1

Biology Module B,

Anchor 2 (part 1)

Distance Learning during Covid-19

BROUGHER/HEMMINGER

2

Genetics Module B, Anchor 2, part 1

To Do List:

1. Peruse online resources 2. Review + highlight key concepts & vocabulary (pages 3-6 of this packet) 3. Answer questions (pages 7-10 of this packet) 4. Read enclosed article + complete article review page

Online Resources: Khan Academy https://www.khanacademy.org/science/high-school-biology/hs-classical-genetics Mr. Hemminger’s Website > Curriculum > Chapter 8 Genes and the Environment https://www.sasd.us/Page/4008 Punnett Square Virtual Lab http://www.glencoe.com/sites/common_assets/science/virtual_labs/E09/E09.html Saving the Tasmanian Devil Interactive https://www.yourgenome.org/interactives/saving-the-devil Heredity Overview Video https://www.youtube.com/watch?v=CBezq1fFUEA Genomics in the News (Coronavirus Spread Article) https://www.the-scientist.com/news-opinion/coronaviruss-genetics-hint-at-its-cryptic-spread-in-communities-67233 Songs of the chapter https://www.youtube.com/watch?v=9G2lvdQiSr4 https://www.youtube.com/watch?v=aCkMQWxPkSc

3

Key Concepts:

- An individual’s characteristics are determined by factors that are passed from one parental generation to the next.

- During gamete formation, the alleles for each gene segregate from each other so that each gamete carries only one allele for each gene.

- Punnett squares use mathematical probability to help predict the genotype and phenotype combinations in genetic crosses.

- The principle of independent assortment states that genes for different traits can segregate independently during the formation of gametes.

- Mendel’s principles of heredity, observed through patterns of inheritance, form the basis of modern genetics.

- Some alleles are neither dominant nor recessive. Many genes exist in several different forms and are therefore said to have multiple alleles. Many traits are produced by the interaction of several genes.

- Environmental conditions can affect gene expression and influence genetically determined traits. - The DNA that makes up genes must be capable of storing, copying, and transmitting the genetic

information in a cell. - DNA is a nucleic acid made up of nucleotides joined into long strands or chains by covalent bonds. - DNA polymerase is an enzyme that joins individual nucleotides to produce a new strand of DNA. - Replication in most prokaryotic cells starts from a single point and proceeds in both directions until the

entire chromosome is copied. - In eukaryotic cells, replication may begin at dozens or even hundreds of places on the DNA molecule,

proceeding in both directions until each chromosome is completely copied. - The main differences between DNA and RNA are that (1) the sugar in RNA is ribose instead of

deoxyribose; (2) RNA is generally single-stranded, not double-stranded; and (3) RNA contains uracil in place of thymine.

- In transcription, segments of DNA serve as templates to produce complementary RNA molecules. - The genetic code is read three “letters” at a time, so that each “word” is three bases long and

corresponds to a single amino acid. - Ribosomes use the sequences of RNA codons to assemble amino acids into polypeptide chains. - The central dogma of molecular biology is that information is transferred from DNA to RNA to protein. - Mutations are heritable changes in genetic information. - The effects of mutations on genes vary widely. Some have little or no effect; some produce beneficial

variations. Some negatively disrupt gene function. - Mutations often produce proteins with new or altered functions that can be useful to organisms in

different or changing environments. - Human genes follow the same Mendelian patterns of inheritance as the genes of other organisms.

Many human traits follow a pattern of simple dominance. The alleles of other human genes display codominant inheritance. Because the X and Y chromosomes determine sex, the genes located on them show a pattern of inheritance called sex-linkage.

- Changes in a gene’s DNA sequence can change proteins by altering their amino acid sequences, which may directly affect one’s phenotype.

- If nondisjunction occurs during meiosis, gametes with an abnormal number of chromosomes may result, leading to a disorder of chromosome numbers.

4

- Recombinant DNA technology – joining together DNA from 2 or more sources – makes it possible to change the genetic composition of living organisms.

- Transgenic organisms can be produced by the insertion of recombinant DNA into the genome of a host organism.

- Ideally, genetic modification could lead to better, less expensive, and more nutrition food as well as less harmful manufacturing processes.

- Recombinant DNA technology is advancing the prevention and treatment of disease. - DNA fingerprinting analyzes sections of DNA that vary widely from one individual to another.

Review – DNA Structure & Replication DNA replication is the molecular mechanism of inheritance. DNA replication occurs during the S phase of mitosis or meiosis. DNA Structure

• DNA is a polymer made from building blocks called nucleotides strung together.

• Each nucleotide consists of a phosphate group, a 5-carbon sugar and a nitrogenous base

• There are 4 nitrogenous bases: adenine (A), guanine (G), thymine (T), and cytosine (C)

• DNA is a double-helix – It contains 2 strands of DNA bonded together that run in opposite directions. The DNA double-helix has the sugar-phosphate backbones on the outside of the double helix and the nitrogenous bases on the inside.

• Complementary Base Pairing – The two strands of DNA are bound together by hydrogen bonds between the bases of the nucleotides. Due to their molecular structure, A allows pair with T, C allows pairs with G.

DNA Replication

• DNA replication is semi-conservative because one old strand if DNA is maintained (conserved) while a new strand is made from the template of the old strand.

• During replication, the double helix separates and each DNA strand serves as a template for a new DNA strand. The new strand is built by adding the complementary nucleotide (using base pairing rules) to the existing template strand.

• Genetic information is conserved during replication because the base pairing rules ensure that the new DNA is an exact copy of the original DNA.

• The genetic code is contained in the specific order of the four base pairs in DNA.

5

Basic rules of gene transmission and expression:

• Genes are elements of DNA that are responsible for observed traits. • In eukaryotes, genes are found in large linear chromosomes. • A chromosome is very long continuous DNA double-helix. • Humans have 23 pairs of chromosomes in somatic (body) cells. Each pair of chromosome represent

homologous chromosomes (one from mom and one from dad). • Diploid organisms (like humans) have two copies of each chromosome and, therefore, 2 copies of each

gene. • Each gene has a specific location on a chromosome. • The two copies of each gene can have a different nucleotide sequence in an organism. • These different versions of a gene are called alleles. Ex. – Attached (f) and free earlobes (F) are different

alleles of a gene. • Homozygous individual – has two copies (two alleles) of a gene that are identical. Ex. – FF • Heterozygous individual – has two different alleles for a gene. Ex – Ff • An organism’s genotype is the type of alleles is has (its genetic composition). • An organism’s phenotype is the appearance and physical expression of its genes.

6

Review – Patterns of Inheritance Genetics – the scientific study of heredity Patterns of Inheritance

• Dominant – A dominant allele is expressed in an organism regardless of the second allele (remember: eukaryotic organisms have 2 copies of each gene).

o Ex. - Free earlobes (F) are dominant to attached earlobes (F) o An individual whose genotype is Ff has a phenotype of free earlobes.

• Recessive – A recessive allele is only expressed if an organism has 2 recessive alleles for the gene. o Ex. – From the example above, a person can only have the phenotype of attached earlobes if they

have the genotype ff. • Co-dominance – Both alleles are fully expressed without one allele dominant over another.

o Ex. – For blood types, the A allele and B allele are codominant. This produces the AB blood group. (However, note that A and B are both dominant over O).

• Incomplete dominance – Both alleles are partially expressed; the resulting phenotype is in between the individual allele phenotypes.

o Ex. – A red snapdragon (R) crossed with a white snapdragon (W) produces pink (RW) offspring. • Sex-linked – Genes for some traits are located on the X chromosome and have no corresponding allele

on the Y chromosome. Since males are XY and only have 1 X chromosome, recessive sex-linked traits are more often observed in males.

o Ex. – color blindness, hemophilia • Polygenic – multiple genes affect the expression of a trait; allows for more variation in phenotypes.

o Ex. – skin color, height • Multiple alleles – several alleles (i.e., more than two) exist in a population and increases the number of

possible genotypes and phenotypes o Ex. – Three alleles exist for blood type – IA, IB and i. The different combination of these alleles

produces the four blood types A, B, AB and O. • Punnett Square – diagram showing the probabilities of the possible outcomes of a genetic cross

Vocabulary: Genetics fertilization allele principle of dominance Trait segregation hybrid gene Gamete probability genotype phenotype Homozygous heterozygous codominance Independent assortment Multiple allele polygenic trait base pairing Incomplete dominance Replication DNA polymerase nucleotides nucleic acid RNA messenger RNA ribosomal RNA RNA polymerase Transfer RNA transcription polypeptide genetic code Codon anticodon translation gene expression Biotechnology PCR genetic marker transgenic Recombinant DNA clone plasmid gene therapy DNA fingerprinting genome autosome sex-linked gene Sex chromosome nondisjunction

7

Basic Mendelian Genetics Questions: 1. Different forms of a gene are called:

A. hybrids B. dominant factors C. alleles D. recessive factors

2. Organisms that have two identical alleles for a particular trait are said to be:

A. hybrid B. heterozygous C. homozygous D. dominant

3. What is the difference between a dominant and recessive allele? 4. State the principle of dominance:

A. How does this explain the phenotype of heterozygous organisms?

B. According to this principle, under what conditions will an organism show a recessive phenotype? 5. State the principle of segregation:

How does this explain how two heterozygous organisms can produce homozygous offspring? 6. State the principle of independent assortment:

8

7. What is a punnett square? How are punnett squares used in genetics?

8. Show the cross between two guinea pigs. One is heterozygous for black color, the other is white. Record

the genotypic and phenotypic ratios of the offspring. Other Patterns of Inheritance Questions: 1. Discuss:

A. Codominance

B. Incomplete Dominance

C. Multiple Alleles

D. Polygenic Traits 2. Why do multiple alleles and polygenic traits produce many different phenotypes for a trait? 3. Can a trait show more than one inheritance pattern?

9

4. You would like to determine if a plant shows codominance or incomplete dominance. What type of cross

would you perform and why? Explain how you would know whether the gene involved showed co- or incomplete dominance.

5. What is the relationship between genes and the environment? DNA Structure Questions: 1. Thoroughly describe the structure of a DNA molecule. Include a visual to support your answer: 2. What are the base pairing rules? If the percentage of adenine in a sample goes up 5 %, what will happen to

the percentage of thymine? What will happen to the percentage of guanine? 3. What are some roles of DNA? Explain how the structure of DNA aids in each role. 4. What happens when a piece of DNA is missing?

A. Genetic information is stored B. Genetic information is transmitted C. Genetic information is lost D. Genetic information is copied

10

DNA Replication Questions: 1. Thoroughly describe the process of DNA replication. 2. Compare DNA replication in prokaryotes vs. eukaryotes. 3. What is base pairing and how is it involved in DNA replication? 4. When a DNA molecule is replicated, how do the new molecules compare to the original molecule? How

does replication ensure that this occurs?

W ABOVE: Scanning electronmicroscope image of SARS-CoV-2 (yellow) emerging from thesurface of human cells (pink)cultured in the lab. WIKIMEDIA,NIAID ROCKY MOUNTAINLABORATORIES (RML), US NIH

Coronavirus’s Genetics Hint at its Cryptic Spread inCommunitiesContact tracing and genetic testing reveal how SARS-CoV-2 circulated among individualsfor weeks, especially in the US, before being detected.

Ashley YeagerMar 6, 2020

hen Emma Hodcro! read that, seemingly out of nowhere, a rash of

cases of the novel coronavirus had popped up in Britain in late

January, she started collecting media reports on them, searching the articles

for clues as to how it had moved to the island nation. Early reports suggested

that a lone traveler from Singapore, who was unaware he was infected with

virus, had visited a French chalet for a few days and had spread the virus to

others at the ski resort. This intrigued Hodcro!, who is half British and a

postdoctoral researcher in evolutionary biologist Richard Neher’s lab at the

University of Basel in Switzerland, where she uses genetics to study and track diseases. She took notes on the

cases that were associated with the infected traveler. “At "rst, there wasn’t that much information and the

story was simple,” she tells The Scientist. But more and more cases kept appearing, and she found it hard to

keep track of who had traveled to which country and when they were diagnosed.

Hodcro! decided to generate an infographic showing the connections between the traveler from Singapore

and the other coronavirus cases emerging in Europe. “I thought, I’ll make an image and see if anyone else

"nds this useful,” she says. She posted the image on Twitter, and “somewhat unexpectedly, it got a lot of

attention,” she says. “People were de"nitely really, really interested in this. So I kept that image updated over

the next week or so.” As she updated it, the graphic showed that at least 21 people were exposed to the virus

at the ski resort the traveler from Singapore visited; 13 of those people ended up developing COVID-19, the

disease caused by the virus. A!er she’d "nished the preliminary work, a colleague of Hodcro! saw it and

suggested she write it up for publication. She posted the paper on February 26; the next day it appeared in

Swiss Medical Weekly.

Hodcro! talked with The Scientist about the work, how its conclusions have been supported by genetic

testing of viral strains from patients, and what it tells us about the spread of the virus, SARS-CoV-2, in other

countries.

The ScientistThe Scientist: What are the main takeaways from your paper?

Home / News & Opinion

Contact tracing showing the spread of SARS-CoV-2 in a particular cluster of patients in Europe.EMMA HODCROFT

Emma Hodcro!: Firstly, that it seems like so many people [at least 13] could be infected by a single person.

It seems like they were infected by the man who traveled from Singapore. So that’s quite a lot of forward

transmission on his part in a fairly short time period; he was only in France for about four days. Of course,

this could be some unusual event that doesn’t normally happen, but it lets us put an outer bound on what is

possible even if it is not common.

The other thing that’s surprising is that, according to the patient statement that he released, the focal patient

never had any symptoms. In his own words, he never felt sick. So he did all of this transmission without ever

having any indication that he was unwell or that he should be taking any precautions to modify his behavior.

It tells us that some infections might be from people who never even know that they’re sick.

Text continues below infographic

TS: Were the cases in this cluster severe or mild?

EH: As far as we can tell, no one from this cluster had severe symptoms. It seems like some people did have

some symptoms, but they were never serious. And that’s also interesting because it shows that if we didn't

know about this outbreak, it’s pretty likely that these people would have kind of written this o# as a bad cold

or the $u. None of them would have ended up going to hospital or signi"cantly changing their behavior.

And again, this indicates that it might be quite hard, and it is becoming quite hard, to contain this virus

because some people don't feel very unwell, such that they would change their behavior or go for testing.

TS: The number of cases has been skyrocketing in several countries, the US included. How doesyour work on this cluster connect with genetic data being reported on NextStrain.org about thisspike in cases?

EH: In the US, from the information available, it still doesn’t seem like the US has really ramped up testing.

We don’t know the number of tests that have been performed because it’s come down o# of the CDC

website, which is a little concerning. But at least the last reports that were given to us show the US was really

lagging behind most countries in the number of tests that it had done.

See “Coronavirus’s Genetics Reveal Its Global Travels”

A few days ago, the research group called the Seattle Flu Study, which is designed to take community

samples from random people who have any kind of cough, runny nose, or cold-like symptoms and look for

the $u—they pivoted and started testing some of the samples for coronavirus. They found a case in the

Seattle area and sequenced the viral genome of the infected person [posted on NextStrain] and showed it

links very closely with another case in the Seattle area that’s from mid-January. And so this strongly suggests

(though we don’t yet know for certain) that there has been ongoing undetected transmission in Seattle since

mid-January and wasn’t picked up because we weren’t looking for it. This has become clearer in the last few

days, as more cases and even deaths have been reported in Washington State. That tells us the virus hasn’t

just appeared in the last few days in the area.

Text continues below graphic

The viral genome of the !rst case in Washington (USA/WA1/2020) is identical to Fujian/8/2020. The genome of the virus from asecond case in Washington (USA/WA2/2020) is identical to the !rst Washington case, except it has three additional mutations.This suggests WA1 was a traveler from China bringing the virus to Snohomish County, Washington in mid-January, where thevirus circulated undetected for about !ve weeks, a timespan that explains why WA2 is so similar genetically, with a fewmutations. The graphic shows the connection to the other cases with viral sequences now available.NEXTSTRAIN.ORG

TS: How do the deaths indicate that the virus has been there for weeks?

EH: This virus causes respiratory illness, which can make you feel unwell for a few days and then you get

better or it can progress. If the illness progresses it can cause lung damage that makes the person more

susceptible to other illnesses, such as bacterial infection. This can be treated too and for many people that

treatment turns the course of the infection, but some don’t and the e#ort can essentially delay their death.

So the infection may have occurred weeks [before a person dies]. This is not something intrinsic to this

virus, however. With respiratory illness, it’s usually something that takes a substantial amount of infection

and lung damage before you succumb to it.

TS: Why is genetic tracing to link cases important?

EH: Sequencing can tell us a lot about what is happening with the virus right now. The Washington samples

are a perfect example. . . . Without having these genomes, we never would have seen this signal of ongoing

transmission, which we saw just before the case explosion in Washington. And on the $ip side we can tell

when cases are coming in from other countries. We have another genome from Washington State that’s

grouping with genomes that we know have a travel history to Italy—so it seems like this could be a case

where [an infected person] came back from Italy.

When you have a very small number of cases of a disease, you can do this just through epidemiological

contact tracing: you can go to everyone and ask questions and "nd out the connections between the cases. As

the case numbers scale up, this becomes very hard to do. With genetic sequencing, we can do this without

having to go and try and "gure out where everyone was at the time of infection. We’ve had an in$ux of

sequences from Brazil, Switzerland, Mexico, Scotland, Germany. These have clustered with sequences from

Italy and have a travel history from Italy and so from that we can show that Italy really is now exporting

cases around the world to multiple countries.

TS: How might public health o!cials use this information? Is it applicable to making decisionsabout containment or air travel?

EH: There’s been a lot of modeling, not only with genetics but epidemiologically in the last few weeks, and

we had pretty strong indications that circulation was wider than publicly thought. At the time, we did try to

some extent to get this message out to government health agencies and the public in general. I do think that

in the future, incorporating a little bit more of that scienti"c expertise perhaps into the public dialogue and

government decision-making could make a big di#erence. The earlier that you can act in an epidemic, you

have more e#ect you can have, because one person goes on to infect a few more people who go on to infect

a few more people. It’s much harder once that has gone up to 10 [infected] people, than if you can stop with

person one.

One thing I would note is that studies have shown that limiting transportation really doesn’t make much of

an impact for outbreaks. Quarantining particular cities, if they seem to be epicenters, can work as a

preventive measure, but as the epidemic scales up, you move past being able to contain it in this sense, [and]

what you end up doing is just disrupting supply routes, interrupting business, making all of these things

much harder.

Editor’s note: This interview has been edited for brevity.

Ashley Yeager is an associate editor at The Scientist. Email her at ayeager@the-scientist.com. Follow her on Twitter

@AshleyJYeager.

Keywords:

coronavirus, COVID-19, disease & medicine, genetic testing, genetics & genomics, infectious disease, News, public health, Q&A,SARS-CoV-2

Brougher 2020

Your NAME: Today’s DATE:

Supporting Idea #1:

Supporting Idea #2:

Author:

Source:

Title of the article:

Publish Date:

Supporting Idea #3:

Supporting Idea #4:

Outcome, ending, or future projections

from this article:

What questions do you have after reading and analyzing this article?

What is the main

point/idea in this article?

Vocabulary:List 3 words from the text that you think someone might

have trouble understanding. Look up and provide the definitions.

1)

2)

3)

The viral genome of the !rst case in Washington (USA/WA1/2020) is identical to Fujian/8/2020. The genome of the virus from asecond case in Washington (USA/WA2/2020) is identical to the !rst Washington case, except it has three additional mutations.This suggests WA1 was a traveler from China bringing the virus to Snohomish County, Washington in mid-January, where thevirus circulated undetected for about !ve weeks, a timespan that explains why WA2 is so similar genetically, with a fewmutations. The graphic shows the connection to the other cases with viral sequences now available.NEXTSTRAIN.ORG

TS: How do the deaths indicate that the virus has been there for weeks?

EH: This virus causes respiratory illness, which can make you feel unwell for a few days and then you get

better or it can progress. If the illness progresses it can cause lung damage that makes the person more

susceptible to other illnesses, such as bacterial infection. This can be treated too and for many people that

treatment turns the course of the infection, but some don’t and the e#ort can essentially delay their death.

So the infection may have occurred weeks [before a person dies]. This is not something intrinsic to this

virus, however. With respiratory illness, it’s usually something that takes a substantial amount of infection

and lung damage before you succumb to it.

TS: Why is genetic tracing to link cases important?

EH: Sequencing can tell us a lot about what is happening with the virus right now. The Washington samples

are a perfect example. . . . Without having these genomes, we never would have seen this signal of ongoing

transmission, which we saw just before the case explosion in Washington. And on the $ip side we can tell

when cases are coming in from other countries. We have another genome from Washington State that’s

grouping with genomes that we know have a travel history to Italy—so it seems like this could be a case

where [an infected person] came back from Italy.

When you have a very small number of cases of a disease, you can do this just through epidemiological

contact tracing: you can go to everyone and ask questions and "nd out the connections between the cases. As

the case numbers scale up, this becomes very hard to do. With genetic sequencing, we can do this without

having to go and try and "gure out where everyone was at the time of infection. We’ve had an in$ux of

sequences from Brazil, Switzerland, Mexico, Scotland, Germany. These have clustered with sequences from

Italy and have a travel history from Italy and so from that we can show that Italy really is now exporting

cases around the world to multiple countries.

TS: How might public health o!cials use this information? Is it applicable to making decisionsabout containment or air travel?

EH: There’s been a lot of modeling, not only with genetics but epidemiologically in the last few weeks, and

we had pretty strong indications that circulation was wider than publicly thought. At the time, we did try to

some extent to get this message out to government health agencies and the public in general. I do think that

in the future, incorporating a little bit more of that scienti"c expertise perhaps into the public dialogue and

government decision-making could make a big di#erence. The earlier that you can act in an epidemic, you

have more e#ect you can have, because one person goes on to infect a few more people who go on to infect

a few more people. It’s much harder once that has gone up to 10 [infected] people, than if you can stop with

person one.

One thing I would note is that studies have shown that limiting transportation really doesn’t make much of

an impact for outbreaks. Quarantining particular cities, if they seem to be epicenters, can work as a

preventive measure, but as the epidemic scales up, you move past being able to contain it in this sense, [and]

what you end up doing is just disrupting supply routes, interrupting business, making all of these things

much harder.

Editor’s note: This interview has been edited for brevity.

Ashley Yeager is an associate editor at The Scientist. Email her at ayeager@the-scientist.com. Follow her on Twitter

@AshleyJYeager.

Keywords:

coronavirus, COVID-19, disease & medicine, genetic testing, genetics & genomics, infectious disease, News, public health, Q&A,SARS-CoV-2

Brougher 2020

Your NAME: Today’s DATE:

Supporting Idea #1:

Supporting Idea #2:

Author:

Source:

Title of the article:

Publish Date:

Supporting Idea #3:

Supporting Idea #4:

Outcome, ending, or future projections

from this article:

What questions do you have after reading and analyzing this article?

What is the main

point/idea in this article?

Vocabulary:List 3 words from the text that you think someone might

have trouble understanding. Look up and provide the definitions.

1)

2)

3)