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HomeClass Notes1,200,000CA670,000

BMSC 200 Lecture Notes - Lecture 5: Hydrogen Bond, Amine, Acid Dissociation Constant

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School
U of S
Department
Biomedical Sciences
Course
BMSC 200
Professor
Yangdong Wei

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Document Summary

Peptides, proteins and nucleic acids are all polymers. The building blocks (monomers) are amino acids (peptides and proteins) and nucleotides (dna and rna). Both the donor-hydrogen-acceptor angle and the distance between the donor and the acceptor atoms can vary quite a bit, and with that the strength of the bond itself. Remember that the hydrogen bond is an electrostatic interaction, and like any electrostatic interaction, its strength depends on the distance between the interacting charges. Ionic product of water, kw= [h+][oh-]= 10-14 , no matter what ph. Therefore if you know ph, you can always calculate [oh-], and, conversely, if you know [oh-] you can always calculate. Example: if ph=4. 0, then [h+]=10-4 m, and [oh-]=10-14/[h+]=10-10m. From the table given at the exam, the pka values of aspartate are: How to calculate the net charge of a triprotic amino acid, when ph equals pka of one of. +) and has a charge of +1, therefore the.

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Related Questions

Match each term with its definition. Each term or definition is used only once

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

right-spiraling common DNA form
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P. Q. R. S. T.

referencing the opposite orientation of hydrogen-bonded DNA strands
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P. Q. R. S. T.

viral particle whose natural host is a prokaryote
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P. Q. R. S. T.

universal holding that the number of purines always equals the number of pyrimidines
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P. Q. R. S. T.

nucleic acid base sequences able to form a double-stranded structure by virtue of matching base pairs
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P. Q. R. S. T.

5’→ 3’ or 3’→ 5’
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P. Q. R. S. T.

nuclease able to cleave phosphodiester linkages in the DNA backbone
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P. Q. R. S. T.

the structure formed by two DNA strands twisted around a common axis in a spiral
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P. Q. R. S. T.

bacterial cycle of phage- infected cells resulting in cell destruction and viral release
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P. Q. R. S. T.

main access site for proteins that recognize specific DNA sequences
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P. Q. R. S. T.

a cytosine modification favoring Z DNA formation
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P. Q. R. S. T.

nucleic acid monomer consisting of a sugar, a phosphate group, and a nitrogenous base
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P. Q. R. S. T.

connects two nucleic acid sugar molecules via an ester bond
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P. Q. R. S. T.

hydrolyzes peptide bonds linking amino acids
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P. Q. R. S. T.

U or C in RNA
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P. Q. R. S. T.

a pentose sugar
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P. Q. R. S. T.

an enzyme that breaks down RNA
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P. Q. R. S. T.

either of the two nucleotide chains of a double helix
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P. Q. R. S. T.

a pyrimidine able to hydrogen bond with adenine
- A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P. Q. R. S. T.

a DNA configuration favored by high ionic strength and GC repeats
A.

protease
B.

lysis
C.

double helix
D.

bacteriophage
E.

complementary
F.

Chargaff’s rule
G.

B DNA
H.

major groove
I.

nucelotide
J.

antiparallel
K.

RNAse
L.

directionality
M.

phosphodiester linkage
N.

ribose
O.

Z DNA
P.

pyrimidine
Q.

methylation
R.

DNAse
S.

uracil
T.

strand

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.

For the following strand of DNA, use the table below to provide: bases for the complementary mRNA and the associated amino acids. What do you notice about the genetic code for proline in the peptide? How would the loss of the first G or switching that G to a T affect the structure and function of this protein?

DNA: GGC CTA CAA GCC GGA ACA GTT ACC GCG TAA CGA

RNA: ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ???

Amino Acid:??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ???
(3 Letters)

Genetic Code Table (mRNA)

1st position
(5' end)

2nd position (middle)

 3rd position
(3' end)
U C A G
U Phe F
Phe F
Leu L
Leu L 		Ser S
Ser S
Ser S
Ser S		 Tyr Y
Tyr Y
STOP
STOP		 Cys C
Cys C
STOP
Trp W 		U
C
A
G
C Leu L
Leu L
Leu L
Leu L		 Pro P
Pro P
Pro P
Pro P		 His H
His H
Gln Q
Gln Q		 Arg R
Arg R
Arg R
Arg R		 U
C
A
G
A Ile I
Ile I
Ile I
Met M 		Thr T
Thr T
Thr T
Thr T		 Asn N
Asn N
Lys K
Lys K		 Ser S
Ser S
Arg R
Arg R		 U
C
A
G
G Val V
Val V
Val V
Val V		 Ala A
Ala A
Ala A
Ala A		 Asp D
Asp D
Glu E
Glu E		 Gly G
Gly G
Gly G
Gly G		 U
C
A
G