BIOL 111 Lab Final

This week's procedures will include:

- Examining plants under the dissecting microscope to look for trichomes -Examining plants under blue light to look for GFP

Which of the following are NOT allowed in lab?

-Applying cosmetics -Chewing gum -Drinking water (or anything else) -Eating food

Which of the following are true statements about Arabidopsis?

-Arabidopsis is easy to grow in a lab -It is a model organism - It is possible to create plants that carry genes not normally found in Arabidopsis

Select the safety statements which apply to this lab.

-Arrive at lab already wearing closed-toed shoes -There are reagents and supplies that require disposal in the biohazardous waste -Loose/dangling clothing/accessories should be removed or contained so they will not fall into experiments -Goggles must be on and covering eyes when any experiments are being done in the lab

Which of the following are common uses for BLAST?

-Comparing my sequence to many thousands of others to try to gain insight into the ancestry of the gene -Determining the function of an unknown gene -Identifying an organism

Based on the phenotypes of the parental plants and F1 plants from the Heredity I lab, which phenotypes are dominant?

-GFP positive -Trichomes

When performing this laboratory exercise, which of the following personal protective equipment (PPE) is requried?

-Goggles -Closed-toed shoes -Gloves

Which of the following values show how closely matched your sequence is to potential matches from the database?

-Identity Score -E-value -Max Score

If a lane does not show any visible DNA, which of the following are plausible reasons there is nothing visible?

-PCR of that sample did not work so there is no DNA fragment to be visualized -The DNA sample did not contain the region PCR was supposed to amplify so there is no DNA fragment to visualize -The lane was accidentally skipped when loading the gel

Of the following, which are sequences you can search the databases of GenBank with?

-Protein -DNA

Which statements about genetics and heredity are TRUE?

-The genotypic and phenotypic frequencies in a cross between AaBb x AaBb are NOT the same -Genotype refers to the alleles an individual possesses

Which of the following are TRUE statements about this week's procedures?

-The plates can grow contaminants in addition to plants so be careful how long the plate is left open -The seeds come from the F1 generation plants and are already fertilized

Based on the phenotypes of the P generation and F1 generation, what are possible phenotypes in the F2 generation?

-Trichomes, GFP positive -Glabrous, GFP positive -Trichomes, no GFP -Glabrous, no GFP

Which of the following are options for comparing sequences on NCBI BLAST?

-tblastn: protein sequence compared to translated nucleotide sequence -Protein BLAST: protein sequence compared to protein sequence - blastx: translated nucleotide sequence compared to protein sequence -Nucleotide BLAST: nucleotide sequence compared to nucleotide sequence

Put the steps of PCR in order...

1. Assemble reaction with template DNA and master mix 2. Denature 3. Anneal 4. Extend

The central dogma of molecular biology. Put the steps in order: the molecules and the processes that create one from the other.

1. DNA 2. Transcription 3. mRNA 4. Translation 5. Protein

Put the following steps of a sequencing experiment in order from start to finish

1. Extract DNA from the organism/cells 2. Run PCR so that there are many copies of the sequence of interest 3. Send samples for sequencing 4. Analyze the sequence using tools like BLAST

There are 270 offspring from a cross of AabB x AaBb. If Mendelian ratios are followed, how many offspring would you expect to have recessive phenotypes for both traits?

16

It is frequently necessary to perform dilutions of a stock solution on the laboratory. If you were instructed to make a 1:20 dilution of a stock solution to arrive at a final volume of 800, how much stock solution would you need to pipette?

40

If you allow a heterozygous tall plant that is heterozygous for purple flowers to self-pollinate, how many tall and purple plants would you expect in the F2 generation if you sample 16 individuals? Both tall and purple flowers are dominant.

9

You set up a dihybrid cross between parents with genotypes AabB x AaBb. You get 16 offspring. If Mendelian ratios are observed, how many offspring do you predict will have the dominant phenotype for both traits?

9

How will the bands on the gel be visualized?

A UV light will make the fluorescence dye attached to the DNA glow

Gel A uses an electrical charge to move B through a gel matrix made of C. This causes fragments to be separated by D.

A= Agarose B= DNA C= further D= large

The A assay can be used to determine expression of B under different environmental conditions. If the gene is expressed and the C is present, D will be broken down and create a E pigment.

A= B-gal B= LacZ C= Enzyme D= ONPG E= Yellow

When you arrive at lab, you need to be wearing A shoes. When it is time to start experiments, you must wear B and, to keep you safe, they must remain over your C while D in the lab is doing experiments.

A= Closed-toed B= Goggles C= Eyes D= Anyone

To examine the A plants for the B of interest, a dissecting scope will be used to look for the presence of C and a D will be used to look for GFP.

A= F2 B= Phenotypes C= Trichomes D= Blue light

A uses a/an B called Taq polymerase to create C of copies of a specific region of D

A= PCR B= Enzyme C= thousands D= DNA

This week, two generations of plants will be observed; the A that were crossed to create the first generation and those offspring called the B generation. The seeds that you will plate are the C generation.

A= Parents B= F1 C= F2

The Arabidopsis will be scored based on presence or absence of two traits. A plant that is A lacks structures called B on its leaves. Plants positive for C will glow green under a special light.

A= glabrous B= trichomes C= GFP (green fluorescent protein)

You are preparing to set up a Punnett square for the cross, AaBb x aabb. The gametes for the first parent would be?

AB, Ab, aB, ab

Which of the following are TRUE statements regarding safety in this week's lab?

Arrive wearing close-toed shoes

Which of the following statements are good examples of following lab safety protocols?

Asking the TA if you can step outside to get a drink of water

This week's lab makes frequent use of a bioinformatic tool called BLAST. What is the acronym BLAST short for?

Basic Local Alignment Search Tool

In the lac operon, the operator functions to

Bind the repressor and prevent lac gene expression

In the lac operon, the repressor

Binds to allolactose and becomes inactive, allowing lac gene expression to occur

Because the Arabidopsis are transgenic (they have had genetic material modified), what is the proper disposal procedure?

Biohazard disposal

Match the function to the name of the lab equipment.

Centrifuge ----> Spins at a high speed to separate things by density (denser stuff moves lower in the tube) Thermocycler ----> Can be programmed to keep samples to keep samples/reactions at specific lengths of time Micropipette ----> measures and transfers very specific, usually small, volumes of fluid accurately Chelex Beads ----> Bind metal ions so they can be removed from the sample

While experiments are being conducted in the lab, which of the following must be worn?

Closed-toed shoes Gloves Goggles

Which genotypes are possible from a cross of parents with the genotypes Dd x DD

DD and Dd

Match the PCR component with its definition.

DNA template ----> The original DNA that you want to copy using PCR Primers ----> Small sections of DNA that match ends of the template so it can be copied Master Mix ----> The solution that contains all the components- including enzymes, nucleic acids, and ions- to build new DNA dNTPs ----> Individual nucleic acids (A,T,C and G) that will be the building blocks when new strands of DNA are made

Match the definitions with the PCR technology

Denaturation ----> The DNA template is heated so the strands separate Annealing ----> The reaction is cooled so the primers can stick to the DNA template Extension ----> The temperature is changed to the ideal temperature for Taq polymerase to build (synthesize) a new strand based on the template Thermocycler ----> The machine that controls the temperature of the reaction and has been programmed to move through the heat and cooling cycles

Which type of microscope is best for observing presence/absence of trichomes?

Dissecting

Identify which of the following statements are true and which are false...

Electrophoresis works by running an electrical charge through the gel [TRUE] DNA has a negative charge [TRUE] Because of its charge, DNA will move towards the negatively charged side of the gel [FALSE] All DNA will move through gel at the exact same rate [FALSE]

Which of the following will be components in your PCR mixture?

Human DNA Master Mix

All used pipet tips and microcentrifuge tubes should be disposed of where?

In the waste bag/bucket on my bench

Why do the cheek cells need to be lysed before setting up PCR?

Lysing breaks open the cells so the DNA is accessible

What is the purpose of PCR?

Make many, many copies of a specific region of DNA

What does PCR stand for?

Polymerase Chain Reaction

Complete the sentences by matching.

Shoes must be ----> closed-toed and cover most of your foot Clothing and jewelry ----> should not dangle Long hair ----> should be tied back To avoid transferring chemicals to sensitive areas ----> avoid touching your face and eyes in lab

What does STR stand for?

Short tandem repeats

What are you trying to amplify using PCR in this experiment?

Short tandem repeats from specific genes

Match the item or reagent to the proper disposal container for this week's experiments.

Spit Cups -----> Biohazard Waste Pipette Tips ----> Biohazard Waste 15 mL tube for pelleting cells ----> Biohazard Waste Gloves ----> Trashcan

What is bioinformatics?

The application of computer technology and associated software to biological data

At the conclusion of this experiment, all used culture materials should be places in what location?

The liquid waste disposal container on the side bench

Why is PCR required before running the DNA on a gel?

Without PCR, there would be too little of the DNA region of interest to see it on the gel

In a prokaryotic operon, the promoter functions to

bind the RNA polymerase

In animals, what type of sequence is commonly used to construct a phylogeny and determine ancestry?

mitochondrial DNA

When heterozygous tall plants with purple flowers self-pollinate to give rise to tall and dwarf plants with purple flowers, it demonstrates the following:

segregation of alleles

When observing plants, trichomes are

small hairs projecting from the leaves