Description
Study Guide
Questions
1. PPT 15, Developmental genetics 4/3/19
a. Slide 1
i. List some things the Hox gene is believed to be responsible for: ii. _____________ are the organism of choice in analyzing genes’ relation with early development
b. Slide 3: What are the steps, in order, of how a cell goes from unspecialized to specialized? What makes each step unique?
c. Slide 6:
i. What are the stages of embryonic development in drosophila, and what makes each stage unique?
ii. True or false: If one of the T1, T2, and T3 segments is formed incorrectly, the function of the overall thorax doesn’t change.
d. Slide 7:
i. What is the general order of development stages for an
organism?:
ii. Which stage do drosophila not experience in development?
iii. True or false: zygotic effect genes are transcribed in an embryo before maternal effect genes are transcribed.
e. Slide 8: _____________________ is used to mutagenize (create mutations in) flies. This is known as a __________ strategy
f. Slide 9
i. True or false: In drosophila, maternal-effect genes are
transcribed before zygotic genes, which are transcribed before homeotic genes
ii. List the groups of maternal-effect genes in drosophila:
iii. List the types of zygotic genes in drosophila in the order that they are transcribed:
Don't forget about the age old question of What is the full meaning of lawn?
We also discuss several other topics like What is an example of an oligopoly?
g. Slide 10: Name the 4 possible phenotypic outcomes of the gap gene in drosophila:
h. Slide 11: true or false: The wild-type phenotype of the pair-rule gene has fewer, larger segments than the mutant type.
i. Slide 12: true or false: the wild-type phenotype of the segment polarity gene is visibly more straight than the mutants.
j. Slide 13: The runt gene in mice is ______. The runt gene in humans is ______
2. PPT 18, Population and Evolutionary Genetics
a. Slide 4 4/5/19
i. True or false: Humans, despite different appearances and
regions of ancestry, are all the same species
ii. _________________ is an example of artificial selection We also discuss several other topics like What is the difference between slander libel and defamation?
If you want to learn more check out What is the meaning of binary relation in the context of discrete mathematics?
b. 4/8/19
i. Slide 8: List the conditions necessary for Hardy-Weinberg
equilibrium:
ii. Slide 12: list the necessary conditions for natural selection
iii. Slide 13: Selection favoring dark beetles over intermediate and light colored beetles is an example of __________ selection
iv. Slide 14: Selection favoring intermediate colored beetles over light and dark beetles is an example of __________ selection
v. Slide 15: Selection favoring light and dark beetles over
intermediate colored beetles is an example of __________
selection
vi. Slide 16: True or false: if a mutation appears in an organism within a large population, the effect will be large.
vii. Slide 17: Migration creates gene ______
viii. Slide 18: The founder effect, genetic bottleneck, and some other random changes in allele frequencies, in small populations, are forms of genetic ______
c. 4/10/19 Don't forget about the age old question of What is an example of conceptualization?
i. Slide 19:
1. For 2 organisms to be of the same species, they must be
able to produce offspring with certain qualities: list and
define them
2. True or false: Nonrandom mating changes the allele
frequency within a population.
3. ____________________ is organisms preferring similar
phenotypes in mates
4. ____________________ is organisms preferring dissimilar
phenotypes in mates We also discuss several other topics like Describe bronsted-lowry acids and bases as proton acceptors.
5. The meaning of inbreeding is
________________________________
ii. Slide 20: True or false: populations of organisms can be found in nature, that stay in Hardy-Weinberg equilibrium.
iii. Slide 21: What do mainstream biologists observe, to determine whether 2 populations are distinct species, and that speciation has occurred in between them?
iv. What are the 2 main categories of reproductive isolation? v. Slide 22: List and describe the types of _____1_____ reproductive isolation
vi. Slide 23: list and describe the types of ______2_____ reproductive isolation
3. PPT 16, Recombinant DNA Technology
a. 4/10/19
i. What are 2 ways to associate a gene to a function?
ii. Slide 3: True or false: there is a colinear relationship between chromosomal location of homeotic genes, and the spatial
pattern in the embryo.
iii. Slide 4: List and describe the 2 clusters of homeotic selector genes on chromosome 3 in drosophila
iv. Slide 5: an altered expression of the _____ gene in drosophila causes the head to be more similar to a thoracic segment than it’s supposed to be. It even causes legs to appear at the head
v. Slide 6: A mutation of the ____ gene leads to 4 wings and 0 balance halteres in drosophila
vi. Slide 7: humans and other vertebrates have how many ___ Hox gene clusters
b. 4/12/19
i. Slide 8: List and describe the effects of well-known Hox gene mutations in humans
ii. In flowers of plants, there are 3 classes of homeotic genes affecting different organs. List the classes and the organs they affect
iii. Slide 12: In embryonic development, cell-cell communication plays an important role. List the parts of a receiving cell, and steps when appropriate, involved in a signal transduction pathway, in the order that they receive a signal
iv. Slide 14: Define recombinant DNA:
v. Slide 15: In order for restriction enzymes to cut DNA, they must detect recognition sequences
1. How many nucleotides usually make up a recognition sequence?
2. Once the DNA is cut, the cut ends can be 1 of 2 notable shapes. List and describe them:
vi. Summarize the most popularly discussed way that a segment of DNA can be copied:
c. 4/15/19
i. Slide 14
1. Define transgenic animals:
2. What is a popular example of transgenic animals?:
ii. Slide 17: List and describe the properties of vectors
iii. Slide 18: What's the purpose of growing bacteria cells in the presence of ampicillin or other antibiotics?
iv. Slide 19:
1. Define genomic library:
2. Define complementary DNA (cDNA) library:
v. Slide 20
1. Why do cleaved DNA fragments and cleaved vectors meet and bond well when scientists are using them to create
plasmids?
2. What most notably makes starting with RNA different from starting with DNA in the process of DNA recombination? vi. Slide 21
1. Summarize the PCR process used to amplify DNA:
2. True or false: the PCR perfectly produces exact copies of DNA.
3. List the ideal temperatures for the following steps in the
PCR
a. Denaturation:
b. Primer Annealing:
c. Primer extension:
vii. Slide 22: A modified nucleotide that can’t form phosphodiester (adjacent, not across) bonds and is called a _________________
viii. Slide 23:
1. If a segment of DNA is inserted into an animal instead of a
bacteria host, the result is ______________
2. Define knockout animals:
4. PPT 17, Genomics, Transcriptomics, and Bioinformatics
a. Slide 4: “# of genes” is referring to the amount of DNA that is actually involved in making proteins, rather than the entire genome. Roughly what percent of DNA in most organisms is responsible for making proteins, and what is the remaining percent that is regulatory,
noncoding, and otherwise irrelevant to making proteins?
b. Slide 7: Define the following
i. Genomics:
ii. Transcriptomics:
iii. Proteomics:
iv. Bioinformatics:
c. Humans and mice are genetically ____% similar
Answers
5. PPT 15, Developmental genetics 4/3/19
a. Slide 1
i. List some things the Hox gene is believed to be responsible for: body form/structure. Pattern maintenance. Turning
invertebrates into vertebrates.
ii. Drosophila are the organism of choice in analyzing genes’
relation with early development
b. Slide 3: What are the steps, in order, of how a cell goes from unspecialized to specialized? What makes each step unique?
i. Specification: long known to be reversible change
ii. Determination: mostly irreversible until recent tech
developments. This step determines the general
category the cell will fall into, but not more specific type and function
iii. Proliferation: cell number increase
iv. Differentiation: morphological, chemical, functional
specialization
c. Slide 6:
i. What are the stages of embryonic development in drosophila, and what makes each stage unique?
1. Initial diploid (2n) zygote stage: 1 nucleus only
2. Syncytium stage: zygote has many nuclei
duplicated from the initial 1
3. Blastula: roughly 100-cell stage. The blastula
develops a blastoderm, which is a lining of cells at
the surface, which serves as skin until the next
developmental stage
4. Embryo stage: segmentation is established
ii. True or false: If one of the T1, T2, and T3 segments is formed incorrectly, the function of the overall thorax doesn’t change. If one of the segments is formed incorrectly, the whole
thorax functions oddly
d. Slide 7:
i. What is the general order of development stages for an
organism?: zygote, embryo, fetus.
ii. Which stage do drosophila not experience in development? Drosophila don’t have a fetus stage.
iii. True or false: zygotic effect genes are transcribed in an embryo before maternal effect genes are transcribed. Maternal-effect genes are transcribed in an egg before fertilization.
Zygotic effect genes are transcribed after fertilization, in response to maternal-effect genes
e. Slide 8: Ethylmethane Sulfonate (EMS) is used to mutagenize (create mutations in) flies. This is known as a screen strategy f. Slide 9
i. True or false: In drosophila, maternal-effect genes are
transcribed before zygotic genes, which are transcribed before homeotic genes
ii. List the groups of maternal-effect genes in drosophila: Anterior group, posterior group, terminal group
iii. List the types of zygotic genes in drosophila in the order that they are transcribed: Gap, pair-rule, segment polarity
g. Slide 10: Name the 4 possible phenotypic outcomes of the gap gene in drosophila: wild type, Kruppel, Hunchback, Knirps
h. Slide 11: true or false: The wild-type phenotype of the pair-rule gene has fewer, larger segments than the mutant type. The mutant phenotype of the pair-rule gene has fewer, larger segments than the wild type
i. Slide 12: true or false: the wild-type phenotype of the segment polarity gene is visibly more straight than the mutants.
j. Slide 13: The runt gene in mice is Cbfa1. The runt gene in humans is RUNX2
6. PPT 18, Population and Evolutionary Genetics
a. Slide 4 4/5/19
i. True or false: Humans, despite different appearances and regions of ancestry, are all the same species
ii. Wild mustard is an example of artificial selection that has led to cauliflower, broccoli, cabbage, among other well
known greens
b. 4/8/19
i. Slide 8: List the conditions necessary for Hardy-Weinberg equilibrium: No natural selection, no mutation, no
migration, large population, and random mating.
ii. Slide 12: list the necessary conditions for natural selection 1. Individuals exhibit phenotypic variation
2. Phenotypic variations are heritable
3. More offspring are produced than can survive
4. Individuals with particular phenotypes survive better and reproduce more
iii. Slide 13: Selection favoring dark beetles over intermediate and light colored beetles is an example of directional selection
iv. Slide 14: Selection favoring intermediate colored beetles over light and dark beetles is an example of stabilizing selection v. Slide 15: Selection favoring light and dark beetles over intermediate colored beetles is an example of disruptive selection
vi. Slide 16: True or false: if a mutation appears in an organism within a large population, the effect will be large. If a mutation appears in an organism within a large population, the effect will be small. If a mutation appears in an organism within a small population, the effect will be large.
vii. Slide 17: Migration creates gene flow
viii. Slide 18: The founder effect, genetic bottleneck, and some other random changes in allele frequencies, in small populations, are forms of genetic drift
c. 4/10/19
i. Slide 19:
1. For 2 organisms to be of the same species, they must be able to produce offspring with certain qualities: list and
define them
a. Viability: capability to survive
b. Fertility: capability to reproduce
2. True or false: Nonrandom mating changes the allele frequency within a population. Nonrandom mating
changes the genotype frequency, but not the allele frequency, within a population.
3. Positive assortive mating is organisms preferring similar phenotypes in mates
4. Negative assortive mating is organisms preferring dissimilar phenotypes in mates
5. The meaning of inbreeding is when mating happens between individuals who are more closely related
to each other than any 2 random individuals in a
population
ii. Slide 20: True or false: populations of organisms can be found in nature, that stay in Hardy-Weinberg equilibrium. There is no existing ideal population, that stays in Hardy-Weinberg equilibrium, to our knowledge
iii. Slide 21: What do mainstream biologists observe, to determine whether 2 populations are distinct species, and that speciation has occurred in between them? Reproductive isolation
iv. What are the 2 main categories of reproductive isolation? Prezygotic and postzygotic isolation
v. Slide 22: List and describe the types of prezygotic reproductive isolation
1. Ecological: habitat differences. Desired or needed
environments are different
2. Mechanical: orientation of different snails makes it difficult
3. Behavioral: courtship rituals. Singing/dancing one
way or another
4. Temporal: morning vs afternoon, spring vs fall
5. Gametic: sperm and egg could come together but
simply cannot make a zygote for other reasons
vi. Slide 23: list and describe the types of postzygotic reproductive isolation
1. Hybrid inviability: hybrid dies
2. Hybrid sterility: hybrid isn’t fertile. Example: mule
3. Hybrid breakdown: hybrid success decreases with
successive generations
7. PPT 16, Recombinant DNA Technology
a. 4/10/19
i. What are 2 ways to associate a gene to a function?
1. Take a gene away and observe change in function.
This is known as knockout
2. Add a gene and observe change in function
ii. Slide 3: True or false: there is a colinear relationship between chromosomal location of homeotic genes, and the spatial
pattern in the embryo.
iii. Slide 4: List and describe the 2 clusters of homeotic selector genes on chromosome 3 in drosophila
1. Antennapedia complex (ANT-C): relates to the head and 1st 2 thoracic segments (T1 and T2).
2. Bithorax complex (BX-C): relates to the posterior of T2 and T3, and the abdominal segments
iv. Slide 5: an altered expression of the Antp gene in drosophila causes the head to be more similar to a thoracic segment than it’s supposed to be. It even causes legs to appear at the head
v. Slide 6: A mutation of the Ubx gene leads to 4 wings and 0 balance halteres in drosophila
vi. Slide 7: humans and other vertebrates have 4 Hox gene clusters
b. 4/12/19
i. Slide 8: List and describe the effects of well-known Hox gene mutations
1. HOXA2: abnormal ears
2. HOXB1: abnormal mouth shape
3. HOXD13: abnormal toes on feet
ii. In flowers of plants, there are 3 classes of homeotic genes affecting different organs. List the classes and the organs they affect
1. Class A: sepals and petals
2. Class B: petals and stamen
3. Class C: stamen and carpel
iii. Slide 12: In embryonic development, cell-cell communication plays an important role. List the parts of a receiving cell, and steps when appropriate, involved in a signal transduction pathway, in the order that they receive a signal
1. Ligand
2. Receptor
3. Signaling cascade
4. Gene expression
5. Cellular response
iv. Slide 14: Define recombinant DNA: molecules produced by artificially joining DNA from different sources
v. Slide 15: In order for restriction enzymes to cut DNA, they must detect recognition sequences
1. How many nucleotides usually make up a recognition sequence? 4-6.
2. Once the DNA is cut, the cut ends can be 1 of 2 notable shapes. List and describe them:
a. Cohesive ends: Not symmetrical, having
“sticky” overhangs with many base pairs
separated. Slide image helps visualize this
b. Blunt ends: symmetrical, no overhangs or
base pairs separated
vi. Summarize the most popularly discussed way that a segment of DNA can be copied: take one segment of DNA, and put it into a bacteria cell. A small unit of DNA in bacteria is called a plasmid. The bacteria will replicate itself rapidly, including the segment of DNA you intended to copy, creating recombinant DNA. You can take this
recombinant DNA and then remove the segments that you want.
c. 4/15/19
i. Slide 14
1. Define transgenic animals: animals with recombinant DNA, whose features often combine the features of 2 different animals that exist naturally in the
environment
2. What is a popular example of transgenic animals?: firefly genes can be combined with DNA of other animals and they end up glowing
ii. Slide 17: List and describe the properties of vectors
1. Contain several restriction sites
2. Independently replicating in host cells
3. Carry a selectable marker gene
4. Contain known sequences for sequencing
iii. Slide 18: What's the purpose of growing bacteria cells in the presence of ampicillin or other antibiotics? To kill bacteria cells that don’t have your plasmids of interest, so that you end up only with the bacteria cells that have the recombinant DNA that you want.
iv. Slide 19:
1. Define genomic library: vectors with DNA fragments from the entire genome, including both coding and noncoding regions
2. Define complementary DNA (cDNA) library: DNA
fragments of expressed genes
v. Slide 20
1. Why do cleaved DNA fragments and cleaved vectors meet and bond well when scientists are using them to create
plasmids? They have been cut with the same
restriction enzymes
2. What most notably makes starting with RNA different from starting with DNA in the process of DNA recombination? Starting with RNA requires reverse transcriptase to create cDNA. Ultimately it ends up leading to a
similar result as starting with DNA
vi. Slide 21
1. Summarize the PCR process used to amplify DNA: RNA primers attach to each of 2 strands of DNA. Next, DNA polymerase brings nucleotides to create
complementary strands, as in DNA replication. This
causes single strands to double. What makes the
PCR different from DNA replication is that it
continues as an exponential process
2. True or false: the PCR perfectly produces exact copies of
DNA. No process in nature is perfect, and mutations
could occur in this process as they do with other
DNA and RNA-related processes.
3. List the ideal temperatures for the following steps in the
PCR
a. Denaturation: 96 degrees C
b. Primer Annealing: 55 degrees C
c. Primer extension: 72 degrees C
vii. Slide 22: A modified nucleotide that can’t form phosphodiester (adjacent, not across) bonds and is called a dideoxynucleotide viii. Slide 23:
1. If a segment of DNA is inserted into an animal instead of a bacteria host, the result is transgenic animals
2. Define knockout animals: genetically modified animals where a gene’s expression is prevented or
eliminated, allowing people to observe what is
phenotypically missing when the gene is absent
8. PPT 17, Genomics, Transcriptomics, and Bioinformatics
a. Slide 4: “# of genes” is referring to the amount of DNA that is actually involved in making proteins, rather than the entire genome. Roughly what percent of DNA in most organisms is responsible for making proteins, and what is the remaining percent that is regulatory, noncoding, and otherwise irrelevant to making proteins? 10% and 90%
b. Slide 7: Define the following
i. Genomics: Analysis of DNA
ii. Transcriptomics: Analysis of RNA
iii. Proteomics: Analysis of proteins
iv. Bioinformatics: Use of math, computer programming, and statistics for the above
c. Humans and mice are genetically 80% similar