IB Bio- Year 1 Summative

Outline the steps of glycolysis

1. Phosphorylation

   1. Glucose + 2ATP → fructose- 1,6-bisphosphate.

   2. ATP is converted into ADP as phosphate group from each ATP attached to the 6C molecule fructose 1,6-bisphosphate (unstable molecule). This makes glucose more unstable (usually very stable) and hence lower activation energy of the reaction.

2. Lysis

   1. The unstable fructose- 1,6- biphosphate (phosphorylated 6C) splits into 2 molecules of 3C (triose phosphate)

3. Oxidation

   1. Hydrogen is removed from each molecule triose phosphate by dehydrogenase enzyme and transferred to coenzyme NAD⁺ (nicotinamide adenine diphosphate) to reduced NAD⁺ (NADP) to form G3P (glycerate-3-phosphate)

4. ATP Formation

   1. Phosphates are transferred from intermediate substrate molecules to form 4 ATP through substrate-link phosphorylation (4 inorganic P + 4 ADP → 4 ATP) 2 molecules of pyruvate = end product (used in next pathway)

   Net gain: 2 ATP, 2 pyruvate, 1 NADP

Outline the steps of anaerobic respiration (alcohol fermentation of yeast)

1. Decarboxylation

   1. Pyruvate from glycolysis removes 1 C to form CO₂

   2. This forms a 2C molecule. (x2 for the other pyruvate molecule) 

2. Oxidation 

   1. NADH from glycolysis is oxidized into NAD which turns the 2C into ethanal = hydrogen acceptor of NADH . This is done by alcohol dehydrogenase 

   2. Ethanal is oxidized again to form ethanol. 

Net gain:

• 2 CO₂

• 2 ethanol 

Outline the steps of anaerobic respiration (lactate) and its function

1. Oxidation Pyruvate from glycolysis is the hydrogen acceptor of NADH (the H⁺). NADH is oxidized into NAD⁺ by lactase dehydrogenase which forms lactate

2. Function. Used in humans when lack of air (exercise). However too much can built up lactate into form of lactic acid which can fatigue muscle.

Outline the steps of the link reaction

Occurs if there is enough oxygen available.

1. Enters to mitochondrial matrix for aerobic respiration.

2. Oxidative carboxylation 2 pyruvate from glycolysis is decarboxylated (removes C) to form 2C compound.

3. 2C compound is oxidized by NAD which reduces it to NADH CoA Coenzyme-A attaches to 2C carbon to form acetyl coenzyme A (acetyl CoA) which enters Krebs Cycle.

Outline the steps of Krebs Cycle

1. Removal of Coenzyme-A

   1. Acetyl CoA’s enzyme is removed. 4C compound from previous Krebs Cycle (oxaloacetate) is joined together to form a 6C compound called citrate

2. Decarboxylation

   1. Citrate is decarboxylated, losing one carbon in the form of CO2. This forms a 5C intermediate. NAD+ is also reduced into NADH by oxidizing the 5C compound.

   2. 5C is converted into a 4C by another decarboxylation (releasing another CO2) and reducing another NAD to NADH 4C undergoes several transformations.

   3. NAD reduced to NADH. FAD reduced to FADH₂ Undergoes substrate-level phosphorylation. (ADP to ATP)

Net products: 1 ATP, 3 NADP, 1 FADH₂, 1 oxaloacetate (redo cycle), 3 CO₂

Outline the steps of electron transport chain in mitochondria

Takes place in inner-membrane of mitochondria

1. Coenzymes

   1. NADH and FADH₂ from Krebs Cycle carries high energy H⁺ ions and electrons 

2. Electron is transported

   1. NADH donates electrons to first protein complex in inner membrane of mitochondria → oxidixed into NAD⁺

   2. FADH₂ donates electrons further down the chain (later carrier) so it produces less ATP

3. Electrochemical gradient

   1. As electrons move along the chain it releases energy that is used to pump protons from NADH and FADH₂ (H⁺ )into the matrix of the innermembrane space

   2. Electrons stay within innermebrane space but H⁺ are pumped out = builds potential energy

4. Chemiosmosis and ATP Production

   1. H⁺  is impermeable to inner membrane and can only go through an enzyme called ATP synthase. 

   2. ATP synthase has ADP and inorganic phosphate attached. H+ goes through the synthase = generates energy to join ADP and inorganic phosphate to form ATP. This process is called chemisomosis.

5. Oxygen as final electron acceptor

   1. At the end of chain electrons are removed to prevent chain from flowing by combining 4H⁺+ and 4 electrons → water.

   2. Without oxygen, ETC can’t pass its electrons so it remains reduced meaning that it prevents carriers from accepting electrons (needs to get rid of spare electrons for new electrons to go through ETC)

   3. As a result NADH and FADH₂ can’t donate electrons and can’t be recylced into NAD⁺ and FAD that are needed for earlier steps of respiration = no glycolysis/Krebs Cycle/ETC = no ATP

Net yield:

Large amounts of ATP per glucose molecule

Outline the steps of cell respiration

1. Glycolysis (cytoplasm)

2. Link Reaction (mitochondrial matrix)

3. Aerobic Respiration OR Krebs Cycle (mitochondrial matrix)

4. Electron Transport Chain (inner membrane of mitochondria)

List the abiotic factors that affect organisms with their habitat

• Salinity

• Temperature

• pH 

• Humidity

• Cloudiness/Turbidity of water  

• Oxygen/CO₂ concentration

• Soil composition

• Light intensity/wavelength

List the adaptaion of leaves for gas exchange in plants

• Waxy cubicle: Prevents water vapor and gas from leaving through the epidermis. Controls gas exchange and water loss.

• Epidermis: Contains stomata for gas exchange. Mostly found in lower epidermis where the temperature is lower which reduces water loss.

• Veins: Xylem vessles transports water necessary for photosyntehsis and transpiration. Photosynthesis requires carbon dioxide to diffuse into the leaf and transpiration involves the loss of water vapor.

• Stomatal guard cells: Controls the opening and closing of stomata which controls gas exchange and water loss

• Air space: Maintain a concentration gradient between

• Spongy mesophyll: Increases SA for gas exchange

List the different tissues in leaves

• Epidermis tissue

  • Formed by single layer of cells (upper and inner that protects inner part of leaf)

  • Lower epidermis has stomata surrounded by 2 guard cells that control gas exchange. Allows diffusion of O₂ and CO₂ gas. 

  • Guard cells becomes turgid when water enters and changes shape = opens stomata. Becomes flaccid when water is lost = water close. 

  • Covered by waxy layer (cuticle) which forms an impermeable barrier 

• Mesophyll tissue

  • Formed by parenchyma cells 

  • Contains chloroplasts where photosynthesis occurs. 

  • Palisade mesophyll= contains chloroplasts for photosyntehsis

  • Sponge mesophyll= contains large aire space between upper epidermis. 

• Vascular tissue 

  • Arranged in vascular bundles 

    • Forms veins in leaves: xylem transports water + mineral ions from roots to leaves, phloem transports products of photosynthesis from leaves to other parts of plants 

List the adaptation of xylem vessels for transport of water: 

• Dead, hollow cells = continuous water column (water molecules can maintain continuous contact via cohesion/adhesion) 

• Lignin (prevents collapse of xylem). Rings alongside xylem. Thickened cellulose wall of xylem strengthened by lignin polymer. Can withstand very low internal pressures without collapsing 

• Pits. Water can pass through and move sideways between vessels. Even if vessel is damaged, water can flow into another vessel and still reach leaves 

Distribution of tissues in a transverse section of stem: 

Xylem: water transport

Phloem: transport of nutrients and organic products from photosynthesis 

Parenchyma: 

• Cortex: Structural support and transport/store nutrients 

• Pith = bulk (no function)  

Vascular bundle: Xylem + Phloem

Epidermis: Thin one cell layer that protects cell and allows semi-permeability of certain substances such as CO₂ and O₂ for photosynthesis  

Cambium: Secondary growth (width) by providing non specialized stem cells 

Endodermis: Boundary between vascular tissue and cortex in root 

List the adaptation of phloem sieve tube and companion cells for translocation of sap: 

Purpose: Efficient translocation(movement) of sugars, amino acids, and other solutes from source (ex: leaf) to sink (ex: root/fruit) via phloem 

Source: Plant oran where photosynthesis occurs 

Sink: Plant organ that requires/stores sugars such as roots/fruits

Assimilate: Products of photosynthesis. Molecules that are being transported 

1. Sieve tubes: Transport pathways for sugars/organic compounds  

   1. Sieve plates: little holes for continuous movement of organic compound 

   2. Cellulose cell wall: strengthens wall to withstand hydrostatic pressure 

   3. No nucleus/vacuole/ribosome: maximizes space for translocation 

   4. Thin cytoplasm: reduces friction for more facilitated movement of assimilate 

2. Companion cells: Load and unload sugars in and out of sieve tubes 

   1. Nucleus/other organelles: Regulate metabolic activities 

   2. Transport proteins: Moves assimilates in and out of cell 

   3. Many mitochondria: ATP for active transport of assimilates in and out of companion cells. 

   4. Plasmodesmata: Link between sieve tube elements for assimilates to move from companion cells to sieve tube

Outline the steps of translocation in cells (phloem) 

Translocation is the loading/unloading of sucrose/other organic compounds from source to phloem 

1. Loading assimilate from source to sink with aid of water from xylem

   1. Active transport loads organic compound into phloem

   2. Water provide hydrostatic pressure that allows assimilate to travel down to roots/other parts of cell to sink due to high concentration of solutes in phloem.  Water comes from neighbouring xylem. 

2. Unloading in sink

   1. Assimilate from phloem goes into sink via companion cell, lowering water potential of cells at sink 

   2. Water moves back to xylem by osmosis = maintain hydrostatic pressure gradient between source and sink

Describe the generation of root pressure in xylem vessels by active transport of mineral ions: 

1. Mineral ions actively transported with ATP into cells of the root cortex and into xylem vessels. 

2. This causes solute concentration in xylem vessels to increase 

3. Water comes from surrounding root cells via osmosis =  hydrostatic pressure (root pressure) through xylem = used for water uptake 

List the advantages and disadvantages of transpiration:

Advantages

• Cooling of plant via transpiration (water evaporates = absorbs heat energy = reduce leaf temperature) 

• Uptake of mineral ions (transpiration pulls water + dissolved minerals from roots to rest of plant 

• Maintain water flow (cont. Stream of water 

• Turgor maintenance (cell rigidity + structure) 

Disadvantages

• Water loss (excessive transpiration in dry/windy conditions = wilting/dehydration)

List the factors for the rate of transpiration: 

Air temperature

• Higher temperature = higher transpiration because high water vapor has more kinetic energy and move around faster so they are likely to move out of the stomata by diffusion 

 

Humidity

• More humidity = decreases transpiration because environment contains high concentration of water vapor = less water diffuse out of leaf (high to low concentration of water) 

Light Intensity

• Higher light intensity = higher rate of transpiration because stomata open more for photosynthesis = more gas exchange (water diffuse out) 

Wind speed

• High wind speed = higher rate of transpiration because water molecules diffuse out of stomata more quickly/blown away from leaf = concentration gradient and more water vapor diffuse out 

Explain how abiotic factors determine range of tolerance: 

• Abiotic factors such as temperature, oxygen/CO₂ concentration, water availability, wind speed, and light intensity impact range of tolerance because it impacts species’ survivability 

• Every species has a range of tolerance 

  • Optimum range where they grow + reproduce best

  • Survive in conditions in a bit above/below

  • Conditions go too far outside the range = not survive 

• Specialists = narrow tolerance range. Survive/thrive in specific conditions

• Generalists = wide tolerance range. Can survive in many environments 

List the adaptations of marram grass in sand dunes (including the challenge and adaptation to overcome it) 

Challenges: Low water availability, high salt/solute concentration, low nutrient levels 

Adaptations: 

• Thick waxy cuticle (waterproof layer that covers epidermis) 

• Sunken stomata in puts to trap water vapor 

• Rolled leaf to prevent exposure of surfaces to wind. Traps water vapor inside rolled leaf. It also has tiny hairs that can trap water

List the adaptations of tress in mangrove swamps (including the challenge and adaptation to overcome it)

Challenges: High salinity, low oxygen availability, low fresh water availability  

Adaptations:

• Aerial root system = parts of roots above water = take in oxygen for respiration  

• Red mangrove = prop roots (stability in unstable soil) + no entry of salt into water-transport systems 

• Black mangrove= Pneumatophores structure that grow vertically up out of water-logged soil & salt water into cells + excrete excess salt through salt glands on leaves

List the conditions required for coral reef formation

Coral reefs:

• Symbiotic relationship between coral polyp (anima) and zooxanthellae algae. Polyp = shelter and algae = photosynthesis + C compound production 

Distribution:

• Limited because coral reefs has narrow range of tolerance for abiotic factors

  • Water depth: Coral reefs can only be form in  shallow depths where light can penetrate water at high enough levels for zooxanthellae to photosynthesize 

  • pH: Too high pH = calcium carbonate of polyps can cause it to dissolve. Corals need carbonate ions to build calcium carbonate. H⁺ ions are only present in low pH levels. 

  • Salinity: Requires slaty water withing 32-42% range

  • Water clarity: Water must be clear enough for light to pass through 

  • Temperature: Low range of temperature (20-28˚C) tolerance. Rising sea temperature causes polyps to expel zooxanthellae = coral bleaching

Define biome and relation to its ecosystems inside it:

• large community of organisms that occurred due to environmental factors. Occurs in large geographical areas. 

• Named after dominant vegetation type. 

• Avg temp + precipitation (rain fall patterns) = sig. Factors in development of biome 

• Climotraph = mean annual rainfall + temperature 

• Ecosystem in biome are very similar

  • Convergent evolution (diff species with diff ancestors adapted to shared abiotic factors + same geographical/environmental challenges) 

List the adaptations of cactus in hot deserts (including the challenge and adaptation to overcome it)

Challenges: Low water availability, hot day and cold night

Adaptations: 

• Thick waxy cuticle = reduce water loss by evap. 

• Spines instead of leaves (reduces SA for water to be lost)

• Cell in stem can expand and store water

• Deep tap root = access to water deep underground. Shallow surface root = fast absorption of water from rainfall 

List the adaptations of fennec fox in hot deserts (including the challenge and adaptation to overcome it)

Challenges: High temperatures, limited water excess, sandstorms 

Adaptations: 

• Large ears (large SA) that have blood vessels that regulates body heat and cool 

• Nocturnal= active at night when it’s cooler

• Kidneys concentrate urine = reduce water loss. Most water is from food

Distinguish between obligate anaerobe, obligate aerobes, and facultative anaerobes: 

Obligate anaerobe: Requires environment with no oxygen in order to survive (ex: skin bacteria) 

Obligate aerobe: Requires environment with continuous supply of  oxygen to survive (ex: plants/animals) 

Facultative anaerobe: Can live in both anaerobic or aerobic environment (ex: yeast)

Define and outline the steps of holozoic nutrition:

Holozoic nutrition = for heterotrophs who requires organic molecules from tissues of other organism. Involves internal digestion 

1. Ingestion=eating 

2. Digestion= breaking down large molecules into smaller molecules 

3. Absorption= transport of molecules from digestive tract to cells 

4. Assimilation= using molecules to build cells + tissues

5. Egestion= waste product excreted 

Distinguish between heterotrophs, autotrophs,  mixotrophs and saprotrophs: 

1. Heterotrophs/Consumers 

   1. Every animal 

   2. Herbivore + Carnivore 

2. Autotrophs

   1. Producers. Synthesizes own nutrients/organic molecules without absorption from other organic molecules

   2. Mainly done by photosynthesis 

3. Mixotrophs

   1. Can do more than one method of nutrition (autotrophy/heterotrophy) 

   2. Obligate mixotrophs: Constantly access to both methods 

   3. Facultative mixotrophs: Survive using only one and supported with another. 

      1. Euglena (single-cell eukaryote) = takes in bacterial cells by endocytosis + digests them using enzymes in lysosomes. Also has light sensitive spot for photosynthesis 

      2. Coral 

4. Saprotrophs

   1. Mostly fungi + bacteria (decomposers) 

   2. Digestion of dead organism/waste material (NOT like detritivores that feed on organic dead material) 

   3. Secretes wide range of digestive enzymes onto food and digests externally

   4. Products of digestion = mineral ions (ammonium + phosphate) and leaves some minerals to surrounding soil for absorption by other organisms 

   5. Without saprotrophs = all nutrients will be in dead/waste matter that is never released. 

Distinguish the nutrients of phototrophic archaea, chemotrophic archaea, and heterotrophic archaea:  

1. Phototrophic archaea

   1. Photoheterotrophs = gain carbon compounds to build cell structure from other organisms. ATP/energy from photosynthesis 

   2. Converts light energy to chemical energy via photosynthesis (proton gradient achieved that produces ATP by ATP synthase = very similar to phosphorylation) 

   3. NOT the same as plant photosynthesis by 

2. Chemotrophic archaea 

   1. Chemoautotrophs = Releases energy from chemicals + produces own carbon compound 

   2. Chemosynthesis = releases energy from chemicals that is transferred to carbon compound. C compound used for ATP synthesis 

   3. Chemicals that are energy sources = hydrogen sulfide, methane, hydrogen gas, ammonia 

   4. Some directly use energy from chemicals for ATP synthesis (chemoheterotrophs = use chemicals to produce ATP but gain C compound from other organisms) 

3. Heterotrophic archaea 

   1. Using energy from breaking down organic compounds from other organisms. Use carbon carbonds to generate Atp 

Explain the relation of dentition and diet:

• Humans are part of hominidae family with gorilla, chimps, orangutans 

• Study of skulls = jaw + dentition/teeth of each species are specialised to particular diet 

  • Chimps = small jaw muscles (softer fruit + animals tissue)

  • Gorilla = strong jaw muscles for biting/griding tough vegetation

• Incisor teeth = cutting/biting

• Canine teeth = pointed + holding/tearing

• Premolar/molars = flat/ridged for grinding 

• Scientists use dentistry to determine diet + ecosystem of extinct species (not super accurate because teeth ≠ always what species eat like humans teeth more like plant-eaters but eat lots of meath, teeth can also be used for competing with mates/defending territory) 

List the adaptions of herbivores in insects and mammals (with examples): 

Insect

• Caterpillar/grasshopper/beetle has mandible mouth part = cut through leaves

• Aphid has stylets that pierce through plant tissues to reach sugary sap in phloem. 

Mammals 

• Flat teeth in order to chew plants

• Rudimentary mammals have specialised stomach with different compartments for increased digestion of plant + specialized community of bacteria in digestive tract for breakdown of cellulose 

• Digestive enzymes in saliva like deer that breaks down plants even more 

• Cautionary sampling = allows to eat new plant without digesting as many toxins for harm

• Neutralizes toxins from plants like deer (protein in saliva that binds to tannis toxin) 

List the plant adaptations against herbivory in plants

Plants can’t move away from herbivores. Herbivory = cause damage to plant leaves = less photosynthesis

1. Mechanical deterrents

   1. Sharp spines (cactus) 

   2. Thick bark = no pierce plant stems

   3. Many tiny hairs on leaves = difficult to pierce in plant tissue 

   4. Nettles have tiny hairs with toxin = irritates skin 

2. Toxin secretion

   1. Tannin toxic = bitter taste + bad impact on digestive 

   2. Alkaloid chemicals (caffeine + nicotine) = toxic effect on growth + nerve impulse 

   3. Foxgloves produce digitalis = affects heart rate of animals 

List the adaptions of prey(with examples):  

1. Chemical

   1. Scent camouflage

      1.  Mongoose = chemical to prevent predator from detecting them 

   2. Toxins

      1. Taste bad/cause harm (poison dart frog + skunk) 

2. Behavioral

   1. Preference for dark/shelter

      1. Avoidance of predator 

   2. Avoidance of location/time

      1. Different activity at day/night depending on predator’s life cycle

   3. Group 

      1. Individual animals difficult to pick out

      2. Mob a predator/attack to drive it away

      3. Warn others (warning call) 

   4. Bluffing 

      1. Pretend to be dead (opossums) 

      2. Appear to be much larger than reality 

3. Physical 

   1. Sense organs

      1. Ability to sense predators nearby 

   2. Body features 

      1. Camouflage (looks like stick) 

      2. Warning colours (confuse/scare predator) 

      3. Mechanical defense (strong calcium shell) 

List the adaptations of trees/lianas/epiphytes/strangler epiphytes/shade tolerant shrubs/herbaceous plants for harvesting light:

Trees

• Prioritizes height in order to get the max amount of sunlight

• Canopy = uppermost layer of plants. Some trees may grow above main canopy. 

• Photosynthesis at high rate to get molecules needed to grow quickly + compete with other plants 

Lianas

• Grows on trunks of trees 

• Roots reaches to soil in order to get nutrition

• Competes with trees for light/nutrients/moisture 

Epiphytes

• Gain nutrients from high in canopy 

• Uses height of trees to increase sunlight absorption by growing high in tree branches. 

• Does not have roots in soil 

• Moss gains water + nutrients from rainwater on tree bark 

Strangler epiphytes

• Begins life at a canopy and grows roots downard to forest floor, allowing them to gain nutrients/water from soil 

• Some orchids have aerial roots and takes nutrients directly from air

• Strangler fig can grow both up+downwards to maximized resources. Can sometimes kill tree hosts by taking all resources 

Shade tolerant shrubs/herbaceous plants 

• Absorb limited range of wavelengths of light only (different photosynthetic pigments) 

• Large leaves to max SA 

• Flowers are brightly coloured/strongly scented for pollinators to recognize clearly 

• Shrubs = woody stems/not tall like trees

• Herbaceous plants (herbs) = no woody stems = soft tissues + turgid cells for support

List the adaptions of predators (with examples):  

1. Chemical

   1. Toxins (snake)

      1. Haemotoxic= circulatory system 

      2. Neurotoxic = nerves

   2. Chemical mimicry (allure prey animals) 

   3. Scent crypsis/camouflage (ambush predators to not be detected by prey) 

2. Behavioral

   1. Pack (cooperate with each other to increase chance of success) 

   2. Ambush (Wait without moving for extended periods and wait for prey to come near like crocodiles) 

   3. Pursuit (use speed like cheetahs/persistent hunting like wolves)  

3. Physical 

   1. Excellent vision (birds of prey that can detect prey movement) 

   2. Body structure 

      1. Long, sharp teeth (catch/hold prey for carnivorous mammals) 

      2. Long limbs/flexible spins for running fast (cheetah) 

      3. Streamline body shape = swimming (swordfish) 

Define what a niche is and distinguish between realized niche and fundamental niche:

Niche- Role of species in environment influenced by biotic (prey/predator) and abiotic factors(oxygen/carbon dioxide is exchanged). One species = one role or else competition. 

Fundamental niche: 

• Full range/possible ways for species to grow without predators + competition  

• Large size

Realized niche: 

• Actual size/range of species 

• Smaller size due to predators and competition 

Define competitive exclusion:

• When two species try to compete with other for one niche. 

• Outcomes: 

  • Other species is extinct/out-competed

  • Other species is forced to occupy a similar different niche 
    

Describe the advantages of light harvesting system for photosynthesis: 

• LHC is part of photosystem which is known as reaction centre as it is where photosynthesis begins. 

• LHC located in thylakoid membrane of plant cells. It contains pigments and accessory pigments that absorb light energy for photosynthesis

  • Pigments(chlorophyll a and b) absorbs red and blue-violet wavelengths from sun

  • Accessory pigments (xanthophyll and carotene) absorbs red wavelengths

• Consists of enzymes that catalyzes formation of ATP from ADP and phosphate & converts oxidized hydrogen carrier NADP⁺ to reduced NADPH + H⁺ 

• Electron carrier molecules 

Distinguish between cyclic and noncyclic photophosphorylation:

Cyclic photophosphorylation: 

• Photosystem I only

• Electron is recycled back to chlorophyll 

• No NADPH production 

• No photolysis

• No oxygen released

• ATP production when NADPH is abundant and not enough NADP⁺ that can be reduced to NADPH 

1. Light hits PI and electrons are excited

2. Electrons pass to ferredoxin (protein) which are electron carriers that transfer electrons back to PSI. During this process 2 ADP is converted to 2 ATP (phosphorylation). 

Noncyclic photophosphorylation (normal light-dependent pathway): 

• Both photosystem I and II 

• Electrons are transferred to NADP⁺ to make NADPH

• Supplies ATP and NADPH for Calvin Cycle  

Outline the steps of light dependent reaction in photosynthesis:

Occurs in the thylakoid membrane of the chloroplast. 

1. Hydrolysis

   1. Light energy causes water molecule to split into hydrogen and oxygen. 

2. Photosystem II 

   1. Pigments (chlorophyll a = primary and b) and accessory pigments such as carotene and xanthophyll absorb red and blue-violet light causing electrons from hydrogen during hydrolysis in photosystem II to be excited 

   2. Excited electrons are passed to electron transport chain in inner membrane of thylakoid

3. ETC and ATP Formation

   1. Electrons flow through ETC, generating energy for H⁺ ions from water into the thylakoid lumen. 

   2. Chemiosmosis is the process in which protons goes against concentration gradient through ATP synthase to produce ATP. By going through ATP synthase, H⁺ ion generates energy needed to join ADP and P_i into ATP. 

4. Photosystem I and NADPH production 

   1. Electrons continue down the transport chain to PSI and gets re-excited by light energy

   2. Excited electrons are used to reduce NADP⁺ to NADPH  which are used for light independent reaction for glucose production. 

Outline the steps of light independent reaction in photosynthesis: 

Occurs in the stroma of the cytoplasm of cell. Depends on ATP and NADPH produced by light dependent reaction.   

1. Carboxylation

   1. Enzyme Rubisco fixes C from CO₂ to 5C molecule called RuBP (ribulose biphosphate) resulting in an unstable 6C molecule

   2. 6C molecule is broken down into two 3C molecules called 3-PGA (3-phosphoglycerate)  

2. Reduction

   1. 3-PGA is phosphorylated by ATP (additional phosphate group added) and reduced by NADPH to form G3P (glycerate-3-phosphate/triose phosphate). Reduced NADPH becomes NADP⁺

3. Organic carbon molecule formation

   1. For every 3 turns of cycle (3 CO₂) = 6 G3P molecules produced (2 each cycle). 1 G3P exits cycle to be made into glucose and other carbohydrates (sucrose, starch) and other 5 is used to regenerate RuBP (5C molecule) 

4. RuBP Regeneration

   1. The remaining 5 G3P (3C each) are rearranged using ATP into 3 RuBP molecules (15C TOTAL)  

Net yield for glucose (3 cycles)

• 1 G3P

• 3 RuBP 

• 6 ADP 

• 6 NADP⁺

Net input: 

• 3 CO₂ 

• 6 ATP (total of six 3-PGA molecules formed)

Describe water potential/solute(osmotic) potential/pressure potential

Water potential 

• Tells where water will flow/move (tendency to move from high solute to low solute concentration) 

• Measured in kPa 

• Relative to pure water at atmospheric pressure (20˚C). Pure water = 0kPa. 

• High water potential = low solute concentration = positive water potential because less water molecules form H-bonds with solute molecules = more water flow/energy 

• Low water potential =  high solute concentration = negative water potential because water molecules form H-bond with solute molecules = less “free” water (in bond now) = less energy available  

• Total water potential = Solute - pressure potential  

Solute/osmotic potential (Ψ_s) 

• Effect of solute on water potential

• Pure water = 0 solute potential 

• Solutes are added to solution = solute potential decreases = more negative 

Pressure potential 

• Physical pressure of water

• Plant cells = positive because of cell wall’s ability to withstand turgor pressure 

• Xylem vessels = negative due to tension (pulling forces during transpiration) 

Distinguish between turgid, flaccid, and plasmolyzed: 

Turgid- Hypotonic solute concentration (inside of cell has higher solute concentration than outside so water moves in). Plant cells are able to withstand water uptake due to strong cell walls but animals cells = cell lysis 

Flaccid- Isotonic solute concentration (solute concentration outside + inside = same)  

Plasmolyzed- Hypertonic solute concentration (outside of cell has higher solute than inside so water moves out). Plant cells: membrane pulls away from cell wall = wilting. Animal cell = cell shrinks 

Explain epigenesis and how it relates to cell differentiation. Distinguish between epigenetics, epigenesis, epigenome, and epigenetic tags : 

• Epigenesis

  • Process in which single-celled zygote develops into complex multicellular organism with specialised cells.

  • Determined by genome of DNA

• Epigenetics

  • Study of heritable changes in gene expression (no alteration to DNA sequence) 

  • Genetic control by factors other than DNA sequence such as chemical modification to chromatid (condensed DNA) called epigenetic tags 

    • Methylation: addition of Acetyl group 

    • Acetylation: addition of CH₃ group 

    • Phosphorylation: addition phosphate group  

• Epigenome

  • All epigenetic tags in organism

  • Epigenome is heritable

Explain the methylation of DNA:

• Histone proteins condense DNA into chromatids.  

• Methyl groups are added to amino acids of histone that can activate/deactivate the gene expression 

• Can also be added to DNA directly

• Methyl group of cytosine bases of promoter region

• Suppresses transcription of inhibited gene by suppression transcription factors 

• Affected by environmental factors such as air pollution, stress, exposure to chemicals etc. that can cause methyl groups to be added which alters the gene expression

Explain imprinting in epigenesis and tigons/ligers: 

• During egg/sperm development, epigenetic tags are removed (mostly) and removes methylation patterns from environmental influences 

• Imprinted gene = Some epigenetic tags are passed down to next generation 

• Tigons

  • Same size/smaller than parents. Female lion discourage growth 

• Ligers

  • Bigger size than parents because lion male encourage growth genes

Outline the role of glycoproteins and ABO blood types:

• Chemical signaller for cell-to-cell recognition. 

• Receptors for cell signalling (hormones/neurotransmitters) 

ABO blood types:

• Acts as antigens that can identify “self” and “not self”

• Not self triggers immune response. Incorrect blood = clumped together + block blood vessels 

• Blood types:

  • Antigen A only accept antibody A  

  • Antigen B only anti-B

  • Antigen AB none 

  • Antigen O all (universal blood donor) 

Outline the role/structure of triglycerides:

• 3 fatty acids joined to 1 glycerol molecule. 1 fatty acid = saturated, other unsaturated 

• Ester bond between OH group of glycerol molecule with COOH of fatty acid

• Ester bond is formed by condensation reaction (water molecule release). 

List the differences between saturated and unsaturated fatty acids:

Saturated

• Single bonds 

• High melting point because packed tightly (solid at room temp) 

• More unhealthier fat because  it can build up lots of cholesterol (bad) 

• Energy storage common in animals

• Straight chains 

Unsaturated 

• At least one double bond

• Low melting point because of kink (can’t pack tightly) = liquid at room temp 

• Healthier fat because improve cholesterol levels 

• Monosaurated = 1 double, poly = more than 2 

• Energy storage common in plants 

• Bent chains from double bond 

List the structure of glycogen, cellulose, and starch:

Glycogen

• Storage polysaccharide in animals  (excess glucose) 

• Made of highly branched 1,4 and 1,6 glycosidic bonds between α-glucose molecules

• More terminal glucose molecules = break down quickly for metabolic needs  

Starch 

• Storage polysaccharide in plants (excess glucose) 

• Made of amylose and amylopectin 

  • Amylose = unbranched, 1,4 glycosidic bonds between α-glucose molecules = compact

  • Amylopectin = branched, 1,4 and 1,6 glycosidic bonds between α-glucose molecules = compact. End = terminal glucose molecules 

Cellulose

• Structural carbohydrate in cell wall of plant (provides strengths + rigidity in plant cell) 

• Straight chain, made of 1,4 glycosidic bonds between β-glucose (H is at bottom of 1’ C) = alternative/inverted structure to form bonds (1 up, other down) 

• Individual chains are bonded together by hydrogen bonds 

• Insoluble in water but water adheres to it

Outline the structure of insulin, collagen, globular/fibrous proteins:

Globular

• Circular + compact 

• Soluble in water because hydrophilic R groups on outside which interact with water molecules 

• Non-polar hydrophobic R group inside 

Insulin 

• Globular protein

• Controls blood glucose levels 

• Has beta

• 2 polypeptide chain (A has 21 amino acid residues + B has 30 amino acid residues) that are held together by 3 disulfide bridges  

Fibrous

• Long strands of polypeptide chains with cross-linkages due to H-bonds

• No tertiary structure

• Large number of hydrophobic R group = insoluble 

• Fibrous = very repetitive amino acid sequence (limited #) = very strong structural (keratin in hair/nails + collagen in connective tissue) 

Collagen 

• Fibrous protein 

• Flexible structure that can form connective tissue (tendons, ligaments, etc.) 

• Insoluble = hydrophobic R group 

• Made of 3 polypeptide chains held together by H-bonds that forms triple helix (lots of tensile strength) + covalent bond that cross links between R groups to make fibrils

• Fibrils are staggered = strength.

List the different structures of proteins and examples

1. Primary structure

   1. Linear sequence of amino acid  that determines the protein shape

   2. Peptide bonds between adjacent amino acids

   3. Determines 3D shape 

 

2. Secondary structure

   1. Formation of complex shape of alpha-helix and beta-pleated sheets

      1. Alpha = coiled shape between amino acids that are close in sequence  

      2. Beta= formed by adjacent polypeptide strange aligned side by side 

   2. Weak H-bonds between COOH and amino groups. Non-adjacent amino acids = change in shape of 

3. Tertiary structure

   1. Interaction between R groups of amino acids

      1. Ionic bond (charge base on H⁺, disulfide bridges, hydrophilic/hydrophobic bonds, H-bond between amino acid/carboxyl groups 

   2. Very specific shape that is important for function (receptor sites in cell membrane/active sites in enzymes) 

4. Quaternary structure

   1. Multiple polypeptide chains

   2. Conjugated proteins (polypeptide + non polypeptide prosthetic group)

      1. Haemoglobin. 

         1. Has haem group that has iron ion (where oxygen binds to) 

         2. Alpha and beta globin subunit (2 pairs of identical chains). 4 in total 

   3. Non-conjugated proteins 

      1. Insulin = 2 chains (A + B) that are held by disulfide bridges 

      2. Collagen= fibrous protein made of 3 polypeptide chains in helix shape

Outline the function/structure of HIV/COVID/Bacteriophage lambda: 

HIV

• Circular shape 

• Antigen binding 

• Antigenic shift 

• 2 RNA strands

• Protein capsid

• Protein (enzyme reverse transcriptase that allows production DNA from viral RNA = retrovirus) 

• Transmitted by direct exchange of body fluids 

  • Blood donation 

  • Sexual intercourse 

• Viral envelope that has lipid bilayer + glycoprotein that act as attachment proteins. Made of host helper T cells 

COVID

• Circular shape 

• Single stranded RNA 

• Envelope outside of capsid 

• Many glycoproteins projecting on exterior 

• Causes respiratory diseases in mammals + birds (transmitted 

Bacteriophage lambda

• Head with capsid that has double-stranded DNA strand 

• Tail + fibre attaches it to host and inject genetic info into cell 

Outline the steps of cytokinesis in plant and animal cells:

Animals:

1. Cleavage furrow formation

   • The cell membrane begins to indent at the center (equator) of the cell.

   • This indentation is called the cleavage furrow.

2. Actin and myosin ring contraction

   • A contractile ring made of actin and myosin proteins forms beneath the membrane.

   • The ring contracts, pulling the membrane inward.

3. Furrow deepens

   • The cleavage furrow deepens progressively as the contractile ring continues to tighten.

4. Separation of cytoplasm

   • The cell is pinched in two, separating the cytoplasm into two daughter cells.

5. Two distinct daughter cells formed

   • Each daughter cell contains a nucleus and roughly equal share of cytoplasm and organelles.

Plants:

1. Vesicle formation

   • Vesicles derived from the Golgi apparatus gather at the center of the cell.

2. Cell plate formation

   • The vesicles fuse to form a cell plate across the middle of the cell.

3. Expansion of the cell plate

   • The cell plate grows outward, eventually reaching and fusing with the existing cell membrane.

4. New cell wall formation

   • The vesicle contents contribute to the construction of a new cell wall (primary wall) between the daughter cells.

5. Two daughter cells formed

   • Each daughter cell is separated by a new section of cell wall, completing cytokinesis.

Outline how vesicles are formed

Types of Vesicles:

1. Peroxisomes

   • Contain enzymes to break down fatty acids and detoxify harmful substances.

2. Lysosomes

   • Contain lytic (digestive) enzymes to digest cellular waste, damaged organelles, or pathogens.

3. Transport vesicles

   • Move molecules within the cell (e.g., between the ER and Golgi).

4. Secretory vesicles

   • Carry substances to the cell membrane for exocytosis (e.g., hormones, neurotransmitters).

Role of Clathrin in Vesicle Formation (Clathrin-Mediated Endocytosis)

1. Clathrin-coated pit formation

   • Clathrin proteins accumulate on the inner surface of the plasma membrane, forming a curved structure called a clathrin-coated pit.

2. Receptor binding

   • Receptor proteins in the membrane bind to specific target molecules (ligands) outside the cell.

3. Pit invagination

   • As more target molecules bind, the pit deepens with the help of the cytoskeleton (actin filaments) and accessory proteins.

4. Vesicle budding

   • The pit eventually pinches off from the membrane, sealing the target molecules inside.

5. Vesicle formation

   • A clathrin-coated vesicle is now free in the cytoplasm, carrying its cargo.

   • Later, the clathrin coat is shed, and the vesicle fuses with the appropriate compartment (e.g., endosome or Golgi)

Outline genetic variation in meiosis

Outline: Genetic Variation in Meiosis 1. Random Orientation (Independent Assortment) – Metaphase I

• During metaphase I, bivalents (paired homologous chromosomes) line up at the cell equator.

• Spindle microtubules grow from opposite poles and attach to centromeres.

• Each homolog in a bivalent is connected to a different pole.

• The orientation of each bivalent is random—either the maternal or paternal chromosome can face either pole.

• The orientation of one bivalent is independent of the others.

• This leads to independent assortment of chromosomes, producing many possible combinations of maternal and paternal chromosomes in gametes.

➡ Result: Different gametes receive different combinations of chromosomes → genetic variation.

2. Crossing Over – Prophase I

• In prophase I, homologous chromosomes pair up in a process called synapsis, forming a bivalent.

• Each chromosome is made of two sister chromatids, so a bivalent contains four chromatids.

• Crossing over occurs between non-sister chromatids (one from each homolog).

• The chromatids break and rejoin at the same location, forming a chiasma (pl. chiasmata).

• This exchanges alleles between maternal and paternal chromatids.

➡ Result: New combinations of alleles on each chromatid → recombinant chromosomes → increased genetic diversity.

3. Importance of Genetic Variation

• Both crossing over and random orientation create genetically unique gametes.

• This variation is essential for:

  • Natural selection

  • Adaptation to changing environments

  • The evolution of species