Agar and Agarose

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Questions and Answers

Match each component with its role in agarose gel electrophoresis:

Agarose = Provides a matrix for DNA separation based on size Electrical Field = Drives DNA migration through the gel DNA Standard (Ladder) = Used to estimate the size of DNA fragments Buffer Solution = Provides ions to carry the electrical current and maintain pH

Match each term with its description in the context of agarose gel electrophoresis:

Cathode = The negatively charged electrode, attracts positively charged molecules Anode = The positively charged electrode, attracts negatively charged molecules Electrophoresis = The movement of charged particles in an electric field Agar = A polysaccharide used to create the gel matrix

Match the following steps with their purpose in preparing an agarose gel:

Melting Agarose in Buffer = Dissolves agarose to form a homogenous solution Pouring into Casting Tray = Shapes the gel into a solid matrix with wells Solidification = Creates the porous structure for DNA separation Submerging in Buffer = Provides conductive environment for electrophoresis

Match each characteristic with either agarose or agaropectin:

Agarose = The purified form of Agar commonly used in electrophoresis Agaropectin = A protein that is associated with the polysaccharide in the original organism Agar = A mixture of agarose and agaropectin Neither = A substance that melts at ~35°C Signup and view all the answers

Match each feature with its role in agarose gel electrophoresis:

Gel Rig = Houses the gel and buffer solution Power Supply = Provides the current needed for electrophoresis Casting Tray = Shapes the agarose gel during solidification Loading Dye = Makes DNA samples visible and aids in loading Signup and view all the answers

Match the function to the term used for gel electrophoresis:

Banana Coupler = Used connect power supply leads to the electrophoresis unit Gel Running = Process of applying an electric field to separate DNA fragments Casting Tray Platform = Supports the casting tray while the agarose gel solidifies Loading Dye = Added to DNA samples to make them denser and visible during loading Signup and view all the answers

Match the description to the result in gel electrophoresis:

Small DNA fragments = Migrate faster and farther through the gel Large DNA fragments = Migrate slower Supercoiled DNA = May migrate at varying speeds relative to linear DNA Linear DNA = Migrates consistently based on its size Signup and view all the answers

Match the description to the technique used in gel electrophoresis:

Ethidium Bromide (EtBr) = Intercalates between DNA base pairs and fluoresces under UV light SYBR Green = Binds to double-stranded DNA and fluoresces UV Transilluminator = Used to visualize fluorescently labeled DNA in the gel Gel Documentation System = Captures images of the gel under UV or visible light Signup and view all the answers

Match the description to the analysis of the results:

Semi-log Plot = Relates migration distance to DNA fragment size DNA Standard Curve = Used to accurately determine fragment sizes Visual Inspection = Provides a quick estimate of fragment sizes Comparison to Marker = Allows approximate size determination Signup and view all the answers

Match the troubleshooting steps with the problem encountered in agarose gel electrophoresis:

No DNA Migration = Check power supply and buffer conductivity Smearing Bands = Ensure proper DNA concentration and avoid overloading the gel Distorted Bands = Check for air bubbles or debris in the gel Uneven Migration = Ensure gel is level and buffer is evenly distributed Signup and view all the answers

Match potential uses of electrophoresis:

DNA Fingerprinting = Use of restriction enzymes to differentiate individuals Determining DNA purity = Observation of distinct, clear bands, versus smears Separation of RNA = Assess RNA Integrity Cloning verification = Confirmation with expected band size Signup and view all the answers

Match the description to what factors are important when using agarose gel:

Agarose Concentration = Affects pore sizes, influencing DNA separation Buffer Solution = Maintains pH and provides ions for conductivity Voltage = Affects the rate of DNA migration Run Time = Determines separation distance of DNA fragments Signup and view all the answers

Match each component to the role in visualizing DNA bands:

Ethidium Bromide = Binds to DNA and fluoresces under UV light UV Transilluminator = Provides UV light to visualize the DNA Gel Documentation System = Captures images of the gel. Loading Dye = Helps to load the DNA Signup and view all the answers

Match potential problems with the proper way to correct:

Incorrect Power Leads = Connect the negative lead of the power supply to the cathode Bubbles in gel = Ensure that gel solution is completely melted and degassed. Gel is not solid = Increase cooling time Overrun Result = Lower voltage Signup and view all the answers

Match the feature with a type of DNA:

Small DNA fragments = Can migrate more quickly through a gel Large DNA fragments = Travel more slowly in gel Supercoiled DNA = Circular, twisted DNA found in bacteria Genomic DNA = All of an organisms DNA and can be digested Signup and view all the answers

Match the description to the application of the product Agar or Agarose:

Agar = Used in microbiology as a solid substrate to contain culture media Agarose = Used in molecular biology to separate large objects Gelatin = Melts at ~35°C Cellulose = Component of plant cell walls Signup and view all the answers

Match each feature with the term used gel electrophoresis:

Banana Coupler = Used connect power supply leads to electrode Casting Tray Platform = Supports/levels the tray while gel solidifies DNA ladder = A standard to reference fragment size against Buffer solution = Maintains appropriate ionic strength for system Signup and view all the answers

Match the description to the step in plotting results of a gel:

Semi-log Plot = Used to display the relationship between base-pairs and distance X-axis Plot = Distance is show on the X axis Y-axis Plot = Base Pairs are shown on the Y axis, on a log scale Trend Line = Used to estimate the size of the fragment Signup and view all the answers

Which of the descriptions is most similar for running DNA on a gel?:

Distance = Base pairs are show on the Y axis, on a log scale Electrical Charge = DNA migrates to positive Run speed = Determined by voltage used to migrate DNA fragments Migration = Rate relies on fragment size Signup and view all the answers

Flashcards

What is Agar?

An extract from algae/seaweed, used as a solid substrate in microbiology and cooking.

Agar's hysteresis property

Agar melts at ~85°C and gels at ~40°-60°C, unlike gelatin, which melts at ~35°C.