Experiment 2: DNA Sequence Polymorphism

Question 1

The DNA sequences of genomes is _____.

Answer 1

Dynamic

Question 2

How will this experiment differ from the first experiment?

Answer 2

In this experiment, sequence differences among individuals of the SAME species will be investigated.

Question 3

Define Polymorphism

Answer 3

If two individuals have sequence differences at the same place in the genome, it is called polymorphism.

Question 4

What is a difference of one nucleotide in a polymorphism called?

Answer 4

A difference of one nucleotide is called a single nucleotide polymorphism (SNP).

Question 5

What is an example of an SNP in humans? Go in detail.

Answer 5

The mutation that results in sickle cell anemia is due to SNP: the normal allele has a glutamic acid codon (GAG) whereas the mutant allele has a valine (GTG) codon at exactly the same place in the protein. This is an example of a non synonymous mutation and, in this case, it is detrimental to protein function.

Question 6

Do SNPs usually change the protein sequence?

Answer 6

No (like TTT and TTC code for phenylalanine).

Question 7

Define Non synonymous mutation.

Answer 7

A nucleotide mutation that alters the amino acid sequence of a protein. NA

Question 8

Define Synonymous Mutation

Answer 8

A nucleotide mutation that does NOT alter the amino acid sequence of a protein.

Question 9

Many synonymous mutations occur at the _____ of a codon

Answer 9

Third Position

Question 10

What are the different types of Polymorphisms?

Answer 10

Single Nucleotide Polymorphism (SNP)-Insertion/Deletion-Transposable Elements (TEs)

Question 11

Define Insertion/Deletion

Answer 11

Occurs when one or more nucleotide of DNA is present in one individual and absent in another.

Question 12

SNPs and Indels are the results of errors during the _____ process.

Answer 12

DNA Replication

Question 13

Define Transposable Elements

Answer 13

DNA sequences that move from one location on the genome to another. They are divided into autonomous and non-autonomous.

Question 14

Explain everything important about Autonomous and Non-Autonomous Transposable Elements

Answer 14

The autonomous element contains the gene encoding transposase enzyme (TPase) necessary for movement of both the autonomous and non autonomous elements. The non-autonomous element lacks a functional TPase gene and depends on the autonomous element for movement.

Question 15

What do the arrows at the ends of the autonomous and non-autonomous transposable elements represent?

Answer 15

Terminal Inverted Repeats

Question 16

Define Terminal Inverted Repeats (TIRs)

Answer 16

A single stranded sequence of nucleotides followed downstream by its reverse complement. TIRs are binding sites of transposase and it is the action of transposase that results in insertion polymorphism. When a TE moves, polymorphism is generated at the site that it left and at the new insertion site.

Question 17

One of the big surprises of the genomics era is that TEs account for over _____ of genomic DNA of many species. Most TEs in a genome are _____ meaning that they can no longer _____. Active TEs have often evolved mechanisms to avoid harming the organism. They insert between genes, into other TEs, or into introns.

Answer 17

50%-Inactive-Move

Question 18

In this experiment, B73 is used as a _____.

Answer 18

Positive Control

Question 19

What does diploid mean in our experiment?

Answer 19

That the 169020 locus occurs twice.

Question 20

The strains without TEs are going to be _____ in length.

Answer 20

Smaller

Question 21

What does the presence of 2 bands entail?

Answer 21

That there is a +/- insertion of the transposable element; heterozygous.

Question 22

What is the function of primers in PCR?

Answer 22

The primers direct the polymerase to the region of DNA for copying

Question 23

What is the function of Taq Polymerase in PCR?

Answer 23

the function of Taq Polymerase is to amplify the DNA for the production of multiple copies of DNA. TA