Amino Acids, Polypeptides and Proteins

8/4/2019 Amino Acids, Polypeptides and Proteins

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Amino acids,Polypeptides and

Proteins



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ProteinsDerived from the Greek word proteios, whichmeans “holding first place” or “firstimportance”

Are instrumental in about everything that anorganism does



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Proteinsare organic compounds composedmainly of carbon, hydrogen, oxygen,

and nitrogen



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FunctionsStructure

Catalysis

Movement

Transport

Hormones

Protection

Storage

Regulation



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FunctionsProteins are the overwhelming enzymes in

a cell and regulate metabolism byselectively accelerating chemicalreactions.



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Function - structureProteins are the main structural materials

for animals



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Chief constituents of skin, bones,hair, and nails

Two important structural proteins –collagen and keratin



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CollagenCollagen is a type of protein.

Fibrous in nature, it connects and supports

other bodily tissues, such as skin,bone, tendons, muscles, and cartilage.

It also supports the internal organs and iseven present in teeth. There are more than 25

types of collagens that naturally occur in thebody.



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KeratinKeratin is an extremely strong protein which

is a major component in skin, hair, nails,hooves, horns, and teeth.

The amino acids which combine toform keratin have several unique properties,and depending on the levels of the various

amino acids, keratin can be inflexible andhard, like hooves, or soft, as is the case withskin.



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KeratinMost of the keratin that people interact with

is actually dead; hair, skin, and nails are allformed from dead cells which the body sheds

as new cells push up from underneath. If thedead cells are kept in good condition, they willserve as an insulating layer to protect thedelicate new keratin below them.



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Keratin Structure



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Function - catalysisVirtually all reactions in living organisms are

catalyzed by proteins called enzymes.

Very slow reaction will happen if enzymes arenot used.



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Function -movement

Muscle expansion and contraction areinvolved in every movement we make.

Muscles are made up of protein moleculescalled myosin and actin.



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Function - transport

A large number of proteins performtransportation duties.

Hemoglobin – protein in the blood –carries oxygen from lungs to the cells andcarbon dioxide from cells to the lungs.



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Function - hormones

Many hormones are proteins, includinginsulin, erythropoietin, and humangrowth hormone.



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Function - protection

When a protein from outside source orother foreign substance – antigen – entersthe body, the body makes its own proteins– antibodies – to counteract the foreignprotein.

Blood clotting is another protective

function carried out by a protein –fibrinogen – without blood clotting, wewill bleed to death from any small wound.



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Function - storage

Some proteins store materials in the waythat starch and glycogen store energy.

Casein in milk and ovalbumin in eggsstore nutrients for newborn mammals andbirds.

Ferritin – a protein in the liver – storesiron.



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Function - regulation

Some proteins not only control theexpression of genes thereby regulating thekind of proteins synthesized in a particularcell, but also dictate when suchmanufacture takes place.



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Function

These are not the only functions of proteins, but they are among the mostimportant.

Any individual needs a great manyproteins to carry out these variedfunctions.

A typical cell contains about 9,000different proteins; the entire human bodyhas about 100,000 different proteins.



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Major types

Fibrous proteins

Insoluble in water

Used mainly for structural purposes

Globular proteinsMore or less soluble in water

Used mainly for nonstructural

purposes



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Some common fibrous and Globular Proteins

Name Occurrence and UseFibrous Proteins( insoluble)

Collagens Animal hide, tendons,connective tissues

Elastins Blood vessels,ligament

Fibrinogen Necessary for bloodclotting

Keratin Skin, wool, feathersetc.



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Some common fibrous and Globular Proteins

Name Occurrence and UseGlobular Proteins(soluble)

Hemoglobin Involve in oxygentransport

Immunoglobulin Involve in immuneresponse

Insulin Hormone forcontrolling glucosemetabolsim

Ribonuclease Enzymes controllingRNA synthesis



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Structure-function

connectionHumans have ten thousands of

different proteins, each with their

own structure and function.Proteins are the most structurally

complex molecules known.

Protein polymers are constructedfrom the same set 0f 20 monomers,called amino acids.



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Amino acids

An organic compound containing anamino group and a carboxyl group

Can be synthesized in the laboratory

Nature is more restrictive and uses20 common amino acids to make up

proteins.



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Amino acids

The sequence of amino acidsdetermines a protein’s shape and

function. The 20 common amino acids found

in proteins are called alpha amino

acids.Amino acid in which the aminogroup is linked to the carbon atom

next to the –COOH carbon.



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Amino acids

12 amino acids are made in thehuman body.

Humans need to consume theother 8 amino acids from sourcessuch as nuts, beans, or meat



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Classification of proteins

Simple Proteins

yield only amino acids when hydrolyzed

Conjugated Proteins

yield amino acids and one or more

additional products



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Some Conjugated Proteins

Name Composition

Glycoproteins Proteins bonded to acabohydrates; e.g. Cellmembrane

Lipoprotein Proteins bonded tofats and oils ( lipid);e.g. cholesterol

Metalloproteins Proteins bonded to ametal ion; e.gcytochrome( biological energy)



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Some Conjugated Proteins

Name Composition

Nucleoproteins Proteins bonded toRNA

Phosphoproteins Proteins bonded to aphosphate group; milkcasein



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Classification according

to polarityNonpolar

hydrophobic

Polar but neutral

hydrophilic

Acidic

hydrophilic

Basic

Hydrophilic



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Amino acids

Several amino acids found inproteins also serve functions distinct

from the formation of peptides andproteins.

Histidine – converted to histamine,

which causes stomach lining tosecrete HCl and is associated withtissue inflammations and colds.



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Amino acids

Tyrosine – converted to dopamine(neurotransmitter), epinephrine

(adrenalin) and thyroxineGlycine and glutamic acid –

chemical messengers between nerve

cells



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Essential amino acidsArginine

Histidine

Isoleucine

Leucine

Lysine

MethioninePhenylalanine

Threonine

Tryptophan

N ti l i



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Non essential aminoacidsAlanine

Asparagine

Aspartate

Cysteine

Glutamate

Glutamine

Glycine

Proline

Serine



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Amino acids

Amino acid units in a given protein arearranged in a definite sequence

The sequence of amino acids establishesthe proteins function.

Missing or misplaced amino acids mayalter the proteins biological function.



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amphoterism

Amphoteric – can act either as anacid or as a base

The alpha-COOH and alpha-NH2groups in amino acids are capable of

ionizing (as are the acidic and basicR-groups of the amino acids).



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Zwitterion (di-ion)

Amino acid with no ionizable R-groupand is electrically neutral



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Formation of

polypeptidesProteins and peptides are polymers

of amino acids linked by “ peptide

bonds”Also called amide bonds or peptide linkage



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Formation of

polypeptidesAmide bonds results from the

condensation of an amino and a

carboxyl group, releasing water The amide group is polar, with

resonance giving partial double bond

characteristics. This helps peptides be soluble even

though the charges are lost during

condensation.



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Formation of

polypeptidesAmino acids are joined together

when a dehydration reaction

removes a hydroxyl group from thecarbonyl end of one amino acid and ahydrogen from the amino group of another.

The resulting covalent bond iscalled a peptide bond .



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Formation of

polypeptidesRepeating the process over and over

creates a long polypeptide chain.

At one end is an amino acid with a freeamino group the N-terminus and at theother is an amino acid with a freecarboxyl group the C-terminus.



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Formation of

polypeptides The repeated sequence (N-C-C) is the polypeptide backbone.

Attached to the backbone are the variousR groups.

Polypeptides range in size from a fewmonomers to thousands.



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Formation of

polypeptidesEach amino acid is called a residue.

The number of amino acids is reflected in a

general designation2 amino acids – dipeptide

3 amino acids – tripeptide

Several amino acids – oligopeptidesMany amino acids – protein or

polypeptides



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TRIPEPTIDE



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Conformation

A proteins’s function depends on itsspecific conformation.

A functional proteins consists of one ormore polypetides that have been preciselytwisted, folded, and coiled into aunique shape.

It is the order of amino acids thatdetermines what three-dimensionalconformation will be.



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Conformation

In almost every case, the function dependson its ability to recognize and bind to someother molecule.

Antibodies bind to a particular foreignsubstances that fir their binding sites.

Enzyme recognize and bind to specific

substrates, facilitating a chemicalreaction.

Neurotransmitters pass signals from

one cell to another by binding to



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conformation

The folding of a protein from a chain of amino acids occurs spontaneously.

The function of protein is an emergentproperty resulting from its specificmolecular order.



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conformation

Three levels of structure: primary,secondary and tertiary structure, areused to organize the folding within a single

polypeptide.

Quarternary structure arises when twoor more polypeptides join to form a

protein.



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Primary structure

The primary structure of a protein is itsunique sequence of amino acids.

Lysozyme, an enzyme that attacksbacteria, consists on a polypeptide chainof 129 amino acids.

The precise structure of a protein is

determined by inherited geneticinformation.



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Primary structure

Even a slight change in primary structurecan affect a protein’s conformation andability to function.

In individuals with sickle cell disease,abnormal hemoglobins, oxygen-carryingproteins, develop because of a single

amino acid substitution. These abnormal hemoglobins crystallize,

deforming the red blood cells andleading to clogs in tiny blood vessels.



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Secondary structure

The secondary structure of a proteinresults from hydrogen bonds at regularintervals along the polypeptide backbone.

Typical shapes that develop fromsecondary structure are coils (an alphahelix) or folds (beta pleated sheets)



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Secondary structure

The structural properties of silk are due tobeta pleated sheets.

The presence of so many hydrogen bondsmakes each silk fiber stronger that steel.



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Tertiary structure

Tertiary structure is determined by avariety of interactions among R groups andbetween R groups and the polypeptide

backbone.

These interactions include hydrogen bondsamong polar and/or charged areas, ionicbonds between charged R groups, and

hydrophobic interactions and van der Waals interactions among hydrophobic Rgroups.



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Tertiary structure

While these interactions are relatively weak,disulfide bridges, strong covalent bondsthat form between the sulfhydryl groups

(SH) of cysteine monomers, stabilize thestructure.



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Quarternary structure

Quarternary structure results from theaggregation of two or more polypeptide subunits.

Collagen – a fibrous protein of threepolypeptides that are supercoiled like a rope.

This provides the structural strength of their role

in connective tissue.Hemoglobin is a globular protein with two

copies of two kinds of polypeptides.



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conformation

A protein’s conformation can change inresponse to the physical and chemicalconditions

Alterations in pH, salt concentration,temperature, or other factors canunravel or denature a protein.

These forces disrupt the hydrogen bonds, ionicbond, and disulfide bridges that maintain theprotein’s shape



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conformation

Some proteins can return to theirfunctional shape after denaturation, butother cannot, especially in the crowded

environment of the cell.



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conformation

In spite of the knowledge of the three-dimensional shapes of over 10,000proteins, it is still difficult to predict the

conformation of a protein from its primarystructure alone.

Most proteins appear to undergo

several intermediate stages beforereaching their “mature”configuration.



conformation

The folding of many proteins is protectedby chaperonin proteins that shield outbad influences.

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Amino Acids, Polypeptides and Proteins