1

EXPLORING PROTEIN EXPLORING PROTEIN STRUCTURE & STRUCTURE &

FUNCTIONFUNCTION

ProteinsProteins

Make up about 15% of the cellMake up about 15% of the cell Have many functions in the Have many functions in the

cellcell EnzymesEnzymes StructuralStructural TransportTransport MotorMotor StorageStorage SignalingSignaling ReceptorsReceptors Gene regulationGene regulation Special functionsSpecial functions

3

Proteins….Proteins….

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

4

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

5

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

6

The globular proteinsThe globular proteins

The 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 – hemoglobin and myosinTransport and storage – hemoglobin and myosin

7

Proteins for cell motility Proteins for cell motility

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

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

8

Eukaryote cells have a cytoskeleton made up of straight hollow cylinders called microtubules (bottom left).

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.

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

9

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

The reaction is The reaction is extremely rapid as extremely rapid as the enzyme lowers the enzyme lowers the energy needed the energy needed to kick-start the to kick-start the reaction (activation reaction (activation energy)energy)

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 speed up reactions - Proteins speed up reactions - EnzymesEnzymes

+2 2

10

Proteins can regulate metabolism Proteins can regulate metabolism – hormones– 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 the Insulin binds to cell membranes and this triggers the cells to absorb glucose for use or for storage as cells to absorb glucose for use or for storage as glycogen in the liver.glycogen in the liver.

Proteins span membranes –protein Proteins span membranes –protein channelschannels

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.

11

Proteins Defend us against Proteins Defend us against pathogens –antibodiespathogens –antibodies

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)

12

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. This is known as gene which join amino acids together to form a polypeptide. This is known as gene expression.expression.

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

13

G T A C T A

Chromosome

The order of bases in DNA is a code for making proteins. The code is read in groups of three

DNAGene

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

AUGAGUAAAGGAGAAGAACUUUUCACUGGAUAM S E E LK G TF G

The protein folds to form its working shape

M

S EK G

E L TF G

M

S

E

K

GE L TF G

M

S

E

K

G

EL

TF

G

M

S

E

K

G

EL

TF

G

M

S

E

K

G

EL

T F

G

CELL

NUCLEUS

Gene Gene ExpressionExpression

M

S

E

K

G

EL

T F

G

T

G

M

S

E

K

G

EL

F

T

G

M

E

K

G

EL

FS

14

The building blocksThe building blocks

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

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

15

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

16

The 20 Amino AcidsThe 20 Amino Acids

The amino acids each have their own shape The amino acids each have their own shape and charge due to their specific R group.and charge due to their specific R group.

View the molecular shape of amino acids by View the molecular shape of amino acids by clicking on the URL link below:clicking on the URL link below:

http://sosnick.uchicago.edu/amino_acids.htmlhttp://sosnick.uchicago.edu/amino_acids.html

Would the shape of a protein be affected if the Would the shape of a protein be affected if the wrong amino acid were added to a growing wrong amino acid were added to a growing protein chain?protein chain?

Amino AcidsAmino AcidsNOTE: You need to know NOTE: You need to know

this tablethis table

Hydrophilic Hydrophobic

18

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

19

Why Investigate Protein Why Investigate Protein Structure?Structure?

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

20

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

21

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

22

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

23

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

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

24

Explore your proteinsExplore your proteinsScientists have worked out the shape of many Scientists have worked out the shape of many

proteins by conducting experiments. When they proteins by conducting experiments. When they have their results, they publish them and this have their results, they publish them and this information is then entered into supercomputing information is then entered into supercomputing systems for people to access.systems for people to access.

You can view the three dimensional structure of You can view the three dimensional structure of some of your proteins using the computer some of your proteins using the computer program Cn3D. If you do not have Cn3D installed program Cn3D. If you do not have Cn3D installed on your computer you can download this free on your computer you can download this free application from the URL link:application from the URL link:

Download Cn3D

CollagenHaemoglobin Amylase

ftp://ftp.ncbi.nlm.nih.gov/cn3d/Cn3D-4.3.1_setup.exe

25

Research another protein. Discuss what you Research another protein. Discuss what you can learn about its structure, function and the can learn about its structure, function and the

organism it comes from using the skills you organism it comes from using the skills you learned today and website resources.learned today and website resources.

You can explore a number of proteins using Cn3D. Go to the You can explore a number of proteins using Cn3D. Go to the following URL: following URL:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structurehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure

In the In the “for”“for” box, try some of the proteins listed below box, try some of the proteins listed below (one at a time) and then hit (one at a time) and then hit “go”.“go”. You will get a list of You will get a list of options. Click on theoptions. Click on the writing in blue writing in blue to select one. A new to select one. A new page will appear. Click on thepage will appear. Click on the View 3D structure View 3D structure button. button. Explore using your Cn3D skills.Explore using your Cn3D skills.

Misc Enzymes Genetics Toxins

Collagen Amylase Endonuclease Ricin

Tubulin Rubisco Taq DNA Polymerase Arsenic

Porphyrin Pepsin Ribosome Tetanus toxin

Prion Alcohol dehydrogenase Helicase Funnel web toxin