Chapter 17 - Metabolism Overview Flashcards
What is metabolism
METABOLISM = CATABOLISM + ANABOLISM
The sum of all the chemical processes occurring in an organism at one time
There are two pathways of metabolism:
Catabolic pathways
Anabolic pathways
What are the two pathways of metabolism
Catabolic pathways
Anabolic pathways
Explain catabolic pathway
•Pathways that release energy by breaking down complex molecules into simpler compounds
–Oxidative degradation of complex molecules
–Energy Yielding
–Captured in the form of ATP
Explain anabolic pathway
•Pathways that consume energy to build larger, complicated molecules from simpler ones
–Assembly of complex biomolecules from simpler precursors
–Biosynthesis
–Energy Requiring
Explain ATP
- Energy molecule used to couple exergonic reactions to endergonic
- Nucleotide with three phosphate groups attached to the ribose sugar
- ATP has a high G
Explain exergonic reaction
Exergonic reactions are spontaneous chemical reactions in which the products are at a lower energy level than the reactants; these reactions release energy.
Explain endergonic reaction
Endergonic reactions are nonspontaneous chemical reactions in which the products are at a higher energy level than the reactants; these reactions consume energy.
What does ATP stand for?
Adenosine Tri-Phosphate
Explain the ATP cycle.
How is ATP formed
What are the different types of ATP hydrolysis seen in cells?
What is the end product of ATP hydrolysis?
- ATP is formed via photosynthesis in phototrophic cells or catabolism in heterotrophic cells.
- 3 different types of ATP hydrolysis?
- Biosynthesis, osmotic work, cell motility/muscle contraction
- Energy-requiring cellular activities are powered by ATP hydrolysis, liberating ADP and Pi.
Explain catabolism vs anabolism
Explain how catabolism breaks down nutriets and what does it give off in this process?
Explain how anabolisms bulds up precursor molecules and what does it require for this process?
Metabolic diversity based on carbon source
Metabolic diversity based on carbon source
Autotrophs
Heterotrops
Metabolic diversity based on energy source
Metabolic diversity based on energy source
Phototrophs
Chemotrophs
How are organisms classified by their oxygen needs?
Aerobes
Anaerobes
What are aerobes
Aerobe:
An organism that require oxygen (O2) as the terminal electron acceptor,
or can grow in an environment with the present of oxygen.
different types:
Obligate aeroboes
What are the different types of aerobes
Obligate Aerobes:
O2 is an obsolute necessity
What are anaerobes
Anaerobe:
An organism that can live without oxygen (O2).
Different type:
Facultative anaerobes
Obligate anaerobes
What are the types of anaerobes?
Obligate Anaerobes
which cannot use oxygen for growth and are even harmed by it
Facultative anaerobes
which can grow without oxygen but can utilize oxygen if it is present
Normally use O2 but can adapt to anaerobic conditions by using other compounds as an electron acceptors
Example E. coli
Explain thioglycollate broth
Fluid Thioglycollate broth is a reducing medium. It contains sodium thioglycollate, which reacts with molecular oxygen keeping free oxygen levels low. The sodium thioglycollate in the broth creates a redox potential in the tube, with higher levels of oxygen at the top of the tube, and a complete absence of oxygen at the bottom of the tube.
To differentiate between oxygen requirements using anaerobic culture media.
What is Thioglycoalte in thioglycolate broth used for in labs?
Thioglycoalte in thioglycolate broth is an anaerobic dulture media
It lets us differentiate between oxygen requirements
After thioglycolate reacts with oxygen throughout the tube, oxygen can penetrate only near the top of the tube where the medium contacts air.
ü Obligate aerobes grow only at the top of such tubes.
ü Facultative organisms grow throughout the tube but best near the top.
ü Microaerophiles grow near the top but not right at the top.
ü Anaerobes grow only near the bottom of the tube, where oxygen cannot penetrate.
Microbes can be classified into 5 groups based on their requirement for air that contains
20% oxygen:
- Obligate aerobes: Require oxygen for growth via respiratory metabolism in
which oxygen is the terminal electron acceptor. - Obligate anaerobes: Can not survive in the presence of oxygen due to lack of
enzymes superoxide and catalase or peroxidase, which detoxify damaging oxygen by-
products such as peroxides and superoxides. Use fermentation or anaerobic
respiration. - Facultative anaerobes: Can grow in oxygen or without. Use oxidative
respiration and fermentation/ anaerobic respiration. - Microaerophiles: Require small amounts of oxygen (5-10%) for respiration but
can not survive in atmospheric oxygen due to limited ability to carry out respiration
or presence of oxygen-sensitive enzymes. - Aerotolerant anaerobes: Can survive in oxygen due to presence of superoxide
dismutase but do not use oxygen as a terminal electron acceptor. Use fermentation
or anaerobic respiration.
Explain the different catagories seen in the picture.
ü Obligate aerobes grow only at the top of such tubes.
ü Facultative organisms grow throughout the tube but best near the top.
ü Microaerophiles grow near the top but not right at the top.
ü Anaerobes grow only near the bottom of the tube, where oxygen cannot penetrate.
What are reactive oxygen species?
Reactive oxygen species (ROS) are chemically-reactive molecules containing oxygen.
Reactive oxygen species can damage proteins, enzymes, DNA
Reactive Oxygen Species (ROS) is a phrase used to describe a number of reactive molecules and free radicals derived from molecular oxygen. The production of oxygen based radicals is the bane to all aerobic species. These molecules, produced as byproducts during the mitochondrial electron transport of aerobic respiration or by oxidoreductase enzymes and metal catalyzed oxidation, have the potential to cause a number of deleterious events.
What are the different types of reactive oxygen species?
- Singlet oxygen
- Superoxide radical (O2-)
- Superoxide dismutase
- Peroxide anion (O22-)
- Catalase
- Hydroxyl Radical (OH.)
Reactive oxygen species can damage proteins, enzymes, DNA
What are the two ways Living organisms obtain their chemical energy?
Livivng organisms obtain their chemeical energy in two ways:
Autotrophs
Heterotrophs
What are autotrophs
Autotroph:
Make their own food
Organisms that are able to utilize carbon dioxide as sole source of carbon for metabolism
Organisms that use inorganic materials as nutrients
such as photoautotroph using light as energy, chemolithoautotroph obtaining energy through oxidation of inorganic material.
What are the different types of autotrophs and define each
photoautotroph
- using light as energy,
chemolithoautotroph
- obtaining energy through oxidation of inorganic material.
What are heterotroph
Heterotroph:
cannot make their own food, so they must eat or absorb it
Heterotrophs are organisms that utilize organic materials as building blocks
Require an organic form of carbon (produced by other living system) such as glucose for their metabolism.
CO2, O2, and H2O are recycled
Explain phototrophs and give an example
Phototrophs:
Phototrophs are photosynthetic organims that use light as a source of energy to drive synthesis of organic molecules
e.g, algae, cyanobacteria.
Explain how the phototrophs and heterotroph cycle works and show what is being recycled in this cycle between these two cells.
Explain chemotrophs and give an example
Chemotrophs:
Organisms that use organic compounds (eg. glucose) or oxidizable inorganic substances (Fe2+, NH4+) for their energy source.
Energy is typically extracted using redox reactions.
e.g., fungi, some sulfur bacteria.
4 categories of organisms based upon carbon and energy source
4 categories of organisms based upon carbon and energy source
Photoautotroph
Photoheterotrophs
Chemoautotrophs
Chemoheterotrophs
Explain chemoautotrophs and give an example
Chemoautotrophs:
Organisms use chemical compounds (inorganic) for energy and carbon dioxide as the main source of carbon,
e.g., nitrifying bacteria, sulfur bacteria, and iron bacteria.
Explain photoautotrophs and give an example
Photoautotrophs:
Organisms use light for energy and carbon dioxide as the main source of carbon,
e.g., algae, plants, cyanobacteria.
Explain Photoheterotrophs and give an example
Photoheterotrophs:
Organisms use light for energy and organic compounds as main source of carbon,
e.g., purple and green nonsulfur bacteria.
What is the carbon source and the energy source of the following organisms?
Photoautotrophs
Photoheterotrophs
Chemoautotrophs
Chemoheterotrophs
Explain metabolic maps
Metabolic maps are a means by which to illustrate the various interconnected chemical pathways in intermediary metabolism.
Metabolic maps comprise dots and lines
In metabollic maps, how are intermediates show?
Intermediates represented as a black dot and each enzyme as a line
In metabollic maps, how are enzyme shown?
Intermediates represented as a black dot and each enzyme as a line
In metabollic maps, what does a dot connected to a single line represent?
A dot connected to a single line = nutrient, a storage form, an end product, or an excretory product
In metabollic maps, what does a dot connected to a two lines represent?
A dot connected to just two lines = intermediate in one pathway and has only one fate in metabolism
In metabollic maps, what does a dot connected to a three lines represent?
A dot connected to three represents an intermediate that has two metabolic fates
What are the two different models of viewing metablic pathway maps?
a) The traditional view of a metabolic pathway is metabolite-centric.
(b) Julia Gerrard has proposed that a protein-centric view is more informative for some purposes.
What are the 3 stages of catabolism? how does catabolic pathways converges to the end products
The three stages of catabolism.
Stage 1: Proteins, polysaccharides, and lipids are broken down into their component building blocks.
Stage 2: The building blocks are degraded into the common product, the acetyl groups of acetyl-CoA.
Stage 3: Catabolism converges to three principal end products: water, carbon dioxide, and ammonia.
Explain amphibolic
What is an example of amphibolic intermediate?
A pathway that is used for both anabolic and catabolic purposes is a central pathway and is called “amphibolic”.
Example: citric acid cycle
In many cases, processes of breakdown and synthesis of molecules share pathways. These pathways are known as amphibolic to show their involvement in both catabolic and anabolic processes
what are the 4 functions of metabolism
metabolism has four functions:
- to obtain chemical energy from food
- to convert nutrients to the precursors of biologically important molecules
- to synthesize the biologically important molecules
- to degrade previously formed molecules that are no longer needed
what is the structure of glucose
What is the formula for glucose?
Glucose ————– C6H12O6
What is the formula for pyruvate?
Pyruvate or pyruvic acid
C3H4O3
Explain the difference between glycolysis vs gluconeogenesis.
Glycolysis:
Catabolism of glucose to pyruvate
Converts one glucose to 2 pyruvate and produces 2 ATP.
Gluconeogenesis:
Metabolic products such as pyruvate and lactate can be salvaged to synthesize glucose.
Biosynthesis of glucose from pyruvate
These two pathways share some enzymes but glyconeogenesis is not the reverse of glycolysis
Explain metabolic oxidation and reduction
catabolism is oxidative, anabolism is reductive.
Oxidation is the loss of electrons.
Oxidative reactions release hydride ions H:-
Oxidative reactions are exergonic
Metabolic energy derives from processes of oxidation and reduction. When energy is consumed in a process, chemical energy is made available for synthesis of ATP as one atom gives up electrons (becomes oxidized) and another atom accepts electrons (becomes reduced).
Explain Hydride ions
Oxidative reactions release Hydride Ions
Hydride ions get transferred in dehydrogenase reactions to NAD+ reducing them to NADH
Explain NAD+ and NADH
NAD+ collects electrons released in catabolism
The oxidative reactions of catabolism release reducing equivalents from these substrates, often in the form of hydride ions.
These hydrides are transferred to NAD+ molecules, reducing them to NADH. NADH in turn passes these reducing equivalents to other acceptors.
The main role of NADH is to transfer electrons to electron acceptor systems
Explain NADPH
NADPH provides the reducing power for anabolic processes
NADPH can be viewed as the carrier of electrons from catabolic reactions to anabolic reactions.
Explain the NADPH cycle
Transfer of reducing equivalents from catabolism to anabolism via the NADPH cycle.
Explain oxidative phosphorylation
Oxidative Phosphorylation is the process of generating ATP couple to NADH + (H+) —–> NAD+
Explain vitamins
Vitamins are essential nutrients required in trace amounts because they cannot be synthesized by the organism
Explain coenzymes
Coenzymes are organic cofactors that are required for the activity of certain enzymes
Coenzymes often contain a vitamin as a component
Coenzymes provide a broader range of catalytic properties for the enzyme.
What experiments can be used to elucidate metabolic pathways?
Metabolic inhibitors were important tools for elucidating the pathway steps.
Mutations also were used to create specific metabolic blocks.
Metabolic pathways can also be elucidated by the use of isotopic forms of elements
How can isotopic tracers can be used as metabolic probes
Metabolic pathways have been elucidated by use of isotopic forms of elements.
Metabolic substrates and intermediates can be “labeled” with a measurable isotope and then “traced” through a series of reactions.
Two types of isotopes have been used in this way.
Radioactive isotopes
Stable “heavy” isotopes - can be separated by mass spec or density gradient.
Prokaryotes vs eukaryotes
Prokaryotic cell
- Do not have organelles or internal memebranes
- Certain metabolic pathways do show localization to specific areas with the cell
- oxidative phosphorylation localized to the plasma membrane
Eukaryotic cell
- Internal membrane bound organelles
- Metabolic pahtways are segregated to different regions within the cell
What are metabolome?
The metabolome is the complete set of low-molecular weight molecules present in an organism or excreted by it under a given set of circumstances.
What are metabolomics?
Metabolomics is the systematic identification and quantitation of all these metabolites in a given organism or sample.
What Food Substances Form the Basis of Human Nutrition? and explain each
Protein is a rich source of nitrogen and also provides essential amino acids.
Carbohydrates provide needed energy and essential components for nucleotides and nucleic acids.
Lipids provide essential fatty acids that are key components of membranes and also important signal molecules.
Fiber – whether soluble or insoluble – can be a beneficial complement in the human diet.
