cmb lect 4 2011 colour 2 slides per page.pdf

8/14/2019 CMB Lect 4 2011 colour 2 slides per page.pdf

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Lecture 4

The structure andcom osition of roteins

BIOSCI 101: Cellular and Molecular Biology

Structure and composition of proteins Functions of proteins (50% or more of the dry

weight of most cells):-- provide many of the structural elements ofthe cell (cytoskeleton)- catalyse most of the reactions in the cell(enzymes)- act as contractile elements (muscle fibres)- act as transporters (membranes)


- act as regulators of cell metabolism(hormones, repressors etc)- act as food reserves (albumin)


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Structure and composition ofproteins (contd)

The diversity of protein function arisesbecause polypeptides fold in complex ways toyield a great diversity of precise 3D structures.This is, in turn, due to the 20 different aminoacids.


Amino acid structures (1)Nonpolar side chains; hydrophob ic

Side chain

Glycine(Gly or G)

Alan in e(Ala or A)

Valine(Val or V)

Leucine(Leu or L)

Isoleucine(I le or I )

BIOSCI 101: Cellular and Molecular BiologyCampbell 5.16a

Methionine(Met or M)

Phenylalanine(Phe or F)

Tryptophan(Trp or W)

Proline(Pro or P)


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Amino acid structures (2)Polar side chains; hydrophi lic

Serine(Ser or S)

Threonine(Thr or T)

Cysteine(Cys or C)

BIOSCI 101: Cellular and Molecular BiologyCampbell 5.16b

Tyrosine(Tyr or Y)

Asparagi ne(Asn or N)

Glutamine(Gln or Q)

Amino acid structures (3)

Electrically ch arged side chains; hydrophilic

Acidic (n egativel y charged)

BIOSCI 101: Cellular and Molecular BiologyCampbell 5.16c

Aspart ic acid(Asp or D)

Glutamic acid(Glu or E)

Lysine(Lys or K)

Arg in in e(Arg or R)

Histidine(His or H)


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Making apolypeptide

chain

Peptide bond

New p eptidebond forming

Sidechains

BIOSCI 101: Cellular and Molecular BiologyCampbell 5.17

Back-bone

Ami no end(N-terminus)

Peptidebond

Carboxyl end(C-terminus)

Proteins havea precise 3D

shape



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Primary ( 1 o ) structure

- the linear arrangement of amino acids

Protein structure

- the polypeptide has an amino terminusand a carboxy terminus- specified by the sequence ofnucleotides in DNA which is convertedinto information in protein via the mRNA



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Aminoacids

Amino end

PrimarystructurePrimary structure of transthyretin


Carboxyl end

Protein structure (contd)



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Protein structure (contd) Secondary (2 o ) structure

- secondary structure is the localised

- consider the backbone of a polypeptide:

+


- the negatively and positively charged ends ofthe polar covalent N-H and C=O bonds canattract each other forming H bonds.

+


- the two most common folding patterns formedby H bonding between atoms of the peptide bondare the -helix and the -pleated sheet

- the actual secondary structure adopted will be


n uence y e groups


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helix

Secondary structure

Hydrogen bond pleated sheet

strand, shown as a flatarrow pointing towardthe carboxyl end


Hydrogen bond

Protein structure (contd) Secondary structure (contd)

(a) the -helix- a rigid cylinder in which each peptide bond isregularly H-bonded to other peptide bondsnearby in the chain- found in the portions of transmembraneproteins that cross the lipid bilayer- occurs in the protein -keratin, found in skin,


hair, nails and feathers


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N-terminus

EXTRACELLULARSIDE

structure of a

transmembraneproteinhelix

C-terminus


CYTOPLASMICSIDE


Secondary structure (contd)

(b) -pleated sheets- an extended polypeptide chain folds back andforth upon itself- held by H-bonds that connect the peptide bondsin neighbouring chains- found in the core of most lobular roteins


- occurs in fibroin, the protein found in silk

(c) random coil - no regular structure - typicalwhen there are bulky R groups


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Protein structure (contd) Tertiary ( 3 o ) structure

-polypeptide chain

- the various segments of helix, pleated sheetand random coil are held in position bya) side chain interactions - hydrogen bondsand ionic bonds between hydrophilic R groupsand interactions between h dro hobic R


groups.b) intramolecular disulphide bonds - formbetween the two -SH groups of neighbouringcysteine residues in a folded polypeptide chain


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Tertiary structure (contd)

- proteins tend to fold in such a way as toarrange their hydrophobic groups towards theinterior and the hydrophilic groups towardsthe exterior of the molecule


Bonds involved in tertiary

structure

Hydrogenbond

Disulfidebridge

Ionic bond

Hydrophobicinteractions andvan der Waalsinteractions


Polypeptidebackbone


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Quaternary ( 4 o ) structure

- the number and relative positions of subunits ina multimeric protein- subunits are held together by interactionsbetween R groups- the subunits may be the same or different


Examples: Collagen (supercoiled triple helix)Human haemoglobin (2 -chains and 2

-chains)Microtubules (tubes of - and -

tubulin dimers)

Quaternary structure

Transthyretinprotein

(four identicalpolypeptides)



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Examples of quaternary structure

Collagen

HemeIron

subunit

subunit

Tubulin

25 nm


Hemoglobin

subunit

Review of protein structureSecondarystructure

Tertiarystructure

Quaternarystructure

Hydrogen bond

helix

pleated sheet strand


Hydrogenbond

Transthyretinpolypeptide

protein


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Chaperonins assist proteins to

fold in cells


Protein structure (contd) Denaturation and hydrolysis

- denaturation is unfolding of the 3-D shape of themolecule due to disruption of 2 o , 3 o and 4 ostructure (breakage of H bonds, hydrophilic andhydrophobic interactions and S=S bonds)- hydrolysis involves destruction of 1 o structure


.- proteins can occasionally be reversiblydenatured (ribonuclease).


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Denaturation and renaturation


Protein structure (contd)- denaturation may be achieved by :-

a) heat - breaks any weak bondb) extremes of pH changes ionisation

patterns of R groupsc) reducing agents - reduce S=S bonds to SHd) organic solvents - disturb hydrophobic and

hydrophilic interactionse) detergents disrupt hydrophobic


interactions

- some examples of denaturation: albumin (eggwhite), collagen (gelatin)


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Test question

The 20 different amino acids found in polypeptides

because of different:1. alpha ( ) carbon atoms.2. asymmetric carbon atoms.3. carboxyl groups attached to the alpha

( ) carbon.


.carbon.

5. amino groups attached to the alpha( ) carbon.

cmb lect 4 2011 colour 2 slides per page.pdf

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