Lecture 4: Metabolism

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Metabolism: sum total of all biochemical processes going on
anabolism: synthesis of chemical compounds
catabolism: breakdown of chemical compounds
- large molecules broken down into smaller molecules
- energy is released
anabolism vs. catabolism: sythesis vs. breakdown
What is the tool of metabolism?: enzymes
enzymes: group of organic molecules (usually proteins) that bring about chemical changes while remaining unchanged
Lowers activation energy of reactions (days vs. seconds): enzymes
What do enzymes allow to happen?: Allow specific reactions to occur- a cell then has the power to control its destiny
- A + B --> C or A + B --> D depending on the enzyme
Are enzymes recycled?: yes
Names of enzymes are usually based on ___?: substrate
Ex:
-Lactase: breaks down lactose
-Peptidase: breaks peptide bonds
-Lipase: hydrolyses lipids
Some enzymes are made up entirely of protein. Give an example of a protein only enzyme.: Lysozyme (129 amino acids, found in saliva and tears, will break bacterial cell walls)
Some enzymes are made of protein and ion. What is the ion component called?: cofactor
give examples of cofactors (Three of them): Mg, Zn, Fe
What enzyme needs a cofactor?: Taq polymerase, which is used for PCR, needs Mg. (If used Mn2+, there would be an error prone PCR)
some enzymes are made of protein and an organic molecule. What is the non protein part called?: Coenzyme
Give two examples of coenzymes: nicotinamide adenine dinucleotide (NAD), flavin adenine dinucleotide (FAD)
Give three different compositions that enzymes come in.: - protein only
- protein and ion
- protein and organic molecule
What is the chemical energy for enzymes?: ATP
- it is like a portable battery
An ATP molecule is composed of adenine and ribose bonded to one another and to three phosphate groups. Breaking the high-energy bond holding the last phosphate group yields ___.: 7.3 kcal/mole ATP
Because ATP molecules are not good for energy storage, they need to store energy in ____ or other compounds until needed: sugars
What two ways do cells release energy out of storage?: 1) metabolic pathway
2) respiration (ex: glucose catabolism)
Metabolic pathway: connected sequence of chemical reactions where product of one reaction is the substrate for the next reaction
respiration. Give the definition and the two types of respiration.: series of biochemical reactions (such as glucose catabolism) which release energy.
1) Aerobic respiration- oxygen present
2) Anaerobic respiration- oxygen absent
Glucose catabolism can occur in either ____ or ____ conditions.: aerobic or anaerobic conditions
Give the summary of glucose metabolism. (equation): C6H12O6 + 6O2 + 38ADP + 38P -->
6CO2 + 6H2O + 38ATP

*C6H12O6 (GLUCOSE)
and 38 ATP
What is the first, second, and third step of glucose metabolism?: glycolysis, TCA cycle, oxidative phosphorylation
In glycolysis, glucose is converted into how many molecules of pyruvic acid?: two
Is oxygen utilized in glycolysis?: no
Where does glycolysis occur?: pathway occurs in cytoplasm
In the TCA cycle, also known as Krebbs, pyruvic acid from glycolysis is converted to ___ after combining with ____.: acetyl-CoA
coenzyme A
oxidative: loss of e- pairs from chemical molecules in sequence (electron transport chain)
phosphorylation: addition of phosphate to ATP
Where does the TCA cycle take place?: cell membrane
The TCA cycle and electron transport is located in the ____of bacteria and ___ of eukaryotes: cell membrane
mitochondria
Which coenzymes transport electron pairs to the cytochromes in the cell membrane?: NADH or FADH2
Cytochromes (cyt A, A3, B, C): protein pigments containing iron ions that accept and release electrons during sequence
Are coenzymes regenerated? If so, why?: Coenzymes are regenerated for reuse
Cytochromes transport e- pairs among themselves, releasing energy which fuels ___ across cell membrane at 3 points.: transport of protons.
Where do protons reenter the cytoplasm?: through a protein channel lined with ATP synthetase
What is the final electron acceptor in the electron transport chain?: oxygen is the final electron acceptor and forms water once it receives the electrons at the end of the electron transport chain.
chemiosmosis: mechanism for ATP formation
Is ATP made through electron transport?: No. So what is the importance of the electron transport chain since no ATP has been made? CHEMIOSMOSIS. The actual mechanism for ATP synthesis comes from the pumping of protons through a process called chemiosmosis.
Describe the process of chiosmosis.: -Energy released at three transition points.
-Energy (proton motive force) powers pumping of protons from cytoplasm across cell membrane.
-Protons build up outside membrane--buildup of positive charge.
-Channels opens up, protons flow reverses.
-Inside of channels lined with ATP synthetase. ATP IS GENERATED!
How much ATP comes directly from glycolysis?: 2 ATP
In the TCA cycle, ATP comes from ___: GTP
Even more ATP is formed from ___ and ___ coming from the TCA cycle going through oxidative phosphorylation.: NADH and FADH2.
How much ATP is formed from NADH?: 3 ATP
How much ATP is formed from FADH2?: 2 ATP. (fewer proton pumps activated)
How do microorganisms eat things other than glucose?: By modifying alternate carbohydrates into something that fits into a common pathway.
Sucrose digested by enzyme sucrase yields ___ and ____.: fructose and glucose. The glucose goes to glycolysis. Fructose converted to F-1-P, enters glycolysis as DHAP.
Lactose converted by lactase into ___ and ___: glucose and galactose. The galactose is converted to G-6-P and enters glycolysis.
When are proteins used for energy sources?: Cells use them for energy when carbohydrates and fats are in short supply.
Proteases breakdown protein into ___.: amino acids

ex: aspartic acid converted to oxaloacetic acid
Amino acids converted to pathway components by ___.: deamination (get rid of amino group).
What are fats?: fats are fatty acids bonded to glycerol
What converts fats into fatty acids and glycerol?: lipase
Lipase converts fats into fatty acids and glycerol. Glycerol converted into ___, which goes into glycolysis.: DHAP
Fatty acid is broken down into 2 carbon units through the process of ___: beta oxidation

-Each 2 carbon unit converted into Acetyl CoA, which goes into TCA cycle
anaerobic respiration: alternative final electron acceptors in the absence of oxygen
Nitrate ion (NO3-) as final e- acceptor yields ____ in E. coli.: Nitrite (NO2-)
Sulfate as final e- acceptor yields ___ in Desulfovibrio.: H2S
CO2 as final e- acceptor yields ____ in methanogens (Methanobacterium, Methanococcus): methane
What are three alternative final electron acceptors in the absence of oxygen (anaerobic respiration)?: Nitrate, sulfate, CO2.
Fermentation is a type of anaerobic respiration. ___ or ___ is final electron acceptor.: pyruvic acid or derivative
Lactic acid fermentation. Pyruvic acid is final electron acceptor. Pyruvic acid converted to _____: lactic acid (Streptococcus lactis)
Alcoholic fermentation. ____ is final electron acceptor.: acetylaldehyde
acetyladehyde, the final electron acceptor in alcoholic fermentation, is converted to ____.: ethyl alcohol (Saccharomyces cerevisiae)
Fermentation: only go through glycolysis. no TCA or oxidation. Energy benefits less (2 ATP) than aerobic respiration, but organism may not have a choice.
Aerobic respiration (glycolysis, TCA cycle, oxidative phosphorylation), yields ___ from 1 molecule of glucose.: 38 ATP
What is the final electron acceptor of aerobic respriation?: oxygen
In anaerobic respiration, oxygen is not the final electron acceptor. Instead, ___, ____, and ___ are the final electron acceptors.: nitrate, sulfate, carbon dioxide
In fermentation, the final electron acceptor is ____ or ___.: pyruvate or pyruvate derivative
Name a type of anabolism.: photosynthesis
In photosyntheses, light energy from photons is converted into ____: chemical energy (ATP and NADPH2)
- light energy is caught by chlorophyll or chlorophyll-like pigments.
chemical energy is used to ____: synthesize glucose
What are two types of photosynthesis?: oxygenic- yields oxygen
anoxygenic- does not yield oxygen
Give an example of a eukaryote that participates in oxygenic photosynthesis.: algae
Give two examples of prokaryotes that participate in oxygenic photosynthesis.: 1) cyanobacteria (photosynthesis in membranes)

2) extreme halophiles (use bacteriorhodopsin instead of a chlorophyll derivative)
halophiles use ____ instead of a chlorophyll derivative for oxygenic photosynthesis.: bacteriorhodopsin
Anoxygenic photosynthesis is a type of photosynthesis that does not yield oxygen. Something other than water is used as a source of hydrogen ions. Green sulfur bacteria (chlorobium limicola) uses ___ as a source of hydrogen ions.: H2S

H2S used as a source of hhydrogen ions, converted to sulfur.
In green sulfur bacteria, bacteriochlorophyll is located in vesicles attached to the plasma membrane called ____.: chlorosomes
Give two examples of organisms that participate in anoxygenic photosynthesis.: 1) Green sulfur bacteria (Chlorobium limicola)

2) Purple sulfur bacteria (rhodobacter sphaeroides)
Purple sulfur bacteria, which participates in anoxygenic photosynthesis, uses ____ as a source of hydrogen ions. It is converted to ___.: small fatty acids (succinate)

fumarate
In purple sulfur bacteria, bacteriochlorophyll pigments are located in folds of the plasma membrane called ____.: intracytoplasmic membranes
Nutritional classifications are based on ____ and _____.: energy source

carbon source
Do photoautotrophs perform anoxygenic or oxygenic phtotosynthesis?: both. photoautotrophs perform anoxygenic or oxygenic photosynthesis.
Where do photoautotrophs gain their energy from?: light
Where do photoautotrophs gain their carbon from?: CO2 provides carbon
Chemoheterotrophs gain their energy from ____ and ____ provide carbon: chemical reactions
organic compounds
photoheterotrophs use ____ as a source of energy.: light
photoheterotrophs use ____ such as ____ as a source of carbon: organic compounds such as alcohols, fatty acids or organic acids
Give two examples of photoheterotrophs: 1) Green nonsulfur bacteria (ex: Chloroflexus)

2) Purple nonsulfur bacteria (ex: Rhodopseudomonas)

*not to get confused w/ green sulfur & purple sulfur bacteria, which are anoxygenic
Chemoautotrophs use ___ as a source of carbon dioxide and ___ reactions to obtain energy from inorganic compounds.: carbon

chemical
For chemoautotrophs, since nergy source is from chemical reactions, _____ rather than photosynthesis.: chemosynthesis
With Chemoautotrophs, nitrifying bacteria preserve nitrogen in the soil in the form of ____: nitrate
- nitrosomonas
ammonium to nitrite

-nitrobacter
nitrite to nitrate
______ is an example of chemolithotroph used in 'biomining': Thiobacillus ferroxidans
Thiobacillus ferroxidans uses CO2 as its carbon source. It is a chemoautotroph. It obtains its energy from oxidizing sulfides of iron sulfides to sulfur, then to sulfuric acid. What does sulfuric acid do?: Sulfuric acid dissolves the insoluble copper and gold from the ore.

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