Annotated Bibliography

Assess sources for your research for your final presentation (for credibility, reliability, and relevance) and list references in proper APA format. That means the sources you use for this assignment should be directly related to the species that you chose in Forum 1 of the class

Assignment Instructions:  The Research Project/Presentation for this class is divided into three major Assignments, 1) annotated bibliography, 2) outline and 3) final presentation. The first part is the annotated bibliography. An annotation is a summary and evaluation, and your annotated bibliography will include a summary and evaluation of some of the sources (or references) you will use for your presentation.

To prepare for this assignment, I recommend that you do the following:

  • Read these directions carefully.
  • Review the sample annotated bibliography provided to you below.
  • Read the grading criteria below. The grading criteria is a detailed evaluation that I will use to assess your performance. It will also help you understand what is expected of you as you prepare your assignment.
  • Message me with any questions!

The reason the annotated bibliography is included as part of the research project is that writing an annotated bibliography is important in that it provides excellent preparation for the final presentation. One of the issues regarding any type of research, especially in biology, is the credibility of the sources used, particularly those obtained from various websites. By forcing you to evaluate each of your potential sources carefully, the annotated bibliography helps you determine if in fact the source you chose is credible and helps you determine how relevant it is to your topic and understand the topic better which will help you develop your presentation.

For this project, you will assess three sources to include:

1) a complete citation for each source,

2) a summary of each source, and

3) an evaluation of each source.

Three sources are required for this assignment (i.e., you are to write an annotation for each source).  However, you must use five or more sources in your final presentation. 

Use this TEMPLATE to summarize and evaluate each of your three sources.

  1. Citation:

Written in APA reference list format. For more help with formatting, see APA handout.

  1. Summary:

What is the purpose of the source, review article, original research? What topics are covered? This section is generally 4-6 sentences that summarize the author’s main point. For more help, see this link on paraphrasing sources.

  1. Evaluation:

After summarizing the article (or research paper or book), it is necessary to evaluate it and state where you found it – its source (e.g., journal, website, etc.).  Briefly answer the following questions in 4-6 sentences:

What is the format or type of source (e.g., peer-reviewed journal paper, website, book)? How reliable is the information in the article, and how credible is the source (e.g., website’s sponsoring organization, journal or book publisher) and the author(s)?

SCIN130 – Introduction to Biology with Lab

 

Annotated Bibliography

 

 

Name:
Course Number:
Presentation Topic:

 

 

 

Source #1

 

Citation

(in APA format)

 

 

 

 

Summary

 

 

 

 

 

 

 

 

 

 

Evaluation

 

 

 

 

 

 

 

 

 

 

 

Source #2

 

 

Citation

(in APA format)

 

 

 

 

Summary

 

 

 

 

 

 

 

 
 

Evaluation

 

 

 

 

 

 

 

 

 

 

 

Source #3

 

 

Citation

(in APA format)

 

 

 

 

Summary

 

 

 

 

 

 

 

 
 

Evaluation

 

 

 

 

 

 

 

 

 

 

American Public University System May 2018

 
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The Epipelagic Is Divided Into Two Components: The Oceanic Waters And The

Question

1 of 25

The epipelagic is divided into two components: the oceanic waters and the

photic zone.

neritic zone.

pelagic realm.

upper photic zone.

subtidal zone.

Question

2 of 25

Most of the primary production carried out in the open ocean is performed by

seaweeds.

kelps.

phytoplankton.

seagrasses.

zooxanthellae.

Question

3 of 25

Net phytoplankton consist mostly of

copepods.

diatoms and dinoflagellates.

nanoplankton.

cyanobacteria (blue-green algae).

nanoplankton and diatoms.

Question

4 of 25

Typically the most abundant group in the zooplankton are the.

larvaceans.

krill.

fish larvae.

nanoplankton.

copepods.

Question

5 of 25

Which of these is least likely to be seen in the epipelagic?

Suspension feeders

Deposit feeders

Primary production

First-level carnivores

Second-level carnivores

Question

6 of 25

Which of these groups builds a mucus “house?”

Copepods

Arrow worms

Larvaceans

Planktonic snails such as pteropods

Snail larvae

Question

7 of 25

Which of the following accounts for about 50% of the primary production in epipelagic waters?

Diatoms

Cyanobacteria

Dinoflagellates

Coccolithophorids

Silicoflagellates

Question

8 of 25

The following are an adaptation to the planktonic way of life except

spines.

small size.

decrease in drag.

substitution of heavy ions by light ones.

gas-filled bladders.

Question

9 of 25

The storage of lipids within the body is an adaptation in plankton since lipids

make cells heavier.

increase body density.

contain air pockets so they help in buoyancy.

contain a larger amount of energy.

are less dense than water.

Question

10 of 25

The neuston consists of animals that

swim against currents.

sink to the bottom portion of the water column.

are top carnivores in the pelagic realm.

spend their entire lives in the plankton.

live at the surface, but remain underwater.

Question

11 of 25

Counter shading is a form of

shading with bioluminescence.

warning coloration.

structural coloration.

protective coloration.

cryptic coloration.

Question

12 of 25

The rete mirabile found in some fishes is involved in.

increasing speed.

decreasing buoyancy.

digesting food.

increasing buoyancy.

conserving body heat.

Question

13 of 25

Zooplankton that migrate vertically

hibernate at night and feed during the day.

feed at the surface during the day, and migrate below the photic zone at night.

feed in the photic zone during the day, and migrate to the surface at night.

stay below the photic zone during the day, and feed at the surface at night.

migrate up and down but always stay below the photic zone.

Question

14 of 25

Most animals in the epipelagic are omnivores. This means that they eat

producers and consumers.

part of the neuston.

zooplankton.

detritus.

phytoplankton.

Question

15 of 25

What is the relationship between dissolved organic matter (DOM) and bacteria in the epipelagic?

Bacteria feed on the DOM, making it available to other animals in the food chain that feed on bacteria.

Bacteria supply most of the DOM.

Bacteria feed on DOM and thus it is unavailable to other animals.

Bacteria cannot utilize DOM and thus feed on detritus, depleting it through most of the epipelagic.

Bacteria cannot utilize DOM, making it available to animals.

Question

16 of 25

The most common limiting nutrient in the ocean is

silicon.

oxygen.

nitrogen.

carbonate.

phosphorus.

Question

17 of 25

The fall bloom in temperate waters is caused when

primary production decreases as nutrients increase.

primary production decreases due to light limitation.

primary production decreases as nutrients decrease.

primary production increases as nutrients increase.

primary production increases as the number of zooplankton increases.

Question

18 of 25

Equatorial upwelling occurs as a result of

temperature changes at the Equator.

the divergence of equatorial surface currents.

the convergence of equatorial surface currents.

winds causing the Ekman transport of surface water offshore.

El Niño conditions north and south of the Equator.

Question

19 of 25

The Southern Oscillation can be best described as

relative changes between two pressure systems.

variation in wind speed over the Pacific Ocean.

relationship between sea-surface and high-altitude pressures.

tidal differences between the Indian and Pacific Oceans.

wind-speed differences along the Equator.

Question

20 of 25

The long spines and projections seen in many epipelagic plankton are used for

feeding.

reproduction.

increasing drag.

increasing buoyancy.

gathering nutrients.

Question

21 of 25

Most epipelagic fish have a tail that is

short and wide.

short and narrow.

short and thin.

high and wide.

high and narrow.

Question

22 of 25

Which of the following adaptations is least likely to be seen in epipelagic fish?

Stiff fins

A smooth, scaleless body

Increased white muscle

Grove in body for fins

Eyes flush with body

Question

23 of 25

The largest source of dissolved organic material (DOM) in the epipelagic is

viruses.

bacteria.

phytoplankton.

zooplankton.

nekton.

Question

24 of 25

The lateral line system in fishes functions in ________________.

sensing vibrations in the water

detecting magnetic lines of force in water

sensing light in aphotic zones

sweeping surrounding water for plankton

bioluminescence

Question

25 of 25

The remote sensing system found in dolphins and some other cetaceans is ___________.

communal mutualistic behavior

extrasensory perception

echolocation

underwater acoustic sensitivity

heightened smell

 

 

 

 
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Biology Solutions 100% A+

Exam 3 Biology 1307

1. True or False. All protists are eukaryotic.

A. true

B. false

2. Chloroplasts arose via _____.

A. endosymbiosis of dinoflagellates

B. endosymbiosis of cyanobacteria

C. endosymbiosis of fungi

D. endosymbiosis of euglenids

3. According to the endosymbiosis theory, how many membranes should a mitochondrion have?

A. One

B. Three

C. Two

D. Zero

4. You are given an unknown organism to identify. It is unicellular and heterotrophic. It is motile, using many short extensions of the cytoplasm. It has well-developed organelles and two nuclei, one large and one small. This organism is most likely to be a ________.

A. foraminiferan

B. diatom

C. ciliate

D. dinoflagellate

E. slime mold

5. Which of the following statements is consistent with the assertion that protists are paraphyletic?

A. There is no common set of synapomorphies that define a protist

B. Protists all share a common set of synapomorphies.

C. Protists are all more primitive than land plants and animals.

D. Protists do not share a single common ancestor.

6. Encouraging the growth (via nutrient fertilization) of photosynthetic protists in marine environments may help reduce global warming because _____.

A. the increased oxygen consumption by large populations of photosynthetic protists will increase photosynthesis in land plants

B. photosynthetic protists are primary consumers in many marine food chains

C. photosynthetic protists fix atmospheric carbon dioxide, decreasing atmospheric carbon dioxide levels

7. Encouraging the growth (via nutrient fertilization) of photosynthetic protists in marine environments may help reduce global warming because ________.

A) photosynthetic protists are primary consumers in many marine food chains

B) photosynthetic protists fix atmospheric carbon dioxide, decreasing atmospheric carbon

dioxide levels

C) the increased oxygen consumption by large populations of photosynthetic protists will increase photosynthesis in land plants

D) photosynthetic protists would release a lot of oxygen, and fertilizing them would increase levels of oxygen in the atmosphere

8. Which of these taxa contains species that produce potent toxins that can cause extensive fish kills, contaminate shellfish, and poison humans?

A. red algae

B. dinoflagellates

C. diplomonads

D. euglenids

9. Which of the following might be a result of adding a secondary consumer to the aquatic ecosystem in the accompanying illustration?

A. a decrease in the number of primary consumers

B. a decrease in the population of decomposers

C. an increase in atmospheric carbon dioxide

D. an increase in the population of scavengers

E. a decrease in the carbon sink

10. The Irish potato famine was caused by an organism that belongs to which species?

A. Phytophtorainfestans

B. Trichomonas vaginalis

C. Giardia spp.

D. Trypanozomacruzi

11. Which of the following eukaryotic lineages contains species that all lack functioning mitochondria?

A. Excavata

B. Rhizaria

C. Amoebozoa

D. Stramenopila

12. Pseudopods that can perform phagocytosis and have the ability to change their shape are generally characteristic of which group?

A. radiolarians

B. amoebas

C. slime molds

D. oomycetes

13. Which of the following is a synapomorphy that defines all green algae and land plants?

A. Seeds B. Vascular tissue C. Cell walls D, Photosynthetic chloroplasts

14. One of the fish in your aquarium dies. Adding which protist to the water would allow you to avoid flushing the dead fish by speeding its decay?

A. an apicomplexan

B. a dinoflagellata

C. a water mold

D. a ciliate

E. a euglenid

15. According to the endosymbiotic theory, why was it adaptive for the larger (host) cell to keep the engulfed cell alive, rather than digesting it as food?

A. The engulfed cell provided the host cell with adenosine triphosphate (ATP).

B. The engulfed cell provided the host cell with carbon dioxide.

C. The engulfed cell allowed the host cell to metabolize glucose.

D. The host cell was able to survive anaerobic conditions with the engulfed cell alive.

E. The host cell would have been poisoned if it had digested the engulfed cell.

16. Alternation of generations occurs in some protists. Which of the following represents the correct sequence of events for this mode of reproduction?

A. gametophyte → gamete → fusion → sporophyte → spore → gametophyte

B. sporophyte → spore fusion → gametophyte → gamete → sporophyte

C. gametophyte → fusion → sporophyte → spore → gamete → gametophyte

D. gamete → fusion → gametophyte →spore → sporophyte → gamete

17. In examining a protist, you notice that it lacks a cell wall, and has movement with cytoplasmic streaming. These data allow you to infer that the species belongs to which of the following protist groups?

A. Excavata

B. Stramenopila

C. Rhizaria

D. Alveolata

E. Amoebozoa

18. Chagas disease is spread by the “kissing bug”. This disease affect 16-18 million people around the world and causes about 50,000 deaths annually and is caused by which protist?

A. Giardia

B. Trichomonas vaginalis

C. Trypanosoma cruzi

D. Plasmodioum

19. Dysentery is caused by _______________ and causes severe diarrhea. It is mostly prevalent in countries with a warm climate and poor sanitary conditions. In some places it is known as “Montezuma’s revenge”. Which of the following protists causes dysentery

A. Entamoeba histolytica

B. Phytophthora infestans

C. Plasmodioum

D. Dinoflagellates

20. What impact will the loss of land plants have on the soil?

A. Increase soil stability

B. Increase soil erosion

C. Increase nutrient levels

D. Decrease surface temperature

21. The major function of the medicinal compounds in plants is to _____.

A. as defense against herbivores

B. attract pollinators for seed dispersal

C. attract insects and birds to spread seeds and fruits

D. defend the plant against microbes

22. The most direct ancestors of land plants were probably _____.

A. liverworts and mosses B. green algae C. kelp (brown alga) D. cyanobacteria

23. What evidence indicates the movement of plants from water to land?

A. sporopollenin to inhibit evaporation from leaves

B. loss of structures that produce spores

C. remnants of chloroplasts from photosynthesizing cells

D. waxy cuticle to decrease evaporation from leaves

24. Which of these time intervals, based on plant fossils, came last (most recently)?

A. carboniferous swamps with giant horsetails and ferns

B. rise and diversification of angiosperms

C. colonization of land by early liverworts and mosses

D. extensive growth of gymnosperm forests

25. Angiosperms are the most successful terrestrial plants. Which of the following features is unique to them and helps account for their success?

A. embryos enclosed within seed coats

B. sperm cells without flagella

C. fruits enclosing seeds which contain the plant embryo

D. wind pollination

26. Protists and bacteria are grouped into different domains because _____.

A. bacteria are not made of cells

B. protists have a membrane-bounded nucleus, which bacterial cells lack

C. protists eat bacteria

D. protists are photosynthetic

27. The term gymnosperm refers to plants _____.

A. with “naked seeds” that do not produce flowers

B. that are non-vascular

C. that flower

D. with seeds protected within a fruit

28. What trait gives seeds an advantage over spores?

A. Protected from the environment

B. Small in size

C. Contain nutrients

D. Long-lived

29. Which of the following was a challenge to the survival of the first land plants?

A. desiccation

B. too much sunlight

C. a shortage of carbon dioxide

D. animal predation

30. _____ are angiosperms.

A. Roses

B. Fiddlehead ferns

C. Sphagnum mosses

D. Pine trees

31. Primary producers such as plants and green algae ____________.

A. Convert solar energy (light) to chemical energy (sugars)

B. Decompose decaying material in soil to produce energy

C. Consume other organisms to produce chemical energy (sugars) and solar energy (light)

D. Produce CO2 by performing photosynthesis

32. Plants provide many ecosystem services including production of oxygen and holding the soil. What is an ecosystem?

A. All the organisms or biotic factors in a particular area

B. All the living and nonliving components in a particular area

C. The nonliving or abiotic components in a particular area

D. All plants and animals in a given region

33. Stoma (plural: stomata) are____________.

A. Small openings called pores surrounded by specialized guard cells

B. Watertight sealants produced by plants to avoid desiccation

C. Specialized organelles in plant cells to perform photosynthesis

D. Modified leaves in a plant to avoid predation by herbivores

34. Flowers, the reproductive organ of a flowering plant, has two key reproductive structures called:

A. Seed and pistil

B. Stamen and fruit

C. Stamen and pistil

D. Seed and anther

35. The three main ways in which pollen is transported from plant to plant or flower to flower are:

A. Animals, wind, water

B. Wind, fungi, water

C. Animals, bees, wind

D. Fungi, water, insects

36. _____________ is a process by which pollen is transferred in plants.

A. Pollen grains

B. Style

C. Pollination

D. Translocation

37. True or False. The female part of the flower is the stamen.

A. True B. False

38. True or False. The main function of the endosperm is to provide nutrients for the embryo plant.

A. True B. False

39. True or False. Plants and not algae are the main primary producers in Earth’s oceans.

A. True B. False

40. True or False. Bryophytes such as mosses lack vascular tissue (xylem and phloem).

A. True B. False

41. Root hairs are most important to a plant because they ________.

A. anchor a plant in the soil

B. store starches

C. increase the surface area for absorption

D. provide a habitat for nitrogen-fixing bacteria

E. contain xylem tissue

42. As fuels, wood and coal ________.

A) are the main fuel sources in industrialized countries today.

B) are both formed from living or fossil plants.

C) are both formed under pressure deep in the Earth.

D) are sustainable as they are even now being made at high rates.

43. Molecular phylogenies show all land plants are a monophyletic group. This suggests ________.

A) there were many different transitions from aquatic to terrestrial habitats

B) wind-pollinated plants arose first

C) land plants have undergone a diversification since they first colonized terrestrial habitats

D) there was a single transition from aquatic to terrestrial habitats

44. Which of these time intervals, based on plant fossils, came last (most recently)?

A) extensive growth of gymnosperm forests

B) Silurian-Devonian explosion with fossils of plant lineages containing most of the major morphological innovations

C) colonization of land by early liverworts and mosses

D) rise and diversification of angiosperms

E) carboniferous swamps with giant horsetails and lycophytes

45. Why are seedless vascular plants considered paraphyletic rather than monophyletic?

A) Some of the groups within the seedless vascular plants are more closely related to each other than to other groups (such as Lycophyta).

B) They share a more recent common ancestor with seeded plants than they do with the non-vascular plants.

C) All of the groups contained within the seedless vascular plants do not have the same ancestor.

D) The group includes their common ancestor but also the seeded descendants of that same ancestor.

46. Which set contains the most closely related terms?

A) megasporangium, megaspore, pollen, ovule

B) microsporangium, microspore, egg, ovary

C) megasporangium, megaspore, egg, ovule

D) microsporangium, microspore, carpel, ovary

47. In the process of alternation of generations, the ________.

A) sporophyte is haploid and produces gametes

B) sporophyte is diploid and produces spores

C) gametophyte is haploid and produces spores

D) gametophyte is diploid and produces gametes

E) spores unite to form a zygote

48. Where are you LEAST likely to see green algae?

A) as pink snow in the mountains in summer

B) growing symbiotically with fungi in lichens or with some invertebrate animals

C) growing independently on dry rock in meadows

D) growing independently on wet rock in ponds and lakes

E) floating in seas and oceans

49. When a mosquito infected with Plasmodium first bites a human, the Plasmodium ________.

A) gametes fuse, forming an oocyst

B) cells infect the human liver cells

C) cells cause lysing of the human red blood cells

D) oocyst undergoes meiosis

50. Carbon dioxide enters the inner spaces of the leaf through the ________.

A) cuticle

B) epidermal trichomes

C) stoma

D) phloem

E) walls of guard cells

51. Which part of a plant absorbs most of the water and minerals taken up from the soil?

A) root cap

B) root hairs

C) the thick parts of the roots near the base of the stem

D) storage roots

E) sections of the root that have secondary xylem

52. When an animal cell is placed in a hypotonic solution and water enters the cell via osmosis, the volume of the cell increases until it bursts. This does NOT happen to plant cells, because ________.

A) they have large central vacuoles, which provide abundant space for storage of incoming water

B) the composition of their plasma membranes differs from that of animal-cell plasma membranes in a way that provides much greater strength

C) they have cell walls, which prevent the entry of water by osmosis

D) they have cell walls, which provide pressure to counteract the pressure of the incoming water

E) certain gated channel proteins embedded in their plasma membranes open as osmotic pressure decreases, allowing excess water to leave the cell

53. Compared to a cell with few aquaporins in its membrane, a cell containing many aquaporins will ________.

A) have a faster rate of osmosis

B) have a lower water potential

C) have a higher water potential

D) have a faster rate of active transport

E) be flaccid

54. Which cells in a root form a protective barrier to the vascular system where all materials must move through the symplast?

A) pericycle

B) cortex

C) epidermis

D) endodermis

E) exodermis

55. You are conducting an experiment on plant growth. You take a plant fresh from the soil that weighs 5 kilograms (kg). Then you dry the plant overnight and determine the dry weight to be 1 kg. Of this dry weight, how much would you expect to be made up of oxygen, carbon, and hydrogen?

A) 1 gram

B) 4 grams

C) 40 grams

D) 960 grams

E) 1 kg

56. Which of the following statements about essential nutrients are TRUE? Essential nutrients ________.

I. are necessary for plant growth and reproduction

II. are required for a specific structure or metabolic function

III.cannot be synthesized by a plant

IV.are produced by symbiotic bacteria

A) I and IV

B) II, III, and IV

C) I, II, and III

D) I, II, III, and IV

57. Which criteria allow biologists to divide chemicals into macronutrients and micronutrients?

A) molecular weight of the element or compound

B) the quantities of each required by plants

C) how they are used in metabolism

D) whether or not they are essential for plant growth

58. A mineral deficiency is likely to affect older leaves more than younger leaves if the ________.

A) mineral is a micronutrient

B) mineral is very mobile within the plant

C) mineral is required for chlorophyll synthesis

D) mineral is a macronutrient

E) older leaves are in direct sunlight

59.Which of the following elements correctly pairs an essential element in plants with its function?

A) nitrogen–component of nucleic acids, proteins, hormones, coenzymes

B) magnesium–component of nucleic acids, phospholipids, ATP

C) phosphorus–cofactor functioning in protein synthesis

D) sulfur–component of DNA; activates some enzymes

60.Why is nitrogen fixation an essential process?

A) Fixed nitrogen is often the limiting factor in plant growth.

B) Nitrogen fixation is very expensive in terms of metabolic energy.

C) Nitrogen-fixing capacity can be genetically engineered.

D) None of the above

61.Nitrogen fixation is a process that ________.

A) recycles nitrogen compounds from dead and decaying materials

B) converts ammonia to ammonium

C) releases nitrate from the rock substrate

D) converts nitrogen gas into ammonia

E) recycles nitrogen compounds from dead and decaying materials and converts ammonia to ammonium

62.Which of the following, if used as a fertilizer, would be most immediately available for plant uptake?

A) NH3

B) N2

C) CN2H2

D) NO3-

63. In what way do nitrogen compounds differ from other minerals needed by plants? Only nitrogen ________.

A) can be lost from the soil

B) can be provided by symbiotic bacteria

C) is needed for protein synthesis

D) is held by cation exchange capacity in the soil

E) can be absorbed by root hairs

64. What is the correct sequence of steps during infection of plants by nitrogen-fixing bacteria?

A) Rhizobia release Nod factors; roots release flavonoids; rhizobia proliferate inside of root hair; infection thread grows into the root cortex; nodule forms.

B) Rhizobia release flavonoids; roots release Nod factors; rhizobia proliferate inside of root hair; infection thread grows into the root cortex; nodule forms.

C) Roots release flavonoids; rhizobia release Nod factors; rhizobia proliferate inside of root hair; nodule forms; infection thread grows into the root cortex.

D) Roots release flavonoids; rhizobia release Nod factors; rhizobia proliferate inside of root hair; infection thread grows into the root cortex; nodule forms.

E) Nodule forms; infection thread grows into the root cortex; rhizobia proliferate inside of root hair; rhizobia release flavonoids and Nod factors.

65. Carnivorous plants have evolved mechanisms that trap and digest small animals. The products of this digestion are used to supplement the plant’s supply of ________.

A) water

B) carbohydrates

C) lipids and steroids

D) nitrogen, nutrient, and other minerals

66. Which of the following statements about nitrogen fixation in root nodules is correct?

A) The plant contributes the nitrogenase enzyme.

B) The process is relatively inexpensive in terms of ATP costs.

C) Leghemoglobin helps maintain a low oxygen concentration within the nodule.

D) The process tends to deplete nitrogen compounds in the soil.

E) The bacteria of the nodule are autotrophic.

67. Most of the dry mass of a plant is derived from ________.

A) NO3- and CO2

B) K+ and CO2

C) PO4 and K+

D) H2O and K+

E) H2O and CO2

 
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>Human-B brain form B-ACBP) (88)

MALQADFDRAAEDVRKLKARPDDGELKELYGLYKQAIVGDINIACPGMLDLKGKAKWEAWNLKKGLSTED

ATSAYISKAKELIEKYGI

>Duck-B brain form B-ACBP) (103)

mfqahllrgtltlsfflhqadfdeaaeevkklktrptdeelkelygfykqatvgdiniecpgmldlkgka

kweawnlkkgiskedamnayiskaktmvekygi

>Bovine-T testis form -ACBP)(86)

mcqvefemacaaikqlkgpvsdqekllvysyykqatqgdcnipappatdlkakakweawnenkgmskmdamriyiakveelkkneag

>Dog-T testis form (74) (T-ACBP)

MCQVEFEMACAAIKQLKGPVSDQEKLLVYSFYKQATQGDCNIPAPPATDVKAKAKWEAWNQNKGMSKMDAHEDL

>C.elegans (85)

mtlsfddaaatvktlktspsndellklyalfkqgtvgdnttdkpgmfdlkgkakwsawdekkglakddaqkayvalveeliakyga

>Barley (93)

MGLKEEFEEYAEKAKTLPDTTTNESKLCLYSLYKQATVGPVNTDRPGLFDLAGKAKWDAW

KSVEAKSKEEAMADYITKVKQLLEEAAAASASS

>Fruitfly1 (86)

MVSEQFNAAAEKVKSLTKRPSDDEFLQLYALFKQASVGDNDTAKPGLLDLKGKAKWEAWNKQKGKSSEAAQQEYITFVEGLVAKYA

>S.cerevisiae (86)

mvsqlfeekakavnelptkpstdellelyalykqatvgdndkekpgifnmkdrykweawenlkgksqedaekeyialvdqliakyss

>A.thaliana (92)

mglkeefeehaekvntltelpsnedllilyglykqakfgpvdtsrpgmfsmkerakwdawkavegksseeamndyitkvkqllevaas

Pabio 536 Lab session and Homework Week 8 Multiple Alignment

1. Perform a multiple alignment using the ACBP liver forms and the ACBP brain forms from this week’s sequence file and show the alignment (ALN file) you obtained (10 points).

2. Compare the pattern of identical residues conserved within the liver forms to those conserved within the brain forms. Are there brain or liver specific residues (ie residues conserved in liver but not in brain or vice versa)? Provide a couple of examples (ie brain: A26, liver: W32)(10 points).

3. A) Determine a “pattern” of liver-specific amino acid residues, ie those amino acids conserved in all liver forms but not in the brain forms. Provide your pattern. (10 points) B) Do a PHI-BLAST search using the human ACBP Liver form in the query and your Liver-specific pattern – limit your output to salmonids. Did you detect a putative liver ACBP form in the salmonid “ atlantic salmon salmo” ? provide the BLAST hit. If you obtain no putative salmon ACBP hits try altering your pattern slightly and redo the PHI-BLAST. If all else fails, do a normal BLAST search with no pattern and exam the hits to see if you can detect a putative liver ACBP form in the salmonid “atlantic salmon salmo”? Provide the BLAST hit. In this last case, how did the salmo sequence differ from your pattern (10 points) C) Do a multiple alignment of all of the liver forms in question 2 plus your putative salmon liver ACBP form – provide the alignment (10 points). D) Discuss the alignment with regard to other liver-specific residues that you did not include in your PHI-BLAST pattern, ie are those conserved as well? Would you consider this putative atlantic salmon ACBP to be a liver form? Discuss (10 points).

4. A) Determine a “pattern” of amino acid residues that are conserved in the ACBP brain forms but not in the liver forms. Provide the pattern (10 points) B) Do a PHI-BLAST search using the human ACBP Brain form in the query and

your Brain-specific pattern – limit your output to salmonids. Did you detect a putative brain ACBP form in the Atlantic salmon (Salmo salar)? If you obtain no putative salmon ACBP hits try altering your pattern slightly and redo the PHI-BLAST. If you still get no putative salmon ACBP hit try doing a protein BLAST without the pattern and look at the hits by eye to determine whether there is a brain form in Salmo salar (hint- you should detect one) (10 points)

C) Do a multiple alignment of all of the brain forms in question 2 plus your putative salmon brain ACBP form – provide the alignment. (10 points)

D) Discuss the alignment with regard to the brain-specific residues? Would you consider this salmon ACBP to be a brain form? Discuss in relationship to your PHI-BLAST pattern and other “brain form”specific characteristics. (10 points)

5. EXTRA CREDIT: Do an alignment of all of the liver and brain form ACBP sequences including the salmon sequences. Identify the identical residues

 

 

conserved within all the sequences and discuss with regard to conservation of the previously characterized “ACBP” motifs (10 points). Can you make any conclusion regarding how the brain and the liver forms differ from each other – relying upon what you know of the structure of ACBP? (no right answer here – something to think about). (10 points)

 
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