Bio C1 (Enzymes/Metabolism, Cell Respiration, Photosynthesis)

C1.1.1 What is the role of enzymes as catalysts?

Enzymes are biological catalysts;
that speeds up reactions;
in living cells;
which allows reactions to occur at much lower temperatures than would be possible otherwise;

C1.1.2—What is metabolism? What is the role of enzymes in metabolism?

metabolism is the complex network of interdependent and interacting chemical reactions occurring in living organisms;
because of enzyme specificity (where one enzyme catalyses on reaction);
many different enzymes are required by living organism;
control over metabolism can be brought about through these enzymes;

C1.1.3—What are anabolic reactions? (Anabolism)

anabolic reactions are those that build up larger molecules from smaller ones;
when macromolecules are built from from monomers by condensation reactions;
including protein synthesis, glycogen formation and photosynthesis;

C1.1.3 What are catabolic reactions? (Catabolism)

catabolic reactions are those that break down larger molecules into smaller ones;
this include hydrolysis of macromolecules into monomers in digestion;
and oxidation of substrates like glucose in respiration;

C1.1.4 What is an active site? What is its role in enzyme catalysis?

An active site is composed of a few amino acids only;
and is part of a globular protein's structure;
many interactions between amino acids within the overall three-dimensional structure of the enzyme ensure that the active site has the necessary properties for catalysis;
the active site binds to substrates;
allowing for reactions to occur;

C1.1.5 How do interactions between substrate and active site to allow induced-fit binding?

As substrates bind to active sites;
both substrate and enzymes change shape;
so that bonds within the substrate are weakened;
in this way the fit is induced;
allowing for catalysis to take place; at a lower energy level than normal;

C1.1.6 What is the role of molecular motion and substrate-active site collisions in enzyme catalysis?

Molecular motion is required for enzyme-substrate collisions to occur successfully;
in order for reactions to occur;
substrates need to collide with the enzyme active site with sufficient energy and at the correct orientation;
however, enzymes can be immobilised by being embedded into membranes;
and sometimes large substrates are immobilised, with enzymes colliding with them instead; e.g. glycogen which is too large to move;

C1.1.7—What is the relationship between the structure of the active site, enzyme-substrate specificity and denaturation?

active sites are have a precise shape;
due to the amino acids that make them up;
leading to a shape that only fits a particular substrate;
they are therefore highly specific;
with one enzyme fitting one substrate(s);
if the shape changes due to denaturing, then the shape of the active site no longer fits the substrate;
leading to a loss of activity of the enzyme;

C1.1.8—What are the effects of temperature on the rate of enzyme activity?

increased temperature increases the chance of enzyme substrate collisions;
so enzyme activity increases as temperature increases;
up to an optimal temperature;
beyond the optimum temperature, increased molecular motion leads to disruption of intermolecular interactions;
loss of tertiary and secondary structure;
therefore changes shape of active site;
so it can no longer bind to substrate;
leading to decreased activity;
until enzyme is completely denatured; and there is no activity;

C1.1.8—What are the effects of pH on the rate of enzyme activity?

altering pH can alter intermolecular interactions within the protein;
between R groups;
e.g. hydrogen bonding;
or within the active site;
enzymes have an optimum pH;
away from this optimum, enzyme activity decreases;
this can be irreversible, leading to total loss of activity;

C1.1.8—What are the effects of substrate concentration on the rate of enzyme activity?

the more substrate, the more product forms;
more substrate-active site collisions;
more substrate can bind to the enzyme active site, so therefore rate of reaction increases;
after a point, all enzyme active sites are bound to substrate (full occupancy of enzyme active sites);
additional substrate will not lead to a greater rate of product formation at this point;

C1.1.9 How can we measurements the rate of enzyme-catalysed reactions? How is it calculated?

by measuring either product formation in a given time;
or substrate usage;
1/time taken gives a measure of the rate of the reaction;

C1.1.10 What is activation energy? What are the effects of enzymes on activation energy?

Activation energy is the amount of energy required to allow a particular reaction to occur;
energy is required to break bonds in substrates;
energy is given out when bonds are formed;
the overall yield (net amount) of energy released or taken in by a reaction can be calculated or shown on a graph;
enzymes reduce the amount of activation energy required;
this means reactions can happen at s sufficient rate at much lower temperatures;

C1.1.11— HL ONLY - What are intracellular and extracellular enzyme-catalysed reactions? What is an example of each?

Intracellular enzyme catalysed reactions take place in cells;
e.g. glycolysis in the cytoplasm and Kreb's cycle in the mitochondria;
extracellular enzyme catalysed reactions take place outside of cells;
e.g. chemical digestion in the gut;

C1.1.12— HL ONLY -What is generated by all reactions of metabolism? Why is this inevitable? How is this useful?

heat generation is inevitable;
because metabolic reactions are not 100% efficient in energy transfer;
Mammals, birds and some other animals depend on this heat production for maintenance of constant body temperature;
homeostasis;

C1.1.13— HL ONLY —What are the two major types of pathway in metabolism?

linear, where one product becomes the reactant in the next reaction;
proceeding to a final product;
e.g. glycolysis
and cyclical, where the final product is again fed back to become the reactant in the first step;
e.g. Krebs cycle and Calvin cycle;

C1.1.14— HL ONLY -What are allosteric sites? What is non-competitive inhibition of enzymes?

allosteric sites are binding site(s) away from the active site of an enzyme;
non-competitive inhibitors are substances that can bind to allosteric site;
this binding is reversible;
the binding causes conformational (shape) changes in the enzyme due to interactions (with tertiary and secondary structures);
which change the shape of the active site enough to prevent catalysis;
reducing the rate of reaction;
but non competitive inhibitors not compete with substrate for the active site;

C1.1.15— HL ONLY -What is competitive inhibition? What is an example of one?

competitive inhibition is when a molecule structurally similar to the substrate binds to the active site;
this prevents the substrate from binding;
eg Statins;
where they compete for the active site of an enzyme involved in cholesterol synthesis, therefore reducing it;

C1.1.15— HL ONLY - How do competitive inhibitors affect the rate of reactions? What does the graph look like and why?

Because non-competitive inhibitors bind at allosteric sites, away from the active site, they do not compete for the active site with the substrate;
they are therefore their binding is not affected by substrate concentration in the same way as competitive inhibitors;
this means inhibition of enzyme activity is maintained even at very high substrate concentration;
meaning a lower rate of enzyme activity; at all substrate concentrations;

C1.1.16— HL ONLY - How are metabolic pathways regulated by feedback inhibition? Use isoleucine as an example

a non-competitive inhibitor binds to allosteric site;
non-competitive inhibitor changes shape of active site;
non-competitive inhibitors do not compete with substrate for the active site;
this means end-product of a pathway can inhibit enzyme needed for the first step in metabolic pathway;
this is negative feedback since increased level of product formation decreases rate of its own production;
the metabolic pathway regulated according to the requirement for its end-product;
the inhibition is reversible;

e.g. Isoleucine is end product;
binds to threonine deaminase enzyme;
stopping threonine from being converted;
which is turn stops production of isoleucine;

C1.1.17— HL ONLY - How is penicillin an example of mechanism-based inhibition? What does it block?

penicillin binds irreversibly;

to transpeptidase enzymes in bacteria;

which are involved in cell wall synthesis;

by creating cross-links between cell wall polysachharides;

penicillin therefore weakens the cell wall and they burst;

killing bacteria;

C1.1.17— HL ONLY - How does resistance to penicillin develop in bacteria?

mutations can occur in bacteria which change the shape of the transpeptidase enzymes;
therefore penicillin cannot bind;
and cell walls are synthesised as normal, making the bacteria penicillin resistant;

C1.2.1—What is the molecule that distributes energy in cells?

ATP;

the full name being adenosine triphosphate;

is a nucleotide that serves as the primary energy carrier in cells;

Its structure, with three phosphate groups, allows for the easy release and storage of energy;

ATP's properties, such as its ability to release energy quickly and in small manageable amounts;

make it ideal for use as the cellular energy currency;

C1.2.2—What life processes within cells are supplied with energy by ATP?

ATP provides energy for various cellular processes including active transport across membranes;

anabolism (synthesis of macromolecules);

the movement of the whole cell;

or cell components, such as chromosomes;

contraction of muscles;

C1.2.3—How is energy released and stored by ATP?

Energy is released when ATP is hydrolyzed to ADP (adenosine diphosphate);

and a phosphate; known as Pi;

Conversely, synthesizing ATP from ADP and phosphate requires energy input;

C1.2.4—How is ATP produced in cells using energy released from carbon compounds? What is the process?

Cell respiration is a biochemical process that produces ATP;

by releasing energy from carbon compounds like glucose and fatty acids;

cell respiration is distinct from gas exchange as it involves a series of reactions that convert biochemical energy from nutrients into ATP; not just breathing in and out;

C1.2.5—What are the differences between anaerobic and aerobic cell respiration in humans?

Anaerobic respiration occurs without oxygen;

producing less ATP and yielding lactic acid as a waste produce;

primarily in the cytoplasm;

Aerobic respiration requires oxygen;

occurs in mitochondria;

and produces more ATP along with carbon dioxide and water as waste;

Both processes use glucose, but only aerobic respiration requires mitochondria;

C1.2.6—What variables affecting the rate of cell respiration?

The rate of cell respiration can be influenced by various factors such as;

temperature, availability of substrates, and oxygen concentration;

Experimental measurements and calculations from data can determine the respiration rate, through measuring oxygen use or carbon dioxide production;

HL ONLY - C1.2.7—What is the role of NAD in cell respiration, particularly in relation to hydrogen and oxidation?

NAD (Nicotinamide adenine dinucleotide) acts as a hydrogen carrier; in cell respiration;

Oxidation occurs when hydrogen, along with its electron, is removed from a substrate (dehydrogenation);

thereby oxidizing the substrate;

NAD is reduced when it gains hydrogen;

HL ONLY - C1.2.8— What is the process used to convert glucose to pyruvate in and what are the products?

In glycolysis;

glucose is converted to pyruvate through stepwise reactions involving phosphorylation; which is adding phosphate;

lysis; breaking the molecule apart;

oxidation; removing hydrogen and oxygen;

and ATP formation;

Each step is catalyzed by a different enzyme;

the net yield is a small amount of ATP and reduced NAD;

Describe glycolysis - IB Question

Occurs in the cytoplasm;

Two ATP used to phosphorylate glucose (phosphorylation);

the glucose is broken down (lysis) into two three-carbon pyruvate molecules;

through removing hydrogen (which has electrons) and adding them to NAD+ (NAD);

this is oxidation of glucose;

with a net yield of 2 pyruvate and 2 ATP;

as four ADP are phosphorylated into four ATP*;

and two reduced NAD (NADH) are produced;

HL ONLY - C1.2.9—How is pyruvate converted to lactate in anaerobic respiration, and why is this significant?

In anaerobic respiration;

pyruvate is converted to lactate to regenerate NAD;

allowing glycolysis to continue.;

This process yields a net of two ATP molecules per glucose molecule;

and is essential for energy production when oxygen is not available;

HL ONLY - C1.2.10—What is the role of anaerobic respiration in yeast, and how is it utilized in brewing and baking?

Anaerobic respiration in yeast is similar to humans except for pyruvate is not used to regenerate NAD;

pyruvate is further broken down;

producing carbon dioxide and alcohol;

The final products of this process are utilized in brewing;

and carbon dioxide makes bread rise in baking;

HL ONLY - C1.2.11—What is the link reaction? Where does it happen? What is produced as a result?

pyruvate enters the mitochondria;

the link reaction occurs in the matrix of the mitochondria;

enzymes remove carbon from pyruvate;

this is decarboxylation;

pyruvate is converted to acetyl CoA;

by joining to CoA enzyme;

by oxidative decarboxylation; (as pyruvate is oxidised as it loses electrons);

Reduced NAD (NADH) and CO2 formed;

fatty acids also can be converted to acetyl CoA;

acetyl CoA then enters the Krebs cycle;

HL ONLY - C1.2.12—What happens in the Krebs cycle? Where does it happen? What is formed as a result?

Krebs cycle occurs in matrix of mitochondria;

acetyl CoA enters the Krebs cycle:

acetyl group (2C) joins a 4C sugar;

oxaloacetate;

to form a 6C sugar;

citrate;

the 6C sugar is then turned into a 5C sugar;

by oxidative decarboxylation;

four oxidations happen and 2 decarboxylations;

oxidation is via dehydrogenation, removing hydrogen from citrate;

which are added to NAD and FAD;

which are reduced by the addition of hydrogen;

to Reduced NAD and Reduced FAD;

decarboxylation is removing carbon dioxide from the sugars;

producing CO2;

the 5C compound is then turned back into the 4C compound oxaloacetate; by oxidative decarboxylation;

What is the net yeild from Krebs?

2 x CO2 are produced per molecule of pyruvate;

3 x reduced NAD and one FADH2 per molecule of pyruvate;

one ATP is produced by substrate-level phosphorylation per molecule of pyruvate;

NADH and FADH2 provide electrons to the electron transport chain;

HL ONLY - C1.2.13—How is energy transferred to the electron transport chain in the mitochondrion? What is made there?

Energy is transferred when reduced NAD;

passes a pair of electrons;

to the first carrier in the electron transport chain;

the electrons carry energy;

the NAD is converted back to NAD;

Reduced NAD is comes from glycolysis, the link reaction, and the Krebs cycle;

HL ONLY - C1.2.14—What is energy from electrons used to do in the electron transport chain? IB essay statements

the electron transport chain receives energy from oxidation reactions from Krebs cycle and glycolysis;

in the form of electrons from Reduced NAD and Reduced FAD;

energy is released as electrons pass from carrier to carrier (in the chain);

the release of energy (from electron flow) is coupled to proton pumping;

protons are pumped into inter-membrane space;

this creates a proton gradient;

HL ONLY - C1.2.15—What is chemiosmosis and how is it lnked to ATP production?

chemiosmosis is the coupling of the energy from the proton gradient; with the production of ATP by ATP synthase;

the protons diffuse down their concentration gradient (across the membrane);

the protons pass through ATP synthase;

the protons return to the matrix;

the flow of protons provides energy for generating ATP;

HL ONLY - C1.2.16—What is oxygen's role in aerobic respiration? Why do we need it for respiration?

In aerobic respiration, oxygen acts as the terminal electron acceptor in the electron transport chain;

the electrons are transferred to oxygen at end of electron transport chain;

It accepts electrons and protons from the matrix of the mitochondrion to produce metabolic water,;

allowing the continuous flow of electrons along the chain; which would otherwise stop due to a build up;

HL ONLY - C.1.2.17—What are the differences between lipids and carbohydrates as respiratory substrates?

Lipids yield more energy per gram compared to carbohydrates;

due to their higher content of oxidizable hydrogen and carbon;

Glycolysis and anaerobic respiration occur only if carbohydrate is the substrate;

with 2C acetyl groups from fatty acids entering the pathway via acetyl-CoA;

C1.3.1—What is photosynthesis? What transformations of energy take place? Using what reactants?

Photosynthesis transforms light energy into chemical energy;

Chlorophyll absorbs light energy;

enabling the synthesis of glucose and oxygen;

from water and carbon dioxide;

this is the way carbon compounds are created;

providing chemical energy for life processes in ecosystems;

C1.3.2—How is carbon dioxide converted into glucose? What else is required?

Using hydrogen from splitting water molecules;

driven by light energy;

The equation is: Carbon Dioxide + Water → Glucose + Oxygen.

C1.3.3—How is oxygen produced from photosynthesis? By what groups of organisms?

Oxygen in photosynthesis is a by-product from splitting water molecules;

This process occurs in plants, algae, and cyanobacteria;

C1.3.4—How can we separate and identify the light-absorbing pigments used in photosynthesis?

Using chromatography which separates and identifies photosynthetic pigments;

Pigments are run using a solvent;

For example propanone;

Pigments are separated by solubility;

and move different distances through the paper;

a Chromatogram is produced;

either by thin-layer or paper chromatography;

C1.3.4—What is an Rf value? How can it be calculated?

Measure the distance from the origin to the pigment;

Measure the distance to the solvent front using a ruler;

Divide the distance to pigment by the distance to the solvent front;

This gives an Rf value;

which can be compared to known pigment samples;

C1.3.5—What is visible light composed of?

Visible light has a range of wavelengths;

these wavelengths are associated with colours;

with violet having the shortest wavelength; 400nm;

and red has the longest wavelength; 700nm

C1.3.5— What wavelengths of light are absorbed by photosynthetic pigments? What happens as a result of the absorption of light energy?

Photosynthetic pigments, like chlorophyll, absorb specific wavelengths of light;

This absorption leads to the excitation of electrons and is crucial for the transformation of light energy into chemical energy in photosynthesis;

chlorophyll absorbs mainly red and blue light, reflecting green light;

C1.3.6—What is an action spectrum? How does the action spectrum appear for chlorophyll?

An action spectrum is a graph showing the rate of photosynthesis when using different wavelengths of light;

Most activity happens in the blue and red wavelengths not in the green middle section);

C1.3.6— What is an absorption spectrum? How does the absoprtion spectrum appear for chlorophyll?

An absorption spectrum is a graph showing the percentage of light absorbed at different wavelengths by a pigment or a group of pigments;

C1.3.6— What are the similarities and differences between action and absorption spectrum?

Both show the impact of different wavelengths of light;

The absorption spectrum shows wavelengths of light absorbed by photosynthetic pigments; whereas the action spectrum indicates the effectiveness of different wavelengths in causing photosynthesis to occur;

C1.3.7—What factors can limit the rate of photosynthesis?

a limiting factor is a factor that can decrease the rate of photosynthesis below its optimum level;

Temperature, carbon dioxide, light intensity;

C1.3.7—How do temperature, carbon dioxide and light intensity affect the rate of photosynthesis? Detailed explanation

Light intensity: rate of photosynthesis increases as light intensity increases;

photosynthetic rate levels-off at high light levels;

as other factors are then limiting;

Carbon dioxide: photosynthetic rate increases as CO2 concentration increases;

up to a maximum when rate levels-off;

Temperature: rate of photosynthesis increases with increase in temperature;

due to more kinetic energy and more successful collisions;

up to maximum level;

high temperatures reduce the rate of photosynthesis;due to denaturing of enzymes;

C1.3.8—How can carbon dioxide enrichment experiments in greenhouses be used to predict future rates of photosynthesis and plant growth?

Concept: In these experiments, plants are grown in controlled greenhouse environments where the CO2 concentration is artificially increased.

Example: A typical experiment might involve growing a crop like wheat or soybeans in a greenhouse with CO2 levels elevated to, say, 700 parts per million (ppm), compared to the current atmospheric level of around 400 ppm.

Observations: Researchers can observe changes in the rate of photosynthesis, plant growth patterns, yield quantity, and quality;

C1.3.8—What are Free Air Carbon-dioxide Experiments (FACE)? How can they be used to predict future rates of photosynthesis and plant growth?

Free Air Carbon-dioxide Experiments (FACE) involve having a network of pipes that give out extra carbon dioxide;

so they are open to the air;

however, plants within the enriched area receive much higher levels of carbon dioxide;

Researchers can observe changes in the rate of photosynthesis, plant growth patterns, yield quantity, and quality;

AHL ONLY - C1.3.9—What are photosystems and how do they generate and emit excited electrons?

Photosystems are molecular arrays of pigment molecules;

they located in membranes of cyanobacteria and within chloroplasts;

in eukaryotes;

They consist of chlorophyll and accessory pigments;

with a special chlorophyll at the reaction centre;

When light is absorbed, the reaction centre emits an excited electron;

which carries energy required for further steps;

AHL ONLY - C1.3.10—What are the advantages of structured arrays of different types of pigment molecules in a photosystem?

The structured array of different pigments in a photosystem is crucial because a single pigment molecule, like chlorophyll, cannot perform photosynthesis independently;

This array allows for efficient light absorption;

and energy transfer within the photosystem;

AHL ONLY - C1.3.11—How and where is oxygen generated by photosynthesis? (Light dependent reactions)

Light dependent reactions:

photolysis of water occurs;

In photosystem II;

generating oxygen, protons, and electrons;

The oxygen is released as a waste product;

while the protons and electrons are used in other steps of photosynthesis;

AHL ONLY - C1.3.12—How and where is ATP produced in photosynthesis? (Light dependent reactions)

Light dependent reactions:

ATP production occurs in the thylakoids;

in chloroplasts;

through using the energy from a proton gradient;

which is generated when excited electrons carrying energy from photosystems;

are used to pump protons into the thylakoid space;

protons diffuse through ATP synthase;

with the kinetic energy turning it, creating ATP from ADP + Pi (inorganic phosphate);

Excited electrons come from either photosystem I in cyclic photophosphorylation;

or photosystem II in non-cyclic photophosphorylation;

AHL ONLY - C1.3.13— What is reduced NADP? Where is it formed? (Light dependent reactions)

Light dependent reactions:

NADP is reduced; by photosystem I; in the stroma;

to reduced NADP;

by accepting two electrons from photosystem I;

and a hydrogen ion from the stroma;

AHL ONLY - C1.3.14—What is chemiosmosis (Light dependent reactions)

Light dependent reactions:

Chemiosmosis is the production of ATP using a gradient of protons;

and energy from electron transport;

Protons diffuse down their concentration gradient;

from the thylakoid space;

through ATP synthase;

producing ATP;

AHL ONLY - C1.3.14—Where do the light-dependent reactions take place?

The light-dependent reactions take place in the thylakoids;

which contain:

Photosystem II;

ATP synthase;

a chain of electron carriers;

Photosystem I;

leading to photolysis of water;

synthesis of ATP by chemiosmosis,;

and reduction of NADP;

AHL ONLY - C1.3.15—What is rubisco? What is its role in carbon fixation? What cycle is involved? (Light-independent reactions)

(Light-independent reactions)

Take place in the stroma of chloroplasts;

Rubisco is the most abundant enzyme on Earth;

it catalyzes the first major step of the Calvin cycle;

the fixation of carbon dioxide; to RuBP;

The calvin cycle then produces glycerate 3-phosphate;

Rubisco operates slowly and inefficiently in low CO2 concentrations;

so high concentrations of Rubisco are needed in the chloroplast stroma are needed;

AHL ONLY - C1.3.16—What is Triose phosphate? How is it formed? What is required?

(Light-independent reactions)

(Light-independent reactions)

In the Calvin cycle, glycerate-3-phosphate (GP);

formed from CO2 fixation;

is converted into triose phosphate (TP).;

This conversion requires energy from ATP;

and reducing power from Reduced NADP respectively;

Triose phosphate is a crucial intermediate;

leading to the synthesis of glucose;

AHL ONLY - C1.3.17—How is RuBP regenerated in the Calvin cycle? What is required?

(Light-independent reactions)

The regeneration of RuBP;

in the Calvin cycle is critical for it to continue;

Regeneration involves converting five out of six molecules of triose phosphate;

back into three molecules of RuBP;

using ATP;

if there is no ATP, then GP accumulates;

AHL ONLY - C1.3.18—How are other carbon compounds produced using products of the Calvin cycle and mineral nutrients? (Light-independent reactions)

The Calvin cycle fixes carbon producing intermediates that serve as precursors for the synthesis of various organic compounds;

like carbohydrates, amino acids, and others;

These compounds are synthesized through metabolic pathways that often trace back to an intermediate of the Calvin cycle;

demonstrating the cycle's central role in the biosynthesis of essential organic molecules.

AHL ONLY - C1.3.19—How do the light-independent reactions reactions depend on the light dependent?

The light-dependent reactions generate ATP and NADPH;

which are essential for the light-independent reactions (Calvin cycle);

A lack of light reduces the light-dependent reactions;

reducing ATP and Reduced NADP supply;

thereby reducing or stopping the Calvin cycle;

if there is no ATP or reduced NADP, then GP accumulates;

Triose Phosphate cannot be made;

so Glucose can't be made;

Not enough Carbon dioxide affects the light-dependent reactions;

as NADP+ cannot be remade by the calvin cycle;

so reduction by photosystem II to reduced NADPH stops;

Previous IB essay on how light-dependent reactions depend on light-independent reactions

reduced NADP (NADPH) is produced in the light-dependent reactions;
through reduction of NADP+ using electrons which are photoactivated; by photosystem II;
ATP is produced;
using the proton gradient created when protons are pumped into thylakoid space by electron carriers;
by photosphorylation;
as light-dependent reactions produce ATP and NADPH, and they are used up and would run out without light;
if there is no ATP and reduced NADP,
Glycerate-3-phosphate cannot be reduced to triose phosphate;
RuBP is therefore not regenerated, (as triose phosphate is used to regenerate RuBP);
and as ATP required for RuBP regeneration from triose phosphate;
carbon dioxide fixation therefore stops;
Glycerate-3-phosphate accumulates;
and there would be no RuBP to add to carbon dioxide;
stomata also close in the dark;
carbon dioxide is therefore not absorbed;