what is a Gene part 1

In what way is information encoded in a DNA molecule?

By the sequence of bases and amino acids.

What features make Neurospora crassa a useful model organism?

It's easy to grow because it requires sugar, salts, biotin. Uses sexual and asexual life cycles.

Erwin Chargaff was an American scientist. In what way is this fact is related to World War II?

It's related to WWII because he was a Jew that fled Germany when Hitler came to power.

What happened when Griffith injected heat-killed S-strain Streptococcus pneumoniae into a mouse? What can you conclude from this result? (Think carefully about this question.)

Mouse survived, so I can conclude that the S-strain can be killed with heat.

Was Rosalind Franklin recognized in any significant way for her contributions in elucidating the three-dimensional structure of DNA? Explain.

No, because she was not eligible for the Nobel prize and her work wasn't seen as significant.

When it was established that chromosomes carry the genetic material, did this mean that the genetic material had to be DNA? Explain.

No, most scientists considered protein to be a more likely candidate than DNA.

Would humans and Neurospora crassa agree as to which amino acids are essential? Explain.

No, some neurospora can make all its own amino acids, whereas humans can only make ½. But some Neurospora can't make amino acid Arginine which us humans can.

Does the second strand of a DNA molecule encode any information not already encoded by the first strand? Explain.

No, the 2nd strand doesn't encode additional info.

Were all the arg- mutants identified by Beadle and Tatum genetically identical? Explain.

No, they were different. All were defective in production of arginine.

What are Chargaff's Rules?

The numbers of A and T residues are always equal and the numbers of G and C residues are always equal.

When T2 bacteriophage was grown in the presence of radioactive sulfur, what viral component became radioactive? Why? Explain.

The protein became radioactive with sulfur because sulfur is present in proteins and not in DNA.

Describe the relationship between biology and natural theology during the time of Gregor Mendel.

The relationship between the 2 is that biology during Mendel's time was mainly a descriptive science and natural theology was developing an understanding of God through observations of nature rather than supposed "divine revelation"

Describe, in terms of the steps of the scientific method, the results of Avery's experiments prior to his incorporation of enzymatic steps.

The results before enzymatic steps were purifying S protein + R cells = no transformation, Purified S RNA + R cells = no transformation, Purified S DNA + R cells = transformation

What were the conclusions of Hershey and Chase regarding the nature of the genetic material?

They concluded that DNA is the genetic material and convinced the scientific community because they used a different system.

What did Hershey and Chase conclude to be the genetic material? In a single sentence, provide their rationale for this conclusion.

They concluded that DNA is the genetic material because they used a system different than Griffith and Avery so the scientific community was finally convinced.

What model organism did Morgan choose for his genetic studies?

He used fruit flies.

Describe two hypotheses that would account for the type of bacteria found during the mouse's autopsy.

1) this transformation only occurred in the presence of dead S bacteria 2) this transformation must have involved the uptake of genetic material from the dead S bacteria

What did Garrod mean by an inborn error of metabolism?

A genetically-determined lack of a specific enzyme.

What subfields of biology were Archibald Garrod's specialty? How old were these fields?

Alkaptonuria, but understood biochemistry and genetics. Biochemistry was established in 1967 and Genetics in mid 19th century.

Describe and compare arg+ and arg- cells.

Arg + = cells can produce their own arginine Arg- = cells require arginine and can't produce it.

Compare Beadle and Tatum's findings with respect to arginine synthesis to Garrod's findings with respect to alkaptonuria. How are they similar?

Beadle and Tatum found that arginine synthesis is possible if a product "downstream" of this "broken" step is added. Lack of any enzyme blocks arginine synthesis. This is similar to Garrod's findings because both findings involve enzymes and their involvement with phenotypes and genetic disorders.

What were Beadle and Tatum's conclusions? How did these conclusions relate to those of Garrod?

Beadle and Tatum found that the arg- phenotype is heritable as a result of a genetic defect and an enzyme is lacking in each mutant and lacking. These related to Garrod's findings as well because he found that the lack of an enzyme made urine black and discolored ears and eyes. Their findings were consistent with the "one gene, one enzyme" hypothesis.

What subfields of biology were George Beadle's specialty?

Biochemistry and Genetics.

What relevant and important changes and/or discoveries in biology had occurred between the time of Mendel's work and the rediscovery of his work? In what ways were these important?

Biology had become a quantitative, experimental science. The behavior of chromosomes during cell division had been studied and was now understood. Mendel's work was recognized.

Describe the symptoms of alkaptonuria.

Black urine and leads to deposition of pigment in ears and eyes.

In what way did Erwin Chargaff's work help Crick and Watson build an accurate three-dimensional model of DNA?

Chargaff's work helped because he analyzed DNA's base composition so that they could accurately build a 3D model of DNA and could pair the 4 bases accurately.

Relate the three classes or arg- mutants to the metabolic pathway for arginine synthesis.

Class 1 = arginine, citrulline, or ornithine Class 2 = arginine or citrulline Class 3 = arginine only Metabolic pathway for arginine = Precursor - ornithine - citrulline - arginine.

Describe, in detail, how Beadle and Tatum identified several arg- mutants.

Discovered through indirect selection for arg- mutants which is a very labor intensive process. None would grow on minimal media and all would grow on minimal media supplemented with amino acid arginine.

Approximately 29% of the nitrogenous bases from the DNA of the cyanobacterium Nostoc punctiforme are adenine. What are the relative frequencies of the other three nitrogenous bases?

G = 19.5% T = 30.3% C = 19.9%

Describe the growth requirements of wild-type Neurospora crassa. What is an auxotrophic mutant and what are its growth requirements?

Growth requirements = sugar, some salts, vitamin biotin. Auxotrophic mutant is a mutant that is unable to produce the amino acid Arginine.

Describe the asexual life cycle of Neurospora crassa.

Haploid asexual life cycle.

What model organism did Mendel choose for his genetic studies?

He chose to use the common garden pea.

What did Griffith conclude had occurred when he injected the mixture into the mouse? What term did he use to describe this phenomenon?

He concluded that there was a bacterial transformation which is a heritable change resulting from the uptake of genetic material from a bacterium's surroundings

Describe the nature of the DNA analyses performed by Erwin Chargaff.

He found that the base composition is consistent within species, but differs between species. This implies that DNA is somehow important and makes it a more credible candidate for the genetic material .

How did Avery interpret the results of his experiment? What was the key criticism of scientists that did not accept Avery's conclusion? How did Avery modify his experiment to address these criticisms?

He interpreted that DNA is likely the transforming agent, but the criticism was that some argued that the transforming agent could be a protein contaminant in the purified DNA. Avery modified his experiment by adding enzymes.

During which century did Gregor Mendel live and perform his genetic experiments?

He lived in the 1800s, so the 19th century.

What observations did Walter Sutton make regarding chromosomes and traits?

He noted that the behavior of chromosomes paralleled the segregation of traits and proposed the chromosome theory of inheritance.

What specific traits was Morgan following when he demonstrated that genes did, in fact, reside upon chromosomes?

He noted that transmission of the white-eyed phenotype correlates with sex determination.

What did Chargaff observe with respect to the relative abundance of each of the four different DNA bases? How did these relative abundances vary within a species? How did these relative abundances vary between species?

He observed that the numbers of A and T residues are always equal and that the numbers of G and C residues are always equal. It varies between species because of molecular unity and diversity which implied that DNA is important.

What basic biological concept was Beadle trying to uncover with is work on Drosophila eye color mutants? How successful was he? Why might this be the case?

He proposed that enzymes affect phenotypes. It was difficult using Drosophila due to the organism's complexity.

Describe Avery's reworked experiment in terms of the steps of the scientific method. What was his conclusion?

He took S DNA + R cells = transformation, S DNA + Protease + R cells = transformation, S DNA + DNase + R cells = no transformation. His conclusion was that the transforming agent was DNA and not protein and DNA is the genetic material

In what way did Gregor Mendel treat science differently than virtually all of his contemporaries?

He treated it differently because he experimented.

Describe an enzyme in terms of its structure, its function, and its specificity. What enzymes did Avery use in this experiment, and what were their specificities?

He used Protease and DNase. Protease = destroy any protein contaminants and DNase = destroy DNA but not protein contaminants

What was Thomas Hunt Morgan's initial reaction to Sutton's chromosome theory of inheritance? Did his view ever change? Explain.

He was initially skeptical of his theory but ultimately verified Sutton's theory.

In what way did Rosalind Franklin's work help Crick and Watson build an accurate three-dimensional model of DNA?

Her work helped them because Wilkens showed Watson Rosalind's x-ray diffraction without her consent as well as showed them her unpublished report.

Were Alfred Hershey and Martha Chase recognized in any significant way for their experiments demonstrating the identity of the genetic material? Explain.

Hershey received a Nobel Prize in 1969 but Chase did not share the prize and Hershey didn't even acknowledge her contributions in his acceptance speech.

What was the primary focus of Frederick Griffith's research with Streptococcus pneumoniae? Was he successful? Explain.

His focus was to attempt to develop a vaccine. He worked with 2 different strains (S strain and R strain)

Why do you think the presence of a glycocalyx would make these bacteria more pathogenic?

I think It's presence makes a bacteria more pathogenic because it's a macromolecule that's attached to the cell membrane. So it creates another barrier and is harder to kill/penetrate.

Why do you think Avery's conclusion was not widely accepted by the scientific community?

I think it was because evidence would have been more compelling if they found it in multiple biological systems and not a single system (which is what Avery and Griffith used) and scientist are not prone to accepting new ideas right away and don't like to be wrong.

Why do you think the importance of Mendel's work was not recognized during Mendel's lifetime?

I think it's because biology was mainly a descriptive science with no experiments and the behavior of chromosomes during cell division had not been studied.

Why do you think the conclusions of Hershey and Chase were accepted by the scientific community much more quickly than the results of Griffith or Avery?

I think they accepted it much more quickly because they used a system different than Griffith and Avery.

How did Garrod establish that alkaptonuria was a genetic disorder?

It was rare in populations, frequent in children of 1st cousin marriages, and displayed recessive pattern of inheritance.

How was Avery's experiment like Griffith's?

It was similar because he also worked with S protein to study transformation. He also focused on DNA, RNA, and Protein.

What was it about this experiment that suggested that DNA was a more likely candidate for the genetic material that protein?

It was that since the genetic material survived extreme heat, so Griffith reasoned that DNA was a more likely candidate than protein.

When was Mendel's work rediscovered?

In 1900.

When did Oswald Avery investigate bacterial transformation, as compared to Frederick Griffith?

In 1944 and Frederick Griffith studied in 1928.

Describe indirect selection and direct selection, comparing each to the other.

Indirect = occurs when the bacteria are cultured in conditions where the growth of the mutant is different from the growth of the wild type. Direct = occurs when the bacteria are cultured in conditions where only the mutant will grow

How did Avery's experiment differ from Griffith's?

It differed because he purified the S DNA which suggested that DNA is the transforming agent.

In a single sentence, describe the process of X-ray crystallography in basic terms.

It examines a sample in crystalline state and are examined by X-ray beam.

What type of organism is Neurospora crassa?

It is a bread mold.

What is a glycocalyx? What is the connection between a glycocalyx and the genetic material?

It is a highly charged layer of membrane-bound biological macromolecules attached to a cell membrane. It's involved in the development and progression of many diseases. The connection is that possessing or not possessing a glycocalyx determines if it's lethal or harmless.

What is a radioisotope? What radioisotopes were used in Hershey and Chase's blender experiment? Why were they used?

It is a radioactive isotope of an element. Hershey and Chase used S-labeled phage and P-labeled phage.

What is a bacteriophage?

It is a virus that infects E. coli

What is a model organism? Why are model organisms important to scientific investigation?

It is an amenable to manipulation and study and the findings can be applied to numerous other species.

In a single sentence, describe Walter Sutton's chromosome theory of inheritance. Please include his justification for this idea within this sentence.

It is that chromosomes contain the genetic material and genes reside on chromosomes .

Explain why a viral infection must constitute a genetic reprogramming.

It must constitute a genetic reprogramming because the cell is converted into a virus-producing factory

What was revealed by an autopsy of the mouse described in the previous question?

It showed that living S cells are recovered from the blood and that the living R cells must have somehow been transformed into S cells.

What was Rosalind Franklin's research focus?

It was analyzing DNA through X-ray crystallography.

How was it demonstrated that the R and S phenotypes of Streptococcus pneumoniae were genetically determined?

It was demonstrated by injecting bacteria into mice. The living S cells (experimental control) = mouse died, the living R cells = mouse survived. The heat-killed S cells = mouse survived.

Describe the structure of T2 bacteriophage.

It's comprised of DNA and protein.

Describe the three key differences between the S strain and the R strain of Streptococcus pneumoniae. Which of these differences are microscopic and which are macroscopic?

S strain = smooth appearance, cells possess a glycocalyx, virulent (lethal) R strain = rough appearance, cells lack a glycocalyx, avirulent (harmless)

What features of DNA's three-dimensional structure did Rosalind Franklin infer from her X-ray crystallography images?

She inferred that the big helix is in several chains, phosphates on the outside, phosphate-phosphate inter-helical bonds disrupted by water. Phosphate links available to proteins.

Did Mendel's discovery of the particulate nature of inheritance bring humankind closer to knowing everything there is to know? Explain.

Somewhat, this is because it raised 2 questions that took a while to be answered, but it provided a framework for our understanding of inheritance patterns

Using whatever combination of words and pictures you desire, describe the three-dimensional structure of DNA.

The 2 strands are antiparallel (parallel but point in opposite orientations) and it's double stranded.

When T2 bacteriophage was grown in the presence of radioactive phosphorus, what viral component became radioactive? Why? Explain.

The DNA became radioactive with phosphorus because phosphorus is abundant in DNA and not in proteins.

In basic terms, describe the composition of a chromosome. What different types of molecules are present within this structure?

The composition of a chromosome contains the genetic material and consists of large amounts of DNA and protein.

What were the conclusions of Garrod, Beadle, and Tatum regarding the connection between genes and phenotypes?

The conclusions were that they all concluded that the lack of an enzyme leads to a mutation and blocks arginine synthesis. They also concluded that the lack of an enzyme coincides with phenotype.

Together, Beadle and Tatum sought to better understand what?

The connection between genes and phenotypes.

In a sentence or two, explain the basic mechanism of DNA replication.

The mechanism is that DNA double-helix unzips and is copied during replication. Hydrogen bonds connecting the 2 strands are relatively easily broken "missing" complementary bases are added.

What happened when Griffith mixed live R-strain Streptococcus pneumoniae with heat-killed S-strain Streptococcus pneumoniae, and injected this mixture into a mouse? What can you conclude from this result?

The mouse died. I can conclude that living S cells must be recovered from the blood.

What happened when Griffith injected live S-strain Streptococcus pneumoniae into a mouse? What can you conclude from this result?

The mouse died. I can conclude that this is due to the main difference of possessing a glycocalyx whereas the R-strain does not. So I can conclude that the S-strain is lethal.

What happened when Griffith injected live R-strain Streptococcus pneumoniae into a mouse? What can you conclude from this result?

The mouse lived. I can conclude that the R-strain doesn't kill due to not possessing a glycocalyx.

The Hershey-Chase blender experiment consisted of two parallel experiments, testing a pair of parallel hypotheses. Describe each hypothesis/experiment in terms of the scientific method. Include the results and conclusions in your description.

They conducted a parallel experiment with S -labled phage and P-labled phage. 1st, they infected E. coli with radiolabeled phage, one with S-labled phage (labeled protein) and one with P-labled phage (labeled DNA). After establishing an infection, they used a blender to remove phage parts loosely associated with the bacterial surface. They separated the cells from the liquid with a centrifuge and the portion of the virus not inside cells remained liquid. They measured radioactivity in pellet and liquid. (radioactive sulfur was found in liquid because protein didn't enter cell) and Radioactive phosphorus was found in pellet (DNA didn't enter the cell).

How may experiments did Crick and Watson perform in their quest to determine DNA's three-dimensional structure?

They did no actual experiments of their own but relied on others' work.

Garrod proposed that the genetic disorder alkaptonuria was due to a metabolic defect. What was the nature of this metabolic defect? (What was missing or nonfunctional in people with alkaptonuria?)

They lacked an enzyme necessary for protein to breakdown and resulted in the accumulation of a chemical that darkens urine.

What did Crick and Watson propose regarding the function of DNA's second strand? Was this prediction accurate?

They proposed that the 2nd strand exists because of replication, yes this was accurate.

When Beadle and Tatum received the Nobel Prize for their work, was it shared with Garrod? Why or why not?

They received the award in 1958 and did not share it with Garrod but they acknowledged him when they received the award.

What did Chargaff's observations suggest regarding DNA's three-dimensional structure?

They suggested a relationship between A & T and between G & C.

In what way did Chargaff's observations suggest that DNA is likely to be an important component of a cell?

They suggested it because he analyzed the base compositions of DNA in a variety of organisms and found that the base composition is consistent within species but differs between species.

In what important way are Neurospora crassa and Drosophila melanogaster different in terms of their genetics? Why is this important?

They're different because Drosophila is difficult due to the organism's complexity but Neurospora is easy to grow. It's important for experimenting with.

In a single sentence, describe Mendel's particulate nature of inheritance, focusing on the importance of the term particulate in his findings.

This is his published work showing that heritable traits resulted from discrete physical particles called "genes" and that characteristics are passed from one generation to the next through transmission of genes. The importance provided the basis for our modern understanding of heredity.

Describe Garrod's one gene - one enzyme hypothesis.

This means that the connection between gene and missing or altered enzymes disrupted metabolic pathways and caused certain phenotypes.

Why is DNA replication termed semiconservative?

This name comes from the fact that semiconservative replication would produce 2 copies that contained 1 of the original strands of DNA and 1 new strand.

Beadle and Tatum searched for rare auxotrophic mutants. By what means did they enhance the mutation rate?

Through permissive media and restrictive media. Permissive = allows the growth of wild-type and mutant cells Restrictive = allows only the growth of wild-type cells

Was Maurice Wilkins recognized in any significant way for his minimal contributions in elucidating the three-dimensional structure of DNA? Explain.

Yes, he shared the Nobel prize with Watson and Crick. Wilkens also used x-ray crystallography to try to discern DNA's 3D structure.

Was Thomas Hunt Morgan recognized in any significant way for his experiments demonstrating the accuracy of the chromosome theory of inheritance? Explain.

Yes, he won the Nobel Prize in 1933.

When was Garrod's hypothesis verified?

Yes, his proposal as demonstrated by other researches in 1941 (George Beadle and Edward Tatum).

Did Beadle and Tatum acknowledge the work of Garrod? How does this compare to the work of Crick, Watson, and Franklin?

Yes, this does not compare to Watson, Crick, and Franklin because Watson and Crick did not recognize Franklin.