t f t n'*

Natural Sciences - Year 1(Salmon)

Biological Molecules - Proteins

Amino ac ids are the monomers o f a l l p ro te ins . A l l amino ac id mo lecu les conta in a toms o f carbon,hydrogen and oxygen together with ni trogen. Some also contain sulphur. Amino acids condensetogether to form long chains known as polypept ides. A protein molecule consists of one or more thanone po lypept ide cha in .

Proteins are therefore a group of organic compounds whose molecules consist of carbon, hydrogen,oxygen, ni trogen and sometimes sulphur atoms. They are condensat ion polymers of amino acids.

Each amino ac id conta ins a carboxy lg roup and an amino group. The par t o f the molecu le wh ich isdi f ferent in every amino acid is known as the R-group. The R-group can vary enormously. Some R-groups are polar, some are non-polar, some contain carboxyl groups and some contain hydroxyl groups.A few, such as cysteine, contain sulphur.

Humans can produce some amino acids in the body by conversion from others. However, some must beeaten as part of our diet. These are cal led essent ial amino acids.

' Behaviour of amino acids in water

When an amino acid dissolves in water, the carboxyl group dissociates, f reeing a hydrogen ion, sobecoming negat ively charged. Meanwhi le the amino group acquires a hydrogen ion and becomesposit ively charged. Therefore the ion formed has both a negat ive and a posit ive charge and is cal led azwitterion.

The abi l i ty to take up hydrogen ions from a solut ion enables the amino acids to take up hydrogen ionsreadi ly from an acid solut ion, so making the solut ion less acid. Amino acids release hydrogen ions readi lyin a lka l ine cond i t ions , so mak ing the so lu t ion less a lka l ine . For th is reason, the amino ac id can ac t as apH buffer. A pH buffer is a substance which can resist a change in the acidi ty or alkal ini ty of i tssurrou nd ings.

Condensat ion of amino acids

Two amino acids condense together, to form a dipept ide. The bond which is formed, l inking the aminoacids, is cal led a pept ide bond.

Further condensat ion react ions between amino acids lead to the formation of long chains cal ledpolypept ides. Amino acids may condense in any order and form chains of any length. Al l polypept idechains formed wi l l have simi lar 'backbones' containing pept ide bonds. Every polypept ide has an 'amino

end' with an amino group and a 'carboxyl end' with a carboxyl group present. However the order of R-groups along di f ferent chains var ies.

There are twenty di f ferent amino acids avai lable and polypept ide chains may be formed with any

number and any di f ferent order of arnino acids. Therefore i t is possible to form an inf ini te number of

d i f fe re nt po lypept ides with d i f ferent propert ies.

The order of R-groups along the polypept ide depends upon the sequence of amino acids forming

monomers in the chain. Every di f ferent polypept ide is formed from a di f ferent sequence of amino acids.

I t is this order of R-groups which determines the shape and the propert ies of the polypept ide.

Levels of protein structure

Primary structure of proteins

This refers to the exact sequence of amino acids in the polypept ide(s) within a protein molecule. Only

peptide bonds are involved in forming this sequence.

Secondary structure of proteins

Parts of the backbone of every polypept ide carry smal l posi t ive or negat ive charges. Hvdroaen bonds

form between these charges.

The secondary structure refers to the shape in al l polypept ides, the same shape can be taken up by

dif ferent polypept ides (or part of them). Therefore the shape is not specif ic to part icular polypept ides.

The shape is regu la r and is repeated a long the cha in .

The two most common types of secondary structure are the alpha-hel ix and the beta-pleated sheet.

ln the alpha-hel ix, the hydrogen bonds are formed between the CO of one amino acid with the NH of an

amino ac id four p laces fu r ther a long the cha in . Th is tw is ts the cha in in to a sp i ra l (he l i ca l ) fo rm where the' twists 'are held in place by the hydrogen bonds. Just a smal l port ion of a short chain may take up this

conf igurat ion or long chains may become twisted into an alpha-hel ix along the whole length. Kerat in,

the inso lub le p ro te in o f ha i r , na i l s and fea thers , has molecu les wh ich are la rge ly in th is shape.

In the beta-pleated sheet, adjacent port ions of di f ferent polypept ide chains, i f formed in opposite

direct ions to each other (ant i -paral lel) , may form a beta-pleated sheet. Hydrogen bonds form between

the -CO groups of one chain and the -NH groups of neighbouring chains. This gives a stronger, but less

elast ic structure than the alpha-hel ix. An example of a protein with a structure largely based upon the

beta-pleated sheet is the protein which makes up si lk ( f ibr ion).

The tertiary structure of proteins

This refers to the shape taken up by the polypept ide chain(s) of some proteins as a result of var ious

bonds between parts of the R-groups of the chains. As every di f ferent polypept ide has a di f ferent order

of R-groups, the bonds form in di f ferent places in every di f ferent polypept ide, leading to di f ferent

sha pes.

There are three types of bond which may be formed between R-groups, and these are mainly

responsible for folding a polypept ide into i ts tert iary structure. They are the hydrogen bond, the ionic

bond, and the d isu lph ide bond.

fhe hvdroaen bond is very common but is the weakest of the three bonds. l t is formed when the

electroposit ive H atoms of the -OH or -NH of one R-group attract the electronegat ive O of a CO group in

another R group.

lonic bonds form between amino and carboxyl parts present on some R-groups. These are stronger than

hydrogen bonds bu t in water they are much weaker than the d isu lph ide bond.

The disulphide bond is a covalent bond which is formed between the R-groups of amino acids such as

cysteine which have -SH groups. This is the strongest bond of the three.

The shape which the chain takes up is also affected by the presence of hydrophobic R-groups which tend

to take up a posit ion away from water protected by other parts of the molecule. Hvdrophobic

. interoctions occur between such groups.

A l lo f these bonds and in te rac t ions tend to cause the pro te in to fo ld in to an i r regu la r , compact , g lobu la r

shape w i th hydroph i l i c par ts on the ou ts ide in an aqueous env i ronment . One molecu le may become

surrounded by a 'shel l 'of water molecules and become separated from others. Such proteins are said to

be soluble forming a 'col loidal ' solut ion. They are referred to as globular proteins. An example of a

globular protein is insul in. Parts of a polypept ide which fold in this way, may already be in the form of an

alpha-hel ix or beta-pleated sheet.

The tert iary structure of every di f ferent polypept ide is di f ferent. The shape is said to be specif ic. The

func t ion o f the pro te in depends upon th is shape.

Not al lproteins fold into a tert iary structure, especial ly i f they have very long polypept ide chains r ich in

hydrophob ic amino ac ids . Pro te ins such as kera t in , co l lagen and f ib ro in a re inso lub le and the molecu lesare unfolded and have a non-specif ic f ibrous structure. They are referred to as f ibrous proteins.

Quaternary structure of proteins

Some proteins are made of more than one polypept ide chain. These chains interact with each other. Thequaternary structure refers to this structure in which more than two or more polypept ide chains areinteract ing. This structure is stabi l ized by the bonds and interact ions which stabi l ize the tert iary

structure. E.g. Haemoglobin

Conjugated proteins

Conjugated proteins have molecules in which polypept ide chain(s) are l inked to a non-protein part ofthe molecule. The non-protein part is cal led the prosthet icgroup. An example of a conjugated protein ishaemoglob in . Th is mo lecu le conta ins four po lypept ide cha ins and four haem groups .

The 'stability' of proteins

A molecule is regarded as chemical ly stable i f i t does not react with other chemicals readi ly, and is notchanged eas i l y by chang ing cond i t ions , such as tempera ture .

The tert iary shape of globular proteins and, therefore, their v i tal propert ies are easi ly al tered. The shapeis dependent upon weak hydrogen and ionic bonds. A r ise in temperature causes the molecules tovibrate more. This disrupts the hydrogen bonds and, as they break, the shape of the molecule al ters.

The hydrogen bonds and ionic bonds are also affected by a change in pH of the solut ion because thechanges in concentrat ion of the posit ively charged hydrogen ions affect the forces of at tract ion holdingthe pro te in mo lecu le in shape.

, So, g lobu la r p ro te ins in so lu t ion are uns tab le as the i r shape is eas i l y changed. l f th is happens, theycannot carry out their funct ions and they are said to be denatured. This is very signi f icant i f the globularproteins are enzymes.

The insoluble f ibrous proteins are much more stable.

Collagen

Col lagen is an important f ibrous protein. l t is a major component of the connect ive t issues of the bodiesof many animals. Connect ive t issues hold other t issues together and are found, for example in tendons,blood vessel wal ls and f ibres holding teeth in gums. Col lagen is also important in bone where i t bindsinorganic crystals together, prevent ing the bones from being br i t t le and easi ly broken.

The col lagen molecule is very stable and extremely strong. Each molecule consists of three polypept idechains wound round each otherto form a tr ip le hel ix ( l ike the strands of a rope twined around eachother). The amino acid sequence in each chain is very regular and is mainly based on repet i t ion of threeamino ac ids . The lengths o f the cha ins and hydrophob ic na ture o f most o f the R-groups make themolecule insoluble. Bonding between the three polypept ide chains gives the molecule strength. Themolecules are further assembled into f ibres. The f ibres are f lexible but cannot be stretched.

Haemoglobin

This is a reddish-purple respiratory pigment which gives blood i ts red colour. l t combines with oxygen toform oxyhaemoglobin which is a br ighter red in colour. l t is a globular protein and one haemoglobinmolecule consists of four polypept ide chains. Each chain is associated with a haem group which containsi ro n .

Adult human haemoglobin consists of four subunits, two alpha chains and two beta chains. With fourpolypept ide chains, haemoglobin has a quaternary structure. The haem group is an example of aprosthet ic group making haemoglobin a conjugated protein.

One oxygen molecule attaches to each haem group and therefore with four haem groups, onehaemoglobin molecule can transport four molecules of oxygen. The f i rst molecule of oxygen to attachdoes so with di f f icul ty and as i t at taches i t distorts the shape of the haemoglobin molecule. Thisdistort ion makes i t easier for other oxygens to attach. The subsequent three molecules of oxygen attachprogressively more quickly. This process is cal led co-operat ive binding.

The release of one of the oxygens from oxyhaemoglobin changes the shape of the haemoglobinmolecule to make release of the other three oxygens increasingly easy.

Biochemical test for the presence of proreins (the biuret test)

This test depends upon the fact that proteins react with alkal ine copper ( l l ) sulphate solut ion to form amauve/ l i lac co loured compound ca l led 'b iu re t ,

Procedure: the food sample is placed in a test tube. An equal volume of biuret reagent is added to the, sample .

l f protein is present, a mauve colour deverops.

The test may also be carr ied out using separate solut ions.

The food sample is placed in a test tube. An equal volum e of 5% potassium hydroxide solut ion is addedand mixed. Two drops o f L% copper su lphate so lu t ion are added and mixed.

l f protein is present, a mauve colour develops.

The role of proteins

Globular proteins

Globular proteins are found in col loidal solut ion or in cel l membranes. Their funct ions are metabol ic(chemical) ' A protein's specif ic shape enables i t to ' f i t 'a part icular, specif ic substance and carry out i tsfunc t ion on tha t subs tance on ly .

Globular proteins act as enzymes. The specif ic act ive si te on the enzyme molecule f i ts i ts substrate,speeding up a react ion involving that substrate.

They also act as carr iers in membranes. Some proteins in membranes combine with specif ic substancesand transport them across the membrane, ei ther by faci l i tated di f fusion or act ive transport .

Globular proteins also act as receptor sites in membranes. These proteins f i t a part icular substance suchas a hormone on the outside of the membrane. This combination tr iggers a part icular reaction inside thecell . For example, insulin f i ts into specif ic receptor sites in cel l membranes, tr iggering cellular reactions

They are also useful as ant ibodies. The specif ic shape of ant ibodies enables them to f i t specif ic ant igenswhen defending the body against disease.

Haemoglobin transports oxygen and myoglobin stores oxygen in muscles. Both are globular proteins

Fibrous proteins

The funct ion of f ibrous proteins, depend upon their insolubi l i ty, strength and f lexible, f ibrous nature

rather than their specif ic shape. Dif ferent f ibrous proteins have sl ight ly di f ferent propert ies. The

funct ions of f ibrous proteins are mainly related to support and movement. Col lagen gives f lexible

strength to tendons, blood vessel wal ls and skin. Elast in gives strength and elast ic i ty to l igaments.

Kerat in is the main substance of hair , feathers and scales. Act in and mvosin are needed for muscle

contraction.

Reference: AS Level Biology - Bradf ield, Dodds, Taylor

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Chapter '1 , Aspects of biochemistry

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