microbiology ch 5 Flashcards
What breaks down complex molecules, provides energy and building blocks for anabolism, and is exergonic and hydrolytic?
Catabolism
What reactions produce more energy than they consume?
Exergonic
These reactions use water and break chemical bonds
Hydrolytic
What do hyrdolytic reactions do?
Break chemical bonds using water
What type of reactions use energy to build complex molecules, are endergonic and use dehydration synthesis?
Anabolism
These reactions consume more energy than they produce
Endergonic
These reactions release water
Dehydration synthesis
What is a metabolic pathway?
Sequence of enzymatically catalyzed chemical reactions in a cell
What determines metabolic pathways?
Enzymes
What are enzymes encoded by?
Genes
These are sequences of enzymatically catalyzed chemical reactions in a cell
Metabolic pathways
Enzymes determine these
Metabolic pathways
Genes encode these
Enzymes
What does collision theory state?
That chemical reactions occur when atoms, ions, and molecules collide
What is the basis of collision theory?
That all atoms, ions, and molecules are continuously moving and colliding with one another
What can the energy transferred by colliding particles do?
Break chemical bonds or form new bonds
This states that chemical reactions occur when atoms, ions, and molecules collide
Collision theory
This explains how chemical reactions occur and how certain factors affect the rates of those reactions
Collision theory
How can chemical bonds be broken or formed?
By the energy transferred to them during collision breaking their electron structures
What is activation energy?
The collision energy required for a chemical reaction to occur
What is reaction rate?
The frequency of collisions containing enough energy to bring about a reaction
What four factors can increase reaction rate?
Enzymes, increasing temperature, increasing pressure, increasing concentration
This is the collision energy needed for chemical reactions to occur
Activation energy
This is the frequency of collisions with enough energy to cause reactions
Reaction rate
Enzymes, or increases in temperature, pressure, or concentration can cause this
Reaction rate increase
What are enzymes?
Biological catalysts
What can catalysts do?
Speed up chemical reactions without being altered
What do enzymes act on?
A specific substrate
How do enzymes increase the rate of reaction?
By lowering activation energy
These are biological catalysts
Enzymes
These can speed up chemical reactions without being changed themselves
Catalysts
What is an enzyme-substrate complex?
Formation of enzyme’s active site and substrate
What happens to the substrate on an enzyme’s active site?
It is transformed, rearranged into products, and released from enzyme
What happens to the enzyme after the substrate is released?
The enzyme is unchanged and can react with other substrates
This is formed by joining a substrate to an enzyme’s active bonding site
Enzyme-substrate complex
What is turnover number?
The number of substrate molecules an enzyme converts to a product per second
How high can enzyme turnover number be?
500,000
What is the general range of enzyme turnover?
1 to 10,000
This is the number of substrate molecules an enzyme converts to a product per second
Turnover number
What do enzyme names typically end with?
-ase
What are enzyme names based on?
The reaction they catalyze
What reactions is oxidoreductase involved with?
Oxidation-reduction reactions
What reactions is transferase involved with?
Transfer of functional groups such as amino, acetyl, and phosphate groups
What reactions is hydrolase involved with?
Hydrolysis
What reactions is lyase involved with?
Removal of atoms without hydrolysis
What reactions is isomerase involved with?
Rearrangement of atoms within a molecule
What reactions is ligase involved with?
Joining of molecules using ATP
This enzyme is involved with oxidation-reduction reactions
Oxidoreductase
This enzyme is involved in functional group transfer
Transferase
This enzyme is involved with hydrolysis
Hydrolase
This enzyme is involved with the removal of atoms without hydrolysis
Lyase
This enzyme is involved with the rearrangement of atoms within a molecule
Isomerase
This enzyme is involved in the joining of molecules using ATP
Ligase
What are coenzymes/cofactors?
Enzyme ‘helpers’/electron carriers
What four factors influence enzyme activity?
Temperature, pH, substrate concentration and inhibitors
How does high temperature influence enzyme activity?
High temperature can denature proteins
What does it mean to denature a protein?
Loss of its characteristic three-dimensional structure (tertiary configuration)
How can extreme pH influence enzyme activity?
By denaturing proteins
Do enzymes have an optimum pH?
Yes
Do enzymes catalyze faster with a higher substrate concentration?
Yes
What is saturation?
When concentration of substrate is high enough for enzyme to catalyze at maximum rate
When substrate concentration is high and enzyme catalyzes at maximum rate, this is reached
Saturation
What do competitive inhibitors do?
Fill active site of an enzyme and compete with substrate
This fill the active site of an enzyme and compete with the substrate
Competitive inhibitors
What do noncompetitive inhibitors do?
Interact with another part of enzyme rather than active site
What is allosteric inhibition?
Interaction of noncompetitive inhibitors with enzyme
What is an allosteric site?
A site other than the active site
How do noncompetitive inhibitors render enzymes nonfunctional?
By altering the shape of the active site
These interact with an allosteric site to render enzyme nonfunctional
Noncompetitive inhibitors
This is a site on an enzyme that is not its active site
Allosteric site
This is the interaction of noncompetitive inhibitors with an enzyme
Allosteric inhibition
What is feedback inhibition?
End-product of reaction allosterically inhibits enzymes from earlier in pathway
This happens when a reaction end-product allosterically inhibits an enzyme at an earlier point in pathway
Feedback inhibition
What are ribozymes?
RNA that function as catalysts by binding to substrates and acting upon them
What are ribozymes used for in cells?
To cut and splice RNA; also involved in protein synthesis in ribosomes
Are ribozymes used up in the reaction?
No
These are RNA that function as catalysts
Ribozymes
These are used in cells to cut/splice RNA and to synthesize proteins and ribosomes
Ribozymes
What is the removal of electrons called?
Oxidation
What is the gain of electrons called?
Reduction
What is the pairing of an oxidation reaction and a reduction reaction called?
Redox reaction
What is oxidation?
Removal of electrons
What is reduction?
Gain of electrons
What is a redox reaction?
An oxidation reaction paired with a reduction reaction
What are removed simultaneously in biological systems?
Electrons and protons
What is an electron and proton the equivalent of?
One hydrogen atom
Biological oxidations are often this type of reaction
Dehydrogenations
What is dehydrogenation?
Loss of hydrogen atoms
How are electrons and protons removed in biological systems?
Simultaneously
What is the equivalent of one hydrogen atom?
One electron and proton
This is the loss of hydrogen atoms
Dehydrogenation
How is ATP generated?
By the phosphorylation of ADP with the input of energy
What is generated by the phosphorylation of ADP with the input of energy?
ATP
What is generated when high-energy PO4- is added to ADP from a phosphorylated compound?
ATP
What has to be added to ADP from a phosphorylated compound to generate ATP?
High-energy PO4-
This transfers electrons from one electron carrier to another
Electron transport chain
The electron transport chain transfers electrons along a membrane, releasing energy to generate this
ATP
What is the process wherein ATP is generated from ADP using energy derived from the electron transport chain?
Chemiosmosis
What is the electron transport chain?
Electrons transferred from one electron carrier to another along a membrane that releases energy to generate ATP
What is chemiosmosis?
The process wherein ATP is generated from ADP using the energy derived from the electron transport chain
In what type of cells does photophosphorylation occur?
In photosynthetic cells with light-trapping pigments
What is the process of photophosphorylation?
Light energy is converted to chemical energy (ATP) during the transfer of electrons (oxidation) from chlorophyll as they pass through a system of carrier molecules
In photosynthetic cells with light-trapping pigments such as chlorophyll, this occurs
Photophosphorylation
In this process, light energy is converted to chemical energy during the transfer of electrons from chlorophyll as they pass through a system of carrier molecules
Photophosphorylation
What are series of enzymatically catalyzed chemical reactions that extract energy from organic compounds and store it in chemical form?
Metabolic pathways
How do metabolic pathways store extracted energy?
As ATP
What is carbohydrate catabolism?
The breakdown of carbohydrate molecules to produce energy
What is the most common carbohydrate energy source used by cells?
Glucose
In addition to glucose, what can microbes use as energy sources?
Lipids and proteins
This is the breakdown of carbohydrate molecules to produce energy
Carbohydrate catabolism
What is the oxidation of glucose to pyruvic acid to produce ATP and NADH?
Glycolysis
What does “glycolysis” mean?
“Splitting sugar”
What is glycolysis?
The oxidation of glucose to pyruvic acid to produce ATP and NADH
What does glycolysis produce?
ATP and NADH
What happens in the preparatory stage of glycolysis?
2 ATP are used, glucose is split to form two molecules, and DHAP is converted to GP
In this stage of glycolysis, 2 ATP are used to split glucose to form one GP and one DHAP, and DHAP is readily converted to GP
Preparatory stage
What two molecules is glucose used to form during the preparatory stage of glycolysis?
Glyceraldehyde 3-phosphate (GP) and dihydroxyacetone phosphate (DHAP)
How many ATP are used during the preparatory stage of glycolysis?
2
Which molecule is converted into which at the end of the preparatory stage of glycolysis?
Dihydroxyacetone phosphate (DHAP) is converted into glyceraldehyde 3-phosphate (GP)
What happens during the energy-conserving stage of glycolysis?
The two GP molecules are oxidized to 2 pyruvic acid molecules, 4 ATP are produced, and 2 NADH are produced
How many glyceraldehyde 3-phosphate (GP) molecules are oxidized into pyruvic acid during the energy-conserving stage of glycolysis?
2
How many pyruvic acid molecules are formed from glyceraldehyde 3-phosphate (GP) during the energy-conserving stage of glycolysis?
2
How many ATP are produced during the energy-conserving stage of glycolysis?
4
How many NADH are produced during the energy-conserving stage of glycolysis?
2
During this stage of glycolysis, two glyceraldehyde 3-phosphate molecules are oxidized to two pyruvic acid molecules, 4 ATP are produced, and 2 NADH are produced
Energy-conserving stage
What is the overall net gain of ATP for each molecule of glucose oxidized during glycolysis?
2
What are the products of this equation: Glucose + 2ATP + 2ADP 2 PO4- + 2NAD+ —>
2 pyruvic acid + 4ATP + 2NADH + 2H
What types of sugar does the pentose phosphate pathway break down?
Pentose and/or glucose
What does the pentose phosphate pathway produce?
NADPH
Does the pentose pathway operate simultaneously with glycolysis?
Yes
What 3 intermediates can the pentose phosphate pathway provide?
Nucleic acids, glucose, certain amino acids
How many molecules of ATP does the pentose phosphate pathway yield for each molecule of glucose oxidized?
1
Which species of bacteria utilizes the pentose phosphate pathway?
E. coli
This pathway breaks down pentose sugars and/or glucose, produces NADPH, can provide intermediates for synthesis reactions, and yields one molecule of ATP per molecule of glucose oxidized
Pentose phosphate pathway
This pathway operates simultaneously with glycolysis
Pentose phosphate pathway
Can the pentose phosphate pathway produce intermediates for synthesis reactions?
Yes
Does the pentose phosphate pathway yield 2 ATP molecules for every 1 glucose molecule oxidized?
No
This pathway is utilized by E. coli
Pentose phosphate pathway
What three molecules does the Entner Doudoroff pathway produce from 1 glucose molecule?
1 NADPH, 1 NADH, and 1 ATP
Does the Entner-Doudoroff pathway operate alongside glycolysis?
No
What three groups of bacteria use the Entner Doudoroff pathway?
Pseudomonas, Rhizobium, and Agrobacterium
From 1 glucose molecule, this pathway produces one molecule each of NADPH, NADH, and ATP
Entner-Doudoroff pathway
This pathway operates independently of glycolysis and the pentose phosphate pathway
Entner-Doudoroff pathway
This pathway occurs in Pseudomonas, Rhizobium, and Agrobacterium
Entner-Doudoroff pathway
What does aerobic respiration use as a final electron acceptor?
Oxygen
What does anaerobic respiration use as a final electron acceptor?
Molecule other than oxygen
What generates ATP in cellular respiration?
Oxidative phosphorylation
In this, oxidation of molecules liberates electrons to operate an electron transport chain
Cellular respiration
What are two requirements for the final electron acceptor in cellular respiration?
Comes from outside the cell and is inorganic
This type of cellular respiration uses oxygen as the final electron acceptor
Aerobic respiration
This type of cellular respiration uses a molecule other than oxygen as the final electron acceptor
Anaerobic respiration
This generates ATP in cellular respiration
Oxidative phosphorylation
What is oxidized during the Krebs cycle?
Pyruvic acid
What does the pyruvic acid used in the Krebs cycle come from?
Glycolysis
What is lost from pyruvic acid during oxidation in the Krebs cycle?
CO2
What is the loss of CO2 called?
Decarboxylation
After decarboxylation in the Krebs cycle, what does the resulting two-carbon compound form?
Acetyl CoA and NADH
What enzyme is used to form acetyl CoA and NADH?
Coenzyme A
What does the oxidation of acetyl CoA produce?
NADH, ATP, and waste CO2
This process transforms pyruvic acid from glycolysis into NADH, ATP, and CO2
Krebs cycle
Pyruvic acid is oxidized and decarboxylated during this process
Krebs cycle
Coenzyme A attaches with a two-carbon compound during the Krebs cycle to form these two molecules
Acetyl CoA and NADH
NADH, ATP, and CO2 are all produced from this process during the Krebs cycle
Oxidation of acetyl CoA
Where does the electron transport chain occur in prokaryotes?
In plasma membrane
Where does the electron transport chain occur in eukaryotes?
Inner mitochondrial membrane
What are three types of carrier molecules in the electron transport chain?
Flavoproteins, cytochromes, and ubiquinones
What happens to carrier molecules as electrons are passed down the electron transport chain?
They are oxidized and reduced
What is done with energy released from electron transport chain?
It is used to produce ATP
In prokaryotes, the electron transport chain occurs here
Plasma membrane
In eukaryotes, the electron transport chain occurs here
Inner mitochondrial membrane
Flavoproteins, cytochromes, and ubiquinones are examples of these
Carrier molecules
These are oxidized and reduced as electrons are passed down the electron transport chain
Carrier molecules
What happens with protons as electrons from NADH are passed down the electron transport chain?
They are pumped across membrane
What does the proton motive force come from?
Proton gradient
What do protons go through when they diffuse across the membrane?
ATP synthase
What is the energy from protons diffusing through ATP synthase used for?
Synthesizing ATP
This is the process of establishing a proton gradient to then diffuse protons through ATP synthase to release the energy needed to synthesize ATP
Chemiosmosis
How many ATP molecules are made from aerobic respiration?
38
How many ADP molecules are used during aerobic respiration?
38
How many molecules of ATP are made from oxidizing one NADH in the electron transport chain?
3
How many molecules of ATP can one FADH2 make?
2
How many NADH molecules are produced throughout carbohydrate catabolism?
12
How many FADH2 molecules are produced throughout carbohydrate catabolism?
2
How many ATP does substrate-level phosphorylation generate throughout carbohydrate catabolism?
4
Does anaerobic respiration yield less energy that aerobic respiration?
Yes
What is fermentation?
Process that releases energy from oxidation of organic molecules, does not require oxygen, does not use the Krebs cycle of ETC, and uses an organic molecule as final electron acceptor
Can fermentation produce as much ATP as cellular respiration?
No
How many molecules of ATP can fermentation produce?
1 or 2
This process releases energy from oxidation of organic molecules, does not require oxygen, does not use the Krebs cycle or electron transport chain, and uses an organic molecule as a final electron acceptor
Fermentation
In fermentation, pyruvic acid is converted into what?
Organic product
What is used as a final electron acceptor in fermentation?
Organic molecule
Does fermentation require oxygen?
No
Does fermentation release energy from oxidation of organic molecules?
Yes
Does fermentation use the Krebs cycle or the electron transport chain?
No
Does fermentation produce 1 or 2 ATP?
Yes
What does lactic acid fermentation produce?
Lactic acid
What does homolactic fermentation produce?
Lactic acid only
What does heterolactic fermentation produce?
Lactic acid and other compounds
What happens to glucose in fermentation?
It is oxidized to pyruvic acid, which is reduced by NADH
This process produces lactic acid
Lactic acid fermentation
This process produces lactic acid only
Homolactic fermentation
This process produces lactic acid and other compounds, doing both alcohol fermentation and lactic acid fermentation
Heterolactic fermentation
This is oxidized to pyruvic acid, which is then reduced by NADH in the fermentation process
Glucose
What does alcohol fermentation produce?
Ethanol + CO2
In this process, glucose is oxidized to pyruvic acid, pyruvic acid is converted to acetaldehyde and CO2, and NADH reduces acetaldehyde to ethanol
Alcohol fermentation
This process produces ethanol and carbon dioxide
Alcohol fermentation
What are proteins degraded into by extracellular proteases and peptidases?
Amino acids
Can amino acids cross plasma membranes?
Yes
What three things are done to amino acids before entering Krebs cycle?
Deamination, decarboxylation, and desulfurization
What is deamination?
Removal of amino group to converted to ammonium ion
What is decarboxylation?
Removal of carboxylic acid
What is desulferization?
Removal of thiol group (-SH)
These degrade proteins into amino acids
Extracellular proteases and peptidases
These cross plasma membranes to be deaminated, decarboxylated, and desulfurized
Amino acids
This is the removal of an amino group to convert into an ammonium ion
Deamination
This is the removal of carboxylic acid
Decarboxylation
This is the removal of a thiol group
Desulferization
How do biochemical tests identify bacteria?
By detecting enzymes
Enzymes involved in what are detected in biochemical tests?
Decarboxylation and dehydrogenation
These identify bacteria by detecting enzymes involved in decarboxylation and dehydrogenation
Biochemical tests
What does an oxidase test identify?
Bacteria that have cytochrome c oxidase
What does a catalase test identify?
Bacteria that have catalase
What does catalase do?
Neutralizes the bacterial effects of hydrogen peroxide
This test identifies bacteria that have cytochrome c oxidase
Oxidase test
This test identifies bacteria that have catalase
Catalase test
This enzyme neutralizes the bacterial effects of hydrogen peroxide
Catalase
What does a fermentation test identify?
Bacteria that catabolize carbohydrate or protein
What happens during a positive fermentation test?
The pH indicator changes color
Why does the pH indicator change color during a positive fermentation test?
Bacteria that catabolize carbohydrates or protein produce acid
This test can also be used with a Durham tube to detect gas production during fermentation
Fermentation test
This test identifies bacteria that catabolize carbohydrates or protein by causing a pH indicator to change color
Fermentation test
This can be used with a fermentation test to detect gas production
Durham tube
What is carbon fixation?
The synthesis of sugar by using carbon atoms from CO2 gas
This is the synthesis of sugar by using carbon atoms from CO2 gas
Carbon fixation
What organisms are oxygenic photosynthesizers?
Plants, algae, cyanobacteria
What organisms are anoxygenic photosynthesizers?
Purple sulfur/green sulfur bacteria
What does anoxygenic photosynthesis use in place of water?
H2S
What does anoxygenic photosynthesis produce instead of oxygen?
12 Sulfur molecules
What happens in light-dependent reactions?
Conversion of light energy into chemical energy
What kind of chemical energy to light-dependent reactions produce?
ATP and NADPH
What happens in light-independent reactions?
ATP and NADPH are used to reduce CO2 to sugar via Calvin-Benson cycle
What is a photosystem made of?
Chlorophyll and other proteins
What are used to reduce CO2 to sugar via the Calvin-Benson cycle?
ATP and NADPH
What is cyclic photophosphorylation?
Return of electrons released from chlorophyll in photosystem 1 back into chlorophyll
During this process, the electrons released from chlorophyll in photosystem 1 eventually return to chlorophyll
Cyclic photophosphorylation
During this process, both photosystems are required and electrons do not return to chlorophyll, but become incorporated into NADH
Non-cyclic photophosphorylation
What type of organisms use non-cyclic photophosphorylation?
Oxygenic organisms
Where do electrons from chlorophyll end up in cyclic photophosphorylation?
Chlorophyll
Where do electrons from chlorophyll end up in non-cyclic photophosphorylation?
NADH
What do phototrophs use to drive ATP production?
Light
What do photoautotrophs do?
Use energy initially obtained from light to fix CO2 to sugar during Calvin-Benson cycle
What do photoheterotrophs use as a source of carbon?
Organic compounds
These use light energy to drive ATP production
Phototrophs
These use energy obtained initially from light in the Calvin-Benson cycle to fix CO2 to sugar
Photoautotrophs
These use organic compounds as a source of carbon
Photoheterotrophs
Are photoheterotrophs anoxygenic?
Yes
What do chemoautotrophs get energy from?
Inorganic chemicals
What do chemoautotrophs use as a carbon source?
CO2
What do chemoautotrophs use energy to do in the Calvin-Benson cycle?
Fix CO2
These obtain energy from inorganic chemicals
Chemoautotrophs
These use CO2 as carbon source
Chemoautotrophs
Energy is used to fix CO2 during this process
Calvin-Benson cycle
What to chemoheterotrophs obtain from organic chemicals?
Carbon and energy
Are chemoheterotrophs medically and economically important?
Yes
These obtain energy and carbon from organic chemicals
Chemoheterotrophs
What are amphibolic pathways?
Metabolic pathways that function in both anabolism and catabolism
What role do amphibolic pathways play?
Amphibolic pathways bridge the reactions that lead to the breakdown and synthesis of carbohydrates, lipids, proteins, and nucleotides
These are metabolic pathways that function in both anabolism and catabolism
Amphibolic pathways
Do many pathways function simultaneously with common intermediates?
Yes
These pathways bridge reactions leading to breakdown/synthesis of carbohydrates, lipids, proteins, and nucleotides
Amphibolic pathways
