Unit 5 Test Review: DNA Replication & Biotech

DNA Replication

100

The enzyme responsible for the majority of new DNA strand synthesis during replication is:

DNA Polymerase III (aka DNA Pol III)

150

The enzyme which removes RNA primers at the end of replication and replaces them with DNA nucleotides is:

DNA Polymerase I (aka DNA Pol I)

200

In DNA replication, each of the original strands of the DNA molecule being replicated acts as a template strand which DNA replication enzymes use to guide synthesis of the new strands. After replication concludes, each of the two new DNA molecules is this made up of one original template strand and one newly-synthesized strand. This mode of molecular replication is described as:

Semiconservative

250

The directionality of DNA molecules impacts how DNA replication enzymes interact with them. In simple terms, we often say that DNA replication enzymes can only "read" DNA in the _____________ direction, and can only build a new DNA strand in the ___________ direction. 

3' to 5' ; 5' to 3'

300

Provide the proper name for the "chunks" of DNA produced during lagging strand synthesis, AND list the name of the enzyme which repairs the gaps between these "chunks."

Okazaki fragments ; DNA Ligase

PCR

100

What does the acronym "PCR" stand for?

Polymerase Chain Reaction

150

What specific enzyme is used during PCR to replicate DNA?

Taq polymerase

200

In PCR, 30 cycles of reactions are carried out to ensure that the original DNA added to the reaction has been copied a sufficient number of times. Each of these 30 cycles consists of 3 specific steps, delineated by controlled temperature changes. Name the 3 steps of a PCR reaction cycle, in order. 

Denaturation, Annealing, Extension (or Elongation)

250

Name the technology / approach that is used to check the results of PCR by separating DNA fragments by their size. 

Gel Electrophoresis

300

Identify what the acronym "STR" stands for, and why STRs are useful areas for targeting by PCR in applications like paternity testing and crime scene investigation. 

STRs = Short Tandem Repeats. Non-coding regions which vary widely between individuals; unlikely for two people to match number of repeats at one STR site, VERY unlikely to match at multiple sites, so can help tell people apart. 

Mutations

100

Name any one example of a mutagen. 

Ionizing Radiation (EM or nuclear), mutagenic Chemicals, specific mutagenic viruses (ex. HPV in humans)

150

Name one human disease / condition which is caused by a specific, heritable genetic mutation. 

Many examples: CF, Sickle Cell, Albinism, PKU, Hemophilia, etc. 

200

Identify where in the human body a mutation must be present in order for it to be heritable. 

Germline cells, aka germ cells (gametes and the cells that produce them in the ovaries and testes)

250

Consider the DNA sequence of the beginning part of Gene Z (sequence is broken up into codons to make it more easily readable):

* ATG AAA TTT GGG CCC

Now examine the following mutations to Gene Z:

Mutation 1: ATG CCC AAA TTT GGG CCC

Mutation 2: ATG AAT TTG GGC CC

Mutation 3: ATG TTT GGG CCC

Which of these mutations would be predicted to have the most severe effect, and why?

Mutation 2, one base deletion resulting in frameshift

300

The vast majority of mutations which occur in human cells have no effect at all on those cells' functions. Identify and outline THREE reasons why this is the case. 

Humans (and most eukaryotes) have DNA repair proteins which fix mutations, most of the genome is non-coding so most mutations do not impact genes, nature of the genetic code means in many cases changing one nucleotide does not change the amino acid the codon encodes, and even if amino acid sequence of a protein is altered by mutation many amino acids are so similar that there may be no biochemical / functional difference

Mutations & Evolution

100

Name the biological theory which states the following:

Individuals with traits more fit for their environment survive and reproduce at rates greater than individuals with traits less fit for their environment. As generations pass, advantageous traits become more common throughout a population (and eventually a species), while disadvantageous traits become less common. 

The Theory of Natural Selection

150

This is the term for a variant of a gene, produced by mutation. Some genes may have only one such variant, whereas other genes may have dozens of variants. All diploid organisms inherit at least two of these for every gene in their genome.  

Allele

200

HOX genes are a set of genes shared by all animals. While these genes differ greatly in their sequence, and different species have different numbers and types of HOX genes, there are still similarities shared between them. The most important detail pertaining to HOX genes is that their core function is the same across all animals; these genes are the master regulators of body development in embryos. Because of these shared sequence and function similarities that span hundreds of millions of years of evolutionary time, we say that the HOX genes are very:

Conserved

250

Sometimes, a gene will acquire so many mutations over generations that it is no longer functional, and ends up producing no protein product at all. This is one way in which some organisms can lack certain traits that close relatives possess. For example, in humans (and bats) our GULO (L-gulono-γ-lactone oxidase) gene underwent this process, and is now nonfunctional and so considered a "psuedogene." What extremely important metabolic cofactor did GULO allow our ancestors to produce?

Vitamin C (ascorbic acid)

300

When conducting DNA comparisons of individuals of the same species, it is best to use PCR primers that target regions that are highly _____________ , but when conducting DNA comparisons of distantly related species it is best to target regions that are highly __________ . 

non-conserved ; conserved

Gene Editing

100

What does the acronym "GMO" stand for?

Genetically Modified Organism

150

The name of the most common type of genetic editing approached currently used today is the ___________ system. 

CRISPR/Cas9

200

This is the name for a genetic edit conducted specifically to induce a DNA repair error and prevent a gene from being able to function.

Gene knockout

250

This is the stage of embryonic development at which a genetic edit must be made in order to ensure ALL cells in that organism will receive the edit. 

Zygote (one cell stage)

300

While targeted genetic edits have only become possible in the last few decades and highly targeted edits have only become possible in the last 10 years, humans have been intentionally modifying species since approximately 10,000 (estimates vary) years ago. What is the name for the approach that they used to create new plant and animal varieties?

Selective Breeding, AKA Artificial Selection

Current Events

100

This is the name of the US Attorney General who recently used a thriving stock market as reason to not fully un-redact the Epstein Files. 

Pam Bondi

150

This is the name of the government agency which was illegally created to "slash the deficit" and reduce the national debt, but which was shut down after only 6 months having actually created (at least) 2 billion dollars of new debt. 

Department of Government Efficiency (DOGE)

200

This is the AI company currently being blacklisted and targeted by the US Department of War for not allowing them to use their AI model to "pull the trigger" on autonomous weapons to end human lives.

Anthropic (owners of Claude AI)

250

This is the AI company which recently agreed (in effect) to allow the US Department of War to use its AI model to "pull the trigger" and be used to fire autonomous weapons to end human lives. 

OpenAI (owners of ChatGPT)

300

This is the name for the narrow region of ocean between Iran and the Gulf states which is currently (mostly) impassable due to the outbreak of war. 

Strait of Hormuz