ProteinsProteins

Dr Una FairbrotherDr Una Fairbrother

DipeptidesDipeptides

Two amino acids are Two amino acids are combined as in the combined as in the diagram, to form a diagram, to form a dipeptide.dipeptide.

Water is the other Water is the other productproduct

PeptidesPeptides

Peptides are normally Peptides are normally written with the written with the terminal amino group terminal amino group (N-terminal) to the left (N-terminal) to the left and the carboxyl and the carboxyl group (C-terminal) to group (C-terminal) to the right.the right.

PolypeptidesPolypeptides

Continued formation of peptide bonds extends Continued formation of peptide bonds extends the molecule to many amino acids linked by the molecule to many amino acids linked by peptide bonds. peptide bonds.

Polymers of amino acids called Polymers of amino acids called POLYPEPTIDES POLYPEPTIDES   

IIndividual units of the polypeptide are called ndividual units of the polypeptide are called amino acid RESIDUESamino acid RESIDUES

Can estimate the no. of amino acid residues in a Can estimate the no. of amino acid residues in a polypeptide or protein by its molecular weight polypeptide or protein by its molecular weight ((MMr). r).

Assume the mean Assume the mean MMr of an amino acid residue r of an amino acid residue is 110 daltonis 110 dalton

Protein Structure or Protein Structure or HierarchyHierarchy

Protein structure is considered at different Protein structure is considered at different levels. levels.

PrimaryPrimary SecondarySecondary Tertiary Tertiary QuaternaryQuaternary

Primary structurePrimary structure

Describes the unique sequence of amino Describes the unique sequence of amino acids which make up the polypeptide(s). acids which make up the polypeptide(s).

i.e a bead necklace where each different i.e a bead necklace where each different coloured bead represents an amino acid. coloured bead represents an amino acid.

The beads can be arranged in any order The beads can be arranged in any order or have any frequencyor have any frequency

Secondary structureSecondary structure

is content of regular or repeating is content of regular or repeating structures i.e. structures i.e. helix and helix and pleated sheets.pleated sheets.

For the For the helix consider the bead helix consider the bead necklace twisted into a coil.necklace twisted into a coil.

The nature and structure of the The nature and structure of the helix was elucidated by Linus helix was elucidated by Linus Pauling and Robert Corey using X-Pauling and Robert Corey using X-ray diffraction analysis and some ray diffraction analysis and some simple chemical rules.simple chemical rules.

polypeptide chain follows a coiled polypeptide chain follows a coiled pathpath

X ray diffractionX ray diffraction

keratin - woolkeratin - wool b- keratin - silkb- keratin - silk

aa bb

helixhelix

Thermodyamically favoured structure - the Thermodyamically favoured structure - the preferred and thus most stable structure of a preferred and thus most stable structure of a polypeptide in the absence of interactionspolypeptide in the absence of interactions

Stabilised by H-bonding between the carbonyl Stabilised by H-bonding between the carbonyl oxygen and amino hydrogen of the peptide oxygen and amino hydrogen of the peptide linkages. linkages.

Each linkage is H-bonded to 2 other linkagesEach linkage is H-bonded to 2 other linkages one three units ahead and one three units behind. one three units ahead and one three units behind.

The H-bonds are approximately parallel to the The H-bonds are approximately parallel to the long axis of the helix.long axis of the helix.

Alpha helixAlpha helix

Each turn has 3.6 amino acid residuesEach turn has 3.6 amino acid residues Each turn extends 5.4Å along the long axisEach turn extends 5.4Å along the long axis Hydrogen bondsHydrogen bonds

are between every fourth amino acid residueare between every fourth amino acid residue lie parallel to the long axislie parallel to the long axis occur between carbonyl oxygens and amino hydrogens within occur between carbonyl oxygens and amino hydrogens within

different peptide linkagesdifferent peptide linkages

10Å 10Å = = 1nm1nm

Helices and other Helices and other structuresstructures

If a protein contains long stretches of If a protein contains long stretches of helix it helix it will be semi-rigid and fibrous. will be semi-rigid and fibrous. E.g E.g keratin found in hair and horn keratin found in hair and horn

Silk or Silk or -Keratin,excreted by the caterpillar of -Keratin,excreted by the caterpillar of the silk moth.the silk moth.

A polypeptide of glycine, alanine, and smaller A polypeptide of glycine, alanine, and smaller amounts of other amino acids called famounts of other amino acids called fibroinibroin

-Keratin molecules do not form a helix-Keratin molecules do not form a helix they lie on top of each other to give ridged they lie on top of each other to give ridged

sheets of linked amino acids, with glycine sheets of linked amino acids, with glycine appearing on only one side of the sheets. appearing on only one side of the sheets.

The sheets then stack one on top of the other. The sheets then stack one on top of the other. This planar structure is felt when you touch the This planar structure is felt when you touch the smooth surface of silk.smooth surface of silk.

pleated sheetspleated sheets

Polypeptide extended, Polypeptide extended, not coilednot coiled polypeptide regions may polypeptide regions may

come to lie alongside each come to lie alongside each other. other.

These regions stabilised These regions stabilised by H-bonds between the by H-bonds between the polypeptide regions. polypeptide regions.

Here, H-bonds are roughly Here, H-bonds are roughly at right-angles to the long at right-angles to the long axis of the polypeptide axis of the polypeptide chain in contrast to the chain in contrast to the helix.helix.

pleated sheet typespleated sheet types

Globular proteinsGlobular proteins

Contain only short regions of Contain only short regions of helix helix No systematic structures. No systematic structures.

single chains,single chains, two or more chains which interact in the two or more chains which interact in the

usual waysusual ways portions of the chains with: helical portions of the chains with: helical

structures, pleated structures, or structures, pleated structures, or completely random structures. completely random structures.

Relatively spherical in shapeRelatively spherical in shape Common globular proteins includeCommon globular proteins include

egg albumin, hemoglobin, myoglobin, egg albumin, hemoglobin, myoglobin, insulin, serum globulins in blood, and insulin, serum globulins in blood, and many enzymes.many enzymes.

Globular proteins and Globular proteins and ProlineProline

(a)Regions can be lined up (a)Regions can be lined up as parallel (N C to N C) or as parallel (N C to N C) or antiparallel (N C to C N)antiparallel (N C to C N)

Proline forces the chain to kink and does Proline forces the chain to kink and does not allow the not allow the helix to continue helix to continue

it is a it is a helix breakerhelix breaker residue. residue. often found in globular proteins at the end often found in globular proteins at the end

of regular sequences where the of regular sequences where the polypeptide chain bends back on itself.polypeptide chain bends back on itself.

(b) proline in green and glycine in yellow. (b) proline in green and glycine in yellow. the side chain of proline forms a ring the side chain of proline forms a ring

attached to the amino N atom (in blue). attached to the amino N atom (in blue). The N atom has no hydrogen so can't act The N atom has no hydrogen so can't act

as an H bond donor. as an H bond donor. This "breaks the chain" of H-bonds in helix This "breaks the chain" of H-bonds in helix

(a)(a)

(b)(b)

Tertiary StructureTertiary Structure

Describes the superfolding Describes the superfolding of the polypeptide. of the polypeptide.

The resultant structure The resultant structure contains regular regions of contains regular regions of secondary structure secondary structure

It is stabilised by a range of It is stabilised by a range of different interactions or different interactions or bonds. bonds.

Bonds in tertiary structureBonds in tertiary structure Hydrogen bondingHydrogen bonding

is between side chains of the amino acid residues is between side chains of the amino acid residues (compare with H-bonding in secondary structure which is (compare with H-bonding in secondary structure which is between peptide linkages)between peptide linkages)

Ionic bonds Ionic bonds between oppositely charged side chains (eg positively between oppositely charged side chains (eg positively

charged lysine residues and negatively charged glutamic charged lysine residues and negatively charged glutamic acid residues).acid residues).

Hydrophobic interactions Hydrophobic interactions between the hydrocarbon side chains in phenylalanine, between the hydrocarbon side chains in phenylalanine,

leucine, isoleucine and valine.leucine, isoleucine and valine. Disulphide bridges Disulphide bridges

between cysteine residues, these are covalent and more between cysteine residues, these are covalent and more difficult to break.difficult to break.

HexokinaseHexokinase

An example of a An example of a protein showing -protein showing -helices, -structure helices, -structure and connecting loopsand connecting loops

Hexokinase Hexokinase phosphorylates phosphorylates glucoseglucose

Bonds and denaturing Bonds and denaturing agentsagents

Bonds o r l inkage s Dena tur ing agen ts

Ion ic bond ( sal t br idge)

-COOH +H 3N

Aci d (- COOH - t o ŠCOO H)

Alk ali (+H3N t o H 2N-)

Disulph ide br idge

-S-S -

Redu cing age nts eg

mer cap toe thano l

(- S-S- to ŠSH H S-)

Hy drophob ic b onds Organ ic s ol ven ts (non po lar) and

de tergen ts

Hy drogen bond s

~C=O ..... ...... H-N~

Urea ( N2N-C=O

|

N H2)

Fo rma tion of unna tural Š S-S-

br idge s

Hea t, ion si ng rad iati on

Str uc tural d ist or ti on Salts of me tals su ch a s c opper ,

lead , mer cur y and cadm ium

Quaternary structureQuaternary structure

(a) the association of (a) the association of individual polypeptide individual polypeptide subunits into a multi-subunits into a multi-subunit or multimeric subunit or multimeric protein.protein.

Polypeptides with surface Polypeptides with surface regions of hydrophobic regions of hydrophobic amino acids will tend to amino acids will tend to associate in order to associate in order to bring those patches bring those patches together and reduce together and reduce interactions with water.interactions with water.

(b) Hexokinase, domain 1 and 2(b) Hexokinase, domain 1 and 2

What stabilises What stabilises quaternary structure?quaternary structure?

Hydrophobic bondingHydrophobic bonding Ionic bondingIonic bonding Hydrogen bondingHydrogen bonding unlike tertiary structure unlike tertiary structure

there is no covalent there is no covalent bonding such as would bonding such as would be obtained with -S-S- be obtained with -S-S- bridgesbridges

SummarySummary