IB Bio Unit C

Enzymes

A protein molecule that acts as a catalyst to increase the rate of a reaction

Lock and Key model

Enzymes are very specifically made to fit with a specific substrate (reactant molecule); its active site binds to the substrate, weakening the bonds and making them more susceptible to altering.

Substrate-active site collision

When a substrate and an active site come together.

Substrate vs. Enzyme movement

Most substrates are small and so move more than the enzyme. Some substrates are large and the enzymes have to move, ex. In DNA replication. Some enzymes are embedded in membranes and are immobilized so substrates must do all of the movement.

Enzyme-substrate specificity

The shape and chemical properties of an enzyme allowing substrate molecules to bind

Denaturation

When temperature or pH increases too greatly (for example), and the shape of the enzyme gets distorted and unable to bind to its substrate.

Catabolism

Breaking down molecules into smaller pieces. Ex. Digestion, cellular respiration

Anabolism

Condensation reaction. The synthesis of molecules to form larger simple ones. Ex. Protein synthesis, the creation of ATP

Enzymes effect on activation energy

decrease activation energy (but NOT enthalpy change)

Extracellular enzymes/Exoenzymes

Enzymes synthesized by ribosomes on the ER and released from the cell to work outside of it. Many break down large macromolecules to be able to pass through cell membranes. Ex. In the digestive tract. This is also how saprotrophs work

Intracellular enzymes

Enzymes synthesized by free ribosomes and work within the cell

Metabolic pathways

The steps which enzymes take to convert reactants into products. Can be cyclic like the Krebs cycle or linear

Inhibitors

Molecules that attach to the enzyme and reduce its ability to bind to substrates

Competitive inhibitors

Attach to the enzyme's active site, competing with the substrate to occupy the site. Ex. Carbon Monoxide (CO)

Non-competitive inhibitors

Attach elsewhere on the enzyme, changing its shape to make it not fit the substrate. Created during enzymic reactions, causing a negative feedback loop (make sure that enzyme does not create too many products)

Allosteric site

A second active site on enzymes where non-competitive inhibitors can bind and cause the enzyme to change shape

Feedback inhibition

Where the product of an enzyme reaction interferes with the enzyme in non-competitive inhibition, slowing down the rate of reaction so final products don't accumulate more than needed

Mechanism-based inhibition

Where a substance is similar to a substrate and permanently binds to the enzyme's active site through covalent bond. Can kill an organism. Some organisms synthesize these to kill others. Ex. Antibiotics, allelopathy

ATP (Adenine triphosphate)

A nucleotide which acts as the cell's energy currency. Soluble in water; Stable at pH levels close to neutral (cytoplasm); Cannot pass freely through the phospholipid bilayer and so can be controlled; Third phosphate group is easily removed and reattached through hydrolysis and condensation; Hydrolysing ATP provides a good amount of energy (enough for cell functions, not too much excess lost as heat)

ATP helps with

Synthesizing macromolecules, Active transport, Movement (mitosis, locomotion)

Aerobic respiration in humans and other animals and plants

Glucose + O2-> CO2 + H2O

Anaerobic respiration in humans, other animals and bacteria

Glucose -> Lactate

Anaerobic respiration in yeast and fungi

Glucose -> Ethanol + CO2

Aerobic vs. Anaerobic respiration

Anaerobic has lower yield (2 ATP/glucose vs. 34). All anaerobic are in the cytoplasm, while aerobic have most in the mitochondria. Aerobic can use fats, etc., while anaerobic can only use glucose.

Oxygen debt

The demand for oxygen that builds up during a period of anaerobic respiration

Electron carriers

Substances that can accept and lose electrons reversibly, often linking oxidations and reductions in cells.

Nicotinamide Adenine Dinucleotide (NAD)

The main electron carrier in respiration. NAD+ + 2H+ + 2 electrons -> NADH + H+. Reduced NAD

Glycolysis

Anaerobic process that breaks down the 6 carbons in glucose into 2 sets of 3 glucose called pyruvate. In the cytoplasm. Takes up one glucose and two ATP. Ends up with 2 pyruvate, 4 ATPs (total; 2 net), and 2 NADHs (reduction)

1.Phosphorylation (+ PO4^3-) to destabilize the glucose.

2.Converted into fructose. Glucose-6-phosphate -> Fructose-6-phosphate.

3.Phosphorylated again.

4.Lysis: Each fructose biphosphate is split to form two triose phosphates Fructose-1, 6-biphosphate -> 2 triose phosphate.

5.Oxidation: Each triose phosphate has a hydrogen atom removed, NAD is reduced, and a second phosphate group is attached

6.The acid's two phosphate groups are transferred to ADP, turning to pyruvate/pyruvic acid

Link Reaction

Between Glycolysis and the Kreb's cycle, in the matrix of the mitochondria. Results in Two acetyl CoA and two NADH+

1.Decarboxylation to turn pyruvate to a two-carbon molecule

2.Oxidation, removing two electrons to make an acetyl group.

3.Binding of the acetyl group to coenzyme A, creating acetyl coenzyme A.

FAD

Another electron and hydrogen carrier which accepts electrons and is reduced

Kreb's Cycle / Citric acid cycle

In the matrix of the mitochondria. Aerobic. The results from each pyruvate are: 3 CO2, 3 NADH, 1 FADH2, 1 ATP. From one glucose (total): 6 CO2, 6 NADH, 2 FADH2, 2 ATP (+ 2 ATP and 2 NADH from glycolysis)
1. Acetyl CoA acetyl groups are transferred to oxaloacetate, forming citric acid
2. Citric acid has two carbons removed in steps, releasing carbon dioxide. It eventually loops back to oxaloacetate.

Electron Transport Cycle

In the cristae of the mitochondria. Aerobic. Turns high electron to low by maintaining a proton gradient. 2.5 ATP per NADH. 1.5 ATP per FADH2
1.The first carrier accepts a pair of electrons from NADH, being reduced and oxidizing the electron carrier. FAD is accepted by a carrier with a higher affinity than the first.
2. These electrons pass from carrier to carrier, gradually releasing energy.
3. The three main carriers pump protons from the matrix to the intermembrane space. First second pump 4 protons per, 3rd pumps 2, total 10 per pair of electrons from NADH. The first carrier does not pump protons from FADH, so only 6 per pair of electrons

Terminal electron acceptor

Molecular oxygen, having the highest affinity and removing electrons from the last electron carrier to complete the process. Produce water in the process.

What happens in the ETC when oxygen runs out?

Electrons are not removed, so ETC are all reduced. NADH accumulates and oxidations stop.

ATP Synthase

A large and complex protein that phosphorylates ADP to produce ATP. Two main regions: Transmembrane subunits embedded in the inner mitochondrial membrane, allowing protons to pass through the membrane and absorbing their energy. Globular and projecting into the matrix, using energy from the protons to catalyse ATP production

Chemiosmosis

Using the proton gradient to synthesize ATP through the ATP synthase. The protons move down the concentration gradient back across the membrane and release energy, which the synthase uses to link a phosphate group to ADP and produce ATP.

Lactate fermentation

Occurs in aerobic beings, and is when NADH converts the pyruvate to lactate/lactic acid. NAD+ is recycled. When muscle cells are working strenuously, the energy exceeds aerobic capabilities; an excess of pyruvate is made without an ability to convert it through the Krebs cycle fast enough, and so it is fermented into lactic acid, which is stored in the muscles (causing cramps, etc.) or the liver until it can be turned back to pyruvate to continue the cycle.

How might animals replenish NAD+ stores?

Lactate fermentation

Fermentation

Anaerobic and occurs primarily in food cells. Ethanol fermentation: Occurs in facultative anaerobes. Pyruvate is converted to ethanal and CO2, and then two hydrogens are transferred from NADH to convert to ethanol. NADH oxidizes to NAD+.

How is fermentation used in baking

To create CO2 bubbles in dough and cause it to rise. Ethanol is cooked out.

How is fermentation used in brewing

To produce ethanol (CO2 rises to the surface and escape). Ends either when all sugar is used up or when ethanol concentration becomes toxic to the yeast.

How is fermentation used for commercial energy

Can be used to convert sugar cane and corn using yeast into bioethanol

Carbohydrates vs Lipids as respiratory substrates

Carbohydrates are capable of both aerobic and anaerobic respiration. Energy yield per gram is 17 kJ. This is less than lipids because over 50% of the mass is oxygen. Breaking down of fatty acids to acetyl groups requires oxygen (anaerobic respiration impossible). Energy yield per gram of aerobic is 37 kJ because nearly 90% of the mass is carbon and hydrogen.

Photosynthesis

The process of converting light energy into chemical energy in carbon compounds (carbs, proteins, lipids, nucleic acids). Carbon dioxide + water -> glucose + oxygen. Hydrogen is needed for this process

Photolysis

Splitting of molecules of water (oxidation) to provide hydrogen ions, oxygen, and electrons. 2H2O -> 4e- + 4H+ + O2

Pigments

Substances which absorb light. White/transparent substances are not pigments, absorbing no light. Black pigments absorb all light, transforming light energy into other forms (ex. Heat)

Photon

A particle or unit of light, a quantity of energy, related to its wavelength. Absorbed by pigment molecules and cause excitation.

Stroma lamellae

Unstacked thylakoids which form connections between thylakoids in grana

Photosystems

The structured arrays of clustered pigments are arranged in within the thylakoid membrane, typically 100 chlorophyll and 30 accessory pigments, as well as an electron-acceptor. Each has a core complex connected to light-harvested antenna complexes

Chlorophyll

The green pigment in chloroplasts, traps light energy. Does not absorb green or yellow light. Special chlorophyll transfers sunlight energy to photosynthesis

Fluorescence

When the light energy absorbed by a pigment is re-emitted as light when the electron drops back to its original energy level.

Reaction centre

A chlorophyll molecule which accepts electrons; all light energy from pigment molecules is passed on to the reaction centre

Advantages of structured arrays of pigments

Increased number of photons absorbed because photons are scattered. Variety of pigments can absorb different wavelengths. Precise and close orientation allows energy to be transferred without fluorescence

Photosystem II (PSII)

Photosystem mostly located in the thylakoid membranes.

P680

A special chlorophyll molecule in the reaction centre of PSII which emits excited electrons and regains them from water photolysis

Oxygen-evolving Complex (OEC)

Contains a group of Manganese, Calcium, and oxygen atoms in the core complex of PSII next to the thylakoid space. Facilitates photolysis when P680 chlorophyll is oxidized. The electrons are transferred to the reaction centre to replace P680, protons are released into the thylakoid space and contribute to a proton gradient, and oxygen diffuses through the cytoplasm and eventually out of the organism (or stomata)

Plastoquinone

An electron carrier in the thylakoid membrane, accepts excited electrons from PSII and two protons from the stroma, becoming plastoquinol.

Plastoquinol

Moves through the membrane to the cytochrome b6f complex, passes two electrons to the complex and two protons into the thylakoid space. Plastoquinol -> plastoquinone returns to photosystem II to collect more

Cytochrome b6f complex

Contains ETC which transfer electrons from the plastoquinol to plastocyanin.

Plastocyanin

Electron carrier, water-soluble and dissolved in the fluid space inside the thylakoid. Picks up an electron from the b6f complex and transfers it to the reaction centre of PSI.

Photosystem I (PSI)

Located in the stroma lamellae membranes. The electrons reaching PSI have lower energy than PSII since energy from them was used to pump protons.

P700

Special chlorophyll molecules in PSI that act as the primary electron donor.

NADP (nicotinamide adenine dinucleotide phosphate)

Identical to NAD but with an extra phosphate group. Reduced NADP is produced by photosystem I.

Light-independent reactions

The reduction of CO2 to glucose (potential chemical energy) with the use of ATP's energy and NADPH's reducing power

Calvin-Benson cycle

The series of reactions by which carbohydrates (such as glucose) are synthesized using NADPH and ATP in the stroma of chloroplasts

Carbon Dioxide Fixation

Converting CO2 to a more complex carbon compound to prevent diffusing out of photosynthesizing cells. The carbon atom in carbon dioxide is chemical bonded to RuBP

Rubisco (ribulose-1, 5-biphosphate carboxylase-oxygenase)

The enzyme which catalyses carbon fixation. Inefficient, so exists in very high concentrations, the most abundant enzyme.

Reduction in calvin-benson cycle

The three-carbon compounds are converted into a higher energy state by being activated by ATP and then reduced by NADPH. Hydrogen is added, the carboxyl group being replaced by an aldehyde group. This creates two molecules of Triose Phosphate. Some of the Triose Phosphate leave the cycle and may be used to make glucose; the rest move onto the next stage. To make glucose, the two are combined to form hexose phosphate, and hexose phosphate can be combined to form starch. This cycle must be completed six times (i.e. with 6 CO2) to synthesize one molecule of glucose. Six CO2 will create 12 triose phosphate molecules; 10 regenerate RuBP, while 2 are used to make glucose

Replacing RuBP

5/6 of the triose phosphate produced, using ATP to convert triose phospahte -> ribulose phosphate -> RuBP

Transport in calvin-benson cycle

Glucose is converted to sucrose for transport. When glucose cannot be transported, it is converted to starch and stored temporarily. When photosynthesis has stopped, the starch is broken down and the glucose is transported.

What can triose phosphate be turned into in the calvin-benson cycle?

Fatty acids, using glycolysis enzymes and link reaction to produce acetyl coA and then linking two-carbon acetyl groups. Glycerol can be made to produce triglycerides. Other carbon compounds can also be produced, although mineral nutrients such as phosphate are often needed to make any other compounds.

How many amino acids can plants synthesize and why?

20 because of the calvin-benson cycle

Limiting steps in photosynthesis

In low light intensity, conversion of glycerate 3-phosphate is limiting. In high light intensity, carbon fixation is limiting.

Absorbance spectrum

A graph that shows the relative amounts of light of different colours that a compound absorbs

Action spectrum

Shows the relative effectiveness of different wavelengths of light for promoting photosynthesis

Free air Carbon Dioxide Enrichment Experiments (FACE)

Experiments which test CO2 concentration on plants in regular conditions. In progress. Attempting to decipher how carbon dioxide impacts plants, as concentration in the air has doubled since the industrial revolution and will likely continue

Banded iron formations

Sedentary rocks formed from iron oxide, caused by iron in the oceans being oxidized by oxygen from photolysis in cyanobacteria

Receptors

Proteins with a site to which a signaling chemical can bind, changing the receptor to stimulate a response

Ligand

A molecule that binds selectively to a specific site on another molecule

Ligand-binding site

The site on a receptor to which a ligand binds

Similarities in enzymes and receptors

Binding occurs at a specific site. Shape and chemical properties of the ligand-binding site match those of the ligand. Enzymes and receptors are unchanged by the binding of a ligand

Differences in enzymes and receptors

Substrates change when they bind to enzymes. Binding is brief. It cycles. Signaling chemicals do not change. They can remain for a long time.

Quorum

A fixed number of individuals needed for a meeting to go ahead.

Quorum sensing

Assessing whether a population is large enough for a group activity. Many bacteria switch behavior when population density rises. Signaling molecules are secreted at a low rate by all cells and diffuse freely, binding to receptors in each cell. When there has been sufficient binding of signaling molecules, gene expression is changed and activities change.

Example of quorum sensing

Vibrio Fischeri. Bacteria which are mutualistic with squid. Provide bioluminescence in large colonies (lessens visibility contrast to the sky) in exchange for amino acids and sugar from the squid. i. Release an autoinducer into the extracellular environment. ii. This binds to LuxR in the cytoplasm in other bacterial cells. iii. After a certain threshold, transcription of DNA synthesizes luciferase. iv. Luciferases catalyzes oxidation that releases energy as bioluminescence.

Hormones

Signaling chemicals produced by specialized cells in glands and transported through the bloodstream. Promote or inhibit certain processes. Long-lasting effect.

Forms of hormones

Amines, peptides, steroids

Endocrine glands

Glands which secrete hormones into the bloodstream, typically capillaries within the gland

Exocrine glands

Glands which secrete hormones out through a duct

Signalling chemicals

Hormones, neurotransmitters, cytokines, and calcium ions

Neurotransmitters

Chemicals that transmit signals across synapses. Secreted by presynaptic and receives by postsynaptic.

Types of neurotransmitters

Amines, gas (nitrous oxide), amino acid (glutamate, glycine)

Synapses

Junctions between two neurons in the nervous system.

Cytokines

Small proteins that act as signaling chemicals. Some can be secreted by almost all cells. Act on the cell that produced them or on a nearby cell. Bind to transmembrane receptors. Roles in inflammation and other immune system responses as well as in cell growth and embryo development.

Calcium ions used for cell signaling in muscle fibers

Ions are pumped into the sarcoplasmic reticulum and generate a high concentration. Calcium channels open in the membrane and ions diffuse out, binding to troponin and causing them to change position to expose actin sites. After nerve impulses stop, calcium is pumped back into the sarcoplasmic reticulum.

Calcium ions used for cell signaling in neurons

Nerve impulse at a presynaptic membrane causes calcium channels to open, diffusing inwards and causing secretion of a neurotransmitter through exocytosis. They are then pumped back out of into the synaptic cleft.

Signaling chemicals must

Have a distinctive shape and chemical properties. Be small and soluble enough to be transported

Intracellular receptors

Located in the cytoplasm or nucleus, have signaling chemicals pass through the plasma membrane. Hydrophilic and so remain dissolved

Active Ligand-Receptor complex

Regulates gene expression by binding to DNA at specific sites, promoting or inhibiting the transcription of particular genes. Is formed when signaling chemicals bind to intracellular receptors

Transmembrane receptors

Located across the membrane with a region extending to the cytoplasm, have signalling chemicals bind on the exterior. Hydrophobic on the surface, attracted to the phospholipids, but hydrophilic in the area inside the cell. Has its shape changed, the inner site becoming catalytically active and producing a secondary messenger. The secondary messenger conveys the signal to effectors, carrying out responses.