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Rediscovering Biology: Molecular to Global Perspectives

Proteins and Proteomics

The proteins made by a cell determine what the cell does. This unit explores some basics of fundamental biochemistry, such as protein structure, interactions, and post-translational modifications. It also introduces the new ‘big-picture’ field of proteomics, exploring the implications of protein expression at levels from species determination to human disease.

The online textbook chapters support and extend the content of each video. The Web version can be viewed as a full chapter or as individual sub-sections, and includes links to glossary terms and other related material.

Explore the archive of animations, images and figures from the videos and online textbook. All of the images can be viewed online or downloaded as jpg files.

Read profiles of the expert scientists featured in the video and find the complete transcripts of the interviews conducted for this unit.
Ned David, Ph.D.
Stanley Fields, Ph.D.
Hunter Fraser
Aaron Hirsh
Leroy Hood, Ph.D.

Chapter Contents

What Is Proteomics?
Introduction to Protein Structure
Determining Protein Structure
Structure and Function Relationships of Proteins
Protein Modification
Genomics-Based Predictions of Cellular Proteins
2D Gel Electrophoresis to Identify Cellular Proteins
Mass Spectrometry to Identify Cellular Proteins
Identifying Protein Interactions
The Yeast Two-Hybrid System
Protein Microarrays
Protein Networks
Proteomes in Different Organisms
Proteomics and Drug Discovery
Ethics and the Economics of Drug Discovery

Unit Glossary

Active site
The specific part of an enzyme that binds the substrate.

Alternative splicing
A biological process in which introns are removed from RNA in different combinations to produce different mRNA molecules from one gene; sometimes called “RNA alternative splicing.”

Catalytic domain
The regions of a protein that interact to form the active or functional site of the protein.

Domain shuffling
The creation of new proteins by bringing different domains together.

The modification of a protein by adding sugar molecules to particular amino acids in the protein.

High-throughput technology
Large-scale methods to purify, identify, and characterize DNA, RNA, proteins and other molecules. These methods are usually automated, allowing rapid analysis of very large numbers of samples.

Interaction domain
A discrete module of a protein that is involved in interactions with other proteins.

Isoelectric point
A discrete module of a protein that is involved in interactions with other proteins.

A discrete module of a protein that is involved in interactions with other proteins.

A molecule that binds to a protein, usually at a specific binding site.

Mass spectrometry
A technique that separates proteins on their mass-to-charge ratio, allowing identification and quantitation of complex mixtures of proteins.

A short region in a protein sequence, which is conserved in many proteins.

Nuclear magnetic resonance (NMR)
A short region in a protein sequence, which is conserved in many proteins.

Peptide mass mapping
A technique for identifying proteins by mass spectrometry; combined with a computer program that matches the information on each peptide’s mass against the mass of theoretical, predicted peptides, based on known proteins in databases.

An enzyme that removes a phosphate group from a molecule, such as a protein.

The addition of a phosphate group to a molecule, such as a protein.

Polyacrylamide gel electrophoresis (PAGE)
A technique used to separate proteins in a gel matrix by their relative movement in an electric field.

Primary structure
The sequence of amino acids that makes up the polypeptide chain.

Protein fingerprinting
The identification of the proteins in a sample by analytical techniques, such as gel electrophoresis and mass spectrometry.

Protein sorting
The processes in which proteins synthesized in the cytosol are further modified and directed to the appropriate cellular location for their particular function.

The complete collection of proteins encoded by the genome of an organism.

Quaternary structure
The association of two or more polypeptides into a larger protein structure.

Secondary structure
The arrangement of the amino acids of a protein into a regular structure, such as an alpha-helix or a beta-sheet.

Tertiary structure
The folding of a polypeptide chain into a three-dimensional structure.

2D gel electrophoresis
A technique for separating proteins to further identify and characterize them. Proteins are separated in the first dimension based on their isoelectric point, and then in the second dimension by molecular weight.

Virtual ligand screening
A computer-based technology that simulates the interaction between proteins and small molecules to identify those that might be pharmaceutically active and useful as drugs.

X-ray crystallography
A method for determining the structure of a molecule, such as a protein, based on the diffraction pattern resulting from focused X-ray radiation onto pure crystals of the molecule.

Yeast two-hybrid system
A method used to identify protein-protein interactions. A protein of interest serves as the “bait” to fish for and bind to unknown proteins, called the “prey.”


Unit Animations

    • shim.gifThe Evolution of Protein-Protein Interactions
      A depiction of how evolution can affect how proteins interact with other proteins.
      View Quicktime Movie
    • The Three-Dimensional Structure of a Protein
      A depiction of the subsets of a protein structure.
      View Quicktime Movie
    • shim.gifVirtual Ligand Screening in Drug Design
      Shows how a computer program can be used to fit potential drug molecules into a site of interest on a protein.
      View Quicktime Movie

Related Resources

Branden, C., and J. Tooze. 1998. Introduction to protein structure. New York: Garland Press.
A non-technical introduction to protein structure.

Ezzell, Carol. 2002. Scientific American: Beyond the human genome.
An e-book that describes the new biology after the human genome.

DeFrancesco, L. 2002. Probing protein interactions. The Scientist 16[8]:28.
Researchers have found them by the thousands, but what do these interactions mean?

Ezzell, C. 2002. Proteins rule. Scientific American 286:40–48.
Biotech’s latest mantra is “proteomics,” as it focuses on how dynamic networks of human proteins control cells and tissues.

Hollon, T. 2002. Software zeroes in on ovarian cancer. The Scientist 16[8]:16.
A proteomic fingerprint with unprecedented diagnostic accuracy becomes a new kind of disease biomarker.

Hopkin, K. 2001. The post-genome project. Scientific American 285:16.
Whether the human proteome will be successfully mapped in three years depends upon how you define “proteome.”

Lewis, R. 2002. Fighting the 10/90 gap. The Scientist 16[10]:22.
Initiative targets the most neglected diseases; how scientists can help.

McCook, A. 2002. Lifting the screen. Scientific American 286:16–17.
An accurate test is not always the best way to find cancer.

Sinclair, B. 2001. Software solutions to proteomics problems. The Scientist15[20]:26.
Researchers find programs to aid every step of research.

Smutzer, G. 2001. Yeast: An attractive, yet simple model. The Scientist15[18]:24.
Researchers use whole genome strategies to characterize unknown genes in yeast.

Stix, G. 1999. Parsing cells. Scientific American 287:36.
Proteomics is an attempt to devise industrial-scale techniques to map the identity and activities of all the proteins in a cell.

Series Directory

Rediscovering Biology: Molecular to Global Perspectives


Produced by Oregon Public Broadcasting. 2003.
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  • ISBN: 1-57680-733-9