Exam 3: What is a Gene? Part 2

Question 1

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

Answer 1

Biochemistry and genetics, not old at all, very new fields. Specifically research Alkaptonuria.

Question 2

Describe the symptoms of alkaptonuria.

Answer 2

Urine that turns black after exposure to air.

Urine contains excessive amounts of homogentisic acid.

Deposition of pigment in ears and eyes.

Question 3

How did Garrod establish that alkaptonuria was a genetic disorder?

Answer 3

Noticed rare in general populations, frequent in children of first-cousin marriages, displayed a pattern of recessive inheritance.

Question 4

What did Garrod mean by an inborn error of metabolism?

Answer 4

Missing or altered enzymes disrupted metabolic pathways and caused certain phenotypes

Question 5

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?)

Answer 5

He proposed that individuals lacked a specific enzyme due to genetic determination. On the pathway from A to D via A->B, B->C, and C->D in which each reaction is catalyzed by an enzyme. One of the enzymes is inactive and as a result one of the products builds up and the reaction pathway is never completed.

Homogentisate 1,2-dioxygenase
This enzyme acts upon
homogentisic acid
Without this enzyme,
homogentisic acid accumulates

Question 6

Describe Garrod’s one gene - one enzyme hypothesis.

Answer 6

Lack of a particular enzyme results in a particular phenotype and the enzyme lacking is due to a genetic defect. The connection between gene and phenotype involves enzymes, thus one gene-one enzyme.

Question 7

When was Garrod’s hypothesis verified?

Answer 7

50 years later

Question 8

How does alkaptonuria specifically work?

Answer 8

Homogentisic acid is an intermediate in the breakdown of two amino acids, phenylalanine and tyrosine. Alkapronurics lack the enzyme Homogentisate 1,2-dioxygenase which acts on homogentistic acid. Which results in an accumulation of homogentisic acid.

Question 9

What subfields of biology were George Beadle’s specialty? How old were these fields?

Answer 9

Biochemistry and genetics, about 50y old by this point.

Question 10

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?

Answer 10

Proposed that enzymes affect phenotypes. Mutations causing missing enzymes changed the phenotype. However the situation was difficult to evaluate due to the complexity of the organism.

Question 11

Together, Beadle and Tatum sought to better understand what?

Answer 11

The connection between genes and phenotypes.

Question 12

In what way is information encoded in a DNA molecule?

Answer 12

DNA encodes information through the order, or sequence, of the nucleotides along each strand. Each base—A, C, T, or G—can be considered as a letter in a four-letter alphabet that spells out biological messages in the chemical structure of the DNA

Question 13

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

Answer 13

No, the second strand does not encode additional information. The base sequence of the first strand dictates the base sequence of the second strand.

Question 14

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

Answer 14

They proposed the function of the second strand was a role in replication. That DNA replicates semi conservatively. Their prediction was accurate.

Question 15

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

Answer 15

DNA replication is semiconservative. Each strand in the double helix acts as a template for synthesis of a new, complementary strand

Question 16

Why is DNA replication termed semiconservative?

Answer 16

Two copies of the original DNA molecule are produced, each copy conserving (replicating) the information from one half of the original DNA molecule. Each copy contains one original strand and one newly synthesized strand.

Question 17

Describe the three 1950s models of DNA replication – Conservative, semi-conservative, and dispersive.

Answer 17

Conservative: one daughter cell is made (composed of copies of the parent cell) and the parent cell is fully conserved (made of the two original strands).

Semi-conservative: two daughter cells made each composed of one original strand and one complementary strand that is made.

Dispersive: the original DNA double helix breaks apart into fragments, and each fragment then serves as a template for a new DNA fragment

Question 18

Briefly describe the Meselson & Stahl experiment investigating DNA replication. What was their conclusion?

Answer 18

E.Coli was cultured for several generations with a presence of 15N. Used “heavy nitrogen” to label parent DNA.

Bacteria then transferred into a media containing only 14N. So newly synthesized DNA was lighter than the older DNA. Labeled with 14N.

Extracted DNA molecules were separated by density using gradient centrifugation. First generation had intermediate density while the second had equal low and intermediate density.

Results consistent with semi-conservative model.

Question 19

What forms of nitrogen were used in the Meselson & Stahl experiment? Why was this important to the experiment?

Answer 19

Heavy nitrogen, 15N. Important because 14N is the most prevalent isotope so the 15N cab be distinguished based on density.

Question 20

What type of organism is Neurospora crassa?

Answer 20

Fungi, type of bread mold.

Question 21

What features make Neurospora crassa a useful model organism?

Answer 21

Easy to grow on minimal media with vitamin biotin added.

Short sexual and asexual life cycles.

Haploid asexual life cycle can make genetic analysis more straightforward.

Question 22

Describe the asexual life cycle of Neurospora crassa.

Answer 22

Haploid asexual life cycle. Individuals have one copy of chromosome and one copy of each gene. Nothing gets masked so easy to see mutations when present.

Question 23

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

Answer 23

Few nutrient requirements and no sexual dimorphism since asexual. Haploidr resulting in limited mutation options and limited genetic makeup made for a much simpler study. Much easier to track mutations.

Question 24

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

Answer 24

No, humans only make half their amino acids; the rest are essential amino acids that must be met through dietary intake. However Neurospora do not have any essential amino acids, they can make all of theirs.

Question 25

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

Answer 25

Wild-type has very few nutritional requirements, sugar, salt, and vitamin biotin. Able to make all of its own amino acids and all vitamins except for biotin. auxotrophic mutants are unable to produce the amino acid arginine therefore it is a growth requirement for the mutants.

Question 26

Describe and compare arg+ and arg- cells.

Answer 26

arg+ are wild types who have the ability to make their own arginine amino acids. Arg- cannot make its own arginine amino acid, must live in an environment where arginine is supplied.

Question 27

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

Answer 27

They subjected Neurospora crassa to x-rays or UV radiation to increase mutations.

Question 28

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

Answer 28

Indirect selection: used when there is no media on which the mutant can grow and the parent cell cannot. e.g mutant requires a growth factor not required by the parent.

Direct selection: used when both the mutant and parent require the same growth factors. a mode of negative natural selection in which an extreme phenotype is favored over other phenotypes, causing the allele frequency to shift over time in the direction of that phenotype.

Question 29

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

Answer 29

1. fungi spread on the surface of plates. Diluted so isolated colonies formed. Plates are minimal media plus arginine plus biotin. Both arg- and arg + will grow.
2. Plates are incubated overnight. Deposited cells divide repeatedly, colonies formed.
3. Colonies blotted with sterile velvet.
4. Colonies transferred to second plate. Minimal media lacking arginine. Only arg + cells will grow, not arg- . Transfer cells to a new plate that’s minimal media with arginine.
5. Plates are incubated overnight.
6. Negative space on the media lacking arginine shows where arg- colonies are on the original plate. Tells you which colonies to pluck.

Question 30

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

Answer 30

No, they each contained different mutations that affected different parts of the arginine synthesis pathway. Same result “no arginine production” however the enzyme that was not produced varied mutation to mutation.

Question 31

After identifying numerous arg- mutants, how did Beadle and Tatum further refine the phenotypes of these mutants? What did they find?

Answer 31

They tested to see if any of the mutants could grow when provided with molecules similar to arginine. Resulted in 3 classes of mutants. Class I: can grow when supply with arginine, citrulline, or ornithine. Class II: can grow when supplied with arginine or citrulline. Class III: can grow when supplied with arginine only.

Question 32

What event converts an arg+ cell to an arg- cell? How many such events are necessary for such a conversion? Explain.

Answer 32

The deactivation of enzymes needed in the arginine production pathway. Only one event of deactivation is needed for such a conversion.

Question 33

How many mutations are most likely present in any given arg- cell? How do you know?

Answer 33

Likely only 1 since molecules similar to arginine can be provided and used by the mutated arg-.

Question 34

Describe the metabolic pathway by which arginine is synthesized from a precursor molecule, indicating where various enzymes are involved.

Answer 34

Enzyme A converts precursor to ornithine, enzyme B converts ornithine to citrulline, enzyme C converts citrulline to arginine.

Question 35

How similar are the molecules arginine, citrulline, and ornithine? Why is this the case?

Answer 35

Very similar, acts as precursors to the production of arginine.

Question 36

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

Answer 36

Class I: Enzyme A that converts precursor to ornithine is inhibited. But if given any precursor after that (arginine, citrulline, or ornithine) it can finish the pathway.

Class II: enzyme B that converts ornithine to citrulline is inhibited. Process stops at ornithine. But can use citrulline or arginine to continue the pathway.

Class III: Enzyme C that converts citrulline to arginine is inhibited. The process stops at citrulline. Can only use arginine, cannot conduct the pathway at all when given precursors.

Question 37

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

Answer 37

Similar findings of “one gene-one enzyme hypothesis”. Both found that a mutation stops a metabolic process somewhere around the way. If you change the mutation you change the gene and the enzyme affected.

Question 38

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

Answer 38

Arg- phenotype is heritable, daughter cells are arg-. Agreed with Garrods conclusion of “inborn error of metabolism”. They concluded that the “one gene-one enzyme hypothesis” is accurate.

Question 39

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

Answer 39

No not shared but they acknowledged him.

Question 40

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

Answer 40

Yes, they acknowledged Archibald Garrod when they received the award. Unlike many previous scientists who failed to acknowledge the work of other scientists who were fundamental to their own results.

Question 41

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

Answer 41

DNA is the genetic material not the proteins.

Question 42

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

Answer 42

Genes act via enzymes.

Question 43

DNA is the genetic material not the proteins.

&

Genes act via enzymes.

Combine the two conclusions above into a unified explanation.

Answer 43

Genes are units of DNA that direct the production or the activity of enzymes.

Question 44

Describe the various ways the one gene - one enzyme hypothesis was revised as we gained a deeper understanding of the structure and function of genes.

Answer 44

Enzymes are a subset of proteins; not all proteins are enzymes. One gene-> one protein

Some proteins possess multiple polypeptide chains; different polypeptides are encoded by different genes. One gene-> one polypeptide.

A given RNA may be spliced in multiple ways; different polypeptides can be produced. One gene-> one or more related polypeptides.

Some genes encode functional RNA molecules such as tRNA or rRNAs. One gene->one or more related polypeptides or a functional RNA molecule

Question 45

What is the modern definition of a gene?

Answer 45

A gene is a unit of DNA that serves as a blueprint for:
A protein, or
A polypeptide, or
A group of related polypeptides, or
A functional RNA molecule

Question 46

Which of the following features does NOT accurately describe wild type Neurospora crassa?

Fungus

Eukaryotic

Model organism

Requires arginine from its environment

Sexually reproducing

ALL of these accurately describe Neurospora crassa

Answer 46

Requires arginine from its environment

Question 47

Considering only the work of Griffith, Aver, Hersey & Chase, Beadle & Tatum, and Garrod, which of the following is the most complete supported statement?

DNA is transcribed into RNA

A gene is a unit of DNA that directs the synthesis of a polypeptide or functional RNA molecule

DNA is the genetic material

DNA directs the activity of enzymes

Genes act through enzumes

None of these statements are supported by the work of the listed scientists

Question 48

Which of the following is an accurate description of “natural theology?”

the study of the natural world without ties to the supernatural

the investigation of ultimate goals in evolution

using divine revelation to develop an understanding of god

the study of biology using purely empirical evidence

ALL these are accurate descriptions of natural theology

the argument for intelligent design

Question 49

Considering only the work of Griffith, Aver, Hersey & Chase, Beadle & Tatum, and Garrod, which of the following is the most complete supported statement?

Question options:

DNA directs the activity of enzymes

DNA is the genetic material

genes act through enzumes

none of these statements are supported by the work of the listed scientists

a gene is a unit of DNA that directs the synthesis of a polypeptide or functional RNA molecule

DNA is transcribed into RNA

Answer 49

DNA directs the activity of enzymes?