1 Examples of protein functionality: Enzymatic catalysis vast - - PDF document

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A primer on the structure and function of proteins

Protein is derived from the Greek “proteios”, for “of first rank” (Jöns J. Berzelius, 1838)

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Examples of protein functionality:

• Enzymatic catalysis
• Transport and Storage
• Motion
• Signaling and communication
• Immunity
• Control of gene expression
• vast majority of reactions catalyzed by enzymes
• enzymes have an enormous influence on reaction

rates

• biochemical reaction rate can be increase by > a

million fold

• enzymes control biochemical reactions ranging

from simple to complex (e.g., replication of a genome)

Examples of protein functionality:

• Enzymatic catalysis
• Transport and Storage
• Motion
• Signaling and communication
• Immunity
• Control of gene expression
• transport of small, but critically important molecules

is carried out by specific proteins.

• examples: haemoglobins to transport oxygen;

myoglobins to transport and store oxygen in muscle.

• over time haemoglobin and myoglobin have evolved

very precise, but divergent functions with respect to their role in oxygen transport within an organism.

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Examples of protein functionality:

• Enzymatic catalysis
• Transport and Storage
• Motion
• Signaling and communication
• Immunity
• Control of gene expression

Examples include: muscle contraction, movement of chromosomes during mitosis and meiosis, the propulsion

• f sperm by flagella.

Examples of protein functionality:

• Enzymatic catalysis
• Transport and Storage
• Motion
• Signaling and communication
• Immunity
• Control of gene expression
• proteins can receive molecular signals
• proteins can transmit molecular signals
• signals are transmitted within proteins by changes

in 3D conformation.

• proteins can “perceive” a change in an

environment and “communicate” this change via a molecular signal.

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Examples of protein functionality:

• Enzymatic catalysis
• Transport and Storage
• Motion
• Signaling and communication
• Immunity
• Control of gene expression
• proteins critical to distinguishing “self” from “non-self”
• recognize and bind foreign proteins
• evolutionary conflict between pathogen and its host
• leads to an evolutionary arms-race

Examples of protein functionality:

• Enzymatic catalysis
• Transport and Storage
• Motion
• Signaling and communication
• Immunity
• Control of gene expression

Precise control of the level of gene expression is essential to the proper growth and function of cells. The incredibly complex process of development from a fertilized egg to a multi-cellular organism such as a human being is under genetic control through the production (expression) and function of proteins such as transcription factors.

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(or how do we get all this functionality from just 20 monomers?)

The number of possible polypeptides is “nearly infinite”:

• polypeptide of 2 aa’s: 202 = 400
• polypeptide of 3 aa’s: 203 = 8000
• most polypeptides: 50 – 2000 aa’s
• polypeptide of 150 aa’s: 20150
• number of possible 3D conformations

is >> number of polypeptides!

A guess at the number of natural polypeptides on earth:

• 10 million species
• average genome of 5,000 genes
• at least 5 x 1010 proteins
• estimated number of 3D folds: 650 –

10,000

• majority of proteins = 1,000 folds

Amino acids as building blocks of proteins

The distribution of natural folds is highly skewed. The usage of foldes could be subject to natural selection.

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Polypeptides are built by using the peptide bond 20 amino acids are defined by 20 unique R-group side-chains

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D E M I CS-S A S CS-H G N Q V L P T R K H Y F W Polar Aromatic Aliphatic Negative Charged Hydrophobic Positive Small Tiny

Overlapping physiochemical properties of amino acids Scales of physiochemical properties are artificial

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The structural hierarchy of a protein can be described at four levels Prosthetic group: any small, non polypeptide, molecule that is tightly bound to a protein

• essential role in protein function
• influence 3D fold
• ex: Heme molecular of haemoglobin.

Globin fold > 800 million years old

• association can be covalent or non-

covalent

• not all proteins have prosthetic

groups

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Post-translational modifications: covalent modifications that affect the structure and function of proteins

• Disulphide bridges
• Polypeptide cleavage
• Modification of amino acid side chains
• Addition of carbohydrates
• Addition of lipids

Enzymes convert preproinsulin into insulin:

• 1. Preproimsulin is cleaved by an enzyme almost immediately after the chain of 108 amino acids is

synthesized.

• 2. Proinsulin is folded in such a way that the state of lowest free energy at this pont is the one in

which the disulfide bridges can be formed.

• 3. Lastly, enzymes remove the C-chain to produce the insulin. By utilizing intermediate stages, the

cell is able to for a stable conformation (insulin) that is not the one with the lowest free energy.

The native conformation of insulin is NOT the one with the lowest free energy

Note: Free energy is a measure of the potential energy of a biological reaction. Free energy determines the direction of the reaction, with the reaction going in the direction of lower free energy.

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30,000 genes of mice and men:

• 1. Effect of mutations in active sites, etc.
• 2. Mix and match regulatory elements
• 3. Alternative splicing
• 4. Post-translational modifications

Protein functionality derives from 3D conformation:

1. Recognize and bind variety of molecules: i. Heme ii. Other native proteins iii. Forgeign proteins iv. RNA and DNA v. Etc.

e.g., regulatory proteins binding directly with DNA

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Protein functionality derives from 3D conformation:

• 2. Complimentary

surfaces or clefts:

i. Very precise 3D surfaces ii. Side chain interactions via physiochemical properties of side- chains

Protein functionality derives from 3D conformation:

• 3. Precise orientation =

increased catalytic power: i. Reaction rate increased > 1 million fold by enzymes ii.

• ptimal distance

iii.

• ptimal orientation

iv. Charged R-groups important in reactions

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Protein functionality derives from 3D conformation:

• 3. Proteins transmit

molecular signals: i. Allosteric control ii. Conformational changes iii. Hg uses this to “perceive” changes in its environment Cancer can be the result of an information transfer system “gone wrong”

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Relationship between coding sequences, functional domains, and tertiary structure of beta globin

DNA Introns

Exon 1 Exon 2 Exon 3

Regulatory Signals

Relationship between coding sequences, functional domains, and tertiary structure of beta globin

DNA Introns

Exon 1 Exon 2 Exon 3

Regulatory Signals

Modularity of protein folds:

Comparison of LDL receptor gene with the C9 complement and EGF genes. Comparison clearly indicates that the LDL receptor gene evolved via a gene fusion. event.

Exon shuffling: