Section $5.$ Answer the following questions on genomics using the information you learned from the lectures. There can be multiple answers per question in this section. Partial credit will be applied and incorrect answers will be penalized such that there is a minimum possible score of $0$ per question.

$20.$ What would happen if you tried to do standard PCR with dideoxy nucleotides and two primers?

A$.$ Amplification would be linear.

B$.$ Amplification would be exponential.

C$.$ Amplification would not occur due to lack of primers.

D$.$ Amplification would fail because TAQ would be unable to add the next base

E$.$ PCR will only work with one primer and two target DNAs.

$21.$ We talked about a variety of chemical modifications to nucleotides that could block reactions or even replication. Which processes had modifications that could be removed to allow the reaction$/$replication to then continue?

A$.$ Dideoxynucleotides in Sanger$-$Dideoxy sequencing.

B$.$ Modified nucleotides in Illumina short$-$read sequencing

C$.$ Deoxynucleotides in nanopore sequencing

D$.$ Nucleotides in bead based synthesis of DNA

E$.$ Nucleotides in Polymerase Chain reaction

$22.$ What are all of the components of a deoxynucleotide that are necessary for Sanger dideoxy sequencing?

A$.$ deoxyribose

B$.$ triphosphate

C$.$ dideoxyribose

D$.$ a chemical fluorescent tag

E$.$ monophosphate

$23.$ Which of the following makes TAQ polymerase good for PCR reactions to amplify and clone DNA?

A$.$ It is able to synthesize DNA in both the $3-5$ and $5-3$ directions, thus

increasing the potential for confused reactions

B$.$ It is able to remain stable at the high temperatures required to denature

DNA.

C$.$ It requires the addition of dNTPs$,$ minerals, or salts to do a PCR reaction

D$.$ It makes a ton of the amplified DNA making it easy to purify.

E$.$ TAQ Polymerase is sloppy and causes mutations

$24.$ A WT chromosome is represented by the genes, $1$ through $9,$ with a

centromere represented by a dot $,$ which looks like $123456789.$ The

researcher finds the following mutant chromosome $12346789.$ What is wrong with this chromosome?

A$.$ Inversion

B$.$ Translocation

C$.$ Deletion

D$.$ Duplication

E$.$ None

$25.$ The mutation in the above WT chromosome resulting in $(12346789)$ could have been caused by the following?

A$.$ Two recombination events between repetitive DNA on homologous

chromosomes.

B$.$ Two identically positioned double stranded breaks in homologous

chromosomes and reunion.

C$.$ A single recombination event between repetitive DNA on homologous

chromosomes.

D$.$ Recombination between repetitive DNA on non$-$homologous chromosomes.

E$.$ Recombination in meiotic inversion loops.

$26.$ Using the above WT chromosome, the researcher finds another mutant

chromosome with the following gene order $12346578$ABC. What is wrong with this chromosome?

A$.$ Inversion

B$.$ Translocation

C$.$ Deletion

D$.$ Duplication

E$.$ None

$27.$ Animals have a single photolyase gene while plants have two copies and one of the copies became a way to measure Ultraviolet radiation $.$ What is the most likely way that these two genes could have arisen?

A$.$ An missense mutation in the single copy of the photolyase gene to make a protein that can measure ultraviolet light.

B$.$ Duplication of the photyolyase gene followed by neo$-$functionalization to a ultraviolet function.

C$.$ Horizontal transfer of the ultraviolet measuring gene from another species into plants

D$.$ Duplication of ancestral genes followed by sub$-$functionalization to express in the presence or absence of ultraviolet light.

E$.$ Independent evolution of the photolyase and ultraviolet genes from scratch.

$28.$ When will the presence of a mutant $12346578$ABCchromosome $($in

comparison to the above WT$)$ probably not be a problem for the organism?

A$.$ Mitosis of a homozygote for the mutation

B$.$ Mitosis of a heterozygote for the mutation

C$.$ Meiosis of a homozygote for the mutation

D$.$ Meiosis of a heterozygote for the mutation

E$.$ It will never be a problem

$29.$ Which of the following genomic changes can be created by recombination based mechanisms?

A$.$ Inversion

B$.$ Translocation

C$.$ Deletion

D$.$ Duplication

E$.$ None.

$30.$ Which of the following function in trans and are required for a

retrotransposon to move?

A$.$ Long Terminal Repeats

B$.$ Transposase promoter

C$.$ Transposase protein

D$.$ RNAP

E$.$ Ribosome.

F$.$ DNA Polymerase.

$31.$ Which of these possible descriptions would fit only a non$-$ replicative DNA transposon?

A$.$ The transposase protein creates double strand cuts at both LTRs and moves the entire transposon to another location independent of replication

B$.$ The transposase protein takes the transposon after it is turned into DNA by Reverse transcriptase and inserts it into the genome,

C$.$ The transposase protein creates single strand cuts at both LTRs and moves the transposon to another location independent of replication.

D$.$ The transposase protein can function in trans to cut at any LTR sequences and move any DNA in between the LTR$.$

E$.$ Immediately after replication, the transposase protein creates double strand cuts at both LTRs and move