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Amino Acids and Proteins
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Amino AcidsProteins: Types and Function
Contractile- Actin & Myosin
Hormonal- Insulin
Protection- Immunoglobins (Antibodies)
Receptors and channels- KcsA
Transport- Haemoglobin
Structural- Collagen
Storage- Ferritin
Enzymes- EcoRV, Catalyst- breakdown, build-up, modifying and signalling
Classifi cation of Proteins
Fibrous
Fibrous proteins are multi-subunit complexes- constitute some of most abundant proteins in nature- keratin, silk
fibre, and collagen
Keratin- homodimer of two helical polypeptides wrapped around each other to form coiled coil
o Right handed but coiled coil dimer is formed from helices wrapping around each other in left-handed
direction
o ~300 amino acid core polypeptide of each keratin subunit consists of 7-amino acid repeating unit-
first and fourth amino acid is hydrophobic
This pattern provides hydrophobic strip that rotates anticlockwise around surface of helix
Two helices have to twist around each other in order to line up to two hydrophobic strips- helices
pack together with extensive hydrophobic interface
o Keratin helix contains ~3.5 amino acids per turn and is slightly more extended than α-helix (3.6
amino acids per turn)
Strength of keratin comes from covalent cross-linking between coiled dimers- resulting disulphide bridge formation
between cysteine residues
Different types of keratin found in nature- differ primarily in number of cysteine residues:
- Hair- flexible and has fewer disulphide bridges between coiled coil dimer than fingernails
- Fingernails- rigid and more durable- extensive disulphide cross-linking between fibres
- Rhinoceros horn- strongest keratin structures- made up keratin subunits containing 18% cysteine
Disulphide bridges in keratin can be broken with REDUCING AGENTS- ammonium thioglycolate
Silk fibroin- consists of multiple protein subunits with repeating secondary structure- β sheets
o Silkworm fibroin from insect Bombyx mori- heterotrimer of three proteins:
- 350kDa fibroin heavy chain- contain large numbers of β-sheets
- Two smaller proteins of ~30 kDa each- Fibroin Light chain- covalently linked to heavy chain by
disulphide bonds
P25 glycoprotein- associated with heavy chain polypeptide chains- contains large number of alanine
and glycine residues
Small sizes of side chains allow β sheets to layer very closely with each other- allow tight packing of protein
subunits
,Amino acid sequence of Fibroin Heavy Chain- reveals stretches of polyalanine residues- followed by hundreds of
repeating tripeptide – Gly-Gly-X (X is often Tyr, Gln or Ser)
Repeating polypeptide sequence facilitates formation of β-strands- fold into β sheets- organise into large arrays
consisting of many stacked β sheets
Collagen- found in soft tissues- hold bones together and major constituent of tendons and cartilage
o Collagen is protein complex consisting of long helical subunits intertwined- form right handed-helix
fibre
o Three helical subunits held together by interstrand cross-links involving hydroxylated lysine residues
o Collagen helix isn’t α-helix strucutre but instead each polypeptide is stretched out left handed helix
with three residues per turn
Collagen is major protein in connective tissue and in cornea of eye
Tendons in soft connective tissue consist of large numbers of cross-linked collagen strand- attach skeletal muscle to
bone
Insoluble- used structurally to give strength or make protective layer
Silk- Durable and Flexibility- web
Coatings- secretory granules, seeds
Intracellular cytoskeleton, extracellular matrix
Globular
Globular proteins are more compact with spherical shapes- may form multi-subunit protein complexes
Bacteriophage ф29 DNA packing motor- consists of 12 identical α subunits that together form concentric
α12 homododecamer complex
o Bacteriophage packing motor guides newly replicated DNA into viral capsid prior to cell lysis
o Asymmetric α-subunit contains two complementary quaternary protein interaction surfaces- permit
adjacent subunits to form interlocking junctions
o The shape of two interaction surfaces- homododecamer closes up on itself to form donut-shaped
macromolecule with hole in middle for DNA molecule to transit
Heterotrimeric G protein complex- involved in cell signalling and heterotetrametric haemoglobin protein complex
– required for O2 transport in animals
Immunoglobin proteins (Antibodies)- consists of two copies each of related protein subunits
o Contain two heavy- chains (H) and two light-chains (L)- form H2L2 heterotetramer
o Biological function of antibodies is to bind to foreign molecyles (non-self)- ANTIGENS- destroyed by
other immume cells that recognise antibody-antigen complex and engulf them
Antigens are bacteria, viruses or pollen molecules that antibodies recognise them as FOREIGN
o ~150-kDa H2L2 protein complex is Y-shaped macromolecule- contains Heavy- and Light- chain
subunits
Disulphide bonds stabilise tertiary and quaternary structures of immunoglobin protein complexes- mild treatment of
antibody molecules with protease- release two types of immuneglobin protein subfragments- retain their structure
and function
- Antigen Binding Fragment (FAB)- Contains entire light chain plus N-terminal half of heavy chain
- Crystallisation Fragnment (Fc)- contains C-terminal half of two heavy chains
Two light-chain polypeptides of immunoglobin complexes are ~25 kDa in mass and contain two distinct permanent
domains
, Variable domain- binds antigen molecules
Constant domain
Variable and constant domain of immunoglobin molecules all have basic protein fold- immunoglobin fold (Ig fold)
Immunoglobin fold is all β-structure consisting of two β sheets- form two layered sandwich
Intermolecular disulphide bonds that covalently link heavy and light chains- most immunoglobin folds contain
intramolecular disulphide bonds between two β-sheets
Soluble- offer dynamic functions
Exact 3D shape is critical in their function
Enzymes- biological catalysts
Transport proteins
Hormones
Defence
Toxins
In membranes
How can proteins have such diversity
Each polypeptide chain is called protein subunit
- These subunits form complexed- associated with each other through multiple noncovalent weak interaction.
Some protein complexes are held together by covalent linkages
Protein subunits can be encoded by different genes and contribute unique chemical/structural properties to protein
complex/they can consist of identical subunits encoded by same gene
A more complicated polymer
One repeating subunit- unreactive
20 different subunits- many possible subunits
Plus variable R groups- sidechains
Amino Acids- basic repeating unit
Amino acids can be covalently linked together as linear chain- type of amide bond- peptide bond
Polypeptide chains- Longer amino acid polymers
Oligopeptides/ Peptides- simply proteins and short polypeptides (usually <20
amino acids)
Some amino acids gave chemical groups that are hydrophobic whereas others
are more hydrophilic
7 amino acids have ionisable chemical groups- can participate in acid-base
reactions
Amino acid side chains can be large and structurally bulky, with long aliphatic groups/ aromatic rings or they can be
quite small and easily pack into tight spaces
When polypeptide chain is exposed in aqueous environment of cell-hydrophobic amino acids tend to cluster in
interior of protein- minimise interactions with water
Hydrophilic amino acids- readily form HYDROGEN BONDS with water- often found at aqueous interface on protein
surface
Hydrophobic effect- acts as driving force for protein to assume its 3D shape
Macromolecule protein structure is stabilised by formation of large numbers of weak non-covalent interactions
, between atoms within protein- energetically favourable folding of linear polypeptide into stable 3D structure-
determines protein function
The functional groups- amino acid side chains- differ in chemical structure, polarity
and charge
Central carbon atom (Cα) of every amino acid except glycine is asymmetrical chiral
centre having four different subunits arranged in tetrahedron
Amino acids are often called α amino acids- have no primary group and carboxyl group attached to Cα- except
proline- amino group is incorporated in to pyrrolidine ring attached to C α
Zwitterionic form
Isoelectric point (pI)- pH at which amino acid carries no net charge
Zwitterion- electroneutral molecule that contains both positive and negative charges
In physiological solution- neutral pH ~7.35
pKa of α carboxyl group of amino acids is ~2.3- α carboxyl group of free amino acid is deprotonated at pH 7
pKaof α amino group is ~9.7- at pH7 nitrogen is protonated and carries positive charge
Protonation- positive charge
Deprotonation- negative charge
Chirality- Stereoisomers/ Optical Isomers
Stereoisomers- molecules with same molecular formula and atomic connectivity but different 3D orientations of
their atoms
- L and D stereoisomers are mirror images of each other- structures can’t be superimposed
Enantiomers- Stereoisomers that mirror images of each other- nonsuperimposable
Almost all amino acids have L configuration
Few short bacterial peptides have been found that contain D-amino acids
Synthesising with mixtures of L and D amino acids would be energy burden to
cell- two sets of enzymes would be required for protein synthesis
RS system
Molecules have absolute S configuration if hierarchical arrangements of chemical groups around chiral Cα-
follow COUNTERCLOCKWISE direction
- Primarily on atomic numbers of atoms attached to chiral C α
- If more than one carbon is linked to chiral centre- numbering system reflects atoms bonded to each of
these atoms
e.g orienting H group away from you- L-alanine has S-configuration- nitrogen atom of NH 3+ group has
highest atomic number, Oxygen atoms on COO - group have higher atomic number than hydrogens on CH 3
group- COO- has higher property than CH3 group
R configuration- hierarchical arrangement of groups around Cα- follows CLOCKWISE orientation
e.g. L-cysteine- sulphur atom attached to side chain has higher atomic number than of oxygen in carboxyl
group- CH2SH group has higher property than COO - group
Cysteine is only L-amino acid with R configuration- all other L-amino acids have S configuration
Chemical and Physical properties of Amino Acids
20 amino acids into 4 general subfamilies that emphasise chemical interaction of amino acids with aqueous
environment of cell:
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