Bio 211 exam 3

Define gender

"Gender" is more difficult to define but can refer to the role of a male or female in society (gender role), or an individual's concept of themselves (gender identity)

Klinefelter Syndrome

(47,XXY) Some male dev. but no sperm, and some female dev. too.

Can also create knockout mice:

(a normal gene is disabled) - Add a disabled copy of the gene of interest with a working copy of an antibiotic-resistance gene - Disabled copy replaces wild-type copy in embryonic stem cells

Transformation

(recombinant and nonrecombinant plasmids taken-up by cells)

Ligation

(seals DNA backbone) plasmid may re-seal without the foreign DNA (= nonrecombinant)

- Sex determination in Drosophila. - Does the Y chromosome determine maleness in flies as it does in humans? - What experiment can you design to determine whether the Y chromosome determines sex in fruit flies?

**You can add the Y chromosome to a female XX fly, and see if it becomes male (to see if the Y is sufficient). You could also take away the Y chromosome from an XY fly, and see if Y is necessary (predict female fly if Y is necessary).

What syndrome results from a 2nd division nondisjunction during meiosis in females (making eggs) after fertilization with a normal Y chromosome? (Draw out the figure below with X chromosomes to figure out the answer)

*Klinefelter, XXY [Y alone not viable]

Tip for finding the number of chromosomes at each stage of mitosis

*day 15 slide 10

Insertions and Deletions (collectively called indels)

- Add (insertions) or remove (deletions) one or more nucleotide pairs - When they occur in coding sequences, may lead to frameshift mutations

Cell Cycle Checkpoints big picture

- Checkpoints exist to make sure that cells are dividing only when appropriate - Major checkpoints just before DNA is replicated (G1/S) and before cells divide (G2/M) - Molecularly, passing through checkpoints involves active CDK/cyclin complexes that phosphorylate target proteins - Many other regulators involved

Cancer cells accumulate mutations

- Each mutation gives the cell an advantage in growth, or eventually spreading - Cancer is achieved when growth is uncontrollable and cells can spread - Causes disease by competing with healthy tissue for space, nutrients

DNA damage checkpoints are crucial for preventing cell proliferation when DNA damage has occurred. The role of DNA checkpoint proteins in the cell cycle is closely tied to the roles of DNA repair enzymes, although these proteins perform different functions. Which cell cycle phases contain critical DNA damage checkpoints? - G2 - M - G0 - G1

- G2 - M - G1

Hemoglobin is a complex protein that contains four polypeptide chains. The normal hemoglobin found in adults, called adult hemoglobin, consists of two alpha and two beta polypeptide chains, which are encoded by different loci. Sickle‑cell hemoglobin, which causes sickle‑cell anemia, arises from a single mutation in the beta chain of adult hemoglobin. Adult hemoglobin and sickle‑cell hemoglobin differ in a single amino acid. The sixth amino acid from one end in adult hemoglobin is glutamic acid, whereas sickle‑cell hemoglobin has valine at this position. After consulting a codon table, indicate the mutant codons that could give rise to sickle‑cell anemia. - GUC - GUG - GAG - GAA - GUA (codon table on back)

- GUG - GUA

Both genes and environmental factors contribute to cancer. The table shows that prostate cancer is 30 times more common among Caucasians from Utah as among Chinese from Shanghai. Briefly outline how to determine if these differences in the incidence of prostate cancer are due to differences in the genetic makeup of the two populations or to differences in their environments. - If the differences are due to the environment only, then people in Utah will have different rates depending on their ethnic background. - If the differences are due to the environment only, then people who migrated from Utah or Shanghai would have rates of cancer determined by their location and not by their place of origin. - If the differences are due to genetic makeup only, then people who migrated from Utah or Shanghai to elsewhere would have a similar cancer rate as people who stayed in Utah or Shanghai. - If the differences are due to genetic makeup only, then all of the people in Shanghai should have similar cancer rates despite different ethnicities. - If the differences are due to the environment only, then Caucasians with prostate cancer from Utah should see a reduction in tumor size after they move to Shanghai. (photo on back)

- If the differences are due to the environment only, then people who migrated from Utah or Shanghai would have rates of cancer determined by their location and not by their place of origin. - If the differences are due to genetic makeup only, then people who migrated from Utah or Shanghai to elsewhere would have a similar cancer rate as people who stayed in Utah or Shanghai.

• If you have an experiment that adds in a factor/gene, then you conclude if the gene is ________________ (pick necessary or sufficient). • If you have an experiment that removes a factor/gene, then you can conclude if the gene is _______________ (pick necessary or sufficient).

- If you have an expt. that ADDS in a factor/gene, then you can conclude if the gene is sufficient. - If you have an expt. that REMOVES a factor/gene, then you can conclude if the gene is necessary.

Select which examples are induced mutations. - Errors in DNA replication cause the formation of point mutations. - Ionizing radiation causes chromosomal fragmentation. - Nitrous acid causes the deamination of adenine to hypoxanthine. - Transposition causes the formation of deletions.

- Ionizing radiation causes chromosomal fragmentation. - Nitrous acid causes the deamination of adenine to hypoxanthine.

Interpreting results of SRY experiment • From this experiment, is SRY necessary for maleness? (Yes/No/Didn't test). • From this experiment, is SRY is sufficient for maleness? (Yes/No/Didn't tese).

- Is SRY is necessary for maleness? - DIDN'T TEST, because they did not take away the Sry gene from a mouse. - Is SRY is sufficient for maleness? - YES, because they ADDED Sry to an XX female, and it was enough to make the mouse look male.

(The Human Genome Project) There were several surprising findings

- Less than 2% of the genome codes for proteins - There are only about 20,000 protein coding genes (alternative splicing) - At least half of our genes show sequence similarity to genes shared by other organisms - The human genomic sequence is 99.9% identical between any two people

(DNA Sequencing Technology) Potential concerns:

- Privacy - Insurance companies - Patenting of genes - Ethics of embryo screening

DNA sequences derived from viruses or foreign DNA are added to CRISPR locus

- RNA transcribed from CRISPR locus directs Cas9 enzyme to cut complementary DNA - Allows cells to cut-up foreign DNA when encountered in the future (serves as adaptive defense system similar to an immune system) - Geneticists have engineered these systems to serve as a molecular editing tool ****Important technical and ethical issues with its use in humans

"Classical" techniques to add or delete genes from organisms:

- Start with recombinant DNA - Add a wild-type or mutant copy of the gene from a plasmid - Knockout a gene

Select the mechanisms used by tumor suppressor proteins to prevent the initiation and progression of cancer. - They act at cell cycle checkpoints to regulate progression through the cycle. - They induce apoptosis in response to DNA damage. - They promote uncontrolled cell division. - They repair base substitutions or breaks in DNA. - They promote cell growth in response to DNA damage.

- They act at cell cycle checkpoints to regulate progression through the cycle. - They induce apoptosis in response to DNA damage. - They repair base substitutions or breaks in DNA.

The Human Y chromosome (questions they were testing to find)

- What gene on Y chr. is testis-determining factor (TDF)? - Are there many candidates?

A codon that specifies the amino acid Gly undergoes a single base substitution to become a nonsense mutation. Use the genetic code to answer the questions below. - What was the starting codon? - What was the new sequence after the mutation? - Was the mutation a transition or a transversion? (photo needed on back)

- What was the starting codon? GGA - What was the new sequence after the mutation? UGA - Was the mutation a transition or a transversion? Transversion

Blue-White Screening:

- White colonies = insert - Blue colonies = no insert

- SRY is translocated to X in rare _________. - SRY is absent from Y in rare __________.

- XX males - XY females - Do these correlations tell us SRY causes maleness, is the TDF?

Which of the mutations described have the potential to cause cancer? - a gain‑of‑function mutation in a proto‑oncogene - a loss‑of‑function mutation in a tumor suppressor gene - a loss‑of‑function mutation in a proto‑oncogene - a gain‑of‑function mutation in a tumor suppressor gene

- a gain‑of‑function mutation in a proto‑oncogene - a loss‑of‑function mutation in a tumor suppressor gene

After using a chemical mutagen to generate mutations in a DNA sequence, scientists noted a mutation from C to T at the 10th position within the coding region of a gene. This mutation led to a change of proline into serine at the fourth position in the resulting peptide. Using this information and the sequences listed, select all the types of mutations that occurred. - missense - spontaneous - induced - transversion - transition - base substitution - silent

- missense - induced - transition - base substitution

(Taco example: Necessary vs sufficient) • If I remove the spicy taco sauce, it is no longer flavorful. Therefore, spicy taco sauce is _____________ for flavor. • However, we don't know from this "experiment" if the sauce is ________ for flavor. • If I give you a plain taco with meat and cheese, it is not flavorful. If I then add spicy taco sauce, it becomes flavorful. That "experiment" tells us the sauce is ___________ for flavor.

- necessary - sufficient - sufficient

In butterflies, sex is determined by the ZW sex‑determination system. Female butterflies are heterogametic and have both a Z sex chromosome and a W sex chromosome for sex determination. In contrast, male butterflies are homogametic and have two Z sex chromosomes. Select all of the relatives from which a female butterfly could have inherited her Z sex chromosome. - paternal grandmother - mother - maternal grandfather - father

- paternal grandmother - father

background rate of spontaneous mutation (due to?) and therefore always...

-(due to?) arise do to errors in replication or background chemical changes -baseline rate of cancer

Translocations can lead to cancer: Philadelphia chromosome

-A reciprocal translocation• c-abl proto-oncogene becomes fused with bcr gene and this hybrid bcr/c-abl oncogene is transcriptionally active; • cell cycle becomes deregulated - results in CML, chronic myelogenous leukemia. • Single white blood cell with translocation event may act as origin. - 5-yr survival, historically = 55%

(nucleotide excision repair) Xeroderma Pigmentosum

-Patients with xeroderma pigmentosum (XP) have defective NER - Sunlight induces pyrimidine dimers; these are normally corrected by NER, but not in XP patients - People w/XP have 1000-2000X greater risk of skin cancer

Which mutant genes are most likely to result in cancer?

-genes that normally regulate whether cells go through the cell cycle -genes that respond to DNA damage and mutations and protect the cell from accumulating mutations.

Meiosis in Flowering Plants pt. 1

-male microsporocytes (2n) microspores (1n) pollen grain (1n) sperm (1n) -female megasporocyte (2n) megaspore (1n) egg (1n) -both embryo (2n) - neither endosperm (3n)

Gametogenesis in Animals

-male spermatogonium (2n) primary spermatocyte (2n) secondary spermatocyte (1n) spermatids (1n) sperm (1n) -female oogonium (2n) primary oocyte (2n) secondary oocyte (1n) ovum (1n)

Use the image below to classify mutations 1-3 as either missense, nonsense, or silent. Which mutation will likely have the greatest effect on the protein? The least effect? (photo on back)

1 = silent (least effect) 2 = nonsense (greatest effect) 3 = missense

(p53) 2 possible responses to DNA damage

1. Acts as a Transcription Factor to activate expression of p21, which inhibits CDK/G1 cyclins to halt the cell cycle; then activates DNA repair. 2. Triggers apoptosis (programmed cell death) if damage can't be repaired.

Cancer Cells Evade Two "Safety" Mechanisms Built into the Cell Cycle

1. Once p53 is inactivated, cells with DNA damage don't arrest in G1 and don't undergo apoptosis. 2. Telomerase enzyme is activated, avoiding the limit to cell divisions imposed by telomere shortening. Contributes to "immortal" tumor cells.

3 groups of molecular techniques used to cut DNA segments:

1. Restriction enzymes (DNA in a tube) 2. Engineered nucleases (whole genome) 3. CRISPR-Cas systems (whole genome)

Mutations occur during replication, at a rate of... Final error rate is... how?

1/100,000 nucleotides. Final error rate is <1/billion nt - how? • Proofreading • DNA repair

Human genome size =

3.2 x 109 bp (3 billion base pairs!)

Sequences recognized by restriction enzymes is typically...

4 to 8 base pairs (bp) long (most are 4 or 6 bp)

Determine the diploid number of chromosomes (2𝑛)(2n) in this species of plant. ***use image on previous slide

6

Cloning

= make many copies

a. In an experiment you mutate the retinoblastoma gene (RB) such that its gene product behaves as if hyper-phosphorylated (too much phosphorylation). A. Which cell-cycle checkpoint is normally regulated by RB? B. Would the mutation result in a stronger or weaker association between RB and E2F? (APPLY) C. Would the transcription of genes necessary for DNA replication be higher or lower? (APPLY)

A. G1/S B. weaker C. higher

Why would a "regular" mitosis be a problem in making gametes?

A. Meiotic cell division generates cells (sperm and eggs) with one-half the genetic material (2n to 1n) - a reduction in chromosome number B. Source of genetic variation!

b. In a healthy individual who gets too much exposure to the sun, the skin often peels. A. What is the environmental source that causes a problem? B. What specific type of mutation often occurs? C. What cellular process is disrupted because of this mutation? D. In response to DNA damage, levels of what tumor suppressor protein increase? E. When this protein is at high levels, what cellular process can it trigger to explain the phenotype of peeling skin? F. Using what you know about the normal role of p53, describe why mutations in p53 are often observed in cases of skin cancer. Do you expect to see peeling skin in these individuals? (APPLY)

A. Sunlight/UV irradiation B. thymine dimers C. DNA replication D. p53 E. apoptosis F. After cells acquire DNA damage from UV, they can't trigger apoptosis (or cell cycle arrest). Therefore, DNA-damaged cells accumulate allowing more mutations to occur, eventually resulting in cancer (no peeling skin expected).

Suppose a DNA base change of an A to a T occurs, and is copied during replication (i.e. inherited by daughter cells). Is this change necessarily a mutation? A. Yes, it is a change in the DNA sequence. B. Yes, if the change occurs in a gamete; otherwise, no. C. Yes, if it occurs in a coding part of a gene; otherwise, no. D. Yes, if it occurs in a coding part of a gene AND alters the amino acid sequence of a protein; otherwise, no. E. Yes, if the change alters the phenotype of the organism; otherwise, no.

A. Yes, it is a change in the DNA sequence.

what is cloning an alternative form of?

Alternative to PCR, if you want to have a stable source of your isolated gene

(How can different mutations be classified?) Location on the chromosome

Autosomal or sex linked?

autosomes vs. sex chromosomes

Autosomes --> All non-sex chromosomes --> Humans have 22 Sex chromosomes --> Determine sex --> Male (XY) and Female (XX)

Ben and Angela are pregnant and discover they will be having twin girls. They are excited about the news. Ben and Angela are from England and have darker pigmentation and brown eyes. They are a little shocked when the first baby comes out with very light skin and blue eyes. The second baby has skin pigmentation similar to her parents and she has brown eyes. A few years later then have another set of twins who also display the same pigmentations as their older sisters. What is the most likely explanation to these observations? A. A random mutation occurred in the early embryo during both pregnancies. B. The same crossing over event during prophase I occurred causing the same mutation, which led to different pigmentations. C. The many genes that code for pigmentation get shuffled during anaphase I. Some of these gene combinations will give rise to different pigmentation levels.

C. The many genes that code for pigmentation get shuffled during anaphase I. Some of these gene combinations will give rise to different pigmentation levels.

"New technique to directly edit the genome:

CRISPRCas based genome editing

Does cancer run in families?

Cancer "runs in families" - known for over 200 years - from pedigrees - but no clear-cut pattern of inheritance - usually one mutant allele of a cancer-causing gene is inherited - predisposes person to cancer - likelihood cancer will develop depends on particular mutant allele, mutations in other genes, and environmental factors

Is cancer a single disease?

Cancer is not a single disease; rather, it is a heterogeneous group of disorders characterized by the presence of cells that do not respond to the normal controls on division.

Cause and Effect of Duplications and Deletions

Chromosomes can misalign during crossing over, leads to duplications and deletions (EX: red-green color blindness)

b. How is the information provided by 23andMe/Ancestry.com different from whole genome sequencing? (See https://www.vox.com/science-and health/2019/1/28/18194560/ancestrydna-23-me-myheritage-science-explainer).

Commercial ancestry tests are based on particular SNPs (single nucleotide polymorphisms), not whole genome sequencing. Based on certain "reference" individuals. Get reports about certain features based on current understanding, not actual sequence. May or may not be correctly interpreting data & don't have complete information. (Would need help interpreting sequence data)

Turner Syndrome

Female dev. but no eggs (45, X)

(SRY experiment) Genotypically _______ Mice Transgenic for SRY are Phenotypically ________.

Female; Male

do frameshift mutations alter phenotype or genotype?

Frameshift mutations alter all amino acids following the mutation, so generally have drastic effects on phenotype

(How can different mutations be classified?) Based on the effect the mutation has on phenotype

Gain or loss of function? Dominant or recessive? How does the trait change?

ionizing radiation

High-energy rays (X-rays, gamma rays, cosmic rays) penetrate tissues and damage DNA --> called ionizing radiation - Change stable molecules into free radicals and reactive ions --> these alter nitrogenous bases and break phosphodiester bonds in DNA - Often cause double-stranded breaks in DNA

b. Dosage compensation in mammals • How many Barr bodies do you expect in: i. An XXY individual ____ ii. An XXXX individual ___ iii. An XO individual ________

How many Barr bodies do you expect in: i. An XXY individual 1 ii. An XXXX individual 3 iii. An XO individual 0

Turner Syndrome (45, X) How often does this occur in female births? Does absence of second X= maleness?

How often does this occur in female births? -1 in 3000 female births Does absence of second X= maleness? - NO

Klinefelter Syndrome (47, XXY) How often does this occur in male births? Is presence of Y sufficient for maleness?

How often does this occur in male births? -2 in 1000 male births Is presence of Y sufficient for maleness? - Partially

Ohno's Hypothesis

KEY POINT: Duplicated chromosome segments may play a role in the evolution of new gene families • Original copy performs original function. • Second (or more) copy can acquire mutations and perform a new function. • Often, mutations in a second copy makes the gene nonfunctional - a pseudogene.

(Induced Mutations: Chemicals) when do these mutations occur?

KEY POINT: These mutations occur during Replication

Chromosomal sex determination (Example human karyotypes)

Karyotypes indicate correlations. X is long chromosome and Y is small

Coding regions

Missense, nonsense, or silent mutation

c. What are some of the limitations of using services like 23andMe to determine risk of genetic disease? Ancestry? How does race play into these limitations? (See above article as well as https://www.vox.com/science-and-health/2018/10/22/17983568/dna-tests-precision-medicine-geneticsgwas-diversity-all-of-us)

Most diseases are polygenic and so very difficult to predict. Ancestry is determined based on comparisons to "reference" individuals and limited studies; also there are many ethnicities missing. Current GWAS studies are mostly limited to people of European background. Claims of precise percentages of ethnic backgrounds are misleading. General risk of misunderstandings about race, which is a social and historical construct, not based on genetics. (80-90% of genetic diversity occurs within races; only ~7% occurs between races).

radiation mutations most frequently involve...

Most frequently involves 2 thymines (thymine dimer)

(Association of Ras with Cancer) mutated in _____% in all cancers.

Mutated in 30% of all cancers: 95% of pancreatic and 45% of colorectal cancers.

___________ play a central role in cancer

Mutations

It's the late 1980s, the Parkers had struggled for years to have children and were told that they would never conceive. They learned that there were many children from the former USSR that were available for adoption. They immediately fell in love with twin infant girls from the city of Kiev. The children's biological parents were from a small town about 100 miles away from Kiev. The parents were reported to be very healthy, with no known inherited family diseases. The Parkers go through the long process of adoption and are finally able to bring their children home (Hailey and Hannah). The children are happy and healthy. Shortly after the twins' 4th birthday they take Hailey to their doctor, Dr. Paul, because she has a sore throat, is hoarse, has a low grade fever, and a swollen throat. Dr. Paul immediately does a Strep test on Hailey and it comes back negative. He starts her on antibiotics and tells them to bring her back in a week if it doesn't get better. a. Do you think that prescribing antibiotics was a good decision in this situation?

NO - only prescribe antibiotics for bacterial infection

Shouldn't XX mammals produce twice the amount of X-linked gene products (proteins) as XY mammals?

NO, because XX mammals "compensate" by inactivating one of their X chromosomes to make a single "dosage" of X-linked genes. KEY point: expression of most, but not all, genes is repressed.

DNA sequencing technology makes it possible for what?

Now possible to sequence entire human genome in a few hours

independent assortment

One of the 2 processes that generate genetic diversity is the random distribution of chromosomes in anaphase I after their random alignment in metaphase I

Similarly, why do XXY individuals have a phenotype?

Overexpression of the genes that were not inactivated on "inactive" X

Where does crossing over occur in meiosis I?

Prophase 1

Crossing over occurs in...

Prophase I of Meiosis I

Why are there four X chromatids at start of meiosis in a female?

Replication occurs before M phase

Gel Electrophoresis

Separates (or resolves) DNA fragments -DNA dye visualizes all DNA

palindromic

Sequences read the same (5'-->3') on complementary strands

(How can different mutations be classified?) Location of the cell

Somatic or germline?

c. Sex testing and athletics. • Maria was born in 1961 and was a world class hurdler from Spain. Starting in 1968 the Olympics required female sex testing. She passed a sex test in 1983 ("certificate of femininity"). In 1985, she took another sex test which found that she was XY. • What are some reasons why Maria might have been an XY woman who was physically female, with no medical intervention?

Some possibilities might include a mutation in the SRY gene or androgen insensitivity syndrome. In Maria's case, it was androgen insensitivity syndrome.

(How can different mutations be classified?) Based on the cause of the mutation

Spontaneous or induced?

(The Human Genome Project) when did it start? When was the first draft completed? when was the finished sequence published?

Started in 1990 --> first draft completed in June 2000 --> finished sequence published in 2003

SRY gene on the Y chromosome was identified as the gene that codes for _______.

TDF (Testis-Determining Factor)

How do we know which chemicals are mutagenic, and likely carcinogenic?

The Ames test - Start with auxotrophic his- bacteria and mix with chemical X. - If a mutation occurs, changing his- to his+, then will see colonies on plates with minimal media - If the addition of chemical results in more colonies, then chemical X is mutagenic (and probably carcinogenic).

sex determination

The mechanism by which sex is established is called sex determination

Aneuploidy (2nd type of chromosome mutation) How often does this mutation occur?

Trisomy 21 Down Syndrome (47, +21) • Characteristic facial patterning, cognitive disability • 1 / 700 live births • recall, XXY and XYY are viable; but the addition of an autosome is much more severe; plants tolerate this better than animals

Tumor suppressors

Tumor suppressors normally stop cells at checkpoints when trouble arises

What syndromes result if the same eggs are fertilized by a sperm with a normal X chromosome?

Turner and XXX

pyrimidine dimers

Ultraviolet (UV) light has less energy than ionizing radiation, but is still mutagenic --> cause pyrimidine dimers

If an XX individual has one X inactivated, then why does Turner syndrome (XO) cause a phenotype?

We now know that in XX individuals, only about 75% of genes on the "inactivated" X chromosome have suppressed expression. Therefore, people with Turner syndrome are missing the expression of those special genes, that are not inactivated in XX females

(How can different mutations be classified?) Based on the type of molecular change

What happens to the DNA? What happens to the protein?

oncogenes

When mutated to oncogenes, drive passage through checkpoints under any condition

(Dosage Compensation in mammals) The _____ chromosome has many more genes than the ___ chromosome

X Y

Sex in flies can be determined using the Ratio of....

X (# X chromosomes): A (# sets of autosomes) • Dosage of genes on X is "counted", whereas autosomes contribute indirectly

To equalize X-chromosome gene expression between the sexes: -Solution in flies:

X-linked genes in ♂ (male) transcribed at twice the level of that in ♀(female)

Polyploidy (3rd type of chromosome mutation)

a change in the number of chromosome sets -Additional sets identical to parents. - Hybridization of closely related species; often sterile. - Very common in plants

Fusion of two gametes at fertilization results in...

a diploid zygote

Meiosis

a special cell division to make gametes (sperm and egg)

p53

a tumor suppressor gene • The "Last Gatekeeper" gene (aka Guardian of the Genome)

A cell in G1 of interphase has 3 pairs of homologous chromosomes. How many chromosomes and how many DNA molecules will be found/cell in the following stages: a) G2 of interphase b) Metaphase I of meiosis c) Prophase of mitosis d) Anaphase I of meiosis e) Anaphase II of meiosis f) Prophase II of meiosis g) After cytokinesis, following mitosis h) After cytokinesis, following meiosis II

a) G2 of interphase 6, 12 b) Metaphase I of meiosis 6, 12 c) Prophase of mitosis 6, 12 d) Anaphase I of meiosis 6, 12 e) Anaphase II of meiosis 6, 6 f) Prophase II of meiosis 3, 6 g) After cytokinesis, following mitosis 6, 6 h) After cytokinesis, following meiosis II 3, 3

a. A species has 2n = 16 chromosomes. How many chromosomes will be found per somatic cell in each of the following mutants in this species? a. Monosomic b. Autotriploid c. Trisomic d. Autotetraploid

a. 15 b. 24 c. 17 d. 32

After the cloning shown in part (a), the plasmids are transformed into bacteria and added to the plates shown below. Assuming that the plasmid contains an antibiotic resistance gene AND the lacZ gene to enable blue-white selection, answer the questions below. (APPLY) A. Which plate, A or B, shows a more efficient ligation?___ B. What color will colonies on plate C be (note the media)? C. Do you expect to see many colonies or only a few on plate D (note the media)? D. What type of negative control would you expect to produce only blue colonies? E. Which aspect of blue-white cloning is a selection? F. Which aspect of blue-white cloning is a screen?

a. B b. White because no X-gal c. Lawn (lots) of bacteria because no ampicillin to kill off non-transformed bacteria d. Do the ligation without the insert (green DNA) and plate on X-gal with ampicillin. You should see 100% blue colonies. e. Using ampicillin in media because it removes non-transformed bacteria f. Using X-gal because it gives colonies blue color when lacZ is intact (failed ligation)

Plasmids are small circular DNA molecules found in bacteria that replicate separately from chromosomes. Why are plasmids essential for recombinant DNA technology? a. DNA from a gene of interest can be inserted into a plasmid, then the modified plasmid can be inserted into a bacterial cell to make many copies of a gene of interest. b. Plasmids can cleave the bonds between DNA strands in DNA molecules in a staggered manner, creating single‑stranded, "sticky" ends of DNA where the gene of interest can attach. c. Plasmids are able to rapidly reproduce exact copies of cells, so they provide a means to acquire a large number of cells that contain a particular gene of interest. d. Plasmids provide the enzymatic action required to denature a molecule of DNA from a gene of interest that can be used in recombinant DNA technology.

a. DNA from a gene of interest can be inserted into a plasmid, then the modified plasmid can be inserted into a bacterial cell to make many copies of a gene of interest.

b. A chromosome has the following segments, where • represents the centromere: A B • C D E F G Describe the specific chromosome mutations required to change this chromosome into each of the following chromosomes. a. A B A B • C D E F G b. A B • C D E A B F G c. A B • C F E D G d. A • C D E F G e. A B • C D E f. A B • E D C F G g. C • B A D E F G

a. Duplication of AB (tandem) b. Duplication of AB (displaced) c. Paracentric inversion of DEF d. Deletion of B e. Deletion of FG f. Paracentric inversion of CDE g. Pericentric inversion of ABC

In the XX‑XO mechanism of sex determination, which of the statements is true? a. Females have two X chromosomes (XX) and males have one X chromosome (XO). b. Males have one chromosome (XO) at high temperatures and two X chromosomes at low temperatures (XX). c. Males have two X chromosomes (XX) and females have one X chromosome (XO). d. Males have one X chromosome and one Y chromosome (XY). e. Females have two Z chromosomes and males have one Z chromosome (ZO).

a. Females have two X chromosomes (XX) and males have one X chromosome (XO).

a. Whole genome sequencing of individuals. A. What are possible advantages to having your whole genome sequenced? B. What are possible disadvantages?

a. Information that could help protect against disease, target use of pharmaceutical, learn about ancestry b. Learn about a disease that there is no way to protect against, privacy, more difficulty with insurance, discrimination by employers, ancestry information might be difficult

a. Which types of chromosome mutations do each of the following statements describe? Choose from duplications, deletions, inversions, and translocations. (One of these is used twice). A. They change the position of DNA sequences in a single chromosome without changing the amount of genetic material B. They increase the amount of genetic material in a particular chromosome C. They move DNA from one chromosome to a nonhomologous chromosome D. They decrease the amount of genetic material in a particular chromosome E. They have a major influence on the evolution of gene families

a. Inversions b. Duplications c. Translocations d. Deletions e. Duplications

Cells in a tumor contain mutated copies of a particular gene that promotes tumor growth. Gene therapy could be used to introduce a normal copy of this gene into the tumor cells. (The original mutation would still be there as well) a. Will this therapy be effective if the mutated gene were an oncogene? b. What if it was a tumor-suppressor gene? c. Why is it more likely that Dr. Karp knows more people who have been diagnosed with, and who have died from, cancer than the typical BIO 211 student?

a. NO. Oncogenes produce overactive proteins that drive cells through the cell cycle checkpoints. There is already too much activity of an oncogene. Adding more will not help, and may make things worse. (Oncogene = "GO" signal/accelerator) b. YES. Tumor suppressors help cells stop at checkpoints, so adding more might help. (Tumor suppressor = "brakes"). c. Because Dr. Karp is older than most BIO 211 students. Cancer is more prevalent in older people, because cancer results from an accumulation of mutations over time. With each cell division, the chance of a mutation during replication increases.

On a separate paper, draw a cell with 3 homologous pairs of chromosomes in G1 and after S phase. Next, draw the four ways the 3 tetrads can line up at the metaphase I plate. Use your drawings to answer the questions below. A. How many different kinds of gametes are possible? (need to keep in mind the chromosomes and chromatids separate during meiosis I and II)? B. How many combinations of chromosomes are possible in humans with 23 chr.?

a. RULE: # of combinations is 2n (n= # homologous pairs) 2^3= 8 b. How many combinations of chromosomes are possible in humans with 23 chr.? 2^ 23= 8,388,608

Use the diagram to answer the questions below. A. What enzyme is represented by the letter A? B. Does the letter B show sticky ends or blunt ends? C. What enzyme is represented by the letter C? D. Is plasmid D recombinant or nonrecombinant? E. Is plasmid E recombinant or nonrecombinant? (photo on back)

a. Restriction enzyme b. Sticky ends c. DNA ligase d. Recombinant e. Nonrecombinant

Hemoglobin is a complex protein that contains four polypeptide chains. The normal hemoglobin found in adults, called adult hemoglobin, consists of two alpha and two beta polypeptide chains, which are encoded by different loci. Sickle‑cell hemoglobin, which causes sickle‑cell anemia, arises from a single mutation in the beta chain of adult hemoglobin. Adult hemoglobin and sickle‑cell hemoglobin differ in a single amino acid. The sixth amino acid from one end in adult hemoglobin is glutamic acid, whereas sickle‑cell hemoglobin has valine at this position. Indicate the type of mutation that gave rise to sickle‑cell anemia. a. a transversion that leads to a missense mutation b. a transition that leads to a neutral mutation c. a frameshift that results from a two‑base deletion d. a transversion that leads to a nonsense mutation e. a transition that leads to a missense mutation

a. a transversion that leads to a missense mutation

Which process results in sister chromatids that are no longer identical? a. crossing over b. DNA replication c. random assortment of homologous chromosomes on the metaphase plate d. crossing over and DNA replication only e. All of the answers are correct.

a. crossing over

Categorize the "mutations" in the 3-letter "codons" below as either: insertion of 1, insertion of 3, deletion of 1, deletion of 3, substitution (missense), substitution (nonsense), substitution (silent), or expanding nucleotide repeats. One type of mutation is not shown. Put an asterisk next to any frameshift mutations. Which mutations have the greatest effect on the protein/sentence? THE ONE BIG FLY HAD ONE RED EYE: Normal a. THE ONE QBI GFL YHA DON ERE DEY b. THE ONE BIG_HAD ONE RED EYE c. THQ ONE BIG FLY HAD ONE RED EYE d. THE ONE BIG FLI HAD ONE RED EYE e. THO NEB IGF LYH ADO NER EDE YE f. THE ONE BIG DRY FLY HAD ONE RED EYE g. THE ONE BIG FLY HAD ONE RED EYE THE ONE BIG FLY FLY HAD ONE RED EYE THE ONE BIG FLY FLY FLY HAD ONE RED EYE

a. insertion (1)* b. deletion (3) c. missense d. silent e. deletion (1)* f. insertion (3) g. expanding repeat Frameshifts have the greatest effect

Consider the diagram. AB∙CDEFG>AB∙CFEDG Which type of inversion is presented in the diagram? a. paracentric b. pericentric c. allelic d. Robertsonian e. heterozygous

a. paracentric

In humans, what normally results in the male sexual phenotype? a. the presence of the SRY gene on the Y chromosome b. the presence of two Z chromosomes (ZZ) c. the presence of only one X chromosome (XO) d. the presence of the Xist gene on the X chromosome e. the presence of one X chromosome and one W chromosome (XW)

a. the presence of the SRY gene on the Y chromosome

Bacteria protect their own DNA from restriction enzymes by..

adding methyl groups to their DNA

After being cut (also called digested) with restriction enzymes, DNA fragments can be separated based on size by __________________.

agarose gel electrophoresis - Small fragments travel faster and will be at the bottom of the gel - Large fragments travel slower and will be at the top of the gel

above baseline rate, environmental agents that promote mutation (mutagens) usually...

also contribute to cancer = carcinogens

Base substitutions

alter a single nucleotide in the DNA

(The Human Genome Project) Attention now focused on...

analyzing & interpreting the vast amount of data gathered in this project

(cloning) Select for bacteria containing...

any plasmid

(p53 mutations) Damaged cells do not undergo...

apoptosis and remain in the body

The number of possible transversions is twice the number of possible transitions, but transitions...

arise more frequently

A geneticist tests the function of a gene called CFTR in mice. She makes a knock-out mouse in which the CFTR gene is deleted. The resulting mouse has a phenotype similar to humans with cystic fibrosis, including abnormal, thick secretions in the lung. The correct interpretation is: a) CFTR is sufficient for proper lung secretions b) CFTR is necessary for proper lung secretions. c) Neither interpretation is supported by this experiment. d) Both interpretations are supported by this experiment.

b) CFTR is necessary for proper lung secretions.

The first cloned cat, Carbon Copy (CC), was tabby, while the cat she was cloned from, Rainbow, was calico. The surrogate mother was a tabby. Select the explanation that best explains why CC would never have been identical in pattern to Rainbow. a. Neither X chromosome is inactivated. b. During embryogenesis, one X chromosome is randomly inactivated in each cell lineage. c. The coat color genes are maternal effect genes, so CC looked like the surrogate. d. The coat color genes are on the mitochondrial genome and inherited with the mother's oocyte.

b. During embryogenesis, one X chromosome is randomly inactivated in each cell lineage.

Identical, or monozygotic, twins develop from a single egg fertilized by a single sperm. Monozygotic twins are genetically identical because they originate from a single zygote that split into two. Caroline Loat and her colleagues examined nine measures of social, behavioral, and cognitive ability in 1000 pairs of both male and female identical twins. Their study found that pairs of male twins tended to be more alike in their prosocial behavior, peer problems, and verbal ability scores than pairs of female twins. Which statement explains this observation? a. Identical male twins express the same X‑linked alleles in their neural cells, because males undergo random X‑inactivation. b. Females are mosaic for the expression of heterozygous X‑linked loci, because females undergo random X‑inactivation. c. Interacting genes on the X and Y chromosomes in the brains of males results in identical twins with more similar behaviors. d. Male twins have similar expression levels of X‑linked genes, because the Y chromosome silences expression of X chromosome genes.

b. Females are mosaic for the expression of heterozygous X‑linked loci, because females undergo random X‑inactivation.

What did Mary Lyon propose about sex chromosomes in mammals? a. The female sexual phenotype will normally result from having two X chromosomes in mammals. b. One X chromosome in each female cell becomes inactivated, and the process of selection is random. c. The X and Y chromosomes will pair with each other during meiosis in males. d. The Y chromosome determines the male sexual phenotype in mammals. e. Genes on the Y chromosome are expressed at very high levels.

b. One X chromosome in each female cell becomes inactivated, and the process of selection is random.

Three days later Hannah wakes her parents up because Hailey is having difficulty breathing and is turning a faint blue. An ambulance comes to take Hailey to the emergency room where they intubate her so she can breathe. The attending physician in the ER is surprised at how large her throat is. She immediately orders a blood test, a neck ultrasound, and does a biopsy of the swollen neck region. The diagnosis: thyroid cancer. The Parkers contact the adoption agency to get some health information on the birth parents. They learn the parents are still relatively healthy and there is no history of cancer in the family except for two distant cousins who were born in 1982 who also have thyroid cancer. b. What caused Hailey's thyroid cancer? (google "ionizing radiation accident Soviet Union 1980s") c. Is the cancer genetically linked to the birth or adoptive parents? d. Is Hannah likely to get thyroid cancer? e. Was the initial mutation a germ line or somatic mutation? f. Is this an example of an induced or spontaneous mutation?

b. Radiation from Chernobyl . (Many kids near Chernobyl got thyroid cancer from drinking milk with radioactive iodine) c. No d. Possible because of exposure to radiation e. somatic f. induced

What happens during anaphase II of meiosis? a. Homologous chromosomes form, and crossing over occurs between them. b. Sister chromatids separate from each other and migrate to opposite ends of the cell. c. Homologous chromosomes separate, but sister chromatids remain joined at their centromeres. d. Homologous chromosomes are randomly arranged in the middle of the cell. e. Sister chromatids are distributed in a single layer across the center of the cell. f. The nuclear membrane begins to form around haploid sets of chromosomes.

b. Sister chromatids separate from each other and migrate to opposite ends of the cell.

Select the definition of polyploidy. a. the addition or loss of less than a full set of chromosomes or chromosome pairs b. a chromosomal complement with at least three complete sets of homologous chromosomes c. a complete chromosome set or an exact multiple of the haploid chromosome set d. the number of chromosome sets that make up a complete genome

b. a chromosomal complement with at least three complete sets of homologous chromosomes

In bearded dragons, sex is determined by which characteristic? a. sex chromosomes only b. both sex chromosomes and temperature c. genes scattered throughout on the nonsex chromosomes (autosomes) d. X and Y chromosomes e. temperature only

b. both sex chromosomes and temperature

In Caenorhabditis elegans, the level of expression of genes on both X chromosomes of females is reduced by half. What phenomenon is this an example of? a. paternal mitochondrial leakage b. dosage compensation c. genomic imprinting d. extranuclear inheritance

b. dosage compensation

Consider the diagram. AB∙CDEFG>AB∙CFEDG Which chromosomal abnormality is represented in the diagram? a. deletion b. inversion c. aneuploidy d. translocation e. duplication

b. inversion

In the lower half of the interactive, change the template DNA strand such that the sequence ...ACAAAC... is changed to ...ACATAC... If this mutation occurred in a protein‑coding gene, how would it be classified? a. nonsense mutation b. missense mutation c. frameshift mutation d. silent mutation

b. missense mutation

Failure to separate for homologous chromosomes or sister chromatids is referred to as ____________. . a. pseudodominance. b. nondisjunction. c. Robertsonian translocation. d. gene dosage effect.

b. nondisjunction.

Select the definition of aneuploidy. a. the number of chromosome sets that make up a complete genome b. the addition or loss of less than a full set of chromosomes or chromosome pairs c. a complete chromosome set or an exact multiple of the haploid chromosome set d. a chromosomal complement with at least three complete sets of homologous chromosomes

b. the addition or loss of less than a full set of chromosomes or chromosome pairs

(cloning) Use __________ as a tool to copy your piece of DNA

bacteria

Gender is not _______.

binary

After replication, homologous chromosomes pair (synapse) to form a...

bivalent; the 4 chromatids form a tetrad.

Monoecious

both male and female reproductive structures within an organism; a plant with both male and female flowers (Arabidopsis)

A geneticist uses a cloning plasmid that contains the lacZ gene and a gene that confers resistance to penicillin. She inserts a piece of foreign DNA into a restriction site located within the lacZ gene and uses the plasmid to transform bacteria. She then grows the bacteria on selective media containing penicillin and X‑gal. Explain how the geneticist can identify bacteria that contain a plasmid with the foreign DNA. a. Bacteria with the desired plasmid produce both blue and white colonies. b. Bacteria with the desired plasmid produce blue colonies. c. Bacteria with the desired plasmid produce white colonies. d. Only bacteria with the desired plasmid produce living colonies.

c. Bacteria with the desired plasmid produce white colonies.

Chromosome duplications and deletions frequently result in abnormal phenotypes or inviable gametes. Which factor is a major contributor to this phenomenon? a. The genes are found in a novel arrangement. b. Recessive diseases are unmasked by additional copies. c. Gene dosage is modified.

c. Gene dosage is modified.

Suppose Alia recently learned that she inherited a mutant RB1 allele from her mother, who had retinoblastoma. RB1 is a tumor suppressor gene that is related to retinoblastoma. Why would Alia be at higher risk for getting retinoblastoma at an earlier age than her sister, Francine, who inherited a normal RB1 allele from their mother? a. If an individual has even one mutation in a tumor suppressor gene, cancer will not be suppressed. b. One mutant allele of a tumor suppressor gene increases the likelihood that the wild-type allele will also mutate. c. Someone with one mutant allele in a tumor suppressor gene only requires a mutation in the one remaining normal allele for tumors to form. d. An individual who inherited two functional alleles of a tumor suppressor gene is less likely to eat highly carcinogenic foods.

c. Someone with one mutant allele in a tumor suppressor gene only requires a mutation in the one remaining normal allele for tumors to form.

What is the likely fate of the acentric fragment (the part not connected to the other chromatids) when the homologous chromosomes separate during anaphase I? a. The segment segregates randomly from those that have centromeres. b. The segment will reinsert itself into the chromosome of the gamete. c. The acentric segment fails to segregate properly and will be lost. d. The segment will translocate to other nonhomologous chromosomes. e. The segment will be duplicated exactly once.

c. The acentric segment fails to segregate properly and will be lost.

A genetic counselor determines that patients with a deletion in a particular region of a chromosome are more likely to develop cancer than other people. Is the gene responsible for the increased risk of cancer a tumor suppressor or a proto-oncogene? a. The gene is a tumor suppressor, because tumor suppressor genes enable the cell to progress into M phase. b. The gene is a proto-oncogene, because proto-oncogenes promote cell division in response to appropriate stimuli. c. The gene is a tumor suppressor, because tumor suppressor genes inhibit or slow the rate of cell division. d. The gene is a proto-oncogene, because proto-oncogenes transmit signals that stimulate the cell cycle.

c. The gene is a tumor suppressor, because tumor suppressor genes inhibit or slow the rate of cell division.

DNA damage checkpoints are crucial for preventing cell proliferation when DNA damage has occurred. The role of DNA checkpoint proteins in the cell cycle is closely tied to the roles of DNA repair enzymes, although these proteins perform different functions. Which of the statements is true for DNA checkpoint proteins and not true for DNA repair enzymes? a. These proteins remove a single nucleotide of damaged DNA. b. These proteins nick the phosphodiester backbone of the damaged DNA. c. These proteins prevent the cell cycle from progressing if damaged DNA is detected. d. These proteins correctly synthesize new DNA strands.

c. These proteins prevent the cell cycle from progressing if damaged DNA is detected.

Why are these effects less noticeable for multisomies and monosomies of the X chromosome in humans? a. The X chromosome does not produce proteins. b. The X chromosome is not necessary for human survival. c. X inactivation only allows one X chromosome to be expressed in any given cell.

c. X inactivation only allows one X chromosome to be expressed in any given cell.

Which type of DNA mutation results in a change in the reading frame of an mRNA? a. substitution of one codon for another b. substitution of one nucleotide with another c. deletion of a single nucleotide d. duplication of a single codon

c. deletion of a single nucleotide

What are the two processes in meiosis that create genetic differences among cells? a. having two rounds of cell division and independent assortment b. independent assortment and going from diploid to haploid c. independent assortment and crossing over d. going from diploid to haploid and having two rounds of cell division e. crossing over and going from diploid to haploid

c. independent assortment and crossing over

A chromosomal translocation refers to a. gain of one extra set of chromosomes from the same species. b. deletion of a chromosomal segment. c. movement of a chromosome segment to a nonhomologous chromosome. d. change in number of individual chromosomes. e. loss of one member of a homologous chromosome pair.

c. movement of a chromosome segment to a nonhomologous chromosome.

Mutant versions of genes that are normally involved in driving the cell cycle are known as a. malignant genes. b. tumor suppressors. c. oncogenes. d. attenuators. e. proto‑oncogenes.

c. oncogenes.

During which phase of meiosis does crossing over occur? a. metaphase II b. telophase II c. prophase I d. telophase I e. anaphase I

c. prophase I

In the lower half of the interactive, change the template DNA strand such that the sequence ...ACAAAC... is changed to ...ACATAC... Which of the terms correctly describes this type of mutation? a. deletion b. insertion c. substitution d. inversion

c. substitution

(Induced Mutations: Chemicals) Intercalating agents

cause frameshift mutations --> Sandwich themselves between bases EX: Benzopyrene (cigarette smoke), charbroiled food

(Induced Mutations: Chemicals) Base analogs

cause transitions --> 5BU (analog of T) normally pairs with A, but can mispair with G (changes T to C)

(Induced Mutations: Chemicals) Alkylating agents

cause transitions --> Chemicals that add methyl or ethyl groups to bases (EX: mustard gas)

(Induced Mutations: Chemicals) Oxidative radicals

cause transversions --> G converted to analog and can mispair with A (changes G to T)

(Induced Mutations: Chemicals) Hydroxylamine

causes transitions --> Adds -OH group to cytosine (C)

On the downside, genetic mutations can lead to...

cell death, genetic disease, and cancer

(Induced Mutations: Radiation) SOS response allows...

cell division to continue- but keeps mutations

frameshift mutations

changes in the reading frame

In dioecious species, sex may be determined...

chromosomally, genetically, or environmentally

In mitosis, _________ holds sister chromatids together

cohesin

(Association of Ras with Cancer) A single amino acid change in Ras protein can cause...

constant stimulation of the pathway, even in the absence of growth factors

Sex is broadly described as male/female, but there is actually more of a...

continuum including intersex

(cloning) Screen for bacteria containing...

correct plasmid

You discovered a mouse gene with an unknown function. You do not know the location or sequence of this gene in the mice genome, but a similar gene has been isolated and sequenced in yeast. How might you determine whether this gene is essential for development in mice? a. Insert a cloned copy of this gene into the yeast genome. If yeast have the same phenotype as mice, the gene must be essential for development in mice. b. Create a targeting vector using a cloned copy of the gene to develop a knockout mouse. If the gene is essential for development, no offspring heterozygous for the knockout will be born. c. Transform a yeast strain deficient for this gene with DNA fragments from a mouse genomic library to determine if a mouse clone can complement the yeast defect. d. Create a targeting vector using a cloned copy of the gene to develop a knockout mouse. If the gene is essential for development, no offspring homozygous for knockout will be born. e. Engineer a transgenic mouse that overexpresses this gene. If the gene is essential for development, no offspring will be born from the transgenic mice.

d. Create a targeting vector using a cloned copy of the gene to develop a knockout mouse. If the gene is essential for development, no offspring homozygous for knockout will be born.

Which description is the best definition of recombinant DNA? a. DNA that contains both the template strand and the newly synthesized DNA strand within a single double‑helix molecule. b. DNA that composes the genome of a cell that is the product of multiple rounds of asexual reproduction. c. DNA that contains segments of DNA as well as segments of RNA within a single DNA molecule. d. DNA that is composed of a combination of DNA nucleotides from two or more organisms.

d. DNA that is composed of a combination of DNA nucleotides from two or more organisms.

DNA damage can occur as a result of exposure to chemicals or ultraviolet radiation. What happens during nucleotide excision repair of damaged DNA? a. Enzymes cut out the damaged gene, copy the same gene from the homologous chromosome, and insert the copy. b. Enzymes delete an incorrect DNA sequence, pull the gap closed, and join the bases on either side of the gap together. c. Enzymes identify a mismatched base in a DNA strand, remove the incorrect base, and insert the correct base. d. Enzymes unwind the DNA, cut out a section on one stand that contains the DNA damage, and resynthesize the section with the correct DNA sequence.

d. Enzymes unwind the DNA, cut out a section on one stand that contains the DNA damage, and resynthesize the section with the correct DNA sequence.

How are DNA fragments separated using gel electrophoresis? a. More highly charged DNA fragments move through the gel more quickly. b. Larger DNA fragments bind more strongly to the gel than do smaller DNA fragments. c. DNA fragments complementary to probes in the gel travel more slowly through the matrix. d. Larger DNA fragments move more slowly through the gel than smaller fragments.

d. Larger DNA fragments move more slowly through the gel than smaller fragments.

Which statement best describes the clonal evolution of tumors? a. If one or more of the required mutations is inherited, fewer additional mutations are required to produce cancer, and the cancer will tend to run in families. b. Environmental factors can contribute to a cell becoming cancerous, and these factors may interact with genetic predispositions to cancer. c. Both oncogenes and tumor‑suppressor genes contribute to cancer but differ in their modes of action and dominance. d. Tumor cells acquire more somatic mutations that allow them to become increasingly more aggressive in their proliferative properties. e. Tumor cells gain the ability to travel to other sites in the body, where they establish secondary tumors.

d. Tumor cells acquire more somatic mutations that allow them to become increasingly more aggressive in their proliferative properties.

Select the definition of a Barr body. a. an inactive Y chromosome b. an inactive autosome c. an active X chromosome d. an inactive X chromosome

d. an inactive X chromosome

What is a restriction enzyme? a. bacterial enzymes that regulate levels of mitosis‑promoting factor to limit the rate of cell division b. enzymes that bind to DNA synthetase molecules to prevent DNA from being replicated c. enzymes that dissociate proteins in the nuclear envelope after mRNA strands exit the nucleus d. enzymes that can cleave DNA molecules at or near a specific nucleotide sequence

d. enzymes that can cleave DNA molecules at or near a specific nucleotide sequence

Anhidrotic ectodermal dysplasia is an X‑linked recessive disorder in humans characterized by small teeth, no sweat glands, and sparse body hair. The trait is usually seen in men, but women who are heterozygous carriers of the trait often have irregular patches of skin with few or no sweat glands (see the illustration). Irregular patches of skin lacking sweat glands in heterozygous female carriers of anhidrotic ectodermal dysplasia are caused by a. inactivation of the X chromosome with the dysplasia allele in the cells of the sweat gland lacking patches. b. the presence of one X chromosome in some cells and the presence of two X chromosomes in other cells. c. nondisjunction of the X chromosome during gametogenesis in the cells of the sweat gland lacking patches. d. inactivation of the X chromosome with the wild‑type allele in the cells of the sweat gland lacking patches. e. the presence of two X chromosomes in some cells and the presence of an X and a Y chromosome in other cells.

d. inactivation of the X chromosome with the wild‑type allele in the cells of the sweat gland lacking patches.

Consider the diagram. AB∙CDEFG>ABC∙BEFG Which type of inversion is presented in the diagram? a. Robertsonian b. paracentric c. allelic d. pericentric e. heterozygous

d. pericentric

In nature, the purpose of the CRISPR‑Cas system is to a. allow a bacterium to incorporate a bacteriophage genome into its genome. b. protect eukaryotic cells from transposon activity. c. replace defective restriction enzyme activity in bacteria. d. protect bacteria and archaea from invading DNA elements. e. allow organisms to edit their own genomes.

d. protect bacteria and archaea from invading DNA elements.

Meiosis converts the ____________ of chromosomes to the ___________.

diploid number (2n); haploid number (n)

Dimers

distort DNA and block replication

Example of independent assortment

drawing a cell with 3 homologous pairs of chromosomes in G1 and after S phase.

What happens during anaphase I of meiosis? a. Homologous chromosomes are randomly arranged in the middle of the cell. b. Homologous chromosomes form, and crossing over occurs between them. c.The nuclear membrane begins to form around haploid sets of chromosomes. d. Sister chromatids are distributed in a single layer across the center of the cell. e. Homologous chromosomes separate, but sister chromatids remain joined at their centromeres. f. Sister chromatids separate from each other and migrate to opposite ends of the cell.

e. Homologous chromosomes separate, but sister chromatids remain joined at their centromeres.

Why does the distribution of the patches of skin lacking sweat glands differ among the females depicted in the illustration, even between the identical twins? a. It is due to placement of sweat glands being affected by environmental factors. b. It is due to random mutations in the two twins. c. It is due to the random determination of the number of Barr bodies in each cell. d. It is due to the pattern of sex determination being different in the two twins. e. It is due to random inactivation of different X chromosomes in different cells.

e. It is due to random inactivation of different X chromosomes in different cells.

How does cancer differ from most other genetic disorders? a. Cancer is always caused by one or more mutations in genes expressed in only one organ system. Most other genetic disorders are the result of mutations that affect all cell types. b. All cancers are the result of epigenetic changes, whereas most other genetic disorders are the result of changes in the DNA sequence. c. Most genetic disorders involve genes that rarely mutate. Most cancers are the result of mutations in rapidly mutating genes, which explains why cancer is so common. d. Mutations that result in defective receptors on the cell surface lead to cancer but not to other genetic disorders. e. Most genetic disorders are inherited through germ cells from parents. Most cancers are, to some extent, the result of mutations in somatic cells that occur during an organism's lifetime.

e. Most genetic disorders are inherited through germ cells from parents. Most cancers are, to some extent, the result of mutations in somatic cells that occur during an organism's lifetime.

After separating a complex mixture of DNA fragments according to size, identifying a specific fragment of interest a. requires an antibody. b. is done on an electrophoretic gel directly. c. requires a probe that is complementary to the entire fragment of interest. d. can be accomplished by Northern blotting. e. can be accomplished by Southern blotting.

e. can be accomplished by Southern blotting.

Meiosis II

equational division; sister chromatids separate

Mutations in which the # of copies of a set of nucleotides increases are ___________ ___________ __________.

expanding nucleotide repeats (EX: FMR-1)

Insertions or deletions that include any multiple of three nucleotides do not cause a __________.

frameshift - Leave the reading frame intact but add or remove amino acids (still may affect phenotype) - If they do not affect reading frame, are called in-frame insertions and in-frame deletions

Robertsonian translocations can cause...

genetic disorders - Some cases of Down syndrome (read in text) - SRY in XX phenotypic males

crossing over and independent assortment create...

genetic variation in meiosis

In general terms, "sex" refers to things like ___________ and ___________.

genitalia and hormones

(Association of Ras with Cancer) A "molecular switch" in the signal transduction pathway connecting...

growth factors to gene expression controlling cell proliferation

Gametes (egg and sperm) contain a ___________ set of chromosomes.

haploid

Spontaneous mutations

happen naturally and randomly and are usually linked to normal biological or chemical processes in the organism - Replication errors (tautomeric shifts, wobble base-pairing, strand slippage) - Spontaneous chemical changes (depurination, deamination) - Rates of spontaneous mutations vary in different organisms

Hermaphroditism

having both sex organs in one organism; or both gametes made in the same flower (C. elegans)

Sex-determining chromosomes are usually not homologous yet behave as...

homologs in meiosis

Barr Bodies

inactivated X chromosomes

Genome information may be beneficial for...

information about genetic disease, personalized medicine, questions about ancestry, etc.

Testis-Determining Factor was the object of...

intense research

CRISPR-Cas system

is a powerful genome editing tool (2020 Nobel prize in Chemistry!) - Can edit DNA genomes in bacteria, yeast, worms, plants, fruit flies, zebrafish, mice, rats, monkeys, humans (and many more) - Occurs naturally in bacteria and archaea to protect against invading DNA elements (bacteriophage, plasmids, etc)

Recombinant DNA technology

is a set of molecular techniques for locating, isolating, altering, and studying DNA segments

(cloning) Can then...

isolate plasmid from bacteria (now have much more than what you started with)

what is the purpose of cloning?

make many copies of the gene of interest, in a form that you can use for further manipulation and study

Nondisjunction can occur during _____.

meiosis

homologous chromosomes, but not sister chromatids, separate in ___________

meiosis I

To look for specific sequences, after running the gel, you can also transfer the DNA in the gel to a...

membrane and use a probe --> Labeled probe binds to (hybridizes with) any fragments with complementary sequences -This procedure is called a Southern blot

(genetic engineering) Common first step:

molecular work • Isolate gene of interest in a tube • Can then perform different manipulations • Put gene back into experimental animal

Restriction enzymes produced...

naturally by bacteria as a defense against viruses

3. More practice with necessary and sufficient a. Another real-life example: Consider two students and the relationship between studying for Exam 3 and final course grades. To answer if studying for exam 3 is necessary to earn a good grade, you have to "delete" the studying. • Student X doesn't study for exam 3. What happens? Student does not earn a good course grade;therefore, studying is ____________ to earn a good course grade. You don't know if studying is ___________ because it didn't happen. To answer if studying for exam 3 is sufficient to earn a good overall course grade, consider student Y who didn't study for exams the first time taking BIO 211, and "ADD" studying for exam 3 during second time taking BIO 211. • Student Y decides to study only for exam 3. What happens? Student Y does not earn a good course grade; therefore, studying for exam 3 was NOT __________ to earn a good grade in the BIO 211 course.

necessary sufficient sufficient

Equally important, mutations in DNA are the source of...

new alleles and provide genetic variation in populations, critical for evolution

Inversions

no gain or loss of genetic material, but may have position effects (gene moved to heterochromatin) or gene may break in half. -Do paracentric or pericentric inversions involve the centromere? Pericentric

Sex can be assigned to...

non-human animals

Crossing over involves the exchange of genetic information between...

non-sister chromatids (chromatids from different homologous chromosomes)

c. Sex testing and athletics. • Maria was born in 1961 and was a world class hurdler from Spain. Starting in 1968 the Olympics required female sex testing. She passed a sex test in 1983 ("certificate of femininity"). In 1985, she took another sex test which found that she was XY. • One of the tests Maria took was a Barr body test. How many Barr bodies did Maria have?

none

Translocations

nonreciprocal and reciprocal

(Connection between lab and lecture) what kind of mutation is che-3?

nonsense substitution

Proto-oncogenes

normally help cells pass through checkpoints, but only when conditions are correct

When p53 is mutated, DNA-damaged cells are...

not arrested in G1 and DNA repair does not take place.

Restriction digest

of plasmid + foreign DNA

How can scientists study genes?

often times use model systems. In model systems can manipulate genes as a way to learn about them

Dioecious

organism is either male or female (ex. humans, some plants)

Gender develops...

over time and can continue to change

What is the most commonly mutated gene in cancers?

p53 mutations (50% in total)

Most recognition sequences are _______________.

palindromic

(cloning) Put your DNA in a form that bacteria will copy:

plasmid

(cloning) Transform bacteria with...

plasmid carrying antibiotic resistance gene

Most frameshift mutations introduce...

premature stop codons, resulting in shortened (truncated) protein

Ras is a..

proto-oncogene

(Types of Substitution) Transition

purine replaced by a purine or pyrimidine with a pyrimidine

(Types of Substitution) Transversion

purine replaced by pyrimidine or pyrimidine replaced by purine

Human genome project spurred...

rapid development of DNA sequencing technology

Restriction enzymes (aka restriction endonucleases)

recognize specific DNA sequences and make double-stranded cuts at these sites (called restriction sites)

Meiosis I

reduction division; homologous chromosomes separate

Induced mutations

result from the influence of an extraneous factor, either natural or artificial § Two major types of inducer - Chemicals - Radiation

(genetic engineering) Manipulate specific genes of interest

reverse genetics

In all cancers, mutations that alter gene expression are...

seen

In anaphase, cohesin is broken down by...

separase, allowing sister chromatids to separate

Sequencing technology has also allowed...

sequencing of other organisms, including microbiome

Gender may or may not align with _______.

sex

In this class we will focus on ______, not _________.

sex not gender

(Sex determination in flies) Y chromosome does not matter for _________; but it is necessary to...

sex; make sperm!

In meiosis, cohesin is protected at the centromeres by...

shugoshin (Japanese for 'guardian spirit') during anaphase I

After crossing over...

sister chromatids are no longer identical

The breakdown of centromeric cohesin allows...

sister chromatids to separate in anaphase II of meiosis

Most cancer mutations are...

somatic; 1% are germ-line

Lyon hypothesis

states that within each XX cell, one of the two X chromosomes is randomly inactivated. question: are male cats calicos? no

(Induced Mutations: Radiation) If replication blocked, cell division...

stops and cells die - UV light kills bacteria - is an effective sterilizing agent

As the genetic material, DNA must be able to...

store, replicate, transmit and decode information

(p53 mutations) This failure to arrest DNA-damaged cells will be repeated in...

subsequent cell cycles permitting other mutations to accumulate, culminating in neoplastic transformation... tumor formation and cancer.

(SRY experiment) Does this experiment tell us whether SRY is necessary or sufficient for maleness?

sufficient

Restriction enzymes are named based on...

the bacterial species from which the enzyme was isolated

The effect of a substitution depends on...

the location of the mutation in the genome

(The Human Genome Project) Sequencing technologies have improved both...

the time and cost needed to sequence individual genomes

Transgenic mice are useful for some studies because...

they are more similar to humans than non-mammalian model organisms

How do mutations convert normal cells into malignant tumors?

through the process of those mutations

(genetic engineering) Random mutagenesis

to do a genetic screen (forward genetics) - we are doing this is lab now

--> transforming a purine into a different purine or a pyrimidine into a different pyrimidine is easier than...

transforming a purine into a pyrimidine, or vice versa

The "home run" experiment by Koopman et al. used _____________.

transgenic mice

An organism that has been permanently altered by the addition of a DNA sequence to its genome is said to be ______________, and the foreign DNA that it carries is called a __________.

transgenic; transgene

How many mutations are needed to cause cancer?

usually multiple mutations

a. Use the rules you wrote down to determine the sex of these flies: • A fruitfly is found that has three sex chromosomes (XXY) and three of each autosome. The sex of this fruitfly is _____ because the ratio of X-chromosomes to autosomes is ____.

• A fruitfly is found that has three sex chromosomes (XXY) and three of each autosome. The sex of this fruitfly is intersex because ratio is 2/3 (between 0.5 and 1.0). • A different fruitfly has three sex chromosomes (XXX) and two sets of autosomes. The sex of this fruitfly is metafemale because ratio is 1.5 (larger than 1.0)

Noncoding regions:

• Intergenic region (in between genes): no effect • Regulatory region (promoter, enhancer, etc.): it depends • Intron: no effect, unless it affects splicing

For each of the terms listed below, answer the following questions A. Is this cell found in plants, animals, or both? B. Male germ cell, female germ cell, or neither? C. Triploid cell (3n), diploid cell (2n) or haploid cell (n)? Terms • Microsporocyte • Spermatid • Oogonium • Megaspore • Spermatogonium • Ovum • Megasporocyte • Sperm • Endosperm

• Microsporocyte plant, male, diploid • Spermatid animal, male, haploid • Oogonium animal, female, diploid • Megaspore plant, female, haploid • Spermatogonium animal, male, diploid • Ovum animal, female, haploid • Megasporocyte plant, female, diploid • Sperm both, male, haploid • Endosperm plant, neither, triploid

The Transgenic Sry Experiment: How It Was Done?

• Nuclei of fertilized XX mouse eggs were injected with Sry gene, then the eggs were transplanted to surrogate mothers. • Sry gene randomly incorporated into a chromosome and was inherited in subsequent cell divisions. • Animals karyotyped after development to adult

Causes of Down Syndrome Most often occurs by nondisjunction (failure of chromosomes to separate) of Chr. 21 during meiosis; in theory could occur in either parent, but 95% of these trisomies have defective egg as source - why?

• People with ovaries are born with all of their eggs, so eggs start aging at birth - amazingly old cells! • Sperm is made continuously starting in puberty

Rb, a tumor suppressor gene regulates G1/S

• RB normally prevents DNA replication (S phase) • When cyclin/CDK is active, allows passage through G1/S checkpoint

questions often asked regarding reverse genetics

• What happens when the gene is removed? • What happens when the wild-type gene is added? • What happens when a mutant gene is added? • What happens when specific alterations are made?