1 Exploring DNA Binding with the Molecule World DNA Binding Lab

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Exploring DNA Binding with the Molecule World DNA

Binding Lab

www.Digital-World-Biology.com

1. Identify major & minor grooves

2. Identify elements

3. Does DNA have a positive or negative charge?

4. Is DNA hydrophobic or hydrophilic?

5. How many distinct molecules are in DNA?

Explore the properties of the example DNA


Pinch & spread fingers apart to zoom in and out

Drag to rotate

Move & resize the DNA to find the major and minor grooves


Tap the palette to view the color key

Identify the elements in DNA


Identify the elements in DNA


Tap the atom icon to see drawing & coloring options

Does DNA have a positive or negative charge?



1. Tap charge

2. Touch the window to apply the change





Is DNA hydrophilic or hydrophobic?

1. Tap Hydrophobicity



Is DNA hydrophilic or hydrophobic?



How many distinct molecules are in DNA?

1. Tap Molecule



How many distinct molecules are in DNA?


How many different bases are in this DNA fragment?

2. Tap Residue

3. Touch the window

1. Tap Tubes


How many different bases are in this DNA fragment?

Each base has a different color. Count the bases to find the number of residues in each chain.


Why study how molecules interact with DNA?

1. All genetic information is stored in DNAA. Proteins bind to DNA to use information

B. Proteins bind DNA to copy it

C. Proteins bind DNA to repair it

2. Proteins that bind DNA are used in biotechnologyA. Restriction enzymes cut DNA

B. DNA polymerases copy DNA (PCR)

3. Some drugs bind to DNA & block replicationA. Anti-cancer drugs – tamoxifen for breast cancer

B. Anti-viral drugs – valacyclovir


What do we know about molecules that bind DNA?

1. Proteins or drugs often bind to specific regions in DNA

A. Some bind to the major groove

B. Some bind in the minor groove

C. Some contact both the major and minor groove

2. Some proteins and / or drugs bind to specific DNA sequences

A. Restriction enzymes

B. Transcription factors


1. How can we determine if a substance is binding to the major groove, or minor groove, or both?


Answer: use different coloring and drawing styles to look at the two examples and see which visualization options show binding most clearly.

Example major groove binding Example minor groove binding


2. How can we tell if the substance bound to DNA is a protein or another kind of chemical, like a drug or something else?Answer: use residue coloring and the color key to see which objects don’t contain amino acid residues.

Example major groove binding Example minor groove binding


Tap the cameraicon

Assessment

Students can send an image in an email or save an image to the photo library, paste it into a document and write about it.

Documents

1 Exploring DNA Binding with the Molecule World DNA Binding Lab