Study Guide

How do hox genes affect the development of embryos?

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  

What are the stages of embryonic development in drosophila, and what makes each stage unique?

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:  

What is the general order of development stages for an organism?

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. Don't forget about the age old question of What does it mean when interest rates are low?
If you want to learn more check out What is meant by productive efficiency?

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  

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. Don't forget about the age old question of Which are the three prohibitions by the production code administration in 1965 that would forbid a film the seal of approval?

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

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. If you want to learn more check out What is the meaning of binary relation in the context of discrete mathematics?

3. ____________________ is organisms preferring similar  

phenotypes in mates

4. ____________________ is organisms preferring dissimilar  

phenotypes in mates

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 headIf you want to learn more check out What is an example of conceptualization?

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 If you want to learn more check out How can one determine which resonance structure is most stable?

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