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OLEMISS / Biology / BIOL 336 / What is the hardy weinberg equilibrium equation?

What is the hardy weinberg equilibrium equation?

What is the hardy weinberg equilibrium equation?

Description

School: University of Mississippi
Department: Biology
Course: Genetics
Professor: Ryan garrick
Term: Fall 2016
Tags: Genetics
Cost: 50
Name: Genetics Final Study Guide
Description: This study guide covers all of the new material that could be on our final exam. Also, unlike my other study guides, this one has all of the answers at the end of the document.
Uploaded: 12/05/2016
12 Pages 51 Views 3 Unlocks
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EXAM 4 NEW MATERIAL REVIEW


What are the hardy weinberg equilibrium equation?



LECTURE 1 – HARDY WEINBERG EQUILIBRIUM

• Can observe evolution by change in frequency of (1)___________

Q: What are the Hardy Weinberg Equilibrium Equation?  A: p2+2pq+q2=1 and p+q=1

• In the HWE equation…

- p2(or pp) represents (2)______________________

o p represents (3)______________________

- 2pq represents (4)______________________

- q2 (or qq) represents (5)______________________

o q represents (6)______________________

• When a population is in HWE, (7)________________ genotype frequencies are  consistent with (8)_________________ genotype frequencies  • Test results of HWE equation, use the (9)______________________


If you reject the null of the chi-square test, what are you saying?



Q: if you reject the null of the chi-square test, what are you saying? A: that one of the HWE assumptions do not hold true: no selection, no  mutation, no immigration, very large pop. size, random mating.  

LECTURE 2 – “Genetic Rediscovery of ‘Extinct’ Galápagos Giant  Tortoise Species”  If you want to learn more check out What should happen if mr>mc?

Previous Work:  

• The discovery of 11 hybrid, reproductively mature tortoises (c. becki) that  proved to have “extinct” giant tortoise (c. elephantopus) ancestry brought up the question that  

(1)____________________________________________________________

Q: Where were the hybrid c. becki discovered? If you want to learn more check out Define institutions.

A: Volcano Wolf, Isabela Island

Q: Where were the c. elephantopus originally located?  


Where were the hybrid c. becki discovered?



A: Floreana Island

Q: What HW assumption could have allowed genes from the  presumed extinct c. elephantopus species appear on a completely  separate island in hybrid species?

A: Probably (2)______________________ because the tortoises used to move  between islands by pirate and whaling ships

Q: What was the biggest finding?

A: 84 younger Volcano Wolf tortoises were hybrids that had at least 1  immediate parent being the c. elephantopusWe also discuss several other topics like When do we use the z-test?

- suggests that:  

(3)__________________________________________________________

LECTURE 3 –> Ch. 20: Developmental Genetics  

 I. Understand the Meaning of Evolutionary Conserved as it   Relates to Hox Genes 

A. Similarity Despite Diversity

• Genes, genetic pathways, and developmental molecular signaling are all  shared across many eukaryotes

B. Developmental Events (Regulated by Genes)

a. specification  

b. determination

c. differentiation  

(1) ________________ – final form and function of the cell  

(2) ________________ – development of cell’s distinct identity (3) ________________ – fixed cell fate

C. Conserved Mechanisms

• Eukaryotes share a set of mechanisms and signaling systems during the  development process

• This mechanism is evolutionarily conserved meaning (4)  ______________________________ ________________________________________ - However, there are modifications… so evolutionarily we are not  identical If you want to learn more check out What are planned contrasts in anova?

• Ways to get differences and biological diversity:

- (5) ________________

- (6) ________________

D. Homeotic (Hox) Genes

• Hox gene – (7)  

________________________________________________________________ - Differential expression can lead to a zebra or a zebra fish - Most organismal lineages are linked by hox gene clusters  We also discuss several other topics like What is an example of self­enhancement in the us?

• We study developmental genetics using Drosophila and apply our  knowledge about the flies to the humans

- Fruit flies do not have many chromosomes  

- Hox genes are on 4 different chromosomes in humans  

o Some are completely identical to those in Drosophila, as well as  mice

• There was a single evolutionary original set of hox genes that was followed  by duplication in subsequent generations

E. Formation of the Adult Body Plan  

• Cannot have all genes on all the time because you need a progression of  gene expression over the life cycle

- 6 main phases in Drosophila development all because genes can turn  on and off If you want to learn more check out What is an advantage for the south?

o (8) __________________________________________

 II. Describe Drosophila Embryonic Development 

A. Drosophila Development

1 – (9) ________________ by 2 haploid nuclei fusing, creating 1 diploid zygote  - diploid zygote is just a single cell with a nucleus  

fusion of nuclei in cell without (10) ________________–> do not become  multiple cells just everything from both all in one cell  

2 – (11) ________________– multinucleated cell because lots of division without  cytokinesis  

3 – migration – nuclei move to outer edge of the single cells creating a  localized “wall” of maternal mRNA and protein  

- some additional cells can form and undergo cellular division 4 – (12) ________________– membranes are formed around the edges where  the many nuclei have lined up  

5 – (13) ________________– pole cells form at posterior end of the cell  - pole cells are a germ cell pre-cursor

6 – (14) ________________ – segment formation influenced by non-germ cell  position  

- front, back, up, down, established according to where the pole cells  were

- hox genes cause the different segments to become limbs such as legs,  wings, abdomen, etc.  

o FIG 20-2

• Hox genes set tone for adult structures specific to some segments and not  others

­ Legs from thoracic segments, etc.  

­ Only kick in right at end once segments formed and you need specific  structures to be built  

During Drosophila Development:  

• Spatial position matters because the cytoplasm is a molecular gradient of  maternal mRNA and protein (heterogeneous gradient)

­ Sets distance from the pole cells, determining segment type and fate  according to location

• transcriptional cascades over time

­ Even if transcription is a continuous process, there’s distinction  between each developmental stage (egg –> embryo –> larva –> pupa  –> adult)

 III. Know the progression of cell fate (ME > gap > pair rule >  segment polarity 

A. Analysis of Embryogenesis  

i. First set of Genes: Maternal effect (ME) genes: 

Q: Why does mother’s cytoplasm has more impact than dad’s when  the cells fuse

A: Mitochondrial (mRNA) RNA that were transcribed in mother’s nucleus gets  exported to her cytoplasm and eventually package into the egg’s cytoplasm ­ With fertilization, zygote has mRNA transcripts and the proteins that  were translated in the mother in the egg’s cytoplasm  

­ Affect zygotic genes, which affects offspring’s phenotype

• Equal contribution of genetic material from each parent to genome of  zygote

• Unequal contribution of mRNA and cytoplasmic proteins  

ii. Second Set of Genes: Zygotic Genes:

Q: What are Zygotic Genes?

A: Zygotic genes include the (15) ________________(which include (16)  ________________ ______________________________________________) and (17)  ________________________

­ transcribed after fertilization  

• Maternal Effect proteins regulate segmentation genes

• Segmentation genes regulate homeotic (hox) genes  

­ gap genes – specify broad regions of differentiation

­ head, thorax, abdomen

­ some overlap

­ each dot in 20-5 is a different nucleus of the multinucleate cell  ­ pair-rule genes – further divide

­ establish bounderies

­ segment polarity genes – define posterior and anterior ends of each  segment

• Hox genes – specify adult-only structures  

**Look at Fig. 20-4 for visual differentiation**

 a. Pair-Rule Genes

• (18) ________________– a zone of interaction among the gene products  (proteins and transcription factors)  

­ co-exist  

• Pair rule genes:  

­ recognize activity by presence of stripes (stripes determine future  segments)

­ stripe in middle (overlap) is what we see when we look at pair-rule  genes

­ this is the area of mRNA transcription

• FIG 20-6

 b. Segment Polarity Genes 

Q: What are segment polarity genes?  

A: The genes that establish polarity and segment identity (what adult  structures they will become) and are active in each band of each segment  B. Hox Mutants  

• When legs form on the thorax it is due to the allele called (19)  _________________________

­ when this allele is mutant and expressed in the head, legs are not  where they are supposed to be, creating a mutant fly  

C. Hox Gene co-linearity  

• Cluster of hox genes – each take care of different segments in final body  plan  

• Order of the genes is linear with location of expression  

­ 3’ genes –> expressed (20) ________________

­ 5’ genes –> expressed (21) ________________

D. Gene Expression Cascades

ME gene products –> activate gap genes

­ ME genes shut off after job is done  

­ Divide into head, thorax, and abdomen

Gap genes –> activate pair-rule genes

­ Segmentation begins

­ Overlap of segments means expression  

Pair rule genes –> activate segmentation polarity genes  ­ Posterior and anterior ends of each segment is distinguished Hox genes –> adult structures  

E. Cell-to-cell Interactions

• Need communication between cells to make sure they are operating  together at the same time and to keep track of what other cells are doing ­ One cell’s signals impacts the transcription in another cell, regulating  rate of gene expression by turning genes on or off

­ Networks of cell-to-cell interactions help rate of differentiation stay in  step with one another

­ Establish polarity and direct differentiation of specific tissues and organs  

 i. Notch Signaling Pathway 

Q: What is the Notch Signaling Pathway?

A: when you have 2 immediately adjacent cells, one with surface proteins  that are notch receptors, the other with surface proteins called delta proteins that fit into the notch receptors and physical contact between the two cells  via delta protein and notch receptor protein 

­ Contact causes the notch receptor to cleave off partly in the cytoplasm side of the protein

­ Broken off piece of receptor protein (NCID) binds to the Su(H)  protein in the nucleus

­ This complex binds to the binding site on DNA  

­ Alters pattern of gene expression by affecting  

transcription and translation  

LECTURE 4 –> Ch. 16: Cancer and Regulation of the Cell Cycle  I. Understand the Properties of Cancer Cells that Distinguish them from “Normal Cells” 

A. Cancer

• A genetic disease that affects (1) ________________

­ these mutations are usually new and not inherited

• Causes uncontrolled growth and division ((2) ________________) ­ diploid parent cells are reproducing constantly and are unable to  withdraw from the cell cycle to avoid going through mitosis  ­ why cancer cells lead to tumors  

• Cancer doesn’t just include genetic mutations in somatic cells but  epigenetics for those cells as well  

B. Mutations Arise in Somatic Cells

• Minimally (3) ________________must strike the genes to cause a cancer cell  to result

­ not just a single mutation

­

Q: How do cancer cells compare to normal functioning cells? A: Look completely messed up due to substitutions, chromosome  translocations, deletions

­ lead to differences in size, color, makeup, and number of chromatids  within each homologous pair  

­ aka they do not look like homologous pairs at all because each  chromatid is very different from its partner

• These cancer-causing mutations not only affect the cell cycle and division  but also DNA repair  

­ if DNA repair isn’t working, number of mutations drastically increases

 II. Know the Key Terms (e.g., proliferation, metastatic growth,  benign, malignant, etc. 

• (4) ________________: cells from one tumor move to a secondary location via  bloodstream, causing a tumor there as well

­ First mutations accumulate to a cancerous cell  

­ Leads to build up to clones of that cancerous cell

­ Additional mutations that give cancerous tumor to detach in some  areas and travel in the bloodstream to another location  

A. Two Main Types of Tumor

• (5) ______________– (early stage of cancer) uncontrollable cell growth and  proliferation only

­ Forms a mass of cells (tumor) that can be surgically removed  • (6) ________________ – (later in cancer) cell proliferation and metastatic  growth  

­ Secondary tumors due to cancer cells traveling through the  bloodstream and sticking elsewhere, making it a lot more difficult to  treat  

B. Cancer Cells are Clonal

Q: What is a unique feature of Cancer cells that one would originally  think to not be true based on the fact that they have uncontrolled  cell division?  

A: The same set of mutations exist in all primary and secondary tumors ­ Each of these cancer cells is identical  

­ Later cancer cells can mutate further

­ Silencing of the X chromosome in cancer cells should be random, but it is not  

C. Requires Multiple Mutations

• The more cell divisions occurring, the higher chance of 6 or more mutations striking same cell

­ Spontaneous mutations rare but absolute number of mutations  increases with cell divisions  

• Because cancer is induced by prolonged/sustained carcinogen (smoking,  UV, etc) exposure, cancer is more prevalent in adults

• Cancer also becomes more malignant over time

­ If you catch it early in its benign state, your chance of survival is  increased  

D. Genomic Instability  

• Lots of chromosomal defects in cancer cells that can sometimes be used to determine the type and stage of cancer

• (7) __________________________ – occurs when translocation occurs between  chromosomes that would not typically pair up  

­ ex: a really short one (chromo. 22) and a really long one (chromo. 9) ­ causing genes to be too close together that normally would not  be at all

­ creates a fusion protein  

­ with chromo 22 and chromo 9, this can lead to  

proteins that create leukemic white blood cells  

E. Chronic Myelogenous Leukemia

Q: Explain Gene ABL.  

A: gene ABL transmits a signal to the cell to grow

­ when fused with gene BCR (creating ABL-BCR) it creates a fusion  protein

­ the fusion protein stimulates the cell to continuously grow and  divide  

F. Hereditary Cancer (= unusual)

• (8) _______________________– hypersensitivity to UV that usually leads to skin cancer caused by a mutation in any of the 7 genes that are involved in DNA  repair

­ pyrimidine dimers never get fixed because nucleotide excision repair  can’t happen.  

Chromatin Modification  

• due to the heritable factors that affect gene expression through  methylation, alteration, and histone modifications

­ do not affect the DNA sequence itself

­ epigenetics  

• Cancer cells have reduced methylation in some locations, allowing more  genes to be  

(9) ________________ when they shouldn’t be

­ Many genes that are usually methylated and not being expressed in  cell’s lifetime have become un-methylated, leading to overexpression  of genes that typically are turned off  

• Also have higher methylation in promotor regions

 III. Recall the Roles of Checkpoints, Apoptosis, and Tumor Suppressor Genes in Preventing Cancer

A. Altered Cell Cycle Regulation

• Cancer cells have no control to stop dividing  

• Cancer cells completely skip over the (10) ________________ (where other  cells exit cell cycle) and keep going through the cycle

• Normal checkpoints at:  

­ (11) _________ to monitor size and DNA quality

­ (12) _________ to monitor DNA synthesis and damage repair  ­ (13) _________ to monitor attachment of centromere and spindles

• Usually if a problem is detected, cell division ceases  

­ In cancer cells, none of these checkpoints work how they’re supposed  to  

­ Checkpoint genes have been mutated  

B. Control of Apoptosis  

• Apoptosis (14) _____________________________

­ Occurs when there is irreparable chromosome damage

­ Cell shrinks and DNA is chopped up, membrane starts to become weaker, nuclear envelope collapses, apoptic body forms, and the  whole cell lysis and then is engulf by other cells.  

• In cancer cells, the genes involved in apoptosis have also been mutated  

C. Proto-oncogenes

• Normally code for transcription factors that regulate gene expression, cell  division proteins that regulate signal transduction, and the cell cycle  regulators  

Q: What normally happens with the oncogenes?

A: in normal cells at the G0 stage, this expression is repressed (because the  cell is withdrawn from cycle and not dividing). In Cancer cells, they are  mutated and over expressed

D. Proto-oncogene Mutations

• oncogene is a cancer-causing gene that came from a proto-oncogene ­ Due to gain of function mutation  

­ Dominant for cancerous phenotype

­ Only one allele needs to be mutated to cause continuous cell  growth and division  

E. Tumor-Suppressor Genes

Q: What are Tumor-Suppressor Genes?

A: These genes normally code for genes that regulate the checkpoints of the  cell cycle and genes that initiate apoptosis if the cell does not pass the  checkpoints

­ In cancer cells they can’t stop the damaged cells from dividing and are  unable to let apoptosis occur to those damaged cells  

­ These are (15) ________________ for the cancer phenotype  

F. p53 Tumor-Suppressor Gene

Q: What are the p53 tumor suppressor genes?  

A: These genes are mutated in more than fifty percent of human cancer  cases. They are

(16) ________________, meaning they have multiple effects. They code for a  transcription factor that will repress or stimulate the transcription of more  than 50 genes

­ Constantly synthesized, rapidly degraded (not a lot present at a time)

• This gene is usually bound to (17) ________ first, which prevents p53 from  becoming active

­ Mdm2 tags p53 so that it is rapidly degraded  

• With chemical damage, double stranded breaks, or repair intermediates,  the p53 protein can disassociate from Mdm2

­ LEADS TO CANCER CELL

Cancer must also metastasize  

­ Must be able to degrade extracellular matrix and basal lamina that  separates tissues

­ Relies on defects in cell adhesion genes

Heritable Cancers

• Can inherit a mutant allele that requires 4-5 more mutations to strike • lots of types, small percentage

• usually inherited as a single mutant  

­ Must also lose heterozygosity  

• need more mutations to arise to fully express cancer

ex: Colon cancer has a multi-step development

Lecture 1 Answers

1. alleles

2. homozygous dominate genotype frequency (AA)

3. dominate allele frequency  

4. heterozygous genotype frequency (Aa)

5. homozygous recessive genotype frequency (aa)

6. recessive allele frequency

7. observed

8. expected

9. Chi-Square test

Lecture 2 Answers

1. Reproductively mature c. elephantopus are likely to still be alive somewhere  

2. Gene flow

3. If some are still relatively young, this suggests that some pure-bread parents must still be alive somewhere

Lecture 3 Answers

1. Differentiation

2. Specification

3. Determination

4. it arose once or a few times a long time ago and is subsequently  shared by descendants

5. mutations

6. gene duplications

7. set of genes with shared function to specify features of final adult body plan

8. embryo, 3 larval stages, pupal, and adult  

9. fertilization

10. nuclear division

11. migration

12. enclosure

13. orientation

14. differential transcription

15. segmentation genes

16. gap genes, pair rule genes, and segment polarity genes 17. homeotic (hox) genes

18. overlap

19. Antennapedia (Antp)

20. Anteriorly  

21. Posteriorly  

Lecture 4 Answers

1. Somatic Cells

2. Proliferation

3. 6+ mutations

4. metastatic growth

5. benign  

6. malignant

7. Philadelphia Chromosome 8. Exoderma pigmentosum 9. Turned on

10. G0 stage

11. G1/S

12. G2/M

13. M

14. Programmed cell death  15. Recessive

16. Pleiotropic

17. Mdm2

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