BIOL 351 CRISPR, DNA Replication, Lab

CRISPR Gene Editing

100

This protein acts as an RNA-guided endonuclease that can cut DNA at specific sites.

Cas9

200

This short DNA sequence adjacent to the target site is required for Cas9 binding and cleavage.

PAM (protospacer adjacent motif)

300

Cas9 requires this co-factor to cleave DNA

Magnesium ion

400

The molecule that is separated via agarose gel electrophoresis in the cleavage assays (Figure 1 of the journal club paper)

Cut/uncut plasmid DNA

500

This experiment demonstrated that the CRISPR-Cas9 system could be repurposed for programmable gene editing.

A single engineered RNA targeting the GFP gene sequence was shown to cut GFP specifically

DNA Replication

100

This enzyme synthesizes short RNA primers required to initiate DNA synthesis on both leading and lagging strands.

DNA primase

200

During DNA synthesis, these two chemical groups are linked together in a covalent bond. 

5' phosphate and 3' hydroxyl

300

These short DNA fragments are later joined together by ligase during replication. Spell the answer.

Okazaki fragments

400

The experiment by Meselson–Stahl showed that DNA replication demonstrates this property

Semi-conservative

500

These are 5 proteins involved in DNA replication

DNA Repair

100

Msh3 is involved in this DNA repair process

Mismatch repair

200

This process involves the loss of adenine and guanine base from DNA, which can result in mis-pairing during DNA replication

Depurination

300

Pyrimidine dimers (i.e. thymine dimers) can be induced by this source of DNA damage

UV light

400

In this DNA repair process, a double stranded DNA end is ligated to the nearest available double-stranded DNA end.

Non-homologous end joining

500

This describes the sequential steps of DNA mismatch repair

DNA damage is recognized, the newly synthesized strand is identified by an existing nick in the backbone, a segment of the new strand is removed by repair proteins, the gap is filled by DNA polymerase, and the strand is sealed by DNA ligase.

Mission Bay & Microbial Communities

100

The goal of the microbial communities lab module in BIOL 351

To investigate how the composition of microorganisms changes across time and place in Mission Bay

200

This instrument uses fluorescent dyes to determine DNA concentration very accurately

Qubit fluorometer

300

The gene that will be amplified and sequenced to determine the microorganism's taxonomic classification

16s rRNA gene

400

This is one reason why it is important to study the microbial communities of Mission Bay

To see how urban runoff might change the composition of microbial communities.

Because different biotic/abiotic conditions might increase the levels of microorganisms that are harmful to human health...

500

This sequencing platform/technology will be used to determine the taxonomic groups of the microorganisms found in Mission Bay

Illumina sequencing

Miscellaneous

100

When DNA replication initiates at a single origin, it results in this # of replication forks

2

200

This DNA repair process fixes double strand breaks and nucleotide sequences are exchanged between similar or identical DNA molecules

Homologous recombination

300

This describes a set of rules used by living cells to translate information encoded within genetic material into proteins.

Genetic code

400

This structural problem arises at the ends of linear chromosomes and is solved by telomerase enzyme in eukaryotes.

End-replication problem

500

This is one application of how PCR has been used in BIOL 351 lab

To amplify MSH3 gene and determine if correct mutation has been made during CRISPR gene editing.

To amplify the 16s rRNA gene from microbial community DNA.