PROTEINS. *Adapted from Biotechnology: Science for the New Millennium by Ellyn Daugherty.

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1 PROTEINS Most biotech products have something to do with proteins either containing amino acids or entire proteins. To manufacture protein products, researchers must understand protein structure and function. Chemical behavior of the protein is studied such as activity, solubility and electrical charge. Once structure and function of the protein is determined, researchers develop and improve methods of isolating, purifying and analyzing the protein. Protein Structure Protein molecules are polymers composed of amino acids (monomer). Every amino acid has the same basic structure, differing only in the R group. The R group primarily determines an amino acid s interaction in a protein chain. There are 20 different amino acids categorized based on the chemical nature of their R groups. The R groups may be charged (+ or -), polar (water-soluble) or nonpolar.

2 Most proteins contain hundreds of amino acids chained together by peptide bonds. A peptide bond is formed between the carboxyl group of one amino acid and the amino group of an adjacent one. Amino acids bond together forming long polypeptide molecules this occurs in the ribosome of a cell. FYI -- Protein Synthesis mrna copies a gene on DNA in the nucleus. mrna travels to the ribosome, the message is transcribed and an amino acids chain is formed. The mrna will determine which amino acid is placed into the polypeptide chain and in what order. The mrna is a complimentary strand of DNA so DNA really determines the sequence of the amino acids. A polypeptide chain is referred to as a protein s primary structure. As a polypeptide chain is formed, it begins to fold into a protein. The three-dimensional folding of a protein depends on how the different amino acids in the chain interact with each other this folding is vital to its function. In the polypeptide chain, hydrogen bonding between hydrogen, oxygen and nitrogen atoms result in alpha helix and beta sheets these helices and folds make up the secondary structure. Additional folding is called tertiary structure is due to the presence of charged or uncharged R groups. The final folding occurs when disulfide bonds form to produce and stabilize tertiary folding in and between polypeptide chains to form the quaternary structure. Most of the folding pattern results from the attraction and repulsion of amino acids within and between polypeptide chains so the amino acid order coded for on the DNA is critical to determining the ultimate structure and function of a protein.

3 Protein Functions Protein Groups Examples Specific Functions Structural Collagen Component of skin, bones, ligaments and tendons. Enzyme Amylase Enzymes speed up the rate of chemical reactions. Transport Hemoglobin Cytochrome C Carries oxygen in blood primary function Moves electrons through the electron transport chain Contractile Myosin & Actin Involved in muscle contraction Hormone Insulin Regulates blood sugar Antibody HER2 antibody Recognizes a breast cancer protein Recognition Gamma globulin gp120 MHC protein Enzymes are proteins that act as catalysts speed up biochemical reactions by building up or breaking down other molecules. The molecules upon which enzymes act are substrates. Enzymes are highly specific each enzyme catalyzes one type of chemical reaction and has one or only a few substrates. Most enzymes require cofactors to operate such as an ion or vitamin (coenzyme). The catalytic action of an enzyme occurs on the active site where the substrate and enzyme bind. Recognizes a variety of foreign proteins Protein on HIV surface Self-recognition proteins on cell surface Several factors affect enzyme activity: (1) Temperature of reaction Each enzyme has an optimum temperature for maximum activity. As temperature decreases, fewer substrates bump into enzymes and the reaction is slower. At high temperatures, too much stress is placed on the H-bonds holding the enzyme shape and the enzyme begins to unravel denaturation occurs. In a lab, most enzymes are kept cold to decrease the chance of denaturation. (2) ph Each enzyme has an optimum ph for maximum activity. In solutions extreme ph, ions may interfere with enzyme activity or cause it to denature. Studying Proteins Proteins are usually colorless and are submicroscopic so researchers must separate them from other molecules and determine their specific characteristic to study them. To develop a process for purifying a protein, a researcher must learn the protein s size, shape, amino acid composition, overall charge and solubility. Several techniques for studying protein characteristics are: Indicator test Biuret reagent, Lowry assay, Bradford assay. Proteins and small DNA molecules are commonly separated on vertical gels made of polyacrylamide the process is called polyacrylamide gel electrophoresis (PAGE). Polyacrylamide gels have a high concentration of molecules (4-18%), so they have a greater ability to separate smaller molecules than an agarose gel. Western Blots are used to determine whether a protein band on a gel is actually the protein of interest. Samples are run on a PAGE gel and then the protein bands are transferred to a blotting membrane (PVDR or nitrocellulose) the membrane is called a blot. The protein bands are colorless and need to be visualized. Using an enzyme linked onto an antibody, the blot protein bands can be colorized.

4 A spectrophotometer measures how much of a specific wavelength of light is absorbed by a material. Different specs produce light of different wavelengths (measured in nanometers) classified as UV specs or visible-light specs (VIS). Specs shine a beam of light on a protein and protein molecules interact with light waves by either absorbing light energy, reflecting the light or the light transmits between the atoms and molecules. The spectrophotometer measures the amount of light transmitted through the sample (transmittance). Transmittance data can be converted to an absorbance value by comparing the absorbance data to standards, the concentration of an unknown protein sample can be determined. o The lambda max is the wavelength of maximum light absorbance for molecules in a sample and is used to measure the amount of a protein in a solution. o To visualize colorless proteins, Bradford reagent can be mixed with colorless proteins and used in a UV spec changes from brown to blue in the presence of a protein. Bradford testing is often used to calculate the protein concentration of unknown samples. Standard protein solutions of known concentrations are mixed with the reagent, and the absorbance is determined and plotted on a graph creating a standard curve. An ELISA, which uses antibodies to recognize specific proteins, can be used to detect and measure the presence and concentration of a specific protein in a mixture. o An ELISA plate with a built-in spectrometer can quickly read the concentration of colorimetric ELISA samples in each well to quantify the amount of color change and protein concentration in several samples. X-ray crystallography determines the 3-dimensional structure. An x-ray beam is shined on a very pure crystal of a protein as the beam hits the protein atoms, the x-ray light is diffracted. A detector records the pattern of x-ray diffracted light. Using a computer, the x-ray diffraction data is interpreted and generates a 3-D image of a protein molecule.

5 Protein Extraction and Purification Purification separates other proteins from the desired proteins usually accomplished through a process called column chromatography. There are two ways to run a column: (1) allow gravity to draw the sample and buffers through the column resin; (2) use pumps to push a sample and buffers through a column. Open-column (gravity-flow) chromatography uses a plastic or glass column packed with resin. Samples and buffers are added to the top of the resin bed works well for small volumes, as in R&D to give an idea of how to scale-up the purification process to larger, more effective columns. Disadvantage to open-column chromatography: buffer runs slow, quantitation (collection of numerical data) is poor for large volumes and molecules do not separate as well. Fast-performance liquid chromatography (FPLC) uses pressure pumps to purify proteins pressure pumping gives faster and better separation of similar compounds. Pumps push the sample and buffer through tubing, into and through the column. As fractions come off the column, they are run through a UV spectrophotometer that determines the protein concentration of each fraction. FPLC can be scaled-up to very large volumes. High-performance liquid chromatography (HPLC) uses tiny columns made of metal that can withstand very high pressures. The columns are packed with minute resin beads, which provide increased surface area for better separation. Using HPLC, technicians can study tiny amounts of proteins, DNA and RNA. The HPLC instrument is highly sophisticated and requires specialized training. Immuno-affinity chromatography uses the specific binding of an antibody to the target protein to selectively purify the protein. The procedure involves immobilizing an antibody to a column material, which then selectively binds the protein, while everything else flows through. The protein can be eluted by changing the ph or the salinity. Factors affecting the resolving power of a column apparatus: (1) The diameter of the channels in the resin beads determine which molecules can be separated. (2) The charge of the resin beads in ion-exchange columns. (3) The type of buffers used: In gel-filtration columns, the buffer is used to carry the sample down the column. In ion-exchange columns, equilibration buffers are used to charge the beads and proteins in the sample. In ion-exchange columns, elution buffer knocks bound proteins off the charged beads. Elution buffers with a high salt concentration can elute molecules off a column. (4) Buffer exchange when a sample is loaded onto a column, it must be in an appropriate buffer. Often the sample will undergo buffer exchange, where the buffering compound in the sample is removed and new buffering compounds take their place. Dialysis may be used for buffer exchange. The dialysis tube must be suspended in the appropriate buffer to the buffers can change several times over several hours. (5) Resin Bed Volume and Sample Concentration amount of resin beads and the column bed must be long enough. Samples are run under various conditions and the fractions are checked using PAGE. Gas Chromatography was one of the first types of chromatography used in biology and chemistry labs. It s not a common practice now in biotechnology, but many companies still use gas chromatography for R&D.

6 HS-AB-2: Describe how characteristics of living organisms are integrated with advanced biotechnology techniques to lead to discovery or production. 2.7 Relate principles of macromolecule structure, physical chemistry and composition to strategies for isolating, analyzing and characterizing protein and DNA. 2.8 Perform methods of protein extraction and purification such as salt precipitation and dialysis, chromatography or antibody purification. 2.9 Design and perform methods of protein measurement, quantification, and characterization such as: Western blot, polyacrylamide gel electrophoresis, ELISA, and UV/VIS spectrophotometry 2.10 Apply the principles of electricity and ionization to successfully migrate charged molecules in ionic buffering systems Describe principles of phase separation in physical chemistry used in high performance liquid chromatography (HPLC) and gas chromatography (GC) for separating mixed analyses. HS-AB-4: Utilize statistical analyses to evaluate molecular separations and manipulations. 4.1 Discuss the importance of appropriate controls, standards, and statistical planning in laboratory applications and experimental design. 4.2 Assess the quality of data including possible sources of bias in their investigations hypotheses, observations, data analyses, and interpretations. 4.3 Compare the standard deviation and the mean of efficacy testing data of two or more biotechnology products. 4.4 Apply linear regression to [deleted] spectrophotometry calibration curve or ELISA standard curve. 4.5 Represent data using Gaussian distributions (normal populations). 4.6 Explain the reliability of data and construct confidence intervals for ph measurements and pipetting accuracy. 4.7 Establish measurement parameters and accuracy determination for real-time PCR or chromatography (HPLC or GC) detection data interpretation. 4.8 Apply significant figures to laboratory assessments and calculations to fall within established criteria.