Metabolism Flashcards
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
2
Q
What is metabolism?
A
taking the molecules from the environment and using this molecules for the parts
3
Q
What is anabolism?
A
Production of macromolecules and chemicals from “building blocks” and energy (ATP). Reducing power is provided by NADH
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
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
6
Q
What is needed to do with some nutrients before incorporating it into cellular material
A
Modification
7
Q
What is the top three molecules that are the most widespread by weight in bacteria?
A
Protein
RNA
Lipid
8
Q
Why there is so much RNA in bacterial cell
A
Because of ribosomes
9
Q
What should we do for a proper growth of the bacterial culture
A
Provide all the nutrients from the environment + water
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
11
Q
Fastidious organism is
A
Have very specific demands, because it cannot produce a lot of things themselves
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)
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
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
15
Q
What is reduction and oxidation
A
Reduction is gain of H+ and electrons
Oxidation is donating hydrogens and electrons
16
Q
What is the best oxidizing agent
A
Oxygen
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
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)
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
20
Q
How NADH is used within the cell
A
In redox reactions
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)
22
Q
What is anhydride bond
A
The bond between phosphorus and oxygen
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)
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
25
What drives ATP synthesis
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
26
What is used in glycolysis and what is the total yield of glycolysis
One molecule of glucose is used ( 6C) to yield 2 pyruvate (3C)
2 ATP)(substrate level phosphorylation), 2 NADH+H+
27
Three stages of glycolysis
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
28
What is the fate of pyruvate if the oxygen is available
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
29
The description of TCA cycle
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
30
Why succinate dehydrogenase is important
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
31
How GTP is used
As it is in some metabolic reactions and can be converted to ATP
32
What are two functions of TCA cycle
Energetic and biosynthetic
| Biosythetic- some of the intermediate molecules will be funneled of the cycle to be used in anabolic processes
33
What reactions are performed to regenerate intermediates in TCA cycle
Anaplerotic pathway
34
What is the net yield of TCA cycle
```
2 CO2
1 GTP (ATP)
3 NADH
1 FADH2
AND
1 NADH and 1 CO2 from pyruvate oxidation
```
35
Two types of producing ATP during respiration
Substrate level phosphorylation
AND
Oxidative phosphorylation
36
What is respiratory chain
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
37
How many complexes are there in the respiratory chain
4
38
Why electron transport chain cannot run without TCA cycle and vice versa?
Because then succinate cannot be oxidized by succinate dehysrogenase in the respiratory chain
39
How does electron transport chain function
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.
40
What is quinone
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
41
What is complex II
Succinate dehydrogenase, that makes FADH2 and then immediately trasnfers electrons and hydrogens to quinone
42
How much protons are transported from matrix to intermembrane space from 1 NADH and 1 FADH2
NADH:10
FADH2:6
43
List all the parts of electron transport chain
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
44
Where is electron transport chain in prokaryotes
in the cell membrane
45
Proton motive force is used for
```
Flagellum rotation( in bacteria)
Transport across the membrane and synthesis of ATP
```
46
How much protons are needed for 1 ATP
3-4 protons
47
What is the equation for proton motive force
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
Why do some bacteria that do not use oxidative phosphorylation still use ATPases
Because they are reversible, hydrolyze ATP to ADP in order to generate proton motive force
49
What is the yield of ATP from glycolysis
2 ATP
| 6ATP
50
What is the yield of ATP from CAC
1 ATP
4 NADH->12 ATP
1 FADH2->2 ATP
Total:15 ATP*2( because two pyruvate)->30 ATP
51
The maximum yield from respiration
38 ATP
52
What is the yield from fermentation
Net yield: 2 ATP
Lactic acid:2 lactate and 2 NAD+
Alcohol: 2 ethanol+2 Co2+2 NAD+
53
In yeast production of ethanol and CO2 depends on what
Inversely proportional to the concentration of O2
54
Why it is important to get right conditions for the yeast when fermenting
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
What does the pentose pathway produce
A large diversity of sugars and regenerate NADPH-reducing power
56
What is the first step in pentose phosphate pathway
Oxidative phase
57
Where does the reactant for the oxidative phase come
Directly from glycolysis (glucose 6-phosphate)
58
In what phase NADPH and sugars are produced
NADPH-oxidative phase
| Sugars- second phase
59
How do organism get NADPH?
The majority of organisms can produce it themselves, but the rest will use pentose phosphate pathway
60
What is the end product of the oxidative phase and the by-products
End product-ribulose 5-phosphate
| By-product - NADPH and CO2
61
How are deoxyribose and ribose for DNA produced
from ribose 5-phosphate in pentose phosphate pathway
62
Where does pentose pathway take place
In the cytoplasm in eukaryotes and prokaryotes
63
If fermentation is taking place, pentose phosphate pathway occurs ___ and if respiring, ppp runs ___
In parallel
64
Why does NADPH produced during pentose phosphate pathway important
Because NADH and FADH2 from respiration will be used in the respiratory chain
NADPH makes sure there is enough reducing agent for anabolism
65
Two roles of TCA cycle
```
Energetic role ( producing reducing equivalents)
Biosynthetic roles - intermediates can be used for anabolic processes
```
66
Examples of biosynthetic role of TCA cycle
Alpha ketoglutarate ->glutamate family and oxaloacetate->aspartate family can be converted to AA
67
The cell needs the intermediates of TCA cycle , but it needs AA at the same time, how does it cope with it
Anaplerotic pathway( converting pyruvate with the help of the reducing power to malate)
68
Where does different cycles occur in eukaryotes and prokaryotes
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
Why do we have different yield for respiration in eukaryotes
Pyruvate needs to actively transported through the inner membrane and so ATP is used -> less yield
70
How does molecules get through the outer membrane
The membrane is porous -> diffusion
71
How does ATP is transported from mitochondria matrix to the intermembrane space
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
What is the cytoplasm
A solution of salts, sugars, AA, nucleotides, and many other substances
73
What can get through the cytoplasmic membrane with simple diffusion
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
What is the way to accumulate molecules against concentration gradient and to transport molecules that are hydrophylic through the membrane
Integral transport proteins
75
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
As soon as glucose molecule gets into the cell, glucose can phosphorylated
76
3 types of transport across the membrane
Simple diffusion
Facilitated diffusion
Active transport
77
Two types of facilitated diffusion
Channel-mediated
| Carrier-mediated
78
Facilitated diffusion transports molecules ___ the gradient, and active transport ____ the gradient
Down the gradient
| Against the gradient
79
What is the determinant where is down the gradient fro uncharged and charged substances
For uncharged: the concentration gradient
| Charged: the concentration gradient and the charge
80
What is the advantage of simple diffusion vs transport and vice versa
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
Transport proteins are very ____ to the molecule they are transfering
Specific
82
In multi-cellular organisms , cells acquires nutrients by ___
In unicellar organisms (bacteria, archea and eukarya) nutrients are usually acquired by ___
```
Facilitated diffusion (from blood/plasma)
Active transport
```
83
What is the specificity of channel-mediated diffusion
Relatively low
84
What is the name for the facilitated diffusion channels than can be closed by the cell
Gated channels
85
How does carrier-mediated channels work?
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
Who does have higher specificity:channel-mediated or carrier-mediated channels
Carrier-mediated
87
What is the active transport
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
Three types of active transport and how they work
- 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
Three types of simple diffusion ( depending on the direction of movement )
Uniporter: one substance one way
Symporter: two substances one way
Antiporter: two substances in different directions
90
The example of symporter and antiporter
Antiporter: when H+ moves in and NA+ moves out
Symporter:Lactose in and H+ in
91
What is the best characterized group translocation system
Phosphoenolpyrivate-dependent sugar phosphotransferase system
92
where is Phosphoenolpyrivate-dependent sugar phosphotransferase system used?
To transport glucose, fructose and mannose in bacteria
PLUS
Responsible for the first step of glycolytic pathway in prokaryotes
93
How do we get phosphate for glucose in Phosphoenolpyrivate-dependent sugar phosphotransferase system
A complex of 5 enzymes.
| Phosphoenolpyruvate gives off phosphate group to the first enzyme and then the cascade until it gets to glucose
94
How many enzymes in Phosphoenolpyrivate-dependent sugar phosphotransferase system are in the cytoplasm, cytoplasmic membrane , etc.
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
ATP binding cassette
| 3 components
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
Where is the binding protein in Gram-positive and Gram-negative bacteria
Gram-negative:free in periplasm
| Gram-positive:anchored in the cytoplasmic membrane
97
What does binding protein do
Binds to the substrate and transfers it to the transporter
98
When does proton motive force is generated
If the respiration is possible - a terminal electron acceptor( electron transport chain) is present
99
If a terminal electron is not present , pmf is generated by
ATPases
100
PMF-dependent transporters are ___ or ___ that use the proton gradient
symporters or antiporters
101
How does pmf and Na+ connected
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
who does use Na+ dependent transport systems
Marine organisms
103
pmf is generated inside of mitochondria in eukaryotes, how do they create another pmf in cytosol
They use ATPases to pump ATP across the cytoplasmic membrane
104
What type of ATPases eukaryotes and prokaryotes have
Prokaryotes and mitochonsria f-type
| eukaryites - p-type
105
What is the difference between f-type and p-type atpases
P type can pump only proton with one ATP hydrolyzed, when F-type can pump 3 protons for 1 ATP hydrolyzed
106
What is endocytoses
The ability to take up large molecules and digest them inside of the cell
107
What is essential endocytosis
Actin filaments
108
Three types of endocytosis
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
What is formed during phagocytosis
Pseudopodium
| and then phagosome ( food particle)
