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 ____.
- 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?
- 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.
- 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 ___
- 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 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
- 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
- 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 ____
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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