Option C - Cells and energy

C.1     Membranes

C.1.1- A series of diagrams may be suitable to demonstrate the structural

C.1.3relationships and how materials are moved. The continuous nature of membranes and the flow of materials through the channels or by vesicles is expected, although the chemical nature of materials is not required. Mention of pores and the fact that some intrinsic proteins are anchored is expected.

Primary: linear sequence of amino acids with peptide linkages. (Regard disulfide bridges as part of the tertiary structure). Names of specific amino acids, mention of L- and D- forms or branching vs. unbranched, are not required, although mention of R side chains leading to polar/non-polar amino acids is needed for 8.5.2. Note that changes in the sequence may have several effects on the overall structure and activity. Mention the almost infinite number of sequences. Secondary: the formation of the a -helix (e.g., keratin – hair, wool, horn, feathers, etc.) and b -pleated sheets (e.g., silk), held together by hydrogen bonds. Tertiary: mention the possibility of creating ‘active sites’, added strength due to ionic bonds and disulfide bridges and the possibility of prosthetic groups and coenzymes. Quaternary: note that most large, non-structural proteins have more than one polypeptide and that it leads to greater range of biological activity.

Limited to polar amino acids leading to proteins with greater hydrophilic tendencies and water solubility due to the hydrogen bond formation; the reverse being true for proteins rich in non-polar amino acids. This should be related to how parts of large globular proteins interact with membranes.

An extension of the ‘lock-and-key’ model. Its importance in the reduction of the activation energy should be mentioned and how it can account for the broad specificity of some enzymes (the ability to bind several substrates).

Graphical representation of both exergonic and endergonic reactions should be covered, but no specific energy values need be recalled. An understanding how to calculate the activation energy of a reaction when reversed is also needed.

Competitive: explained by an inhibiting molecule so similar to the substrate molecule that it binds to the active site so preventing the substrate binding. Examples: inhibition of butanedioic acid (succinate) dehydrogenase by propanedioic acid (malonate) in the Krebs cycle; sulfonamide Prontosil™ (an antibiotic) inhibits folic acid synthesis in bacteria.

Non-competitive: limited to an inhibitor molecule binding to an enzyme (not to its active site) that results in a confonnational change in its active site resulting in a change in activity. Examples include Hg²⁺, Ag⁺, Cu²⁺ and CN- ion inhibition of many enzymes (including those like cytochrome oxidase) by binding to –SH groups, thereby breaking –S-S- linkages; nerve gases like sarin and DFP inactivate ethanoyl (acetyl) cholinesterase; Lisinopril™ lowers high blood pressure by inhibiting the enzyme ACE which manufactures angiotensin II.

C.3.5 Explain the role of allostery with respect to feedback inhibition and the control of metabolic pathways.

Allostery as a form of non-competitive inhibition. Mention that all allosteric enzymes consist of two or more polypeptides whose shape can be altered by the binding of effectors to an allosteric state, thereby increasing or decreasing its activity. Metabolites can act as allosteric inhibitors of enzymes earlier in a metabolic pathway and regulate metabolism according to the requirements of organisms; a form of negative feedback. One example is ATP inhibition of phosphofructokinase (glycolysis); another is inhibition of aspartate carbamoyltransferase (ATCase) (which catalyses the first step in pyrimidine synthesis). ATP is a positive modulator and CTP a negative modulator. Graphical representation of allosteric enzyme action is not required.

 

 

Notes: The terms used and the chemical nomencalture specified will be used in examinations. No alternatives will be required. Nor is any detail required beyond that listed.

C.4.2 State that photosynthesis consists of light-dependent and light-independent reactions.

Not "light" and "dark" reactions.

C.4.3 Explain the light-dependent reactions including the photoactivation of Photosystem II, photolysis of water, electron transport, cyclic and non-cyclic photophosphorylation, photoactivation of Photosystem I and reduction of NADP⁺.

C.4.4 Explain photophosphorylation in terms of chemiosmosis (cross reference 9.1.4).

9.2.3- Chlorophylll a molecules in PsII (mainly in the grana)

1. absorb tlight 9.2.4 mainly at 680 nm, electrons are excited and (therefore more easily) removed by a chain of electron carriers 9oxidising agents – names not required). This process is couples (aided by the no, Chl a ⁺ molecules) with the photolysis (splitting) of water so thata oxygen, protons and electrons are released. (The latter reduce Chl a ⁺ back to Chl a ). The protons (H⁺ ions) are pumped to the inside of the thylakoids, they accumulate (pH drops) and eventually move out to the stroma through protein channels in the ATP synthetase enzymes providing energy for ATP synthesis (non-cyclic photophosphorylation). Some of the protons release are converted to NADPH which acts later as a reducing agent. Chlorophyll a molecules in PS I (in intergranal lamellae) absorb light mainly at 700 nm and can control a cycling of electrons via carriers so that ATP is formed (chemiosmosis) but not NADPH (and this is called cyclic photophosphorylation).

C.4.5 Explain the light-inependent reactions including the roles of ribulose bisphosphate (RuBP) carboxylase, reduction of glycerate 3-phosphate (GP) to triose phosphate (TP or GALP), NADPH + H ⁺, ATP, regenration of RuBP and synthesis of carbohydrate and other products.

In the stroma of the chloroplasts the ATP provides energy, and the NADPH energy and reducing power for biosyntehsis using carbon dioxide. The Calvin cycle in which the five-carbon molecules RuBP acts as the CO₂ acceptor (catalysed by RuBP carboxylase) is important, (then forming two 3 carbon molecules – GP) but the intermedaites can be given the initials GP and TP or (GALP). Note that the reduction of GP (removal of O) to TP requires H and most of the energy from NADPH (and some from ATP). TP can be converted to clucose, sucrose, starch, fatty acids, amino acids and other products. (It could be noted that GP and TP are also intermediates in glycolysis). Some of the TP is used, via intermediates, to regenerate more RuBP, a process that involves some more ATP. Details of experimental procedures to elucidate the stages are not required.

C.4.6 Outline the differences in carbon dioxide fixation between C₃, C₄ and CAM plants, noting their adaptive significance.

9.2.5 describes the C₃ pathway since a three carbon compound (GP) is the first rrecognisable product after the fixation of CO₂ . C₄ pathway uses propenoate 2-phosphate (PEP – a 3C compound) to manufacture a four carbon compound (2-oxobutanedioate-oxaloacetate). The enzyme that carries out this process (PEP carboxylase) ahs a greater affinity for CO₂ that RuBP carboxylase so that it can be fixed at much lower concentrations. CAM (Crassulacean Acid Metabolism) is an adaptation where some plants living in dry areas keep their stomata closed during the day (to conserve water). They open them at night and fix the CO₂ using PEP carboxylase to eventually form various organic acids which are later decarboxylated releasing the CO₂ for synthesis. These are particularly adapted to high light, high temperature and drought. Histological details are not required nor details of photorespiration.

C.4.7 State one crop plant example for each of the following: a C₃, C₄ and CAM plant.

C₃: rice and most temperate region crops, wheat, potatoes.

CAM: pineapple, prickly pear, vanilla orchid.

C.5 Cell respiration (4h)

Notes: Most standard textbooks cover the process (often in great detail). It is important to sort out a vision of ‘the wood from the trees’ and to point out the universal nature of enzymes, ATP and the process (Theme).

C.5.1 Outline that oxidation involves the loss of electrons from an element whereas reduction involves gain in electrons, and that oxidation frequently involves gaining oxygen or losing hydrogen; whereas reduction frequently involves loss of oxygen or gain in hydrogen.

Mnemonic: Oxidation is Loss (of electrons), Reduction is Gain (in electrons) [OIL RIG]

C.5.2 Outline what is achieved by the process of glycolysis including phosphorylation, lysis, oxidation and ATP formation.

In the cytoplasm, one hexose sugar is converted into two three-carbon atom compounds 2-oxopropanoate (pyruvate) with a net gain of two ATP and two NADH + H⁺

Phosphorylation is a process in which ATP is made in vivo (in glycolysis the process is "substrate level phosphorylation")