Agenda: 3/26 Warm-up: Bill Nye – Understanding DNA Homework: pp. 19 – 23 Answer Questions on p. 23 Warm-up: Bill Nye – Understanding DNA DNA: Structure and Function Overview: Reading & notes Components Building a model - Computer Model - Paper model Preparation for tomato extraction

Video: Understanding DNA https://www.youtube.com/watch?v=J33JS-15MDc

Class Notebook Page # 3/26 DNA Structure & Function

DNA → RNA → Protein “Central Dogma” DNA and Biotechnology DNA → RNA → Protein “Central Dogma”

DNA Structure and Function Requires an understanding of: Backbone structure and direction Bases names, structure and pairing Difference in bonds: covalent bonds and hydrogen bonds Requires Memorization

The structure of the DNA provides the function. How does the structure of DNA allow it to be the instructional book of life?

Video- describing DNA DNA – packed into chromosomes http://www.dnalc.org/resources/3d/08-how-dna-is-packaged-advanced.html

Chemical structure of DNA http://www.hhmi.org/biointeractive/disease/dna_chem_structure.html HHMI's BioInteractive - The Chemical Structure of DNA

DNA: structure determines function Chemical Structure Composition Type of atoms Names Bonds Covalent bonds Hydrogen bonds Backbone Bases Helix

DNA structure – major parts S = sugars (deoxyribose) P = Phosphate group Nitrogenous Bases: A= adenine C= cytosine G= guanine T = thymine

Chemical composition Types of atoms? Combined to make macromolecules Extremely strong forces hold the atoms together Covalent bonds Why are covalent bonds important?

The carbons on the sugar are numbered The carbons on the sugar are numbered. The linkage between the phosphate group and the deoxyribose sugar are covalent bonds.

How is it put together? 3’ end joins the 5’ end of another base The carbons on the sugar are numbered. These linkages are covalent bond between the phosphate and sugar groups in the backbone Note how the molecules are represented. The pentagons show the shape of the sugar but do not label the carbons.

Directional DNA strands in the double helix are oriented in opposite directions 5’ -3’ strand with 3’ – 5’ strand (based on carbon bonds)

Structure of C and T Structure of A and G Structure of A and G Structure of A and G Two Base Types: Compare and contrast the 2 groups What do they have in common? How are they different?

2 types of bases Purines Pyrimidine Adenine and guanine Pyrimidine Cytosine and thymine In the DNA helix, certain bases are complementary. What does this mean? Which bases are complementary? Why? What would happen if they were randomly paired?

Hydrogen bonds: relatively weak forces that hold the bases together in the double helix.

Hydrogen bonds in the double helix How are the hydrogen bonds different from the covalent bonds? Why are 2 types of bonds important for the functioning of DNA?

Building a Model http://learn.genetics.utah.edu/content/begin/dna/builddna/ Molecular machines copy DNA Your body produces billions of new cells every day. Each time one of your cells divides, it must first copy the genetic information contained within its nucleus. Copying the genetic information in one cell using this activity would take more than 95 years*, yet molecular machines in your cells accomplish this feat in about 6 to 8 hours. In order to speed up the copying process, DNA replication begins at multiple locations along each chromosome. The two DNA strands are pulled apart and copied in both directions at the rate of about 50 nucleotides per second.**

Complementary base pairing These models are based on the molecular structure of real nucleotides. The grey and white circles on the models represent partial positive and negative charges that form hydrogen bonds between complementary bases. These bonds work kind of like tiny magnets to hold the two DNA strands together. Complementary base-pairing ensures that DNA strands are copied accurately, with just a few errors for each round of replication. Forces between neighboring nucleotides stack the bases on top of one another and twist the DNA strands into a double-helix.

Building a DNA Model Build a DNA Molecule http://learn.genetics.utah.edu/content/begin/dna/builddna/

Watson: creating the model http://www.hhmi.org/biointeractive/media/DNAi_watson_basepairing-sm.wmv

Biotech Objectives for a DNA model: Label the functional groups on the sugars and carbons to determine the 5’ and 3’ Know the components of the DNA “backbone” & where they bond Determine the location and function of hydrogen bonds Demonstrate that the molecular structure & shape of the complementary pairs is critical Identify the purine and pyrimidine bases & sizes Know the names of the bases (not just letters)

Your model will be similar to this.

DNA Model

Review Problem 19: The DNA molecule is shaped like a twisted ladder. :: DNA Learning Center http://www.dnalc.org/view/16441-Problem-19-The-DNA-molecule-is-shaped-like-a-twisted-ladder-.html

Questions about the model What base does adenine pair with? What base does guanine pair with? What is the smallest unit of DNA called? What is the shape of the DNA model?

Suppose you know that the sequence of bases on one DNA strand is AGCTCAG. What is the sequence on the opposite strand? Referring to the above question, suppose that the 5’-most base on the given strand is the first A from the left to the right. What would the 5’-most base on the opposite strand? Assume that a 100 base pair DNA double helix segment contains 45 cytosines. How many adenines are there?