Glossary of Lecture 4: Metabolism

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sum total of all biochemical processes going on
synthesis of chemical compounds
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?
group of organic molecules (usually proteins) that bring about chemical changes while remaining unchanged
Lowers activation energy of reactions (days vs. seconds)
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?
Names of enzymes are usually based on ___?
-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?
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?
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?
- 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
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

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?
Is oxygen utilized in glycolysis?
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 ____.
coenzyme A
loss of e- pairs from chemical molecules in sequence (electron transport chain)
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
Which coenzymes transport electron pairs to the cytochromes in the cell membrane?
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.
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?
In the TCA cycle, ATP comes from ___
Even more ATP is formed from ___ and ___ coming from the TCA cycle going through oxidative phosphorylation.
How much ATP is formed from NADH?
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 converts fats into fatty acids and glycerol. Glycerol converted into ___, which goes into glycolysis.
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.
CO2 as final e- acceptor yields ____ in methanogens (Methanobacterium, Methanococcus)
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.
acetyladehyde, the final electron acceptor in alcoholic fermentation, is converted to ____.
ethyl alcohol (Saccharomyces cerevisiae)
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?
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.
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.
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.
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 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 ____.
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)

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?
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.
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.

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

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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