HW 1

Define genetics and explain how humans had an implicit understanding of genetics 10,000 years ago.

• Genetics, is the study of heredity and hereditary material. (Gregor Mendel)

• Domestication and selective breeding.

• Genetic, study of heredity and hereditary material

• Domestication and selective breeding

Define the idea of epigenesis. Who is credited with the modern explanation of this idea? Does the homunculus theory of heredity include epigenesis? Does Aristotle’s theory of heredity include epigenesis? Explain.

• Epigenesis, substances within the embryo differentiate into body tissues, rather than body tissues being preformed. 

• William Harvey is credited with the first modern explanation of epigenesis.

• No, the homunculus theory is saying that the sperm contains a miniature human which suggest that all the body tissues is preformed, but epigenesis is talking that the substances within the embryo differentiate into body tissues (new structure and function emerge over time) counter the idea of the organism being preform.

• Yes, the Aristotle is basically talking about the semen contains “vital heat” and will cook and shapes the menstrual blood into an embryo, suggest that function and structure emerge from an initially formless embryo, which align with epigenesis that new structure and function emerge over time rather than preformed entity. 

• Epigenesis, substance within the embryo differentiate into body tissues, rather than body tissues being performed

• William harvey

• No, homunculus theory → sperm contain miniature human

• Yes, Aristotle → semen cook and shape menstrual blood → embryo

What is germ plasm theory? How does it differ from the homunculus and ovist theories?

• Germ plasm theory suggests that ovaries and testes each contain full sets of genetic information, and that sperm and egg cells carry the information brought together in fertilization. (by August Weissman)

• Germ plasm theory suggests that genetic information is transmitted through germ cells which carry the hereditary material(germ plasm). Homunculus theory is a type of preformnist suggests a tiny fully formed human(homunculus) exists within a sperm cell. Ovist theory is very similar to the homunculus theory which suggests a perfectly formed miniature human is in the egg cell and will grow when it gets stimulated by the semen. 

  • Differ: germ plasm theory suggests epigenesis while homunculus theory and ovist theory don’t. Als the source of heredity is different

• Germ plasm theory → ovaries and testes contain genetic info → sperm and egg carry the info → brought together into fertilization.

• Germ plasm theory → germ contain genetic info and brought together into fertilization

• Homunculus theory → miniature human in sperm 

• Ovist theory → miniature human in egg 

What were the key contributions of Edmund Beecher Wilson and Archibal Garrod to genetics?

• Edmund Beecher Wilson proposes that “nuclein” is the hereditary material. And that inheritance may, perhaps, be affected by the physical transmission of a particular chemical compound from parent to offspring. (suggest heredity as a biochemical process)

• Archibald Garrod was the first to propose a link between genetics and metabolic disorders through his study of alkaptonuria.

  • proposed that Alkaptonuria followed the Mendelian excessive inheritance pattern and is the result of missing or malfunctioning enzymes in metabolic pathways. (defect in the breakdown of HGA)

• Edmund beecher wilson → nuclein is hereditary material

• Archibald Garrod → link genetic with metabolic disorders (alkaptonuria)

What are the two main ideas behind cell theory? Which scientists made these contributions?

• The two main ideas behind cell theory are that 1. All life is made of cells (Schleiden and Schwann) 2. All cells come from other cells (Rudolph Virchow) 

• All life is made of cells (Schleiden and schwann)

• All cells come from other cells (Rudolph Virchow)

What is the idea of spontaneous generation? Who refuted it?

• Spontaneous generation states that life will arise de novo from nonliving matter. 

• Pasteur refuted the idea.

• Spontaneous generation → life arise from nonliving matter

• Pasteur refuted the idea

Explain the “fixity of species” idea. How does Darwin’s theory of evolution by natural selection contradict this idea?

• The fixity of species mainly aligns with the idea of special creation, which states that all species have not changed since they were formed. Darwin suggested that species are not fixed, but rather, they change over time through natural selection.

• Fixity of species → all species have not change 

• Darwin → species are not fixed → change through natural selection.

 Outline the core argument of evolution by natural selection as 3 premises and 3 conclusions.

• Premise 1: species are variable, and some of this variation is heritable(can be passed from parent to offspring) 

• Premise 2: some of this heritable variation is meaningful in terms of survival and reproduction. 

• Premise 3: Species tend to “over-reproduce” or produce more offspring than the environment can support.

• Conclusion 1: There will be a “struggle for existence among offspring.

• Conclusion 2: Individuals with variations that are most suited to the environment will enjoy higher reproductive success than individuals with less favorable variations. 

• Conclusion 3: The population will change over time as adaptive traits accumulate.

Darwin believed in blending inheritance. What was Jenkin’s argument for this idea being incompatible with natural selection?

• Blending inheritance is when the offspring tend to have trait values near the average of the parents. 

• Fleeming Jenkin argues that adaptive evolution is not compatible with blending inheritance because it does not matter how advantageous a new variant is, it will tend to be diluted out each generation.

• Adaptive evolution is not compatible with blending inheritance → does not matter how advantageous a new variant is, it will tend to be diluted out each generation 

Mendel showed inheritance was “particulate”. Who championed Mendel’s ideas in the early 1900s?

• William Bateson was a supporter of the universality of Mendelian inheritance, 

  • All traits are fundamentally inherited(rules of Mendelian inheritance)

• William Bateson → supports universality of Mendelian inheritance. 

 Define chromosome and homologous pairs. How does the idea of homologous pairs relate to haploidy and diploidy?

• Chromosome is a large linear DNA molecule that contains genetic information. (made up of DNA and protein)

• Homologous pairs refer to a set of 2 chromosomes that are similar in shape, size, and genetic content; one is maternal, and the other is a paternal copy of a chromosome. 

• In haploidy, there are no homologous pairs as there is only one set of chromosomes, while in diploidy, homologous pairs are present, reflecting the contribution of both the maternal and paternal genetic information. 

• Chromosomes → large linear DNA contain genetic info.

• Homologous pairs → a set of 2 similar chromosome → one is maternal and the other is paternal

• Haploidy → no homologous pairs 

• Diploidy → homologous pairs present

Define gene and allele.

• Genes, are the functional unit of heredity

• Allele, is the alternative form of a gene

What are two key differences between mitosis and meiosis?

• Mitosis, is the replication and equal division of chromosomes into 2 daughter cells (Both 2 N)

• Meiosis, is 2 rounds of division yielding 4 haploid(having only one copy of each gene in the genome) gametes(reproductive cells, egg, and sperm).

• Key difference: mitosis produces 2 identical diploid daughter cells for growth and repair, while meiosis produces 4 genetically diverse haploid gametes for sexual reproduction, involving 2 rounds of division.

• Mitosis → 2 identical diploid daughter cell(2N) → growth and repair → 1 round division

• Meiosis → 4 genetically diverse haploid gametes(N) → sexual reproduction → 2 round division

 Name one of the scientists who developed the chromosomal theory of inheritance. What observations prompted this theory?

• Sutton and Boveri developed the chromosomal theory of inheritance(genetic information is encoded on chromosomes).

• The observation of the behavior of the chromosomes was exactly analogous to how Mendel described the behavior of genes during gamete formation. Which led to the hypothesizing of the chromosomal theory of inheritance.

• Sutton and Boveri 

• Behavior of the chromosome →(same) behavior of genes during gamete formation.

 How can Mendelian factors explain the inheritance of a continuous character? Name one scientist who demonstrated this idea.

• Herman Nilsson-Ehle and Edward East demonstrated the idea.

• Biometricians(scientists who specialize in the application of statistic methods to biological data) believe that continuous characters(traits or features in organisms that can take on the range of values) could not be explained by Mendelian inheritance, but later, one what work of Herman Nilsson-Ehle and Edward East showed that it can actually explain inheritance of continuous characters by multiple Mendelian Factor, (polygenic inheritance, multiple gene involve and the combination of alleles would determine the final phenotype)

• Herman Nilsson -Ehle and Edward East

• Multiple Mendelian Factor → multiple gene involved and combination of alleles → determine the phenotype

Define mutation. How do the concepts of “gene” and “allele” apply to the case of the white-eyed fly mutation?

• Mutation, is any heritable change. (source of all genetic variation)(Thomas Hunt Morgan)

• The gene for eye color is in the X chromosome, and there are 2 alleles which include the mutant allele white(r) and Red(R) alleles(the alternative forms of a gene that differ in DNA sequence and thus will affect the phenotype). A combination of 2 alleles will result in different Genotypes (the genetic makeup of an organism), which can be RR, Rr, rr. And of course, different genotypes will result in different Phenotypes ( the physical manifestation of genotypes).

• Mutation → any heritable change 

  • Gene for eye color → 2 alleles (R or r) → combination of 2 alleles → different genotype → different phenotype. 

Before DNA was shown to be the hereditary material, many hypothesized that proteins were the hereditary material. What is the logic behind this idea?

• Chromosomes are 50%~ proteins, 50% ~DNA, and since there are 20 different monomers in proteins(amino acids) which is more than 4 different monomers in DNA (Nucleotides), many hypothesized that proteins were the hereditary material due to greater sequence complexity.

• Experiments By Avery, McCarty, and MaCleod in Bacteria and the Hershey-Chase experiment, demonstrate hereditary material was DNA.

  • Proteins have 20 different monomers, DNA have 4 different monomers. → greater sequence complexity.

What are the three components of a nucleotide?

• Nucleotides(the basic unit of DNA and RNA) have 3 components, which is a phosphate, a ribose/deoxyribose sugar, a nitrogenous base.

  • Phosphate, ribose/deoxyribose sugar, nitrogenous base

How are nucleotides linked in a strand? Is this bond covalent or noncovalent? How are strands of DNA held together? Is this bond covalent or noncovalent?

• Nucleotides are linked in a strand by covalent Phosphodiester bonds. 

• Strands of DNA are held together by noncovalent hydrogen bonds. They exist as a complementary(A always pairs with T with 2 H bond, C always pairs with G with 3 H bond), antiparallel(one strand 5’ to 3’, another strand 3’ to 5’), duplex(double strand molecule).

• Nucleotide → by covalent phosphodiester bonds

• Strands of DNA → by noncovalent H bonds

Explain base complementarity. How does this relate to the mechanism of DNA replication? If 20% of a genome is A, what are the percentages of the other nucleotides?

• Base complementarity refers to specific pairings between nucleotide bases in DNA. A always pairs with T with a 2 H bond, and C always pairs with G with a 3 H bond. So if 20% of a genome is A, there will be another 20% as T, 30% as C, and 30% as G.

• The high specificity of the nucleotide pairing makes replication highly accurate, and it can replicate perfectly with just a single strand of DNA.

• Base complementarity → specific pairings between nucleotide bases in DNA. 

• 20 % T, 30% G 30% C

• High specificity → highly accurate replication.

Sketch a two-nucleotide antiparallel DNA duplex (4 nucleotides). A simple cartoon that shows 5’ 3’ polarity, complementary base pairs, the three components of a nucleotide, and an indication of H-bonds between strands is sufficient.

What are three structural differences between RNA and DNA?

• RNA has ribose instead of deoxyribose

• RNA has uracil instead of thymine

• RNA is typically single-stranded rather than double-helix structure. 

• RNA → ribose, uracil, single-stranded

• DNA → deoxyribose, thymine, double-helix 

  DNA contains the heredity information

• RNA carries the information to the ribosome

Diagram the central dogma of molecular biology. Label where transcription and translation occur.

• DNA→RNA→Protein

• Transcription from DNA to RNA, translation from RNA to Protein(use genetic code)

• DNA –(transcription)→ RNA –(translation)→ protein

What is the role of tRNAs in translation?

• tRNA is the molecule that “Translate” the language(genetic code) of DNA/RNA into the protein.

• tRNA → translate mRNA into protein by genetic code

 Trace the etiology of sickle cell disease using the central dogma. how does a DNA change in the hemoglobin gene lead to the sickle cell phenotype?

• Sickle cell disease is a genetic disorder that affects the hemoglobin(the protein in red blood cells responsible for carrying oxygen throughout the body), this disorder affects the beta subunit globin of hemoglobin, leading to red blood cells becoming fragile with sickle shape.

• The wrong DNA sequence leads to the wrong amino acid formation of hemoglobin. (translate into wrong amino acid)

• Wrong DNA sequence → wrong amino acid formation of hemoglobin.

. Describe gel electrophoresis. What does it assay with respect to DNA?

• Gel electrophoresis is a fundamental technique used in genetics research. It can differentiate the size of DNA or proteins by their migration pattern(larger molecules migrate more slowly than smaller ones).

• Gel electrophoresis (technique for separating DNA and protein based on size) → differentiate the size of DNA or protein by their migration pattern

Why can the study of model organisms usually be transferrable to our knowledge of human biology?

• Because all life shares a common ancestor (LUCA - Last Universal Common Ancestor). 

  • The central dogma and the genetic code evidence this

  • Usually used organisms that have fast generation times and can be genetically manipulated easily.

• All life shares a common ancestor → LUCA - last Universal Common ancestor.

Explain three pieces of evidence that exist for a single origin of life on earth. What might we expect to be different for each piece of evidence described if there were independent origins of life?

• All life is composed of a common set of chemical parts(DNA, RNA, amino acids) and structures(membrane-bound cells)

• All life contains genetic information that uses a nearly universal genetic code to specify how proteins are assembled.

• All life extracts energy from their environment

• All life replicates its genetic information in the same manner

• All life shares structural similarities among a fundamental set of genes

• All life evolves through gradual changes in their genetic information

Carl Woese and colleagues examined rDNA genes, common to all forms of life, and based on similarity, devised the three-domain model of life on Earth.