Biological Chemistry

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1

Atom

The smallest particle of an element that still contains all the properties of the element

2

Atomic number

The number of protons

3

Atomic mass

The weight of the atom

# of protons + # of neutrons

4

An atom is neutral when the number of __________ equals the number of __________.

Electrons

Protons

5

Ion?

An atom that has an unequal amount of electrons and protons

6

Isotope

Each of two or more forms of the same element that contain equal numbers of protons but different numbers of neutrons in their nuclei, and hence differ in relative atomic mass. Usually unstable.

7

Molecule

The smallest unit of a substance (more than 1 atom) having its own properties.

8

Electron energy levels

The discrete levels surrounding the nucleus

9

Inner electrons have _________ energy and outer electrons have _________ energy.

Lower

Higher

10

Valence electrons

Electrons within the outermost energy level

11

When are atoms reactive?

When their valence shell isn't full

12

What are two types of strong chemical bonds?

Covalent

Ionic

13

Ionic bond

The transfer of electrons

14

Covalent bond

The sharing of electrons

15

Two types of covalent bonds

1. Polar: unequal sharing of electrons

2. Nonpolar: equal sharing of electrons

16

Three biologically important weak bonds

1. Hydrogen bonds

2. Van-der-Waals interactions

3. Hydrophobic Interactions

17

Hydrogen bonds

Polar covalent bonding as a single hydrogen is shared between electronegative atoms N or O. This is a weak electrostatic interaction.

H2O

18

Van-der-Waals interactions

Occurs between electrically neutral molecules when they are very close together, due to slight perturbations of electron distributions

19

Hydrophobic interactions

Occurs between groups that are insoluble in water; these nonpolar groups tend to clump together minimizing their exposure to H2O

20

Hydrogen bonds alone are very __________, but together as a whole ___________.

Weak

Strong

21

The DNA back bone is held together by __________ bonds.

Hydrogen

22

1. A and T are held together by a __________ bond.

2. G and C are held together by a __________ bond.

1. Double

2. Triple

23

pH is the measure of __________ concentration

Hydrogen

24

What is the equation for pH?

pH = -log10 [ H+ Concentration ]

25

__________ + log10 [OH-] = -14

log10 [H+] + log10 [OH-] = -14

26

When does pOH equal pH?

When pH is 7, at neutrality.

27

1. If a solution is neutral and H+ is added then the pH goes toward __________.

2. If the solution is neutral and OH- is added the the pH goes towards __________.

1

14

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1. Acid

2. Base

3. Salt

1. Acid: Proton donor

2. Base: Proton acceptor

3. Salt: Dissociates but releases neither OH- of H+

29

Buffer

Has the ability to minimize pH fluctuations by:

1. Bonding to H+ as H+concentration rises, therefore removing them from the solution.

2. Releasing H+ into solution as the concentration of H+ begins to fall

30

Chemical reactions

The rearrangement of atoms often involving making or breaking of chemical bonds

31

Most organisms are __________ - __________% water.

75 - 85%

32

Give 5 reasons why water is important

1. Water is a gold solvent, dissolves but is inert

2. High surface tension due to hydrogen bonding (capillary action)

3. High heat capacity due to hydrogen bonds absorbing heat from chemical reactions (maintains body temperature)

4. High heat of vaporization due to many hydrogen bonds

5. Ice is less dense than liquid water so ice floats

33

How do water molecules come together?

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Hydrogen bond forms between the H of one water molecule and the O of the other.

34

CO2 is considered __________ even though it contains carbon, due to its structure.

Inorganic

35

Give two reasons why CO2 is important

1. Used by green plants together with H2O and light to manufacture complex organic molecules for food

2. Major by-product of metabolism of aerobic organisms

36

Give two reasons why O2 is important

1. Required by most living organisms for maintenance of life

2. Needed fro oxidation of nutrient molecules - extracting usable energy from them

37

Carbon has __________ valence electrons

4

38

Why is carbon so unique?

1. Forms single, double, and triple bonds with itself

2. Forms double bonds with O and N

3. Forms triple bonds with N

39

Carbon is very __________.

Stable

40

__________, __________, __________, and __________ are the lightest elements that form covalent bonds.

C, H, O, and N

41

Describe how carbon compounds exhibit great structural diversity

they can form rings, straight and bent chains, branched chains, and stereoisomers

42

What are stereoisomers?

Same elemental content but different spatial arrangement

43

Amphipathic

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Both hydrophobic and hydrophilic in one molecule

44

Amphoteric

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Both positive and negative charge in the same molecule

45
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1. What functional group is this?

2. Is it polar or nonpolar?

1. Carboxyl group

2. Polar

46
card image

1. What functional group is this?

2. Is it polar or nonpolar?

1. Amino group

2. Polar

47
card image

1. What functional group is this?

2. Is it polar or nonpolar?

1. Hydroxyl group

2. Polar

48
card image

1. What functional group is this?

2. Is it polar or nonpolar?

1. Sulfhydryl group

2. Polar

49

Macromolecules

Carbohydrates (sugars, starches, cellulose, chitin)

50

What is another word for a macromolecule?

A polymer

51

Polymers are made by jioning many similar or identical small molecules called __________.

Monomers

52

Monomer

Basic building block molecules

Simple sugars (monoscaccharides) many contain 3, 5, 6 or more carbons

53

Glucose and fructose are monosaccarides containing __________ carbons

6

54

What are the two forms of monosaccarides?

1. Aldosugars: have an aldehyde functional group (H-C=O)

2. Ketosugars: Have a ketone functional group (C=O)

55

What is the difference between α-D-glucose and β-D-glucose?

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α-D-glucose has its hydroxyl on carbon 1 pointing downward

β-D-glucose has its hydroxyl on carbon 1 pointing upward

56

Condensation dehydration reaction

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Reaction that builds a molecule by losing water

57

Hydrolysis reaction

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Reaction that breaks a molecule down by adding water

58

2 monosaccharides can be covalently bonded together to form a disaccharide through __________ __________ __________

Condensation dehydration reaction

59

When 2 monosaccharides are bonded together to form a disaccharide the resulting bond is called a __________ bond

Glycosidic

60

3 examples of gylcosidic bonds:

1. Glucose + Glucose =

2. Glucose + Fructose =

3. Glucose + Galactose =

1. Glucose + Glucose = Maltose

2. Glucose + Fructose = Sucrose

3. Glucose + Galactose = Lactose

61
card image

What monosaccharide is this?

Fructose

62

Condensation dehydration, and hydrolysis reactions are very important in __________.

Digestion

63

Through repeated condensation reaction, you can build __________ which are polymers of monosaccharides.

Polysaccharides

64

What is the difference between an α-1,4-glycosidic linkage and a β-1,4-glcosidic linkage?

card image

α-1,4-glycosidic linkage connects two α sugars

β-1,4-glcosidic linkage connects α sugar and one sugar

65

What enzyme breaks glycosidic linkages?

Amylase

66

Glycogen

Principal carbohydrate storage product in animals

Highly branched glucose glucose polymer

67

What is the most common linkage in glycogen?

Polymer of α-D-glucose liked by α-1,4-linkages

68
card image

Describe this image

This is glycogen. Each end of glycogen produces 2 molecules of glucose, that's why there is so many ends

69

Glycogen is stored mainly in your __________ and __________.

Liver

Muscles

70

Function of glycogen in liver

Source of glucose to maintain blood sugar levels

71

Function of glycogen in muscles

Serves as fuel to generate ATP for muscle contraction

72

Starch

Principle carbohydrate storage product of higher plants. Glucose polymer , unbranched amylose, and branched amylopectin

73

Amylopectin has what type of linkage?

α-1,6 linkages

74

Starch deposits are usually 10-30% __________ and 70-90% __________

Amylose

Amylopectin

75

Starch deposits are stored as __________ in chloroplasts or __________.

Granules

Amyloplasts

76

Cellulose is highly __________.

Insoluble

77

Cellulose function

The structural carbohydrate in plants

78

Cellulose is a repeating monomer of _____-_____-glucose with _____-_____, _____-linkages

Cellulose is a repeating monomer of β-D-glucose with β-1,4-linkages

79

Can mammals utilize cellulose as food? why or why not?

No. Mammals lack the enzymes to break it down

80

How are goats and sheep able to break down cellulose?

They contain bacteria and protozoa in their rumen that break it down into a form they can use

81

NAG - formed by what?

NAM - requires what?

NAG - formed by acetylation of amino acids

NAM - requires further addition of 3C-lactyl group to carbon atom 3

82

Chitin

The exoskeleton of insects

Consists of NAG units joined by β-1,4-linkages

83

Lipids are composed mostly or _______, _______, and _______.

Carbon, Hydrogen and Oxygen

84

Lipids are a heterogeneous group of substances (fats, oils, sterols) lumped together because...

of the solubility in organic substances and H2O insolubility.

85

Lipids are important as _______ molecules and __________ components

Fuel

Structural

86

What are the 5 types of lipids

1. Triglycerides

2. Phospholipids

3. Sterols

4. Sphingolipids

5. Glycosphingolipids

87

What are fatty acids?

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Long, unbranched hydrocarbon chains with a single carboxyl group at one end.

88

Fatty acids have a __________ hydrocarbon chain and a __________ carboxyl group.

Hydrophobic

Hydrophilic

89

What is a triglyceride?

card image

Glycerol and 3 fatty acids that come together though ester linkages

90

What is an ester linkage?

card image
91

Fatty acids chains can vary in length and degree of __________.

Saturation

92

Describe saturated fatty acid chains

Contain no double bounds and every C is attached to its maximum number of H's

93

What is the general formula for saturated fatty acids?

CnH2nO2

-For chains with "n" carbons

94

Describe how the saturated fatty acid chain sits

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Chains are straight, long, and packed tightly together

95

Describe unsaturated fatty acid chains

Contain one or a few double bonds

96

How does the double bonds in unsaturated fatty acids affect their shape?

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The double bonds cause kinks in the chain preventing it from being tightly packed

97

Fatty Acids are __________.

Amphipathic

98

Fats

Contain mostly saturated fatty acids

Solid or semisolid at room temperature

Found in animals

99

Oils

In plants triglycerides usually liquid

Predominantly unsaturated and liquid because of the kinks

100

What is a phospholipid?

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A glycerol + 2 fatty acids + phosphate group

101

The phosphate is attached to the glycerol via __________ __________ linkage

Phosphate ester

102

What can be added to the phosphate of a phospholipid?

An R group

103

What are sterols?

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4 joined rings differing in numbers and positions of double bonds and functional groups

104

Four types of steroid hormones

1. Adrenocortical hormones

2. Sex hormones

3. Vitamin D and Bile acids

4. Cholesterol

105

Adrenocortical hormones

Any hormone secreted by the adrenal cortex

106

Sex hormones

Estrogen

Progesterone

Testosterone

107

Vitamin D and the bile acids

Involved in lipid digestion in the intestine

108

Cholesterol

Found in plasma membrane but not in internal membranes; largely hydrophobic with only a OH group to confer hydrophilicity at 1 end of the molecule

109

Sphingolipids

Found in animals and based on the amino alcohol sphingosine instead of glycerol

110

How are sphingolipids formed?

When fatty acid attached is called a ceramide and has polar region flanked by 2 long nonpolar tails

111

Glycosphingolipids

Contains sugar on the head

Cerebrosides and gangliosides

112

Cerebrosides

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one sugar on the head

113

Gangliosides

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more complex sugar head groups

114

How do lipids behave in water?

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They form a micelle

115

If two or more micelles fuse then what is formed?

A phospholipid bilayer

116

Nucleic acids make up __________

genes

117

Nucleic acids form polymers of ____________ (DNA and RNA)

Polynucleotides

118

Three things that make up nucleotides

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1. Negatively charged phosphate group

2. Sugar (pentose)

3. Nitrogenous base

119
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What sugar is this?

Deoxyribose

120
card image

What sugar is this?

Oxyribose

121

What does a phosphate group look like?

card image
122

What are the 5 nitrogenous bases?

Adenine

Guanine

Thymidine

Cytosine

Uracil

123

1. Name the purines

2. Name the Pyrimidines

1. Adenine, Guanine

2. Thymidine, Cytosine, Uracil

124

How can tell the difference between purines and pyrimidines?

Purines have 2 rings

Pyrimidines have 1 ring

125

What is a nucleoside?

Sugar + Base

126

What is a nucleotide?

Sugar + Base + Phosphate

127

1. Thymine is in _______

2. Uracil is in _______

1. DNA

2. RNA

128

DNA is antiparallel what does that mean?

Runs in opposite directions

129

A and T make what type of bond?

Double hydrogen bond

130

C and G make what type of bond

Triple hydrogen bond

131

1. The backbone of DNA is __________.

2. The bases on DNA are _________.

1. Hydrophilic

2. Hydrophobic

132

Name and describe the 3 levels of DNA structue

Primary - Sequence of nitrogen bases

Secondary - 3D base pair interactions (double helix)

Tertiary - Supercoiling

133

RNA is usually __________-stranded

single

134

Ribosomal RNA

Protein synthesis

135

Transfer RNA

Brings amino acid to the cytoprotein

136

Messenger RNA

Carries the code from DNA to ribosomes to build proteins

137

What are proteins made of?

polymers of amino acids

138

What linkage can't mammals break?

β-linkages

139

What is the generalized amino acid structure?

card image
140

What does the generalized amino acid look like at Physiological pH

card image
141

What are the 4 classifications of amino acids?

1. Polar charged

2. Polar uncharged

3. Nonpolar

4. Unique

142

Describe polar charged amino acids

Contain hydrophilic R groups that act as strong organic acids and bases

- Lysine, arginine, aspartic acid, glutamic acid, histidine

143

Describe Polar uncharged amino acids

Contain Hydrophilic R groups that are weakly acidic or basic.

- asparagine, glutamine, theronin, serine, cysteine

144

Describe Nonpolar amino acids

Contain hydrophobic R groups, tends to form an inner core of soluble proteins

- Valine, leucine, isoleucine, tryptophan

145

Describe the unique amino acids

Glycine - fits into both hydrophobic and hydrophilic environments

Cysteine - R group is polar, uncharged in character

Proline - R group is hydrophobic in character, creates kinks in polypeptide chains