Biochemistry B Flashcards
ATP Cycle
Hydrolysis: a water molecule gets added to a molecule of adenosine triphosphate. ATP gets split into ADP and Pi after releasing energy.
Dehydration Synthesis (Condensation): ADP and Pi release a water molecule through acquiring energy to become ATP.
What is ATP?
Light energy, comes from the sun. Fuels anything that requires energy: reactions, transport, etc.
Cellular respiration involves…
Numerous small exothermic reactions, with small activation energies. A controlled release of energy from organic compounds (glucose mainly, but lipids and proteins too), ro produce ATP
Why is cellular respiration not just a single large step?
Free energy would be released, the glucose would burn up in combustion. The free energy needs to be stored for later usage
Cellular respiration is a creation or transferral or energy?
Transferral, NOT creation
Aerobic Respiration Summary
Utilizing ozygen to completely break down glucose in the mitochondria for a larger ATP yield
Regulation of Cellular Respiration
End Product Inhibition, with ATP being the end product
Redox Reactions
Oxidation - reduction
The reducing agent vs the reduced
The reducing agent loses electrons, the reduced gains electrons
The oxidizing agent vs the oxidized
The oxidizing agent gains electrons, the oxidized loses electrons
Oxidation
Loss of electrons and hydrogen atoms, gain of oxygen atoms
Reduction
Gain of electrons and hydrogen atoms, loss of oxygen atoms
2 Reversible reactions in cellular respiration
NAD+ + 2 electrons and 2 hydrogen ions -> NADH + hydrogen ion
FAD + 2 electrons and 2 hydrogen ions -> FADH2
NADH
Nicotinamide adenine dinucleotide
FADH2
Flavin adenine dinucleotide
Electrons carriers and process of electron transfer
Transport electrons between different molecules.
- NAD+ within a cell along two hydrogen atoms
- NAD+ is reduced to NAD by accepting an electron from a hydrogen atom
- It picks up another hydrogen atom (an electron and a hydrogen ion) to become NADH
- NADH carries the electrons to a later stage of respiration and drops them off, becoming oxidized
NAD+ gets … by picking up 2 electrons and a hydrogen ion
NADH gets … by dropping off 2 electrons and a hydrogen ion
Reduced, oxidized
Glycolysis is the …
Splitting of sugar
3 Stages of Glycolysis
Activation, splitting and oxidation
Glycolysis Activation
2 molecules of ATP are hydrolysed into 2ADP + 2Pi. This is used to activate a molecule of glucose. Glucose forms fructose - 1, 6 - bisphosphate, or F1, 6 - BP, an unstable intermediate molecule.
Glycolysis Splitting
F1, 6 - BP is split into DHAP and molecule of G3P, both 3 carbon molecules. All the DHAP are eventually converted into G3P.
Glycolysis Oxidation
Restructuring to remove energy in a series of steps. Glucose is converted into two molecules of pyruvate and two molecules of water.
2 NAD+ picks up four hydrogen ions and four electrons to become 2 NADH + H+
4 ADP + 4 Pi becomes 4 ATP
Glycolysis ATP Net Gain
2 ATP
Pyruvate Oxidation
A molecule of pyruvate (C3H4O3) is decarboxylated to become acetate (C2H4O). Coenzyme A is added to acetate to help the enzyme stabilize the molecule and restructure it temporarily, and a NAD+ molecule is reduced. Acetyl - CoA is formed.
Pyruvate Oxidation Chemical Equation
2 pyruvate + 2 NAD+ -> 2 Acetyl Co - A + 2 NADH + 2 CO2
Substrate Level Phosphorylation
A metabolic reaction in which a phosphorylated compound transfers its phosphate group to ADP for ATP synthesis. Pi is an inorganic phosphate, not attached to anything, usually just floating in the cytoplasm. An enzyme catalyzes the phosphorylation, and it needs an input of energy.
3 Stages of Krebs Cycle
Restructuring, redox, substrate level phosphorylation (same as glycolysis)
Krebs Cycle Process (5 Steps)
- Acetyl - CoA loses CoA
- Oxaloacetate (C4H4O5) forms citrate (6 carbon) with acetic acid
- Citrate undergoes decarboxylation twice (to provide energy for step 4), fueled by the reduction of 2 NAD+, becoming a 4 carbon molecule
- Restructuring to provide energy for: one ADP -> ATP, one FAD -> FADH2, one NAD+ -> NADH.
- Oxaloacetate formed
Oxidative phosphorylation is named so because…
The energy to synthesize ATP is derived from the oxidation of NADH and FADH2
Purpose of the electron transport chain
Releases the energy stored within the reduced electron carriers in order to synthesize ATP by adding Pi to ADP.
Oxidative Phosphorylation Process (8 Steps)
- E carriers release electrons to the ETC
- As the e- move throguh the chain they lose energy, transferred to the hydrogen pumps within the chain
- The pumps use this energy to pump H+ from the matrix into the intermembrane space
- Accumulation of hydrogen ions creates and electrochemical gradient, or a proton motive force
- Chemiosmosis: H+ return to the matrix throguh the transmembrane enzyme ATP synthase
- H+ trigger a phosphorylation reaction, adding Pi to ADP as they pass through ATP synthase
- The de - energized electrons aer removed from the chain by oxygen, allowing new energy electrons to enter the chain
- Oxygen also binds matrix protons to form water, maintaining the hydrogen gradient
FADH2 is slightly more … than NADH
Electronegative
NADH is reduced at the xth hydrogen pump, FADH2 is reduced at the yth hydrogen pump
x: first
y: second
Phosphorylation is an catabolic vs anabolic, exothermic vs endothermic reaction
Anabolic, endothermic
Anaerobic respiration occurs when…
A biological system reaches a maximum rate at transporting oxygen to the cells and aerobic respiration becomes limiting
How do some organisms (bacteria) survive on anaerobic respiration alone?
They don’t need that much energy
First Stage of Anaerobic Respiration
Activation and splitting stages of glycolysis
Lactic Acid Fermentation occurs in…
Humans
Lactic Acid Fermentation
- After glycolysis, the 2 pyruvate regenerate NAD+ by converting into 2 lactate
- Lactate dehydrogenase converts lactate, oxidizing 2 NADH
- Lactate becomes a waste product, stored in the liver and reused as energy
Alcohol fermentation is done by x, y and z only
Archaea, yeast and bacterial cells
Alcohol Fermentation Process
- 2 pyruvate decarboxylated by pyruvate decarboxylase to lose 2CO2
- Becomes 2 acetaldehyde
- Acetaldehyde converted into 2 ethanol by alcohol dehydrogenase
- 2 NADH oxidized
Photosyntehsis Equation
6CO2 + 6H2O -> C6H12O6 + 6O2
Photosynthesis is…
An anabolic reaction that converts light into chemical energy. The cell either directly uses the ATP or to build carbohydrates.
The chloroplast has one/two membranes
Two
Cytoplasm of the chloroplast
Stroma
Thylakoids
Contain chlorophyll for undergoing photosynthesis
Grana
Stacks of thylakoids
Stromal lamella
Connect grana
Different colors of light are defined by the…
Wavelength
Function of pigments in chloroplasts
Absorb light energy in photosynthesis
Different pigments are required to absorb different…
Wavelengths of light
Does the color of the wavelength affect the speed at which it travels?
No
Action Spectrum for Photosynthesis
Rate of photosynthesis for all the wavelengths as a percentage of the maximum possible rate
Leafs reflect x light, absorbing other colors
Green
Leafs can’t survive under x light while y light is applicable for everything
X: green
Y: white
Absorption Spectrum for Photosynthesis
Rate of photosynthesis for each wavelength
When a chemical process depends on more than one essential condition being favorable, the rate of reaction will be limited by the factor that is nearest…
Its minimum value
Rate of photosynthesis can be measured by…
Amount of oxygen created, carbon dioxide fixed, biomass gained
Photosynthesis Limiting Factors
Light intensity, carbon dioxide concentration and temperature
Photosynthesis Limiting Factor: Light Intensity
Logarithmic curve. At the plateau, enzymes etc. are already working at their maximum rate. Low intensity results in insufficient ATP production
Photosynthesis Limiting Factor: Carbon Dioxide
Logarithmic curve, eventually plateaus.
Photosynthesis Limiting Factor: Temperature
Slightly slanted normal distribution towards a higher temeprature. Low temperatures provide insufficient energy for molecules and will prohibit reactions from occuring. At higher temperatures, enzymes and other proteins denature,
Primordial Earth’s Atmosphere
Reducing atmosphere, low O2 levels. Lacked O2 and other oxidizing gasses (gasses with high oxidation states). Consists of hydrogen, CO
Early life as anaerobic or aerobic?
Anaerobic
Organism that first performed photosynthesis
Cyanobacteria, small photosynthetic, containing chlorophyll
What occured after oxygen levels rose in the primordial earth?
Ozone layer formed, shielding the Earth from UV
After the formation of the ozone layer, soluble x compounds in oceans were y, forming insoluble x oxides
X: iron
Y: oxidized
Once the iron oxides precipitated onto the seabed,
Oxygen accumulated in the atmosphere once all the iron was consumed
Banded iron formations
Rock layers rich in iron ore
Oxygen gas in the atmosphere lead to the production of …
Oxidized compounds in the oceans, e.g. carbon dioxide
Respirometer Usage Process (3 Steps)
- Organism or germinating seed enclosed in a sealed container undergoes cellular respiration to become energy
- The colored liquid moves as oxygen is consumed as a change in pressure, measured by a scale
- Carbon dioxide produced is absorbed by soda lime (an alkali metal oxide)
3 Conditions for Germination
Water for activating hormones and enzymes,
Temperature for enzymes not to denature,
Oxygen for respiration
Location of Light Dependent Reactions
Thylakoid membranes (similar to electron transport chain)
Light dependent reactions require… to occur
Sunlight
Light Dependent Reactions Process (6 Steps)
- Light strikes photosystem II, with a maximum wavelength of 680 nanometers
- An electron is supplied to PSII by the splitting of water, and gets passed to PSI
- At PSI: electrons lost most light energy and needs to be excited again
- Light trikes PSI, with a maximum absorption at 700 nm (more photoexcitation than PSII)
- Electron is received by the electron carrier NADP+, reducing it into NADPH
- The movement of hydrogen ions down a gradient through ATP synthase: chemiosmosis, photophosphorylation
Photoexcitation
Photosystems capture the light energy and convert it to high energy electrons, with H2O being the source of the electrons
Location of the Light Independent Reactions/ Calvin Cycle
Stroma (cytoplasm of the chloroplast)
Light Independent Reactions/ Calvin Cycle (4 Steps)
Carbon Fixation
1. 3C added to 3 rubisco bisphosphate, catalyzed by rubisco
2. Quickly splits into 6 molecules of 3PGA (phosphoglycerate)
Reduction
3. 6 3PGA reduced to 6 G3P when 6ATP are hydrolysed and 6NADPH oxidized
Regeneration
4. 1 G3P comes out to be used for glucose, 5 to regenerate rubisco bisphosphate; 3 ATP hydrolyzed
Calvin’s Assumption
If an organism such as the green algae was provided with only CO2 labeled with a radioactive carbon source, C14, it could be determined if CO2 was the starting material for building carbohydrates during photosynthesis
Calvin’s Experiment Setup
Lollipop Apparatus
- Round container for algae, with an air outlet
- Two light bulbs on either side of the lollipop, inducing photosynthesis
- Thick glass pane between the container and light source to insulate heat and prevent algal death
- C14 in hydrogen carbonate ion solution injected
- Air and CO2 pumped in
- Algal container opened periodically into a flask containing ethanol to kill cells in the sample, stopping metabolic processes without killing the products
- Dead algal samples are analyzed
Radioactive Labelling
C14 contiains an unstable combination of neutrons and protons, thus an excess amount of energy in the nucleus. It regains stability by releasing energy as radiation through radioactive decay.
Type of decay C14 undergoes
Beta decay: a neutron turns into a proton and releases a high energy electron (beta particle)
2D Paper Chromatography
Mixture separated using a solvent, then the paper rotated 90 degrees and separated again with a different solvent
Autoradiography and the Calvin Cycle
The electron leaves an image, with different blotches in different locations where products are made. Any radioactive carbon compounds on the chromatogram were identified by comparing different periods of light exposure, the order by which carbon compounds are generated. A sequence of events can be deducted: the Calvin Cycle
2D Paper Chromatography in Calvin’s Experiment
Used to separate small organic compounds that were the products of carbon fixation to see where C14 is.
