Chapter 4 Flashcards
1
Q
What is metabolism
A
The sum total of all chemical reactions that occur in a cell
2
Q
What are metabolites
A
The small molecules involved in metabolism
3
Q
What are catabolic reactions
A
Energy-releasing metabolic reactions (breakdown of food)
4
Q
What are anabolic reactions
A
Energy-requiring metabolic reactions (building up)
5
Q
What are nutrients
A
Supply of monomers (or precursors of) required by cells for growth
6
Q
What nutrients do autotrophs require
A
They get their carbon from inorganic sources (CO2). They may require only inorganic molecules (water, CO2, salts, and trace metals) and can make everything they need from CO2
7
Q
What nutrients do heterotrophs require
A
They get their carbon from organic sources. They require organic molecules and obtain them from autotrophs
8
Q
What are macronutrients
A
Nutrients required in large amounts
9
Q
What are micronutrients
A
Nutrients required in trace amount
10
Q
What are the essential elements
A
Hydrogen, Carbon, Nitrogen, Oxygen, Phosphorus, Sulfur, and Selinium
11
Q
Describe Carbon and the major classes of macromolecules that require carbon
A
It is required by ALL cells, a typical bacteria cell is 50% carbon, it is a major element in ALL classes of macromolecules (sugars, AA, lipids, and nucleotides). Heterotrophs use organic carbon and Autotrophs use inorganic carbon (CO2)
12
Q
Describe Nitrogen
A
Typical bacteria cell is 12% nitrogen, it is a key element in proteins, nucleic acids, and other cell constituents. Nitrogen gas is very stable because of triple covalent bond
13
Q
How is nitrogen used by organisms
A
Some prokaryotes can fix nitrogen from the air by converting N2 into NH4, a usable form of nitrogen. NH4 can also be converted to NO3, another usable form of nitrogen
14
Q
Describe Phosphorus
A
It is used in nueclic acids and phospholipids
15
Q
Describe Sulfur
A
Sulfur-containing amino acids (cysteine and methionine) and also in Vitamins and coenzyme A
16
Q
Describe Sodium
A
Major monovalent cation (Na+)
17
Q
Describe Potassium
A
Major monovalent cation (K+) and is required by some enzymes for activity
18
Q
Describe Magnesium
A
Divalent cation (Mg 2+), stabilizes ribosomes, membranes, and nucleic acids, and also required for many enzymes
19
Q
Describe Calcium
A
Divalent cation (Ca 2+), helps stabilize cell walls in microbes and plays a key role in heat stability of endospores. And very small amounts required as cofactors for certain enzymes
20
Q
Describe Iron
A
Key component of cytochromes and FeS proteins involved in electron transport in respiration and photosynthesis.
21
Q
What are siderophores
A
Iron is not very soluble and cells produce particular iron-binding organic molecules (siderophores) that bind iron in the environment and bring it into the cell
22
Q
What are growth factors
A
Organic compounds required in small amounts by certain organisms. Vitamins, amino acids, purines, and pyrimidines. Function to allow for enzymatic activity of certain enzymes
23
Q
Do autotrophs need growth factors
A
Many autotrophs that get CO2 from the environment typically require zero growth factors, they can make everything that they need.
24
Q
What are vitamins
A
They are small, nonprotein, organic molcules commonly required growth factors, most function as coenzymes
25
What are coenzymes
Coenzymes are nonprotein organic, carbon-based molecules required for enzyme activity. Many enzymes are just the seqeunce of amino acid and its not enough to catalyze the reaction, so you need a specialized molecule to associate with the polypeptide chain of the enzyme and vitamins are one type of coenzyme.
26
What is culture media
Nutrient solutions used to grow microbes in the laboratory, must know or determine the nutritional requirements for each microbe
27
What are the classes of components of media
Defined and Complex media
28
What is defined media
The precise chemical composition is known
29
What is complex media
Composed of digests of chemically undefined substances. May know the exact composition of some chemicals but stuff like yeast, blood, and meat extracts, you won't know the exact compositions of.
30
What is selective media
Only allows the growth of certain strains, contains compounds that selectively inhibit growth of some microbes but not others. Nutrient present is one that only target organism can use, or toxic nutrient is present that will kill non-target organisms.
31
What is differential media
Certain strains can be identified because they show visible difference. Contains an indicator, usually a dye, that detects particular chemical reactions occurring during growth of certain microbes. Can differentiate between different organisms between shape or color, and target and non-target organisms will look different due to something like an indicator
32
What is a pure culture
Culture containing only a single kind of microbe, a clonal population. All genomes present in cells in a pure culture will be extremely similar, but there will be natural mutations
33
What are contaminants
Unwanted organisms in a culture
34
How can cells be grown
Cells can be grown in liquid or solid culture media.
35
How is solid media prepared
Solid media are prepared by addition of gelling agent (agar or gelatin)
36
What happens when cells are grown in solid media
When grown on solid media, cells form isolated masses called colonies
37
What is sterilization
Want to sterilize equipment before using it because microbes are everywhere and you do not want contamination.
38
What are two methods of sterilization
Heat (autocalve, a specialized pressure cooker) and Filtration
39
What is Aseptic (Sterile) Technique
Sterilization technique to prevent contamination. When you want to innoculate a broth:
1. Flame your loop
2. Unscrew cap from broth
3. Flame the tip of the tube
4. Innoculate the broth with loop
5. Flame the tip of the tube again
6. Screw cap back on tube
40
What are pure culture techniques for isolation of single colonies
Streak plate, pour plate, and spread plate
41
What do free-energy calculations not provide information on
Reaction rates
42
What is activation energy
The every required to bring all molecules in a chemical reaction into the reactive states.
43
What is a catalysis
It is usually required to breach activation energy barrier.
44
What is a catalyst
A substance that lowers the activation energy of a reaction, increases the reaction rate, and does NOT affect energetics or equilibrium of a reaction
45
What is a spontaneous reaction
Exothermic
46
What is a non-spontaneous reaction
Endothermic
47
What is the speed of a reaction with a high activation energy
The reaction is slow
48
What are enzymes and what kind of bonds do they form with substrates
They are biological catalysts, typically proteins (some RNAs), are highly specific for substrates and bonds made, and typically rely on weak bonds between enzymes and substrates: hydrogen bonds, van der Waals forces and hydrophobic interactions
49
What is the active site
The region of enzyme that binds substrate. The substrate is recognized by its shape of its bond at the active site
50
What are small nonprotein molecules that participate in catalysis but are not substrates
Prosthetic groups and coenzymes
51
What are prosthetic groups
Attached to enzymes. They bind tightly to enzymes and usually bind covalently or permenently (Heme group in cytochromes)
52
What are coenzymes
Diffusable. They are loosely bound to enzymes, derivatives of vitamins (NAD+/NADH). Coenzymes can be reversibly oxidized and reduced
53
How do cells get chemical energy to run their metabolism
Energy from redox reactions are used in synthesis of energy-rich compounds, redox occurs in pairs
54
What is an electron donor
The substance oxidized in a redox reaction
55
What is an electron accepter
The substance reduced in a redox reaction
56
What is reduction potential
E0, tendency to donate electrons, the more negative the number, the greater tendency to donate electrons, the more positive, the great tendency to accept electrons.
57
What are electron carriers
NAD+/NADH are both electron acceptors and donors. When electrons are transfered to NAD+ it is reduced, and when NADH donates the electron it is oxidized
58
What is the redox tower
Represents the range of possible reduction potentials. The reduced substances at the top (food) donate electrons and the oxidized substances at the bottom accept electrons. The farther the electrons "drop" the greater the amount of energy released. Most electronegative molecules at the bottom (NO3-, Fe3+, and O2)
59
What are the two classes of electron carriers
Prosthetic groups and Coenzymes
60
What is the evolutionary selection for carriers
Electron carriers can carry electrons to an electron acceptor on a different enzyme that's specialized for the second transfer. You just need one enzyme for each donor and one enzyme for each receptor
61
CHemical energy released in redox reactions is primarily stored in what phosphorylated compounds for a short period of time
ATP (prime currnecy), PEP, G6P, and Acetyl-CoA
62
What is needed for long-term storage of energy
Involved insoluble polymers that can be later oxidized to generate ATP
63
What are some examples of insoluble polymers used for energy storage in prokaryotes
Glycogen, PHB, and PHA
64
What are some examples of insoluble polymers used for energy storage in eukaryotes
Starch, Glycogen, and Lipids
65
What are the two reaction pathways used for energy conservation in chemoorganotrophs
Fermentation and Respiration
66
What is fermentation
Substrate-level phosphorylation; ATP directly synthesized from an energy-rich intermediate. (ATP made from glycolysis, no ATP actually made in fermentation itself) Pryruvate is converted to lactic acid or ethanol in order to recycle the NADH to NAD+
67
What is respiration
Oxidative phosphorylation; ATP produced from proton motive force across membrane which is generated by electron transport from reduced food molecules
68
What is Glycolysis
Pathway for catabolism of glucose, anaerobic process, and has 3 stages: glucose consumed, 2 ATPs made, and fermentation products generation.
69
What happens after Glycolysis
Glycolysis is the first process of breaking down sugar and will diverge depending on whether or not there is an external electron acceptor (oxygen, nitrate). If there is no acceptor then fermentation will take place, can't use electron carriers if you don't have an end "sink" to put all the electrons at the end
70
What are the substrates in Glycolysis
Glucose molecule, 2 ATPs, inorganic phosphate, and NAD+
71
What are the products in Glycolysis
Net gain of two ATP molecules (4 ATPs are made), 2 Pyruvates and 2 NADH
72
What is the work done in Glycolysis
A 6 carbon sugar is split into 2, 3 carbon molecules (pyruvate), and in this process we have made a net total of 2 ATPs. These chemical reactions require a reduction of NAD+ to NADH and if there is no external electron carriers then the reaction will stop because all the NAD+ available would have been converted to NADH
73
What is Aerobic Respiration
Oxidation using O2 as the terminal electron acceptor, it yields much more ATP than fermentation
74
What are electron transport systems
On the membrane, electron transport proteins (Fe and FeS cofactors associated) mediate transfer of electrons from reduced electron carriers (reduced by metabolism of food molecules) and the energy released during transfer is used to create PMF which is then used to synthesize ATP
75
Where does electron transport take place in bacteria
On the cytoplasmic membrane
76
What is exergonic
Energy releasing
77
What is endergonic
Energy absorbing
78
How are electron carriers arranged in the membrane
In order of their reduction potential, each transfer is exergonic. Organized in order of increasing oxidizing power.
79
What does the final electron carrier do
The final carrier in the chain donates the electrons and protons to the terminal electron acceptor, which for aerobes is oxygen
80
In the ETC what are the substrates
Oxygen and Electron Carriers
81
In the ETC what are the products
Water
82
In the ETC what is the work done
The electron transfers work to produce a proton motive force by pumping protons to the outside of the cell. Results in generation of pH gradient and an electrochemical potential across the membrane (PMF)
83
Where do these pumped protons originate from
The NADH and the dissociation of water
84
Once the PMF is generated what are the conditions outside
Electrically positive and acidic
85
Once the PMF is generated what are the conditions inside
Electrically negative and alkaline
86
What is ATP Synthase (ATPase)
Protein complex that uses PMF to make ATP. It is a large enzyme composed of separate proteins and is anchored in the membrane. As the H+ lose their energy by diffusing down their electrochemical gradient, the energy is captured by the ATPase enzyme to combine ADP and P to make ATP. It has a turning mechanism
87
What are the substrates for ATP synthase
H+ protons, ADP, and phosphate
88
What are the products for ATP synthase
ATP
89
What is the citric acid cycle
Pathway through which pyruvate is completely oxidized to CO2, provides energy in the form of ATP, NADH, and FADH2
90
What are the substrates of the citric acid cycle
Pyruvate, phosphate and electron carriers: 4 NAD+, 1 FAD, 1 GDP, and Acetly-CoA
91
What are the products of the citric acid cycle
3 CO2, 4 NADH, 1 FADH2, and 1 GTP
92
What is the work done in the citric acid cycle
It is to make the electron carriers, 4 NADH, 1 FADH2, and GTP, they still have a lot of energy and can lose that energy when its transferred in the ETC
93
How many ATP's do you get from Glycolysis
Substrate Level: Net gain of 2 ATPs
| Oxidative Level: 2 NADH -> 6 ATPs
94
How many ATP's do you get from Citric Acid Cycle
Substrate Level: 1 GTP -> 1 ATP
| Oxidative Level: 4 NADH -> 12 ATPs and 1 FADHS -> 2 ATPs
95
How many ATP's total do you get from Aerobic Respiration
38 ATPs total (counting GTP as ATP) per glucose molecule. Glycolysis runs once but CAC runs twice
96
What compounds made in the CAC are available for biosynthetic purposes
a-Ketoglutarate, OAA, Succinyl-CoA, and Acetyl-CoA
97
What are the 5 mechanisms in which microorganism generate energy
Fermentation, Aerobic respiration, Anaerobic respiration, Chemolithotrophy, and Phototrophy
98
What is the energy generation process for chemoorganotrophs
Chemoorganotrophy means that you get energy from ORGANIC compounds, if there is no oxygen present you can do fermentation, in the presence of oxygen you can do aerobic respiration. You breakdown organic compounds to make CO2 to make ATP and NADPH
99
What is the energy generation process for chemolithotrophs
Means that you get energy from INORGANIC compounds, can be aerobic or anaerobic and proceed like chemoorganotrophs
100
What is the energy generation process for photoheterotrophs
Light energy is used in the ETC to generate ATP and NADH to be used with ORGANIC compounds in biosynthesis
101
What is the energy generation process for photoautrophs
Light is used in the ETC to generate ATP and NADH to be used with INORGANIC compounds (CO2) in biosynthesis
102
What is Anaerobic Respiration
The use of electron acceptors other than oxygen, Nitrate, Ferric Iron, Sulfate, Carbonate, and some organic compounds. There is generally less energy released compared to aerobic respiration. Still involved ETC, PMF, and ATPase
103
What is chemolithotrophy
Uses inorganic chemicals as electron donors (food). Begins with oxidation of inorganic electron donor, often autotrophic uses CO2 as carbon source
104
What is phototrophy
Uses light as an energy source
105
What is photophosphorylation
Light-mediated ATP synthesis
106
What are photoautotrophs
Uses redundant NADH and ATP for assimilation of CO2 for biosynthesis
107
What are photoheterotrophs
Uses ATP generated by photophosphorylation for assimilation of organic carbon from environment for biosynthesis
108
What are the 2 major modes of enzyme regulation
Amount and Activity
109
What is amount in enzyme regulation
Regulation at the gene level
110
What is activity in enzyme regulation
Temporary activation or inactivation of enzymes through changes in protein structure
111
What is feedback inhibition
Mechanism for turning off the reactions in a biosynthetic pathway. Usually the end product of the pathway binds to the first enzyme in the pathway, to inhibit activity
112
What is an allosteric enzyme
The enzyme that is inhibited in feedback inhibition.
113
What binding sites do enzymes have
An active site for substrate to bind to make product and an allosteric site for regulation
114
Why is feedback inhibition important
The cell doesn't want to waste energy making more end products than it needs, so when the cell has a certain number of end products it will shutdown the pathway
115
How does the end product regulate the enzyme
When the end product binds to the allosteric site, it changes the shape of the protein so the substrate can't bind to the active site and it can no longer carry out the catalytic reaction
116
What are covalent modifications
Method of regulating biosynthetic enzymes. Regulation involved a small molecule attached to or removed from the protein, which results in conformational change that inhibits or activates activation.
117
What are some covalent modifications
AMP, ADP, PO4 2-, and CH3
118
What regulates covalent modifications
Signal transduction pathway that causes a covalent modification of an enzyme, attaches a functional group or small molecule to the enzyme that results in a change in the shape, can turn the enzyme on or off
119
What is electronegativty
The tendency for a molecule to accept electrons. They are at the bottom at the redox tower. The more electronegative a molecule is, the more likely it is to accept electrons
120
In glycolysis what is the fermentated nutrient and its product(s)
The fermentated nutrient is the electron donor and the product is the electron acceptor
121
Where is oxygen in the redox tower.
Oxygen is at the very bottom of the tower, oxygen is the most electronegative molecule in the tower
122
What are a-ketoglutarate and OAA used for
Precursors for amino acids and OAA is also converted to phosphoenolyryruvate, a precursor of glucose
123
What is Succinyl-CoA used for
Required for synthesis of cytochromes, chlorophyl and other tetrapyrrole compounds
124
What is Acetly-Coa used for
Necessary for fatty acid biosynthesis
