Metabolism p1 and 2 Flashcards
Energy and metabolism
Thermodynamics: the study of energy flow in physical and biological processes
Living things continually capture, store and use energy for their survival
- Movement, growth, reproduction, digestion, heat, movement across cells etc
Metabolism
-Refers to all chemical reactions that change or transform matter and energy in cells
- main function is to breakdown energy-rich compounds ex glucose, and convert the energy into a useable form ex. ATP
Coupled reactions
- energy from catabolic reactions is used to power anablic reactions
ATP
Adenosine triphosphate
- the primary source of free energy in living cells
-structure: nitrogenous base adenine attached to the 5 carbon sugar ribose, which is attached to a chain of 3 phosphate groups
How is energy obtained from ATP?
- enzyme called ATPase catalyses the hydrolisis of the phosphate on ther terminal end of molecule, making ADP
- One Pi (inorganic phosphate) molecule is released with a ton of energy
- The energy is not always freely released; the Pi can go on to phosphorylate (add a phosphate to) other molecules changing their shape and making them more active (like in active transport)
- Phosphates repel eachother due to negative charge, so it takes a great deal of energy to add on the third phosphate, which is then where energy is stored and later released
Electron carriers
- redox reactions are coupled reactions: compounds that pick up electrons from energy rich compounds and then donate them to low-energy compounds
- the electron carrier is then recycled
Compound that accepts electrons –> reduced
Compound that loses electrons –> oxidized
Electrongs that pass from one atom to another carry energy with them
- reduced form of a molecule has higher energy
- electrons are said to carry reducing power
- NAD+ picks up two e- and one H+ to become NADH
The big picture of cellular respiration
- photoautorophs, like green plants, transform light energy into chemical potential energy (glucose and other carbs)
- Heterotrophs (animals, fungi, bacteria) rely on autotrophs for energy
- glucose is the primary energy source for almost all organisms. The energy that is extracted by enzymes doing redox reactions.
- When the bonds are broken, more stable compounds are formed and so energy is released
- Released energy is ‘trapped’ and stored as ATP (34% of it)
Aerobic cellular respiration
- Aerobic means oxygen is used
- Accomplished by 20 chemical reactions
- Glucose and oxygen don’t just react spontaneously, they have to overcome the activation energy barrier
Endergonic reactions
Chemical reaction that does not proceed spontaneously, requires energy. ex. photosynthesis
Exergonic reactions
Chemical reaction that releases energy, it tends to proceed spontaneously. ex. cellular respiration
Substrate level phosphorylation
- When ATP is formed through the direct transfer of Pi to ADP using an enzyme
- results in the generation of less energy than oxidative phosphorylation (happens during etc)
Structure of mitochondria
Mitochondria are often described as the powerhouses of the cell because of their central role in the synthesis of ATP a vital source of energy for the body.
Composed of:
- Double membrane (inner is folded into finger-like projections called cristae, houses the ETC and the outer membrane)
- Intermembrane space (between inner and outer membrane, location of the H+ gradient)
- Matrix
- mtDNA
Matrix of the mitochondria
- contains mDNA and ribosomes responsable for the synthesis of around %15 of mitochondrial proteins
- the remaining mitochondrial proteins are encoded in the nucleus and are transported into the mitochondria in an unfolded state, where they take on their final folded structure
Where does pyruvate oxidation take place?
- the 2 pyruvate molecules made in glycolysis are transported to the matrix through the mitochondrial membranes using facilitated diffusion (2 pyruvate oxidations per glucose)
Where does glycolysis take place?
- in the cytoplasm, is the only stage of cellular respiration that’s anaerobic
Where does the Kreb’s cycle take place?
- In the mitochondrial matrix (2 per glucose)
- At the end of Kreb’s, the original glucose molecule is entirely consumed and all energy is now stored as ATP and in the electron carriers (aka coenzymes) NADH and FADH2 or released as body heat
- CO2 diffuses out as waste (6 og carbon atoms are now CO2 molecules)
Where is the etc?
- It makes up the inner mitochondrial membrane
- Each mitochondria has many ETCs
- protein complexes are organized by electronegativity (weakest attraction to strongest at the end) to establish the electronegativity gradient
NADH vs FADH2
- NADH will transfer electrons to the first protein complex (NADH dehydrogenase) in the ETC and so pumps 3 hydrogens per molecule
- FADH transfers its electrons to Q (the second protein in the ETC) and so it pumps 2 hydrogens per molecule –> produces less energy bc it skips the first protein complex
Cytosolic vs mitochondrial NADH
- the inner mitochondrial membrane is impermeable to NADH
- So NADH made in glycolysis must be shuttled via a transport protein into the matrix. In doing so, it becomes FADH
ATP tally
- 4 made by substrate level phosphorylation 2 in glycolysis, 2 in krebs)
Oxidative phosphorylation
- 24 ATP from NADH (6 by pyruvate oxidation, 18 from krebs, none from glycolysis bc it turns into FADH2)
- 8 ATP made from FADH2 (4 from the glycolysis NADH, and 4 from krebs)
In total, 36 ATP is made per one glucose molecule.
Extra info etc
- For ATP to be produced, an H+ resevoir must be maintained
- This means electrons must be continually moving through the ETC
- To keep electrons moving, oxygen must be present to accept them at the end of the chain
- if there is no oxygen, electrons become ‘clogged’
- H+ ions wont be pumped, chemiosmosis stops, so ATP synthase stops, and NADH/FADH2 can’t give up their electrons so they can’t be recycled. The organism will die if oxygen is witheld for too long
Chemiosmosis
- The electrochemical gradient generated during electron transport stores free energy (called proton-motive force PMF)
- inner mitochondrial membrane is impermeable to H+ ions
- PMF forces protons through ATP synthase and the energy from thus drives the synthesis of ATP from ADP and Pi in the matrix
- one ATP is generated per proton pumped into the intermembrane space, so 3 ATP per NADH and 2 ATP per FADH2
- After ATP is made, it is transferred through the mitochondrial membrane by facilitated diffusion into the cytoplasm so it can do things like active transport
Metabolic rate
- Amount of energy consumed by an organism in a given time
- Also a measure of the overall rate at which cellular repiration occurs
- Increases when work is done, but is not “zero” at rest due to functions such as: breathing, maintenance of body temp, muscle contraction, and brain function
Basal metabolic rate
- Amount of energy needed to keep an organism alive (accounts for 60-%70 of energy used in one day)
- Is measured by kJ per square meter body surface per hour
- Increases from birth and first year, then gradually decreases, also affected by fitness and health
Change in metabolic rate due to age
- metabolic rate decreases with age because we become more efficient at doing tasks and our activity level declines, which causes a loss in muscle tissue so energy requirements diminish
- when activity level declines, our bodies have more unused ATP which allosterically inhibits certain enzymes in cellular respiration, slowing consumption of glucose. Depeding on which pathway is inhibited, any existing acyteyl-coA can then be used to make fat (lipogenesis)
Carbs in cellular respiration
- broken down by enzymes like amylase to make glucose
- enters in glycolysis
Proteins in cellular respiration
- proteases (like pepsin and trypsin) break proteins down into amino acids
- Amino acids are then deaminated, which means the amino group is removed
- depending on the amino acid, they can enter in glycolysis, pyruvate oxydation or krebs
Fats in cellular respiration
- lipase enzymes break fats down into fatty acids and glycerol
- glycerol is converted to make G3P and used in glycolysis
- Fatty acids enter the mitochondria and the carbon atoms are removed 2 at a time, making AcetylcoA
Lactate fermentation
- some single celled organisms and animal muscles undergo lactate fermentation temporarily after deprivation of O2
- NADH reacts with pyruvate to oxidize it, returning to NAD+
- Lactate in bacteria is secreted and becomes acidic
- lactate in animal muscle must be reoxidized to protect tissue from acidity. O2 is needed to allow lactate to be metabolized in oxidative pathways.
Ethanol fermentation
- Yeast and some bacteria can function aerobically and anearobically
- Fermentation by brewers yeast is used in industry fir baking and alcoholic beverages
What is anaerobic respiration and fermentation
Anaerobic respiration: A metabolic pathway in which an inorganic molecule other than O2 is used as the final electron acceptor during chemiosomotic sythesis of ATP
Fermentation: A cellular respiration pathway that transfers electrons from NADH to an organic acceptor molecule.
The absorption of light energy
When any form of matter absorbs light energy, the light is absorbed in the form of packets called photons. Photons carry specific amounts of energy. Each wavelength (colour) of visible light is associated with photons of one distinct amount of energy. Longer wave length photons have smaller amounts of energy and shorter have more energy. The wavelength of a photon/colour of light that an atom/molecule can absorb is determined by the energy level of the electrons in that atom/molecule. It can only absorb a photon if it has the exact same energy level.
Leaves
- the photosynthetic organs of plants
-structure maximizes surface area exposed to sunlight and limits distance between gases - Have a waxy cuticle to protect from over absorption of water/excessive sunlight
- have special photosynthetic cells called mesophyll
- have “guard cells” that create tiny openings called stomata that regulate exchange of CO2 and O2 and allow water vapour to enter or escape by transpiration
- have vascular bundles “veins” that transport water and minerals to roots and leaves and carry carbohydrates from the leaves to the roots
The light reaction
Three key parts:
- Photoexcitation: absorption of a photon and excitation of an electron of chlorophyll
- Electron transport: transfer of the excited electron through a series of membrane bound electron carriers, resulting in the pumping of a proton through the photosynthetic membrane, which creates an H+ resevoir and eventually reduces and electron acceptor
- Chemiosmosis: the movement of protons through ATP synthase complex to drive the phosphorylation of ADP to ATP
Pigments
- Green coloured pigments are known as chlorophyll that absorb light (reflects green absorbs other colours)’
Components: - Porphyrin ring
- Mg at centre
- Alternating single and double bonds
- Delocalized electrons absorb light and begin photosynthesis
- Hydrocarbon tail
- Anchors the chlorophyll molecule in
the membrane
(because its non-polar like the
phospholipid tails)
- Anchors the chlorophyll molecule in
Part 1: photoexcitation
Excitation: the absorption of energy by an electron
- Ground state –> excited state
- higher potential energy
Fluorescence: rapid loss of energy (in the form of light)
- chlorophyll molecules do not fluoresce when in the membrane because the excited electron is captured by the primary electron acceptor (why plants don’t glow in the sunlight
Redox reaction: chlorophyll is oxidized, primary acceptor is reduced
Photosystem
Photosystem: Complex of chlorophyll molecules accessoru pigments and proteins embedded in the thylakoid membrane
Two parts:
- Antenna complex: a number of chlorophyll molecules and accessory pigments
- Reaction centre
Reaction centre
- A transmembrane protein complex containing chlorophyll a whose electrons absorb light energy and begin the process of photosynthesis
- Electron is raised to a higher energy level
- Electron is transferred to the primary electron acceptor
Antenna complex
- A number of chlorophyll molecules and accessory pigments embedded in the thylakoid membrane
- Absorbs a photon and transfers the energy from pigment to pigment until it reaches a chlorophyll molecule in an area known as the reaction centre
Photosystems
Photosystem 1
- Chlorophyll a is called P700 (absorption spectrum peaks at wavelength of 700 nm -red light)
Photosystem 2 –> comes first
- Chlorophyll a is called P680 (absorption spectrum peaks at wavelength of 680 nm - red light)
Stage 1 of photosynthesis: Non-cyclic electron flow and chemiosomosis
Where does it happen –> on the thylakoid membrane and in the lumen (aka thylakoid space)
- Electrons don’t return to starting place
Calvin cycle
Light independent process in which CO2 from the atmosphere is captured and modified by the addition of hydrogen to form C-C covalent bonds of carbs. The incorporation of CO2 into organic compounds is known as carbon fixation. The energy for this comes from the first phase of the photosynthetic process.
- Eventually produces one molecule of glucose from 2 calvin cycles
- happens in the stroma
Process of non-cyclic electron transport:
- energy from the sun (photon) strikes PSII exciting an electron in chlorophyll
- The energized electron is picked up by Q aka PQ (plastoquinone)
- Electrons lost by PSII due to these photons are replaced by Z, which is an enzyme that splits H2O. Electrons go to PSII and H+ goes into thylakoid space, O2 is waste
- PQ passes electrons to bc-f complex causing it to pump H+ into the thylakoid space using the electrons energy
- H+ gradient inside lumen leads to synthesis of ATP via ATPase thanks to PMF and chemiosomosis
- PC (carrier) picks up electrons and passes them to PSI they will then be struck again by photons
- Electrons struck by photons are picked up by Fd (carrier) and taken to FNR (ferredoxin-NADP reductase) which will make NADPH
