Download EXPLORING PROTEIN STRUCTURE

EXPLORING PROTEIN
STRUCTURE
A teaching tool for introducing students to protein structure.
1
Proteins….
A protein hormone which helps to
regulate your blood sugar levels
If there is a job to be
done in the
molecular world of
our cells, usually that
job is done by a
protein.
CATALASE
An enzyme which removes
Hydrogen peroxide from your body
so it does not become toxic
Examples of proteins include hormones acting as
messengers; enzymes speeding up reactions; cell
receptors acting as ‘antennae’; antibodies fighting foreign
invaders; membrane channels allowing specific molecules
to enter or leave a cell; they make up the muscles for
moving; let you grow hair, ligaments and fingernails; and
let you see (the lens of your eye is pure crystalised
protein).
Source:
http://courses.washington.edu/conj/protein/insulin2.gif
http://www.biochem.ucl.ac.uk/bsm/pdbsum/1gwf/main.html
2
Proteins can be fibrous
or globular
Let’s explore the diversity of protein structure and function by
investigating some examples
3
Fibrous proteins have a structural role
•Collagen
is the most abundant protein in
vertebrates. Collagen fibers are a major
portion of tendons, bone and skin. Alpha
helices of collagen make up a triple helix
structure giving it tough and flexible
properties.
•Fibroin
fibers make the silk spun by spiders
and silk worms stronger weight for weight
than steel! The soft and flexible properties
come from the beta structure.
•Keratin
is a tough insoluble protein that
makes up the quills of echidna, your hair and
nails and the rattle of a rattle snake. The
structure comes from alpha helices that are
cross-linked by disulfide bonds.
Source:http://www.prideofindia.net/images/nails.jpg
http://opbs.okstate.edu/~petracek/2002%20protein%20structure%20function/CH06/Fig%2006-12.GIF
http://my.webmd.com/hw/health_guide_atoz/zm2662.asp?printing=true
4
The globular proteins
The globular proteins have a number of biologically important roles.
They include:
1. Cell motility – proteins link together to form filaments which make
movement possible.
2. Organic catalysts in biochemical reactions – enzymes
3. Regulatory proteins – hormones, transcription factors
4. Membrane proteins – MHC markers, protein channels, gap
junctions
5. Defense against pathogens – poisons/toxins, antibodies,
complement
5
Proteins for cell motility
Above: Myosin (red) and actin filaments
(green) in coordinated muscle contraction.
Right: Actin bound to the mysoin binding
site (groove in red part of myosin protein).
Add energy (ATP) and myosin moves,
moving actin with it.
Source: http://www.ebsa.org/npbsn41/maf_home.html
http://sun0.mpimf-
6
Proteins in the Cell Cytoskeleton
Eukaryote cells have a cytoskeleton made up of straight hollow
cylinders called microtubules (bottom left).
Tubulin
forms
helical
filaments
They help cells maintain their shape, they act like conveyer belts
moving organelles around in the cytoplasm, and they participate in
forming spindle fibres in cell division.
Microtubules are composed of filaments of the protein, tubulin (top
left) . These filaments are compressed like springs allowing
microtubules to ‘stretch and contract’.
13 of these filaments attach side to side, a little like the slats in a
barrel, to form a microtubule. This barrel shaped structure gives
strength to the microtubule.
Source:
heidelberg.mpg.de/shared/docs/staff/user/0001/24.php3?department=01&LANG=en
http://www.fz-juelich.de/ibi/ibi-1/Cellular_signaling/
http://cpmcnet.columbia.edu/dept/gsas/anatomy/Faculty/Gundersen/main.html
7
Proteins speed up reactions - Enzymes
2
2
Catalase speeds up the
breakdown of
hydrogen peroxide,
(H2O2) a toxic by
product of metabolic
reactions, to the
harmless substances,
water and oxygen.
The reaction is extremely
rapid as the enzyme
lowers the energy
needed to kick-start
the reaction (activation
energy)
+
No catalyst =
Input of 71kJ energy required
Energy
Activation
Energy
With catalase
= Input of 8 kJ energy required
Substrate
Product
Progress of reaction
8
Proteins can regulate metabolism – hormones
When your body detects an increase in the sugar
content of blood after a meal, the hormone
insulin is released from cells in the pancreas.
Insulin binds to cell membranes and this triggers the
cells to absorb glucose for use or for storage as
glycogen in the liver.
Proteins span membranes –protein channels
The CFTR membrane protein is an ion channel that
regulates the flow of chloride ions.
Not enough of this protein gets inserted into the
membranes of people suffering Cystic fibrosis. This causes
secretions to become thick as they are not hydrated. The
lungs and secretory ducts become blocked as a
consequence.
Source: http://www.biology.arizona.edu/biochemistry/tutorials/chemistry/page2.html
http://www.cbp.pitt.edu/bradbury/projects.htm
9
Proteins Defend us against pathogens –
antibodies
Left: Antibodies like IgG found in
humans, recognise and bind to
groups of molecules or epitopes
found on foreign invaders.
Right: The binding site of an antigen
protein (left) interacting with the
epitope of a foreign antigen (green)
Source: http://www.biology.arizona.edu/immunology/tutorials/antibody/FR.html
http://tutor.lscf.ucsb.edu/instdev/sears/immunology/info/sears-ab.htm
http://www.spilya.com/research/
http://www.umass.edu/microbio/chime/
10
Making Proteins
How are such a diverse range of proteins possible? The
code for making a protein is found in your genes (on
your DNA). This genetic code is copied onto a
messenger RNA molecule. The mRNA code is read in
multiples of 3 (a codon) by ribosomes which join amino
acids together to form a polypeptide. This is known as
gene expression.
Source: http://genetics.nbii.gov/Basic1.html
11
The protein folds
to form its
working shape
Gene Expression
Gene
DNA
G T
NUCLEUS
Chromosome
CELL
A C T A
The order of bases in
DNA is a code for
making proteins. The
code is read in groups of
three
AUGAGUAAAGGAGAAGAACUUUUCACUGGAUA
M
S
K
E
E
L
F
T
Cell machinery
copies the code
making an mRNA
molecule. This
moves into the
cytoplasm.
Ribosomes read the
code and accurately
join Amino acids
together to make a
protein
12
The building blocks
The amino acids for making new proteins come from
the proteins that you eat and digest. Every time you
eat a burger (vege or beef), you break the proteins
down into single amino acids ready for use in
building new proteins. And yes, proteins have the
job of digesting proteins, they are known as
proteases.
There are only 20 different amino acids but they can
be joined together in many different combinations
to form the diverse range of proteins that exist on
this planet
13
Amino Acids
An amino acid is a relatively small molecule with characteristic groups of
atoms that determine its chemical behaviour.
The structural formula of an amino acid is shown at the end of the animation
below. The R group is the only part that differs between the 20 amino acids.
Phenylalanine
Cysteine
Alanine
Glycine
Valine
Amino
H3H
C
H N
H
S
H H
CH
3
C
H H
R
C C O H
H O
Acid
14
Making a Polypeptide
R
H2N
C
H
O H
H N
C
O
Peptide Bond
R
H2N
C
O
N
C
C
O¯H
H
H N
R
Peptide Bond Peptide Bond
H
C
O
O
C
R
C
H
N
O H
H
C
C
O
O H
H N
C
C
O H
O
R
R
C
R
O H
C
O
Polypeptide
Growth
Polypeptide production = Condensation Reaction (dehyrdation synthesis)
15
Why Investigate Protein Structure?
Proteins are complex molecules whose
structure can be discussed in terms of:
primary structure
secondary structure
tertiary structure
quaternary structure
The structure of proteins is important as
the shape of a protein allows it to
perform its particular role or function
16
Protein Primary Structure
The primary structure is the sequence of amino acids that are linked
together. The linear structure is called a polypeptide
http://www.mywiseowl.com/articles/Image:Protein-primary-structure.png
17
Protein Secondary Structure
The secondary structure of proteins consists of:
alpha helices
beta sheets
Random coils – usually form the binding and active sites of proteins
Source: http://www.rothamsted.bbsrc.ac.uk/notebook/courses/guide/prot.htm#I
18
Protein Tertiary Structure
Involves the way the random coils, alpha
helices and beta sheets fold in respect to
each other.
This shape is held in place by bonds such as
•
weak Hydrogen bonds between amino
acids that lie close to each other,
•
strong ionic bonds between R groups
with positive and negative charges, and
•
disulfide bridges (strong covalent S-S
bonds)
Amino acids that were distant in the primary
structure may now become very close to
each other after the folding has taken
place
Source: io.uwinnipeg.ca/~simmons/ cm1503/proteins.htm
The subunit of a more complex protein has
now been formed. It may be globular or
fibrous. It now has its functional shape or
conformation.
19
Protein Quaternary Structure
This is packing of the protein subunits to
form the final protein complex. For
example, the human hemoglobin
molecule is a tetramer made up of
two alpha and two beta polypeptide
chains (right)
Source: www.ibri.org/Books/
Pun_Evolution/Chapter2/2.6.htm
This is also when the protein associates
with non-proteic groups. For example,
carbohydrates can be added to form a
glycoprotein
Source:
www.cem.msu.edu/~parrill/movies/neur
am.GIF
20