1. DNA Structure and Packaging (Review)
Molecular Genetics Unit

2. 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?

3. 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)

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

5. 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?

6. 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?

7. 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’

8. 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?

9. 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'

10. 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

11. The DNA backbone Putting the DNA backbone together5′
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′

12. 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′

13. 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?

14. 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

15. 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

17. 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

18. 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

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

20. This will be important!
Plasmids

21. 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