Metabolism Flashcards
(62 cards)
1
Q
What is the definition of metabolism?
A
All chemical reactions that occur within a living organism.
2
Q
What is a catabolic reaction?
A
- Degradative reactions that release energy (exergonic) by breaking down large, complex molecules into smaller ones
- Often involves hydrolysis, breaking bonds with water
- Transfer energy from complex molecules to ATP
- Often coupled to ATP synthesis - ADP + Pi + Energy –> ATP
3
Q
What is an anabolic reaction?
A
- Biosynthetic reactions that build large complex molecules from simpler ones
- Require energy (endergonic) and often involve dehydration synthesis
- Transfer energy from ATP to complex molecules
- Often coupled to ATP hydrolysis - ATP –> ADP + Pi + Energy
4
Q
Describe the coupling of catabolic and anabolic reactions.
A
- Catabolic reactions provide the energy needed to drive anabolic reactions.
- ATP stores energy from catabolic reactions and releases it to drive anabolic reactions.
- Only part of energy released in catabolism is available for work, the rest is lost as heat
5
Q
What are enzymes?
A
- Highly specific, usally catalyze only one or a few closely related chemical reactions
- Extremely effecient (Speed up 10 billion times more than without enzyme)
- Most are reversible unless they catalyze highly exergonic or endergonic reactions (these typically function in one direction).
6
Q
What is turnover number?
A
Number of substrate molecules an enzyme molecule converts to product each second.
7
Q
Describe the difference between prosthetic groups and coenzymes.
A
- Prosthetic groups bind tightly to their enzymes usually covalently and permanently.
- Coenzymes are loosely and often transiently bound to enzymes.
8
Q
The rate of a chemical reaction depends on…
A
Temperature, pressure, substrate, concentration, pH, and several other factors
9
Q
What is energy of activation (Ea)?
A
- The amount of energy that is required to trigger a chemical reaction.
- Enzymes speed up chemical reactions by decreasing their Ea - allows reaction to proceed
10
Q
Describe what free energy (Delta G) is regarding enzymes.
A
Exergonic vs. Endergonic. Reveals whether energy is released or required in a reaction.
11
Q
What are the six classes of enzymes?
A
Oxidoreductases, transferases, hydrolase, lyase, isomerase, ligase.
12
Q
What do oxidoreductases do?
A
Catalyze oxidation-reduction reactions. Includes dehydrogenases and oxidases.
13
Q
What do transferases do?
A
Transfer functional groups (amino, phosphate, etc.)
14
Q
What do hydrolyases do?
A
Hydrolysis, break bonds by adding water.
15
Q
What do lyases do?
A
Remove groups of atoms without hydrolysis.
16
Q
What do isomerases do?
A
Rearrange atoms within a molecule.
17
Q
What do ligases do?
A
Join two molecules, usually with energy provided by ATP hydrolysis.
18
Q
Describe the relationship of cofactors to enzymes.
A
- Holoenzyme = apoenzyme (protein portion) + cofactor (nonprotein portion)
- Cofactors may be a metal ion (Mg2+, Ca2+, etc.) or an organic molecule (coenzyme, often derived from vitamins, ie… NAD+, NADP+, coenzyme A)
19
Q
Mechanism of enzymatic action.
A
- Enzyme contains an active site that binds specifically to substrate, E-S complex forms
- Substrate molecule transformed by rearrangement of existing atoms, breakdown of substrate molecule, and/or combination with another substrate molecule
- Products of reaction no longer fit active site and are released
- Unchanged enzyme is free to bind to more substrate molecules
20
Q
Shape and enzyme function.
A
Enzymes are protein molecules and their 3D shape is essential for their function. The shape of the active site must not be altered so that it can bind specifically to the substrate.
21
Q
How does temperature affect enzyme function?
A
- Most enzymes have an optimal temperature
- Enzymatic activity increases with increasing temperature
- At low temps, most reactions proceed slowly - slow particle movement
- At high temps, reactions slow down because the enzyme is denatured (breakage of H and noncovalent bonds)
22
Q
How does pH affect enzyme function?
A
- Most enzymes have an optimum pH
- Above or below this value activity slows down
- Extreme changes in pH cause denaturation
23
Q
How does substrate concentration affect enzyme function?
A
- Enzymes act at max. rate at high substrate concentration
- Saturation point: substrate concentration at which enzyme is acting at max. rate possible
24
Q
How do inhibitors affect enzyme function?
A
- Inhibit enzyme activity
- Competitive inhibitors - bind to enzyme active site
- Noncompetitive inhibitors - bind to an allosteric site
25
What is feedback inhibition?
* Some allosteric inhibitors stop cell from making more of a product than it needs
* The end product of a series of reactions, inhibits the activity of an earlier enzyme
* Feedback inhibition is used to regulate ATP, amino acid, nucleotide, and vitamin synthesis by the cell
26
What are ribozymes?
* Catalytic RNA molecules
* Have active sites that bind to substrates
* Discovered in 1982
* Act on RNA substrates by cutting and splicing them
27
What is oxidation?
* Removal of electrons or H atoms
* Addition of oxygen
* Associated with loss of energy
28
What is reduction?
* Gain of electrons or H atoms
* Loss of oxygen
* Associated with gain of energy
29
What are redox reactions?
* Reactions in which both oxidation and reduction occur
* Electron transfer reactions - transferred from an electron donor in one half reaction to an electron acceptor in a second half reaction
* Aerobic respiration is an example of an redox reaction
30
Reduction potential (E0) and reducing power
* Ability to donate electrons during electron transfer reactions
* The greater the difference in the reduction potentials of the two half reactions in a redox couple, the more energy will be available to the cell
* E0 - the tendency of a compound to accept or release electron
* Reactions often employ coenzymes as electron shuttles (ie... NAD+/NADH)
31
What are the three different mechanisms of ATP phosphorylation?
1. Substrate-level phosphorylation
2. Oxidative phosphorylation
3. Photophosphorylation
32
Describe substrate-level phosphorylation.
* Direct transfer of phosphate from phosphorylated compound to ADP
* Does not require intact membranes
* Generates small amount of energy (ATP) during aerobic respiration
* Occurs in cytoplasm
33
Describe oxidative phosphorylation.
* Involves electron transport chain, in which electrons are transferred from organic compounds to electron carriers to a final electron acceptor - PMF generated
* Occurs on membranes
* A LOT of ATP is generated through chemiosmosis
* Generates most of the ATP in aerobic respiration
34
What is the proton motive force?
An electrochemical gradient formed by energy conserving reactions that transport protons outside the cytoplasmic membrane - creates force that is ultimately used to synthesize ATP.
35
Describe photophosphorylation.
* Occurs in photosynthetic cells only
* Convert solar energy (light) into chemical energy (ATP and NADPH)
* Also involves electron transport chain
* Occurs in some plants and bacteria (typically not pathogenic)
36
What is cellular respiration?
* ATP generating process in which food molecules are oxidized
* Requires ETC
* Final electron acceptor is an inorganic molecule (oxygen for aerobic, very efficient; something different for anaerobic [Fe, S, carbonate], inefficient)
37
All mechanisms of energy conservation except --- are linked to the ----
Fermentation, Proton Motive Force
38
What is fermentation?
* Releases energy from sugars or other organic molecules
* Does not require oxygen, but may occur in its presence
* Does not require TCA or ETC
* Final electron acceptor is **organic**
* Inefficient - produces small amount of ATP (1-2 ATP from glycolysis)
* End products are energy rich organic molecules (lactic acid, alcohol) - wastes
39
Describe aerobic respiration.
* Glucose + oxygen --> CO2 + H2O + ATP
* Most energy efficient catabolic process
* Oxygen is final electron acceptor
* Occurs in cytoplasm, ETC occurs on PM
* 3 stages: Glycolysis, TCA, ETC
40
Describe glycolysis.
* Glucose (6C) is split and oxidize to two molecules of pyruvate (3C) - don't lose any carbons
* Have to expend ATP to "prime the pump"
* Does not require oxygen
* Net yield: 2 (NAD+ is reduced) NADH, 2 ATP (substrate level phosphorylation), 2 pyruvate
41
Describe the TCA cycle.
* Before cycle, pyruvate loses 1 carbon (CO2) to become acetyl CoA (2C)
* Acetyl CoA joins oxaloacetate (4C) to form citric acid (6C)
* 8 oxidation-reduction reactions, transfer energy to electron carrier molecules - C is lost as CO2 in redox reactions
* Oxaloacetate is regenerated in final step
* Int. are used for other biosynthetic pathways (ie... forming A.A.)
* Net yield per 1 glucose: 2 GTP (ATP), 8 NADH, 2 FADH2, 6 CO2
42
Describe the ETC.
* Main Goals: Make ATP and recycle electron carriers
* Electrons from NADH and FADH2 are released to chain of electron carriers
* Electron carriers are on cell membrane (PM of bacteria or IM of eukaryotes)
* Final electron acceptor is O2
* Proton gradient is generated across membrane as electrons flow down chain (Protons on outer surface of membrane, OH- accumulated on cytoplasmic side - creates pH difference)
* ATP made by ATP synthase (chemiosmosis) - requires intact membranes
* Net ATP yield: 2 FADH2 = 2 ATP each (4), 10 NADH = 3 ATP each (30)
43
How are carriers within the ETC organized?
* Embedded in the membrane in order of their increasingly positive reduction
* Electrons are passed on from lower potential carriers to higher potential carriers until at the end of the chain they ultimately reduce a terminal electron acceptor.
44
ATP yield per glucose molecule
Around 38 for prokaryotes, 36 for eukaryotes. Yield is lower in eukaryotic because transport of pyruvic acid into mt requires energy.
45
ATP hydrolysis and synthesis
The biosynthesis of energy rich compounds function to trap free energy and their hydrolysis releases this energy to drive endergonic reactions.
46
The ETC allows for 3 main things to occur...
1. Allow bacteria to move flagella
2. H+ linked to transport (anti + symporters)
3. Can affect/regulate pH
47
Describe the difference between ETC inhibitors and uncouplers.
Inhibitors can stop transfer of electrons from one carrier to another (CN - cyt. B). Uncouplers interculate between phopholipids (dinitrophenol, EtBr).
48
What is the final electron acceptor in anaerobic respiration?
* NOT oxygen, instead its inorganic
* Some possibilities include: Fe (next best), nitrate, sulfate, carbonate
49
Describe the effiency of anaerobic respiration.
* It is a very inefficient process (2 ATP/glucose)
* Only some of TCA cycle can work without O2
* Some carriers in ETC won't work without O2
* For these reasons... anaerobes tend to grow more slowly than aerobes
50
What are some reasons that some organisms have to do anaerobic respiration?
* Lack enzymes or cytochromes that use O2
* O2 can inactivate certain enzymes
* O2 itself have have toxic radicals
51
What organisms carry out lactic acid fermentation? What is it used for?
* Carried out by Lactobacillus and Streptococcus
* Can result in food spoilage and used to make yogurt, sauerkraut, and pickles
* Also the cause of dental carries
* Essential to maintaining health of human large intesting and vagina
52
What organisms carry out alcohol fermentation (ie... ethanol)?
Carried out by yeast and bacteria.
53
What is the biggest reason that organisms ferment?
The have to recycle their NAD+ (NADH to NAD+) so it can be used in glycolysis.
54
Where do fats and proteins enter to be broken down? Why does this matter?
* Fats are typically broken down using beta oxidation (2C at a time) and enter as acetyl CoA (can also enter in parts of glycolysis).
* Proteins are broken down in to A.A. and typically enter into the TCA cycle (can also enter other places)
55
Describe light dependent reactions.
* Light energy is trapped by chlorophyll
* Water is split into O and H
* NADP+ reduced to NADPH
* ATP is made
56
Describe light independent reactions.
* Do not require light
* CO2 from air is fixed and used to make sugar
* Sugar is synthesized, using ATP and NADPH
57
What are phototrophs?
Light is primary energy source.
58
What are chemotrophs?
Oxidation of chemical compounds as primary energy source.
59
What are autotrophs?
Use CO2 as primary carbon source.
60
What are heterotrophs?
Use organic C as primary carbon source.
61
What are chemoorganotrophs?
Obtain energy from organic molecules.
62
What are chemolithotrophs?
Obtain energy from inorganic molecules.
