Pabio/Meded 536 Protein BLAST and Motifs

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Pabio/Meded 536 Protein BLAST and Motifs – Homework Purpose: Become familiar with Protein BLAST queries of the NCBI non-redundant databases, using the human acyl-CoA binding protein as a query. To examine the range of BLAST hits, we will restrict the output to C. elegans sequences. We will examine the BLAST alignment outputs for a number of the top BLAST hits and relate the alignments to the amino acid conservation that is obvious from multiple alignment of the human, bovine, duck and yeast ACBP family members (see alignment link in question 7). Examine this alignment and identify recognizable conserved motifs which you will use as the basis for determining homology of the C.elegans sequences with the ACBP protein family. Initially you will evaluate the C.elegans hits by eye, looking for conservation of your chosen motifs. Provide your assessment and indicate your reasons. Then you will take each C.elegans sequence you believe has homology to the ACBP family and do a new protein BLAST search against the Conserved Domain database (you can do this analysis as a protein BLAST search against the non-redundant database, since your protein will be automatically searched against the Conserved Domain database – or you can link to the Conserved Domain database and do the search directly from the links at this site.) You will do two different analyses using the information from the Conserved Domain search. First, reevaluate your assessment of the homology of the C. elegans sequences to the ACBP family. Second, determine whether these C.elegans sequences have any other motif recognized by the conserved domain search. You will then use the multiple repetition PSI-BLAST search, which computes an ACBP-specific scoring matrix based on the aligned ACBP sequences, in an attempt to identify additional C.elegans sequences that are distantly related to the ACBP family. Using all this information you will determine whether C.elegans has an ortholog of human ACBP, providing your criteria. In addition, you will determine how many of the C.elegans sequences contain a recognizable ACBP domain. From this make a guess as to the evolution of the C.elegans ACBP family. Finally, you will use PHI-BLAST, to combine a pattern search (A pattern you have determined from the alignment linked in question 7) with BLAST to again search the non-redundant protein database (limited to C.elegans sequences) to evaluate how PHI-BLAST can be used to detect distant similarities. The first extra credit question will test your ability to compare BLAST results for ACBP family members in humans and drosophilia to determine the evolutionary history of ACBP in these organisms and whether they differ from the C.elegans ACBP family members. The second extra credit question will introduce you to phylogenetic analysis.

1. Retrieve the Acyl-CoA Binding protein (human) sequence (87 amino acids) from the class sequence link or this link and do a standard Protein BLAST search against the NCBI Non-Redundant protein database. IMPORTANT- limited for only the Caenorhabiditis elegans sequences. (In the organism box, start typing “caen” and then choose Caenorhabiditis elegans from the list. – your analysis should only find a restricted number of C. elegans hits). Prepare a table giving the accession numbers, number of amino acids in the protein and Evalues for the

 

 

top 10 BLAST hits. How many ACBP family members are detected? What was your criteria? (Evalue score? Sequence title? (10 pts)

2. Examine the alignments of the top 10 C.elegans hits resulting from your search above. Using your knowledge of the conservation of motifs in the ACBP gene family (see ACBP conservation alignment) determine whether any of the alignments reveal homology to the conserved ACBP motifs (Two motifs YxxYKQA and KWxAW are provided in the ACBP alignment) ? In your table in question 1, add a column for each motif and indicate whether either either motif is found in these 10 C.elegans sequences (Y/N/?). How many ACBP-related sequences do you think are in C.elegans? (10 pts)

3. Take each of the C. elegans in question 2 that you have determined to be related to ACBP (those labeled with a Yes in your table) and determine whether they have a ACBP motif that is detected by the Conserved Domain Search (use each sequence in a BLAST search against the Conserved Domain database). Add a column in your table above (BLAST-CD) and indicate whether there is a conserved ACBP domain detected by BLAST (Y/N). How does this compare to your analysis of the sequence alignments? (10 pts) Do any of these proteins have more than one recognizable functional domain (The BLAST search against the CD database will show you this)? Add a column to your table (Other domains) and indicate the domain name (10 pts). Do the same analysis for the remaining BLAST hits of the top 10 that you determined in question 1 and 2 to not be related to ACBP. Indicate the domains detected by BLAST for these sequences and indicate these results in your table (ACBP? Other?). (10 pts). How many ACBP-related sequences do you now think are in C.elegans?

4. Use the ACBP human protein sequence to do a PSI BLAST search of the non- redundant protein database, limiting to C.elegans.. The PSI BLAST results will select all protein matches above a selected E-value to be used in determining a new ACBP-specific scoring matrix. Use the default setting and perform the second iteration of the PSI-BLAST search. Add a new column to your table (PSI- E) and indicate the new E values determined for your top 10 C.elegans hits in your table. Is there a new C.elegans sequence that has a significant E-value that was not readily detected in the original protein BLAST search? From this analysis, how many C.elegans sequences do you think are related to human ACBP? (10 pts)

5. Does C. elegans have an ortholog of ACBP? State your reasons and provide your criteria and ID. An Evalue alone is not sufficient. (10 pts).

6. Provide a short explanation regarding the evolutionary history of the ACBP homologs in C. elegans, discussing gene duplication, conservation of structure and function, and structural similarities between homologs –only based on the data from your analysis (20 pts).

7. Determine an amino acid pattern that is conserved in the N-terminal domain of the ACBP orthologs in the linked alignment which is also found in your “top” choice of the ACBP ortholog in c.elegans (CLICK HERE for alignment). What is your pattern? Do a PHI-BLAST search using the human ACBP as the probe, and insert your pattern to be searched. Limit the search to C. elegans sequences. How many of the C.elegans ACBP-like sequences contain your pattern? Would you

 

 

consider this pattern specific to ACBP orthologs? Do a PHI-BLAST search with this pattern using the C.elegans ACBP “ortholog” as a probe, limiting your search to human sequences. How many “different” (ie coming from different genes/chromosomes) human sequences match this pattern? Discuss, especially in relationship to orthology between the human and c.elegans sequences. (10 pts).

8. Extra credit – can you determine a pattern that is found in more than 4 of the C.elegans ACBP-like sequences? What is it? Do a PHI-BLAST search with the pattern and one of these four sequences as query, limiting your search to C.elegans. How many C.elegans ACBP-like sequences is it found in (10 pts). Do the same search but limit to human sequences. Are there any human ACBP-like sequences that contain this pattern. Provide one example.(10 pts)?

 
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Cumulative Biology Final Exam

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BIO101_MH_V4 | Topic 14: Review

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Started on Wednesday, July 17, 2019, 11:00 PM State Finished

Completed on Wednesday, July 17, 2019, 11:06 PM Time taken 5 mins 42 secs

Grade 87.50 out of 350.00 (25%)

The structure of valine, an amino acid, is shown. What portion of the valine molecule is indicated by the shaded area?

Select one: a. amino group

b. carbon chain

c. carboxyl group

d. R group

 

 

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Question 4 Correct

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Nucleotides are composed of

Select one: a. adenosine triphosphate, pentose sugars, and phosphates.

b. DNA, ribose sugars and polypeptides.

c. nitrogen-containing bases, phosphates, and peptides.

d. phosphates, pentose sugars, and nitrogen-containing bases.

What are the primary constituents of cell membranes?

Select one: a. carbohydrates

b. lipids

c. minerals

d. proteins

Which of the following is an organic catalyst and usually a protein?

Select one: a. ATP

b. coenzyme

c. enzyme

d. substrate

 

 

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Which of the following cell organelles is the site of the citric acid cycle?

Select one: a. Golgi apparatus

b. mitochondria

c. nucleus

d. ribosome

What is the degradation product of heme?

Select one: a. bile pigment

b. globin

c. iron

d. porphyrin

During photosynthesis, which of the following happens?

Select one: a. Carbon dioxide is reduced to glucose.

b. Chloroplasts convert solar energy to ADP.

c. Hydrogen atoms reduce water to glucose.

d. Water is hydrolyzed.

 

 

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Question 8 Correct

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Question 9 Correct

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Question 10 Incorrect

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Which of these are the photosynthetic organs of a plant?

Select one: a. cones

b. fruits

c. leaves

d. seeds

Which of these is an end product of photosynthesis?

Select one: a. ATP

b. carbon dioxide

c. glucose

d. water

What is the total number of ATP molecules produced by the citric acid cycle?

Select one: a. 2

b. 4

c. 16

d. 256

 

 

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Question 11 Correct

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Question 12 Incorrect

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Question 13 Incorrect

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In cellular respiration, what percentage of the available energy is transferred from glucose to ATP?

Select one: a. 17%

b. 28%

c. 39%

d. 63%

Based on their characteristics, mitochondria could be evolutionary remnants of which type of microorganism?

Select one: a. bacteria

b. fungi

c. protozoa

d. virus

In cellular respiration, what is the end product of chemiosmosis?

Select one: a. ATP

b. glucose

c. NADH

d. pyruvic acid

 

 

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Question 14 Incorrect

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Question 15 Incorrect

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Question 16 Incorrect

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The primary cell wall of plants is composed of which of the following?

Select one: a. cellulose

b. chitin

c. lignin

d. phospholipid

What unique structural property of cellulose makes it largely indigestible by humans?

Select one: a. addition of chitin, another structural polysaccharide

b. alternating positioning of oxygen atoms in linked glucose

c. branched chains of linked glucose

d. covalent bonding between glucose units, providing extra stability

How do peripheral proteins play a role in the plasma membrane?

Select one: a. They often play a structural role, helping stabilize and shape the plasma membrane.

b. They allow ions to �ow directly through the membrane.

c. They bind with glycoproteins for cell recognition in immune responses.

d. They bind with a carrier protein to facilitate membrane transport.

 

 

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Question 17 Correct

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Question 18 Incorrect

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At the end of meiosis I, how many chromosomes from each homologous parental pair does one daughter cell contain?

Select one: a. 1

b. 2

c. 3

d. 4

In meiosis, crossing-over of genetic material between two non-sister chromatids occurs during

Select one: a. anaphase I.

b. metaphase II.

c. prophase I.

d. telophase II.

 

 

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Question 19 Incorrect

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In the phase of mitosis depicted in the �gure, which of the following is occurring?

Select one: a. Chromatids are crossing over.

b. Chromosomes are aligning on the plates.

c. Daughter cells are being formed.

d. Sister chromatids are separating.

 

 

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Question 20 Incorrect

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In the representation of a DNA molecule shown below, what parts of the nucleotides are indicated by the colors red, green, blue, and yellow?

Select one: a. nitrogenous base

b. pentose sugar

c. phosphate

d. ribose sugar

 

 

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Question 21 Correct

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Question 22 Incorrect

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Using the Punnett square, what is the phenotypic ratio of tall plants to short plants?

Select one: a. 1:1

b. 2:1

c. 3:1

d. 1:3

Which of the following causes of mutations occurs when nucleotide pairs are replicated?

Select one: a. errors in replication

b. mutagens

c. transposons

d. gene expression

 

 

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Question 23 Incorrect

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Question 24 Correct

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Question 25 Incorrect

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In the following mutation the letter “C” was deleted from the sequence of codons. Instead of reading “THE CAT ATE THE RAT” the sequence reads “THE ATA TET HER AT.” Which of the following types of mutation is this?

Select one: a. deletion mutation

b. frameshift mutation

c. point mutation

d. protein mutation

Which of the following is an estimate of the number of pairs of DNA bases in the human genome?

Select one: a. 300,000 pairs

b. 5.8 million pairs

c. 3.2 billion pairs

d. 6.4 trillion pairs

Which type of bacteria is produced by biotechnology to express a cloned gene?

Select one: a. aerobic

b. pathogenic

c. peritrichous

d. transgenic

 

 

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Question 26 Incorrect

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In this illustration of the stem of a plant, the arrow points to which structure?

Select one: a. auxiliary bud

 

 

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b. node

c. petiole

d. terminal bud

Which type of root is used by certain plants for food storage?

Select one: a. adventitious

b. �brous

c. pneumatophore

d. tap

Which of the following processes involves evaporation of water from the leaves?

Select one: a. osmosis

b. respiration

c. translocation

d. transpiration

According to the cohesion-tension model, how does xylem transport work in plants?

Select one: a. Tension created by atmospheric pressure pushes water up the xylem.

b. Tension created by transpiration in the leaves pulls water along the xylem.

c. Water entering the root cells creates negative pressure that pushes water up the xylem.

d. Water is actively transported up the xylem by gravity.

 

 

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Question 30 Correct

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Question 31 Correct

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Which of the following types of tropism is exhibited by the plant shown in the photograph?

Select one: a. negative gravitropism

b. negative phototropism

c. positive phototropism

d. positive gravitoprism

Which plant hormone facilitates ripening of fruits?

Select one: a. abscisic acid

b. auxin

c. ethylene

d. gibberellin

 

 

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Question 32 Incorrect

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Question 33 Incorrect

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Referring to the diagram, what is the correct order of labeling for the boxes (1-4) depicting alternation of generations in �owering plants?

Select one: a. (1) meiosis, (2) mitosis, (3) fertilization, (4) mitosis

b. (1) meiosis, (2) mitosis, (3) mitosis, (4) meiosis

c. (1) mitosis, (2) meiosis, (3) fertilization, (4) mitosis

d. (1) mitosis, (2) meiosis, (3) meiosis, (4) mitosis

In plant reproduction, what is the eudicot structure that provides nutrition to the embryo?

Select one: a. cotyledon

b. hypocotyl

c. plumule

d. radicle

 

 

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Question 35 Incorrect

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Which of the following parts of a �ower protect the bud as the �ower develops?

Select one: a. anthers

b. ovaries

c. petals

d. sepals

An animal exhibits the following characteristics: tentacles, radial symmetry, and incomplete digestive tract. This animal would be classi�ed in which phylum?

Select one: a. Cnidaria

b. Platyhelminthes

c. Porifera

d. Rotifera

 

 

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Question 36 Incorrect

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According to the cladogram shown, what two characteristics distinguish lizards from gorillas?

Select one: a. an amniotic membrane and hair

b. bipedalism and a tail

c. hairlessness and a tail

d. jaws and lungs

 

 

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Question 37 Incorrect

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Question 38 Incorrect

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In the context of evolution, which type of selection is depicted in the graph?

Select one: a. directional selection

b. disruptive selection

c. natural selection

d. stabilizing selection

According to the Hardy-Weinberg principle, allele frequencies in a gene pool will remain at equilibrium as long as there is

Select one: a. interbreeding between populations.

b. frequent mutation.

c. genetic drift.

d. random mating.

 

 

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Question 39 Incorrect

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Question 41 Correct

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Spores are found in which part of a mushroom?

Select one: a. hyphae

b. lamellae

c. pileus

d. stipe

Which of the following types of mammal has a cloaca?

Select one: a. marsupial

b. monotreme

c. Placental

d. Testudinata

The blastopore develops into the anus in which of these invertebrates?

Select one: a. cockroach

b. earthworm

c. sea cucumber

d. squid

 

 

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Question 42 Incorrect

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According to the replacement model, where did the Homo sapiens in Europe migrate from?

Select one: a. Africa

b. Asia

c. Europe

d. North America

Which of the following human ancestors were the �rst to make tools?

Select one: a. Ardipithecines

b. Australopithecines

c. Homo erectus

d. Homo habilis

Which type of tissue lines the cavities of the human body?

Select one: a. connective

b. epithelial

c. muscular

d. nervous

 

 

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Question 45 Incorrect

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Question 46 Correct

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Question 47 Incorrect

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In the human body, which of these is a matrix of white �bers in connective tissue?

Select one: a. actin

b. collagen

c. elastic

d. myosin

Which term refers to the outermost layer of human skin?

Select one: a. dermis

b. subcutaneous

c. epidermis

d. follicle

In the human respiratory system, exchange of oxygen and carbon dioxide occurs in the

Select one: a. alveoli.

b. bronchi.

c. bronchioles.

d. trachea.

 

 

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Question 48 Incorrect

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Question 50 Correct

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In human reproduction, nutrient-rich blood is transported from the placenta to the fetus by the

Select one: a. foramen ovale.

b. inferior vena cava.

c. umbilical artery.

d. umbilical vein.

Which of the following female reproductive organs produces oocytes?

Select one: a. cervix

b. ovaries

c. oviducts

d. uterus

A typical human somatic cell contains how many chromosomes?

Select one: a. 22

b. 23

c. 46

d. 47

 

 

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Question 51 Incorrect

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Question 52 Incorrect

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What must primary mRNA undergo to become mature mRNA?

Select one: a. processing provided by tRNA molecules

b. processing to remove introns and join exons

c. processing to remove exons and join introns

d. translation into codon of amino acids

The addition of a poly-A tail and a guanine cap to a primary mRNA exempli�es which level of gene control in eukaryotes?

Select one: a. transcriptional

b. post-transcriptional

c. translational

d. post-translational

 

 

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Question 53 Correct

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In the food web shown in the �gure, which of the following are the primary consumers?

Select one: a. bald eagle and osprey

b. phytoplankton, submerged aquatic vegetation, and vegetation

c. small planktivorous �sh, benthic invertebrates, herbivorous ducks, geese and mute swans

d. gulls, wading birds, large piscivorous �sh, sea ducks, and tundra swan

 

 

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Question 54 Incorrect

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Question 55 Correct

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Question 56 Incorrect

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Which of the following is the order of energy �ow within an ecosystem?

Select one: a. decomposers ⇒ consumers ⇒ producers

b. producers ⇒ consumers ⇒ decomposers

c. producers ⇒ decomposers ⇒ carnivores

d. decomposers ⇒ producers ⇒ consumers

In the ocean, coral reefs are found in which zone?

Select one: a. abyssal

b. bathypelagic

c. epipelagic

d. mesopelagic

Of Earth’s terrestrial biomes, which one is hot in the summer, cold in the winter, gets moderate annual precipitation, and has good soil for agriculture?

Select one: a. grasslands

b. shrublands

c. taiga

d. tundra

 

 

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Question 57 Incorrect

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Question 58 Incorrect

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Question 59 Incorrect

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Which protists are responsible for causing red tide?

Select one: a. diatoms

b. dino�agellates

c. �agellates

d. sporozoans

Which of the following is a density-dependent regulating factor on the population of a community?

Select one: a. availability of space

b. competition

c. temperature range

d. water supply

Which type of learning occurs when a dog stops eating butter�ies because he gets sick every time he eats one?

Select one: a. classical conditioning

b. operant conditioning

c. unconditioned response

d. imprinting

 

 

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Question 60 Correct

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To communicate the location of a food source, a honey bee returns to its hive and performs a dance while the other bees gather around and touch it with their antennae. By touching the returning bee with their antennae, what form of communication are the bees exhibiting?

Select one: a. auditory

b. chemical

c. tactile

d. visual

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Human Body Systems Worksheet

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Human Body Systems Worksheet

Fill in the table for each system. You must identify the system by the organs present. Be as concise as possible.

Name and main function of the system:

      

 
Main organs of the system:

These are provided. Use this information to fill in the remainder of the table.

 Mouth, esophagus, stomach, small intestine, large intestine, rectum, anus

Salivary glands, pancreas, liver, gall bladder
What each organ does:

      

 
How the system affects other body systems or is affected by other systems

(Describe one interaction with another organ system)

      
One disease of the system:

      

 
Name and main function of the system:

      

 
Main organs of the system:

These are provided. Use this information to fill in the remainder of the table.

 kidney
What each organ does:

      

 
How the system affects other body systems or is affected by other systems

(Describe one interaction with another organ system)

      
One disease of the system:

      

 
Name and main function of the system:

      

 
Main organs of the system:

These are provided. Use this information to fill in the remainder of the table.

 Scrotum, testes, vas deferens, urethra, penis

Ovaries, fallopian tube, uterus, vagina
What each organ does:

      

 
How the system affects other body systems or is affected by other systems

(Describe one interaction with another organ system)

      
One disease of the system:

      

 
Name and main function of the system:

      

 
Main organs of the system:

These are provided. Use this information to fill in the remainder of the table.

 Bone, joints
What each organ does:

      

 
How the system affects other body systems or is affected by other systems

(Describe one interaction with another organ system)

      
One disease of the system:

      

 
Name and main function of the system:

      

 
Main organs of the system:

These are provided. Use this information to fill in the remainder of the table.

 Skeletal muscle
What each organ does:

      

 
How the system affects other body systems or is affected by other systems

(Describe one interaction with another organ system)

      
One disease of the system:

      

 
Name and main function of the system:

      

 
Main organs of the system:

These are provided. Use this information to fill in the remainder of the table.

 lungs
What each organ does:

      

 
How the system affects other body systems or is affected by other systems

(Describe one interaction with another organ system)

      
One disease of the system:

      

 
Name and main function of the system:

      

 
Main organs of the system:

These are provided. Use this information to fill in the remainder of the table.

 Heart, arteries, veins, capillaries
What each organ does:

      

 
How the system affects other body systems or is affected by other systems

(Describe one interaction with another organ system)

      
One disease of the system:

      

 

 

Name and main function of the system:

      

 
Main organs of the system:

These are provided. Use this information to fill in the remainder of the table.

 Lymph nodes
What each organ does:

      

 
How the system affects other body systems or is affected by other systems

(Describe one interaction with another organ system)

      
One disease of the system:

      

 
Name and main function of the system:

      

 
Main organs of the system:

These are provided. Use this information to fill in the remainder of the table.

 Hypothalamus, pituitary, thyroid, parathyroid, pancreas, adrenal glands, testes, ovaries
What each organ does:

      

 
How the system affects other body systems or is affected by other systems

(Describe one interaction with another organ system)

      
One disease of the system:

      
 
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Health Questions

/in /by
1.   Practitioners that have specialized training in the musculoskeletal system are called
A. occupational therapists.
B. physical therapists.
C. rehabilitation specialists.
D. chiropractors.

 

 

2.   The Health Care and Education Reconciliation Act of 2010 was mandated under the
A. Office of the Inspector General.
B. American Health Information Management Association (AHIMA).
C. Medicare Act of 1965.
D. Affordable Care Act (ACA).

 

 

7.   Heat, water, sound, and ultrasound procedures are often administered by
A. dental assistants.
B. nurses aides.
C. medical assistants.
D. physical therapy aides.

 

 

8.   What term is used to refer to the process of communicating with people from different health care backgrounds?
A. Professional coarctation
B. Interprofessional or interdisciplinary collaboration
C. Health care interdisciplinary communication
D. Peer-to-peer review

 

 

10.   Which one of the following statements indicates that an individual understands how health insurance coverage works?
A. “Because of the Affordable Care Act (ACA), I don’t need to apply for health care insurance.”
B. “Because I work in a hospital, I’m eligible for Medicaid coverage.”
C. “Because I’m 60 years old, I can get Medicare coverage.”
D. “Because my father served in the military, I’m eligible for TRICARE insurance.”

 

 

12.   Identifying key beliefs and cultures is a/an
A. professional characteristic of a health care worker.
B. element of becoming culturally sensitive.
C. component of nursing treatment in the ICU.
D. necessary for the administration of religious rites.

 

 

18.   What is the purpose of the Health Insurance Portability and Accountability Act (HIPAA)?
A. To determine the scope of practice for health care workers
B. To protect doctors against malpractice suits
C. To protect and enhance the privacy of the patient
D. To ensure health care workers’ safety on the job

 

 

19.   Which one of the following statements about the responsibilities of medical billers and coders is correct?
A. They use three code sets: ICD, CPT, and HCPCS.
B. They play a minor role in health care reimbursement.
C. They create documentation required for reimbursement from only third-party payers.
D. They should not examine patient records.

 

 

20.   Which one of the following health care workers would be employed to provide services at a rehabilitation center?
A. Louisa, a medical coder
B. Maria, a speech pathology assistant
C. Patrick, a pharmacy technician
D. Jim, a health information manager
 
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