IB Biology SL 2025 FULL SET

Taking together all 8 units and compiling into one big set...

How is water the medium of life?

It is thought that the first cells came from water, specifically oceans. During formation of first cells, a small batch of water was enclosed in a membrane, allowing for substances to dissolve and chemical reactions to occur, which allows the processes of life to occur

Why does water have a polarity?

Within a water molecule, there is an unequal sharing of electrons (more on the oxygen than hydrogen), causing one side to be more “negatively charged” and the other “positively charged”

How does water stick together through cohesion?

Water sticks together because of the mutual attractions between the water molecules (caused by hydrogen bonds)

How does water stick to surfaces through adhesion?

Hydrogen bonds form between the water molecules and surfaces of solids composed of polar molecules, allowing them to stick together

How are the solvent properties of water linked to its role as a medium for metabolism and for transport in plants and animals?

The polar nature forms shells around charged and polar molecules, preventing them from clumping together and remaining in solution

In metabolism, substances are dissolved in the cytoplasm. Dissolved enzymes catalyze metabolic reactions, and the solutes move around and interact

In transport, xylem and phloem sap transport mineral ions and sucrose respectively to the plant. In animals, blood transports glucose, amino acids, oxygen, and fat molecules (coated in phospholipids to prevent contact between water and fat)

What are the Physical Properties of Water to consider?

Buoyancy, Viscosity, Thermal Conductivity, and Specific Heat

Black-throated loon (Gavia arctica) and its interaction with water

Since the loon flies more often than it swims, it requires more aerodynamic wings to fly efficiently, while its feet are not that strong. Additionally, since air has a much lower thermal conductivity, it can maintain its body temperature easier

Ringed Seal (Pusa Hispida) and its interaction with water

Since the seal swims more, it requires strong flippers to be able to move through a more viscous medium. However, since water has a higher specific heat capacity, it provides a more stable thermal environment despite water having higher thermal conductivity

Chemical Properties of Carbon Atoms

Can form up to 4 covalent bonds with elements such as H, O, N or P, and these covalent bonds can chain up to any length. The covalent bonds can spread out as far to make a tetrahedral shape

Sometimes, carbon’s bond angles can form rings, whether it’s all carbon or with other elements

Polysaccharides

A chain of monosaccharides

Polypeptides

A chain of amino acids

Nucleic Acids

A chain of nucleotides

Digestion of Polymers into Monomers via Hydrolysis

Polymers are deconstructed so that monomers can be used to build new polymers or as a source of energy

Polysaccharides deconstruct into monosaccharides

Polypeptides deconstruct into amino acids

Nucleic Acids deconstruct into nucleotides

Form & Function of Monosaccharides

Between 3-7 carbon atoms

Pentoses have 5, Hexoses have 6. Typically they’ll also have one oxygen in the carbon ring

Monosaccharides can connect to other monosaccharides to create polysaccharides. Glucose is a well-known one

Polysaccharides as Energy Storage Compounds

Branched structures of starch and glycogen allow them to be relatively compact despite their large mass, storing large amounts of energy without taking up much space

Structure of Cellulose

Composed of beta-glucose (typically more than 10,000 glucose subunits), and is only linked by 1-4 glycosidic bonds

Since they are not branched, they can only connect if it’s a pattern of regular-inverted

These form straight chains called microfibrils, which have very high tensile strength

Glycoproteins in cell-cell Recognition

Composed of polypeptides with carbohydrate attached (typically an oligosaccharide, which is a monosaccharide linked with glycosidic bonds)

The carbohydrate is the part that is displayed, allowing cells to recognize other cells

Lipids

Diverse group of substances that dissolve in non-polar solvents, such as ethanol, toluene and propanone

Common groups include oils, fats, waxes, and steroids

Triglycerides

Made by combining 3 fatty acids and one glycerol

Each of the fatty acids are linked via condensation reactions, so 3 water molecules are produced. Since the hydrophilic parts are used up during this reaction, triglycerides are hydrophobic

Depending on the type of fatty acids, triglycerides can be fats or oils

Phospholipids

Similar to triglycerides, but there are two fatty acids linked to the glycerol, with the third group instead being a phosphate group

Saturated Fatty Acids

Fatty acids that have all single covalent bonds between the carbon atoms, allowing it to contain as much hydrogen as possible

Monounsaturated Fatty Acids

Fatty acids that have one double covalent bond amongst the carbon atoms

Polyunsaturated Fatty Acids

Fatty acids that have more than one double covalent bond amongst the carbon atoms

How are triglycerides used in adipose tissue for energy storage and thermal insulation?

They are chemically stable, so they don’t lose energy

They are immiscible in water, so they naturally form droplets in the cytoplasm and don’t have effects on the osmosis

They release twice as much energy per gram in cell respiration as carbohydrate

They can be used as insulators

They are liquid at room temperature, acting as shock absorbers

Formation of Phospholipid Bilayers

The hydrocarbon tails of phospholipids are attracted more to each other because they are hydrophobic, causing the “tails” to attract each other while the heads face the opposite directions

They form the basis of cell structures

Amphipathic

When part of a molecule is hydrophobic and another part is hydrophilic

Examples of non-polar molecules to pass through phospholipid bilayer

Steroids are the most common that can pass through phospholipid bilayers

Steroids are composed of 4 fused rings of carbon atoms (3 cyclohexane and 1 cyclopentane giving a total of 17 C atoms)

Their hydrophobic properties allow them to pass through phospholipid bilayers

Structure of Amino Acid

Central carbon atom called the alpha carbon, with 4 single covalent bonds

One is to a nitrogen atom of an amine group.

The second is to a carbon atom of a carboxyl group (-COOH)

A third goes to another hydrogen atom

A fourth links it to a side chain called an R group

Condensation reactions forming dipeptides and longer chains of amino acids

Dipeptides are formed with two amino acids and a condensation reaction. Polypeptides are formed with more than two

These are formed via peptide bonds

Dietary Requirements for Amino Acids

20 different amino acids are used by ribosomes to make polypeptides (plants make, animals obtain)

9 of 20 are essential in humans, this can be obtained by eating animal-based foods such as fish, meat, milk or eggs

How Many Combinations are Possible for Amino Acids?

For a polypeptide with n amino acids, there are 20ⁿ possibilities

Effect of pH and temperature on Protein Structures

High temperatures causes vibrations within the molecule that can break intermolecular bonds or interactions, changing the shape of the protein. Proteins vary in their heat tolerance

Acidic and alkaline pHs can cause the positive and negative charges on the R-group to change, breaking ionic bonds or causing new ones to form.

Denaturation

When the bonds and interactions are broken between molecules that cause the protein to not be able to return to its original state

What is DNA?

Deoxyribonucleic acid, a molecule that carries genetic code

Covalent bonds forms between the phosphate group and pentose sugar on each nucleotide to form a DNA backbone

Names of Nitrogenous Bases

C - Cytosine

T - Thymine

G - Guanine

A - Adenine (only in DNA)

U - Uracil (only in RNA)

Complementary Base Pairing as A Role For Double Helix Strands

Adenine pairs with Thymine (Uracil in RNA)

Cytosine pairs with Guanine

Since the nucleotides run antiparallel, one must be inverted in order to be able to form hydrogen bonds, so they adopt a helical shape

Differences between DNA & RNA

DNA has two polymers, RNA has one polymer

DNA is double-stranded, RNA is single-stranded

DNA has a deoxyribose pentose sugar, while RNA has a ribose pentose sugar

Complementary Base Pairing as A Role for Replicating Genetic Info

Since the nitrogenous bases can only pair with one other base, it allows an exact copy to be made during replication for DNA or transcription for RNA

Diversity of DNA

There are 4ⁿ possibilities of bases depending on how long the sequence is

Additionally, DNA molecules can be any length, adding to the potential diversity

Conservation of genetic code across all life forms

Through the use of codons (sequence of three bases), organisms use 64 codons to code for amino acids in order to carry out life functions.

The incredible thing is, with a few minor exceptions, all living organisms and all viruses use the same genetic code

Hydrogen Bond

An intermolecular force that, in the context of water, forms when a slightly positive hydrogen atom in one polar molecule is attracted to a slightly negative oxygen atom of another polar molecule

Cohesion in Xylem

Allows the transport of water under tension in plants

Continuous columns of water that are drawn up generate tension between soil particles and water molecules

Water in xylem can withstand tensions because hydrogen bonds make it cohesive

Cohesion on Water Surfaces

Water molecules are much more attracted to each other than air molecules, creating an elastic membrane. This allows certain things to be able to float on water

Water striders walk on the surface of the water

Capillary Action in Plants

The process where water molecules “move” through surfaces thanks to its strong suction forces on polar areas

In plants, water adheres to the cellulose, so any wall that dries out is automatically rewetted

Buoyancy

The upward force that is exerted on an immersed object

Since living organisms have a density close to water, it allows them to live in water habitats, as they don’t need to use much energy to float

Viscosity

The stickiness of a fluid, which determines how easily it can flow

Pure water has a higher viscosity than organic solvents because hydrogen bonds cause internal friction

Seawater has a higher viscosity than freshwater because of the dissolved salts

Viscosity of air is about 50x smaller than that of water at the same temperature

Thermal Conductivity

The rate at which heat passes through a material

Water has a relatively high thermal conductivity. The high water content of blood allows it to carry heats to other parts of the body where it is generated to other parts that need more heat

Specific Heat

The heat required to raise the temperature of 1g of a material by 1C or 1K (kelvin)

Specific heat capacity of water is 4.18Jg^-1K^-1

Water has a high heat capacity because of the hydrogen bonds resisting molecular motion

Alpha-Glucose

Made of glycogen molecules in liver or muscle cells that are branched. They can contain up to 60,000

When drawing a diagram of these, the OH is on the top of the 4th carbon

Beta-Glucose

Cellulose molecules found in plant cell walls that are unbranched chains. They can contain 15,000 or more

When drawing a diagram of these, the H is on the top of the 4th carbon

Starch

Energy molecule used in plants composed of alpha-glucose. Can contain more than a hundred thousand glucose subunits

Amylose - one type that’s an unbranched chain linked by 1-4 glycosidic bonds, which form a helical chain

Amylopectin - same structure but some 1-6 glycosidic bonds to make it branched

Glycogen

Energy molecule used in animals composed of alpha-glucose

Linked by 1-4 glycosidic bonds and branched by 1-6 glycosidic bonds

Can contain tens of thousands of glucose subunits

Hydrophilic

Substances that are more attracted to water and therefore dissolve in water

Hydrophobic

Substances that are more attracted to other molecules and therefore do not dissolve in water

Oils

Type of lipid that has a melting point below 20C, so they solidify at low temperatures

Fats

Type of lipid that melts between 20C and 37C so they are solid at room temperature and liquid at body temperature

Waxes

Type of lipid that melts above 37C, so they liquify at high temperatures

Steroids

Type of lipid that is a molecule, typically known with a 4-ring structure

Ester Bonds

Formed when fatty acids link with the glycerol in the triglyceride. Forms when an acid links with the hydroxyl group (-OH) in an alcohol

Cis-Fatty Acids

When hydrogen atoms lie on the same side of the two double-bonded carbon atoms in unsaturated fatty acids

Since they all lie on the same side, there is a bend in the hydrocarbon chain at the double bond, so they cannot pack as tightly. So, cis-unsaturated fatty acids are typically oils

Trans-Fatty Acids

When hydrogen atoms are on opposite sides. Because of this, there is no bend in the hydrocarbon chain, allowing them to have a higher melting point

Peptide Bonds

The process where amino acids are linked by joining the carbon from the carboxyl group and the nitrogen from the amine group

Ribosomes catalyze this reaction in cells

Essential Amino Acids

An amino acid that cannot be synthesized in sufficient quantities by the organism so they must obtain from eating

Non-Essential Amino Acids

An amino acid that can be synthesized through metabolic pathways by the organism

Beta-Endorphin

Natural pain killer secreted by the pituitary gland that is a polypeptide composed of 31 amino acids

Insulin

Small protein that contains two short polypeptides, one with 21 amino acids and another with 30 amino acids

Alpha Amylase

The enzyme in saliva that starts the digestion of starch

Single polypeptide of 496 amino acids, with one chloride ion and one calcium ion associated

Titin

Part of the structure of the muscle

34,350 amino acids in humans, 35,213 amino acids in mice

Nucleotide

Consist of 3 parts: pentose sugar, phosphate group and a nitrogenous base

RNA

Ribonucleic Acid that is a single, unbranched polymer of nucleotides

Examples of Monosaccharides

Glucose, Fructose, Galactose

Examples of Disaccharides

Maltose, Lactose, Sucrose

Examples of Polysaccharides

Starches, Fibers, Glycogen

Glycerol Layout

Fatty Acid Layout

What is the role of enzymes?

Enzymes convert substrates into products

What role do enzymes play in metabolism?

Almost all metabolic reactions are catalyzed by an enzyme, with each enzyme catalyzing one specific reaction (called specificity)

Living organisms need to make a large number of different enzymes

By controlling the amount of enzymes, the organism can control how fast or slow the metabolic processes happen

Anabolic Reactions

When monomers are constructed into macromolecules, building up energy using ATP

Protein synthesis by ribosomes

DNA synthesis

Synthesis of starch, cellulose, glycogen

Catabolic Reactions

When macromolecules break down into monomers, releasing energy (ATP) in the process

Digestion of food

Cell respiration

Digestion of complex carbon compounds

Enzymes as globular proteins with an active site for catalysis

The 3D shape of enzymes has chemical properties that allow them to be catalysts

Substrates must bind to the active site, which varies in size, and the enzymes perform chemical processes to create the products, which are released

A few amino acids are needed at the active site to create the chemical conditions (usually brought together by folding of the polypeptides)

Interactions between substrate and active site to allow induced-fit binding

When the substrate binds to the active site, interactions between the substrate and the active site cause bond angles and lengths to be altered, causing the 3D shape to change as well (induced-fit bonding)

These changes make it easier for bonds within them to break and new bonds to form, converting substrates into products

Role of molecular motion and substrate-active site collisions in enzyme catalysis

Since the substrates and enzymes move in random directions, these collisions only happen occasionally

While some enzymes have chemical properties to draw substances or change their alignment, successful collisions only happen when the substrate and active site are aligned

Typically, the enzymes move around since they are smaller. However, there are instances where the enzymes are immobilized and the substrate needs to move by itself

Relationships between the structure of the active site, enzyme-substrate specificity, and denaturation

The shape and chemical properties of an enzyme’s active site allow substrate molecules to bind, but not other molecules (enzyme-substrate specificity)

Some enzymes only bind to the same substrate (glucose only goes to glucokinase), while others can bind to a group (hexokinase can bind with any hexose sugar)

Since the shape of the active sites rely on relatively weak interactions between amino acids within the protein, heat and acidity can change these shapes, causing denaturation

Effects of temperature, pH, and substrate concentration on the rate of enzyme activity

The higher the temperature, the more kinetic energy both the substrates and enzymes have, therefore higher enzyme activity. However, there comes a point where the temperature is too high and the enzymes lose their shape

Usually enzymes have an optimal pH for activity. Once the pH falls outside their optimal range, enzyme activity slows because of denaturation

The higher the substrate concentration, the slower the rate of enzyme activity since more sites are occupied at once

Measurements in enzyme-catalysed reactions

Typically, measurements for catalyzed reactions are recorded in the change in the amount of the chemical divided by time (millimoles per second gives us mmol s^-1)

Effect of enzymes on activation energy

Since chemical reactions are not single-step processes, activation energy is needed for substrates to convert to products

Without enzymes, the activation energy is much greater in the exothermic process

With enzymes, the exothermic process releases the same net amount of energy, but requires less activation energy

What is ATP?

A nucleotide that consists of the base adenine, 5-carbon ribose sugar, and 3 phosphate groups

Often described as the energy currency of the cell

Soluble in water and is stable at pH levels near neutral

Cannot pass freely through the phospholipid bilayer, so the rate at which they leave or enter the cell can be controlled

The 3rd phosphate can be easily removed or reattached. When it’s removed, there is a small amount of energy released, but it’s enough to fulfill many processes

What does ATP support?

Synthesizing macromolecules - linking monomers together requires energy, therefore the conversion of ATP to ADP releases the energy needed.

Active Transport - Pumping ions or particles across a membrane against the concentration gradient requires energy

Movements - in order for cells to move, they need energy, therefore ATP

Energy transfers during interconversions between ATP and ADP

When ATP converts to ADP, there is a net release of energy (endergonic). This energy is small, but enough to fulfill many processes. The extra phosphate is sometimes linked to another molecule to fulfill a reaction

When ADP converts to ATP, energy is needed (exergonic). This can come from cell respiration, photosynthesis or chemosynthesis

Cell Respiration Process

Carbon compounds are oxidized to release energy and this energy is used to create ATP

Respiration requires oxygen and produces carbon dioxide (called gas exchange)

Glucose breaks down to pyruvate, which breaks down to acetyl, and finally carbon dioxide

Aerobic Cell Respiration

Glucose and oxygen convert to carbon dioxide and water, which converts ADP to ATP

C₆H₁₂O₆ + 6O₂ → 6CO₂ +6H₂O + energy (ATP)

The pyruvate enters the mitochondria to be oxidized further

Anaerobic Cell Respiration

Glucose simply breaks down, producing lactate in animals and some bacteria and ethanol in yeast and fungi

Lactate: C₆H₁₂O₆ → 2C₃H₆O₃ + ATP

Ethanol: C₆H₁₂O₆ → 2C₂H₅OH + 2CO₂ + ATP

Variables affecting rate of cell respiration

Oxygen uptake

Carbon dioxide production

Consumption of glucose or other respiratory substrates

Transformation of light energy to chemical energy when carbon compounds are produced in photosynthesis

Some organisms, such as plants, are able to make all carbon compounds they need only using light energy, carbon dioxide and water

Photosynthesis

The process where light energy is converted to chemical energy in carbon compounds

Carbon compounds include: carbohydrates, proteins, lipids and nucleic acids

Photosynthesis Equation

6CO₂ + 6H₂O + light energy → C₆H₁₂O₆ + 6CO₂

Why does oxygen form during photosynthesis?

Oxygen is produced because of the photolysis that splits water molecules. This increases the concentration of oxygen in chloroplasts, so oxygen diffuses out

Water molecules need to split because the hydrogen is used for the reduction reaction that converts carbon dioxide to glucose

Equation: 2H₂O → 4e^- + 4H⁺ + O₂

Separation and identification of photosynthetic pigments by chromatography

Thin layer chromatography can be used to reveal the pigments of leaf tissue by putting it into solvent and the solution will separate the different types of pigments

Absorption of specific wavelengths of light by photosynthetic pigments

Specific pigments in plants absorb certain wavelengths of light while reflect others. This is why us humans view certain flowers in certain colors, since they reflect that specific wavelength while absorbing others for photosynthesis

Similarities and Differences between Absorption and Action Spectra

Absorption Spectrum - a graph showing the percentage of light absorbed at each wavelength by a pigment

Action Spectra - a graph showing the rate of photosynthesis at each wavelength of light

One can use both graphs to determine at what wavelength the most photosynthesis occurs