Basic Biological Molecules

8/10/2019 Basic Biological Molecules

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10.1 - Biological molecules

Biochemistry is the study of the chemicals of living organisms. Biochemistry gives us anunderstanding of how biological systems work.

Organic Compounds of Biological Significance

There are 4 main organic compounds of biological significance

Elements

Carbohydrates C H O

Lipids C H O

roteins C H O !

!ucleic acids C H O

These are macromolecules " giant molecules made from many repeating units# it is therefore called apolymer

The e$ception to this are lipids %not composed of a repeating unit&

The repeating units are called monomers

The same type of unit can be used to build different types of chains " long' short' straight' branched

Polymer Monomer

Carbohydrates olysaccharide (onosaccharide

roteins rotein )mino acids

!ucleic acids !ucleotides

Lipids are composed of units of fatty acid and glycerol

Carbohydrates

Overhead " Classification of COH from Biol *ci +,- " Copy into notes

lements in carbohydrates are carbon' hydrogen and o$ygen

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There are always twice as many H atoms as O atoms per carbohydrate molecule

/eneral formula 0 %CH-1& n

2unction of carbohydrates is the storage and liberation of energy. ) few e.g. cellulose have astructural role

Monosaccharides monomers!

)ll monosaccharides are sweet and soluble

The cannot be hydrolysed %B3O! 5O6!& to sugars of a smaller si7e

/eneral formula " %CH-O&n

(onosaccharides are classified according to the number of carbon atoms in the molecule

8 carbon molecule " triose monosaccharide

9 carbon molecule " pentose monosaccharide

: carbon molecule " he$ose monosaccharide

/lucose is a monoaccharide " this is the sugar found in animal blood. 2ructose has the sameformula but is a different shape. *ucrose is the most common sugar in plants and is a disaccharide

*ee handout;overhead" structure of monosaccharides

"SOME#"SM

)n important structural characteristic of monosaccharides %e.g. glucose& is the occurrence ofisomerism


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OH group is below the plane of the ring = isomer " glucose

H below 0 Beta

Hydro$yl and hydrogen groups have swapped places

OH group is above the plane of the ring = glucose

*ee Overhead

The e$istence of and isomers leads to greater chemical variety and is of importance in for

e$ample the formation of starch and cellulose

Both types occur naturally and result in considerable biological differences when they form polymers

$etecting monosaccharides

There are a number of simple tests to identify groups of carbohydrates. (ost are effective if carriedout on a solution or suspension of COH.


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$isaccharides

)ll are sweet' soluble in water and form crystals but can also be hydrolysed %broken down& intosugars of smaller si7e

%ormation of disaccharides

*ee life sciences on file

+. (onosaccharides align %usually he$oses&-. Hydrogen atom removed from OH group at position + of monosaccharide8. Hydrogen atom removed from OH group at position 4 of ad@acent monosaccharide4. O$ygen atom removed from one of OH groups9. This results in the formation of a covalent bond. The covalent bond is called a /LACO*


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Polysaccharides

2unction chiefly as food ; energy stores and structural materials. .g. starch ; glycogen ; cellulose

)ll polysaccharides are insoluble' unsweet and cannot be crystallised but can be broken down intosugars of a smaller si7e

%ormation of Polysaccharides

(any monosaccharides combine together %+111s&. The number of monosaccharides which combineis variable and the chain may be branched or unbranched.

The chains may be folded' making them compact' inert and ideal for storage.

The si7e of the molecules makes them insoluble " another feature that suits storage purposesbecause it e$erts no osmotic influence on the cells and does not diffuse.

The properties of the polysaccharide depend on the number of monosaccharide units and how theyare @oined together. .g. glucose can be @oined together in many different ways to form differentcompounds

*ee life sciences on file;overhead " formation of starch

+. 5isaccharides align-. /lycosidic bonds form between ad@acent disaccharides by condensation forming long chain

polysaccharide molecules

&ypes of polysaccharide

)ll the following are polymers of glucose

a& S&'#C( C:(+1O9!n

*tarch is a reserve of food formed from any e$cess glucose produced in photosynthesis. $cessglucose must be stored as it an important source of energy

*tarch molecule is a long chain of +=4 linked = glucose units. The chain %long' unbranched& is then

coiled into a heli$ forming a cylinder in which most of the OH groups pro@ect to the inside

*hape of molecule = !o bonds form between starch molecules so not very good structurally

2unctions " found in plant cells only

*tarch molecules accumulate to form granules called grains or plastids %common in seeds&

$erts no osmotic effect because does not dissolve in water

$etecting starch

*tarch ? iodine;potassium iodide Blue;black colour

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O3Hydrolysis

*tarch solution ? )mylase (altose ?(altase 0 )lucose*+,e ith Benedicts

B )/CO)E C:(+1O9!n 'nimal starch!

/lycogen consists of a long chain of glucose molecules linked by +=4 or +=: glycosidic bonds

2unction " short term storage COH in animals. *tored in muscle and liver cells %centres of highmetabolic activity&. Can form up to +1 of liver mass. /lycogen needs to be converted to glucosewhen needed

/lycogen ? /lycogenase glucose

Conversion is controlled by hormones

*lightly more soluble than starch %shorter chains and more highly branched&' e$ists as granules in thecytoplasm " close to *3

C CE2OSE

Cellulose consists of long chains of = glucose molecules.

Chains are straight and run parallel with cross linkages in between them. The hydrogen bonds

between the glucose chains are weak but the number of them are what gives the cellulose its

strength. These give cellulose its stability and make it a good structural material. This also makes ithard to digest

The long straight polysaccharide chains are bonded together by hydrogen bonds to form micelles

The micelles group together to from microfibrils %:1=D1 cellulose molecules& which group together toform fibres of cellulose %high tensile strength&

Cell walls have several fibre layers running in different directions " again this provides strength

2unctions= structural material in plants e.g. cell walls plant cells " up to 91 of plant cell wall iscellulose " it is the most abundant organic molecule on earth

Cellulose fibres form a mesh often filled with organic material %matri$&

To make impermeable the matri$ must be plugged %it is of course important that the matri$ is notplugged in plant cells so the walls remain permeable&

.g. lignin " $ylemBoth impermeable to water

*uberin " bark

(an uses fibres from plants e.g. cotton

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$etecting cellulose

Cellulose ? *chult7s solution 0 purple

O3

Cellulose ? Cellulase glucose %test with Benedicts&

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P#O&E"S

lant foods tend to be rich in COH' animal foods tend to be rich in protein and fat.

These are organic compounds with a large ((

!umber of proteins is limitless because there are over -1 different amino acids

roteins are often specific to each species %glucose is glucose in any species but proteins can bedifferent&.


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)ll amino acids are colourless' crystalline solids which are soluble in water where they form ions

*ee life science on file;Overhead

Properties of amino acids

1. B2%%E#") 'C&"O

roteins are buffers %resists tendency to alter pH in acid;alkaline solution& This is due to the structureof the amino acids subunits in that amino acids have acid and basic properties

The amino group is basic

The carbo$yl group is acidic

Therefore if an amino acid is in acid conditions the H-! acts as a hydrogen acceptor thereforereducing acidity

2ood containing all essential amino acids " first class protein e.g. meat' soya' and pulses5 soya this is ho ,egetarians can cope ith a meat free diet!

2ood containing some essential amino acids " second class proteins e.g. veg

ssential amino acids are no more important than those mammals can synthesis' they are simplyessential because they cannot be synthesised my mammals

6. 'M"O 'C"$S C' BE PO'#7O PO'#

)mino acids can be classified according to whether they attract;repel water

%O#M'&"O O% ' P#O&E"

*ee life sciences on file;Overhead



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+. - amino acids %monomers& align

-. )n OH %hydro$yl group& is lost from the COOH %carbo$yl group& of one of the amino acids and a His lost from the amino group %!H-& of the other amino acid. ) molecule of H-O is removed%condensation& and the - amino acids become @oined by a peptide bond to form a dipeptide%covalent carbon=nitrogen bond& 3esult 0 a peptide is formed

8. Continued condensation reactions lead to the addition of more amino acids resulting in theformation of a long chain of amino acids called a polypeptide chain %a protein molecule&. )polypeptide chain may be many +11s amino acids. The type of polypeptide chain formeddepends upon the se>uence of amino acids in the chain. olypeptides can be linked by peptidebonds to give proteins of +111s of aa

!B the synthesis of polypeptide chains takes place on the surface of ribosomes. %the amino acidsfloat free in the cytoplasm " taken into the body during absorption& The instructions needed for these>uence of the amino acids in the polypeptide come from the 5!) in the nucleus " the informationis transported out to the ribosome in the form of m3!). Once peptide bonds have formed the proteinfolds into a particular shape because of 4 other bond types " ionic' disulphide' hydrogen and covalent

bonds

&he primary structure of proteins

roteins have a wide variety of functions and properties. These depend on the type and order of aawithin the protein. There are over +1111 different proteins.

The primary structure of proteins is the type and se>uence of amino acids in the polypeptide chainand determines the properties and shape of the protein and therefore its biological function. ach

protein shows a characteristic number and se>uence of amino acids

.g. rimary structure of


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This is the secondary structure. The shape of the molecule is maintained by weak hydrogen bondsbetween the loops. H?0 electropositive' O 0 electronegative. ach bond is weak but the number ofthem means they have a considerable role in maintaining the shape and stability of the protein. Hbonds are easily broken by high temperatures " this has important conse>uences for livingorganisms

&herefore secondary structure is formed hen a primary structure is modified by coiling5pleating5 looping etc. Secondary structures are less fle8ible

.g. collagen " triple heli$ " 8 chains put together in a heli$.g. 5!) %double heli$& " - chains put together in heli$

&ertiary structure of proteins

5ue to bending and twisting of polypeptide heli$ into a compact' globular structure " held togetherwith weak chemical bonds

6hen a secondary structure e.g. heli$ is folded a more compact tertiary structure is formed with adefinite and precise 85 structure

.g. myoglobin %con@ugated protein&

only protein part shown

Tertiary protein structure is stabilised byH Bondsuaternary structure. Thelinking of polypeptide chains together forms the >uaternary structure. .g. human haemoglobin is a

protein consisting of - polypeptide chains and - polypeptide chains arranged around an iron

containing haem group


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Classification of proteins

Because of the comple$ity of protein molecules and their diversity of function' it is very difficult toclassify them in a single' well defined fashion. One way however is to classify them according to theirstructure " as either 2uence

unaffected though& altering the physical;chemical and biological properties of the protein. Can betemporary or permanent

e.g. protein ? e$cessive heat denatured protein %the H bonds holdingspiral together are destroyed because the atoms in theprotein vibrate more therefore

shape of molecule is irreversibly alteredi.e. spiral opens&

Other denaturing agentsE

*trong acids;alkalis %affects ionic bonds&)lcohol)cetone organic chemicalsIrea



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*alts of heavy metals e.g. silver ; mercury(echanical force

5enatured proteins are insoluble

%unction of proteins

+. forming structures for growth' repair' support and movement e.g. cell membranes' hair' nails'

feathers' hooves' tendons-. buffers8. transport " haemoglobin " o$ygen4. proteins can be broken down to release energy %deamination&9. regulators " en7ymes ; hormones:. food %nutrition&D. n7ymes involved in e$cretion e.g. ureaseG. *ensitivity and co=ordination e.g. hormones. 3eproductive hormones e.g. prolactin

(ydrolysing en:ymesroteins can be hydrolysed %by addition of water& breaking the peptide bonds which hold the aminoacid together

rotein ? n7yme )mino )cids

$etecting proteins

Biuret detects peptide links therefore all proteins are positive.

Biuret " OH ? Cu*O4 urple 0 positive



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"P"$S

These are not polymers like COH and proteins but large molecules made of fatty acids and analcohol %usually glycerol&

5o contain C H O and @oined by condensation reactions

(ost fat molecules have 8 fa @oined to + glycerol molecule and are called triglycerides

lements in lipids 0 C H O

They are insoluble in water but dissolve readily in organic solvents like acetone' alcohol

!umber of O atoms relatively small ratio HEO 0 -E+

(a@or function is energy storage. 2at is stored when animals hibernate' it also acts as an insulator.lants store lipids as oils e.g. in seeds

&ypes of lipids

Lipids

/lycerol based !on glycerol based

*imple Comple$ e.g. wa$es.g. fats;oils e.g. phospholipids steroids

.g. lecithin

Structure of lipids

Lipids are compounds of an alcohol and fatty acids formed by condensation reactions

(ost common alcohol is glycerol " general formula C8HGO8. /lycerol has 8 OH groups' each ofwhich can combine with a fatty acid forming a T3


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2atty acids have general formula 3 " COOH

3emainder of molecule is a hydrocarbon chain of varying length. This chain is hydrophobic and willnot dissolve in water

- groups

1. Saturated fatty acid

(a$imum number of H atoms " all bonds used. !o double bond in chain. Isually solid at roomtemp %animal fats&

.g. stearic acid C+DH89COOH

Hydrocarbon chain carbo$yl group

+. 2nsaturated fatty acid. (ore than + double bond in chain. Isually li>uid at room temp %plantfats&

.g. Oleic acid C+DH88COOH

Oleic acid %chief constituent of olive oil& does not contain ma$imum number of hydrogen atomsbecause it has double bond connecting - of the C atoms in the chain

!B oils contain a high proportion of unsaturated fatty acids e.g. linseed oil " D1 unsaturated2ats contain a high proportion of saturated fatty acids e.g. cocoa butter " D9 saturated

!ote " hydrocarbon chains can be long therefore form the tail 0 The tails are HA53OHOB


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Triglycerides are non polar therefore no uneven distribution of charge in the molecule therefore theydo not form hydrogen bonds with water therefore do not dissolve. They are less dense than waterand therefore float

The lipid which is formed depends on the fatty acids used

&ypes of lipids

a& 2ats " water insoluble. 2atty acids mainly saturated. *olid at room temp

b& Oils " water insoluble. 2atty acids mainly unsaturated. Li>uid at room temp

c& hospholipids " lipids which contain phosphorus and nitrogen in addition to C H and O

Phospholipids

These are lipids in which + of the fatty acid groups is replaced by phosphoric acid %H8O4&.

There are therefore - fa and + phosphate group attached to the glycerol.

These are special because phosphoric acid carries an electric charge and is HA53OH


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source of energy " stored fat;oilcan be used in respirationsource of water " released when fat o$idisedheat insulator " when under skin " fat conducts heat very slowly so helping to retain body heatprotects organs " kidneys are embedded in fatlong=term food store " oil in seed " stored because there is a high yield on breakdownused to make other molecules like hormonestransport fat soluble vitamins around the body e.g. Fit 5

b& phospholipidsstructural " unit membranes

ipids and the diet

The human body can synthesise most fatty acids from the products of carbohydrate and proteinmetabolism.

But there are certain unsaturated fatty acids which man cannot synthesis therefore known asessential fatty acids e.g. linleic fa; linoleic fa.

2ood which are rich in essential fatty acids are vegetable ; seed oils

&esting for lipids

Emulsion test" add 9cm8ethanol and shake. ositive result 0 milky suspension. This is becausebeing insoluble in water and less dense' oil would float if added to water. Oil here is dissolved inalcohol within which it is soluble. 6hen water is added the alcohol ? oil mi$es with water

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Chromatography

Chromatography is a common techni>ue used to separate mi$tures of compounds " for e$ample eggalbumin which is a protein made up of several different amino acids

The most commonly used chromatography employs either absorbent paper or a dried thin layer ofpowder on glass or plastic.

*pots of the mi$ture are put at one end in a concentrated form then the chromatogram is dipped intoa suitable solvent. The solvent moves through the paper by capillarity until it reaches the spots ofmi$ture.

The compounds in the mi$ture dissolve in the solvent and are carried with the solvent as it soaksfurther through the chromatogram.

5epending on its properties each compound will move at a characteristic speed. 6hen thechromatogram is removed the distance moved by the solvent is marked %solvent front&

*olvent 2ront

Origin

*olvent

Chromatography Tank

The component compounds can be determined using 3f %3elative front& values. very compoundhas a characteristic 3f value

3f value 0 5istance moved by compound

5istance moved by solvent front



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ach amino acid has a characteristic 3f valueE

)mino acid 3f value

Lysine 1.+4)rginine 1.-1)spartic acid 1.-4/lycine 1.-:

*erine 1.-D/lutamic acid 1.81Threonine 1.89)lanine 1.8Groline 1.48Tyrosine 1.49(ethionine 1.99Faline 1.:1henylalanine 1.:G


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ueous solution

By contrast' non polar molecules like lipids are repelled by water and group together in its presence.These are HA53OHOBuired to raise the temperature of + kg of water by+oC



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6ater has a high heat capacity which means a large increase in heat energy results in a relativelysmall rise in temperature. This is because much of the energy is used in breaking the hydrogenbonds which restrict the movement of the molecules

Temperature changes within water are minimised as a result of its high heat capacity

Biochemical processes therefore operate over a smaller temperature range' proceeding at moreconstant rates and are less likely to be inhibited by e$tremes of temperature

6ater also provides a very constant e$ternal environment for many cells and organisms

This property means water has a high heat of vaporisation % i.e. needs a lot of to convert from ali>uid to a gas& and a high heat of fusion %i.e. needs a lot of to convert from a solid to a li>uid&

$ensity and %ree:ing Properties

The density of water decreases below 4oC and so ice tends to float. uid form

*ince ice floats it forms at the surface first and the bottom last. This has important conse>uences fororganisms living in water in clod climates or with cold seasons

(igh surface tension and cohesion

Cohesion is the force whereby individual molecules stick together

)t the surface of a li>uid' a force called surface tension e$ists between the molecules as a result ofcohesive forces between the molecules

These cause the surface of the li>uid to occupy the least possible area %ideally a sphere&

6ater has a higher surface tension than any other li>uid


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Review Questions:

1. &h' is (a!er considered !o )e a polar *olecule+ &ha! !'pe o, )ond occurs )e!(een (a!er *olecules+2. -plain (h' ice ,loa!s on li/uid (a!er. &ha! alue does !his hae+3. is!inguish )e!(een an acid and a )ase. Gie an ea*ple o, each.4. Solu!ions (i!h a p o, less !han " are !er*ed (hereas !hose solu!ions (i!h a p grea!er !han " are !er*ed . As !hep scale decreases !here is a

,old increase in h'drogen ion concen!ra!ion ,or eer' p uni!.

$. e,ine a )u,,er. &ha! is !he ,unc!ion o, a )u,,er solu!ion+%. is!inguish )e!(een deh'dra!ion s'n!hesis and h'drol'sis.". &ha! is !he ,unc!ion5s6 o, pro!eins+8. &ha! are !he 2 ,unc!ional groups in a*ino acids+ o( do a*ino acids di,,er+9. &ha! !'pe o, )ond 7oins 2 a*ino acids !oge!her+ escri)e (hich par!s are 7oined.

10. Co*pare a dipep!ide a pol'pep!ide and a pro!ein *olecule.11. is!inguish )e!(een !he pri*ar' secondar' !er!iar' and /ua!ernar' s!ruc!ure o, a pro!ein.12. &ha! is !he di,,erence a*ong *onosaccharides disaccharides and pol'saccharides.13. is! 2 sugars each ,or *onosaccharides disaccharides and pol'saccharides.14. &ha! is !he role o, s!arch gl'cogen and cellulose in cells+1$. Are lipids solu)le in (a!er+ is!inguish )e!(een ,a!s and oils as !'pes o, lipid. o( are !he' ,or*ed+

1%. -plain !he di,,erence )e!(een a sa!ura!ed and an unsa!ura!ed ,a!!' acid.1". &ha! is a soap+ &h' does soap cause oil !o disperse in (a!er+ &ha! is *ean! )' e*ulsi,ica!ion+18. o( is !he phospholipid )ila'er arranged in !he cell *e*)rane+19. &ha! is uni/ue a)ou! !he s!ruc!ure o, s!eroids+ is! seeral ea*ples o, s!eroids.20. is! 2 !'pes o, nucleic acids. u*an genes are co*posed o, (hich !'pe+21. Gie !he co*ponen!s o, eer' nucleo!ide. &ha! dis!inguishes A ,ro* A+

Objectives Test

Completion and Short Answer Questions

1. e,ine an acid )ase and sal!.

a. acid

). )ase

c. sal!

2. :, !he h'drogen ion concen!ra!ion ;


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$. o( do liing !hings preen! rapid and dras!ic changes in p+

%. &ha! are !he 4 classes o, )iological 5organic6 *olecules+

". o, !he classes in ans(er 1" (hich@

a. are MST concerned (i!h energ'+

). one ,or*s *os! enB'*es+

c. one *aes up genes+

d. are long!er* energ' s!orage+

8. &ri!e !he (ordsaturatedand !he (ordunsaturated)enea!h !he appropria!e s!ruc!ure.

9. a)el !he diagra* (i!h !he ,ollo(ing !er*s@synthesis, hydrolysis, macromolecule, monomers.



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10. &hich $ *olecules in /ues!ion 9 (ould )e associa!ed (i!h par! 5a6 in !his diagra*+

11. &hich 4 *olecules (ould )e associa!ed (i!h par! 5c6 in !his diagra*+

12. &hen *an' glucose *olecules are 7oined !he *acro*olecule

resul!s. &hen *an' a*ino acids are 7oined !he *acro*olecule

resul!s. &hen gl'cerol and ,a!!' acids are 7oined resul!. &hen

nucleo!ides 7oin !he *acro*olecules resul!.

13. :n !his h'drol'!ic reac!ion (ri!e in !he na*e o, !he *olecule re/uired on !he le,! and !he a!o*s re/uired on !he righ!.

14. The diagra* )elo( is an a*ino acid. &ri!e !he (ord aminoand !he (or acid on !he appropria!e line.



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1$. The diagra* )elo( is a dipep!ide. Circle !he pep!ide )ond.

1%. eels o, pro!ein s!ruc!ure.

The linear se/uence o, a*ino acids in a pro!ein cons!i!u!es !he

s!ruc!ure. The !'pe o, )ond !ha! lins !he a*ino acids is a5n6

)ond. The ,unc!ional groups on a a*ino acid !ha! (ill 7oin !o ,or* !his )ond are !er*ed

. The group !ha!represen!s !he side chains on !he pro!ein

*olecule is !he . The group !ha! represen!s !he side chains on !he pro!ein *olecule is

!he group.

1". The diagra* )elo( represen!s !he s!ruc!ure o, a nucleo!ide. &ri!e !he (ords base, sugar, andphosphoic acid )eside !he

appropria!e s!ruc!ures.

18. a. !his is !he pri*ar's!ruc!ure o, a s!rand.

&hich le!!ers represen!s !he )ac)one+

&hich le!!er5s6 represen!5s6 !he ni!rogenous )ase+

). &hich *olecule (ould!he le!!er s s!and ,or+

&ha! speci,ic *olecule is S in A+

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&ha!speci,ic *olecule is S in A+

&hich nucleic acid (ouldre/uire a dou)le s!rand+

19. Acids hae a p !ha! is !han " (hereas )aseshae a p !ha! is

!han ".

20. A! p " ;elo( p " (hich o, !hese is grea!er+

21. An unsa!ura!ed ,a!!' acid con!ains less !han a sa!ura!ed,a!!' acid.

22. &hen gl'cerol co*)ines (i!h 3 ,a!!' acids a*olecule resul!s.

23. arelipids con!aining phosphorous !ha! are er' i*por!an! in cell *e*)ranes.

24. is !hespli!!ing o, a )ond (i!hin a larger *olecule )' !he addi!ion o, (a!er.

2$. is !heac! o, dispersing one li/uid in ano!her as ,a! in (a!er.

Matching@ Ma!ch !he ,ollo(ing ans(ers !o one or *ore o, !he (ords )elo(.a. a*ino acid 5or *ore !han one6 ). gl'cerolc. glucose 5or *ore !han one6 d. ,a!!' acide. nucleo!ide 5or *ore !han one6 ,. )o!h gl'cerol and ,a!!' acids

A. nucleic acid pro!ein pol'saccharide

dissacharide cellulose.

>. /uic energ' gene enB'*e

long!er* s!ored energ' plan! cell (all

C. pep!ide )ond unsa!ura!edri)ose

Gl'cogen h'drogen )ond

h'drocar)on 5onl' h'drogen and car)on6

Matching. Ma!ch !he ,ollo(ing ans(ers !o !he diagra*s )elo(.a. a*ino acid 5or *ore !han one6 ). gl'cerol

c. glucose 5or *ore !han one6 d. ,a!!' acide. nucleo!ide 5or *ore !han one6 ,. )o!h gl'cerol and ,a!!' acids

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Basic Biological Molecules

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