Genetics Lab Final

T/F The most commonly used sequencing technique was developed in 1977 by Dr. Fred Sanger and is called Chain Termination sequencing.

True

The final step in the ELS program is to "develop" your gel so that the DNA fragments become visible. This technique uses a small amount of radioactive phosphorus and is called ___________.

autoradiography

What is the Mode of Inheritance in the pedigree below?

autosomal dominant

In an X-linked Recessive trait, why are more males affected than females?

males need only one copy of the defective allele where females require two copies, one on each X chromosome.

This week's exercise will examine nucleotide variation in six species of ________?

mammals

Changes to nucleotides in the second position of codons most frequently results in ___________ mutations.

missense

The source of the DNA used in this laboratory exercise will be ________

mitochondrial DNA

T/F The Dihybrid Recessive Backcross is the primary cross that we will use throughout this laboratory to examine linkage.

true

T/F The most useful cross for solving a 3-point mapping problem is the Trihybrid Recessive Backcross.

true

T/F The ratio 3:1 is a phenotypic "signature" for the Dominant/Recessive Mode of Inheritance.

true

T/F When using microsatellites as genetic markers, as we do in this lab exercise, it is easy to identify heterozygotes because they all show 2 bands.

true

Think about this weeks lab a little bit and in your own words, CONCISELY explain why it is so important to control the time of gel electrophoresis. Address it from the point of what might happen if the gel runs too short of a time versus too long of a time.

1. not enough resolution/separation of the band fragments if the gel runs too short making it difficult to interpret and 2. loss of data if bands are run off the end of the gel

In a recent survey of students in General Genetics, 97 identified themselves are female and 114 as male. Use Chi-Squared analysis to determine if this sample fits an expected ratio of 1:1. The Observed Chi-Squared calculated from these data is ____?

1.37

tall red bent 300 wild 280 red bent 41 tall 39 tall bent 20 tall red 210 red 21 bent 200 The distance between the locus for tall (a) and the locus for red (b) is ______ map units?

10.9

A total of 416 offspring are produced. Some are red and some are blue. Given the cross that you made, you expected a ratio of 3 red : 1 blue. How many blue offspring did you expect from the 416 progeny?

104

In a recent survey of students in General Genetics, 511 identified themselves are female and 396 as male. Use Chi-Squared analysis to determine if this sample fits an expected ratio of 1:1. The Observed Chi-Squared calculated from these data is ____?

14.58

The Fly Colony module used this week has a major difference from the previous weeks. Once you select a F1 offspring to use as an F2 parent, the program automatically selects the other parent to be a Dihybrid Double Recessive genotype. This choice assures that the expected final assortment ratio will always be _______ ratio.

1:1:1:1

A fruitfly is found to have the genotype FFGGHhRR. How many different gamete genotypes could this fly produce?

2

For this week's exercise, you will be selecting which module at the start of the Fly Colony program?

2-point cross

In fruit flies, bristle shape is found to be incompletely dominant with wild being homozygous (+,+), mildly bent being heterozygous (+,b) and fully bent bristles being homozygous (b,b). For mandible size, wild type is heterozygous (+,m), short is homozygous (+,+) and long is homozygous (m,m). Assume that two mildly bristled, wild mandibled flies (standard F1 cross) are mated, how many of their 432 progeny would you expect to be wild bristled, short mandibled?

27

Codons always consist of how many nucleotides?

3

In a typical Medical Pedigree, how many generations are documented?

3

A total of 416 offspring are produced. Some are red and some are blue. Given the cross that you made, you expected a ratio of 3 red : 1 blue. How many red offspring did you expect from the 416 progeny?

312

In fruit flies, bristle shape is found to be incompletely dominant with wild being homozygous (+,+), mildly bent being heterozygous (+,b) and fully bent bristles being homozygous (b,b). For eye color, orange is dominant over wild in a simple Mendelian fashion. Assume that two mildly bristled, orange eyed flies (standard F1 cross) are mated, how many of their 560 progeny would you expect to be wild bristled, wild eyed?

35

A fruitfly is found to have the genotype DdEeFF. How many different gamete genotypes could this fly produce?

4

A fruitfly is found to have the genotype RRSSTTUUWwYy. How many different gamete genotypes could this fly produce?

4

Fruitflies have _________ PAIRS of chromosomes.

4

In fruit flies, bristle shape is found to be incompletely dominant with wild being homozygous (+,+), mildly bent being heterozygous (+,b) and fully bent bristles being homozygous (b,b). For eye color, orange is dominant over wild in a simple Mendelian fashion. Assume that two mildly bristled, orange eyed flies (standard F1 cross) are mated, how many of their 720 progeny would you expect to be bent bristled, wild eyed?

45

In a recent survey of students in General Genetics, 214 identified themselves are female and 168 as male. Use Chi-Squared analysis to determine if this sample fits an expected ratio of 1:1. The Observed Chi-Squared calculated from these data is ____?

5.54

tall red bent 300 wild 280 red bent 41 tall 39 tall bent 20 tall red 210 red 21 bent 200 The distance between the locus for tall (a) and the locus for bent (c) is ________ map units?

51.5

A total of 2608 offspring are produced. Some are red and some are blue. Given the cross that you made, you expected a ratio of 3 red : 1 blue. How many blue offspring did you expect from the 2608 progeny?

653

In peas, Round seeds are dominant over Wrinkled, and Yellow is dominant over Green. A wrinkled, yellow (aaBb) plant is crossed with a round, yellow(AaBb) plant and a large number of offspring are produced. Given the results below, calculate the overall Chi-Squared (observed) value for these data. Hint: You will first need to determine the expected Phenotypic ratio for this cross. Choose the closest answer. Offspring Phenotypes 250 Wrinkled, Yellow 150 Wrinkled, Green 250 Round, Yellow 150 Round, Green

66.67

In peas, Round seeds are dominant over Wrinkled, and Yellow is dominant over Green. A wrinkled, yellow (aaBb) plant is crossed with a round, yellow(AaBb) plant and a large number of offspring are produced. Given the results below, calculate the overall Chi-Squared (observed) value for these data. Hint: You will first need to determine the expected Phenotypic ratio for this cross. Choose the closest answer. Offspring Phenotypes 799 Wrinkled, Yellow 221 Wrinkled, Green 816 Round, Yellow 132 Round, Green

68.67

A fruitfly is found to have the genotype AABbCcDdEE. How many different gamete genotypes could this fly produce?

8

The diploid (2n) number for fruit flies is ____ ?

8

In peas, Round seeds are dominant over Wrinkled, and Yellow is dominant over Green. A wrinkled, yellow (aaBb) plant is crossed with a round, yellow(AaBb) plant and a large number of offspring are produced. Given the results below, calculate the overall Chi-Squared (observed) value for these data. Hint: You will first need to determine the expected Phenotypic ratio for this cross. Choose the closest answer. Offspring Phenotypes 473 Wrinkled, Yellow 139 Wrinkled, Green 481 Round, Yellow 123 Round, Green

8.65

In fruit flies, bristle shape is found to be incompletely dominant with wild being homozygous (+,+), mildly bent being heterozygous (+,b) and fully bent bristles being homozygous (b,b). For mandible size, wild type is heterozygous (+,m), short is homozygous (+,+) and long is homozygous (m,m). Assume that two mildly bristled, wild mandibled flies (standard F1 cross) are mated, how many of their 640 progeny would you expect to be bent bristled, wild mandibled?

80

What is a PEDIGREE and what information can you obtain from it?

A PEDIGREE is a simple line drawing containing symbols that denote gender, birth order, generation, mating and genetic conditions. PEDIGREES are diagrams that convert a family's history into medical information in a standardized format.

In Drosophila, Wild Eye (A) is dominant over Sepia Eye (a) while Wild Wing (B) is dominant over Rough Wing (b). In your exercise using the Electronic Fly Colony you select the following Parental PHENOTYPIC cross: Wild eye, Wild wing Male x Sepia eye, Rough wing Female. What would be the GENOTYPES of the parents used in this cross? SELECT ALL THAT APPLY!!

AABB male X aabb female AaBb male X aabb female

To determine the identity of your DNA samples, we will be using a search program provided by the NIH (National Institute of Health). This program is called __________.

BLAST

The codon that generally indicates the start of a gene is _____.

ATG

The universal Start Codon is ______ and codes for the amino acid _____.

AUG; methionine

To begin work for this exercise, you will produce dsDNA and reverse complement strands of DNA using the computer program ___________.

BioEdit

____________ is a technique for determining the precise order of the nucleotides in a DNA fragment

DNA Sequencing

What is the primary purpose of heating your samples prior to loading them to the gel?

Denature the DNA into single strands.

The last area that you should include in any scientific report is the ____________. This area is very important because it is where you describe in your own words how the observed results relate to what you expected the results to be. This area will be graded very carefully.

Discussion/Conclusion

The scientific (genus species) name for the fruitfly (or red-eyed pomace fly) is?

Drosophila melanogaster

You will be using a new computer program this week called ELS which stands for ________ ________ _______.

Electrophoresis Learning System

T/F A sperm cell produced by a male fruit fly has 4 autosomes.

False

T/F To provide a common access point for all sequences, the National Institute of Health created a free repository called GeneStore.

False

White eye color is believed to be a sex-linked trait in fruit flies. Briefly describe what cross or crosses you would perform to prove test this hypothesis. Indicate what outcome you would expect if the trait is sex-linked as proposed.

In order to determine if eye color is a sex-linked trait in fruit flies, you could start with true breeding parents to determine the F1 generation and then do a self cross to determine their offspring. After finding those results, you could do a reciprocal cross and then self their offspring to see if the parent is different than expected. If the trait is sex-linked as proposed males would show the recessive trait instead of female because they lack the second X chromosome where as females have a second X chromosome.

Three loci are found to be located (linked) on Chromosome 2 in fruit flies. At locus 1, wild is dominant over tall (a). For locus 2, wild is dominant over red (b) and for locus 3, wild is dominant over bent (c). Assume that a standard linkage cross is made and the following progeny are produced: tall red bent 300 wild 280 red bent 41 tall 39 tall bent 20 tall red 210 red 21 bent 200 Based on these data, match each of the following phenotypes with the appropriate label: Parental Single Crossover Double Crossover

Parental: tall red bent Single Crossover: tall red Double Crossover: tall bent

For this week's exercise, we will be using the _______ or similarity-based method of tree construction, specifically the ___________ algorithm.

Phenetic / Nearest Neighbor

PCR is a laboratory technique that allows geneticists to precisely generate millions of copies of small fragments of DNA. The letters PCR are an abbreviation for ____________.

Polymerase Chain Reaction

The figure below represents a sequencing gel. "Read the gel and determine the DNA sequence for this individual sample. In the space below, carefully type in all the bases of this sequence. Type the sequence in as "GACCGC..........". Please use upper case letters and do not leave a space between the letters.

Read gel from bottom to top

Which of the following would NOT be considered a Stop codon?

TAT

The ability of one (1) amino acid to be coded by more than one (1) codon is best described by which concept?

The genetic code is degenerate.

The Consensus Model of a Eukaryotic Gene contains?

Transcribed region, enhancer, TATA box, and introns

Starting at INITIATION, concisely describe the major activities in the process of TRANSLATION. Be sure to include all of the major components, enzymes etc. in the order that they would be expected to appear during the process.

Translation is the process of going from RNA to protein and occurs during the G1 or G2 phase. Starting with initiation, the 40S ribosome binds to the start codon and then the 60S ribosome adds to form the 80S ribosome complex. Next is elongation. tRNA molecules enter the A site of the 40S subunit by the use of elongation factors and GTP. Initiation factors prevent some tRNAs from entering. A phosphate is released from GTP which releases elongation factors. This causes a peptide bond to form between amino acids in P and A sites. This process continues in the 5' to 3' direction (translocation). The tRNA travels through the ribosome complex from the P site to the E site and is then released into the cytoplasm to be reused. This will continue to occur until a peptide chain is formed. After the chain forms, the ribosome complex searches for a stop codon. Release factors are attached to the A site of the ribosome and causes the peptide chain, ribosome, and mRNA to be released. At the end of the process, a protein is formed. Initiation - Small Subunit of Ribosome#xD; RNA#xD; t-RNA into P site with MET#xD; Large Subunit of Ribsome -- completes Ribosome#xD; #xD; Elongation -- t-RNAs move into A site#xD; Peptidyl Transferase forms peptide bonds#xD; Ribosome shifts one codon opening A site again#xD; Process repeats#xD; #xD; Termination -- Stop code encountered#xD; no t-RNA available#xD; Entire unit disassociates

The term HOLANDRIC refers to what type of inheritance?

Y-linked

tall red bent 300 wild 280 red bent 41 tall 39 tall bent 20 tall red 210 red 21 bent 200 The order of the three loci in the cross above is _________?

a-b-c

What does the following symbol signify in a standard pedigree?

affected male

Mendel's Second Principle describes the interaction of 2 or more loci and is call the Principle of Independent ______________.

assortment

_________ is the field of research that combines Genetics, Mathematics and Computer Science. One goal of this research is to identify genes and gene regions.

bioinformatics

Aminoacyl synthetase is an enzyme involved in __________.

charging of tRNAs

Exercise 1 in this week's lab uses different starting crosses to examine the concept of __________.

configuration

A ______________ is produced by examining and comparing each nucleotide at each position across the sequences of a data set.

consensus sequence

The ____ Site is found at the start of an Inton and commonly contains the nucleotides GC.

donor

Phylogenetic "trees" are also know as phenograms and cladograms but the most general term for such graphs is _____________.

dendrograms

The Sanger sequencing technique relies on 5 main components: DNA template, a DNA primer, four deoxynucleoside triphosphates, DNA polymerase and ________________.

di-deoxynucleotides

__________ is a series of techniques by which biomolecules can be separated based on size, length and/or shape.

electrophoresis

________ are regions of a "gene" that remain in the final matured message.

exons

T/F All loci located on Chromosome Pair 4 of fruit flies would exhibit sex-linked mode of inheritance.

false

T/F Chromosome pair 4 functions as the sex chromosomes in fruit flies.

false

T/F Relative to the sex chromosomes, human males are the homogametic gender.

false

T/F TATA boxes are found in the Regulator region of Eukaryotic Genes and primarily control the Rate and Copy Number during gene transcription.

false

T/F The area of the written report where you are expected to fully describe how you set up your experiment is called the Results.

false

A gain or loss of a nucleotide from a mRNA frequently results in a __________ mutation.

frameshift

With a few exceptions that we will discuss later in the course, the flies used as Parentals (P) in the flylab will always be homozygous. This insures that the genotype of all offspring in the first Filial (F1) generation will be?

heterozygotes

The GENOTYPE of the affected son and daughter at the bottom of the following pedigree is _______?

homozygous recessive

Mutations caused or induced by external factors, usually chemical or environmental are termed _________.

induced mutations

Female fruitflies can easily be distinguished from males because female are ________ compared to males,

larger

The fragments of DNA we will be examining this week in lab will be separated based on fragment _____________.

length

In this Laboratory we will be testing predictions derived from the ______ Hypothesis.

mutation buffering

Regions of genes that are actually transcripted are called ________.

open reading frames

What is the Mode of Inheritance in the following pedigree?

sex-linked

Assortment Ratios can be produced from two or more Segregation Ratios using _____________.

the product rule

An exchange of a purine for a purine or a pyrimidine for a pyrimidine would be termed a ________ mutation.

transition

____________ is the conversion of mRNA to Amino Acids.

translation

Replacement of a purine by a pyrimidine would be an example of a ________ mutation.

transversion

T/F Acceptor Sites are found at the end of Introns and are commonly found to contain the nucleotides AG.

true

T/F Bioinformatics the area of science that represents a merger of computer science, mathematics and biology.

true

T/F During this exercise, rejection of the predicted dihybrid ratio indicates that the two loci are linked on the same chromosome.

true

T/F The DNA fragments used in this will exhibit a very simple mode of inheritance, which is co-dominance.

true

The Genotyping that we will be using in this exercise provides us with an example of how science can help solve a problem. Genotyping also provides us with another critical lesson, namely that

uncertainty exists in all scientific studies

By the end of this week's lab, you are expected to have completed a _________.

written report