Transcript Dr Una Fairbrother

Proteins
Dr Una Fairbrother
Dipeptides
Two amino acids are
combined as in the
diagram, to form a
dipeptide.
 Water is the other
product

Peptides

Peptides are normally
written with the
terminal amino group
(N-terminal) to the left
and the carboxyl
group (C-terminal) to
the right.
Polypeptides
 Continued
formation of peptide bonds extends
the molecule to many amino acids linked by
peptide bonds.
 Polymers of amino acids called
POLYPEPTIDES
 Individual units of the polypeptide are called
amino acid RESIDUES
 Can estimate the no. of amino acid residues in a
polypeptide or protein by its molecular weight
(Mr).
 Assume the mean Mr of an amino acid residue
is 110 dalton
Protein Structure or
Hierarchy
 Protein
structure is considered at different
levels.
 Primary
 Secondary
 Tertiary
 Quaternary
Primary structure
 Describes
the unique sequence of amino
acids which make up the polypeptide(s).
 i.e a bead necklace where each different
coloured bead represents an amino acid.
 The beads can be arranged in any order
or have any frequency
Secondary structure
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is content of regular or repeating
structures i.e. a helix and b
pleated sheets.
For the a helix consider the bead
necklace twisted into a coil.
The nature and structure of the a
helix was elucidated by Linus
Pauling and Robert Corey using Xray diffraction analysis and some
simple chemical rules.
polypeptide chain follows a coiled
path
X ray diffraction
a-keratin - wool
 b- keratin - silk

a
b
a helix
 Thermodyamically
favoured structure - the
preferred and thus most stable structure of a
polypeptide in the absence of interactions
 Stabilised by H-bonding between the carbonyl
oxygen and amino hydrogen of the peptide
linkages.
 Each linkage is H-bonded to 2 other linkages


one three units ahead and one three units behind.
The H-bonds are approximately parallel to the
long axis of the helix.
Alpha helix
10Å =
1nm

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
Each turn has 3.6 amino acid residues
Each turn extends 5.4Å along the long axis
Hydrogen bonds

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
are between every fourth amino acid residue
lie parallel to the long axis
occur between carbonyl oxygens and amino hydrogens within
different peptide linkages
Helices and other
structures
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If a protein contains long stretches of a helix it
will be semi-rigid and fibrous.
 E.g a keratin found in hair and horn
Silk or b-Keratin,excreted by the caterpillar of
the silk moth.
A polypeptide of glycine, alanine, and smaller
amounts of other amino acids called fibroin
b-Keratin molecules do not form a helix
they lie on top of each other to give ridged
sheets of linked amino acids, with glycine
appearing on only one side of the sheets.
The sheets then stack one on top of the other.
This planar structure is felt when you touch the
smooth surface of silk.
b pleated sheets

Polypeptide extended,
not coiled

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polypeptide regions may
come to lie alongside each
other.
These regions stabilised
by H-bonds between the
polypeptide regions.
Here, H-bonds are roughly
at right-angles to the long
axis of the polypeptide
chain in contrast to the a
helix.
b pleated sheet types
Globular proteins

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Contain only short regions of a helix
No systematic structures.
 single chains,
 two or more chains which interact in the
usual ways
 portions of the chains with: helical
structures, pleated structures, or
completely random structures.
Relatively spherical in shape
Common globular proteins include
 egg albumin, hemoglobin, myoglobin,
insulin, serum globulins in blood, and
many enzymes.
Globular proteins and
Proline
(a)

(a)Regions can be lined up
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(b)
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as parallel (N C to N C) or
antiparallel (N C to C N)
Proline forces the chain to kink and does
not allow the a helix to continue
it is a helix breaker residue.
often found in globular proteins at the end
of regular sequences where the
polypeptide chain bends back on itself.
(b) proline in green and glycine in yellow.
the side chain of proline forms a ring
attached to the amino N atom (in blue).
The N atom has no hydrogen so can't act
as an H bond donor.
This "breaks the chain" of H-bonds in helix
Tertiary Structure

Describes the superfolding
of the polypeptide.

The resultant structure
contains regular regions of
secondary structure

It is stabilised by a range of
different interactions or
bonds.
Bonds in tertiary structure

Hydrogen bonding
 is
between side chains of the amino acid residues
(compare with H-bonding in secondary structure which is
between peptide linkages)

Ionic bonds
 between
oppositely charged side chains (eg positively
charged lysine residues and negatively charged glutamic
acid residues).

Hydrophobic interactions
 between
the hydrocarbon side chains in phenylalanine,
leucine, isoleucine and valine.

Disulphide bridges
 between
cysteine residues, these are covalent and more
difficult to break.
Hexokinase
An example of a
protein showing helices, -structure
and connecting loops
 Hexokinase
phosphorylates
glucose

Bonds and denaturing
agents
Bonds o r l inkage s
Dena tur ing agen ts
Ion ic bond ( sal t br idge)
-COOH +H 3 N
Disulph ide br idge
-S-S -
Aci d (- COOH - t o ŠCOO H)
Alk ali ( + H 3 N t o H 2 N-)
Redu cing age nt s eg
mer cap toe thano l
(- S-S- to ŠSH H S-)
Organ ic s ol ven ts (non po lar) and
de tergen ts
Urea ( N 2 N-C=O
|
N H 2)
Hea t, ion si ng rad iati on
Hy drophob ic b onds
Hy drogen bond s
~C=O ..... ...... H-N~
Fo rma tion of unna tural Š S-Sbr idge s
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 structure

(a) the association of
individual polypeptide
subunits into a multisubunit or multimeric
protein.

Polypeptides with surface
regions of hydrophobic
amino acids will tend to
associate in order to
bring those patches
together and reduce
interactions with water.
(b) Hexokinase, domain 1 and 2
What stabilises
quaternary structure?
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Hydrophobic bonding
Ionic bonding
Hydrogen bonding
unlike tertiary structure
there is no covalent
bonding such as would
be obtained with -S-Sbridges
Summary