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BIOLOGY 151 Chapter 10.2-10.4: bio textbook 10.2-10.4

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UW-Madison
Department
Biology
Course
BIOLOGY 151
Professor
Donna Fernandez

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Document Summary

I (ll_ +- jq, l-f j 0 0. 11 ev~or yotic ce11s tno_ vt ch leo11+ 2 cytosr~l t()c) f. le. ,~t

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Related Questions

- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P.

Step 1.
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P.

Step 2.
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P.

Step 3.
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P.

Step 4.
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P.

Step 5.
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P.

Step 6.
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P.

Step 7.
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P.

Step 8.
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P.

Step 9.
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P.

Step 10.
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P.

Step 11.
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P.

Step 12.
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P.

Step 13.
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P.

Step 14.
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P.

Step 15.
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P.

Step 16.
A.

Don appropriate personal protective equipment (PPE).
B.

Aseptically transfer 1 mL from dilution tube 2 to dilution tube 3 and mix well. This is a 10-5 cumulative dilution.
C.

Aseptically transfer 1.0 mL from dilution tube 4 to dilution tube 5 and mix well. This is a 10-7 cumulative dilution.
D.

Aseptically transfer 0.1 mL from dilution tube 1 to dilution tube 2 and mix well. The cumulative dilution of the culture is 10-4.
E.

Allow the inocula to soak into the plates before proceeding.
F.

Aseptically transfer 0.1 mL from dilution tube 2 to plate A1. Using the spread plate technique, disperse the sample evenly over the entire surface of the agar.
G.

Aseptically transfer 1 mL from dilution tube 3 to dilution tube 4 and mix well. This is a 10-6 cumulative dilution.
H.

Obtain eight plates, organize them int four pairs and label them A1, A2, B1, B2, etc.
I.

Keep accurate records in your lab notebook.

Clean up the lab benches, doff PPE, and wash hands.
J.

Repeate the procedure with plate A2 and label both plates "10-5mL of original sample," or simply "10-5"

Notice that transferring 0.1 mL counts as a dilution!! The tube was a 10-4 dilution, but the plate is a 10-5 dilution!!
K.

Invert the plates so they are "agar up" to prevent condensation from ruining the plates.
L.

Repeat the aseptic transfer, spread plate technique, and label schematic for dilutions tubes 3, 4, and 5, and plates B, C, and D.
M.

Incubate the plates at 35℃ for 24 to 48 hours.
N.

Obtain five dilution tubes and label them 1–5, respectively. Make sure they remain covered until needed.
O.

Aseptically add 9.9 mL sterile water to dilution tubes 1 & 2. Cover when finished. Aseptically add 9.0 mL sterile water to dilution tubes 3, 4, and 5. Cover when finished.
P.

Mix the broth culture an aseptically transfer 0.1 mL to dilution tube 1. Mix dilution tube 1 well. This is a 10-2 dilution

NEED HELP PLEASE. CAN YOU PLEASE DO IT ALL NOT JUST ANSWER ONE.

MY ANIMALS ARE: HUMAN, KANGAROO, RHESUS MONKEY, BULLFROG, LAMPREY, SNAPPING TURTLE, TUNA, AND EARTHWORM

Step 3: Cytochrome c Analysis

Scientists have found that almost all living organisms have a gene that codes for a protein called Cytochrome c. This chart lists the amino acids found in the Cytochrome c protein of some of the organisms on your cladogram.

Note: not all the organisms you used will be in the chart; as such, you can focus this analysis on the animals that are in the chart. If you only chose three animals that are in the chart, you should probably extend your amino acid analysis to include a couple animals that aren’t on your cladogram.

You will use the data provided in this chart to compare and analyze the amino acid sequences for Cytochrome c among these organisms. Be sure that your comparison considers the entire amino acid sequence, through amino acid 112, and not just the first lines of the chart. Once you have compared the sequences, you will write a discussion about your findings.

Amino Acid Sequences in Cytochome-C Proteins

1-30

Amino Acid Position Number

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

29

30

Human, Chimpanzee

-

-

-

-

-

-

-

-

G

D

V

E

K

G

K

K

I

F

I

M

K

C

S

Q

C

H

T

V

E

K

Rhesus Monkey

-

-

-

-

-

-

-

-

G

D

V

E

K

G

K

K

I

F

I

M

K

C

S

Q

C

H

T

V

E

K

Horse

-

-

-

-

-

-

-

-

G

D

V

E

K

G

K

K

I

F

V

Q

K

C

A

Q

C

H

T

V

E

K

Pig, Cow, Sheep

-

-

-

-

-

-

-

-

G

D

V

E

K

G

K

K

I

F

V

Q

K

C

A

Q

C

H

T

V

E

K

Dog

-

-

-

-

-

-

-

-

G

D

V

E

K

G

K

K

I

F

V

Q

K

C

A

Q

C

H

T

V

E

K

Gray Whale

-

-

-

-

-

-

-

-

G

D

V

E

K

G

K

K

I

F

V

Q

K

C

A

Q

C

H

T

V

E

K

Rabbit

-

-

-

-

-

-

-

-

G

D

V

E

K

G

K

K

I

F

V

Q

K

C

A

Q

C

H

T

V

E

K

Kangaroo

-

-

-

-

-

-

-

-

G

D

V

E

K

G

K

K

I

F

V

Q

K

C

A

Q

C

H

T

V

E

K

Penguin

-

-

-

-

-

-

-

-

G

D

I

E

K

G

K

K

I

F

V

Q

K

C

S

O

C

H

T

V

E

K

Snapping Turtle

-

-

-

-

-

-

-

-

G

D

V

E

K

G

K

K

I

F

V

Q

K

C

A

Q

C

H

T

V

E

K

Bullfrog

-

-

-

-

-

-

-

-

G

D

V

E

K

G

K

K

I

F

V

Q

K

C

A

Q

C

H

T

C

E

K

Tuna

-

-

-

-

-

-

-

-

G

D

V

A

K

G

K

K

T

F

V

Q

K

C

A

Q

C

H

T

V

E

N

31-60

Amino Acid Position Number

31

32

33

34

35

36

37

38

39

40

41

42

43

44

45

46

47

48

49

50

51

52

53

54

55

56

57

58

59

60

Human, Chimpanzee

G

G

K

H

K

T

G

P

N

L

H

G

L

F

G

R

K

T

G

Q

A

P

G

Y

S

Y

T

A

A

N

Rhesus Monkey

G

G

K

H

K

T

G

P

N

L

H

G

L

F

G

R

K

T

G

Q

A

P

G

Y

S

Y

T

A

A

N

Horse

G

G

K

H

K

T

G

P

N

L

H

G

L

F

G

R

K

T

G

Q

A

P

G

F

T

Y

T

D

A

N

Pig, Cow, Sheep

G

G

K

H

K

T

G

P

N

L

H

G

L

F

G

R

K

T

G

Q

A

P

G

F

S

Y

T

D

A

N

Dog

G

G

K

H

K

T

G

P

N

L

H

G

L

F

G

R

K

T

G

Q

A

P

G

F

S

Y

T

D

A

N

Gray Whale

G

G

K

H

K

T

G

P

N

L

H

G

L

F

G

R

K

T

G

Q

A

V

G

F

S

Y

T

D

A

N

Rabbit

G

G

K

H

K

T

G

P

N

L

H

G

L

F

G

R

K

T

G

Q

A

V

G

F

S

Y

T

D

A

N

Kangaroo

G

G

K

H

K

T

G

P

N

L

N

G

I

F

G

R

K

T

G

Q

A

P

G

F

T

Y

T

D

A

N

Penguin

G

G

K

H

K

T

G

P

N

L

H

G

I

F

G

R

K

T

G

Q

A

E

G

F

S

Y

T

D

A

N

Snapping Turtle

G

G

K

H

K

T

G

P

N

L

N

G

L

I

G

R

K

T

G

Q

A

E

G

F

S

Y

T

E

A

N

Rattlesnake

G

G

K

H

K

T

G

P

N

L

H

G

L

F

G

R

K

T

G

Q

A

V

G

Y

S

Y

T

A

A

N

Bullfrog

G

G

K

H

K

V

G

P

N

L

Y

G

L

I

G

R

K

T

G

Q

A

A

G

F

S

Y

T

D

A

N

Tuna

G

G

K

H

K

V

G

P

N

L

W

G

L

F

G

R

K

T

G

Q

A

E

G

Y

S

Y

T

D

A

N

61-90

Amino Acid Position Number

61

62

63

64

65

66

67

38

69

70

71

72

73

74

75

76

77

78

79

80

81

82

83

84

85

86

87

88

89

90

Human, Chimpanzee

K

N

K

G

I

I

W

G

E

D

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Rhesus Monkey

K

N

K

G

I

T

W

G

E

D

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Horse

K

N

K

G

I

T

W

K

E

E

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Pig, Cow, Sheep

K

N

K

G

I

T

W

G

E

E

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Dog

K

N

K

G

I

T

W

G

E

E

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Gray Whale

K

N

K

G

I

T

W

G

E

E

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Rabbit

K

N

K

G

I

T

W

G

E

D

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Kangaroo

K

N

K

G

I

I

W

G

E

D

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Penguin

K

N

K

G

I

T

W

G

E

D

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Snapping Turtle

K

N

K

G

I

T

W

G

E

E

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Rattlesnake

K

N

K

G

I

I

W

G

D

D

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

V

F

Bullfrog

K

N

K

G

I

T

W

G

E

D

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Tuna

K

S

K

G

I

V

W

N

N

D

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

91-112

Amino Acid Position Number

91

92

93

94

95

96

97

98

99

100

101

102

103

104

105

106

107

108

109

110

111

112

Human, Chimpanzee

V

G

I

K

K

K

E

E

R

A

D

L

I

A

Y

L

K

K

A

T

N

E

Rhesus Monkey

V

G

I

K

K

K

E

E

R

A

D

L

I

A

Y

L

K

K

A

T

N

E

Horse

A

G

I

K

K

K

T

E

R

E

D

L

I

A

Y

L

K

K

A

T

N

E

Common Zebra

A

G

I

K

K

K

T

E

R

E

D

L

I

A

Y

L

K

K

A

T

N

E

Pig, Cow, Sheep

A

G

I

K

K

K

G

E

R

E

D

L

I

A

Y

L

K

K

A

T

N

E

Dog

A

G

I

K

K

T

G

E

R

A

D

L

I

A

Y

L

K

K

A

T

K

E

Gray Whale

A

G

I

K

K

K

G

E

R

A

D

L

I

A

Y

L

K

K

A

T

N

E

Rabbit

A

G

I

K

K

K

D

E

R

A

D

L

I

A

Y

L

K

K

A

T

N

E

Kangaroo

A

G

I

K

K

K

G

E

R

A

D

L

I

A

Y

L

K

K

A

T

N

E

Penguin

A

G

I

K

K

K

S

E

R

A

D

L

I

A

Y

L

K

D

A

T

S

K

Snapping Turtle

A

G

I

K

K

K

A

E

R

A

D

L

I

A

Y

L

K

D

A

T

S

K

Rattlesnake

T

G

L

K

K

K

K

E

R

T

D

L

I

A

Y

L

K

E

A

T

A

K

Bullfrog

A

G

I

K

K

K

G

E

R

Q

D

L

I

A

Y

L

K

S

A

C

S

K

Tuna

A

G

I

K

K

K

G

E

R

Q

D

L

V

A

Y

L

K

S

A

T

S

-

More information:

Cytochrome c is a protein used in cellular respiration by most eukaryotes, which is why it's a very common protein to use for comparisons. You don't need to know anything about cellular respiration or the protein itself to do this analysis; just remember that a protein is a specific chain of amino acids.

Which amino acids are found, and the order in which they're found (their sequence), determine the shape, structure, and function of the protein. Also remember that an amino acid sequence is directly determined by the DNA sequence, so similarities in one also indicate similarities in the other.

Please note that the entire sequence of 112 amino acids represents one protein, and this sequence data is all one chart, not four. As such, your analysis should consider the sequence as a whole, and not amino acids 1 – 30, then amino acids 31 – 60, etc.

Be careful not to read too much into the differences you find. Since this analysis only looks at one protein, you will not be able to connect differences here to specific differences in traits between organisms. In other words, it might be that all animals with a placenta have a “V” at a particular location, while animals without a placenta have either a “C” or a “K.” That similarity helps us confirm that those animals with a placenta are more closely related to each other than to the others, but the “V” does not code for the placenta, nor is it related to that particular trait at all.

How to Analyze the Data

While you analyze the data that you are given to identify similarities and differences, be sure to use specific data to draw your comparisons, hypotheses, and discussions from. It is especially helpful to quantitatively compare data. A good way to do this, or at least to start, is to pick one species as a starting point or ‘baseline’ and then compare the amount of differences between that and each other species. Be careful, though, about the conclusions you draw – if species B and C each have 5 differences from species A, then they could have anywhere from 0 to 10 differences with each other!

Once you’ve compared each animal to a baseline animal, you should also compare other pairs of species so that you can discuss their specific relationships. If you only have a few animals with data to analyze in part C, you could simply make this comparison for every pair. If you have 6 or 7 animals, then you could pick just a few pairs to compare.

There are other legitimate ways to form quantitative data – for instance, you could focus on specific locations where most animals have the same amino acid, but some are different. These types of analysis tend to be harder to interpret, though. If you choose to use them, I suggest that you still complete at least some of the above types of analysis as well.

The discussion topics that I'm looking for are:

Use the chart to compare the amino acid sequences for the organisms. Do this in a way that lets you obtain quantitative (numerical) data; see above for suggestions.

Hypothesize about how closely related the different organisms are, based on the amino acid data in the chart.

In particular, focus on organisms that are also found on your phylogenetic tree, but you may choose to discuss others, too. That would be especially helpful if you used only three or four of the organisms that are also in the chart, or if one or more organisms that you did not include in your tree jump out at you as being especially similar or especially different from the ones you did include.

This does not need to be in the form of a formal hypothesis; that is, you do not need to put this in “if/then/because” form.

Because “how closely related” can be interpreted in many ways, it’s often helpful to put this in relative terms: “Animal D is the closest relative to Animal A.” “Animals C and B are more closely related to each other than either one is to Animal D.”

Discuss how this analysis compares to the relationships that were shown on your phylogenetic tree.

To start, does the Cytochrome c data agree or disagree with the relationships shown on the tree?

Remember that "discuss" means more than simply identifying whether the relationships are the same or different as what is shown. You can also suggest why they're likely the same, or what possible differences could imply, if anything. See the note at the end of “More Information” above – don’t read TOO MUCH into any one piece of data!

If your amino acid analysis included animals that weren’t on your cladogram, you could use your amino acid data to speculate where they likely “fit” on the cladogram.

The phrase “common ancestor” should show up somewhere in this discussion.

Please be aware that Step 3 should be written as a short essay, not a list or set of questions and answers. You may include a chart or table for the quantitative data you identified, but the key findings should also be written in sentence form. Once you’ve finished writing this, please proofread for spelling, grammar, and writing clarity.

Step 3 should be a sizeable portion of this portfolio. I expect that your analysis should be about 250 – 400 words long in order to thoroughly analyze the data and discuss the questions.

Matching

1- restriction enzyme

2- codon

3- mRNA

4- Cosmids

5- Ribosomal RNA

6- RNA primers

7- SNP

8- Z-DNA

9- Gyrase

10- Euchromatin

11- Palindromes

12- Helicases

--------------------

A- Cuts DNA at CCCGGG

B- Highly compacted chromatin

C- Cloning vector

D- Topoisomerases

E Lagging strand DNA replication

F- Pharmacogenomics

G= Minimum unit of genetic sense

H- Immunogenic from DNA

I- Poorly compacted chromatin

J- Inverted DNA repeats

K- Strand seperations

L- Minimum functional genetic unit.

M- Structural component of ribosome.