibrils to form a collagen fiber - spontaneous - fibers are visible under light microscope

Primary linkage

Covalent (amide, peptide)

Tertiary linkages

Covelalent H bond, ionic, vanderwall and hydrophobic

Reducing agent

DD and mercatoethaonl - have sulfur containing groups (perm)

Processing of collagen

DNA is copied into mRNA (transcription) - mRNA copies into proteins (translation) Proteins are formed proline and lysine resides are hydroxylated - where every you have OH lysine you will be adding glycosylation so glucose and galactose are added glycoslatyed lysine resides - pro alhpa chains ensemble (c terminal and N terminal disulfide linkages) - now triple helical in center C terminal and N terminal no organization still disrentained - those must be removed - cleavage- procollagen peptidases comes off in the cytosol - tropocollagen not complete also most there - need cross links - N terminals are removed adn leaved us with tropocollaen Enzymatic processes : - enzymes for hydroxylation adn cross linking - IMPORTANT!!! [ copper and iron containing - hydroxylation - iron /proline/(ascorbate vitamin c ) prolyl hydroxylase / ] [lysil oxidase - crosslinking- allysine reside will be bound to regular lysine and forms a complex and cross linked product inhance the strength / oxidize lysine with oxygen and copper tp create lysine oxidase (copper contains) gives you allysine residue.

Loss of structural intergerrity with accompanying loss of activity is called

Denaturation

Food goes into stomach then small intestine

Digestive enzymes come into small intestine and originate in the pancreases- secretin and CCK these are hormones- not important for us right now - Secretin and Cholecystokinin are hormones produced from small intestine

Search for the minimum is not renadon and is a step wise progress because the

Direction toward the native structure is thermodynamically most favorable

Elastin

Highly hydrophobic protien about 750 AA long - glycine and proline rich- elastic in nature - cross links - - not glycosylation and has some OH proline but not OH lysine - random conformation and rubber like structure - give tissues their elasticity -elastin is crosslined and desmosine made of 4 lysine and is the typical crosslink - 3 L lysine resides and 1 unmodified Lysine - desmoise cross link - major components of skin blood vessels and lungs

Network-forming collagens

IV- basement membrane VIII- corneal and vascular endothelium (1,2,3,4 really important )

Fibril-associated collagens

IX- cartilage XII- tendon, ligaments, some other tissues

Protein diseases - misfolding

If we have defects in the chaperones misfolded proteins will accumulate adn aggregate - create amyloid fibrils accumulation - looking for a cure Amyloid beta peptide precursor form - accumulation of the amyloid fibrils is called amyloidoses

Temperature and protein unfolding

Impact: apomyoglobin heme group - as you increase temp at certain temp you wil have Tm= or half is unfolded.

London Dispersion

Medium-range weak attraction between all atoms contributes significantly to the stability in the interior of the protein - doesn't have to be charges, don't have to be polar - location and time of interaction depends on interaction - have to have a minumin distance. Between them - attractive forces - Ligand interactions

Reduction of disulfide bonds

Mercatan ethnol breaks S-S bonds reduces them adn makes them inactive

Cyanogen bromide determines

Methionine

Cyanogen bromides binds specific to

Methionine- mass spectroscopy for chemical digestion - identifying protein sequences. Bind then cleave using edmans Reagant

Pepsin targets

Mostly Phe

The structure of the 3D proteins is called the

Native fold

collagen IV

Network- basement membrane

A common feature of amyloidoses if that

Normally soluble proteins are converted into insoluble fibrils rich beta sheets

Simple

Only 1 poylpeptide chains

parallel or antiparallel sheets

Orientation of the two chains within a sheet are porridge - in parallel beta sheets h bonds are weaker in the same direction - anti parallel are much stronger H bonds in opposite directions

Type I collegen genetic diseases

Osteogenesis imperfects - weak bones that fracture easily - brittle bone disease mild form usually - could be mutations in either alpha cartilage chains

Cross linking involves

Outside cell - just like hydroxylation it is enzyme mediated lysial oxidase and contains copper (metal) lysil oxidase will remove the alpha amino group for lysine - red bean not properly cooked can leaded to lacramisrm - bean contains a neuro toxins and is an inhibitor to lysine oxidase- you will not have mature collagen crosslinks so it is immature and it isn't as ridigid so they get a mild form of paralysis

Trypsin source

Pancrease

Chmeotrypsis source

Pancreases

Outside cells lecture

Peptides removed from ends with peptidases - cleaved the extension peptides - assembly of fibrils don't need enzymes - cross linking - lysl oxidase( oxidizes lysine) builds the strength also has lysine cross Links along with disulfide linkages - collagen crosslinks are effected and they get a crippling disease need a cane or crutches

Edman degradation revolutionized the field of proteins

Phenyl isothiocyanate- idetifgites the terminal amino acid ex alaine. N terminal sequencing. Will label the N terminal then enables it then you'd an cleave it using acid hydrolysis. And realse amino acid.

Review for quiz

Primary- sequence of amino acids - compotisino adn sequence - named from N terminus to C terminus- 2D transcription and translation - covalent (amide adnd peptide) Secondary- spatial arrangment- interaction with hydrogen bonds - between carbonyl oxygen and amide hydrogen of another - alpha helix and beta sheets- bent or straight line (antiparallel) Teritary- 3D arrangement Quantanry structure- interactions with subunits - Peptide bonds- trans, ridged, dipole - uncharged and polar - N terminus postive and C terminus is negative R groups are responsible for charge - resonance N terminus sequencing eddmans degradation - alanine N terminus gets labeled phenyl-isothiocyanate cleaves with acid hydrolysis - repeat - trypsin digestion- specific cleavage sites- lysine and Arginie- 2 arginine in an oliogo peptide - will see 3 fragments 2 cleavage points- Use edmans still accelate the process with trypsin — cyanobromide will tag methionine - acid hydrolysis and start edmans - insulin - peptidal hormone 2 peptide chains- disulfide linakages - diffrent states- preproinsulin (inactive) goes to ER gets rid of signal sequence and gains disulfide bonds get pro insulin goes to golgi gets rid of C peptide insulin Alpha helices and beta sheets- hydrogen bonds stabilze Hydrogen bonds formed every 4th peptide - amide hydrogens - R groups protrude in alpha helices Beta sheets- stretched out chains- hydrogen bonds stabilzed nicely - antiparallel stronger - parallel weaker - proline and glycine (kink, steric hindrance breaking points) see proline in turns - glycine super tiny and can create instability - beta sheets - valine, isoleucine , tyrosine , cysteine, and tryptophan at turn can see proline Motifs are assemblies or aggregates of 2nd structure elements in proteins- alpha beta barrel - reocurring structures - Tertiary structure- hydrophobic interactions (aromatic) and bulky) - fibrous and globular - disulfide bonds -hydrogen bond- ionic bond - insulin had disulfide- hydrophobic - electrostatic interaction serine and glutamate (hydrogen) - aspartate and lysine (ionic bond) negative and a postive - fibrous secondary structure - coils - protofilament- protofirbil - keratin - collagen is a super coil - elastin is simple it has desmoisine crosslinks - globular- teritary adn quantanry - myoglobin - hemoglobin has 4 polypeptides (quantanry) Collagen - proline, glycine or OH proline Most common is glycine - right handed super helices - find in extracellualr matrix of CT- crosslinks or dislfuide bridges - hydroxylation (prolyl hydroxlyase- proline or lysine- require iron , ascorbate, (vitamin C reductant) addding hydroxyl group metals enzyme - corsslinking - lysine oxidase - copper contains - causing deamination of lysine residue- cross links are important - neurotoxin in Beans- lacrisime - 1,2,3,4,- fibril adn networkin - type 1 most abundant - bones, skin, tendons type 2- cartilage and discs IVD, type 3 - skin, muscles nad blood vessels lethal in collagen 3 aortic rupture - type 4 basement membrane- pathogen protection, cancer cells tough basement membrane cancer will localize Type 1 disease- brittle bone disease- varies in life -osteogenesisi Type 2- birds- confriodysplasis- abnormal cartilage Type 3-4- mutations in blood vessels - 3- lethal type 5 - hyper mobile joints pretzels folding - desmosine- 3 a lysine resides with 1 regular lysine- nice network - desmosine crosslinks adds elasticity - bubble like network - flexibility and elasticity in protein - glycine and proline- not glycoslated no OH lysine - quantnary structure - - denatureation - breaking hydrogen bonds - will unfold a protein - leads to loss in structure adn desaturation - you can revert back usually no return - like extreme ph and temp-

Specific resides sights

Proline sight for hydroxylation adn lysine - after hydroxylation you have gycolsytaltion - adding a sugar - form of monosaccharides- glucose and glactose are added on to lysine OH- coiling and wrapping but ends are diss organized- processing to be done - collagen is extracellualr matrix mineralized and rigidity etc. - all inside cell right now - once its out you have procollagen peptidases they chop off disordered ends -

Structure of the protein is partially dictated nu the

Properties of the peptide bond

Irregular arrangements of the polypeptide chain is called the

Random coil

Irregular arrangement of the poly peptide chain is called

Random coils

It is mathematically impossible for protien folding to occur by

Randomly trying every conformation until the lowest energy one is found (levinthal's paradox)

Hydrophobic effect

Realse of eater modules from the structured salvation layer around the molecule as protein folds increases the net entropy

The peptide bond is a

Resonance hybrid of two canonical structures

Peptide linkages

Resonance they are always going back and forward between oxygen and nitrogen bond with carbons double and single.

AA sequence of Ribonuclease

Ribonuclease A cysteine can still interact wiht distant due to folding -

Peptide bonds are

Rigid. Ones ingaded in the peptide bond- trans configuration. Dipolar nature. Other bonds are flexible like c alpha c and a alpha N. Very stable molecules so we need enzymes to break amide linkages

Quantanry linkages

Same as teritary for monomers sub7nits noncovalent interactions

Chymotrypsinogen —> chymotrypsin Trypsinogen —> trypsin Procatboxypepdiase —> carboxypeptidase Protelastase —>> elastase

Secretin tells pancreas to make bicarbonate ions

Prion convorsation

They tell proteins to fold wrong one apple spoils the whole batch

Virtually all peptide bonds in proteins occur in this

Trans configuration and

Peptide bonds

Trans, ridge, and dipole. Need robust to break them

Detemination of primary structure

Triptic digestion- breaks down lysine and Arginie it will be cleaved- shorted oil I go pepetides then you Start edmans sequencing. Cyanogen bromide identifies methionine- you use chemical instead of enzyme removes residues of methionine cleave with acid hydrolysis - realse - trypitic more popular - all modifications of edmans sequencing

Chymotrypsinogen activation

Trypsin and chymotrypsin

Trypsin Digestion

Trypsin cleaves peptide bonds it cleaves specifically- lysine or Arginie it will cleave at those locations. Polypeptide chain and you add tripsyin to is. Lysine and Arginie number you can predict the number of peptides. Number of peptides formed 2 lysine or a lysine or Arginie or 2 Arginie- if there is 1 you see 2 if there is 2 you will see 3. Trypsin located at n terminus.

Small intestine produces Enteropeptidase or enterokinase

Trypsionogen (enteropeptidase) trypsin —> increases and this activates other zymogen and it will set the stage once you have trypsin it will activate all other molecules - now they have specific sites where they cleave poly peptide chains trypsin cleave at Arginie and lysine Trypsin )breaks down amino acids Chymotryposingen—> chymotrypsin Trypsin always works at the N terminus C terminus its carboxyl pepridases (B is arginine adn lysine at C terminus) Chymotrypsin (TRP, Tyr, Phe, Met, Leu)

Teritary stuctures cont.

Type of interactions- almost every possibly internation present - hydrogen disulfide hydrophobic etc. Communication doesn't need to be close distance is not an issue cause of the folds - covalent linkages - disulfide and amide linkages - cysteine resides form disulfide bonds - hydrophobic interactions interior or the protein is where they are localized (branching, aromatic and aliphatic methionine and alinaine ) - hydrogen bonds serine hydroxyl groups with gluatamate carboxyl groups - ionic bonds aspartate and lysine postive adn negative molecules

Fibril forming collagen

Types I, II, III 1- skin bone, tendon, blood vessels, cornea 2- cartilage, intervertebral disc, vitreous body 3- blood vessels, skin, muscle

Native state —> addition of urea and meta cap to-ethanol —>

Unfolded state; inactive. Disulfide cross links reduced to yield cystine residues —> remove urea and metocapto-ethanol —> back to native state disulfide cross links correctly reformed. Adding in hydrogen bonds breaks the sulfur bonds

Zymogen activation (precursor of digestive enzymes inactive enzymes they need an activator)

What triggers there realse - CCK As food comes into small intestine small intestine will send out signals CCK to pancreases and secretin to pancreases in response to secretin it makes bicarbonate ions an the CCK responds and sends out digestive enzyme precursors (zymogen)

chief cells

produce pepsinogen

Three collagen chains intertwine into

right-handed superhelical triple helix