Lecture Midterm 2 Flashcards
(381 cards)
1
Q
What is metabolism?
A
Sum of all chemical processes within a cell includes both catabolic and anabolic reactions
2
Q
What is anabolism?
A
Biosynthetic reactions smaller substances are joined together, using energy to synthesize larger substances, such as macromolecules for cell structure and products like enzymes organelles, etc.
3
Q
What is catabolism?
A
Degradative reactions were large substances are broken down into smaller substances to release energy into supply building blocks for making macromolecules
4
Q
What are the goals of metabolism?
A
Through a process of redox reactions catabolize substances, and then utilize them through another series of redox reactions into substances that are usable for the cell.
5
Q
What is oxidation?
A
A loss of electrons to an electron acceptor
6
Q
What is reduction?
A
A gain of electrons from an electron donor
7
Q
What is a redox reaction?
A
A reaction in which products are derived from oxidized and reduced substances they frequently involve electron or hydrogen carriers
8
Q
What is a metabolic pathway?
A
Hey series of chemical reactions where the product of the first reaction is the substrate for the subsequent enzyme catalyze step
9
Q
Why does metabolism occurs in a stepwise manner?
A
So that its process can be regulated, and over or under production can be mitigated
10
Q
What are enzymes?
A
Protein catalysts or RNA catalysts that increase reaction rates by lowering the activation energy of chemical reactions
11
Q
What is the function of enzymes?
A
Increase reaction rates by lowering activation energy needed for chemical reactions
12
Q
What are the components of enzymes?
A
Specialized proteins
13
Q
How are enzymes named?
A
By adding the suffix – ase they are named according to their substrate, and or function
14
Q
How do enzymes work?
A
They are substrate specific, meaning that they act on a single substrate or closely related shape, charge or size, and generally catalyze a single reaction
15
Q
Name the enzyme that is involved in the first stage of glycolysis?
A
Hexose kinase
16
Q
Name the enzyme that is involved in the pentose phosphate pathway?
A
Hexose kinase, G6PD (glucose six phosphate dehydrogenase)
17
Q
Name the enzyme that is involved in the Entner-Doudouroff pathway.
A
Hexose kinase
18
Q
What are the starting an end products of glycolysis?
A
Starting products: one molecule of glucose
End products: two molecules of pyruvate, 2 ATP 2 NADH
19
Q
What are the stages of glycolysis?
A
There are three main stages, the energy investment stage where ATP is input to start the process, the lysis stage where the six carbon glucose molecule is split into 2 3 carbon pyruvate and the third is the energy conserving or pay off stage where ATP is produced canceling out the initial investment of ATP, and having a net gain of two ATP molecules
20
Q
How many ATP are produced per molecule of glucose in glycolysis
A
Two ATP
21
Q
How many NADH are produced in glycolysis?
A
2 NADH
22
Q
What is the purpose of glycolysis?
A
Catabolized glucose and ready the products for further catabolization to eventually produce an end product of ATP
23
Q
Where does glycolysis occur in the cell?
A
In the cytoplasm
24
Q
Does glycolysis require oxygen?
A
No, it is an anaerobic process
25
What is the starting molecule in the pentose phosphate pathway?
Glucose
26
What is the primary purpose of the pentose phosphate pathway?
To synthesize NADPH for used within red blood cells
27
What is the enzyme that if mutated can cause hemolytic anemia in humans?
Glucose six phosphate dehydrogenase G6PD
28
What can trigger episodes of hemolytic anemia and people who have the mutation?
Infection, certain medications such as primaquine, sulfa drugs, fava beans, henna
29
Are there advantages of having hemolytic anemia mutation?
Yes, this particular mutation provides protection against malaria
30
What is the starting molecule in the Entner Doudouroff pathway?
Glucose
31
What is the intermediate product produced by the Entner Doudouroff pathway?
2-keto-3-deoxy-6-Phosphogluconic acid (KDPG)
32
How is the Entner Doudouroff pathway used for diagnosing bacterial infections?
Only a few types of pathogens utilize the Entner Doudoroff pathway, such as pseudomonas aeroginosa and enterococcus faecalis. Samples are retained from the patient and KDPG is looked for to inform for possible treatment.
33
What is the pathways main purpose in the Entner Doudouroff pathway?
To produce pyruvic acid to be utilized in the Krebs cycle or fermentation
34
What must happen to pyruvate for it to enter the Krebs cycle?
It has to become acetyl Coa
35
What are the starting and end products of the Krebs cycle?
36
How many ATP are produced per turn in the Krebs cycle per glucose?
1, it takes to turns for every glucose molecule so a total of 2 ATP are synthesized for every glucose molecule in the Krebs cycle
37
How many NADH are produced per turn per glucose in the Krebs cycle?
3
38
What is the purpose of the Krebs cycle?
To transfer energy from acetyl-CoA to NAD+ and FAD to then be used in an electron transport chain
39
What is an electron transport chain?
It is a stepwise process in which electron carriers are put with proteins in redox reactions to allow for more synthesis of ATP
40
What are the components and carrier molecules in the electron transport chain?
NADH, FADH2, oxygen
41
What is chemiosmosis?
It can be considered a molecular machine that converts the hydronium gradient into ATP energy
42
What is proton motive, force and what does it do?
It is a buildup in the chemosmotic gradient of hydronium ions in the innermembrane of the mitochondrial matrix which then pushes the hydronium ions back through the membrane, in a specific protein (ATP synthase) resulting in the formation of ADP to ATP
43
What is the terminal electron acceptor of anaerobic ETC?
It would be an inorganic molecule such as sulfate, nitrate, or carbon dioxide 
44
What is used as the terminal electron acceptor of an aerobic ETC?
Oxygen
45
How many ATP’s are made from each type of ETC?
As much as 38 ATP depending on organism
46
What is the purpose of an electron transport chain?
To accept electrons from electron carriers and transfer them to other electronic scepters, and also use energy released from electron transfer to create a proton gradient across the membrane
47
Can an organism have more than a one electron transport chain? Why wouldn’t want to?
Yes, it can it can have an anaerobic electron transport chain as well as an aerobic electron transport chain. It would want this to be able to utilize different environments to keep energy production happening regardless of oxygen availability.
48
What is fermentation?
A process that does not utilize the Krebs cycle or an electron transport chain. Instead, it uses an organic molecule like pyruvic acid as the final electron acceptor to regenerate NAD+ without oxygen
49
What is the starting molecule in fermentation?
Glucose
50
What are some of the end products of fermentation?
NAD+, reduced organic molecule some of which are consumable to humans such as ethanol, acidic acid, and lactic acid
51
What is the purpose of fermentation?
Regeneration of NAD+ for continued glycolysis
52
How was fermentation important in recent post World War II history?
Chaim Weizmann held the patents for the best ways to utilize acetone butanol fermentation. He was approached by the British government who wanted to utilize those patents during the war, he said he would allow it, but his one stipulation was that a state of Israel be created to protect Jews after the war when Israel was created, he was the first president of the state of Israel.
53
How are proteins catabolized?
First, they are hydrolyzed from proteins structure and peptide bonds are broken to put them into individual amino acids, then beta oxidation.
54
How are fats catabolized?
Lipase splits glycerol from the fatty acids, fatty acids are then catabolized via beta oxidation, resulting in 14 to 17 ATP per cycle of beta oxidation
55
How many ATP are generated per cycle of beta oxidation?
14-17
56
Why is it called beta oxidation?
With each turn of the beta oxidation cycle, the beta carbon on the fatty acid chain is cleaved off
57
What are the reactants and end products in photosynthesis?
6CO2+6H2O+light= C6H12O6+ 6O2
58
What are photo systems?
Cells arrange numerous molecules of chlorophyll and other pigments in a protein matrix to form light harvesting matrices.
59
What is chlorophyll?
A pigment molecule that captures light energy to be utilized during photosynthesis. It has a light absorbing active site, a porphyrin ring with a magnesium ion, and a hydrocarbon tail.
60
In regards to photosynthesis what are the dark reactions and what are the products?
These are the reactions that do not need light as a reactant.
61
How many CO2, ATP, and NADPH does it take to make a molecule of glucose with photosynthesis?
6 CO2 -> glyceraldehyde three phosphate (2G3P are needed for one glucose)
18 ATP
12 NADPH
62
Which photo center is responsible for oxidative photosynthesis?
Photosystem two
63
Which photo system to all photo synthetic organisms have?
Photosystem one which is utilized for cyclic photophosphorylation
64
What is the importance of oxidative photosynthesis?
It creates oxygen as a byproduct, so they can be considered carbon fixers since they take in CO2 and release O2
65
What is cyclic photophosphorylation?
It is found in all photosynthetic organisms. It uses photosystem one. It does not generate oxygen. Light comes into the photo system and hits the chlorophyll which excites electrons, those electrons are picked up by electron carriers and brought through the electron transport chain as they do, they lose energy. Energy is able to be harvested from these electron carriers through ATP synthase pumping energy through to convert ADP to ATP. Remaining electrons then re-enter chlorophyll, where they become excited again from the incoming light energy, and complete the cycle again.
66
How does cyclic photophosphorylation work?
It utilizes an electron transport chain, energy is used to pump protons across the membrane, and then proton motive force is used by pumping protons through the membrane to generate ATP from ADP.
67
What is noncyclic photophosphorylation and how does it work?
Utilizes photosystem one and photosystem two. Chlorophyll in photosystem two reacts with light first, then a hydrolysis reaction occurs with water to yield protons (2 hydronium, ions, and one oxygen.) then in photosystem one they follow the same steps as cyclic photophosphorylation. overall, this system will produce ATP, NADPH, and oxygen. 
68
What is an amphibolic pathway?
It is a pathway that can be used both in catabolism or anabolism. Glucose as an example: going into glycolysis-glycolysis can be run in a forward reaction or can be reversed to produce metabolites such as carbohydrates nucleotides, sugar, carrying nucleotides or carbohydrates lake peptidoglycan or glycogen
69
Is it possible for some pathways to be both anabolic and catabolic?
Yes, it is possible. An example of this is taking acetyl CoA and siphoning some of it off in the Krebs cycle to make fatty acids, or taking alpha ketoglutaric acid to make amino acids, or oxaloacetic acid to make amino acids while still continuing to break down remaining acetyl Coa to make ATP.
70
Name three types of photoautotrophs
Algae, green plants, cyanobacteria
71
Name six groups that are chemoheterotrophs
Humans, animals, fungi, some types of bacteria, some archaea, some protozoa
72
What do chemoheterotroph lack?
The ability to synthesize their own food
73
What do photoautotrophs have?
The ability to synthesize their own food utilizing chlorophyll and light
74
What are three types of photosynthetic pigments?
Chlorophylls, bacteriochlorophylls, ???
75
What is an electron carrier?
Molecules that can be used to carry hydronium ions in a redox reaction for ATP synthesis
76
What is a cytochrome?
Proteins that contain porphyrin rings complex with iron
77
What is a flavoprotein?
Proteins containing Flavin
78
What is a ubiquinones?
Ubiquitous, lipid soluble, nonprotein electron carriers derived from vitamin K
79
What are metal containing proteins?
Proteins complex to metal ions, such as iron and sulfur
80
What is an apoenzyme?
An enzyme without a cofactor or coenzyme
81
What is a Holoenzyme?
Apoenzyme+cofactor+coenzyme=holoenzyme (active form)
82
What are coenzymes and cofactors?
Substances required by some enzymes for full activity
83
Which atom represents electron transfer?
Hydrogen
84
What is a reducing agent?
It is the electron donor in a redox reaction
85
What is an oxidizing agent?
It is the electron acceptor in a redox reaction
86
Name 3 H carriers that are frequently used in redox reactions in ATP synthesis?
NAD+ NADP, FAD
87
Name three things that cells require energy for?
Biosynthesis/anabolism, motility, active transport
88
What is substrate level phosphorylation?
The formation of ATP by directly transferring a phosphate group to ADP from an intermediate substrate, using catabolism
89
Why must NADH be regenerated?
The cell supply of NAD plus is finite, using it up results in a shut down of glycolysis
90
What are the two other names for the Krebs cycle?
Tricarboxylic acid cycle and citric acid cycle
91
Denaturation of a protein by heat or pH destroys what level of structure in an amino acid?
It’s 3-D structure
92
What is NAD?
Nicotinamide adenine dinucleotide
93
What is NADP?
An electron carrier used in the pentose phosphate pathway, for anabolic reactions. It is utilized as a cofactor. NADP stands for nicotinamide adenine dinucleotide phosphate.
94
What is FAD?
Flavin adenine dinucleotide (FAD) is a cofactor for cytochrome-b5 reductase, the enzyme that maintains hemoglobin in its functional reduced state, and for glutathione reductase, an enzyme that also protects erythrocytes from oxidative damage.
95
Where are electron carriers located in prokaryotes?
They are located in the cell membrane
96
Where are electron carriers located in eukaryotes?
They are located in the inner mitochondrial membrane
97
What does Endergonic mean?
It means that it requires energy
98
What are three things that anabolism is needed for?
Growth, repair, reproduction
99
What are three things that catabolism is needed for?
Movement, transport, anabolism
100
What does Exergonic mean?
Releasing energy
101
How is catabolism exogonic?
It breaks chemical bonds to release energy
102
How is energy stored?
As a teepee or PEP
103
Explain how ADP becomes ATP
ADP is phosphorylated in the energy released is used to make ATP
104
How is energy released for anabolism?
A phosphate bond is broken in ATP
105
In macromolecules, where is the energy found?
Energy is spread over all of the nutrients chemical bonds
106
What type of energy does anabolism require?
Concentrated energy like the energy found in phosphate bonds of ATP
107
What do we call RNA that can act as an enzyme?
Ribozyme
108
What is an example of RNA acting as an enzyme?
RRNA is what actually bonds the peptides together, so this is an example of RNA, being an enzyme, also known as a ribozyme
109
What is the chemical function of a kinase?
It adds phosphate to molecules
110
What is the function of an active site?
It is where the substrate binds to an enzyme
111
Why is the 3-D structure of a protein important?
The 3-D structure of a protein is what allows it to bind to an active site on an enzyme. If the shape doesn’t match the enzyme, the protein will not be able to bind with its active site, and the help of the reaction won’t happen
112
What is an example of a coenzyme?
Niacin
113
What is an example of a cofactor?
magnesium
114
Is a cofactor organic or inorganic
Inorganic
115
Is a coenzyme organic or inorganic?
Organic
116
Who is Bruce Ames and what does he propose?
A scientist, who advocates for a metabolic tuneup with megadoses of vitamins, and supplements to help mitigate the aging process.
117
How does thiamine (vitamin B one) help people with the metabolic disorder maple syrup urine disease?
Taking a super dose of thiamine, basically forces the substrate to binds to the active site of the enzyme correctly
118
What is pellagra?
A vitamin deficiency disease when someone is deficient in vitamin B3 also known as nicotinamide. If our body doesn’t have enough nicotinamide, it cannot make NAD insufficient quantities. This inhibits catabolism and by default also inhibits anabolism.
119
What is the characteristic presentation of pellagra?
The most notable is skin lesions
120
What is the result of pellagra if it remains untreated?
It can result in death
121
What are four factors that influence the rate of enzymatic reactions?
Temperature, pH, enzyme and substrate concentrations, inhibitors
122
What is the optimum temperature for a psychrophile?
4°C
123
What is the optimum temperature for a mesophile?
37°C
124
What is the optimum temperature for a thermophile?
95°C
125
Human pathogens are more likely to be what type of phile?
Mesophile
126
What is the optimal pH for pepsin
Two
127
What is the optimal pH for urease?
Seven
128
What is the optimal pH for trypsin
10
129
What are the three types of inhibitors?
Competitive inhibitors, non-competitive inhibitors, negative feedback inhibitors
130
Do inhibitors denature enzymes?
No
131
What is an inhibitor?
A substance that decreases or eliminates an enzymes function
132
What is a competitive inhibitor?
It’s an inhibitor that has a similar three dimensional shape as a substrate. It takes the place of the substrate in the active site, and makes it so that the substrate no longer can bind to the enzyme
133
Is it possible for a substrate to outcompete a competitive inhibitor?
Yes, it is possible if the inhibitor is reversible, if it is irreversible, it can’t
134
Is penicillin an irreversible or reversible competitive inhibitor?
It is an irreversible competitive inhibitor.
135
How does sulfa drug function as a competitive inhibitor of bacteria?
It is a competitive inhibitor of Folick acid synthesis enzymes, these are a precursor of nucleotides so if you don’t allow folic acid to be synthesized, nucleotides cannot be built and cell proliferation cannot continue.
136
What is the role of PABA?
It is a substrate for the enzyme involved in folate synthesis
137
What is the role of folate?
It is used to make nucleotides
138
What does PABA stand for?
Para-aminobenzoic acid
139
Why are sulfa drugs not toxic to humans?
Sulfa drugs target, folate synthesis and humans import folate also known as vitamin B9 through our diet
140
What is an allosteric inhibitor or noncompetitive inhibitor?
It is an inhibitor that binds to an alternate site on the enzyme, known as the allosteric site
141
How does an allosteric inhibitor work?
It causes an alteration of the active site so that the enzyme can’t function
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What is an example of a noncompetitive inhibitor?
Lead, Pb
143
How does feedback inhibition function?
End products of the metabolic pathway, build up, and then inhibit the first enzyme in the pathway
144
What does NAD stand for?
Nicotinamide adenine dinucleotide
145
Why is the redox reaction for NAD important?
There is a finite amount of NAD so when it converts to NADH, the cells have to get more NAD
146
What happens in step one of glycolysis?
Glucose has a phosphate from ATP directly, transferred onto it, leaving glucose, six phosphate and ADP
147
What happens in step three of glycolysis?
ATP is used to transfer a phosphate onto fructose, six phosphate, resulting in fructose 1-6 diphosphate and ADP
148
What happens in step four of glycolysis?
Fructose 1-6 diphosphate is broken into two separate molecules dihydroxyacetone phosphate, (DHAP)and glyceraldehyde, three phosphate, known as GP
149
What happens in step seven of glycolysis?
Two ATP are made by transferring the phosphate group to 2 ADP
150
What happens in step eight of glycolysis
Isomerization moves phosphate to the interior to produce PEP also known as Phosphophenolpyruvic acid
151
What happens in step 10 of glycolysis?
Two ATP are made by transferring phosphates from 2 PEP to 2 ADP
152
Name two alternatives to glycolysis
Pentose, phosphate pathway, Entner Doudoroff pathway
153
What can ribose five phosphate be utilized for?
Synthesis of nucleotides
154
During the pentose phosphate pathway, what can ribulose five phosphate be sent to?
The Calvin Benson cycle of photosynthesis
155
What is the importance of erythrose 4 phosphate in the pentose phosphate pathway?
It can be utilized in the synthesis of amino acids
156
What is the main role of the pentose phosphate pathway with NADPH?
The pentose phosphate pathway is mainly a synthetic pathway, allowing for the formation of NADPH, which then can be used by red blood cells.
157
What is the role of glutathione?
It protects red blood cells from oxidative stress
158
What reduces glutathione?
NADPH
159
What happens if there is a G6PD deficiency?
NADPH is not synthesized and therefore glutathione is not reduced which doesn’t allow for oxidative stress within a red blood cell to be reduced.
160
What type of organism utilizes the Entner Doudoroff pathway?
Prokaryotes
161
The pathogen pseudomonas aeroginosa is typically found in what types of patients
Burn patients, patients with cystic fibrosis
162
Enterococcus faecalis
Causes endocarditis, mainly in people with congenital malformations of the valves (heart murmur) as well as people who have had prosthetic valves or recreational drug usage intravenously
163
Which glucose metabolic pathway would be the best target for an antibiotic for use in humans?
164
Why does pyruvate need to be changed into acetyl-CoA to enter the Krebs cycle?
Only two carbon molecules can enter the Krebs cycle, so pyruvate needs to be oxidized and decarboxylated
165
What is added to make acetyl-CoA?
CoA
166
What is the end product of the synthesis of acetyl CoA?
Two acetyl CoA, 2 CO2, 2 NADH for every glucose molecule
167
Where do prokaryotes generate ATP?
Between cell wall and cytoplasm
168
In total how many ATP are produced during aerobic respiration, and specifically how many during each step in the process?
A total of 38 ATP are synthesized during aerobic respiration. Two from glycolysis, two from the Krebs cycle, 34 from the electron transport chain under optimal conditions.
169
What are some molecules that can inhibit the electron transport chain?
Mercury, Demirel, cyanide, carbon monoxide
170
How can urinalysis be utilized to check for an E. coli infection?
By looking for a high presence of nitrates in urine, understanding that that is a byproduct of anaerobic respiration utilized by E. coli
171
What is triple sugar iron medium?
It is utilized in forcing bacteria to culture within an anaerobic environment. The byproduct from certain bacteria in an anaerobic environment is hydrogen sulfide,, which then combines with the ferrous sulfate in the medium to produce ferrous sulfide, and it registers as a black precipitate, this informs for bacterial classification as not all bacteria, utilize anaerobic respiration, and of those that do not all of them utilize hydrogen sulfide.
172
Why is it important to be familiar with the different fermentation pathways?
Not all organisms can have all types of fermentation pathways, therefore, microbes can be identified or profiled by their specific fermentation pathway. This can inform for identification and possible treatments.
173
All E. coli strains look the same under a microscope, how is it possible to differentiate between strains of E. coli?
E. coli can be tested for its ability to ferment different types of sugars such as sorbitol. E. coli 0157 cannot ferment sorbitol but other strains can. It will test negative on a PR sorbitol test.
174
What does a positive PR sorbitol test look like?
It will be yellow with some gas in the small tube, indicating that fermentation has taken place.
175
What does a negative PR sorbitol test look like?
It will be red with no gas present in the little tube
176
What is a protease?
A digestive enzyme secreted by a cell to assist in catabolizing larger molecules, such as proteins
177
What type of reaction to the protease utilize?
Hydrolysis reaction
178
What has to happen to amino acids before they can enter the cell?
Deamination needs to happen and for certain amino acids desulfurylation (methionine
179
What is a genetic disorder that stems from the inability to metabolize amino acids?
Phenylketonuria which stems from an inability to metabolize phenylalanine. Untreated children will experience mental retardation. Treatment course is diet modification with the aim of consuming low levels of phenylalanine. parents also receive counseling to not give children anything containing aspartame.
180
What is the cause of maple syrup urine disease?
It is the inability to process branched amino acids such as valine, isoleucine, and Lucine. These accumulate and cause damage to the brain and respiratory system.
181
Where are photosystems found in prokaryotes?
In the infoldings of the cytoplasmic membrane
182
Where are photosystems found in eukaryotes?
In the infoldings of the inner membrane of chloroplasts
183
What is the definition of a macrobe?
Kingdoms animalia, fungi, plantae, and the remainder of eukarya
184
What is the definition of a microbe?
Micro organisms that cannot be seen by the naked eye, and can only be seen under a microscope these are found within the domains bacteria, and Archaea as well as single celled eukaryotic protists.
185
What are some characteristics of a microbe?
They can be unicellular or multicellular. They can’t be seen with naked eyes, but are visible by microscope. They are able to adapt to their environment, respond to stimuli, carry out, metabolism, and carry out growth.
186
Why do microbes, especially bacteria, have diverse habitats?
They have small size, they need only small amounts of nutrients they are metabolically diverse, and they have tolerance for a wide range of physical conditions
187
What are three necessary things required by all organisms?
Food, water, shelter
188
What are the four groups based on sources of carbon and energy?
Photoautotrophs (energy from light, carbon from environment)
Chemoautotrophs (energy from chemicals, carbon from environment)
Photoheterotrophs (energy from light, carbon from organic compounds)
Chemoheterotrophs (energy and carbon from organic compounds)
189
What are the essential elements and trace elements?
Carbon, hydrogen, oxygen, nitrogen, phosphate, sulfur are the principal elements. Trace elements are zinc, magnesium, manganese.
190
What are the enzymes that are involved in detoxifying toxic oxygen forms?
Superoxide radical (O2-) an enzyme called superoxide dismutase is used in the following reaction:
2O2-+2H+=2H2O2+O2
Peroxide and ion is formed by superoxide dismutase during metabolism. Catalase detoxifies the peroxide in the following reaction:
2H2O2=2H2O+ O2
191
How are microbes classified based on aerobicity?
As anaerobes and aerobes which is referring to the way that they metabolize energy
192
How does temperature affect microbial growth?
It can denature proteins, would affect the 3-D configuration of biological molecules.This can happen with enzymes as well as phospholipids in membranes.
cold slows enzymes down.
keep in mind the minimum, maximum, and optimum growth temperatures of microbes.
193
How does pH affect microbial growth?
Hydronium ions and hydroxide ions interfere with hydrogen bonding of proteins and nucleic acids. Specifically it destroys the tertiary and quaternary protein structure, and destroys nucleic acid structure.
194
How does tonicity affect microbial growth?
It restricts organisms to living within certain environments, some will only grow in a hypertonic environment, others will only grow an isotonic environments, and others will only grow in a hypotonic environment. 
195
How does atmospheric pressure affect microbial growth?
High pressure induces confirmational changes in the cell membranes. It can also modify biochemical reactions, as well as the genetic mechanism of microorganisms, which then reduces the microbial count.
196
How is microbial growth measured?
It is exponentially measured
197
What are the phases of microbial growth (standard growth curve.)
The lag phase, the log or exponential phase, the stationary phase, and the death or decline phase
198
What is carbon utilized for in microbial growth and nutrition?
It is an energy source and the building blocks for carbohydrates, fats, proteins
199
How is nitrogen utilized in microbial growth
It is found in amino acids, purines and pyrimidines
200
What do cyanobacteria do with nitrogen?
Intakes N2 and reduces it to NH3, which is nitrogen fixation, and is an essential component of soil fertilization.
201
What do Rhizobium do with nitrogen?
It takes an N2 and convert it to NH3 which is essential for soil and is nitrogen fixation
202
How is oxygen utilized in microbial growth and nutrition?
It is the final electron acceptor of the electron transport chain in aerobic respiration. It is used with carbohydrates. There are also toxic forms of oxygen formed during aerobic respiration.
203
What are the toxic forms of oxygen formed during aerobic respiration?
Superoxide radical (O2-) an enzyme called superoxide dismutase is used in the following reaction:
2O2-+2H+=2H2O2+O2
Peroxide anion is formed by superoxide dismutase during metabolism. Catalase or perioxidase detoxifies the peroxide in the following reaction:
2H2O2=2H2O+ O2 (gas)
204
What is sulfur utilized for in metabolism and synthesis?
Cysteine, methionine, coenzymes, iron sulfide proteins in electron transport chains. This forms disulfide bonds that are critical to the tertiary structure of proteins and in vitamins, such as thiamin and biotin.
205
What is phosphate utilized for in microbial nutrition and synthesis?
Nucleic acids, ATP, phospholipids, some proteins
206
What are the trace elements involved as enzyme cofactors?
Copper (Cu), iron (Fe), zinc (Zn), cobalt (Co), sodium (Na), chlorine (Cl), potassium (K)
207
What is cobalt used for as a cofactor?
Vitamin B 12
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What is iron used for as a cofactor
Heme and the electron transport chain cytochromes
209
What is the definition of a growth factor?
Organic substances required in small amounts organisms can’t synthesize them themselves vitamins, and essential amino acids, purines and pyrimidines for some organisms, cholesterol, NADH, and heme are also growth factors for some organisms.
210
What are psychrophiles?
Cold lovers they grow best below 15°C. Some grow well as low as 0°C.
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What are mesophiles?
They grow best at 20 to 40°C. Most pathogens are metafiles there optimal temperature is 37°C.
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What are thermophiles
Microbes that grow best about 45°C. Some can grow as high as 110°C
213
What are acidophiles?
They are acid lovers they grow best at a pH of 0.1-5.4.
214
What are neutrophiles?
Microbes that grow best at a pH of 5.4-8.0 this includes most human pathogens.
215
What are alkaliphiles?
They are microbes that are based lovers. They grow best at a pH of 7-11.5.
216
What is the purpose of water within microbes?
It is utilized to dissolve enzymes and nutrients, and serves an important role in metabolism, most cells die without water, there are also physical effects of water such as osmotic pressure and hydrostatic pressure.
217
What is osmotic pressure
The pressure exerted on a semi permeable membrane by a solution containing solutes that cannot freely cross the membrane. These are separated into isotonic, hypotonic, and hypertonic solutions.
218
What is a hyper osmotic environment?
An environment which is saltier in the extracellular fluid than the intracellular fluid. The result of this is cells shrinking due to water loss, which is known as plasmolysis or creation.
219
What is a hypo osmotic environment?
It is when the inside of the cell does saltier than the extracellular fluid. Cells will take on water walled cells, such as bacteria, plants or fungi, become swollen cells without walls will burst
220
What does a halophile?
A microbe that requires a high salt concentration, between 10 to 35% to survive and grow
221
What is the relationship and hydrostatic pressure between meters of depth and ATM?
For every 10 m of depth water pressure will increase one ATM, one ATM is roughly equivalent to 15 psi
222
Can bacteria survive high levels of hydrostatic pressure?
Yes, bacteria can survive to a depth of 7000 m. Some bacteria known as barophiles require pressure to grow
223
What are the three types of ecological associations with microbes?
1. Antagonistic
2. Synergistic
3. Symbiotic
224
And microbial relationships what is the definition of antagonistic?
In which one organism harms, or kills another
225
In microbial relationships, what is the definition of synergistic?
Members cooperate to reap the benefits in excess of those gotten one living alone. each member can live separately, however
226
In microbial relationships what is the definition of symbiotic?
Organisms live in close, nutritional and or physical contact and are independent. Members usually don’t live apart from the relationship.
227
What is quorum sensing?
Organisms living with biofilm respond to signals from fellow organisms through the biofilm and respond with new behaviors.
228
What is the culture technique for anaerobic cultures?
Reducing media contain oxygen binding compounds like thioglycolate
229
What is the special culture technique for low oxygen culture for microaerophiles and capnophiles?
Use carbon dioxide, incubators, and candle jars
230
What are three ways that you can preserve cultures?
Refrigeration, deep, freezing, freeze drying
231
How does growth in microbial populations occur?
Through binary fission, the cell duplicates, its components, and splits into two daughter cells. Growth is logarithmic.
232
What is the definition of lag phase on a growth curve?
The period of time in which microbes are gathering nutrients no anabolism is occurring
233
What is the definition of log phase on a growth curve?
This is the anabolic phase when bacteria are actively growing. Due to binary fission, this happens at an exponential rate.
234
What do the X and Y axis represent on a growth curve?
The X axis represents time, the Y axis represents growth
235
Do all cells divide at the same time and microbial growth?
No, division is nonsynchronous
236
Why is the log phase a finite duration?
As the number of bacteria increase, nutrients are depleted and bacterial waste accumulates
237
What is a limiting factor in the log phase?
The rate of energy production from ATP
238
What are the characteristics of the stationary phase in a growth curve?
Nutrients are limited, waste can be at toxic levels for bacteria, oxygen is inadequate, pH levels are sub optimal, new cells produce at a rate of old cells death
239
What are the characteristics of the decline or death phase?
Waste have built up, nutrients are depleted, growth cannot be sustained, cell death continues to occur
240
What is colonial growth?
Exponential growth on a solid surface, leading to colony formation. All cells in the colony or descendants of the original founding sell. The colony is the same as a clone. All phases of the growth curve occur simultaneously throughout the colony, but growth is nonsynchronous.
241
What is the viable cell measure method?
Placing a known volume of culture onto a plate and allowing it to grow, count the colonies on the plate, then multiply by the dilution rate used, multiply that by the amount of culture that was pleated and this will give you the viable microbes in the sample.
242
What is the membrane filtration growth measure?
This is utilized if your sample looks to dilute for serial, dilution and viable plate count you take a known amount of sample to be filtered and attach a membrane filter to a vacuum the membrane filter retains the sells. Those cells are transferred to a culture, medium incubated, and the colonies are counted.
243
What is the Petroff-Hauser counting chamber?
This is a special type of microbial slide that allows for visual accounting methods to be utilized. Pipette some of the bacterial suspension onto the slide. cover with the special cover slip and examine under oil immersion. Count all of the cells in the 5 x 5 grid and then multiply by 10 to the fourth. This does not differentiate between viable and non-viable cells.
244
What are electronic counters?
Utilizing a light source and a light sensitive detector, also known as a spectrophotometer and inoculated broth, culture is placed between the light source, and the light sensitive detector, based on the amount of light absorbed by the detector calculations are able to be made regarding the amount of microbial growth in the inoculated broth culture. This does not distinguish between viable and dead cells.
245
What are three indirect methods of measuring microbial growth?
Turbidy-measuring with a spectrophotometer
Measure metabolic products
By dry weight measurement
246
What is the definition of microbial growth?
The increase in a population of microbes
247
What are the requirements of microbial growth?
Temperature either the minimum optimum or maximum, pH within acceptable ranges, osmotic pressure within acceptable ranges and hydrostatic pressure within acceptable ranges.
248
Which methods of measuring microbial growth can distinguish between living and dead cells?
Serial, dilution, metabolic activity, and membrane filtration
249
Oxygen in the atmosphere is essential for human life. How can some bacteria grow in the absence of oxygen?
Some bacteria thrive in anaerobic conditions and utilize anaerobic pathways for energy synthesis
250
What effect does temperature have on lipid containing membranes of cells and organelles?
If the temperature is too low membranes become rigid and fragile. If the temperature is too high, membranes become to fluid, and cannot contain the cell or organelle.
251
What is an example of a psychotroph?
Listeria monocytogenes
252
What is an example of a thermophile?
Thermus aquaticus
253
What are psychotropics most likely responsible for?
Food spoilage within refrigerators
254
Based on the growth pattern seen here, are these bacteria psychrophiles, mesophiles, or thermophiles, and would they be likely to cause human disease?
Growth is best occurring at 37°C, which is characteristic of a mesophile. Yes, they would be likely to cause human disease because most pathogens are mesophiles.
255
At what pH do most bacteria and protozoa grow optimally?
They are neutrophiles and grow best at a pH of 6.5-7.5.
256
How do humans use acidophiles to our benefit?
They are utilized in food preservation by preventing further microbial growth, such as lacto fermentation utilized to make pickled vegetables and other foods.
257
What are the two groups that organisms are categorized into based on their carbon source?
Autotrophs which have an inorganic source of carbon like carbon dioxide, and heterotrophs, which have an organic source of carbon like found in proteins and carbohydrates.
258
What are the two groups that organisms are categorized into based on their energy source?
Phototrophs which get their energy from light, and chemotrophs which get their energy from redox reactions of inorganic and organic chemicals
259
What is familial amyotrophic lateral sclerosis?
It is a form of ALS that is a genetic mutation of the super oxide dismutase enzyme, which then renders the person unable to detoxify superoxide.
260
What is Acatalasia?
It is a mutation that results in people being unable to produce the enzyme catalase, complications include increased periodontal disease and oral gangrene
261
What are the four classification based on oxygen requirements?
Aerobes: metabolize aerobically, obligate aerobes that require 02
anaerobes: metabolize anaerobically, obligate that are poisoned by O2
facultative anaerobes: can metabolize aerobically and anaerobically
aerotolerant anaerobes: metabolize anaerobically, can detoxify oxygen’s poisonous forms
262
Explain how bacteria growing in a thioglycolate medium helps with classification based on oxygen requirements?
Obligate anaerobes will grow towards the bottom
obligate aerobes will grow towards the top
facultative anaerobes will have a higher concentration at the top, but will be dispersed throughout, aerotolerant anaerobes will be evenly dispersed throughout the medium
263
Why have the majority of prokaryotes never been grown in culture?
Due to their complex growth requirements it is very difficult to culture prokaryotes
264
What are the six types of general culture media?
Defined media, complex media, selective media, differential media, anaerobic media, transport media
265
What type of microbes can utilize defined media?
Microbes that have a high level of enzymatic ability and are able to break down organic compounds found in the agar to utilize as nutrients for growth
266
What is complex media?
A type of media that can be used by micro organisms that have some ability for metabolizing things like glucose or broken down proteins, but not to the extent of microbes that can grow in defined media
267
What is selective media?
A type of media that will suppress the growth of certain microbes, while allowing for other microbes to grow. An example of this would be altering the pH of the media to suppress bacterial growth and encourage fungal growth.
268
What is differential media?
A type of media that gives the ability to distinguish between microbes. You can give something to the microbes to utilize in a fermentation pathway and see which microbes can utilize carbon for example in fermentation, and which ones cannot.
269
What is anaerobic media?
A media that creates an anaerobic environment to protect obligate anaerobes
270
What is transport media?
Commonly used in a clinical environment, it is media that would allow for transport, while not inhibiting growth of the microbial specimen
271
What type of microorganisms are grown with animal and cell culture?
Obligate intracellular parasites such as viruses,
fastidious microbes
Rickettsias
chlamydias
272
What is the protocol for being able to culture a capnophiles?
Specimens are placed in media inside of a large jar, which then has a lid placed on it. Inside the jar is also a candle burning, which will use up most of the oxygen and produce high amounts of CO2. This creates in an ideal environment for capnophiles, such as neisseria gonorrhoeae.
273
What is reducing media?
A type of media that will reduce certain chemicals in the microbial environment that could possibly inhibit growth. This can also be achieved if oxygen reduction is needed by using anaerobic containers
274
How is bariatric medicine utilized for patients with gas gangrene?
Gas gangrene is typically seen in diabetic patients hyperbaric medicine is oxygen with pressure and the hope is that oxygen will be forced into the tissue that is infected with gas, gangrene and heal. Some of the tissue lessening the need for amputation.
275
What is the numerical range of colonies that is considered statistically acceptable in a viable plate count?
Between 30 and 300
276
What is pyorrhea and what is an example of where it can be seen within the human body?
Pus secretions from tissues, in later stage dental infections it can accompany gingivitis
277
What are the five main stages in biofilm formation?
Attachment, irreversible attachment and cell to cell adhesion, proliferation, maturation, dispersion
278
In biofilms, what is the slime or hydrogel referred to as?
EPS, which stands for extracellular polymeric substance
279
What is the EPS in biofilms often made of?
A substance often made of glycocalyx material
280
What does EPS allow microbes
Share nutrients, resist drying, resist antibiotics, resist host defenses, take shelter from other harmful factors
281
How can patients with catheters become ill with pathogens if the bacterial numbers during the initial introduction are too low to cause outright infection?
It’s possible that the low bacterial numbers during initial introduction, adhere to bio film, growing on the surface of the indwelling catheters, and that bacteria slowly proliferates to a point where infection is possible.
282
Definition of genes
Pieces of DNA that carry instructions to produce proteins (or RNA)
283
What are nucleic acids
Polymers of ribonucleotides (RNA) or deoxyribonucleotides (DNA)
284
Which bases are purines?
Adenine and Guanine
285
Which bases are pyramidines
Cytosine and Thymine
286
How are nucleic acid bases linked to sugar phosphate bonds?
Phosphodiester bonds
287
Which “end of the bases is free?
The 3’ end
288
What is antiparallel?
DNA strands are oriented in opposing directions to each other, they are antiparallel
289
How is replication semi conservative?
Because each strand is copied so that the 2 new molecules each have one new strand and one old strand
290
What is the role of DNA helicase?
DNA strands at the origin are separated (H-bonds broken)
291
What is the role of DNA polymerase?
1. adds bases 5’ → 3’
2. Binds to the DNA at the replication fork and adds nucleotides (dATP, etc) to the hydroxyl at the 3’-end of the RNA primer.
3. It also proofreads and can remove the wrong bases, but errors do still occur.
292
Why can’t bases be added 3’ → 5’?
can’t add 3’ → 5’ b/c no free hydroxyl at 5’ end
293
What role does Primase play?
Primase (enzyme) synthesizes a short length of RNA complementary to the template
294
What is the role of DNA ligase?
DNA ligase seals the short gaps in the sugar-phosphate backbone between the Okazaki fragments to make a whole DNA strand
295
What is an Okazaki fragment?
Short DNAs are made (100-1,000 base DNA fragments)
296
What does DNA methylation do for prokaryotes?
Protects against virus infection in prokaryotes
297
What does DNA methylation do for Eukaryotes?
controls gene expression in eukaryotes
298
What is the definition of Genotype?
what genes an organism has
299
What is phenotype?
Physical features and traits eg., metabolism, morphology
300
How does genotype effect phenotype?
genotype determines phenotype by encoding RNA which contains instructions for proteins
301
What does RNA Polymerase do?
1. DNA strands are separated by RNA polymerase (H-bonds between bases broken)
2. Pairs ribonucleotides (ATP, etc) with the complementary bases on the DNA strands in 5’ → 3’ direction
302
What are the components of prokaryotic genomes?
1. Genes are contained in two structures: chromosomes, which are circular and large, and within plasmids, which are circular and small. 2. They have a single copy of each chromosome known as a haploid. They also have a single copy of each gene.
303
How is prokaryotic DNA arranged?
The DNA is compacted into a nucleoid
304
What are plasmids?
They are small molecules of DNA that replicate independently they carry information required for their own replication and often for one or more cellular traits
305
What are some types of plasmids?
Fertility factors (F): conjugation pili
Resistance factors (R): beta lactamase
Bacteriocin factors: E. coli colicins
Virulence plasmids colon Salmonella modulates immune system to prevent being killed
306
How are plasmids important to the cell?
They carry the information for one or more type of cellular trait, for example, antibiotic resistance. This gives the cell survival advantages.
307
What are components of eukaryotic genomes?
Nuclear DNA, which is chromosomal DNA and extranuclear DNA like what is found in mitochondria, chloroplasts and plasmids
308
How is eukaryotic nuclear DNA arranged?
Chromosomes are linear and they are located in the nucleus. They typically have more than one chromosome per cell eukaryotic cells usually have two copies of each chromosome known as the diploid, and they have two copies of each gene also known as a diploid.
309
How is eukaryotic DNA packaged? Why is it packaged this way?
DNA is wrapped around histone cubes to form nucleosomes. those are linked with short stretches of DNA and histones called Linker DNA. These are linked together over and over to create chromatin fibers. These fibers can be loosely packed if they are active genes, or if they are inactive, they are tightly packed. These can be highly condensed and chromosomes are made up of these chromatin fibers.
310
What does it mean when something is diploid?
311
Why is it advantageous to be diploid?
312
What are DNA and RNA made of?
313
What are the parts of nucleotides?
314
Which nucleotides are in DNA?
315
Which nucleotides are in RNA?
316
What forms the DNA backbone?
317
What forms the rungs or cross pieces of DNA?
318
In which direction are new nucleotides added to a growing molecule, and why must they be added this way?
319
What is replication?
320
What are the main players of replication and what are their functions?
321
During replication, what is the template?
322
What is the product of replication?
323
Where does replication begin?
324
Why is the leading strand synthesis continuous?
325
Why is the lagging strand synthesis discontinuous?
326
What is transcription?
327
Name the players of transcription and their function
328
What is the template during transcription?
329
What is the product of transcription?
330
Where does transcription begin?
331
How is transcription terminated?
332
What are the types of RNA and what is the function of each?
333
How does eukaryotic transcription differ from prokaryotic transcription?
334
What is a cap and what does it do?
335
What is polyadenylation and what is its function?
336
What is a splicesome and what is its function?
337
What are introns and exons?
338
What is alternative splicing and what is the advantage of it?
339
What is translation?
340
What are the players in translation and what is the function of each?
341
Where does translation begin?
342
What is the blueprint of translation and what is the product?
343
What is the genetic code in translation?
344
What does redundancy in the genetic code and why is it important?
345
What is the start codon and what amino acid doesn’t specify?
346
What are stop codons and why does translation terminate at them?
347
What are termination factors and how do they work?
348
What is central dogma?
It states that the flow of genetic information stems from DNA, which is then transcribed to make mRNA and then translated, and from that translation process proteins are created. It also states that it is a unidirectional process.
349
How are prokaryotic genes organized?
350
What is an operon?
351
What is an inducible operon?
352
What is a repressible operon?
353
What are the two levels at what did gene expression can be regulated?
354
Why would cells want to regulate gene expression?
355
What is riboswitch and how does it work?
356
What is siRNA and how does it work?
357
What is mutation?
358
How do mutations occur?
359
What is a mutagen?
360
What kinds of mutagens are there and what type of mutations do they cause?
361
What is the Ames test and how does it work?
362
What are the mechanisms of DNA repair and how does each work?
363
What are some diseases that can result from DNA repair defects?
364
What is horizontal gene transfer?
365
What are the three mechanisms for horizontal gene transfer?
366
How is DNA transferred in each mechanism of horizontal gene transfer?
367
How much DNA could be transferred with an each mechanism for horizontal gene transfer?
368
Which mechanisms of horizontal gene transfer feature dead donors?
369
Which mechanisms of horizontal gene transfer feature live donors?
370
What is the clinical significance of horizontal gene transfer?
371
What is the evolutionary significance of horizontal gene transfer?
372
What are transposons?
373
How can we identify areas were transposition has occurred?
374
What sort of mutation is caused by transposons?
375
Why are transposons of clinical importance?
376
To what larger class of mobile genetic element do transposons belong?
377
What is euchromatin?
It is the loosely packed or active portion of chromatin fibers
378
What is heterochromatin?
It is the inactive or tightly packed chromatin fibers in eukaryotic chromosomal packaging
379
What are similarities between extranuclear DNA of eukaryotes and DNA of prokaryotes?
Mitochondria and chloroplasts have circular DNA like prokaryotes. This makes sense because we believe that mitochondria and chloroplasts likely came from prokaryotic cells earlier on.
380
What percentage of RNA and proteins do mitochondria and chloroplasts code for?
Only about 5%
381
True or false some fungi and protozoa also carry plasmids
True
