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EXPLORING EXPLORING PROTEIN PROTEIN

STRUCTURESTRUCTUREA teaching tool for introducing students to protein

structure.

The final slide contains links to the files and programs students need to complete activities using Cn3D to view

proteins.

Save this Power Point to your desktop prior to beginning the show.

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PROTEINSPROTEINS

Examples of proteins include hormones acting as Examples of proteins include hormones acting as messengers; enzymes speeding up reactions; cell messengers; enzymes speeding up reactions; cell

receptors acting as ‘antennae’; antibodies fighting foreign receptors acting as ‘antennae’; antibodies fighting foreign invaders; membrane channels allowing specific invaders; membrane channels allowing specific

molecules to enter or leave a cell; they make up the molecules to enter or leave a cell; they make up the muscles for moving; let you grow hair, ligaments and muscles for moving; let you grow hair, ligaments and

fingernails; and let you see (the lens of your eye is pure fingernails; and let you see (the lens of your eye is pure crystalised protein).crystalised protein).

Source: http://courses.washington.edu/conj/protein/insulin2.gif

http://www.biochem.ucl.ac.uk/bsm/pdbsum/1gwf/main.html

If there is a job to be If there is a job to be done in the molecular done in the molecular

world of our cells, world of our cells, usually that job is done usually that job is done

by a protein.by a protein. CATALASE

An enzyme which removes Hydrogen peroxide from your body so it does not become toxic

A protein hormone which helps to regulate your blood sugar levels

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Proteins can be Proteins can be fibrous or globularfibrous or globular

Let’s explore the diversity of protein structure and function by investigating some examples

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Fibrous proteins have a Fibrous proteins have a structural rolestructural role

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

•Collagen is the most abundant protein in Collagen is the most abundant protein in vertebrates. Collagen fibers are a major vertebrates. Collagen fibers are a major portion of tendons, bone and skin. Alpha portion of tendons, bone and skin. Alpha helices of collagen make up a triple helix helices of collagen make up a triple helix structure giving it tough and flexible structure giving it tough and flexible properties.properties.

•Fibroin fibers make the silk spun by spiders Fibroin fibers make the silk spun by spiders and silk worms stronger weight for weight and silk worms stronger weight for weight than steel! The soft and flexible properties than steel! The soft and flexible properties come from the beta structure.come from the beta structure.

•Keratin is a tough insoluble protein that Keratin is a tough insoluble protein that makes up the quills of echidna, your hair and makes up the quills of echidna, your hair and nails and the rattle of a rattle snake. The nails and the rattle of a rattle snake. The structure comes from alpha helices that are structure comes from alpha helices that are cross-linked by disulfide bonds.cross-linked by disulfide bonds.

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The globular proteinsThe globular proteinsThe The globularglobular proteins have a number of biologically important roles. They proteins have a number of biologically important roles. They

include:include:

Cell motility – proteins link together to form filaments which make movement Cell motility – proteins link together to form filaments which make movement possible.possible.

Organic catalysts in biochemical reactions – Organic catalysts in biochemical reactions – enzymesenzymes

Regulatory proteins – Regulatory proteins – hormoneshormones, transcription factors, transcription factors

Membrane proteins – MHC markers, Membrane proteins – MHC markers, protein channelsprotein channels, gap junctions, gap junctions

Defense against pathogens – poisons/toxins, Defense against pathogens – poisons/toxins, antibodiesantibodies, complement, complement

Transport and storage – haemoglobin and myosinTransport and storage – haemoglobin and myosin

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Proteins for cell motility – proteins can link Proteins for cell motility – proteins can link together to form filaments that make together to form filaments that make

movement possible.movement possible.

Source: http://www.ebsa.org/npbsn41/maf_home.htmlhttp://sun0.mpimf-

Above: Myosin (red) and actin filaments (green) in coordinated muscle contraction.

Right: Actin bound to the myosin binding site (groove in red part of myosin protein).

Add energy and myosin moves, moving actin with it.

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The cell cytoskeleton contains microtubules that can contract to make cell movement possible. Microtubules are composed of filaments of the protein, tubulin (far left). They form an alpha helix that behaves a little like a ‘spring’ allowing filaments to ‘stretch and contract’. This is how cells control movement of their organelles, of chromosomes in cell division and of flagella and cilia.

Tubulin forms helical

filaments

Source: heidelberg.mpg.de/shared/docs/staff/user/0001/24.php3?department=01&LANG=enhttp://www.fz-juelich.de/ibi/ibi-1/Cellular_signaling/http://cpmcnet.columbia.edu/dept/gsas/anatomy/Faculty/Gundersen/main.html

Proteins in the Cell Cytoskeleton

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CatalaseCatalase catalyses the breakdown of hydrogen peroxide, (Hcatalyses the breakdown of hydrogen peroxide, (H22OO22) a toxic by product of metabolic ) a toxic by product of metabolic reactions, to the harmless substances, water and oxygen. reactions, to the harmless substances, water and oxygen.

The reaction is extremely rapid as the enzyme lowers the activation energy for forming the The reaction is extremely rapid as the enzyme lowers the activation energy for forming the products water and oxygen from the substrate molecule hydrogen peroxide.products water and oxygen from the substrate molecule hydrogen peroxide.

Energy

Progress of reaction

Substrate Product

No catalyst = No catalyst = Input of 71kJ energy requiredInput of 71kJ energy required

Activation Energy

With catalase With catalase = Input of 8 kJ energy required= Input of 8 kJ energy required

Proteins with catalytic behaviours - EnzymesProteins with catalytic behaviours - Enzymes

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Proteins can regulate metabolism – hormonesProteins can regulate metabolism – hormones

When your body detects an increase in the sugar When your body detects an increase in the sugar content of blood after a meal, the hormone content of blood after a meal, the hormone insulin is released from cells in the pancreas. insulin is released from cells in the pancreas.

Insulin binds to cell membranes and this triggers Insulin binds to cell membranes and this triggers them to absorb glucose for use or for storage as them to absorb glucose for use or for storage as glycogen in the liver.glycogen in the liver.

Proteins in cell membranes –protein channelsProteins in cell membranes –protein channels

Source: http://www.biology.arizona.edu/biochemistry/tutorials/chemistry/page2.htmlhttp://www.cbp.pitt.edu/bradbury/projects.htm

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.

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Proteins Defend us against pathogens –Proteins Defend us against pathogens –antibodiesantibodies

Source: http://www.biology.arizona.edu/immunology/tutorials/antibody/FR.htmlhttp://tutor.lscf.ucsb.edu/instdev/sears/immunology/info/sears-ab.htmhttp://www.spilya.com/research/http://www.umass.edu/microbio/chime/

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)

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Making ProteinsMaking Proteins

How are such a diverse range of proteins possible? The code for making a protein is How are such a diverse range of proteins possible? The code for making a protein is found in your found in your genesgenes (on your DNA). This (on your DNA). This genetic codegenetic code is copied onto a messenger is copied onto a messenger RNA molecule. The mRNA code is read in multiples of 3 (a RNA molecule. The mRNA code is read in multiples of 3 (a codoncodon) by ) by ribosomes ribosomes which join amino acids together to form a polypeptide.which join amino acids together to form a polypeptide.

Source: http://genetics.nbii.gov/Basic1.html

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The building blocksThe building blocks

The The amino acidsamino acids for making new proteins come from for making new proteins come from the proteins that you eat and digest. Every time you the proteins that you eat and digest. Every time you eat a burger (vegie or beef), you break the proteins eat a burger (vegie or beef), you break the proteins down into single amino acids ready for use in building down into single amino acids ready for use in building new proteins. And yes, proteins have the job of new proteins. And yes, proteins have the job of digesting proteins, they are known as proteases.digesting proteins, they are known as proteases.

There are only There are only 20 different amino acids20 different amino acids (see slide 12) (see slide 12) but they can be joined together in many different but they can be joined together in many different combinations to form the diverse range of proteins combinations to form the diverse range of proteins that exist on this planetthat exist on this planet

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Amino AcidsAmino AcidsAn amino acid is a relatively small molecule with characteristic groups of An amino acid is a relatively small molecule with characteristic groups of atoms that determine its chemical behaviour.atoms that determine its chemical behaviour.

The structural formula of an amino acid is shown at the end of the animation The structural formula of an amino acid is shown at the end of the animation

below. below. The The R groupR group is the only part that differs between the 20 amino acids. is the only part that differs between the 20 amino acids.

O

RO

H

HH

H N C CH3C

CH3

C HC

H

H H

GlycineAlanineValineCysteinePhenylalanine

H

H

C

S

H HCH H

Amino Acid

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Making a PolypeptideMaking a Polypeptide

H2NC

O

C

R

C

O

CO¯H

R

N

H

HO H

O HH N

C

O

C

RH

O HH

C

O

C

R

N

H

NC

O

C

R

H2NC

O

C

R H

O HO HN

C

O

C

R

H2NC

O

C

R H

NC

O

C

RH

Peptide Bond Peptide BondPeptide Bond

Polypeptide production = Condensation Reaction

PolypeptideGrowth

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Why Investigate Protein Structure?Why Investigate Protein Structure?

Proteins are complex molecules whose Proteins are complex molecules whose structure can be discussed in terms of:structure can be discussed in terms of:

primary structureprimary structuresecondary structuresecondary structuretertiary structuretertiary structurequaternary structurequaternary structure

The structure of proteins is important as The structure of proteins is important as the the shapeshape of a protein allows it to of a protein allows it to perform its particular role or perform its particular role or functionfunction

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Protein Primary StructureProtein Primary StructureThe The primary structureprimary structure is the sequence of amino acids that are linked is the sequence of amino acids that are linked

together. The linear structure is called a polypeptidetogether. The linear structure is called a polypeptide

http://www.mywiseowl.com/articles/Image:Protein-primary-structure.png

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Protein Secondary StructureProtein Secondary StructureThe secondary structure of proteins consists of:The secondary structure of proteins consists of:

alpha helicesalpha helicesbeta sheetsbeta sheetsRandom coils – usually form the binding and active sites of proteinsRandom coils – usually form the binding and active sites of proteins

Source: http://www.rothamsted.bbsrc.ac.uk/notebook/courses/guide/prot.htm#I

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Protein Tertiary StructureProtein Tertiary Structure

Involves the way the random coils, alpha Involves the way the random coils, alpha helices and beta sheets fold in respect to helices and beta sheets fold in respect to each other. each other.

This shape is held in place by bonds such asThis shape is held in place by bonds such as• weak weak Hydrogen bondsHydrogen bonds between amino between amino

acids that lie close to each other, acids that lie close to each other, • strong strong ionic bondsionic bonds between R groups between R groups

with positive and negative charges, andwith positive and negative charges, and• disulfide bridgesdisulfide bridges (strong covalent S-S (strong covalent S-S

bonds)bonds)

Amino acids that were distant in the primary Amino acids that were distant in the primary structure may now become very close to structure may now become very close to each other after the folding has taken each other after the folding has taken placeplace

The subunit of a more complex protein has The subunit of a more complex protein has now been formed. It may be globular or now been formed. It may be globular or fibrous. It now has its functional shape or fibrous. It now has its functional shape or conformationconformation..

Source: io.uwinnipeg.ca/~simmons/ cm1503/proteins.htm

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Protein Quaternary StructureProtein Quaternary Structure

This is packing of the protein subunits to This is packing of the protein subunits to form the final protein complex. For form the final protein complex. For example, the human hemoglobin example, the human hemoglobin molecule is a tetramer made up of molecule is a tetramer made up of two alpha and two beta polypeptide two alpha and two beta polypeptide chains (right)chains (right)

Source: www.cem.msu.edu/~parrill/movies/neuram.GIF

This is also when the protein associates with non-proteic groups. For example, carbohydrates can be added to form a glycoprotein

Source: www.ibri.org/Books/ Pun_Evolution/Chapter2/2.6.htm

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Exploring the 3D Structure of Exploring the 3D Structure of HaemoglobinHaemoglobin

We will now explore the structure of Haemoglobin using Cn3D. Click on We will now explore the structure of Haemoglobin using Cn3D. Click on the button to get the instructions on how to do thisthe button to get the instructions on how to do this

Instructions for viewing Cn3D

To complete this activity, you must have Cn3D installed on your computer. If you do not have Cn3D installed on your computer you can download this

free application from the URL http://ncbi.nih.gov/Structure/CN3D/cn3d.shtml

Click here to view Haemoglobin in Cn3D