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BIMM 120 > Chapter 4 > Flashcards

Chapter 4 Flashcards

1
Q

What is metabolism

A

The sum total of all chemical reactions that occur in a cell

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2
Q

What are metabolites

A

The small molecules involved in metabolism

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3
Q

What are catabolic reactions

A

Energy-releasing metabolic reactions (breakdown of food)

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4
Q

What are anabolic reactions

A

Energy-requiring metabolic reactions (building up)

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5
Q

What are nutrients

A

Supply of monomers (or precursors of) required by cells for growth

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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

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7
Q

What nutrients do heterotrophs require

A

They get their carbon from organic sources. They require organic molecules and obtain them from autotrophs

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8
Q

What are macronutrients

A

Nutrients required in large amounts

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9
Q

What are micronutrients

A

Nutrients required in trace amount

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10
Q

What are the essential elements

A

Hydrogen, Carbon, Nitrogen, Oxygen, Phosphorus, Sulfur, and Selinium

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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)

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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

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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

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14
Q

Describe Phosphorus

A

It is used in nueclic acids and phospholipids

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15
Q

Describe Sulfur

A

Sulfur-containing amino acids (cysteine and methionine) and also in Vitamins and coenzyme A

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16
Q

Describe Sodium

A

Major monovalent cation (Na+)

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17
Q

Describe Potassium

A

Major monovalent cation (K+) and is required by some enzymes for activity

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18
Q

Describe Magnesium

A

Divalent cation (Mg 2+), stabilizes ribosomes, membranes, and nucleic acids, and also required for many enzymes

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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

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20
Q

Describe Iron

A

Key component of cytochromes and FeS proteins involved in electron transport in respiration and photosynthesis.

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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

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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

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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.

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24
Q

What are vitamins

A

They are small, nonprotein, organic molcules commonly required growth factors, most function as coenzymes

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25
Q

What are coenzymes

A

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.

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26
Q

What is culture media

A

Nutrient solutions used to grow microbes in the laboratory, must know or determine the nutritional requirements for each microbe

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27
Q

What are the classes of components of media

A

Defined and Complex media

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28
Q

What is defined media

A

The precise chemical composition is known

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29
Q

What is complex media

A

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.

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30
Q

What is selective media

A

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.

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31
Q

What is differential media

A

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

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32
Q

What is a pure culture

A

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

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33
Q

What are contaminants

A

Unwanted organisms in a culture

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34
Q

How can cells be grown

A

Cells can be grown in liquid or solid culture media.

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35
Q

How is solid media prepared

A

Solid media are prepared by addition of gelling agent (agar or gelatin)

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36
Q

What happens when cells are grown in solid media

A

When grown on solid media, cells form isolated masses called colonies

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37
Q

What is sterilization

A

Want to sterilize equipment before using it because microbes are everywhere and you do not want contamination.

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38
Q

What are two methods of sterilization

A

Heat (autocalve, a specialized pressure cooker) and Filtration

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39
Q

What is Aseptic (Sterile) Technique

A

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
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40
Q

What are pure culture techniques for isolation of single colonies

A

Streak plate, pour plate, and spread plate

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41
Q

What do free-energy calculations not provide information on

A

Reaction rates

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42
Q

What is activation energy

A

The every required to bring all molecules in a chemical reaction into the reactive states.

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43
Q

What is a catalysis

A

It is usually required to breach activation energy barrier.

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44
Q

What is a catalyst

A

A substance that lowers the activation energy of a reaction, increases the reaction rate, and does NOT affect energetics or equilibrium of a reaction

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45
Q

What is a spontaneous reaction

A

Exothermic

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46
Q

What is a non-spontaneous reaction

A

Endothermic

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47
Q

What is the speed of a reaction with a high activation energy

A

The reaction is slow

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48
Q

What are enzymes and what kind of bonds do they form with substrates

A

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

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49
Q

What is the active site

A

The region of enzyme that binds substrate. The substrate is recognized by its shape of its bond at the active site

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50
Q

What are small nonprotein molecules that participate in catalysis but are not substrates

A

Prosthetic groups and coenzymes

51
Q

What are prosthetic groups

A

Attached to enzymes. They bind tightly to enzymes and usually bind covalently or permenently (Heme group in cytochromes)

52
Q

What are coenzymes

A

Diffusable. They are loosely bound to enzymes, derivatives of vitamins (NAD+/NADH). Coenzymes can be reversibly oxidized and reduced

53
Q

How do cells get chemical energy to run their metabolism

A

Energy from redox reactions are used in synthesis of energy-rich compounds, redox occurs in pairs

54
Q

What is an electron donor

A

The substance oxidized in a redox reaction

55
Q

What is an electron accepter

A

The substance reduced in a redox reaction

56
Q

What is reduction potential

A

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
Q

What are electron carriers

A

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
Q

What is the redox tower

A

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
Q

What are the two classes of electron carriers

A

Prosthetic groups and Coenzymes

60
Q

What is the evolutionary selection for carriers

A

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
Q

CHemical energy released in redox reactions is primarily stored in what phosphorylated compounds for a short period of time

A

ATP (prime currnecy), PEP, G6P, and Acetyl-CoA

62
Q

What is needed for long-term storage of energy

A

Involved insoluble polymers that can be later oxidized to generate ATP

63
Q

What are some examples of insoluble polymers used for energy storage in prokaryotes

A

Glycogen, PHB, and PHA

64
Q

What are some examples of insoluble polymers used for energy storage in eukaryotes

A

Starch, Glycogen, and Lipids

65
Q

What are the two reaction pathways used for energy conservation in chemoorganotrophs

A

Fermentation and Respiration

66
Q

What is fermentation

A

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
Q

What is respiration

A

Oxidative phosphorylation; ATP produced from proton motive force across membrane which is generated by electron transport from reduced food molecules

68
Q

What is Glycolysis

A

Pathway for catabolism of glucose, anaerobic process, and has 3 stages: glucose consumed, 2 ATPs made, and fermentation products generation.

69
Q

What happens after Glycolysis

A

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
Q

What are the substrates in Glycolysis

A

Glucose molecule, 2 ATPs, inorganic phosphate, and NAD+

71
Q

What are the products in Glycolysis

A

Net gain of two ATP molecules (4 ATPs are made), 2 Pyruvates and 2 NADH

72
Q

What is the work done in Glycolysis

A

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
Q

What is Aerobic Respiration

A

Oxidation using O2 as the terminal electron acceptor, it yields much more ATP than fermentation

74
Q

What are electron transport systems

A

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
Q

Where does electron transport take place in bacteria

A

On the cytoplasmic membrane

76
Q

What is exergonic

A

Energy releasing

77
Q

What is endergonic

A

Energy absorbing

78
Q

How are electron carriers arranged in the membrane

A

In order of their reduction potential, each transfer is exergonic. Organized in order of increasing oxidizing power.

79
Q

What does the final electron carrier do

A

The final carrier in the chain donates the electrons and protons to the terminal electron acceptor, which for aerobes is oxygen

80
Q

In the ETC what are the substrates

A

Oxygen and Electron Carriers

81
Q

In the ETC what are the products

A

Water

82
Q

In the ETC what is the work done

A

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
Q

Where do these pumped protons originate from

A

The NADH and the dissociation of water

84
Q

Once the PMF is generated what are the conditions outside

A

Electrically positive and acidic

85
Q

Once the PMF is generated what are the conditions inside

A

Electrically negative and alkaline

86
Q

What is ATP Synthase (ATPase)

A

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
Q

What are the substrates for ATP synthase

A

H+ protons, ADP, and phosphate

88
Q

What are the products for ATP synthase

A

ATP

89
Q

What is the citric acid cycle

A

Pathway through which pyruvate is completely oxidized to CO2, provides energy in the form of ATP, NADH, and FADH2

90
Q

What are the substrates of the citric acid cycle

A

Pyruvate, phosphate and electron carriers: 4 NAD+, 1 FAD, 1 GDP, and Acetly-CoA

91
Q

What are the products of the citric acid cycle

A

3 CO2, 4 NADH, 1 FADH2, and 1 GTP

92
Q

What is the work done in the citric acid cycle

A

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
Q

How many ATP’s do you get from Glycolysis

A

Substrate Level: Net gain of 2 ATPs

Oxidative Level: 2 NADH -> 6 ATPs

94
Q

How many ATP’s do you get from Citric Acid Cycle

A

Substrate Level: 1 GTP -> 1 ATP

Oxidative Level: 4 NADH -> 12 ATPs and 1 FADHS -> 2 ATPs

95
Q

How many ATP’s total do you get from Aerobic Respiration

A

38 ATPs total (counting GTP as ATP) per glucose molecule. Glycolysis runs once but CAC runs twice

96
Q

What compounds made in the CAC are available for biosynthetic purposes

A

a-Ketoglutarate, OAA, Succinyl-CoA, and Acetyl-CoA

97
Q

What are the 5 mechanisms in which microorganism generate energy

A

Fermentation, Aerobic respiration, Anaerobic respiration, Chemolithotrophy, and Phototrophy

98
Q

What is the energy generation process for chemoorganotrophs

A

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
Q

What is the energy generation process for chemolithotrophs

A

Means that you get energy from INORGANIC compounds, can be aerobic or anaerobic and proceed like chemoorganotrophs

100
Q

What is the energy generation process for photoheterotrophs

A

Light energy is used in the ETC to generate ATP and NADH to be used with ORGANIC compounds in biosynthesis

101
Q

What is the energy generation process for photoautrophs

A

Light is used in the ETC to generate ATP and NADH to be used with INORGANIC compounds (CO2) in biosynthesis

102
Q

What is Anaerobic Respiration

A

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
Q

What is chemolithotrophy

A

Uses inorganic chemicals as electron donors (food). Begins with oxidation of inorganic electron donor, often autotrophic uses CO2 as carbon source

104
Q

What is phototrophy

A

Uses light as an energy source

105
Q

What is photophosphorylation

A

Light-mediated ATP synthesis

106
Q

What are photoautotrophs

A

Uses redundant NADH and ATP for assimilation of CO2 for biosynthesis

107
Q

What are photoheterotrophs

A

Uses ATP generated by photophosphorylation for assimilation of organic carbon from environment for biosynthesis

108
Q

What are the 2 major modes of enzyme regulation

A

Amount and Activity

109
Q

What is amount in enzyme regulation

A

Regulation at the gene level

110
Q

What is activity in enzyme regulation

A

Temporary activation or inactivation of enzymes through changes in protein structure

111
Q

What is feedback inhibition

A

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
Q

What is an allosteric enzyme

A

The enzyme that is inhibited in feedback inhibition.

113
Q

What binding sites do enzymes have

A

An active site for substrate to bind to make product and an allosteric site for regulation

114
Q

Why is feedback inhibition important

A

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
Q

How does the end product regulate the enzyme

A

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
Q

What are covalent modifications

A

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
Q

What are some covalent modifications

A

AMP, ADP, PO4 2-, and CH3

118
Q

What regulates covalent modifications

A

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
Q

What is electronegativty

A

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
Q

In glycolysis what is the fermentated nutrient and its product(s)

A

The fermentated nutrient is the electron donor and the product is the electron acceptor

121
Q

Where is oxygen in the redox tower.

A

Oxygen is at the very bottom of the tower, oxygen is the most electronegative molecule in the tower

122
Q

What are a-ketoglutarate and OAA used for

A

Precursors for amino acids and OAA is also converted to phosphoenolyryruvate, a precursor of glucose

123
Q

What is Succinyl-CoA used for

A

Required for synthesis of cytochromes, chlorophyl and other tetrapyrrole compounds

124
Q

What is Acetly-Coa used for

A

Necessary for fatty acid biosynthesis

BIMM 120 (17 decks)

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