DNA Structure and Packaging (Review) Molecular Genetics Unit

Nucleotides 3 parts nitrogen base (C-N ring) pentose sugar (5C) ribose in RNA deoxyribose in DNA phosphate (PO4) group DNA & RNA are negatively charged: Don’t cross membranes. Contain DNA within nucleus Need help transporting mRNA across nuclear envelope. Also use this property in gel electrophoresis. Are nucleic acids charged molecules?

Types of nucleotides 2 types of nucleotides different nitrogen bases purines double ring N base adenine (A) guanine (G) pyrimidines single ring N base cytosine (C) thymine (T) uracil (U)

Building the polymer Make sure this is all added to your note.

Modern DNA Model Backbone sugar to PO4 bond phosphodiester bond new base added to sugar of previous base polymer grows in one direction N bases hang off the sugar-phosphate backbone Make sure you add this to your diagram. Can you count which carbon it is that had the phosphodiester bond? Can you tell which is a purine and which is a pyrimidine? Penguin Answer: because it's going to bond to a complimentary strand of DNA Dangling bases? Why is this important?

Pairing of nucleotides Nucleotides bond between DNA strands H bonds purine :: pyrimidine A :: T 2 H bonds G :: C 3 H bonds Penguin Answer: The 2 strands are complementary. One becomes the template of the other & each can be a template to recreate the whole molecule. Matching bases? Why is this important?

DNA Structure If you know the sequence of one strand, you can find the sequence of the complementary strand: 5’ – ATGCCGTA – 3’ 3’ – TACGGCAT – 5’ 5’ – GCATCGTTA – 3’ 3’ – CGTAGCAAT – 5’

DNA molecule Double helix H bonds between bases join the 2 strands A :: T C :: G H bonds = biology’s weak bond • easy to unzip double helix for replication and then re-zip for storage • easy to unzip to “read” gene and then re-zip for storage H bonds? Why is this important?

Antiparallel DNA is antiparallel—has directionality Building a DNA molecule Antiparallel DNA is antiparallel—has directionality 5’ carbon—phosphate group 3’ carbon—OH group Test with pen ... is it these three components, or is it these three? Which phosphate group belongs to which sugar? Also, don't forget the pointy sugar rule in terms of 5' and 3'

Directionality of DNA You need to number the carbons! nucleotide it matters! nucleotide PO4 N base Try filling out this diagram on back of your handout first. 5′ CH2 This will be IMPORTANT!! O 4′ 1′ Pentose 3′ 2′ OH

The DNA backbone Putting the DNA backbone together 5′ The DNA backbone PO4 Putting the DNA backbone together refer to the 3′ and 5′ ends of the DNA the last trailing carbon base CH2 5′ O 4′ 1′ C 3′ 2′ O –O P O Sounds trivial, but… this will be IMPORTANT!! O base CH2 5′ O 4′ 1′ 3′ 2′ OH 3′

Anti-parallel strands Nucleotides in DNA backbone are bonded from phosphate to sugar between 3′ & 5′ carbons DNA molecule has “direction” complementary strand runs in opposite direction 5′ 3′ 3′ 5′

Bonding in DNA 5′ 3′ 3′ 5′ hydrogen bonds covalent phosphodiester ….strong or weak bonds? How do the bonds fit the mechanism for copying DNA?

Nucleosomes “Beads on a string” How DNA is packaged 8 histone molecules Nucleosomes “Beads on a string” 1st level of DNA packing histone proteins 8 protein molecules many positively charged amino acids arginine & lysine bind tightly to negatively charged DNA Play video from playlist How DNA is packaged

Terminology: DNA Packaging Histone: structural proteins Nucleosome: section of DNA wrapped around histones Chromatin: DNA + structural proteins histones Chromatid: when a chromosome duplicates there are 2 chromatids Centromere: holds chromatids together Chromosome: highly condensed chromatin DNA centromere nucleosome chromatid chromatid chromatin

DNA packing as gene control Degree of packing of DNA regulates transcription tightly wrapped around histones no transcription genes turned off Not required to memorize heterochromatin darker DNA (H) = tightly packed euchromatin lighter DNA (E) = loosely packed H E

Bacterial genome Single circular chromosome haploid naked DNA no histone proteins ~1/1000 DNA of eukaryote Genome = all the DNA of an organism Eukaryotes • 1000 times more DNA • only 10 times more genes - introns, spacers, inefficiency 2005-2006

DNA of Prokaryotic Cells Nucleoid—structure in bacteria that contains chromosomal DNA Circular bacterial chromosome Bacterial Chromsomal Compaction

This will be important! Plasmids 2005-200

Plasmids Plasmids small supplemental circles of DNA carry extra genes self-replicating carry extra genes 2-30 genes can be exchanged between bacteria bacterial sex!! rapid evolution antibiotic resistance can be imported from environment Mini-chromosomes 2005-2