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microbial biochemistry Flashcards

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1
Q

what the most abundant elements in cells (macronutrients)

A

hydrogen
carbon
oxygen
nitrogen
phosphorus
sulfur

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2
Q

what are the micronutrients in cells?

A

sodium
potassium
magnesium
zinc
iron
calcium
molybdenum
copper
cobalt
manganese
vanadium

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3
Q

what are the 4 most abundant elements in living matter

A

carbon
nitrogen
oxygen
hydrogen

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4
Q

what does the low atomic number mean for elements I living mattre

A

they are capable of forming strong bonds with other atoms to produce molecules

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5
Q

how many chemical bonds does carbon form

A

4

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6
Q

how many chemical bonds does nitrogen form

A

3

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7
Q

how many chemical bonds does oxygen form

A

2

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8
Q

how many chemical bonds does hydrogen form

A

1

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9
Q

what do oxygen, sulfur and nitrogen have when they are bonded together

A

one or ore lone pairs of electrons

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10
Q

what differentiates organic compounds from inorganic compounds

A

organic compounds contain carbon, inorganic compounds do not.

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11
Q

what is the exception to the organic compounds rule

A

carbon oxides and carbonates are considered inorganic because even though they contain carbon they do not contain hydrogen

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12
Q

what percent of the dry weight of a living cel is inorganic compounds

A

1-1.5%

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13
Q

do inorganic molecules form cell structures

A

no

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14
Q

where does most carbon found in organic molecules come from

A

inorganic carbon sources such as carbon dioxide

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15
Q

what holds carbon skeletons together

A

covalent bonds

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16
Q

what do organic molecules do

A

form cells and chemical reactions that facilitate life

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17
Q

what are biomolecules

A

molecules that are part of living matter, contain carbon the building block of life

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18
Q

what makes carbon unique

A

it has four valence electrons and can form four single covalent bonds with up to four other atoms at the same time

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19
Q

what does carbon usually bond with

A

oxygen
hydrogen
nitrogen
sulfur
phosphorus
carbon

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20
Q

What is the simplest organic compound

A

methane

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21
Q

what is binds in methane

A

carbon only binds to hydrogen

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22
Q

what is a carbon skeleton

A

when carbon atoms bond together in large numbers making a chain

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23
Q

what shape is a carbon skeleton

A

straight, branched or ring shaped

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24
Q

What is an isomer

A

molecules with the same atomic makeup but different structural arrangement of atoms

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25
Q

what makes isomers important

A

the structure of a molecule is directly related to its function

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26
Q

what is a structural formula

A

graphic representation of the molecular structure showing how atoms are arranged

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27
Q

what is a structural isomer

A

compound with an identical molecular formula but differ in bonding sequence

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28
Q

what is an example of structural isomers

A

glucose, galactose and fructose

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29
Q

what is the chemical formula of glucose, galactose and fructose

A

C6H12O6

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30
Q

What is a stereoisomer

A

isomer that differs in spatial arrangement of atoms

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31
Q

what are enantiomers

A

molecules that have chirality where structures are non superimposable mirror images of eachother

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32
Q

how are L-aspartame and D-aspartame related

A

they are enantiomers

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33
Q

how are l-aspartame and d aspartame different

A

L aspartame is sweet
d aspartame is tasteless

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34
Q

how are dextromethoprphan and levomethorphan related

A

they are enantiomers

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35
Q

what is dextromethorphan

A

a cough suppressant

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36
Q

what is levomethorphan

A

analgesic similar to codeine

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37
Q

what are enantiomers sometimes called

A

optical isomers because they can rotate the plane of polarized light

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38
Q

what is an enantiomer that rotates light clockwise

A

(+) d forms

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39
Q

what is a enantiomer that rotates light counter clockwise

A

(-) L forms

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40
Q

where do d and l forms come from

A

dexter (right)
leaves (left)

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41
Q

what are functional groups

A

groups of atoms within molecules that are categorized by specific chemical composition and the chemical reactions they perform

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42
Q

what does r in a functional group represent

A

residue and the remainder of the molecule.

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43
Q

what compounds is aldehyde found in

A

carbohydrates

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44
Q

what compounds are amide found in

A

proteins

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45
Q

what compounds is amino found in

A

amino acids, proteins

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46
Q

what compounds are carbonyl found in

A

ketones, aldehydes, carboxylic acids, amides

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47
Q

what commands are carboxylic acid found in

A

amino acids, proteins, fatty acids

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48
Q

what compounds is ester found in

A

lipids, nucleic acids

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49
Q

what compounds is ether found in

A

disaccharides, polysaccharides, lipids

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50
Q

what compound is hydroxyl found in

A

alcohols, monosaccharides, amino acids, nucleic acids

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51
Q

what compound is ketone found in

A

carbohydrates

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52
Q

what compound is methyl found in

A

methylated compounds such as methyl alcohol’s and methyl esters

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53
Q

what compounds are phosphate found in

A

nucleic acids, phospholipids, ATP

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54
Q

what group is sulfhydryl found in

A

amino acids, proteins

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55
Q

what are monomers

A

smaller molecules that are building blocks of macromolecules

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56
Q

what are polymers

A

macromolecules that result from linking monomers

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57
Q

what is dehydration synthesis

A

a chemical reaction where monomer molecules bind end to end that results in water molecules as a biproduct

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58
Q

what is an example of dehydration synethesis

A

2 glucose combining to form maltose and a water molecule

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59
Q

What do carbohydrates do

A

energy storage, receptors, food, structural role in plants, fungal cell walls, exoskeletons of insects

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60
Q

functions of lipids

A

energy storage, membrane structure, insulation, hormones, pigments

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61
Q

nucleic acids function

A

storage and transfer of genetic information

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62
Q

proteins function

A

enzyme, structure, receptors, transport, structural role in the cytoskeleton of a cel and extracellular matrix.

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63
Q

what are the most abundant biomolecules on earth

A

carbohydrates

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64
Q

what are carbohydrates primarily a combination of

A

carbon and water

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65
Q

what is the empirical formula of many carbs

A

(CH2O)n

n is the number of repeated units

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66
Q

what do all carbohydrates contain

A

carbon
hydrogen and
oxygen

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67
Q

what do some carbohydrates contain

A

nitrogen
phosphorus and/or
sulfur

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68
Q

what are carbohydrates often called

A

saccharides

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69
Q

what are the simplest carbohydrates

A

monosaccharides (simple sugars)

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70
Q

what are monosaccharides

A

monomers for the synthesis of polymers or complex carbohydrates

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71
Q

what are monosaccharides classified based on

A

the number of carbons in the molecule

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72
Q

what is the most abundant monosaccharide in nature

A

hexose D-glucose

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73
Q

what is a common hexose monosaccharide

A

galactose

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74
Q

what is galactose used to make

A

disaccharide milk sugar lactose and the fruit sugar fructose

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75
Q

when are monosaccharides with 4 or more carbon atoms more stable

A

when they adopt a cyclic or ring structure

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76
Q

what causes rings in monosaccharides

A

chemical reactions between functional groups on opposite ends of the sugars flexible carbon chain, mostly the carbonyl group and hydroxyl group

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77
Q

what does glucose form

A

a 6 membered ring

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78
Q

what forms a disaccharide

A

two monosaccharides chemically bonded

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79
Q

what is a glycosidic bond

A

covalent bond between two monosaccharides

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80
Q

what do glycosidic bonds form between

A

hydroxyl groups of two saccharide molecules

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81
Q

what are common disaccharides

A

grain sugar maltose,
milk sugar lactose
table sugar sucrose

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82
Q

what is maltose made of

A

two glucose molecules

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83
Q

what is lactose made of

A

a galactose and a glucose molecule

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84
Q

what is sucrose made of

A

a glucose and fructose molecule

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84
Q

what is another name for polysaccharides

A

glycans

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85
Q

what are polysaccharides

A

large polymers composed of hundreds of monosaccharides

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86
Q

what makes polysaccharides different from mono and disaccharides

A

they are not sweet and generally not soluble in water

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87
Q

what do polysaccharides have in common with disaccharides

A

they are linked together by glycosidic bonds

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88
Q

what are the most biologically important polysaccharides

A

starch
glycogen
cellulose

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89
Q

what is cellulose composed of

A

a linear chain of glucose molecules

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90
Q

what is glycogen

A

the primary energy storage molecule in animals and bacteria

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91
Q

what is starch

A

energy in plants

92
Q

what are the differences between starch, glycogen and cellulose

A

different structure
different orientation of glycosidic linkages

93
Q

what are fatty acids

A

lipids that contain long-chain hydrocarbons terminated with a carboxylic acid functional group

94
Q

what makes fatty acids hydrophobic (non polar)

A

the long hydrocarbon chain

95
Q

what is a saturated fatty acid

A

fatty acid with hydrocarbon chains that only have single bonds

96
Q

what is it called a saturated fatty acid

A

they have the greatest number of hydrogen atoms possible (saturated with hydrogen)

97
Q

what is an unsaturated fatty acid

A

fatty acids with hydrocarbon chains with at least one double bond (fewer hydrogen atoms)

98
Q

describe the backbone of a saturated fatty acid

A

straight, flexible carbon backbone

99
Q

describe skeleton of unsaturated fatty acid

A

have kinks in their carbon skeleton because the double bond causes a rigid bend in the carbon skeleton

100
Q

how does temperature affect saturated fatty acids

A

they are solid at room temperature

101
Q

how does temperature affect unsaturated fatty acids

A

they are liquids at room temperature

102
Q

when is a triglyceride formed

A

when three fatty acids are chemically linked to a glycerol molecule

103
Q

what are triglycerides components of

A

adipose tissue and sebum

104
Q

what are triglycerides classified as

A

simple lipids

105
Q

why are triglycerides simple lipids

A

they are formed from just two types of compounds, glycerol and fatty acids

106
Q

what makes a phospholipid hydrophilic

A

the negatively charged phosphate group gibing it a strong attraction to water

107
Q

what is the head of a phospholipid

A

they hydrophilic portion

108
Q

what is the the tail of a phospholipid

A

the long hydrocarbon chain

109
Q

what is amphipathic

A

a molecule with a hydrophobic portion and a hydrophilic moiety

110
Q

what is a glycolipid

A

a carbohydrate bonded to a lipids head group

111
Q

what are the substituents on the glycerol backbone

A

long hydrocarbon chains

112
Q

what makes a phospholipid hydrophilic

A

the negative charge of the phosphate group

113
Q

What are micelles

A

spherical assemblies containing hydrophobic interior of phospholipid tails and an outer surface of polar heads

114
Q

what are lipid-bilayer sheets

A

large, two dimensional assemblies of phospholipids congregated tail to tail

115
Q

what do lipid bilayers make up

A

cell membranes and many intracellular components

116
Q

what do lipid bilayer spheres make up

A

structural basis of vesicles and liposomes

117
Q

What are isoprenoids

A

branched lipids also referred to as terpenoids

118
Q

what are isoprenoids formed by

A

chemical modifications of the isoprene molecule

119
Q

where are long chain isoprenoids found

A

hydrophobic oils and waxes (sebaceous glands resulting in sebum)

120
Q

what does sebum consist of

A

triacylglycerol, was esters and hydrocarbon squalene

121
Q

what are steroids

A

a type of lipid that is a complex ring structure found in cell membranes and some function as hormones

122
Q

what is the most common type of steroids

A

sterols

123
Q

what are sterols

A

steroids containing an OH group

124
Q

are sterols hydrophobic

A

mainly hydrophobic but have hydrophilic hydroxyl groups

125
Q

what is the most common sterol in animal tissue

A

cholesterol

126
Q

what does cholesterol consist of

A

four rings with a double bond in one of the rings and a hydroxyl group at the sterol-defining position

127
Q

what is the function of cholesterol

A

to strengthen cell membranes

128
Q

do prokaryotes produce cholesterol

A

not usually

129
Q

what do bacteria produce that are similar to cholesterol

A

hopanoids

130
Q

what are haponoids

A

multiringed structures that strengthen bacterial membranes

131
Q

what is the fungi and protozoa equivalent of cholesterol

A

ergosterol

132
Q

What is an amino acid

A

a hydrogen atom, a carboxyl group and an amino group bonded to the same carbon atom

133
Q

what is the fourth group connected to the a carbon in an amino acid

A

a residue or side chain, represented by the letter r

134
Q

what is a residue

A

a monomer that results when two or more amino acids combine and remove water molecules

135
Q

what is the primary structure of a protein

A

a peptide chain

136
Q

what is a peptide chain made of

A

amino acid residues

137
Q

what do the unique characteristics of functional groups and r groups allow components of amino acids to form

A

hydrogen, ionic and disulfide bonds and polar/nonpolar interactions

138
Q

what forms a peptide bond and a water molecule

A

amino acids chemically bonded together by the reaction of the carboxylic acid group of one molecule to the amine group of another

139
Q

what are peptides

A

molecules formed by chemically linking 50 or fewer amino acids

140
Q

what is a dipeptide

A

two amino acids

141
Q

what is a tripeptide

A

three amino acids

142
Q

what is an oligopeptide

A

up to approxiamately 20 amino acids

143
Q

what is a polypeptide

A

up to approximately 50 amino acids

144
Q

what is a protein

A

when a large amount of amino acids or multiple polypeptides are used as building subunits

145
Q

what allows for diversity of proteins

A

the number of monomers, variety of r groups on each amino acid

146
Q

what determines the shape of a protein

A

the size and amino acid sequence

147
Q

what is critical to a proteins function

A

shape

148
Q

what is the primary structure of a protein

A

the sequence of amino acids that make up the polypeptide chain

149
Q

describe the chain of amino acids that forms a proteins primary structure

A

flexible due to bonds that hold the amino acids together

150
Q

What forms the secondary structure

A

when a chain of amino acids is long, hydrogen bonding may occur between amine and carbonyl functional groups within the peptide backbone excluding r side group resulingin folding of the polypeptide chain into helices and sheets

151
Q

what are the most common secondary structures

A

a-helix and b-pleated sheet

152
Q

what happens in the a-helix structure

A

the helix is held by hydrogen bonds between the oxygen atom in a carbonyl group of one amino acid and the hydrogen atom of the amino group that is just four amino acid units farther along the chain

153
Q

what happens in b-pleated sheets

A

the pleats are formed by similar hydrogen bonds between continuous sequences of carbonyl and amino groups that are further separated on the backbone of the polypeptide chain

154
Q

what is the tertiary structure

A

a large scale, three dimensional shape of a single polypeptide chain

155
Q

what determines the tertiary structure

A

interactions between amino acids residues that are far apart in the chain

156
Q

what is a disulfide bridge

A

bonds between sulfhydryl functional groups on amino acid side groups, hydrogen bonds bonds, ionic bonds and hydrophobic interactions between non polar side chains

157
Q

what do disulfide bridges interactions determine

A

the 3 dimensional shape of the protein and its function

158
Q

what is protein folding

A

the process where a polypeptide chain assumes a large-scale three dimensional shape

159
Q

what is a native structure

A

folded proteins that are fully functional in their normal biological role

160
Q

what is denaturation

A

the loss of secondary structure and tertiary structure without the loss of the primary structure

161
Q

what are protein subunits

A

assemblies of several separate polypeptides

162
Q

what are quaternary structure

A

interactions that hold protein subunits together

163
Q

what is an example of a quaternary structure

A

hemoglobin

164
Q

what is a conjugated protein

A

a class of protein with a nonprotein portion

165
Q

What are a biochemical reactions used to identify microorganisms?

A

carbon utilization and other metabolic tests

166
Q

what does biology system identify

A

cells based on their ability to metabolize certain biochemicals and their physiological properties such as ph and chemical sensitivity

167
Q

how does MALDI-TOF identify microorganism based on

A

the specimens mass spectrum and comparing it to a database of thousands of microorganisms

168
Q

how is a MALDI-TOF prepared

A

uses disposable MALDI plates where microorganism is mixed with a specialized matrix reagent

169
Q

what happens to the sample in the MALDU-TOF system

A

it is irradiated with a high intensity pulsed ultraviolet laser resulting in the ejection of gaseous ions generated from the various chemical constituents of the microorganism

170
Q

what happens to the gas ions in the MALDI-TOF test

A

they are collected and accelerated through the mass spectrometer, the ions traveling at a velocity determined by their mass to charge ration reaching the detector at different times

171
Q

What happens in a FAME analysis

A

fatty acids are extracted from the membranes of microorganisms, chemically altered to form volatile methyl esters and analyzed by gas chromatography. the GC chromatogram is compared with other results

172
Q

What does a FAME analysis analyze

A

lipid profile of microbes

173
Q

what does a PLFA analysis do

A

it saponifies phospholipids of membranes that then undergoes FAME analysis

174
Q

what is proteomic analysis

A

identification based on proteins produced under specific growth conditions within the Human body

175
Q

how does protonic analysis work

A

proteins from the pathogen are separated by high-pressure liquid chromatography and then digested to yield smaller peptide fragments then identified using mass spectrometry

176
Q

how are microorganisms identified by glycoproteins

A

antibodies and other carb binding proteins attach to specific carbs on the cell surface causing them to clump together then serological tests are conducted

177
Q

Which of the following is the name for molecules whose structures are nonsuperimposable mirror images?
structural isomers
monomers
polymers
enantiomers

A
178
Q

By definition, carbohydrates contain which elements?
carbon and hydrogen
carbon, hydrogen, and nitrogen
carbon, hydrogen, and oxygen
carbon and oxygen

A
179
Q

Monosaccharides may link together to form polysaccharides by forming which type of bond?
hydrogen
peptide
ionic
glycosidic

A
180
Q

Molecules bearing both polar and nonpolar groups are said to be which of the following?
hydrophilic
amphipathic
hydrophobic
polyfunctional

A
181
Q

Which of the following describes lipids?
a source of nutrients for organisms
energy-storage molecules
molecules having structural role in membranes
molecules that are part of hormones and pigments
all of the above

A
182
Q

Which of the following groups varies among different amino acids?
hydrogen atom
carboxyl group
R group
amino group

A
183
Q

The amino acids present in proteins differ in which of the following?
size
shape
side groups
all of the above

A
184
Q

Which of the following bonds are not involved in tertiary structure?
peptide bonds
ionic bonds
hydrophobic interactions
hydrogen bonds

A
185
Q

Which of the following characteristics/compounds is not considered to be a phenotypic biochemical characteristic used of microbial identification?
poly-β-hydroxybutyrate
small-subunit (16S) rRNA gene
carbon utilization
lipid composition

A
186
Q

Proteomic analysis is a methodology that deals with which of the following?
the analysis of proteins functioning as enzymes within the cell
analysis of transport proteins in the cell
the analysis of integral proteins of the cell membrane
the study of all accumulated proteins of an organism

A
187
Q

Which method involves the generation of gas phase ions from intact microorganisms?
FAME
PLFA
MALDI-TOF
Lancefield group testing

A
188
Q

Which method involves the analysis of membrane-bound carbohydrates?
FAME
PLFA
MALDI-TOF
Lancefield group testing

A
189
Q

Which method involves conversion of a microbe’s lipids to volatile compounds for analysis by gas chromatography?
FAME
proteomic analysis
MALDI-TOF
Lancefield group testing

A
190
Q

true or false
Aldehydes, amides, carboxylic acids, esters, and ketones all contain carbonyl groups.

A
191
Q

true or false
Two molecules containing the same types and numbers of atoms but different bonding sequences are called enantiomers.

A
192
Q

true or false
Lipids are a naturally occurring group of substances that are not soluble in water but are freely soluble in organic solvents.

A
193
Q

true or false
Fatty acids having no double bonds are called “unsaturated.”

A
194
Q

true or false
A triglyceride is formed by joining three glycerol molecules to a fatty acid backbone in a dehydration reaction.

A
195
Q

true or false
A change in one amino acid in a protein sequence always results in a loss of function.

A
196
Q

true or false
MALDI-TOF relies on obtaining a unique mass spectrum for the bacteria tested and then checking the acquired mass spectrum against the spectrum databases registered in the analysis software to identify the microorganism.

A
197
Q

true or false
Lancefield group tests can identify microbes using antibodies that specifically bind cell-surface proteins.

A
198
Q

Waxes contain esters formed from long-chain __________ and saturated __________, and they may also contain substituted hydrocarbons.

A
199
Q

Cholesterol is the most common member of the __________ group, found in animal tissues; it has a tetracyclic carbon ring system with a __________ bond in one of the rings and one free __________group.

A
200
Q

The sequence of amino acids in a protein is called its __________.

A
201
Q

Denaturation implies the loss of the __________ and __________ structures without the loss of the __________ structure.

A
202
Q

A FAME analysis involves the conversion of _______ to more volatile _____ for analysis using ____________.

A
203
Q

Why are carbon, nitrogen, oxygen, and hydrogen the most abundant elements in living matter and, therefore, considered macronutrients?

A
204
Q

What are monosaccharides, disaccharides, and polysaccharides?

A
205
Q

Describe the structure of a typical phospholipid. Are these molecules polar or nonpolar?

A
206
Q

Compare MALDI-TOF, FAME, and PLFA, and explain how each technique would be used to identify pathogens.

A
207
Q

What binds carbon, hydrogen, and oxygen

A

covalent bonds

208
Q

why are covalent bonds used

A

because ionic bonds dissolve in water

209
Q

what do covalent bonds with molecules give cells

A

potential energy

210
Q

what is a common characteristic of monomers

A

they have two opposing sides, a hydroxyl group on one end and a hydrogen on the other end

211
Q

why do monomers have a hydroxyl group on one end and a hydrogen on the other

A

atoms need to be removed to make a binding site for monomers to come together the molecules form water because it is safe for the cell

212
Q

what does dehydration synthesis mean

A

water is removed to put things together

213
Q

what does a hydroxyl group do to a molecule

A

add to the poarity

214
Q

what does polarity refer to

A

the electromagnetic pull that hydrogen and oxygen gives to a molecule when bound together

215
Q

what does oxygen electrons do to the oxygen side of the molecule

A

it pulls the electrons a wiggle ore causing the oxygen side to be more negatively charged than the hydrogen side

216
Q

what does polarity make a molecule

A

hydrophilic

217
Q

what makes carbs easily mixed and dissolved in water

A

multiple hydroxyl groups

218
Q

why dont fatty acids have polarity

A

they do not have hydroxyl groups even though the glycerol portion does the long fatty acids make it hydrophobic

219
Q

what does the term saturated refer to

A

there are no double bonds along the carbon chain so ore sites for hydrogen to bond

saturated with hydrogen

220
Q

what does an unsaturated fatty acid have

A

at least one double bond on the carbon chain

221
Q

what do double bonds do to the carbon chain

A

make them bend so they cannot pack tightly

222
Q

what do increased double bonds give to fatty acids

A

overall fluidity

223
Q

what is the ratio of carbs hydrogen to oxygen

A

one oxygen for every 2 hydrogen

224
Q

what is the bond between the hydroxyl group of a glycerol and the carboxylic acid group of a fatty acid called

A

ester linkage

225
Q

what is the bond that forms between they hydroxyl groups of a monosaccharide called

A

glycosidic bond

226
Q

what is the bond between the amino group of one amino acid and the carboxylic acid group of the next called

A

peptide bond

227
Q
A

Microbiology (15 decks)

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