Week 4 Nucleic Acids

DNA

Double-stranded polymer of deoxyribonucleotides that resides in the nucleus

RNA

Single-stranded chain of ribonucleotides transcribed in the nucleus and translated in the cytoplasm

Prokaryotes vs Eukaryotes DNA Location

Eukaryotes store DNA in the nucleus with small amounts of DNA in the mitochondria and chloroplast while prokaryotes store DNA in the cytoplasm

How do viruses work?

• VIruses can use DNA or RNA for their genetic information

• Viruses “hijack” the replication machinery of their host where they use the host cell’s replication ability to make copies of viral genetic material and viral proteins

Plasmid

Circular DNA molecules that can enter bacterial cells and replicate independently of the bacteria’s genome

Plasmid Uses

• Can causes antibiotic resistance in a bacteria or alter virulence in the bacteria that receives them

• Used in genetic engineering because they are able to transfer genes

Nucleotide Structure

Nitrogenous base + pentose sugar + phosphate group(s)

What phosphate groups can be used in a nucleotide?

• NTP, NDP, NMP

• More phosphates = more energy

Nucleoside

• Like a nucleotide but without a phosphate group

• heterocyclic ring attached to a sugar

Pentose Sugars

• 5 carbon sugars

• Carbons are numbered from the most oxidized to least oxidized

• C1 is the most oxidized, C5 is the least oxidized

Deoxyribose vs Ribose

Deoxyribose has hydrogen at C2, ribose has OH at C2

Purines

Double ring formed from pyrimidine with an imidazole ring, include adenine and guanine

Pyrimidines

Single ring derived from 1, 3-diazine: cytosine and thymine in DNA or cytosine and uracil in RNA

DNA vs RNA Sugar

RNA has an OH at carbon 2 and DNA has an H at carbon 2

DNA Base Pairing

• DNA has complementary base pairing between purines and pyrimidines across strands held together by hydrogen bonds:

• Adenine pairs with Thymine

• Guanine pairs with Cytosine

DNA Hydrogen Bond Strength

Hydrogen bonds between base pairs are strong enough to contribute to DNA structure but weak enough that they can be separated and re-attached

GC vs AT Stability

G-C has 3 hydrogen bonds and is more stable than A-T which has 2. Guanine-cytosine bond predicts melting temperature

RNA Base Pairing Difference (and structure)

• Has uracil instead of thymine

• Uracil has an H instead of methyl CH₃ on C5

• Uracil binds to adenine

Phosphodiester Bond

• Between the 3’ carbon and 5’ carbon in the sugar-phosphate backbone

• Formed by a condensation reaction between an acid an alcohol

• These bonds are strong and stable covalent bonds

DNA Charge

• DNA is negatively charged because the phosphate group in DNA loses a hydrogen ion leaving the phosphate with a negative charge

• DNA has a pKa of 1 to 2

What does DNA easily bind to?

Amino acids with positively charged R groups which include arginine, lysing and histidine. DNA binding proteins typically have positive charges.

Sense (coding) strand

DNA strand which has the same sequence as mRNA

Antisense strand

DNA strand used as a template for making mRNA

Grooves on DNA helix

• Due to twisting of helix, spaces or grooves form along the surface

• Bases within the grooves are exposed and can interact (bind) with proteins through hydrogen bonds

• The major groove is wider and more accessible where most proteins will bind through

DNA Packing Need

Each cell contains about 2 meters of DNA that must fit inside the nucleus

Histones

Positively charged proteins (rich in arginine and lysine) that DNA binds to for packing

Nucleosome

DNA wrapped around histone proteins (“beads on a string”) to form a solenoid structure (coil)

Histone 1 Role

Binds to linker DNA between nucleosomes to lock packing in place

Euchromatin

Relatively loosely packed DNA that is actively transcribed

Heterochromatin

Densely packed DNA that is transcriptionally silent

Chromosomes

Fully condensed DNA only visible during mitosis

Karyogram

Photo profile of an individual’s chromosomes

mRNA

• Messenger RNA that carries coding instructions copied from DNA for protein synthesis

• Transcribed from the template “antisense'“ strand of DNA

rRNA

• Ribosomal RNA that forms the structural and functional core of ribosomes which are the cell’s protein-making machines

• 50% of all RNA in a cell is rRNA

Eukaryotic Large Ribosomal Subunit

contains the tRNA binding sites and active site for peptidyl transferase

Eukaryotic Small Ribosomal Subunit

responsible for the binding and the reading of the mRNA during translation

Prokaryotic Ribosome

Has a large (50S) subunit and a small subunit (40S)

tRNA function

• tRNAs match their amino acid by having the correct anticodon attached to their 3’ end

• The anticodon is complementary to the mRNA sequence so the code can be read and the correct amino acid can be added to the polypeptide chain