Unit 3: Biochemistry Flashcards
Includes: Respiration, Photosynthesis and Protein synthesis
Outline why organisms need to respire with reference to active transport and metabolic reactions
Metabolism: The chemical reactions in cells required to sustain life. Catabolism- breaking down of molecules. Anabolism-building of molecules
Active Transport: Moving molecules where they don’t want to go. Required for some of the steps of respiration
Know that ATP provides the immediate source of energy for biological processes
ATP- Adenosine 5’ Triphosphate: ATP is an energy carrying molecule, energy released by catabolic reactions is temporarily stored, in most cases this is as a chemical bond in “carrier molecules” that can diffuse rapidly throughout the cell. NADH and FADH2 are also important energy carrying molecules in respiration. Most important and versatile of the activated carriers in cells. A ribonucleotide. Terminal group is frequently split off by hydrolysis
Explain the importance of coenzymes in respiration, with reference to NAD and coenzyme A
NAD- Nicotinamide Adenine Dinucleotide: pick up energy in the form of 2 electrons and a proton(H+). Can be regarded as electron donors/acceptors.
Outline the process of glycolysis(and where it takes place)
Lysis means splitting apart. Glycolysis means splitting glucose apart. Yields a small amount of ATP. Occurs in the cytoplasm. Does not require oxygen, therefore happens in both aerobic and anaerobic conditions. Generates pyruvate- required for the next step in the mitochondria. Also generate lactate- anaerobic respiration. Costs ATP(phosphates are added to glucose). Generates ATP(phosphates are added to ATP). Each phase consists of multiple enzymatic steps.
1. Phosphorylation of hexose(glucose) to hexose bisphosphate(fructose bisphosphate).
2. Splitting of hexose(fructose) bisphosphate into two triose phosphate molecules(glyceraldehyde phosphate).
3. Oxidation to pyruvate, producing a small yield of ATP and reduced NAD.
Products: For a single molecule of glucose(hexose): 2 ATP, 2 NADH(reduced NAD+), 2 Pyruvate(-triose). Pyruvate is actively transported into the mitochondria(aerobic). Under anaerobic conditions, pyruvate remains in the cytoplasm.
State that, during aerobic respiration, pyruvate is actively transported into mitochondria
In eukaryotic cells, the pyruvate molecules produced at the end of glycolysis are transported into mitochondria, which are the sites of cellular respiration. There, pyruvate will be transformed into a acetyl group that will be picked up and activated by a carrier compound called coenzyme A.
Transport into the mitochondria. Transported with a proton, down the proton concentration gradient. This gradient is maintained by proton pumping(more later) costing energy(active transport).
Explain how the structure of mitochondria enables them to carry out their function
Outer membrane: smooth, composed of equal amounts of phospholipids and proteins. Contains porins- integral membrane proteins that allow the passage of small molecules. Porins render the outer membrane freely permeable to nutrient molecules, ions, ATP and ADP.
Inner membrane: folded multiple times(known as the cristae), number varies by cell types, he cristae and proteins are the site of various chemical reactions, including the production of ATP. Cristae increase surface area available for these reactions(on average give a 5-fold increase in surface area), Only permeable to oxygen and ATP, other molecules move across by transport proteins in a regulated manner.
Intermembrane space: space between the outer and inner membranes, it has largely the same composition as the cytoplasm but a difference in protein content.
Matrix: a complex mixture of proteins and enzymes, important for the synthesis of ATP molecules. Produced in the matrix with mitochondrial DNA(mtDNA), Not encoded by the genomic DNA(gDNA) in the nucleus.
Outline the link reaction(and where it takes place)
Pyruvate cannot directly enter the TCA cycle. Conversion to acetate. Linked to coenzyme A(CoA)- coenzyme required for lots of enzyme reactions. Acetyl CoA can enter the TCA cycle.
Decarboxylation: catalysed by pyruvate decarboxylase. Removal of a carboxyl group(lost as carbon dioxide).
Dehydrogenation: catalysed by pyruvate dehydrogenase. Removal of protons, accepted by NAD+.
CoA addition: coenzyme A joined to acetate- acetyl coenzyme A. Allows acetate to enter the TCA cycle.
For each glucose molecule entering glycolysis 2 pyruvate molecules are generated.
Products: For a single molecule of pyruvate- 1 ATP(substrate level phosphorylation), 4 NADH(reduced NAD+), 1 FADH2(Reduced FAD+), and 3 CO2
For a single molecule of glucose- 2 ATP(substrate level phosphorylation, 8 NADH(reduced NAD+), 2 FADH+(reduced FAD+), and 6 CO2.
Outline the Krebs(TCA) cycle(and where it takes place), including the key steps of decarboxylation and dehydrogenation, NAD and FAD reduction, and substrate level phosphorylation
First sequenced by Hans Krebs in 1937.
Acetyl CoA from the link reaction combines with Oxaloacetate forming Citrate. Citrate is decarboxylated and dehydrogenated forming a-ketoglutarate, CO2 and NADH. a-ketoglutarate is decarboxylated and dehydrogenated forming Oxaloacetate, CO2, NADH, FADH2, and ATP. Oxaloacetate can start the cycle again.
Products: For a single molecule of pyruvate- 1 ATP(substrate level phosphorylation), 4 NADH(reduced NAD+), 1 FADH2(Reduced FAD+), and 3 CO2
For a single molecule of glucose- 2 ATP(substrate level phosphorylation, 8 NADH(reduced NAD+), 2 FADH+(reduced FAD+), and 6 CO2.
Outline the process of oxidative phosphorylation(and where it takes place)
Electron transport chain: electrons are passed from one member of the transport chain to another in a series of redox reactions. Produces a proton gradient.
1. Supply of electrons: NADH and FADH2- reduced in previous steps, carry electrons. Transfer their electrons to the beginning of the transport chain. Become oxidised again(i.e. revert to NAD+ and FAD+). To be reused in other steps of respiration(cycle of redox reactions.
2. Electron transfer and proton pumping: electrons are passed down the chain of proteins(cytochromes and redox enzymes). Electrons move to a lower energy level. Releasing their energy. Some of the energy pumps protons(H+ ions) from the matrix into the inter membrane space. This pumping establishes and electrochemical gradient the same principle as a concentration gradient.
3. Splitting oxygen to form water: At the end of the electron transport chain electrons are transferred to molecular oxygen(O2). Oxygen splits in half and reacts with 2 H+ to form water (H2O).
Chemiosmosis: Proton gradient used to produce ATP
Outline the process of chemiosmosis, with reference to the electron transport chain, proton gradients and ATP synthase
Gradient-driven synthesis of ATP. The ETC established a proton electrochemical gradient. Protons(H+ ions) flow back down this gradient into the matrix. They pass through the enzyme ATP synthase. This drives the enzyme to synthesize ATP. ATP synthase also part of ATP production by photosynthesis. ATP synthase activity involves a physical rotation. Also used in bacteria which maintain an electrochemical gradient between the cytoplasm and their environment. Closely linked to bacterial motor proteins which use an electrochemical gradient to drive rotation of an attached flagellum for movement.
Explain how oxygen is the final electron acceptor in aerobic respiration
Oxygen combines with electrons and protons to form water, which is crucial to prevent the backup of electrons in the electron transport chain and allow the continued flow and production of ATP.
Explain the theoretical maximum yield of ATP per molecule of glucose, and why it is rarely achieved in aerobic respiration
ATP yield per glucose molecule by oxidative phosphorylation- 26+4=30 ATP. 2 FADH2 can each repoduce 2 molecules of ATP plus 4 ATP per glucose molecule by substrate level phosphorylation. Total yield per glucose molecule=34 ATP. Oxidative phosphorylation is not possible in anaerobic conditions, significantly less energy produced.
Explain why anaerobic respiration produces a much lower yield of ATP than aerobic respiration
Energy required for active transport into mitochondria- ADP, NADH, pyruvate.
Energy required for active transport out of mitochondria- ATP.
Dissipation of the proton gradient(leaky membrane)- protons which leak out of mitochondria are wasted instead of driving ATP production.
Define the terms autotroph and heterotroph
Autotroph: an organism that is able to form nutritional organic substances from simple inorganic substances such as carbon dioxide.
Heterotroph: an organism deriving its nutritional requirements from complex organic substances
Define the term photosynthetic pigment and discuss its role in photosynthesis
The nature of sunlight: the segment most important to life is between 380nm- 750 nm and is known as visible light. The atmosphere is selective and only allows visible light to pass through.
The action spectrum: demonstrated in 1883 by Theodor W. Engelmann. Reveal which wavelengths of light are photosynthetically important. The action spectrum resembles the absorption spectrum of chlorophyll a and the accessory pigments. Showed that light in the violet-blue and red portions of the spectrum is most effective.
