Pra U STPM Biology Term1 CC039142a

Biology Term 1 STPM Chapter 6 Photosynthesis 6 192 Absorption Spectrum and Action Spectrum Absorption spectrum 1. Absorption spectrum of a photosynthetic pigment e.g. chlorophyll is the percent of light absorbed plotted against the visible wavelengths of light i.e. from 200 nm to 800 nm. 2. The absorption spectrum is obtained by using a spectrophotometer. Pure pigment or mixture is put a standard test tube which is then put inside the meter. Different wavelengths of light are shone through it and percent of absorption is obtained as shown in Figure 6.3. White light Refracting prism 1 2 3 4 Refracting prism Slit moves to pass light of selected wavelength Chlorophyll solution Photoelectric tube Galvanometer High percent of absorbance Blue light Chlorophyll a Carotenoids % of absorbance by chlorophyll Wavelength of light (nm) 400 500 600 700 Chlorophyll b Rate of photosyntesis Figure 6.3 Absorption and action spectrum

Biology Term 1 STPM Chapter 6 Photosynthesis 6 193 3. From the absorption spectrum of chlorophyll, it is found that it has two peaks at 450 nm and 680 nm. 4. If the absorption spectrum of carotenoids is studied, it is found that it only peaks at 450 nm. 5. However, if the absorption spectrum of a leaf extract is studied then it has two peaks at 450 nm and 680 nm. 6. The above three absorption spectra show that leaf contains photosynthetic pigments that absorb red light around 450 nm and blue light around 680 nm. Green light is the least absorbed giving leaves its green colour. 7. An absorption spectrum is a visual representation of how well a particular pigment absorbs different wavelengths of visible light. Absorption spectra of various photosynthetic pigment can reveal the role of each pigment during light absorption. Action spectrum 1. Action spectrum of a photosynthetic pigment e.g. chlorophyll is the rate of photosynthesis plotted against the visible wavelengths of light i.e. from 200 nm to 800 nm. 2. This action spectrum is obtained by using the pure pigment or mixture mixed with an electron acceptor e.g. bromothymol blue. It is then exposed to different wavelengths of light. The time taken for a standard concentration of pigment and indicator solution to turn colourless is taken as the rate of photosynthesis. The amount of oxygen given out can also be used to determine the rate. 3. If the absorption spectrum of a leaf extract is compared with its respective action spectrum, the two spectra will resemble each other as in Figure 6.3. Blue and red light are mostly absorbed and similarly, blue and red light cause the highest rate of photosynthesis. 4. This shows that blue and red light that are optimally absorbed by pigments of the extract are the ones that provide most energy for photosynthesis. The pigments convert the blue and red light energies into chemical energy in the form of organic substances during photosynthesis. 6.2 Light-dependent Reactions The light-dependent reactions can be summarised by a Z diagram as shown in Figure 6.4 and divided into smaller component processes as described below. Absorption spectrum and action spectrum 1. Absorption spectrum (a) Percent absorbance is plotted against wavelengths of 200 – 800 nm (b) Chlorophyll absorbs more blue and red, least green light (c) This is due to chlorophyll molecule vibrates differently in different wavelengths (d) Leaf is green due to green light not absorbed (e) Absorption spectrum reveal the role of each pigment 2. Action spectrum (a) Rate of photosynthesis plotted against wavelengths 200 – 800 nm. (b) Fastest rate at blue and red, slowest rate at green (c) Action spectrum corresponds (same shape) absorption spectrum (d) This is due to wavelengths that are absorbed can be used for photosynthesis. Summary Students should be able to: (a) explain photo-activation of chlorophyll a resulting in photolysis of water; (b) explain the cyclic and non-cyclic photophosphorylation including electron transport system resulting in the production of ATP and NADPH. Learning Outcomes

Biology Term 1 STPM Chapter 6 Photosynthesis 6 194 e– H2O pC Plastocyanin Reaction center H+ Proton gradient formed for ATP synthesis 2H+ + –– O2 Water-splitting enzyme Reaction centre e– e– e– Fd Fd Ferredoxin NADP reductase NADP+ +H+ NADPH e– Light cyclic photophosphorylation Excited reaction center Plastoquinone Ferredoxin Q Excited reaction center 1 2 Light Photosystem II b6–f complex b6–f complex Photosystem I NADP reductase P680 P700 Figure 6.4 Summary of light dependent stage Photo-activation of Chlorophyll a 1. The first process can be described from photoactivation of photosystem II. (a) This is a process in which the pigments in photosystem II (as in Figure 6.4) absorb light and the molecules get excited. (b) The energy level in each molecule is raised and energy is passed from one to another until it reaches the reaction centre where electrons are released. Only chlorophyll a P700 can absorb light and release electron in photosystem II. (c) The electrons are transferred to an electron receptor called plastoquinone and then to a system of electron carriers or electron transport system in the internal membrane of chloroplast. (d) The electron transport system is also called b6-f complex which acts as a proton pump, pumping protons into the thylakoid space. The protons are then used to form ATP from ADP and phosphate in a process called photophosphorylation. (e) The electrons which return back to photosystem II come from photolysis of water. This is done by a water splitting enzyme that removes electrons from water. (f) The enzyme passes the electrons from water to the reaction centre of photosystem II forming oxygen, which is then released. 2H2 O → 2H+ + O2 (g) The hydrogen ions formed increase the proton gradient inside the thylakoid. Photoactivation of chlorophyll 1. Chlorophyll molecules in photosystem absorb light 2. They get “energised” and pass energy to one another 3. Chlorophyll a P680 and P700 at reaction centres can only release electrons 4. Electrons are then received by receptors and passes to electron carriers 5. The electron transport chain creates proton gradient for ATP formation from ADP and Pi Summary

Biology Term 1 STPM Chapter 6 Photosynthesis 6 195 2015, 2017 2. The next process is photoactivation of photosystem I. (a) This is a process in which light is absorbed by the pigments in photosystem I. (b) As in photosystem II, the pigment molecules get excited and their energy level is raised. (c) Energy is passed from one molecule to another and finally reaches the reaction centre where electrons are released. Only chlorophyll a P680 can absorb light and release electrons in photosystem I. (d) The electrons are received by electron receptor called ferredoxin where they can be used for cyclic and non-cyclic photophosphorylation. Cyclic and Non-cyclic Photophosphorylation 1. The cyclic photophosphorylation has its electrons return to the same reaction centre where they are released. (a) This is a process in which the electrons released by photosystem I are passed to ferredoxin and to a system of electron carriers or proton pump, the b6 -f complex. (b) The energy released is used to form ATP from ADP and phosphate. (c) The electrons are then passed to plastocyanin and finally back to the same reaction centre i.e. photosystem I. (d) The process is as shown in Figure 6.5. e– e– e– P700 Reaction centre Light Energy of electrons Excited reaction centre Fd ADP Electron acceptor Plastocyanin Ferredoxin ATP Photosystem b6–f complex b6–f complex pC Figure 6.5 Cyclic photophosphorylation 2. The non-cyclic photophosphorylation of photosystem I occurs as follows: 2018 (a) The electrons released are also passed to a ferredoxin and it passes the electrons to an enzyme called NADP reductase found in the membrane. (b) Two of the electrons combine with NADP+ and H+ on the outside of the thylakoid membrane forming NADPH. This process further increases the proton gradient between the inside and the outside of the thylakoid. Cylic and non-cyclic photophosphorylation Cyclic Non-cyclic 1. In PS I only In PS I and PS II 2. Electron goes back to original P700 Electron does not go back 3. Forms only ATP Froms ATP and NADPH 4. No photolysis Photolysis replace loss electron in PS II 5. Electron acceptor is ferredoxin Electron acceptor is ferredoxin and plastoquinone Summary

Biology Term 1 STPM Chapter 6 Photosynthesis 6 196 (c) The electrons therefore, do not go back to the reaction centre where they came from. (d) The reaction centre gets back their electrons from photosystem II. (see Figure 6.3) 3. Non-cyclic photophosphorylation in photosystem II is as follows: (a) The electrons do not go back to the reaction centre of photosystem II but passed to a copper containing protein called plastocyanin then to the reaction centre of photosystem I. (b) Photophosphorylation in the chloroplast is by a process called chemiosmosis. The thylakoid space contains high proton (H+) concentration as a result of proton pump and water is also split to form it. When the proton passes down concentration gradient to the stroma through a channel protein of enzyme ATP synthase, ATP is formed from ADP and phosphate. (c) Therefore, the electrons are transported by the electron transport system and energy is converted and used for phosphorylation i.e. to form a phosphoester bond between phosphate and ADP producing ATP. Further increase in proton concentration gradient is from proton pump and is used in formation of NADPH outside the thylakoid membrane. This promotes the formation of ATP by chemiosmosis. The process can be summarised as shown in Figure 6.6. Exam Tips Remember that you should be able to write an essay on the detailed process of light dependent stage. Remember the answers to test yourself 1 and the roles of NADPH and ATP (STPM 2005 structured question). Thylakoid membrane Light Stroma Antenne complex Q Light pC Fd Ferredoxin H+ + NADP+ NADPH ADP H+ ATP H+ H+ H+ Proton gradient H2O Water - splitting enzyme –– O2 2 Thylakoid space 1 H+ H+ 2 Plastoquinone Plastocyanin Photosystem II b6–f complex Photosystem I NADP reductase ATP synthase Figure 6.6 Light dependent stage and chemiosomosis 4. After the light dependent stage, ATP and NADPH are formed together with oxygen that is released from leaves. The ATP and NADPH2 will be used for the light independent stage.

Biology Term 1 STPM Chapter 6 Photosynthesis 6 197 Quick Check 1 1. What is meant by (a) photoactivation of photosystem I? (b) photoactivation of photosystem II? (c) cyclic photophosphorylation? (d) non-cyclic photophosphorylation? (e) photolysis of water? 6.3 Light-independent Reactions The light-independent reaction/dark reaction is also known as the Calvin cycle. Calvin Cycle 1. Calvin cycle is a cyclic process in which carbon dioxide is fixed to form glucose as shown in Figure 6.7. Starch Glucose Sucrose Fructose 2 PGAL 12 PGAL 10 PGAL Calvin cycle 12 ADP 12NADPH 12 ATP + 12H2O 12NADP+ 6 RuBP Intermediate 12 PGA 6 ATP 6 ADP + 6Pi 6 H2O 6CO2 Figure 6.7 Summary of light-independent reaction 2. The process consists of the following reactions: (a) Ribulose bisphosphate (RuBP) acts as a receptor of carbon dioxide forming a temporary six-carbon molecule, which is unstable and immediately breaks down to form two phosphoglyceric acids (PGA) or phosphoglycerate. Learning Outcomes Students should be able to: (a) describe Calvin cycle; (b) explain photorespiration; (c) describe the anatomical structure of C4 leaf (Krantz anatomy) in comparison to C3 leaf; (d) explain carbon dioxide fixation in C4 plants and Crassulacean Acid Metabolism (CAM) plants; (e) differentiate the metabolism of C3 , C4 and CAM plants. 2013 2011 INFO The Calvin Cycyle

Biology Term 1 STPM Chapter 6 Photosynthesis 6 198 (b) PGA is a three-carbon organic acid. The process is called carbon fixation or carboxylation and is catalysed by RuBP carboxylase (rubisco). RuBP carboxylase RuBP + CO2 + H2 O → [6C molecule] → 2PGA 3. The PGA then undergoes a reduction reaction as follows: (a) PGA (with –COOH group) is reduced to form phosphoglyceraldehyde (PGAL) or triose phosphate (TP). (b) NADPH and ATP are required and the process is catalysed by an oxidoreductase as follows. PGA (–COOH) PGAL (–CHO) NADPH NADP ATP ADP + Pi 4. A portion of the PGAL is used to regenerate RuBP. (a) The process is complex and cyclic called Calvin cycle. (b) 6CO2 + 6H2 O + 6RuBP are required to form 12 PGAL in which 10 of them are used to regenerate 6 RuBP that are used initially. (c) Therefore, for every six turns of Calvin cycle, 2 of the 12 PGAL molecules leave the cycle to be used in glucose or hexose synthesis. (d) The process of carbon fixation can be represented as follows: 6CO2 6H2O 12 NADPH2 18ATP + 12PGAL 12NADP + 12H2O 18ADP + 18Pi 5. The summary of photosynthesis is as shown in Figure 6.8. Photorespiration 1. Photorespiration is when RuBP carboxylase (rubisco) catalyses the conversion of RuBP and oxygen instead of carbon dioxide during the light independent stage of photosynthesis. 2. This results in the formation of phosphoglycolate, phosphoglycerate and hydrogen ions instead of only phosphoglycerate as follows: RuBP + O2 → Phosphoglycolate + Phosphoglycerate + 2H+ 3. Photorespiration is a wasteful process because the phosphoglycolate formed is more difficult to recycle and has to move from the chloroplast to the peroxisomes, and then to the mitochondria, undergoing many reactions on the way, before the atoms can return into the Calvin cycle in the chloroplast again. 4. Photorespiration produces no ATP and leads to a net loss of carbon and nitrogen (as ammonia), slowing plant growth. ATP is in fact used. 5. Photorespiration occurs when carbon dioxide levels are low, for example, when the stomata are closed to prevent water loss during drought. In most plants, photorespiration increases as temperature increases. Exam Tips Remember the diagrams and detailed process of light independent stage in the formation of carbohydrates Calvin cycle 1. RuBP + CO2 → temporary C6 compound → 2PGA 2. Rubisco catalyses this carbon fixation 3. PGA → PGAL requring NADPH and ATP 4. Some PGAL form glucose, sucrose and starch and some regenerate RuBP Summary Photorespiration 1. RuBP + O2 → PGA and phosphoglycolate 2. Phosphoglycolate uses up ATP 3. No ATP is produced 4. Occurs when O2 increases 5. RuBP is wasted Summary 2014 INFO Photorespiration

Biology Term 1 STPM Chapter 6 Photosynthesis 6 199 P680 e– H O2 P700 Plastocyanin Reaction centre H+ Proton gradient formed for ATP synthesis 2H+ + –– O2 Water-splitting enzyme Reaction centre e– e– e– Fd Fd Ferredoxin NADP reductase NADP++H+ NADPH NADP+ e– Light cydio photophos- phorylation Excited Reaction centre Plastoquinone Light-dependent Reaction Q Excited reaction centre 1 2 Light Photosystem II b6–f b complex 6–f complex Photosystem I NADP reductase Starch Glucose 2 PGAL CO2 H O2 Calvin cycle Light-independent Reaction6 ATP Sucrose Fructose 6 ADP + 6Pi Fats 10 PGAL RUBP Intermediate 12 PGA ADP 12 PGAL Fatty acids Protein pC Glycerol Amino acids Acetyl CoA Figure 6.8 Summary of photosyntheses 2011

Biology Term 1 STPM Chapter 6 Photosynthesis 6 200 6. This occurs when oxygen concentration is high and it becomes a competitive inhibitor of RuBP. 7. Photorespiration uses up RuBP instead of producing sugar. Thus, photorespiration may reduce the potential yield of photosynthesis in C3 plants by up to 50%. 8. Hence, it reduces efficiency of photosynthesis and occurs in the beginning step of the Calvin-Benson cycle in C3 plants. Plants that favour the reduction of oxygen and increase in carbon dioxide concentration would reduce photorespiration. C4 Leaf Compared with C3 Leaf 1. Example of a leaf C3 plant is Helianthus (sunflower) as shown in Figure 6.9. Mid-rid prominent Collenchyma More stoma on lower epidermis Spongy mesophyll Mesophyll palisade Figure 6.9 Leaf of C3 plant 2. Example of a C4 plant leaf is Zea mays (maize) as shown below. Parallel venation Very elongated leaf Bundle sheath Sclerenchyma Cross section of leaf Figure 6.10 Leaf of C4 plant 3. Anatomy differences are summarised in the table below. Table 6.1 Anatomy differences between a C3 and a C4 leaf Characters C3 leaf C4 leaf Mid-rib It is prominent and big It is not prominent Kranz’s anatomy It is not exhibited It is exhibited Mesophyll Two types, palisade and spongy mesophylls are involved There is only one type of mesophyll Bundle sheath It is absent or not distinct It is distinct Chloroplast One type of chloroplast is found in two different types of mesophylls Two types of it, one each in mesophyll and bundle sheath cells Vascular bundle It is a network of different sizes It is parallel type of two sizes Supporting tissue It uses collenchyma It uses sclerenchyma C4 leaf compared with C3 leaf C4 leaf with parallel venation, with bundle sheath containing different chloroplasts with 1 type of mesophyll, uses sclerenchyma for support and stomata distributed equally on both epidermis Summary Exam Tips Remember the anatomy of C4 leaf and compare with that of C3 plant. Exam Tips Remember Kranz’s anatomy using maize leaf as an example. (Maize molecular bundle features – STPM 2007 essay question) Exam Tips Remember the detailed anatomy of C3 leaf. 2013 2018

Biology Term 1 STPM Chapter 6 Photosynthesis 6 201 Characters C3 leaf C4 leaf Stoma density It is more dense on the lower epidermis It is equal on both epidermis Intercellular spaces More, especially in spongy mesophyll Little, only near stoma 4. Kranz’s anatomy is exhibited in C4 plants. Kranz’s (= crown) anatomy is the internal structure of Gramineae leaves, which have a ring of bundle sheath cells surrounding the vascular tissue. Leaves with Kranz’s anatomy exhibit dimorphic chloroplasts, i.e. two different types each in mesophyll cells and bundle sheath cells. 5. Differences between the chloroplasts found in that of the mesophyll and that of bundle sheath are summarised in the table below. Table 6.2 Differences between chloroplasts of mesophyll and bundle sheath Characteristic Chloroplasts of mesophyll Chloroplasts of bundle sheath i Granal activities They are higher They have none or little activity ii Photosystem II It is active, produces plenty of ATP, NADPH and O2 It is not active, produces little NADPH and O2 iii RuBP carboxylase It has almost none It is of high concentration iv CO2 fixation It is nil It is active v Starch There is little starch There is abundant starch C4 Plants and CAM Plants C4 plants 1. C4 plants like Gramineae, which include grass, cereal, sugar cane and bamboo carry out an additional process of carbon fixation called Hatch-Slack pathway. 2. It can be defined as a process that transports carbon dioxide and hydrogen ions from the mesophyll cells to the inner bundle sheath cells. 3. The process is as shown in Figure 6.11. (a) In the beginning, fixation of CO2 occurs. (i) Carbon dioxide from the atmosphere is fixed by phosphoenol pyruvate (PEP), a three carbon molecule. (ii) This happens in the protoplast of the mesophyll cells. (iii) The process is catalysed by PEP carboxylase, which is very efficient. It has a low Km and is not affected by oxygen concentration. (iv) The product is oxaloacetate, which is a four carbon acid. PEP carboxylase CO2 + PEP (3C) → oxaloacetate (4C) 2015 INFO C3 , C4 and CAM Plants

Biology Term 1 STPM Chapter 6 Photosynthesis 6 202 CO2 CO2 + CO2 + PEP (3C) Pyruvate (3C) 2ADP 2ATP NADP NADP g b f e RuBP carboxylase Calvin cycle d c a NADPH NADPH Malate (4C) Pyruvate (3C) Malate (4C) RuBP PGAL Carbohydrate Bundle sheath cell Mesophyll cell PGA Oxaloacetate (4C) Figure 6.11 Hatch-Slack pathway (b) Then, reduction of oxaloacetate occurs. Oxaloacetate is reduced to form malate with the help of NADPH. Oxaloacetate (4C) + NADPH → malate (4C) Oxaloacetate may also be converted into aspartate and amino acid by transamination. (c) Transport of malate (may include aspartate) to bundle sheath cell occurs. (i) Malate is transported from the mesophyll cell to the bundle sheath cell through the plasmodesmata. (ii) Malate then diffuses into the chloroplast. (d) Malate undergoes decarboxylation and carbon dioxide is released. (i) It is decarboxylated to form pyruvate with the help of decarboxylase. (ii) NADP is required forming NADPH2 . NADP NADPH Malate (4C) → pyruvate (3C) + CO2 (Aspartate can be deaminated and decarboxylated to form pyruvate) (e) Fixation of carbon dioxide occurs again. (i) The carbon dioxide released is used for normal carbon fixation. (ii) RuBp is used as an acceptor, catalysed by RuBP carboxylase. (iii) Here, the RuBP carboxylase is very efficient because the carbon dioxide is higher in concentration. This is due to carbon dioxide is released by enzymatic reactions. 2013 2010 2017

Biology Term 1 STPM Chapter 6 Photosynthesis 6 203 (f) Pyruvate formed is translocated back to mesophyll cell through the plasmodesmata in the cell wall. (g) Once the pyruvate is back in the mesophyll cell, it is converted back to PEP. Two molecules of ATP are required. Pyruvate + 2ATP → PEP + 2ADP (h) Therefore, the Hatch-Slack pathway can be summarised as a process in which one molecule of carbon dioxide and two hydrogen ions are transferred using two molecules of ATP. 4. C4 plants photosynthesise faster under high optimum temperature of 25°C to 35°C with low photorespiration. C4 plants use low carbon dioxide to have high photosynthesis rate and save more water without needing to open the stomata bigger. CAM plants 1. CAM plants belong to family of Crassulaceae that includes Bryophyllum which open their stomata during the night and close during the day. Other plants that can carry out this process are pineapple and cacti. 2. The process of CAM (Crassulacean acid metabolism) that occurs in the mesophyll cell is as shown in Figure 6.12. CO2 PEP a c f h PGAL g PGA b Oxaloacetate ADP NADP Malate Pyruvate NADPH NADP CO2 d RuBP ATP e NADPH Glucose i Starch Night Day Stoma open Stoma close Calvin cycle Figure 6.12 Crassulascean acid metabolism 3. (a) At night, stomata are open and carbon dioxide is accepted by PEP to form oxaloacetate as in Hatch-Slack pathway. (b) The oxaloacetate is then reduced to malate that requires NADPH. (c) The malate is stored in the sap vacuole and the process of its formation occurs throughout the night. (d) During the day when there is light, photosynthesis takes place with carbon dioxide released from malate by decarboxylation. (e) The carbon dioxide is fixed by RuBP to form PGA, which undergoes Calvin cycle and formation of glucose and starch. Exam Tips Remember the comparison between the C4 cycle of C3 plant and C4 plant. (2006 STPM structured question)

Biology Term 1 STPM Chapter 6 Photosynthesis 6 204 (f) The pyruvate formed after the decarboxylation of malate can also be converted to starch and stored during the day. (g) At night, the starch is hydrolysed to maltose and then glucose, which is converted to PEP to start the cycle again. (h) The significance of the whole process is to enable the plant to carry out photosynthesis despite the closed stomata during the day. The plant is well adapted to live in dry regions with this metabolism. 4. CAM plants have higher water efficiency under arid conditions. They can temporarily survive in drought by closing their stomata during day and night yet they can fix carbon dioxide during the day with stored malate. Differences between the Carbon Dioxide Fixation in C4 and CAM Plants Mesophyll cell Calvin Cycle Starch CO2 CO2 Bundlesheath cell Malate Night Calvin Cycle Starch CO2 CO2 Day Malate C4 plant CAM plant C4 plant CAM plant 1. PEP carboxylase is used PEP carboxylase is used 2. Malate is formed during the day Malate is formed during the night 3. Malated is not stored Stored in sap vacuole 4. Malate releases CO2 in bundle sheath Malate releases CO2 in same cell 5. Spatial (space) separation of C fixation in maize Temporal (time) separation of C fixation in cactus Exam Tips Remember the detailed process of CAM and its significance. (2009 STPM essay question)

Biology Term 1 STPM Chapter 6 Photosynthesis 6 205 Differences Between the Metabolism of C3 , C4 and CAM Plants The differences between the metabolism of C3 , C4 and CAM plants are summarised in the table below: Plant type C3 C4 CAM 1. Primary carboxylase Rubisco PEP carboxylase PEP carboxylase 2. Primary CO2 acceptor RuBP PEP PEP 3. Carbon fixation occurs in Chloroplasts of mesophyll cells during the day Cytoplasm of mesophyll cells during the day Cytoplasm of mesophyll cells during the night when stomata open 4. The first stable products of carbon fixation are Phosphoglycerate then is converted into phosphoglyceraldehyde Oxaloacetate then is converted into malate Oxaloacetate then is converted into malate 5. Malate is stored No No, it is moved to bundle sheath cells Malate is stored throughout the night in sap vacuole 6. Malate releases carbon dioxide No In the bundle sheath cells In the stroma of chloroplasts 7. Secondary carboxylase  None Rubisco separated  in space (bundle sheath) Rubisco separated  in time (during the day) 8. ATP formed Low High High 9. Transpiration rate High Low Low 10. Light compensation point 5 Wm-2 < 1 Wm-2 < 1 Wm-2 11. Photorespiration rate  High (30% of net photosynthesis) Low to undetectable Low to undetectable 12. Optimum temperature 25 o C 35 oC or more 35 oC or more 13. Productivity (tonnes/ha/yr) ~20 ~30 ~30 Quick Check 2 1. What is meant by Kranz’s anatomy?

Biology Term 1 STPM Chapter 6 Photosynthesis 6 206 6.4 Limiting Factors Limiting Factors of Photosynthesis 1. Light intensity affects the rate of photosynthesis. (a) The effect of light intensity on the rate of photosynthesis is shown in Figure 6.13. 2018 Rate of photosynthesis Light intensity / lux Figure 6.13 The effect of light intensity on rate of photosynthesis (b) When light intensity is low, the rate of photosynthesis is proportional to light intensity. This is because the light supplies energy for photosynthesis. Light also causes stomata to open to allow carbon dioxide to diffuse in. (c) At a higher light intensity and depending on the type of plants, the rate of photosynthesis becomes maximum due to atmospheric carbon dioxide which is always a limiting factor at 0.04%. (d) If the carbon dioxide concentration is increased to 0.4%, the rate of photosynthesis increase a few times as shown in Figure 6.14. Rate of photosynthesis Light intensity / lux 0.04% CO2 at 25°C 0.4% CO2 at 25°C Figure 6.14 The effects of light intensity at different CO2 concentrations (e) If the light intensity is further increased, the rate of photosynthesis falls rapidly as the temperature may be too high denaturing enzymes and destroys chlorophyll by photo-oxidation. 2. Temperature is an important factor in photosynthesis. (a) The effect of different temperatures on the rate of photosynthesis is shown in Figure 6.15. Limiting factors of photosynthesis 1. Factors in short supply 2. Factor if increased, increases rate 3. Factor if increased, rate remains – another factor is limiting 4. Low light intensity, low temperature and low CO2 concentration – limiting factors 5. Increase light intensity CO2 is always limiting 6. Too high light intensity = too high temperature is also limiting – due to denaturation of enzymes Summary Students should be able to: (a) explain limiting factors of photosynthesis (light intensity, carbon dioxide concentration and temperature); (b) relate the roles of C3 , C4 and CAM plants in increasing carbon dioxide emission and global warming. Learning Outcomes

Biology Term 1 STPM Chapter 6 Photosynthesis 6 207 Rate of photosynthesis 0 40 Temperature / °C 10 20 30 Figure 6.15 The effect of temperature on photosynthesis (b) At 0 °C, photosynthesis is very low because there is very little kinetic energy for any enzymatic reaction to take place. (c) At optimum temperature, which may be between 25 °C to 40 °C, the rate of photosynthesis is maximum. This is because such temperature provides the most suitable amount of kinetic energy for reactions to take place. The enzymes are in the best shapes and the reacting molecules have the most effective collision. (d) Between 0 °C to optimum temperature, the temperature quotient (Q10) is equal to 2. This means for every 10 °C increase in temperature, there is a corresponding double increase in the rate of photosynthesis. (e) When the temperature is increased further, there is a rapid decrease in the rate of photosynthesis. This is because enzymes are denatured by high temperature. (f) All the effects of temperature are true only if the light intensity is optimal. Under low light intensity, there is minimal effect on the rate of photosynthesis if the temperature is increased say from 10 °C to 30 °C. This is because the light dependent stage of photosynthesis is a photochemical reaction that is minimally affected by temperature. 3. Carbon dioxide concentration is always a limiting factor. (a) The effect of carbon dioxide concentration on the rate of photosynthesis is shown in Figure 6.16. Rate of photosynthesis 0.2 0 0.4 0.6 0.8 1.0 CO2 concentration / % Figure 6.16 The effect of CO2 concentration on photosynthesis (b) When the carbon dioxide concentration is increased from 0 to 0.1%, the rate of photosynthesis increases proportionally if light intensity is not limiting. This is because carbon dioxide is a reactant for the process. Exam Tips Remember the meaning of limiting factor, when the factors become limiting.

Biology Term 1 STPM Chapter 6 Photosynthesis 6 208 (c) 0.1% of carbon dioxide concentration is optimum. (d) If the concentration is increased from 0.1 to 1%, the rate of photosynthesis remains more or less the same as other factor may be limiting. (e) Further increase in concentration of carbon dioxide concentration will result in a rapid decrease in the rate of photosynthesis. This is because too much carbon dioxide dissolved in water, produces too low a pH that denatures enzymes. Roles of C3 , C4 and CAM Plants in High CO2 Emission 1. Most plants in the world are C3 plants with ribulose bisphosphate carboxylase in the stroma of chloroplasts to fix carbon dioxide. The first product is a three carbon (C3 ) phosphoglyceric acid (PGA). 2. These C3 plants play a very important role to reduce inceasing carbon dioxide emission and global warming. The majority of tropical rain forest plants are C3 plants. They have high photosynthetic rate as the light intensity is high, the environment temperature is high and plenty supply of water. 3. They increase in the rate of carbon fixation when carbon dioxide concentration increases. C3 plants carboxylase would work more efficiently as it has high Km and more carbon dioxide is fixed. They would manage to reduce photorespiration as carbon dioxide is increased. 4. These tropical rainforest trees with a big canopy in spongy forest floor should not be destroyed. They help to absorb more carbon dioxide and soak up with water both in the plant as well as the soil to reduce global warming. More of these trees should be planted so they would transpire more in order to reduce global warming. 5. C4 plants are grass family with PEP carboxylase to fix carbon dioxide in the cytoplasm of mesophyll cells to fix carbon dioxide. The first product is a four carbon (C4 ) acid. They are not the main plants in the tropics. Only in temperate grasslands of Africa, North and South America and the Steppes of Asia do they play seasonal summer role in more carbon fixation. 6. The role of these plants is not as important as C3 plants. This is due to PEP carboxylase as low KM, already work at a high rate at low carbon dioxide concentration and found not to have increased their rate at higher carbon dioxide concentration. 7. Planting more C4 drought resistant cereal crops like maize and sorghum helps to increase food production at higher warm temperature. Besides, plants that can withstand high salt content play more important role in the future as the tides of the world start to increase in height. Roles of C3 , C4 and CAM plants in high CO2 emission and global warming 1. More C3 forest plants can reduce more carbon emission 2. More C4 plants cannot reduce CO2 concentration 3. C4 drought resistant plants maintain food production 4. CAM plants can cut down CO2 in semidesert land 5. Plants that tolerate high salt concentration can reduce CO2 in increasing sea level Summary

Biology Term 1 STPM Chapter 6 Photosynthesis 6 209 8. CAM plants such as cacti have PEP carboxylase like C4 plants. They open their stomata at night to fix carbon dioxide. They are well adapted to live in arid land. 9. Cacti play an important role in hot arid areas where the night temperature is cool. They close their stomata to cut down transpiration during they day. Systematic planting of economic important cacti to cut down carbon emission is possible. 10. As the sea level increases, C3 mangrove plants can help to reduce carbon dioxide concentration. C4 crop plants adapted in increasing salt concentration are also important to produce more food. Both help to reduce global temperature through more transpiration and photosynthesis of absorbing more carbon dioxide. Exam Tips Remember that plants with compensation point in the presence of very low light intensity, temperature and carbon dioxide concentration is very efficient in photosynthesis. Quick Check 3 1. Explain factors that affect photosynthesis other than light, temperature and carbon dioxide concentration. 2. Explain the significance of compensation point. Objective Questions 1. What are the phases required during photosynthesis? A Photosystem I and II B Photosystem and photolysis of water C Dark and the carbon fixation reactions D Light and the carbon fixation reactions 2. The diagram shows the light dependent stage of photosynthesis. Primary acceptor Primary acceptor P680 P700 NADP+ + 2H+ 2H+ + —O2 1 2 2e– H2O ATP Light NADPH + H+ NADP+ reductase Light 2e– Cytochrome complex P Q R 2e– 2e– Which combination is true of P, Q and R? P Q R A Ferredoxin Plastocyanin Plastoquinone B Ferredoxin Plastoquinone Plastocyanin C Plastocyanin Plastoquinone Ferredoxin D Plastoquinone Plastocyanin Ferredoxin 3. Which statement is not true in the Z diagram of light dependent reaction below? 4e– 4e– Q P e– e– e– Quinone Ferredoxin 2 NADP+ 2 NDPH2 Sunlight Sunlight PS II PS I P680 P700 I NADP+ is oxidised in non-cyclic photophosphorylation II P680 and P700 are oxidised after their electrons are raised to higher energy levels STPM PRACTICE 6

Biology Term 1 STPM Chapter 6 Photosynthesis 6 210 III ATP are synthesised in steps P and Q IV The products of cyclic photophosphorylation is NADPH, ATP and oxygen A I and IV B II and III C III and IV D II, III and IV 4. Which would be first radioactive product if a rice plant leaf is exposed to radioactive carbon dioxide? A Oxaloacetate B Malate C Phosphoenol pyruvate D Phosphoglycerate 5. Which combination is true of the number of molecules of CO2 , ATP and NADPH used in the Calvin cycle to synthesise one glucose molecule? CO2 ATP NADPH A 6 12 18 B 6 18 12 C 12 18 6 D 18 6 12 6. Which are true of cyclic photophosphorylation? I It involves only photosystem I II It involves photolysis of water III It produces NADPH IV It produces ATP A I and III B I and IV C II and III D II and IV 7. The diagram shows a process which occurs in CAM plants. Sugar Calvin cycle CO2 y x Which about the diagram is not correct? A Process X occurs at night. B Process Y occurs in mesophyll cells. C Calvin cycle occurs in bundle sheath cells. D Y combines with ribulose-1, 5-bisphosphate carboxylase in the Calvin cycle. 8. The following scheme shows a pathway in the amino acid formation in a plant. CO2 RuBP P Q R S Amino acid Which compound is represented by P, Q, R and S in the above scheme? P Q R S A Pyruvate Phosphoglyceraldehyde Phosphoglycerate Acetyl CoA B Phosphoglyceraldehyde Acetyl CoA Phosphoglycerate Pyruvate C Phosphoglycerate Phosphoglyceraldehyde Acetyl CoA Pyruvate D Phosphoglycerate Phosphoglyceraldehyde Pyruvate Acetyl CoA 9. C4 plants are more efficient in photosynthesis than C3 plants due to A ribulose-1,5-bisphosphate carboxylase has a higher affinity towards carbon dioxide. B its first intermediate product of carbon dioxide fixation is oxaloacetate. C carbon dioxide fixation occurs at night. D its photorespiration rate is reduced.

Biology Term 1 STPM Chapter 6 Photosynthesis 6 211 10. The diagram shows a process in C4 plants. Cell Y Cell Z X Triose phosphate Calvin cycle Carbon process CO2 Which statements are true of the above process are correct? I X is malate. II Y is a mesophyll cell. III Z is a bundle sheath cell. IV It occurs in CAM plants. A I and III C II and III B I and IV D II and IV 11. Which about C4 plants is correct? A Photorespiration increases in the presence of oxygen. B The PEP carboxylase is more active in the dark. C Carbon fixation occurs twice. D The leaves have one type of chloroplast. 12. Which difference is not true between C3 and C4 plants? C3 plants C4 plants A Involves rubisco Involves PEP carboxylase B The first product is PGA The first product is malate C CO2 acceptor is C5 CO2 acceptor is C3 D Carbon fixation occurs in cytoplasm Carbon fixation occurs in chloroplast 13. The diagram shows a carbon fixation in the leaf of a plant. Phosphoenolpyruvate carboxylase Mesophyll cell Bundle Sheath cell Phosphoenolpyruvate (3C) Z X Y CO2 CO2 What do X, Y and Z represent? X Y Z A Malate Oxaloacetate Pyruvate B Malate Pyruvate Oxaloacetate C Oxaloacetate Malate Pyruvate D Pyruvate Oxaloacetate Malate 14. Which combination is correct? Non-cyclic photophosphorylation Cyclic photophosphorylation Non-cyclic and cyclic photophosphorylation A ATP is produced NADPH is not formed O2 is produced B O2 is produced ATP is produced NADPH is not formed C O2 is produced NADPH is not formed ATP is produced D ATP is produced O2 is produced NADPH is not formed 15. Which graph shows the absorption of carotenoid? A C Absorption Wavelength Absorption Wavelength B D Absorption Wavelength Absorption Wavelength

Biology Term 1 STPM Chapter 6 Photosynthesis 6 212 16. Which statement is true for point Y, which is known as the compensation point? Light intensity Y Respiration Photosynthesis 0 Rate of use / production of sugar I Y represents the basic rate of respiration II At Y, the rate of production of sugar is higher than its rate of use III At Y, the rate of photosynthesis is same as the rate of respiration IV Y represents the total net production of sugar A I and II C II and IV B I and III D III and IV 17. Which type of plant can have rubisco bound with carbon dioxide and oxygen? A CAM plants B C3 plants C C4 plants D C4 and CAM plants 18. What is the chief factor that produces the curves P, Q and R in the curves below? CO2 concentration Rate of photosynthesis P Q R A Temperature B Light C Water D Oxygen 19. The graph below shows a relationship of rate of photosynthesis against environmental factor X. Rate of photosynthesis/ arbitrary units X X may represent: I temperature II oxygen concentration III light intensity IV carbon dioxide concentration A I and III C II and III B I and IV D III and IV 20. An absorption spectrum of photosynthetic pigments I, II and III is shown in the graph below. Absorbance of light by chloroplast pigments 400 500 600 700 I II III Wavelength of light / nm What combination is true of the pigments I, II and III? I II III A Carotenoids Chlorophyll a Chlorophyll b B Carotenoids Chlorophyll b Chlorophyll a C Chlorophyll a Chlorophyll b Carotenoids D Chlorophyll b Carotenoids Chlorophyll a 21. Which is correct about pineapple? I Carbon fixation occurs at night II Photorespiration is minimised III Stomata are closed at night IV Krantz anatomy exists A I and II B I and IV C II and III D III and IV

Biology Term 1 STPM Chapter 6 Photosynthesis 6 213 22. Phases I, II and III of the Calvin cycle are shown in the diagram below. NADP+ CO2 NADPH ADP ATP PGA RuBP PGAL Glucose IIII II ADP ATP Which processes regarding the three phases of the Calvin cycle are correct? I II III A Fixation of CO2 Regeneration of RuBP Reduction of CO2 B Fixation of CO2 Reduction of CO2 Regeneration of RuBP C Reduction of CO2 Fixation of CO2 Regeneration of RuBP D Regeneration of RuBP Fixation of CO2 Reduction of CO2 Structured Questions 1. The diagram below shows the process of photophosphorylation during light reaction in plants. H2O 1 2 2H+ + –O2 2e– D B Primary acceptor Primary acceptor Cytochrome complex Pq Fd Pc C A (a) Name the systems A and C and the products B and D. [4] (b) Describe the process of production of B and D. [4] (c) What happens to the products B and D after the light reaction? [2]

Biology Term 1 STPM Chapter 6 Photosynthesis 6 214 2. The diagram below shows the C4 cycle of a plant. HCO3 – Phosphoenolpyruvate Oxaloacetate Pyruvate W Y , Z Cell P CO2 + Pyruvate Phosphoglyceraldehyde Calvin cycle Hexose phosphate X QCell (a) Name enzymes W and X. [2] (b) Name metabolites Y and Z. [2] (c) Name cells P and Q. [2] (d) Describe the processes that occur in cell P. [3] (e) State the importance of C4 cycle to the plant. [3] Essay Questions 1. (a) Describe anatomical differences between the leaf of C3 and C4 plants. [4] (b) Describe the light dependent reaction in photosynthesis which does not involve photolysis of water. [8] (c) List three limiting factors that affect the rate of photosynthesis. [3] 2. (a) What are the differences between the metabolic pathways of C3 and C4 plants in the production of carbohydrate? [8] (b) Explain the role of carbon dioxide in the control of the rate of photosynthesis. [7] 3. (a) ATP and NADPH are required for the synthesis of glucose in plants. Describe how these two molecules are produced during photosynthesis. [9] (b) Explain how high concentration of oxygen affects photosynthesis of C3 plants. [6]

Biology Term 1 STPM Chapter 6 Photosynthesis 6 215 1 1. (a) Photoactivation of photosystem I is a process in which light of longer wavelength up to 700 nm is absorbed by the pigments in photosystem I. The pigment molecules get excited and their energy level is raised. Energy is passed from one molecule to another and finally reaches the reaction centre where electrons are released. The electrons are received by electron receptors where they can be used for cyclic and non-cyclic photophosphorylation. (b) Photoactivation of photosystem II is a process in which light of shorter wavelength up to 680 nm is absorbed by the pigments in photosystem II. This is a process in which the pigments in photosystem I absorb light and the molecules get excited. The energy level in each molecule is raised and energy is passed from one to another until it reaches the reaction centre where electrons are liberated. The electrons are received by electron receptors where they can be used for only non-cyclic photophosphorylation. (c) Cyclic photophosphorylation is a process in which the electrons released by photosystem I are finally passed back to the same reaction centre i.e. of photosystem I after they are used for formation of ATP. This is the way for plants to generate a lot of ATP. (d) Non-cyclic photophosphorylation is a process in which the electrons liberated by photosystem are not passed back to the same reaction centre. This occurs in both photosystems I and II. For photosystem II, the electrons go to photosystem I getting them back from water. For photosystem I, the electrons go to coenzyme NADP+ getting them back from photosystem II. (e) Photolysis of water is a process in which water is split during the light dependent stage of photosynthesis. This process occurs in the space of the thylakoid and catalysed by a water splitting enzyme. The enzyme passes the electrons from water to the reaction centre of photosystem II forming oxygen, which is liberated. The hydrogen ions formed increase the proton gradient inside the thylakoid for the use in ATP formation by chemiosmosis. 2 1. Kranz’s anatomy is exhibited in C4 plants. It is the internal structure of Gramineae leaves, which have a ANSWERS ring of bundle sheath cells surrounding the vascular tissue. Leaves with Kranz’s anatomy exhibit dimorphic chloroplasts, i.e. two different types each in mesophyll cells and bundle sheath cells. 3 1. Water supply is a factor as water is a raw material for photosynthesis. Mineral ions especially phosphate is also required directly for the formation of ATP. Other mineral ions such as sulphate, iron, potassium, sodium and magnesium may not be directly involved but the lack of these ions would affect the rate of photosynthesis. 2. The significance of it is as an indicator of the efficiency of photosynthesis. The rate of photosynthesis above the compensation point means the plant can make excess food more than it can sustain basic need. Therefore, if light intensity is used as a factor to determine its compensation point, a plant with compensation at low intensity means its light absorption and conversion system is very efficient. Its temperature, carbon dioxide or water utilisation efficiency is also good if the compensation point occurs at such low unfavourable conditions. STPM Practice 6 Objective Questions 1. A 2. C 3. A 4. B 5. C 6. B 7. C 8. D 9. D 10. D 11. B 12. D 13. C 14. C 15. D 16. B 17. B 18. B 19. D 20. C 21. A 22. B Structured Questions 1. (a) A. Phytosystem II B. ATP C. Photosystem I D. NADPH (b) • When electrons are passed through the cytochrome complex, H+ ions are pumped into thylakoid spaces. • H+ ions gradient is created to allow H+ ions to diffuse through ATP synthase to form ATP from ADP and inorganic phosphate. • Electrons passed from Fd (ferrodoxin) are accepted by electron carrier (NADP reductase) of the electron transport chain.

Biology Term 1 STPM Chapter 6 Photosynthesis 6 216 • Enzyme combines electron, H+ ion from stroma and NADP+ to form NADPH. (c) • ATP is used to convert PGA to PGAL and to regenerate RuBP in the Calvin cycle • NADPH is used to reduce PGA to PGAL and to form organic acids. 2. (a) W: PEP carboxylase, X: RuBP carboxylase (b) Malate and alanine (c) P: mesophyll cell; Q: bundle sheath cell (d) Carbon dioxide reacts with phosphoenolpyruvate catalysed by PEP carboxylase to form oxaloacetate. Oxaloacetate is then converted into malate or aspartate with the help of NADPH. Malate and aspartate diffuse into the bundle sheath cell through the plasmodesmata. (e) It enables the plant to fix carbon dioxide even at low concentration as PEP carboxylase has low Km. It enables more carbon dioxide to accumulate in the bundle sheath cell so that carbon dioxide can be fixed by RuBP carboxylase more efficiently. It reduces photorespiration as PEP carboxylase is not affected by oxygen released by photolysis of water and RuBP is in the bundle sheath cell. Essay questions 1. (a) • C3 plants show Kranz anatomy whereas C4 plants do not • C3 plants have palisade and spongy mesophyll whereas C4 plants have one type • C3 plants usually have no bundle sheath whereas C4 plants have • C3 plants have collenchyma as supporting tissue whereas those of C4 plants are sclerenchyma (b) • The light dependent reactions that do not involve photolysis of water are cyclic and noncyclic photophosphorylation occurring in photosystem I • During cyclic photophosphorylation electrons released from the reaction centre P700 are accepted by ferredoxin and passed to b6-f complex • Hydrogen ions are released from the complex into the thylakoid space for ATP formation • The electrons then released from the b6-f complex are accepted by plastocyanin back P700 reaction centre • During non-cyclic photophosphorylation the electrons released from P700 are also accepted by ferredoxin but pass to NADP reductase • NADP reductase makes use of the electrons, hydrogen ions outside the thylakoid to form NADPH from NADP • The reduction of hydrogen ions outside the thylakoid also creates hydrogen ion concentration gradient • This allows the hydrogen ions to pass through ATP synthase to form ATP on the outside of thylakoid (c) • One limiting factor is light concentration as light is essential as energy source • Another is carbon dioxide concentration as it is the raw material • Suitable temperature is also essential as enzymes require suitable temperature to act in the light independent reactions 2. (a) • C3 plants carry out the same metabolic pathway in chloroplast of all mesophyll cells whereas C4 plants carry out different pathways in mesophyll and bundle sheath cells. • C3 plants have one type of chloroplast whereas C4 plants have two types of chloroplast to carry the pathways. • C4 plants have mesophyll chloroplasts more for light dependent process and bundle sheath chloroplasts more for light independent process. • C3 plants have only one RuBP carboxylase whereas C4 plants have one extra PEP carboxylase for carbon fixation. • C4 plants have PEP carboxylase for carbon fixation in the cytoplasm of mesophyll cells not in chloroplast. • The product of PEP carboxylation is oxaloacetate, C4 not C3 acid. • Oxaloacetate is then converted into malate that diffuses into bundle sheath cells whereas C3 plants have no such conversion and diffusion. • O2 produced in C4 plants do not interfere the RuBP carboxylase as the enzyme is in the bundle sheath cells, unlike C3 plants in the same chloroplast so more photorespiration. (b) • Higher CO2 concentration increases the rate of photosynthesis. • This is due to CO2 is the substrate to form carbohydrate. • CO2 in the atmosphere with the concentration of 0.04% is always a limiting factor, not diffusing fast enough in full sunlight. • So, if the stomata are closed in water stress, the rate of photosynthesis will decrease. • CO2 has to bind with RuBP carboxylase to form a temporary C6 compound that splits to form PGA. • Since RuBP carboxylase has high Km, a high concentration of CO2 can only produce higher rate. • However, high concentration i.e 1% of CO2 reduces the pH and will denatures the enzyme, thus reduces the rate of photosynthesis.

217 Section A [15 marks] Bahagian A [15 markah] Answer all questions in this section. Jawab semua soalan dalam bahagian ini. 1. Which chemical produces variation in DNA molecules? Bahan kimia manakah menghasilkan variasi dalam molekul-molekul DNA? I Phosphate group Kumpulan fosfat II Pentose sugar Kumpulan pentose III Pyrimidine Pirimidina IV Purine Purina A I and II C II and III I dan II II dan III B I and IV D III and IV I dan IV III dan IV 2. Guanine makes up 8% of the nucleotides in a sample of DNA. What is the percentage of thymine in the sample? Guanina membentuk 8% nukleotida dalam suatu sampel DNA. Apakah peratus timina dalam sampel tersebut? A 42 B 28 C 44 D 56 3. The diagram below shows part of a polymer. Gambar rajah di bawah menunjukkan sebahagian daripada sejenis polimer. C N C H H H2N CH3 CH3 C C C H O OH Which molecule is used to break the bond indicated by the arrow? Molekul yang manakah digunakan untuk memutuskan ikatan yang ditunjukkan dengan anak panah? A Amino acid C Peptide Asid amino Peptida B Amylase D Water Amilase Air 4. What differentiates prokaryotic from eukaryotic cells? Apakah yang membezakan antara sel prokariotik dengan sel eukariotik? A The presence or absence of ribosomes Kehadiran atau ketiadaan ribosom B The ability of the cell to carry out cellular metabolism Kebolehan sel untuk menjalankan metabolisme sel C The presence or absence of a rigid cell wall Kehadiran atau ketiadaan dinding sel yang tegar D Whether or not the cell is partitioned by internal membranes Sama ada sel dibahagikan mengikut membran internal atau tidak 5. The pH of the intermembrane space of mitochondria is lower than the matrix of mitochondria due to the pH di ruang antara membran mitokondria adalah lebih rendah daripada di matriks mitokondria kerana A Accumulation of lactic acid during anaerobic respiration Pengumpulan asid laktik semasa respirasi anerobik STPM Model Paper (964/1)

218 Biology Term 1 STPM Model Paper (964/1) B High concentration of pyruvic acid in the matrix Kepekatan asid piruvik yang tinggi dalam matriks C High concentration of H+ due to chemiosmosis Kepekatan H+ yang tinggi disebabkan kimiosmosis D High production of ATP Penghasilan ATP yang tinggi 6. By which process does glucose move into the red blood cells from plasma? Apakah proses yang berlaku apabila glukosa diserap masuk dari plasma ke dalam sel darah merah? A Osmosis Osmosis B Endocytosis Endositosis C Facilitated diffusion Resapan berbantu D Active transport Pengangkutan aktif 7. Strips of potato tuber tissue were immersed in distilled water and in sucrose solutions of different concentrations. The graph shows the percentage change in length of the strips. Jalur kentang direndamkan ke dalam air suling dan larutan sukrosa yang berlainan kepekatan. Graf berikut menunjukkan peratusan perubahan panjang jalur kentang. Change in length of strips / % Perubahan panjang jalur / % 0 1 2 3 4 5 –20 Time / hours Masa / jam Distilled water Air suling 0.1 mol dm–3 0.1 mol dm–3 0.3 mol dm–3 0.3 mol dm–3 –10 0 10 20 Which statement explains the change that occurr in the potato strips immersed in 0.1 mol dm–3 sucrose solution? Pernyataan yang manakah menjelaskan perubahan yang berlaku dalam jalur kentang yang direndam di dalam 0.1 mol dm–3 larutan sukrosa? A Sucrose molecules diffused into the potato cells. Molekul sukrosa meresap ke dalam sel ubi kentang. B Sucrose molecules were actively transported into the potato cells. Molekul sukrosa diangkat secara aktif ke dalam sel ubi kentang. C The water potential of the sucrose solution was less negative than the water potential inside the cells. Keupayaan air larutan sukrosa adalah kurang negatif daripada keupayaan air di dalam sel. D The water potential of the sucrose solution was more negative than the water potential inside the cells. Keupayaan air larutan sukrosa adalah lebih negatif daripada keupayaan air di dalam sel. 8. Which part of a phospholipid molecule makes up most of the thickness of a plasma membrane? Bahagian molekul fosfolipid yang manakah memberi ketebalan membran plasma yang paling tinggi? A Glycerol Gliserol B Hydrophilic head Kepala hidrofilik C Hydrocarbon chains Rantai hidrokarbon D Phosphate group Kumpulan fosfat 9. The initial rate of a reaction catalysed by an enzyme was measured at various substrate concentrations. Which graph shows the effect of a low concentration of noncompetitive inhibitor on the reaction? Kadar awal tindak balas dimangkinkan oleh enzim diukur pada kepekatan berbeza. Graf yang manakah menunjukkan kesan kepekatan perencat tak bersaingan kepada tindak balas?

219 Biology Term 1 STPM Model Paper (964/1) Key: uninhibited reaction/Tindak balas tak terencat inhibited reaction/Tindak balas terencat A Initial rate of reaction Kadar awal tindak balas Substrate concentration Kepekatan substrat B Substrate concentration Kepekatan substrat Initial rate of reaction Kadar awal tindak balas C Substrate concentration Kepekatan substrat Initial rate of reaction Kadar awal tindak balas D Substrate concentration Kepekatan substrat Initial rate of reaction Kadar awal tindak balas 10. A plant cell is placed in a solution with a less negative water potential than the cell contents. Which change occurs in the cell and what causes the change? Suatu sel tumbuhan diletakkan di dalam larutan yang mempunyai keupayaan air yang kurang negatif daripada kandungan sel. Apakah perubahan yang berlaku kepada sel tersebut dan apakah sebabnya? Change Perubahan Cause Sebab A Cell becomes more flaccid Sel menjadi lebih flasid Solution diffuses out of the cell Larutan meresap keluar daripada sel B Cell becomes more flaccid Sel menjadi lebih flasid Water diffuses out of the cell Air meresap keluar daripada sel C Cell becomes more turgid Sel menjadi lebih segah Solution diffuses into of the cell Larutan meresap ke dalam sel D Cell becomes more turgid Sel menjadi lebih segah Water diffuses into cell Air meresap ke dalam sel 11. The table shows the respective solute and pressure potential values of cell X and cell Y. Jadual menunjukkan nilai keupayaan pelarut dan keupayaan tekanan bagi sel X dan Y. Cell X/ Sel X Cell Y/ Sel Y = –16 kPa = –12 kPa = 8 kPa = 2 kPa Which value of water potential in cell X and Y, and the direction of water movement is correct? Nilai keupayaan tekanan bagi sel X dan Y serta arah pergerakan air yang manakah betul? Cell P/ kPa Sel P/ kPa Cell Q/ kPa Sel Q/ kPa Water movement Pergerakan air A 8 10 Q → P B –8 –10 P → Q C –16 –12 P → Q D –24 14 Q → P

220 Biology Term 1 STPM Model Paper (964/1) 12. Which class of enzyme forms aminoacyltRNA? Apakah kelas enzim yang membentuk aminoacyltRNA? A Ligase Ligase B Lyase Liase C Transferase Transferase D Oxidoreductase Oksidoreduktase 13. Which of the following about enzyme immobilisation is correct? Antara yang berikut, yang manakah benar tentang pentakmobilan enzim ? I The enzymes can remain active at high temperatures Enzim kekal aktif pada suhu yang tinggi II The products do not need to be purified Hasil tidak perlu ditulenkan III Inhibits the metabolic pathway Menghalang laluan metabolik IV Reversible reaction Tindak balas berbalik A I and II I dan II B I and IV I dan IV C II and III II dan III D III and IV III dan IV 14. During the chemiosmosis, when is ATP being synthesised? Bilakah ATP dihasilkan semasa kemiosmosis? A Hydrogen ions are pumped from the mitochondrial matrix into the intermembrane space Ion hidrogen dipamkan dari matriks mitokondria ke ruang antara membran B Hydrogen ions flow back from the intermembrane space into the mitochondrial matrix Ion hidrogen meresap keluar dari ruang antara membran ke matriks mitokondria C Electron carrier accepts electrons and then transfers the electrons to the next electron carrier Pembawa elektron menerima elektronelektron dan memindahkannya kepada pembawa elektron yang lain. D Oxygen accepts electrons and protons to form water Oksigen menerima elektron-elektron dan proton-proton untuk membentuk air 15. Which statement is true of the dark reaction stage of photosynthesis? Pernyataan yang manakah benar tentang tindak balas gelap semasa fotosintesis? A ATP and NADPH are formed when electrons leave the reaction centres of photosystem ATP dan NADPH terbentuk apabila elektronelektron keluar dari pusat reaksi fotosistem B ATP is required for the conversion of carbon dioxide to triose phosphate sugar ATP diperlukan untuk menukarkan karbon dioksida kepada gula fosfat triosa C Water molecule is required for the formation of oxygen and reduction of carbon dioxide Molekul air diperlukan untuk pembentukan oksigen dan penurunan karbon dioksida D Water molecule is oxidised to oxygen and NADP+ is reduced to NADPH Molekul air dioksidakan kepada oksigen dan NADP+ diturunkan kepada NADPH

221 Biology Term 1 STPM Model Paper (964/1) Section B [15 marks] Bahagian B [15 markah] Answer all questions in this section. Jawab semua soalan dalam bahagian ini. 16. The diagram below shows a technique of an enzyme immobilisation. Rajah di bawah menunjukkan suatu teknik imobilisasi enzim. + + + + + + + (a) Explain enzyme immobilisation. Terangkan imobilisasi enzim. [2 marks / 2 markah] (b) State the enzyme immobilising technique used above. Nyatakan teknik imobilisasi enzim yang digunakan di atas. [1 mark / 1 markah] (c) Name one possible interaction shown by the technique above. Namakan satu interaksi yang mungkin berlaku dalam teknik di atas. [1 mark / 1 markah] (d) Glucose isomerase is stable at 65o C for almost a year but denatures within a few hours at 45o C for free enzyme. Explain how enzyme becomes more stable when immobilised. Enzim isomerase glukosa stabil pada 65o C selama setahun tetapi ternyahasli dalam masa beberapa jam pada 45o C bagi enzim yang tidak diimobilisasi. Terangkan bagaimana enzim menjadi lebih stabil apabila diimobilisasi. [2 marks / 2 markah] 17. The diagram below shows the structure of ATP. Gambar rajah di bawah menunjukkan struktur ATP. O O– O P O CH2 O H N C N NH2 N C C N C C C C H OH OH H H H H O O– P O O– O– P O

222 Biology Term 1 STPM Model Paper (964/1) (a) Describe the main structural features of the molecule. Huraikan sifat-sifat utama molekul ini. [3 marks / 3 markah] (b) Explain how ATP is able to transfer energy in cells. Terangkan bagaimana ATP dapat memindahkan tenaga dalam sel. [3 marks / 3 markah] (c) Explain how ATP is synthesised in mitochondria. Terangkan bagaimana mitokondria mensintesiskan ATP. [3 marks / 3 markah] Section C [30 marks] Bahagian C [30 markah] Answer any two questions in this section. Jawab mana-mana dua soalan daripada bahagian ini. 18. (a) Explain how the structures of collagen molecules are related to its functions. Terangkan bagaimana struktur molekul kolagen mempunyai kaitan dengan fungsinya. [5 marks / 5 markah] (b) Describe a procedure to separate the organelles of animal cell. Terangkan satu prosedur untuk mengasingkan organel-organel dari sel haiwan.[10 marks / 10 markah] 19. (a) Explain how enzymes lower the activation energy. Terangkan bagaimana enzim merendahkan tenaga pengaktifan. [8 marks / 8 markah] (b) Explain the similarities and differences of how oxidoreductase and transferase work with the help of examples. Terangkan persamaan dan perbezaan bagaimana oksidoreduktase dan transferase bertindak dengan menyebut contoh-contoh. [7 marks / 7 markah] 20. (a) Describe the structure of photosystems and explain how a photosystem functions in cyclic photophosphorylation. Huraikan struktur fotosistem dan terangkan bagaimana suatu fotosistem berfungsi dalam pemfotofosforilaan. [9 marks / 9 markah] (b) Explain briefly how reduced NADP is formed in the light-dependent stage of photosynthesis and is used in the light-independent stage. Terangkan secara ringkas bagaimana NADP penurun terbentuk dalam peringkat cahaya dan digunakan dalam peringkat bebas cahaya. [6 marks / 6 markah]

223 Biology Term 1 STPM Model Paper (964/1) Objective Questions 1. D 2. A 3. D 4. D 5. C 6. C 7. C 8. C 9. A 10. D 11. A 12. C 13. A 14. B 15. B Structured Questions 16. (a) Enzyme immobilisation is the technique of binding enzyme molecules to solid medium. Thus, the enzyme can be used continuously to carry out industrial process. (b) Adsorption (c) Entrapment (d) The enzyme molecules vibrate less as they are bound to solid. They are protected when the temperature is higher. They do not move about to be affected by other factors 17. (a) • It is a nucleotide. • It has adenine. • It has three phosphate groups. • It has a ribose. (b) • It is synthesised from ADP and inorganic phosphate (Pi ). • It is a soluble molecule and diffuses rapidly. • On hydrolysis of the third phosphate energy released. • It acts as an intermediary between energy yielding and energy requiring reactions. [maximum 3] (c) • It is synthesised by oxidative phosphorylation. • NADH moves to crista and transfers electrons to the electron transport chain. • H+ are pumped into the inter-membrane space to create H+ gradient. • Chemiosmosis resulting ADP and Pi forming ATP. Essay Questions 18. (a) • The structure of collagen consists of fibrous protein forming fibre to hold different tissues together as under the skin. • Each molecule of collagen is made up of only secondary structure twisted together with two similar molecules to have greater strength . • The tripolypeptide unit is further lengthened by disulfide bonds with similar units to form longer fibre for stronger binding of tissues. • Such collagen fibres can cross-linked together to form even larger fibres as found in the tendon and ligaments to produce high tensile strength. • Collagen fibres also cross-linked with other fibrous proteins for attachment firmly between two bones at the joints. (b) • The procedure to separate organelles is by differential centrifugation after the tissue such as liver is homogenised. • Homogenisation is by sophisticated ultrasound homogeniser to break up the cells without breaking organelles. • Chilled buffer is added before homogenisation to maintain the structures and functions of organelles and enzymes. • The homogenate obtained is centrifuged for 10 minutes at 600 g force so nucleic will be spun down. • The supernatant is then centrifuged at 10,000 g force for 20 minutes to spin down mitochondria, ER and Golgi bodies. • Then, the supernatant is further spun with 100,000 g force for 60 minutes to obtain ribosomes, microtubules and microfilaments. • The nuclei obtained may be mixed with unbroken cells that need further centrifugation to obtain higher concentration. • Similarly, mitochondria need to be separated from ER and Golgi bodies. • Ribosomes are most difficult to obtain as they exist as separated subunits or combined • To separate the two subunits of ribosomes, magnesium free buffer has to be used by ultracentrifugation using gel. 19. (a) • At body temperature, the barrier of activation energy prevents reaction e.g. the breakdown of glycogen to occur. • Enzyme e.g. phosphorylase lowers the barrier and permits the reaction to occur at that temperature. • Enzymes allow substrate to bind to their active sites to form complex. • Then the enzymes act directly or indirectly on the substrate molecules. • They break and reform certain bonds of the substrate to form the product. • An enzyme may bring two reactive substrate molecules together in its active site and a larger product is formed. • The enzyme molecule orientates two reacting substrate molecules so that the product can be easily formed. ANSWERS

224 Biology Term 1 STPM Model Paper (964/1) • The enzyme provides a micro-environment at the active site to change substrate to product. (b) • Both have active sites to bind to the substrate to form complexes. • Both involve at least two substrate molecules in which sub-atomic particles, atoms or molecules are transferred. • Both will break bonds of substrate before atoms or molecules are transferred. • Oxidoreductase transfers electron, H+ ion or oxygen atom whereas transferase transfer any molecule. • An example of oxidoreductase is cytochrome oxidase that transfers and combines electron, H+ ion and oxygen to form water whereas an example of transferase is hexokinase that transfers phosphate from ATP to glucose. • Another example is succinate dehydrogenase in which H+ ions are removed whereas another example of transferase is transaminase that transfers amino group from amino acid to a keto acid. • Dehydrogenase requires a hydrogen acceptor such as a coenzyme NAD+ or FAD whereas ordinary transferase does not require a coenzyme. 20. (a) • Photosystems have pigments arranged in light harvesting clusters. • The primary pigment chlorophyll a is at the reaction centre. • P700 is found in PI, absorbs at 700 (nm). • P680 is found in PII, absorbs at 680 (nm). • Accessory pigments, chlorophyll b and carotenoids, surround, primary pigment. • All accessory pigments can absorb light and pass energy to primary pigment. • PI is involved in cyclic photophosphorylation. • Light is absorbed results in electrons getting excited. • Electrons are emitted from P700. • The electrons are passed to the chains of electron carriers. • ATP synthesis occurs. • The electron returns to P700. (b) • Photolysis of water occurs. • The process releases H+. • This occurs at PII. • Electrons are released by PI. • Both combine with NADP to form NADPH. • NADPH is used to reduce PGA to become PGAL.

A absorption spectrum The graph of percent of light absorbed by a pigment plotted against wavelengths of visible light. action spectrum The graph of photosynthesis rate by a pigment plotted against wavelengths of visible light. activation energy The initial or minimum energy that must be possessed by atoms or molecules in order to react. active site The specific portion of an enzyme that attaches to the substrate by means of weak chemical bonds. active transport The movement of a substance across a biological membrane against its concentration or electrochemical gradient, with the help of ATP and specific transport proteins. adenosine triphosphate (ATP) An adenine-containing nucleoside triphosphate that releases free energy when its phosphate bonds are hydrolysed. adenylyl cyclase An enzyme that converts ATP to cyclic AMP in response to a chemical signal. aldehyde An organic molecule with a carbonyl group located at the end of the carbon skeleton. allosteric site A specific receptor site on an enzyme molecule that binds to chemical resulting a change in the shape of the enzyme, making it either more or less receptive to the substrate on the active site. alpha helix A spiral shape constituting one form of the secondary structure of proteins, arising from a specific hydrogenbonding structure. amino acid An organic molecule possessing both carboxyl and amino groups. amino group A functional group that consists of a nitrogen atom bonded to two hydrogen atoms that can act as a base in solution. aminoacyl—tRNA synthetases (synthases – USA) A family of enzymes, at least one for each amino acid, that catalyses the attachment of an amino acid to its specific tRNA molecule. amphipathic molecule A molecule that has both hydrophilic region and hydrophobic region. anabolism Within a cell or organism, the sum of all biosynthetic reactions in which larger molecules are formed from smaller ones. anaerobic Lacking oxygen; referring to an organism, environment, or cellular process that lacks oxygen. anticodon The triplet on one end of a tRNA molecule that recognises a particular complementary codon on an mRNA molecule. apical meristem Undifferentiated tissue in the tips of roots and shoots that where the cells can continue to divide. B basement membrane The layer of fine protein fibres beneath epithelial cells. buffer A substance that consists of acid and base forms in a solution and that minimises changes in pH when extraneous acids or bases are added to the solution. C C4 plant A plant that prefaces the Calvin cycle with reactions that incorporate CO2 into four-carbon compounds, the end-product of which supplies CO2 for the Calvin cycle. Calvin cycle The second of two major stages in photosynthesis involving atmospheric CO2 fixation and reduction of the fixed carbon into carbohydrate in a cyclic series of reactions. 225

Biology Term 1 STPM Glossary CAM plant A plant that uses crassulacean acid metabolism, an adaptation for photosynthesis in arid conditions where carbon dioxide entering open stomata during the night is converted into organic acids, which release CO2 for the Calvin cycle during the day, when stomata are closed. carbon fixation The incorporation of carbon from CO2 into an organic compound by an autotrophic organism. carbonyl group A functional group present in aldehydes and ketones, consisting of a carbon atom double-bonded to an oxygen atom. carboxyl group A functional group present in organic acids, consisting of a single carbon atom double-bonded to an oxygen atom and also bonded to a hydroxyl group. carotenoids Accessory pigments, yellow and orange, in the chloroplasts of plants; by absorbing wavelengths of light that chlorophyll cannot, they broaden the spectrum of colors that can drive photosynthesis. cartilage A type of flexible connective tissue with an abundance of collagenous fibers embedded in chondrin. cell fractionation The disruption of a cell and separation of its organelles by centrifugation. cell plate A double membrane across the midline of a dividing plant cell, between which the new cell wall forms during cytokinesis. cell theory All living things are composed of cells; cells arise only from other cells. chemiosmosis The production of ATP using the energy of hydrogen ion gradients across membranes to phosphorylate ADP. chemoautotroph An organism that needs only carbon dioxide as a carbon source but which obtains energy by oxidizing inorganic substances. chemosynthetic Applied to autotrophic bacteria that use the energy released by specific inorganic reactions to power their life processes, including the synthesis of organic molecules. cholesterol A steroid that forms an essential component of animal cell membranes and acts as a precursor molecule for the synthesis of other biologically important steroids. chromatin The complex of DNA and proteins that is soluble in water. codon A three-nucleotide sequence of mRNA that specifies a particular amino acid or termination signal. coenzyme An organic molecule serving as a cofactor working freely or attached with enzyme. cofactor Any non-protein molecule or ion that is required for the proper functioning of an enzyme. collagen A glycoprotein in the extra-cellular matrix of animal cells that forms strong fibres, found extensively in connective tissue and bone. competitive inhibitor A substance that reduces the activity of an enzyme by entering the active site in place of the substrate whose structure it resembles. concentration gradient A difference in the density of a chemical substance. condensation reaction A reaction in which two molecules become covalently bonded to each other through the loss of a small molecule, usually water; also called dehydration reaction. cork A secondary tissue that is a major constituent of bark in woody and some herbaceous plants; made up of flattened cells, dead at maturity; restricts gas and water exchange and protects the vascular tissues from injury. cytoskeleton A network of microtubules, microfilaments, and intermediate filaments that branch throughout the cytoplasm and serve a variety of mechanical and transport functions. cytosol The semi-fluid portion of the cytoplasm. D daughter cell A cell that is the offspring of a cell that has undergone mitosis or meiosis. 226

Biology Term 1 STPM Glossary denaturation For proteins, a process in which a protein unravels and loses its native conformation, thereby becoming biologically inactive. DNA polymerase An enzyme that catalyses the elongation of new DNA during replication by the addition of nucleotides to the existing chain. double helix The form of DNA with two adjacent polynucleotide strands wound into a spiral shape. E electric potential The difference in the amount of electric charge between a region of positive charge and a region of negative charge usually across a membrane. electron carrier Several membrane molecules in the electron transport chains that form ATP from ADP and inorganic phosphate. electron microscope (EM) A microscope that focuses an electron beam through or on the surface of a specimen, resulting in high resolution. electron transport chain A sequence of electron-carrier membrane molecules that shuttle electrons that used to make ATP from ADP and inorganic phosphate. enzyme A class of proteins serving as catalysts, chemical agents that change the rate of a reaction without being consumed by the reaction. equilibrium The state of a system in which no further net change is occurring; result of counterbalancing forward and backward processes. eukaryotic cell A type of cell with a membrane-enclosed nucleus and membrane-enclosed organelles, present in protists, plants, fungi and animals. eukaryote An organism whose cells contain membrane-bound organelles and whose DNA is enclosed in a cell nucleus and is associated with proteins. exocrine glands Glands, such as sweat glands and digestive glands, that secrete their products into ducts that empty onto surfaces, such as the skin, or into cavities, such as the interior of the stomach. exocytosis The cellular secretion of macromolecules by the fusion of vesicles with the plasma membrane. F facilitated diffusion The spontaneous passage of molecules and ions, bound to specific carrier proteins, across a biological membrane down their concentration gradients. FAD Abbreviation of flavin adenine dinucleotide, a cofactor which is a prosthetic group of succinate dehydrogenase. fatty acid A long carbon chain carboxylic acid. Fatty acids vary in length and in the number and location of double bonds; three fatty acids linked to a glycerol molecule form fat. fermentation A catabolic process that makes a limited amount of ATP from glucose without an electron transport chain and that produces a characteristic end-product, such as ethyl alcohol or lactic acid. fibrous protein Structural protein in which the polypeptide chain is coiled along one dimension to form strands or block. fluid mosaic model The model of cell membrane structure, which envisions the membrane as a mosaic of individually inserted protein molecules drifting laterally in a fluid bilayer of phospholipids. functional group A specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and usually involved in chemical reactions. G gel electrophoresis The separation of nucleic acids or proteins, on the basis of their size and electrical charge through an electrical field in a gel. globular protein A polypeptide chain folded into a roughly spherical shape and is soluble in water. glycogen An extensively branched glucose storage polysaccharide found in the liver and muscle of animals. glycolipids Lipids with a simple sugar or short carbohydrate chain 227

Biology Term 1 STPM Glossary glycoprotein A protein with covalently attached carbohydrate. Golgi apparatus An organelle in eukaryotic cells consisting of stacks of flat membranous sacs that modify and package material into vesicles. Gram stain A staining method that distinguishes between two different kinds of bacterial cell walls. H Haversian system One of many structural units of vertebrate bone, consisting of concentric layers of mineralised bone matrix surrounding lacunae, which contain osteocytes, and a central canal, which contains blood vessels and nerves. heat of vaporisation The amount of heat required to change a given amount of a liquid into a gas. heterochromatin A high proportion of histone mixed with DNA soluble in interphase nucleus. histamine A substance released by injured cells that causes blood vessels to dilate during an inflammatory response. histone A small protein with a high proportion of positively charged amino acids that binds to the negatively charged DNA to form chromosomes. hydrogen bond A type of weak chemical bond formed when the slightly positive hydrogen atom of a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule. hydrolysis A chemical process that splits molecules by the addition of water. hydrophilic Having an affinity for water. hydrophobic Having an aversion to water; tending to coalesce and form droplets in water. hydroxyl group A functional group consisting of a hydrogen atom joined to an oxygen atom by a polar covalent bond. Molecules possessing this group are soluble in water and are called alcohols. I induced fit The change in shape of the active site of an enzyme so that it binds more snugly to the substrate, induced by entry of the substrate. ingestion A heterotrophic mode of nutrition in which food is inserted into a cell or body. interleukin Proteins secreted by macrophages or helper T cells required in specific immune response. intermediate filament A component of the cytoskeleton that includes all filaments intermediate in size between microtubules and microfilaments. K Krebs cycle The second major stage in cellular respiration involving eight steps that completes the metabolic breakdown of glucose molecules to carbon dioxides within the mitochondrion. L lamella Layer, thin sheet. light-dependent reactions The reactions of the first stage of photosynthesis, in which light energy is captured by chlorophyll molecules and converted to chemical energy stored in ATP and NADPH molecules. light-independent reactions The carbon-fixing reactions of the second stage of photosynthesis; energy stored in ATP and NADPH by the light-dependent reactions is used to reduce carbon from carbon dioxide to simple sugars. light microscope (LM) An optical instrument with lenses that uses light to magnify images of specimens. light reactions The steps in photosynthesis that occur on the internal membranes of the chloroplast and convert solar energy to the chemical energy of ATP and NADPH, evolving oxygen in the process. lignin A polysaccharide mixed in the cellulose matrix forming hard impervious secondary plant cell walls. lipid One of a family of compounds, including fats, phospholipids, and steroids, that are insoluble in water. 228

Biology Term 1 STPM Glossary lipoprotein A protein bonded to a lipid; includes the low-density lipoproteins (LDLs) and high-density lipoproteins (HDLs) that transport fats and cholesterol in blood. lymphocyte A white blood cell that completes its development in the bone marrow forming B cell or the one that matures in the thymus is called T cell. M macromolecule A big biopolymer formed by the joining of smaller molecules, usually by condensation synthesis e.g. polysaccharides, proteins, and nucleic acids. macrophage A big white blood cell that moves through tissue, engulfing bacteria and dead cells by phagocytosis. meristem Plant tissue that are undifferentiated and can divide. mesophyll The ground tissue of a leaf, sandwiched between the upper and lower epidermis and is specialised for photosynthesis. messenger RNA (mRNA) A type of RNA synthesised using DNA as template specifies the primary structure of a protein. microfilament A solid rod of actin protein in the cytoplasm of almost all eukaryotic cells making up part of the cytoskeleton and acting alone or with myosin to cause cell contraction. microtubule A hollow rod of tubulin protein in the cytoplasm of all eukaryotic cells and in cilia, flagella, and the cytoskeleton. microvillus pl. microvilli One of many fine, fingerlike projections of the absorptive epithelial cells that increase their surface area. middle lamella A thin layer of adhesive extracellular material, primarily pectins, found between the primary walls of adjacent plant cells. monomer The subunit that serves as the building block of a polymer. monosaccharide The simple sugars, active alone or serving as a monomer for disaccharides and polysaccharides. myosin A type of protein filament that interacts with actin filaments to cause cell contraction. N NAD+ (nicotinamide adenine dinucleotide) Abbreviation of nicotinamide adenine dinucleotide, a coenzyme present to help enzymes transfer hydrogen atoms during respiration. NADP Abbreviation of nicotinamide adenine dinucleotide phosphate, a coenzyme that functions as an electron acceptor in the light dependent reactions of photosynthesis. nodes of Ranvier The small gaps in the myelin sheath between successive glial cells along the axon of a neuron; also, the site of high concentration of voltage-gated ion channels. Non-competitive inhibitor A substance that reduces the activity of an enzyme by binding to a location usually not the active site, changing its conformation so that it no longer binds to the substrate. Non-cyclic photophosphorylation The production of ATP by electron flow where the electron emitted does not return. nucleic acid A polymer consisting of many nucleotide monomers forming DNA or RNA. nucleoid region The region in a prokaryotic cell consisting of a concentrated mass of DNA. nucleolus A specialised structure in the nucleus, formed from various chromosomes and active in the synthesis of ribosomes. nucleoside An organic molecule consisting of a nitrogenous base joined to a five-carbon sugar. nucleosome The basic, beadlike unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound around a protein core of histone. nucleotide The building block of a nucleic acid, consisting of a five-carbon sugar covently bonded to a nitrogenous base and a phosphate group. O organelle One of several formed bodies with a specialised function, suspended in the cytoplasm and found in eukaryotic cells. 229

Biology Term 1 STPM Glossary osmosis The diffusion of water across a partially permeable membrane from a place of high water potential to a place of low water potential. oxidative phosphorylation The production of ATP from ADP and inorganic phosphate by electron transport chain in the presence of oxygen. oxygen debt In muscle, the cumulative deficit of oxygen that develops during strenuous exercise when the supply of oxygen is inadequate for the demand; ATP is produced anaerobically by glycolysis, and the resulting pyruvic acid is converted to lactic acid, which is subsequently metabolized when adequate oxygen is available. P pacemaker The sinoatrial (SA) node, a specialised region of the right atrium of the mammalian heart that sets the rate of contraction. palisade cells In plant leaves, the columnar, chloroplast-containing parenchyma cells of the mesophyll. parenchyma A relatively unspecialized plant cell type that carries out most of the metabolism, synthesises and stores organic products, and develops into more differentiated cell types. partial pressures The concentration of gases; a fraction of total pressure. passive transport The diffusion of a substance across a biological membrane without the use of ATP. peptide bond The covalent bond between two amino acid units, formed by condensation synthesis. peptidoglycan A type of polymer in bacterial cell walls consisting of modified sugars cross-linked by short polypeptides. Periderm (cork tissue) The protective coat that replaces the epidermis in plants during secondary growth. peroxisome A microbody containing enzymes that transfer hydrogen from various substrates to oxygen, producing and then degrading hydrogen peroxide. phagocytosis A type of endocytosis involving large, particulate substances. phloem The portion of the vascular system in plants consisting of living cells arranged into elongated tubes that transport sugar and other organic nutrients throughout the plant. phospholipids Lipid consist of a polar, hydrophilic head with phosphate bonded with glycerol and fatty acids forming non-polar, hydrophobic tails. phosphorylation Addition of a phosphate group or groups to a molecule. photoautotroph An organism that uses light energy to drive the synthesis of organic compounds from carbon dioxide. photorespiration A metabolic pathway that consumes oxygen, releases carbon dioxide, generates no ATP, and decreases photosynthetic output; generally occurs on hot, dry, bright days, when stomata close and the oxygen concentration in the leaf exceeds that of carbon dioxide. photosystem The light-harvesting unit in photosynthesis, located on the thylakoid membrane of the chloroplast and consisting of the antenna complex, the reaction-centre chlorophyll a, and the primary electron acceptor. pinocytosis A type of endocytosis in which the cell ingests extracellular fluid and its dissolved solutes. pith The core of the central vascular cylinder of monocot roots, consisting of parenchyma cells, which are ringed by vascular tissue; ground tissue interior to vascular bundles in dicot stems. plasma membrane The membrane at the boundary of every cell that acts as a selective barrier, thereby regulating the cell’s chemical composition. plasmid A small ring of DNA that carries accessory genes separate from those of a bacterial chromosome. Also found in some eukaryotes, such as yeast. plasmodesma pl. plasmodesmata An open channel in the cell wall of plants through which strands of cytosol connect from adjacent cells. plasmolysis A phenomenon in walled cells in which the cytoplasm shrivels and the plasma membrane pulls away from the cell wall when the cell loses water to a hypertonic environment. 230

Biology Term 1 STPM Glossary plastid One of a family of closely related plant organelles, including chloroplasts, chromoplasts, and amyloplasts (leucoplasts). pleated sheet One form of the secondary structure of proteins in which the polypeptide chain folds back and forth, or where two regions of the chain lie parallel to each other and are held together by hydrogen bonds. polar Having parts or areas with opposed or contrasting properties, such as positive and negative charges, head and tail. polar molecule A molecule (such as water) with opposite charges on opposite sides. polymerase An enzyme, such as DNA polymerase or RNA polymerase, that catalyzes the synthesis of a polymer from its subunits. polynucleotide A polymer made up of many nucleotides covalently bonded together. polypeptide A polymer (chain) of many amino acids linked together by peptide bonds. polysaccharide A polymer of up to over a thousand monosaccharides, formed by condensation synthesis. prokaryotic cell A primitive type of cell lacking a membrane-enclosed nucleus and membrane-enclosed organelles found only in bacteria. Q quarternary structure The particular shape of a complex protein with more than one polypeptide chain. R reducing agent The electron donor in a redox reaction. resolution The closest distance between two points can be distinguished as two separate points. respiration The breakdown and energy release from fuel molecules. ribonucleic acid (RNA) A type of nucleic acid consisting of nucleotide monomers with a ribose sugar and the nitrogenous bases adenine (A), cytosine (C), guanine (G), and uracil (U); usually single-stranded; functions in protein synthesis and as the genome of some viruses. ribosomal RNA (rRNA) The most abundant type of RNA together with proteins form the ribosomes structures. ribosome A cell organelle constructed in the nucleolus, functioning as the site of protein synthesis in the cytoplasm. Consists of rRNA and protein molecules, which make up two subunits. RNA polymerase An enzyme that links together the growing chain of ribonucleotides during transcription. S SA (sinoatrial) node The pacemaker of the heart, located in the wall of the right atrium. saturated fatty acid A fatty acid in which all carbons in the hydrocarbon tail are connected by single bonds with maximum number of hydrogen atoms that can attach to the carbon skeleton. sclereid A short, irregular sclerenchyma cell in nutshells and seed coats and scattered through the parenchyma of some plants. sclerenchyma cell A rigid, supportive plant cell type usually lacking protoplasts and possessing thick secondary walls strengthened by lignin at maturity. secondary structure The localised, repetitive coiling or folding of the polypeptide backbone of a protein due to hydrogen bond formation between peptide linkages. secretion The discharge of molecules synthesised by the cell. semilunar valve A valve located at the two exits of the heart, where the aorta leaves the left ventricle and the pulmonary artery leaves the right ventricle. sex chromosomes The pair of chromosomes responsible for determining the sex of an individual. sister chromatids Replicated forms of a chromosome joined together by the centromere and eventually separated during mitosis or meiosis II. smooth ER That portion of the endoplasmic reticulum that is free of ribosomes. 231

Biology Term 1 STPM Glossary sodium-potassium pump A special transport protein in the plasma membrane that transports sodium out of and potassium into the cell against their concentration gradients. somatic cell Any non-gamete (a sperm or egg) cell in a multicellular organism. spectrophotometer An instrument that measures the percent absorbance of light of different wavelengths and by a pigment solution. steroids A class of lipids characterised by a carbon skeleton consisting of four rings with various functional groups attached. striated muscle Skeletal voluntary muscle and cardiac muscle with striped appearance, which reflects the arrangement of contractile filaments. T tertiary structure Three dimensional shape of a protein molecule due to interactions of side chains involving hydrophobic interactions, ionic bonds, hydrogen bonds, and disulfide bonds. thylakoid A circular flattened membrane sac inside the chloroplast that are stacked to form a granum. tonoplast A membrane that encloses the central vacuole in a plant cell, separating the cytosol from the cell sap. tracheid A water-conducting and supportive element of xylem composed of long, thin cells with tapered ends and walls hardened with lignin. transcription The synthesis of RNA on a DNA template. transfer RNA (tRNA) An RNA molecule that picks up specific amino acids and recognising the appropriate codons in the mRNA. translation The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. turgid Firm as a result of the entry of water from a hypotonic environment. turgor pressure The force directed against a cell wall after the influx of water and the swelling of a walled cell due to osmosis. U unsaturated fatty acid A fatty acid possessing one or more double bonds between the carbons in the hydrocarbon tail reducing the number of hydrogen atoms attached to the carbon skeleton. V vacuole A membrane-enclosed sac taking up most of the interior of a mature plant cell and containing water and a variety of inorganic and organic substances. vascular Containing or concerning vessels that conduct fluid. vascular bundle In plants, a group of longitudinal supporting and conducting tissues (xylem and phloem). vascular cambium A continuous cylinder of meristematic cells surrounding the xylem and pith that produces secondary xylem and phloem. vascular tissue (xylem and phloem) Plant tissue consisting of cells joined into tubes that transport water and nutrients throughout the plant body. visible light That portion of the electromagnetic spectrum detected as various colours by the human eye, ranging in wavelength from about 400 nm to about 700 nm. W water potential The physical property determining the direction in which water will flow, governed by solute concentration and applied pressure. wavelength The distance between crests of waves, such as those of the light spectrum. X xylem The tube-shaped, non-living vascular tissue in plants that carries water and minerals from the roots to the rest of the plant. Y yeast A unicellular fungus that lives in liquid or moist habitats, primarily reproducing asexually by simple cell division or by budding of a parent cell. 232