genetics lab final - quiz, jeopardy, in-class review

T/F: BRCA1 and BRCA2 genes normally act as tumor suppressors, by helping in regulation of cell division

True

Which of the following databases is publically available to find variations in a gene that has clinical significance.

a. Nucleotide

b. Protein

c. ClinVar

d. Domains and structures

ClinVar

T/F: The picture of chromosome below shows the P arm of the chromosome

True

T/F: The following sequence is considered to be in FASTA format.

>NP_009225.1 breast cancer type 1 susceptibility protein isoform 1 [Homo sapiens]

MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQS

True

T/F: In bioinformatics, Query coverage refers to the value given as a percentage (0-100%), how much of the length of your sequence of interest (query sequence) aligns with the length of a reference sequence.

True

T/F: The direction of adding nucleotides in a PCR reaction is from 3' to 5' end of the template DNA

False

The purpose of adding bromophenol blue to the DNA loading dye is to

Allow monitoring the DNA migration on the gel during electrophoresis.

As you learned in the fast plant genotyping lab, the wild type should give a band for 280 bp and if there is mutation, it should give a band for 150bp. Based on the figure below what is the genotype of the seedling in lane # 4 with the arrow that has two bands.

Heterozygous for wild type and DFR

T/F: The insertion in the DFR gene leads to green colored seedling.

True

T/F: While screening plants for segregation of a phenotype/trait this generation of seeds/plants is used.

T2

The gene you are studying in the lab for sleep experiment is:

PER3

You are studying a population in Hardy-Weinberg equilibrium, for a gene with two alleles, p and q. The frequency of p allele is 0.46 then what would be the frequency of the heterozygous?

0.496

Which one of the following is NOT a characteristic of VNTRs?

a. Useful in genetics, biology research, forensics, and DNA fingerprinting

b. Repeats vary in sizes from as low as 6bp to as much as 100bp

c. They cut DNA at specific sites

d. These loci contain DNA seqences organized as a tandem repeats

c. They cut DNA at specific sites

T/F: In a population that is not evolving, the frequencies of different alleles within a population are expected to remain the same over time.

True

T/F: Per3 carrying 4 copies of this repeat may be associated with a preference for evening, while having 5 repeats may be associated with a preference for morning.

True

The function of isopropanol in the miniprep DNA isolation we performed in the lab is

Precipitate DNA

If you transformed bacteria with a plasmid carrying the kanamycin (Kan) resistance gene and a gene for Lac Z under the control of an arabinose-dependent promoter, what media should you use to observe the blue colored colonies?

LB+Kan+X-gal+Arabinose

In the bacterial transformation lab, you transformed E. coli with the pRK242 plasmid. You were very happy to see colonies the next day on your plate. Now you isolated plasmid DNA from the cultures of your transformed cells and want to make sure the plasmid is correct. You set up a restriction digest with an enzyme BamHI to validate the plasmid. Here is the plasmid map, based on this what sizes of fragments do you expect to see on your gel?

2700 bp and 2300bp

You and your friend isolated plasmid DNA from a bactureail culture and measured the concentration on a nanodrop. The concentration your of the plasmid is 500ng/ul with a 260/280 ration of 2.02 and that of your friend's is 15ng/ul. Since your DNA has better concentration you offer your your plasmid DNA to your friend. You both use 1 ug of this DNA to perform two restriction enzyme digests that should give you two bands. Your friend ran their gel and saw two nice bands, but your gel looks like the one below.

What might have gone wrong with the gel?

Placed gel towards the wrong electrode

T/F: The restriction enzyme EcoRI cuts the DNA at specific sites which have palindromic DNA sequences.

True

T/F: In E. coli Lac Z gene codes for Cas-9 endonuclease.

False

In a CRISPR mediated gene editing experiment, which one the components is required for recognizing the gene to be edited.

sgRNA

In prokaryotes, the CRISPR-Cas9 microbial defense system this sequence is inserted in CRISPR region of the bacterial genome as a signature for future infections.

spacer

Which of the following reactions will have an edited gene.

a. The reaction that has donor DNA and guide RNA

b. The reaction that has donor DNA, guide RNA, HDR machinery

c. The reaction that has donor DNA, guide RNA, HDR machinery and Cas-9 nuclease

d. The reaction that has Cas -9, donor DNA and guide RNA

c. The reaction that has donor DNA, guide RNA, HDR machinery and Cas-9 nuclease

T/F: Protospacer is the DNA region that is targeted for cleavage by the CRISPR system.

True

To identify genetically modified ingredients from food, we used ____ region of the T-DNA to amplify using a PCR

35S promoter

> or carat symbol in front of a DNA sequence suggests that the sequence is in this format:

FASTA sequence

Plasmid pLux is digested with restriction enzymes EcoRI and Xba I and the digest is run on an agarose gel. The sizes of bands you see on the gel would be:

1442bp and 11567bp

The direction of adding nucleotides in a PCR reaction is _____.

5’ to 3’

The mathematical representation of Hardy-Weinberg equation that predicts the genotypic frequencies for a population that is not evolving is:

p^2 + 2pq + q^2 = 1

The genomic DNA extraction from corn chips in the GMO lab uses this chemical as the strong reducing agent:

Beta mercapoethanol

A gene with the location code 6p21.34 is on the ____ arm of chromosome ____.

Short arm, chromosome 6

In bioinformatics, this refers to the value given as a percentage (0-100%), how much of the length of your sequence of interest (query sequence) aligns with the length of a reference sequence.

Query coverage

BRCA1 and BRCA2 genes normally act as ____, by helping in regulation of cell division.

Tumor suppressors

If the DNA concentration from the nanodrop measurement is 300ng/ul. How many uls will be needed to make 1 ug of DNA?

3.3 ul

During plasmid DNA extraction procedure, this chemical was used to lyse the cells.

NaOH

In a gene, a mutation at this location would lead to the most significant effect on the phenotype?

Closer to the 5’ end

This component allows for the identification of organisms or cells which exhibit successful transformation (between transformed and untransformed cells)

Selective marker

In CRISPR gene editing, Cas-9 endonuclease cuts 3 bps upstream of this sequence.

PAM

This type of promoter is always on in every single cell.

Constitutive promoter

With regards to the sleep regulation, which two genes act as transcriptional regulators of per genes?

CLOCK and BMAL

In gel electrophoresis this compound was added as a DNA stain to allow for visualization under UV light.

SYBRsafe

In Ti plasmid mediated genetic transformation which part of the Ti plasmid is inserted into a plant genome.

T DNA

Four people perform a sleep analysis by amplifying the PER3 gene. You observe the samples on the gel below after the PCR reaction. For sample 3: the phenotype of this person would be a:

Intermediates

A mixture of DNA and proteins with a condensed structure that allows the genetic code for an entire organism to fit in the nucleus of the cell.

Chromatin

In CRISPR gene editing, this component helps to identify the gene for cas 9 nuclease to cut.

Guide RNA

Morning preference phenotype is associated with these many VNTR repeats in an individual.

5

The molecular mechanism for onset of Huntington Disease depends on _____?

CAG repeats

If heat shock is needed to open the cells so the plasmids can enter, the reason why we place the cells on ice for a few minutes after heat shock is:

Reseals the membrane

In the figure below A and B represent what parts of a gene?

A is exon, B is intron

What do the mRNA sequences UAA, UAG, and UGA code for?

Stop codon

T/F: An organism with one extra set of chromosomes is considered to have Trisomy.

False

If you transformed bacteria with a plasmid carrying the kanamycin (Kan) resistance gene and a gene for GFP under the control of an arabinose-dependent promoter, what media can you use to observe the bacteria glow?

Arabinose + LB agar

A cross between yellow and white flowers yields all yellow flowers in the F1 generation. When F1 are selfed, they produce 105 yellow flowers and 45 white flowers. Calculate the chi-square value for the F2 generation seeds. If the critical chi square value is 3.84, what will be the outcome for the null hypothesis?

Chi square = 2, fail to reject the null

Eukaryotic cells utilize ____ _____ to create multiple different proteins from one mRNA sequence!

Alternative splicing

Exons

Expressed, exit nucleus

Introns

In nucleus

How much of the length of your sequence of interest aligns with the length of a result sequence, higher = similar length

Query coverage (Value given as a percentage (0-100%))

How many of the nucleotides in your sequence of interest is identical to the result sequence, higher = similar sequence

Max identity (Value given as a percentage (0-100%))

Describes random background noise of a search, lower value = better resul

E-value

Looking at the E-value data in the table below, which one of the bacteria carries the gene for the protein against which the search was performed?

Bacterium #2

T/F: The insertion in the DFR gene leads to green colored seedling.

True

Cell resuspension buffer-GTW-glucose function

Keeps the buffer isotonic to prevent cells from exploding/shrinking

Tris function

Keeps pH to 8.0

EDTA functions

Chelates ions (Magnesium), keeps DNAse from functioning

RNAse function

Removes RNA

NaOH function

Neutralizes chromosomal and plasmid DNA

SDS function

Denatures the cell membrane

Isopropanol function

Induces the precipitation of DNA by forming stable ionic bonds with phosphate groups in the presence of high concentrations of monovalent cations

70% ethanol function

Removes residual salt and enhances downstream application

You are setting up a restriction enzyme digestion and need 1 μg (1000 ng) of plasmid DNA for the reaction. The concentration of your plasmid DNA, measured using a Nanodrop, is 250 ng/μL. How many microliters (μl) of DNA will you add to the digestion reaction?

Volume = 1000 ng/250 ng/ul = 4 ul

Gel electrophoresis

Technique used to separate DNA fragment(s) by size, with larger fragments not traveling as far as smaller fragments

Resolution (gel electrophoresis)

Depends on agarose concentration

Electricity (gel electrophoresis)

We utilize the negative nature of DNA to “pull” the DNA through the gel (run to red/positive node)

DNA dye (gel electrophoresis)

Allows us to see our DNA at the end of the experiment, we used SYBRsafe; ethidium bromide can also be used

You ordered plasmid B from a company and want to clone your gene of interest into it. Before you start cloning, you confirm that the plasmid is correct by performing a restriction digestion reaction and visualizing the reaction on an agarose gel. If you digested plasmid B with the restriction enzyme HindIII, how many bands will you see on the gel based on the plasmid map below and of what sizes? See the plasmid map below

Two bands; 2500bp and 1500bp

What does CRISPR editing need to take place?

gRNA, donor DNA, repair mechanism

How do you know which cells are transformed?

Need other antibiotic than the cells are resistant to