Microbiology Unit 2

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1

Radioisotope

has two extra neutrons and results in an unstable nucleus that will undergo beta decay.

2

Products when 1 neutron decays

1 proton, a beta particle, and energy

3

pH scale

used to measure the levels (concentration) of H+ ions in a solution

4

Formula to calculate pH

-log10 [H+]

5

Neutral pH

7

6

One water molecule has:

one H+ and one OH-
H+ = OH-
neutral pH

7

Acid

has a higher concentration of H+ than OH-

8

Base (alkaline)

has a higher concentration of OH- than H+

9

Range of pH scale

0-14
No unit qualifiers

10

pH scale of measurement

logarithmic scale

11

0-6.9 =

acidic

12

7.1-14 =

basic

13

Functional Groups

interact and form chemical bonds (chemical reactions)
important role in the structure and function of the molecule

14

Hydroxyl Group

OH (oxygen and hydrogen)

15

Alcohols

molecules containing hydroxyl groups

16

Methyl Alcohol

methanol
wood alcohol
used as a preservative

17

Ethyl Alcohol

ethyl
drinkable alcohol
used as a decolorizer

18

Isopropyl Alcohol

isopropyl
rubbing alcohol
used as a decolorizer

19

Reagent Alcohol

combination of methyl, ethyl, and isopropyl alcohol

20

Carbonyl Group

CO
carbon and oxygen (double covalent bond)

21

Aldehyde

terminal carbonyl

22

Ketone

internal carbonyl

23

Terminal Carbonyl

a tail

24

Internal Carbonyl

centered between 2 ends

25

Carboxyl Group

COOH
one carbonyl group + one hydroxyl group

26

Characteristics of a Carboxyl Group

H+ donor
organic acid

27

Amino Group

NH2

28

Amines

amino-group molecules

29

Characteristics of Amino Group

weak bases
H+ acceptor

30

Phosphate Group

PO4

31

Characteristics of Phosphate Group

lots of negative charge
interactive functional group
(how much potential energy is available to do work = free energy released)

32

Sulfhydryl Group

SH
sulfer atom attached to a hydrogen

33

Thiols

any molecule that has a sulfhydryl group

34

Characteristics of Sulfhydryl Group

archae bacteria use as a source of food
found in skunk odors, rotten eggs, and trash
use an iron indicator to determine

35

Four Functional Groups

carbohydrates, lipids, proteins, and nucleic acids

36

Carbohydrates

often polar/hydrophilic
have glycosidic bonds

37

Polar

when placed in water they will develop a partial positive or negative charge

38

Hydrophilic

"water loving"
interacts easily with water

39

Isomer

same molecular formula but different chemical structure

40

Examples of isomers

glucose, fructose, and galactose

41

Glycosidic bond

link 2 or more monosaccharides (covalent bond)

42

Building blocks of Carbohydrates

monosaccharides

43

Monosaccharides

glucose, and fructose

44

Smallest Monosaccharide

glycerol

45

6 Carbon chain

mannitol

46

5 Carbon ring

deoxyribose (H) & ribose (OH)

47

Disaccharides

sucrose, lactose, and maltose

48

Polysaccharides

starch, glycogen, and cellulose

49

Starch

sugar storage in plants

50

Glycogen

sugar storage in animals

51

Cellulose

cell wall material for plants

52

Glycosidic bond

link 2 or more monosaccharides (covalent bonds)

53

Lipids

are often non polar and hydrophobic

54

Lipids

composed of carbons and hydrogens
contain less oxygen than carbohydrates

55

Nonpolar

no distribution of charge

56

Hydrophobic

avoids water

57

Triglycerides

neutral lipids
phospholipids
steroids
oils
waxes

58

Phospholipids

construct of biological membranes

59

Esther bond

linkage between fatty acid and glycerol

60

Types of steroids

cholesterol
testosterone
estrogen
Vitamin D

61

Dehydration reaction

releases water as a product

62

Steroids

a four ring structure

63

Phospholipid

2/3 - fatty acid attachment (hydrophobic)
1/3 - other charged side group (hydrophilic)

64

When will phospholipids form a micelle?

in an aqueous solution

65

Micelle

single layer of phospholipids that have formed a compartment

66

Liposome

2 layers of non polar fatty acids tails facing each other
AKA lipid bilayer

67

Proteins

have the greatest diversity of structure

68

Peptide bond

covalent bonds between 2 or more peptides

69

Primary structure

peptide bonds
looks like a straight cord

70

Secondary structure

begins to coil and fold
looks like a coiled phone cord

71

Types of secondary structures

alpha helix (curly cord)
beta-plated sheet (fan-like)

72

Tertiary structure

tanged coiled and folds
due to interactions of side groups

73

Myoglobin

oxygen holding molecule
may have non-protein (prosthetic group) or metal ions attached (captures oxygen)

74

Quaternary structure

ex. hemoglobin
each have their own prosthetic group

75

Globular

rounded
ex. hemoglobin & moglobin

76

Fibrous

linear
ex. collagen

77

Proteins can be:

scaffolding (gives cell shape and passageways)
transport
molecular motors
motility
enzymes
defenses
receptors/ligands

78

Temperature & pH

range of minimum, optimum, and maximum

79

pH denatures proteins at:

minimum and maximum

80

temperature denatures proteins at:

maximum & become irreversibly damaged

81

Protein denaturation

when you exceed temp. and pH maximum, there is a loss of biological activity
a typical protein that goes through this will not regain activity

82

Amphibolic metabolic pathway

contains anabolic and catabolic pathways

83

metabolism

sum of all biochemical reactions

84

anabolism

biosynthesis
taking small molecules & free energy & making things the cell could use

85

catabolism

taking a large molecule & breaking it down releasing small molecules & free energy

86

Metabolism of fats

beta oxidation

87

Metabolism of carbohydrates

glycolysis

88

Metabolism of proteins

amino acid catabolism

89

Enzymes

structured to facilitate the change of substrate (reactant) by presence of an active site to combined enzyme-substrate complex to product

90

Enzymes have a high degree of...

specificity for substrate

91

Enzyme-substrate

very specific for substrate has a flexible fit

92

Enzymes

help form or break chemical bonds
can participate in multiple chemical reactions
reactions occur with less energy used
reactions occur faster

93

Energy of activation

the amount of energy required

94

Enzyme suffix

-ase & -zyme

95

Controlling enzymes

inhibitors and activators

96

Active site

where the substrate fits

97

coenzyme

derived from vitamins

98

cofactors

derived from minerals

99

Aponenzyme

scaffolding to which everything is attached to (usually protein and a small amount of RNA)

100

Competitive inhibitor

similar shape to block active site; metabolism is stopped

101

Noncompetitive inhibitor

attach themselves to allosteric site and changes the shape of the active site

102

Glycolysis

not dependent upon the presence of oxygen
1.) substrate phosphorylation from ATP (ATP converted to ADP)
2.) breaking a 6-carbon molecule, glucose, into 2-3 carbon molecules
3.) transfer of 2 electrons to NAD (turns in to NADH+)
4.) capture energy in ATP

103

ATP

source of PO4 (phosphate groups)

104

Glucose

kinase phosphorylates (attached to a phosphate atom)

105

Isomerase

Glucose - P => Fructose - P

106

Products of glycolysis

2 net yield of NADH
2 net yield of ATP (substrate phosphorylation)
2 pyruvate

107

Dephosphoralation

removal of a phosphate

108

substrate phosphoralation

transferred from one organic molecule to another

109

What can a cell do with pyruvic acid?

fermentation & TCA & respiration

110

Homolactic acid fermentation

produces lactic acid

111

Bacteria that perform homolactic acid fermentation

Lactobacillus & streptococcus

112

Alcoholic fermentation

produces ethyl alcohol & CO2

113

Bacteria that perform alcoholic fermentation

saccharomyces (yeast)

114

mixed-acid fermentation

produces acetic acid, succinct acid, ethyl alcohol, CO2, & hydrogen

115

Bacteria that perform mixed-acid fermentation

escherichia, acetobacter, shigella

116

Propionic fermentation

produces propionic acid, acetic acid, & CO2

117

Bacteria that perform propionic fermentation

Propionibacterium
swiss cheese

118

Butanediol fermentation

produces butanedial & CO2

119

Bacteria that perform butanediol fermentation

enterobacter & klebsiella

120

Butyric-butylic fermentation

produces butyric acid butanol, isopropyl alcohol, acetone, and CO2

121

Bacteria that perform butyric-butylic fermentation

clostridium
solvents & gangreeene

122

microbial or ecological succession

yeast => lactic acid bacteria => acetic acid bacteria

123

Alcoholic fermentation

reduces bitterness
saccharomyces cerevisiae

124

lactic acid fermentation

lactobacillus & streptococcus

125

Products of citric acid cycle per 1 acetyl group

3 NADH
1 FADH2
2 CO2
1 GTP <=> ATP - substrate phosphorlaytion
12 net ATP

126

Cellular respiration

electron pairs donated from NADH and FADH2
electron transport and terminal electron acceptor = oxygen or inorganic molecule (If anaerobic)
proton motive force used to make ATP
ADP + Pi (ATPsynthase) yields ATP

127

Chemiosmosis

movement of hydrogen ions (protons) increase changes pH (acidic)

128

ATPsynthase allows protons...

to move back into the cell.

129

Oxidative phorphorylation

use inorganic phosphate groups

130

Beta oxidation

catabolism of a neutral lipid (separates glycerol backbone and shuttles it into glycolysis)

131

hydrocarbons

manufacture acetyl-COa from 2 carbon units. transported by coenzyme a

132

2 carbons in the krebs cycle =

12 ATP

133

Lipase

enzyme that breaks down lipids

134

Protease

breaks down proteins

135

Bioremediation

microbes cleaning up

136

Bioreclamation

environment returning to normal due to cleaning

137

Decarboxylation

removing carboxyl group
leaves a two carbon group to be given to krebs cycle

138

biosynthesis

building molecules, manufacturing amino acids, carbohydrates, nitrogenous bases (almost every intermediate)

139

Chemical energy for bioluminescence

special enzymes that use ATP & release light (locate in specific structures)
ex. angler fish

140

generation time

time it takes to grow from one generation to the next (one cell to two cells)
normally about 20-30 minutes

141

Lag phase

no change in number of bacteria (internally active)

142

Log phase

cell development (rapid increase in numbers)

143

Stationary phase

same number of cells dying that are being produced

144

Death phase

more cells dying than are being produced

145

Direct microscopic cell count

Petro F-Hauser counting chambers - specialized gritted slides that we place a known amount of bacteria
problem: only know number or absent or presence of bacteria, not alive or not

146

Viable cell counts
plate counts

qualitative (quadrant streak) & qualitative (urine streak)
answers yes or no for bacteria

147

Membrane filtration

has a ton of pores placed in a funnel & liquid is vacuumed through
anything trapped on the surface is placed on an agar plate, which can be colonized & counted
liquid in the bottom is sterilized
used in water and waste water management

148

Turbidity

cloudiness of a liquid that could be due to microorganisms (shine light through to determine blockage of light)

149

Most Probable Number (MPN)

determine presence of microbes in water or liquid
based on statistical numbers and estimates
different concentrations
incubate and look for turbidity

150

Psychrophile

cold lover 4 to 30 degrees Celsius

151

Mesophile

body temp
35-37 degrees celsius

152

Thermophile

40 to 60 degrees celsius

153

Hyperthermophile

80 to 110 degrees celsius

154

Acidophile

below pH of 7

155

Alkalophile

above pH of 7

156

Thermoplasma acidophilum

hot
often grows in sulferous, acidic environment (yellow stone)

157

Alcaligenes faecalis

cold

158

Barophilic

grows under extreme pressure

159

example of barophilic

methanococcus jannaschii

160

Obligate aerobe

must have oxygen for growth

161

Pellicle

growth of the organism at the top

162

Metabolic pathway of obligate aerobe

cellular or aerobic respiration
terminal electron acceptor = oxygen

163

Facultative anaerobe

oxygen required but may be used
most versital and thus most often associated with causing disease

164

How many ATP are produced during aerobic respiration per glucose?

38 ATP

165

How many ATP are produced during fermentation per glucose?

2 ATP

166

Aerotolerant anaerobe

oxygen is not used
cloudiness is the same throughout

167

metabolic process of aerotolerant anaerobes

fermentation

168

Obligate (strict) anaerobe

oxygen kills these anaerobes
no growth in the oxygen rich zone

169

metabolic pathways for obligate anaerobes

fermentation

170

Clostridium tetani

obligate anaerobe causes tetanus (lockjaw)

171

Microaerophile

requires less oxygen
2% - 6% oxygen required

172

metabolic pathways used by microaerophile

fermentation and cellular respiration

173

Capnophilic

"carbon dioxide loving"
5% CO2

174

example of capnophilic bacteria

neisseria species
causes gohnorreia

175

Organic compounds

biological molecules that contain carbon

176

Organic molecules commonly include:

carbon, hydrogen, oxygen, and nitrogen

177

Inorganic molecules

molecules that do not contain carbon

178

Molecular formula for glucose

C6 H12 06

179

Chemical bonds

linkages made between the atoms in molecules

180

An atom comprises:

a nucleus orbited by negatively charged electrons

181

Protons

positively charged

182

Neutrons

no charge

183

Nucleus is made up of:

protons and neutrons

184

Ionic bonds

result from the electrostatic attraction between two ions of opposite charge

185

Ions form when:

they have lost or gained an electron

186

Cation

ion with a positive charge
lost an electron

187

Anion

ion with a negative charge
gained an electron

188

Covalent bond

forms when electron pairs between two atoms are shared

189

Hydrogen bond

weak H to O or H to N attractions between different molecules

190

Hydrogen bonding is important:

in the formation of a wide variety of biological molecules such as proteins and nucleic acids (DNA)

191

Disulfide bond

AKA sulfer bridge
is a single covalent bond between two sulfur containing atoms

192

Cysteine

a sulphur containing amino acid