Biochem Lecture 2- Nucleic Acids

What is negentropy?

Living things must extract energy from high order states in their environment to combat their own thermodynamic breakdown (increase in entropy) due to the second law of thermodynamics.

Describe an experiment that proved DNA carries heritable information. Who did the experiment?

Normally when injected with a rough strain (non-virulent) and a heat killed smooth strain (virulent) a mouse will die, but when injected with those and DNAse (chews up DNA) the mouse lives, still dies in the presence of proteinases. Oswald Avery.

What is the Central Dogma?

Replication: DNA>transcription>RNA>translation>protein. Reverse transcriptase turns RNA into DNA.

What are functions of nucleotides?

Building block of nucleic acids, energy unit (ATP and GTP), involved in biosynthesis (UDP-glucose in glycogenesus), signal transduction.

What are examples of how nucleotides used in signal transduction?

cAMP second messenger to activate certain protein kinases, ATP provides phosphate in protein phosphorylation, adenosine binding to sleep-promoting adenosine receptor.

What is the structure of nucleotides?

Phosphate: 5’ carbon-bonded phosphates, Sugar: 5-carbon sugar, Nitrogenous base.

What is the structural difference between RNA and DNA, which is more stable?

RNA has an OH group where DNA has a H on the 2’ carbon. DNA is more stable in aqueous solution due to missing OH.

What is the difference between purines and pyrimidines?

Purines have 2 rings (adenine and guanine), pyrimidines have 1 ring (cytosine uracil and thymine).

How are nucleotides named?

When bonded to sugar names are: Adenosine, Guanosine, Thymidine, Uridine, Cytidine. If it is DNA add deoxy- prefix.

What is the structure of polynucleotides?

Written from 5’ to 3’ direction. Phosphodiester bond connects the phosphates and sugars, the formation is catalyzed by polymerase.

Describe the experiment that supports semiconservate DNA replication.

Bacteria were incubated with a heavy nitrogen isotope, the density of their DNA was taken and then they were moved to be with lower nitrogen isotopes and their DNA density was measured after each replication. The next generation had a density halfway between each, the next had 50/50 at each density, the next had 75 at the light density and 25 at the heavy density.

What is the organization of eukaryotic genomes?

Compression of DNA is done through wrapping DNA around histones, which coil themselves into nucleosomes. Condensed chromatin is visible during metaphase, chromatin becomes de-condensed during interphase (cell growth) which allows for transcription and replication.

What disease is caused by DNA replication problems?

Huntington’s disease is caused by trinucleotide expansion during DNA replication, a similar problem occurs in a gene in FTD/ALS.

What are the steps to PCR?

DNA template with sequence of interest, primers, dNTPs, and polymerase are heat cycled where the DNA denatures due to the heat, the primers attach to the sequence, and polymerase attaches the dNTPs. Normal polymerase degrades with heat, so Tach polymerase is used.

Describe CRISPR/Cas9 genome editing.

Cas9 binds gRNA to the desired sequence and makes a double strand DNA break. This can lead to deletions or insertions or it can be used to add donor DNA into a system.

What is the structure and function of mRNA?

Has a 5’ cap and a poly A tail (allows RNA to be amplified witha poly T primer). It is modified during transcription.

What was the main issue with the triple helical model of DNA?

It placed all of the negatively charged backbone groups in close proximity.

List the alternate forms of DNA structure and their appearance

Alpha- dehydrated, squished and flat, Beta- common aqueous form, Z- less narrow, complexed with proteins.

Describe how the double helix of DNA can be reversibly melted.

As heated the helix unwinds due to the kinetic energy of the heated water colliding with it, it is able to rewind as the temperature goes back to normal.

How are nucleotide analogs used as therapeutic agents?

The reverse transcriptase, for example in HIV, is less selective in the nucleotides they grab and will take the analogs which create a non-functional DNA. Cancer replicates more and is more likely to take up toxic nucleoides, chemotherapy.

Whar is the structure and function of tRNA?

It has an anti-codon end that recognizes the codon in mRNA, and has an amino acid attachment site that picks up amino acids, this is necessary for translation. Looks like a clover.