Biological Molecules Student Notes

8/16/2019 Biological Molecules Student Notes

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10.1 - Biological molecules

Biochemistry is _________________________________________________________________.

Biochemistry gives us an understanding of how biological systems work.

Organic Compounds of Biological Significance

There are 4 main organic compounds of biological significance

Elements

Carbohydrates

Lipids

Proteins

ucleic acids

These are macromolecules ! giant molecules made from many repeating units" it is therefore called a _______________________

The e#ception to this are ____________________ $not composed of a repeating unit%

The repeating units are called ____________________

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

Polymer Monomer

Carbohydrates Polysaccharide ________________

Proteins Protein ________________

ucleic acids ucleotides

Lipids are composed of units of fatty acid and glycerol ! 'T P'L()*+,

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Carbohydrates

*lements in carbohydrates are carbon& hydrogen and o#ygen

There are always _____________ as many - atoms as ' atoms per carbohydrate molecule

eneral formula / $C-01% n

2unction of carbohydrates is the storage and liberation of ____________. 3 few e.g. cellulose have astructural role

Monosaccharides monomers!

3ll monosaccharides are sweet and soluble

The cannot be hydrolysed $B+'* 5'6% to sugars of a smaller si7e

eneral formula ! $C-0'%n

)onosaccharides are classified according to the number of ________ ________ in the molecule

8 carbon molecule ! triose monosaccharide

9 carbon molecule ! pentose monosaccharide

: carbon molecule ! he#ose monosaccharide


Classification of Carbohydrates;


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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

"SOME#"SM

3n important structural characteristic of monosaccharides $e.g. glucose% is the occurrence ofisomerism

carbonatom

*.g. when glucose forms a ring structure the hydro#yl group may be present above or below theplane of the ring structure


- above / 3lpha

'- group is below the plane of the ring ? isomer ! α glucose

- below / Beta

-ydro#yl and hydrogen groups have swapped places

'- group is above the plane of the ring ? β glucose


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The e#istence of α and β isomers leads to greater chemical variety and is of importance in for

e#ample the formation of ____________ and ________________

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 carried

out on a solution or suspension of C'-.

of monosaccharide8. -ydrogen atom removed from '- group at position 4 of adacent monosaccharide4. '#ygen atom removed from one of '- groups9. This results in the formation of a covalent bond. The covalent bond is called a L(C',?4 glycosidic bond

'T* ! The bonding involves the removal of water. This is a dehydration or condensation reaction. The reactions are controlled by en7ymes.


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3ny 0 monosaccharides may be linked in this way to form a disaccharide of which maltose& sucroseand lactose are the most common

Condensation


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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

&ypes of polysaccharide

3ll the following are polymers of ________________

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

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

,tarch molecule is a long chain of >?4 linked α ? glucose units. The chain $long& unbranched% is then

coiled into a ______________ forming a cylinder in which most of the '- groups proect 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%. Compact

*#erts no _______________ effect because does not dissolve in water

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>. 5isaccharides align0. lycosidic bonds form between adacent disaccharides by condensation forming long chain polysaccharide molecules

,tructure of ,tarch;


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$etecting starch

,tarch A iodine=potassium iodide __________________ $if positive%

B )*+CO)E, C:(>1O9!n 'nimal starch!

lycogen consists of a long chain of α glucose molecules linked by >?4 or >?: glycosidic bonds

2unction ! short term storage C'- in animals. ,tored in ____________ and ____________ cells$centres of high metabolic activity%.

Can form up to >1E of liver mass.

lycogen needs to be converted to glucose when needed

lycogen A lycogenase glucose

Conversion is controlled by hormones

C CE***OSE

Cellulose consists of long chains of β ? glucose molecules.

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

between the β 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?F1 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

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,tructure of Cellulose#

,tructure of lycogen


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2unctions? structural material in plants e.g. cell walls plant cells ! up to 91E 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 ! #ylem} Both impermeable to water

,uberin ! bark

$etecting cellulose

Cellulose A ,chult7Ds solution / ________________ $if positive%



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*"P"$S

These are ___________ polymers like C'- and proteins but large molecules made of fatty acids andan alcohol $usually ________________%

5o contain C - ' and oined by condensation reactions

)ost fat molecules have 8 fa oined to > glycerol molecule and are called _________________

*lements in lipids / C - '

They are _______________ in water but dissolve readily in organic solvents like acetone& alcohol

umber of ' atoms relatively small ratio -;' / 0;>

)aor function is ______________ _______________. 2at is stored when animals hibernate& it alsoacts as an insulator. Plants store lipids as oils e.g. in seeds

&ypes of lipidsLipids

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 _______________ reactions

)ost common alcohol is glycerol ! general formula C8-G'8. lycerol has 8 '- groups& each ofwhich can combine with a __________ ___________ forming a T+


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%atty acids

2atty acids have general formula

+emainder of molecule $+% is a hydrocarbon chain of varying length. This chain is ______________and will not dissolve in water

0 groups

1. Saturated fatty acid

)a#imum number of - atoms ! all bonds used. o double bond in chain. Hsually solid at roomtemp $animal fats%

*.g. stearic acid C>F-89C''-

Carbo#yl group -ydrocarbon chain

. nsaturated fatty acid. )ore than > double bond in chain. Hsually li@uid at room temp $plantfats%

*.g. 'leic acid C>F-88C''-

'leic acid $chief constituent of olive oil% does not contain ma#imum number of hydrogen atomsbecause it has double bond connecting 0 of the C atoms in the chain

B oils contain a high proportion of unsaturated fatty acids e.g. linseed oil ! F1E unsaturated2ats contain a high proportion of saturated fatty acids e.g. cocoa butter ! F9 saturated

ote ! hydrocarbon chains can be long therefore form the tail / The tails are -(5+'P-'B


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%ormation of lipids

Triglycerides are _____ _____________therefore no uneven distribution of charge in the moleculetherefore they do not form hydrogen bonds with water therefore ______ __________ dissolve. Theyare less dense than water and therefore float

The lipid which is formed depends on the ____________ ______________

&ypes of lipids

a% 2ats ! water insoluble. 2atty acids mainly saturated. ,olid at room temp

b! 'ils ! water insoluble. 2atty acids mainly unsaturated. Li@uid at room temp

c% Phospholipids ! lipids which contain phosphorus and nitrogen in addition to C - and '

Phospholipids

These are lipids in which > of the fatty acid groups is replaced by ____________ ________ $-8P'4%.

There are therefore 0 fa and > phosphate group attached to the glycerol.

These are special because phosphoric acid carries an electric charge and is ________________$attracts water% and ______________ dissolve in water.

The phosphoric acid group is carried in the head of the phospholipid& making the head soluble inwater.

This is in contrast to the rest of the molecule which is _________________ $repels water%.


>. Three fatty acids become aligned beside one glycerol molecule$the carbo#yl end of the fatty acid points towards the hydro#yl ends $8 in glycerol% of the glycerol molecule%0. *ach of the hydro#yl groups of the glycerol molecule loses an h atom8. *ach of the carbo#yl groups of the 8 fatty acids loses a hydro#yl group

This results in the formation of three o#ygen bonds $ester bonds% and the resulting loss of three water molecules

$ester bonds are therefore formed by condensation%


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This means that phospholipids float on the surface of the water with the fa tails in the air $will notdissolve%.

6hen shaken in water the phospholipids cluster together with tails pointing inwards forming aglobule. This characteristic is important in the formation of membranes.

The addition of a phosphate group gives the lipid polarity $i.e. ADve and !Ive ends to molecule

5ue to polarity phospholipids have become part of cell membranes

%unctions of lipids

a% = b% fats=oilssource 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 heat

protects 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. Jit 5

c! 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 as ___________________ 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 9cm8 _______________ and shake. Positive result / _________________.This is because being insoluble in water and less dense& oil would float if added to water. 'il here isdissolved in alcohol within which it is soluble. 6hen water is added the alcohol A oil mi#es with water


*.g.

Positive end $water insolublehydrophobic%

egative end $water soluble ! hydrophilic%


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P#O&E",S

Plant foods tend to be rich in C'-& 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 01 different amino acids

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


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3lanine + group / C-8 Jaline + group ! C8-F

3ll amino acids are colourless& crystalline solids which are soluble in water where they form ions

Properties of amino acids

• Buffering 3ction

Proteins are buffers $____________________________________________________%

This is due to the structure of the amino acids subunits in that amino acids have acid and basicproperties

The amino group is ___________

The carbo#yl group is ______________

Therefore if an amino acid is in acid conditions the -0 acts as a hydrogen acceptor thereforereducing acidity


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

• 3mino 3cids can be Polar = on polar

3mino acids can be classified according to whether they attract=repel water

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

B the synthesis of polypeptide chains takes place on the surface of _______________. $the aminoacids float free in the cytoplasm ! taken into the body during absorption% The instructions needed forthe se@uence of the amino acids in the polypeptide come from the ________ in the nucleus ! theinformation is transported out to the ribosome in the form of m+3. 'nce peptide bonds have

formed the protein folds into a particular shape because of 4 other bond types ! ionic& disulphide&hydrogen and covalent bonds


>. 0 amino acids $monomers% align

0. 3n '- $hydro#yl group% is lost from the C''- $carbo#yl group% of one of the amino acids and a - is lost from theamino group $-0% of the other amino acid. 3 molecule of -0' is removed $condensation% and the 0 amino acidsbecome oined by a peptide bond to form a dipeptide $covalent carbon?nitrogen bond% +esult / a peptide is formed

8. Continued condensation reactions lead to the addition of more amino acids resulting in the formation of a longchain of amino acids called a polypeptide chain $a protein molecule%. 3 polypeptide chain may be many >11Dsamino acids. The type of polypeptide chain formed depends upon the se@uence of amino acids in the chain.Polypeptides can be linked by peptide bonds to give proteins of >111Ds of aa


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&he primary structure of proteins

Proteins 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.

&he primary structure of proteins is the type and se5uence of amino acids in the polypeptidechain and determines the properties and shape of the protein and therefore its biologicalfunction. *ach protein shows a characteristic number and se@uence of amino acids

The information on primary structure is contained in genes in the nucleic acid $protein synthesis%

&he secondary structure of proteins

&his is the shape 3hich the polypeptide chain forms as a result of ( bonding. &his is theamino acids in the polypeptide chains interacting

)ost common is an e#tended spiral spring $ α heli#%

This is the secondary structure. The shape of the molecule is maintained by weak hydrogen bondsbetween the loops. - / electropositive& ' / electronegative. *ach bond is weak but the number ofthem means they have a considerable role in maintaining the shape and stability of the protein. -bonds are easily broken by high temperatures ! this has important conse@uences for livingorganisms

&herefore secondary structure is formed 3hen a primary structure is modified by coiling2pleating2 looping etc. Secondary structures are less fle6ible

*.g. collagen ! triple heli# ! 8 chains put together in a heli#*.g. 53 $double heli#% ! 0 chains put together in heli#

&ertiary structure of proteins

$ue to bending and t3isting of polypeptide heli6 into a compact2 globular structure heldtogether 3ith 3ea chemical bonds



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

*.g. myoglobin $conugated protein%

• only protein part shown

Tertiary protein structure is stabilised by- Bonds


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lobular Proteins

. can act as buffers because of free C''- and 0- groups0. very large therefore will not go into solution only into colloidal suspension forming viscous sticky

substances8. all proteins can be denatured $changed from normal state ! loss of 85 shape& aa se@uence

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

e.g. protein A e#cessive heat denatured protein $the - bonds holdingspiral together are destroyed because the atoms in theprotein vibrate more therefore

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

'ther denaturing agents;

,trong acids=alkalis $affects ionic bonds% 3lcohol 3cetone organic chemicals

Hrea,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

0. buffers

8. transport ! haemoglobin ! o#ygen4. proteins can be broken down to release energy $deamination%9. regulators ! en7ymes = hormones:. food $nutrition%F. *n7ymes involved in e#cretion e.g. ureaseG. ,ensitivity and co?ordination e.g. hormonesK. +eproductive hormones e.g. prolactin

(ydrolysing en8ymes

Proteins can be ____________________ $by addition of water% breaking the peptide bonds whichhold the amino acid together



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Protein A *n7yme 3mino 3cids

$etecting proteins

_______________ detects peptide links therefore all proteins are positive.

Biuret ! '- A Cu,'4 Purple / positive



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Chromatography

Chromatography is a common techni@ue used to _________________________________________ 2or e#ample egg albumin 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 _______________ in the solvent and are carried with the solvent as itsoaks further through the chromatogram.

5epending on its properties each compound will move at a _______________ __________. 6henthe chromatogram is removed the distance moved by the solvent is marked $solvent front%

The component compounds can be determined using +f $_____________ ____________% values.*very compound has a characteristic +f value

#f 4alue 9 $istance mo4ed by compound

$istance mo4ed by sol4ent front


,olvent 2ront

Components ofCompound

'rigin

,olvent

Chromatography Tank


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*ach amino acid has a characteristic +f value;

3mino acid +f value

Lysine 1.>4 3rginine 1.01 3spartic acid 1.04lycine 1.0:,erine 1.0Flutamic acid 1.81Threonine 1.89

3lanine 1.8GProline 1.48Tyrosine 1.49)ethionine 1.99Jaline 1.:1Phenylalanine 1.:G


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:ater

6ithout water life could not e#ist on this planet.

.0.

The chemical and physical properties of water are unusual and due mostly to its small __________&its _________________ and to ________________ bonding between its molecules

Polarity is _________________________________________________


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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 ________________ 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 %ree8ing Properties

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

Biological Molecules Student Notes

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