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Introductory Microbiology > Metabolism > Flashcards

Metabolism Flashcards

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1
Q

What is catabolism?

A

Generation of energy ( ATP) and reducing power ( NADH) from nutrients. By-products of catabolism may be used as precursor molecules for anabolism . “Break down” of molecules

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2
Q

What is metabolism?

A

taking the molecules from the environment and using this molecules for the parts

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3
Q

What is anabolism?

A

Production of macromolecules and chemicals from “building blocks” and energy (ATP). Reducing power is provided by NADH

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4
Q

The result of the catabolic pathway and what anabolic pathway uses

A

Catabolic: useful forms of energy, lost heat, blocks for biosynthesis
Anabolic pathway uses: blocks and energy

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5
Q

What are five essential chemical elements for life?

What happens if some of those elements are missing

A 
Hydrogen
Carbon
Nitrogen
Oxygen
Phosphorus
Sulfur
Selenium
If not available, the organism will manage to live for some time, but not reproduce
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6
Q

What is needed to do with some nutrients before incorporating it into cellular material

A

Modification

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7
Q

What is the top three molecules that are the most widespread by weight in bacteria?

A

Protein
RNA
Lipid

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8
Q

Why there is so much RNA in bacterial cell

A

Because of ribosomes

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9
Q

What should we do for a proper growth of the bacterial culture

A

Provide all the nutrients from the environment + water

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10
Q

Defined vs complex culture medium

A

Complex: we do not exactly how much of each ingredient is there, but we know for sure that the bacteria reproduce there happily

In a defined mixture we know for sure how much of each ingredient we have

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11
Q

Fastidious organism is

A

Have very specific demands, because it cannot produce a lot of things themselves

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12
Q

How will you recognize an anabolic pathway and a catabolic pathway

A

Anabolic - uses ATP and reducing power, but not all the steps are using them, can be coupled with the catabolic pathway
Catabolic- produces ATP and reducing power (NAD(P)H)

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13
Q

What are enzymes

A

Biologic catalyst that are very specific for the substrate , they lower the activation energy , but does not change the free energy of the reactants or product

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14
Q

How does enzyme lower activation energy

A

It will undergo conformational change that will put a stress on the bond and break it up

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15
Q

What is reduction and oxidation

A

Reduction is gain of H+ and electrons

Oxidation is donating hydrogens and electrons

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16
Q

What is the best oxidizing agent

A

Oxygen

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17
Q

What is the reduction potential and “redox” tower

A

Reduction potential - a measurement of the tendency to donate or accept electrons.

At the top of the tower , substances are more willingly to donate electrons and in the down to accept

The energy is released when electrons are passed by down stream the tower

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18
Q

What is NAD

A

Nicotinamide adenine dinucleotide
As it is a dinucleotide , it has two nucleotides
One nucleotide Consists of sugar(ribose), phosphate group and a base( adenine in one nucleotide and nucleotide in the other nucleotide)

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19
Q

Why NAD is important

A

It is able to carry electrons around the organism by uptaking 2 hydrogens
NAD+ can accept 2 electrons and one proton, but the electrons come with 2 protons
So NAD+ accepts one hydrogen and the other is carried with it

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20
Q

How NADH is used within the cell

A

In redox reactions

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21
Q

What are energy rich compounds and what are their source of energy

A 
Phosphoenolpyruvate(anhydride bond)
Adenosine triphosphate(ATP)(ester bond and anhydride bond)
Glucose 6-phosphate (ester-bond)
Acetyl CoA(thioester bond)
Acetyl phosphate (anhydride bond)
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22
Q

What is anhydride bond

A

The bond between phosphorus and oxygen

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23
Q

What are three basic catabolic pathways that produce everything needed for the anabolism

A 
Glycolytic pathway (glycolysis)
Pentose phosphate pathway( hexose monophospahte pathway)
Tricarboxylic pathway ( TCA, citric acid cycle)
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24
Q

What are two possibilities for ATP synthesis

A

Fermentation: anaerobically, organic compounds are electron donors and acceptors. ATP is produced by phosphate level phopshorylation

Respiration:aerobically. organic compunds are oxidized to CO2 woth O2 as the electron acceptor. Most of the ATP is produced by oxidative phosphorylation

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25
Q

What drives ATP synthesis

A

The difference in charge + the difference in the chemical gradient . The outside is more acidic (more H+), the inside is more basic (less H+) and considered negative

Another name is proton motive force

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26
Q

What is used in glycolysis and what is the total yield of glycolysis

A

One molecule of glucose is used ( 6C) to yield 2 pyruvate (3C)
2 ATP)(substrate level phosphorylation), 2 NADH+H+

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27
Q

Three stages of glycolysis

A

The first stage: we are preparing high energy molecule- investment stage, using ATP
The second stage:we take advantage of this preparatory work in order to create ATP- pay off phase
The third stage: regeneration of NAD+ by reducing pyruvate to waste product ( ethanol or lactic acid )-fermentation in the absence of oxygen

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28
Q

What is the fate of pyruvate if the oxygen is available

A

Pyruvate is going to be converted to acetyl - coA and CO2 by the pyruvate dehydrogenase complex
Acetyl -CoA is fed into TCA cycle and fully oxidized to CO2

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29
Q

The description of TCA cycle

A

Acetyl-CoA ( 2c) +oxaloacetate (4c) losses 2 C in the form of CO2 and get to oxaloacetate once again, forming a loop

During the cycle , 3 NADH is produced, 1 FADH2 and 1 GTP

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30
Q

Why succinate dehydrogenase is important

A

It is used not only in the TCA cycle , but also in electron transport chain,
Succinate dehydrogenase is a enzyme ( protein-complex) that is anchored in the membrane

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31
Q

How GTP is used

A

As it is in some metabolic reactions and can be converted to ATP

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32
Q

What are two functions of TCA cycle

A

Energetic and biosynthetic

Biosythetic- some of the intermediate molecules will be funneled of the cycle to be used in anabolic processes

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33
Q

What reactions are performed to regenerate intermediates in TCA cycle

A

Anaplerotic pathway

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34
Q

What is the net yield of TCA cycle

A 
2 CO2
1 GTP (ATP)
3 NADH
1 FADH2
AND 
1 NADH and 1 CO2 from pyruvate oxidation
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35
Q

Two types of producing ATP during respiration

A

Substrate level phosphorylation
AND
Oxidative phosphorylation

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36
Q

What is respiratory chain

A

Series of hydrogen and electron carriers that can undergo oxidation-reduction.
The enzymes are arranged in the down stream pattern of the redox tower
The electrons aare being brought to the respiratory chain by NADH or in case of FADH2 it is already associated with the respiratory chain

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37
Q

How many complexes are there in the respiratory chain

A

4

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38
Q

Why electron transport chain cannot run without TCA cycle and vice versa?

A

Because then succinate cannot be oxidized by succinate dehysrogenase in the respiratory chain

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39
Q

How does electron transport chain function

A

The alternating system of electrons and proton carriers

NADH brings electrons to complex 1. NADH dehydrogenase transfers is both protons and electrons to FMN.
The next carier is the iron-sulphur complex that carry only electrons, so hydrogens get pumped out in the intermembrane space.

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40
Q

What is quinone

A

A part of electron transport chain that can diffuse in the lipid bilayer.
As it does not have hydrogens to receive, it takes them from the matrix,
When quinone passes electrons to Fe-S complex in complex 3, 4 hydrogens are pumped out

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41
Q

What is complex II

A

Succinate dehydrogenase, that makes FADH2 and then immediately trasnfers electrons and hydrogens to quinone

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42
Q

How much protons are transported from matrix to intermembrane space from 1 NADH and 1 FADH2

A

NADH:10
FADH2:6

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43
Q

List all the parts of electron transport chain

A

Complex I: NADH dehysrogenase,FMN(hydrogen+electrons),Fe-S complex(electrons only)
Quinone( hydrogen+electrons)
Complex II:succinate dehydrogenase ,FAD( hydrogen carrier)
Complex III:cytochrome bc1,Fe-S
Cytochrome C
Complex IV:electron carrier, terminal oxidase

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44
Q

Where is electron transport chain in prokaryotes

A

in the cell membrane

45
Q

Proton motive force is used for

A 
Flagellum rotation( in bacteria)
Transport across the membrane and synthesis of ATP
46
Q

How much protons are needed for 1 ATP

A

3-4 protons

47
Q

What is the equation for proton motive force

A

delta p=delta w-z*deltapH

Delta W= membrane potential ( electrical component)

deltapH=transmembrane pH gradient

Z is a factor to convert pH to mV

48
Q

Why do some bacteria that do not use oxidative phosphorylation still use ATPases

A

Because they are reversible, hydrolyze ATP to ADP in order to generate proton motive force

49
Q

What is the yield of ATP from glycolysis

A

2 ATP

6ATP

50
Q

What is the yield of ATP from CAC

A

1 ATP
4 NADH->12 ATP
1 FADH2->2 ATP
Total:15 ATP*2( because two pyruvate)->30 ATP

51
Q

The maximum yield from respiration

A

38 ATP

52
Q

What is the yield from fermentation

A

Net yield: 2 ATP
Lactic acid:2 lactate and 2 NAD+
Alcohol: 2 ethanol+2 Co2+2 NAD+

53
Q

In yeast production of ethanol and CO2 depends on what

A

Inversely proportional to the concentration of O2

54
Q

Why it is important to get right conditions for the yeast when fermenting

A

When there is a lot of oxygen, we are not going to get a lot of ethanol and CO2
In the absence of oxygen, the yeast population grows slowly because fermentation yields little ATP

55
Q

What does the pentose pathway produce

A

A large diversity of sugars and regenerate NADPH-reducing power

56
Q

What is the first step in pentose phosphate pathway

A

Oxidative phase

57
Q

Where does the reactant for the oxidative phase come

A

Directly from glycolysis (glucose 6-phosphate)

58
Q

In what phase NADPH and sugars are produced

A

NADPH-oxidative phase

Sugars- second phase

59
Q

How do organism get NADPH?

A

The majority of organisms can produce it themselves, but the rest will use pentose phosphate pathway

60
Q

What is the end product of the oxidative phase and the by-products

A

End product-ribulose 5-phosphate

By-product - NADPH and CO2

61
Q

How are deoxyribose and ribose for DNA produced

A

from ribose 5-phosphate in pentose phosphate pathway

62
Q

Where does pentose pathway take place

A

In the cytoplasm in eukaryotes and prokaryotes

63
Q

If fermentation is taking place, pentose phosphate pathway occurs ___ and if respiring, ppp runs ___

A

In parallel

64
Q

Why does NADPH produced during pentose phosphate pathway important

A

Because NADH and FADH2 from respiration will be used in the respiratory chain

NADPH makes sure there is enough reducing agent for anabolism

65
Q

Two roles of TCA cycle

A 
Energetic role ( producing reducing equivalents)
Biosynthetic roles - intermediates can be used for anabolic processes
66
Q

Examples of biosynthetic role of TCA cycle

A

Alpha ketoglutarate ->glutamate family and oxaloacetate->aspartate family can be converted to AA

67
Q

The cell needs the intermediates of TCA cycle , but it needs AA at the same time, how does it cope with it

A

Anaplerotic pathway( converting pyruvate with the help of the reducing power to malate)

68
Q

Where does different cycles occur in eukaryotes and prokaryotes

A

Eukaryotes: TCA cycle, respiratory chain and oxidative phosphorylation->mitochondria, glycolysis and fermentation in cytoplasm

Prokaryotes: respiratory chain in the cytoplasmic membrane, everything else in the cytoplasm
Pentose phosphate pathway occurs in the cytoplasm in both prokaryotes and eukaryotes

69
Q

Why do we have different yield for respiration in eukaryotes

A

Pyruvate needs to actively transported through the inner membrane and so ATP is used -> less yield

70
Q

How does molecules get through the outer membrane

A

The membrane is porous -> diffusion

71
Q

How does ATP is transported from mitochondria matrix to the intermembrane space

A

Translocase that transports ATP out and the same time ADP+P in
To get ATP to cytoplasm is not a problem due to the pores

72
Q

What is the cytoplasm

A

A solution of salts, sugars, AA, nucleotides, and many other substances

73
Q

What can get through the cytoplasmic membrane with simple diffusion

A

Some small molecules ( O2,CO2) can diffuse through the membrane
Water, helped by aquaporins( only water , not ions)
NOT: charged molecules or hydrophylic molecules

74
Q

What is the way to accumulate molecules against concentration gradient and to transport molecules that are hydrophylic through the membrane

A

Integral transport proteins

75
Q

Glucose is pretty fairly good in diffusing through the membrane on its own, so as it can get in , it can get out.
What is done to prevent it

A

As soon as glucose molecule gets into the cell, glucose can phosphorylated

76
Q

3 types of transport across the membrane

A

Simple diffusion
Facilitated diffusion
Active transport

77
Q

Two types of facilitated diffusion

A

Channel-mediated

Carrier-mediated

78
Q

Facilitated diffusion transports molecules ___ the gradient, and active transport ____ the gradient

A

Down the gradient

Against the gradient

79
Q

What is the determinant where is down the gradient fro uncharged and charged substances

A

For uncharged: the concentration gradient

Charged: the concentration gradient and the charge

80
Q

What is the advantage of simple diffusion vs transport and vice versa

A

Transport with proteins is much faster
But at some point of time all proteins will be saturated and the rate will enter “plateau”, when diffusion does not depend on that

81
Q

Transport proteins are very ____ to the molecule they are transfering

A

Specific

82
Q

In multi-cellular organisms , cells acquires nutrients by ___
In unicellar organisms (bacteria, archea and eukarya) nutrients are usually acquired by ___

A 
Facilitated diffusion (from blood/plasma)
Active transport
83
Q

What is the specificity of channel-mediated diffusion

A

Relatively low

84
Q

What is the name for the facilitated diffusion channels than can be closed by the cell

A

Gated channels

85
Q

How does carrier-mediated channels work?

A

The binding of the substrate on one side of the membrane induces a conformational change in the carrier

The substrate is released on the other side

86
Q

Who does have higher specificity:channel-mediated or carrier-mediated channels

A

Carrier-mediated

87
Q

What is the active transport

A

When the substrate is transported against the concentration gradient. The transport uses energt for that. It is needed to accumulate solutes against the concentration gradient

88
Q

Three types of active transport and how they work

A
  • Simple transport: Driven by the energy of the proton motive force
  • Group translocation: Chemical modification of the transported substance driven by phosphoenolpyruvate
  • ABC(ATP binding cassette) transporter: Periplasmic binding proteins are involved and energy comes from ATP
89
Q

Three types of simple diffusion ( depending on the direction of movement )

A

Uniporter: one substance one way
Symporter: two substances one way
Antiporter: two substances in different directions

90
Q

The example of symporter and antiporter

A

Antiporter: when H+ moves in and NA+ moves out
Symporter:Lactose in and H+ in

91
Q

What is the best characterized group translocation system

A

Phosphoenolpyrivate-dependent sugar phosphotransferase system

92
Q

where is Phosphoenolpyrivate-dependent sugar phosphotransferase system used?

A

To transport glucose, fructose and mannose in bacteria

PLUS

Responsible for the first step of glycolytic pathway in prokaryotes

93
Q

How do we get phosphate for glucose in Phosphoenolpyrivate-dependent sugar phosphotransferase system

A

A complex of 5 enzymes.

Phosphoenolpyruvate gives off phosphate group to the first enzyme and then the cascade until it gets to glucose

94
Q

How many enzymes in Phosphoenolpyrivate-dependent sugar phosphotransferase system are in the cytoplasm, cytoplasmic membrane , etc.

A

3 enzymes are in the cytoplasm

the forth one is closely associated with the membrane , but not embedded in the membrane. The last one is the membrane

95
Q

ATP binding cassette

3 components

A

1) a substrate-specific binding protein that has very high affinity for a specific substrate ( or a class of substrates)
2) A membrane-spanning protein, the active transport carrier
3) An ATP-hydrolyzing protein that provides the energy for active transport

96
Q

Where is the binding protein in Gram-positive and Gram-negative bacteria

A

Gram-negative:free in periplasm

Gram-positive:anchored in the cytoplasmic membrane

97
Q

What does binding protein do

A

Binds to the substrate and transfers it to the transporter

98
Q

When does proton motive force is generated

A

If the respiration is possible - a terminal electron acceptor( electron transport chain) is present

99
Q

If a terminal electron is not present , pmf is generated by

A

ATPases

100
Q

PMF-dependent transporters are ___ or ___ that use the proton gradient

A

symporters or antiporters

101
Q

How does pmf and Na+ connected

A

Pmf can be used to generate a gradient of Na+ that is used by some transporters as a source of energy ( when H+ is transported inside of the cell, Na+ can be pumped out, creating the gradient, that will be used after)

102
Q

who does use Na+ dependent transport systems

A

Marine organisms

103
Q

pmf is generated inside of mitochondria in eukaryotes, how do they create another pmf in cytosol

A

They use ATPases to pump ATP across the cytoplasmic membrane

104
Q

What type of ATPases eukaryotes and prokaryotes have

A

Prokaryotes and mitochonsria f-type

eukaryites - p-type

105
Q

What is the difference between f-type and p-type atpases

A

P type can pump only proton with one ATP hydrolyzed, when F-type can pump 3 protons for 1 ATP hydrolyzed

106
Q

What is endocytoses

A

The ability to take up large molecules and digest them inside of the cell

107
Q

What is essential endocytosis

A

Actin filaments

108
Q

Three types of endocytosis

A

Phagocytosis (solid particle, in order to digest the particle inside the cell)
Pinocytosis (extracellular liquid)
Receptor-mediated endocytosis, when receptor senses the particle and uptakes it

109
Q

What is formed during phagocytosis

A

Pseudopodium

and then phagosome ( food particle)

Introductory Microbiology (21 decks)

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