biochemistry is… - du portfolio

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Biochemistry is…“… the study of the

chemical processes/reactions that occur within living organisms.”

“…a summation of the molecular interactions occurring in all forms of life…”

Biochemistry of Proteins class, 2004“… the study of the chemistry done in the human body.”

Biochemistry

“Biochemistry asks how the remarkable properties of living organisms arise from the thousands of different lifeless biomolecules”

“The study of biochemistry shows how the collection of inanimate molecules that constitute living organisms interact to maintain and perpetuate life animated solely by the physical and chemical laws that govern the nonliving universe”

Nelson and Cox, 2004

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Biochemistry“The essence of biological processes – the basis of

the uniformity of living system – is in its most fundamental sense molecular interactions; in other words, the chemistry that takes place between molecules.”

“Biochemistry is the chemistry that takes place within living systems”

Berg, Tymoczko, and Stryer, 2003

Name: Tube worms

Location: First discovered on the Galapagos Rift off the coast of Ecuador

Description: In 1977, scientists first discovered entire communities of

organisms flourishing miles below the surface of the ocean, around

openings in the ocean floor out of which hot, mineral-rich water erupts.

The openingshost a variety of strange and amazing organisms that have

adapted to immense pressure, total darkness, and proximity to super-

heated water that reaches 662 degrees F.

Biochemistry is the chemistry of life.

Name: Methane Ice Worms

Location: Gulf of Mexico, 80 miles off

the coast of Louisiana

Description: In 1997, vast colonies of

strange, rosy-pink worms 1-2 inches in

length were found burrowing in mounds

of methane-rich ice erupting from the sea

floor in the Gulf of Mexico.

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1. A high degree of chemical complexity and microscopic organization.

2. Systems for extracting, transforming and using energy from the environment. Life is opposing entropy.

3. Mechanisms for sensing and responding to alterations in their surroundings.

4. Diverse living organisms share common chemical features.

Three domains of Life

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Source of energy and source of carbon

Autotrophs - which can utilize, inorganic nutrients or light as a source of energy.

Heterotrophs - which require organic compounds as a source of energy.

Photoautotrophs - which use light as an energy source and CO2 as the carbon source.

Photoheterotrophs- which use light as the energy source and reduced organic compounds as a carbon source.

Source of energy and source of carbon

Chemoautorophs - which use inorganic chemicals as an energy source and CO2 as a principal carbon source.

Chemoheterotrophs - which use organic compounds as an energy source as well as a principal carbon source.

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Bacterial Cells

Gram-negative cell has an additional layer and the outside of the cell appears convoluted.

Gram-positive wall is much thicker and its external appearance is smoother.

Gram-positive and gram-negative cells do share one thing in common that is unique to bacteria - peptidoglycan.

streptococci E. coli

Animal cells

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Cellular organization and hierarchy.

1A 8 A

1

H

1.01

2A 3 A 4 A 5 A 6 A 7 A

2

He

4.00

3

Li

6.94

4

Be

9.01

5

B

10.81

6

C

12.01

7

N

14.01

8

O

16.00

9

F

19.00

10

Ne

20.18

11

Na

22.99

12

Mg

24.31

3 B 4 B 5 B 6 B 7B 8B 1 B 2 B

13

Al

26.98

14

Si

28.09

15

P

30.97

16

S

32.07

17

Cl

35.45

18

Ar

39.95

19

K

39.10

20

Ca

40.08

21

Sc

44.96

22

Ti

47.88

23

V

50.94

24

Cr

52.00

25

Mn

54.94

26

Fe

55.85

27

Co

58.93

28

Ni

58.71

29

Cu

63.55

30

Zn

65.38

31

Ga

69.72

32

Ge

72.59

33

As

74.92

34

Se

78.96

35

Br

79.90

36

Kr

83.80

37

Rb

85.47

38

Sr

87.62

39

Y

88.91

40

Zr

91.22

41

Nb

92.91

42

Mo

95.94

43

Tc

(98)

44

Ru

101.1

45

Rh

102.9

46

Pd

106.4

47

Ag

107.9

48

Cd

112.4

49

In

114.8

50

Sn

118.7

51

Sb

121.8

52

Te

127.6

53

I

126.9

54

Xe

131.3

55

Cs

132.9

56

Ba

137.3

57

La*

138.9

72

Hf

178.5

73

Ta

180.9

74

W

183.9

75

Re

186.2

76

Os

190.2

77

Ir

192.2

78

Pt

195.1

79

Au

197.0

80

Hg

200.6

81

Tl

204.4

82

Pb

207.2

83

Bi

209.0

84

Po

(209)

85

At

(210)

86

Rn

(222)

87

Fr

(223)

88

Ra

226.0

89

Acª

227.0

104

Rf

(261)

105

Db

(262)

106

Sg

(263)

107

Bh

(262)

108

Hs

(265)

109

Mt

(266)

110

(269)

111

(272)

Only about 30 elements are essential to organisms.

1. Bulk elements H, Na, K, Ca, C, N, O, P, S, and Cl

2. Trace elements Mg, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Mo, Se, and I

3. Most abundant H, O, N and C (99% of the cellular mass)Form the strongest bonds.

Trace elements

Bulk elements

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Representatives of the organic compounds cellular materials are constructed from

1. Amino acids

2. Nucleic Acids

glycine phenylalanine

adenine cytosine

3. Fatty acids/Lipids

4. Carbohydrates/Sugars

Phosphatidylcholine

Tetradecanoic acid, myristic acid

Glucose

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Chemical Bonds in Biochemistry

1. Covalent bonds

2. Electrostatic interactions

3. van der Waals interactions

4. Hydrogen bonds

5. Hydophobic interactions (will be discussed later)

1. Covalent bonds

Formed by the sharing of a pair of e- between adjacent atoms.bond length = 1.54Ǻ bond energy = 348 kJ mol-1

Energy must be expended to break covalent bonds.

Bond energy of a triple bond > double bond > single bond

bond length = 1.34Ǻ bond energy = 614 kJ mol-1

bond length = 1.20Ǻ bond energy = 839 kJ mol-

Chemical reactions are the breaking and/or forming of covalent bonds.

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2. Electrostatic Interactions (ion-ion)Depends on the electric charge on atoms.

Energy = kq1q2/Dr Coulomb’s law

where q1 and q2 = charges of atomsr = distance between atomsD = dielectric constant of the mediumk = proportionality constant = 332

Na+1 Cl-1r

q1 q2

Electrostatic interaction between 2 atoms each bearing -1 or +1 charges, at a distance of 3Ǻ in water (D = 80).

Long-range effect because the energy falls off as 1/r.

mol

kcalE 4.1

380

1)1)(332(

3. Hydrogen bonds – fundamentaly electrostatic interactionsRelatively weak interactions that are responsible for many of the properties of water.

H-atom is partially shared between two electonegative atoms (N or O).

H-bond donor – the atom the hydrogen is most tightly associated withH-bond acceptor – less tightly linked to the hydrogen

The electonegative atom to which the H is covalently bonded pulls e-

away from the H-atom giving the H-atom a partial positive charge (δ+). The H-atom can then interact with an atom having a partial negative charge (δ-).

These interactions are much weaker than covalent bondsE = 1-3 kcal mol-1

bond distance = 1.5-2.6 Ǻ

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0.9 Å 2.0 Å

180˚

Hydrogen

bond donor

Hydrogen

bond acceptor

4. van der Waals interactionsBasis of the interaction is the distribution of electronic charge around an atom changes with time.

Charge distribution is transiently asymmetric and acts via electrostatic interactions to induce asymmetry on neighboring atoms.

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The attraction between two atoms increases as they come closer to each other until they are separated by the van der Waals contact distance at shorter distances repulsion dominates.

Energies are quite small 0.5 – 1.0 kcal mol-1 per atom pair.

But can be substantial when summed over a large of atoms at the surface of two large molecules.

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