Foundational Biology

compartmentalisation

The division of cellular functions into separate membrane-bound compartments, allowing for specialised environments and increased efficiency within a eukaryotic cell.

nucleus

The membrane-bound compartment that contains the cell's genetic material and regulates gene expression and cell division.

nucleus structure

surrounded by a double membrane/nuclear envelope. Presence of nuclear poles that control movement of molecules across envelope. Contains the most DNA in the cell. Continuous/attached to the rough ER.

nucleolus

small dense spherical subregion of nucleus with transcribing/ribosomal genes

chromosome

long strands of DNA supercoiled and covered in histones. carries genetic information. found in nucleus, important for heredity, gene expression and cell division.

chromosome structure

made up of a chromatin, complex of histone and DNA which condenses to form chromosomes. held together by kinetochore, makes the centromere. 2 identical sister chromatids make a chromosome.

origin of nucleus

from invagination (inward fold) of plasma membrane around nucleotide of ancient prokaryote. looks millions of years. forming both nucleus and ER.

nucleoid

religion on prokaryotic cells, not surrounded by membrane. contains single circular DNA molecule, not formed into chromosomes.

mitochondrion.

a cell may have several or 1 large one. it is surrounded by 2 membranes, outer membrane and inner membrane, with the inner projections of it called the cristae. carry out aerobic respiration of all eukaryotes.

plastid

A plastid is a broad category of double-membrane organelles in plant and algae cells. eg. a chloroplast is a specific type of plastid specialised for photosynthesis

what is life

Living things are made of common elements and organised into cells. They contain genetic information, grow and change, respond to their environment, and carry out chemical reactions to build and use molecules. They obtain and use energy to survive, and exist in populations that can evolve over time.

cell theory

A fundamental unifying theory of biology stating that all living organisms are made of cells, cells are the basic unit of life, all cells arise from pre-existing cells, and thus modern cells evolved from a common ancestor.

evolution

The process where variation among individuals leads to differential reproduction, causing populations to change over time leading to evolution.

where did life come from

Theory 1: arisen spontaneously on Earth, environmental conditions enabled the formation of organic molecules from inorganic substances (e.g. DNA bases), supported by experiments like the Miller–Urey experiment (simulated early Earth’s conditions)

Theory 2: originated extraterrestrially arriving via meteorites such as the Murchison meteorite, which contains organic compounds associated with living systems.

formation of life

Hadean period: Earth formed, when the first oceans developed, little to no oxygen

Archean period: Life began, water present ~3.8 billion years ago, early prokaryotes (e.g. cyanobacteria) appearing around 3.5 billion years ago. 1.4 billion years later, unicellular eukaryotes evolved

Cambrian period: ~600 million years ago, more complex life began to diversify, terrestrial animals.

stromatolites

Layered structures formed by cyanobacteria, often called “living fossils,” that provide evidence of early life on Earth.

large time gap between bacteria, unicellular eukaryotes and terrestrial animals

• no ozone layer

• temperature conditions not optimial

• poor oxygen atmosphere

photosynthesis

• 6CO₂ + 6H₂O ⇌ C₆H₁₂O₆ + 6O₂

• Carbon dioxide and water are converted into glucose and oxygen using energy (light)

UV radiation types

• UV-A, UV-B, UV-C

• UV-C = most harmful to organisms

• UV-A, UV-B = least harmful

• can cause DNA damage and mutations

Early life protection from UV

water absorbed and reduced radiation, protecting organisms which is why they remained aquatic

How did oxygen first build up in the atmosphere

• cyanobacteria undergo photosynthesis, overtime CO₂ in the atmosphere is being cycled out and O₂ replacing it (for cellular respiration

forming the ozone layer

• UV radiation splits oxygen molecules: O₂ → O + O

• oxygen radicals then collide with O2: O + O₂ = O₃

• ozone molecules accumulate in the stratosphere forming a protective ozone layer

• took 1.5 billion years

function of ozone layer

• absorb mostly UV-C

• partially absorbs UV-A and UV-B

• massively deceasing harmful radiation onto earth’s surface and life

Cambrian Explosion

• rapid diversification of life, 541 mya

• major animal groups and major body structures first appeared

• triggered by ozone layer formation

• mostly fossils from this period due to the beginning of hard shell and exoskeletons (previous were soft-bodies and less likely to fossilise)

taxonomy

• the system used to classify and organise living organisms based on shared characteristics

• highest level of classification → 3 domains of life (Eukarya, Archaea, Bacteria

kingdoms of life

• used to group organisms in the Eukarya domain

• 6 kingdoms overall (Animalia, Plantae, Fungi, Protista, Bacteria, Archaea

Animalia

• multicellular

• heterotrophic (must acquire food)

• no cell walls

• most can move

Plantae

• multicellular

• autotrophic (make own food, photosynthesis)

• cell walls (made of cellulose)

• mostly non-motile

Fungi

• heterotrophic (absorb nutrients)

• cell walls (made of chitin)

• mostly decomposers

Protists

• mostly single celled eukaryotes

• can be plant like, animal like or fungus like

Prokaryotes

simple, unicellular organisms (bacteria and archaea) that do not have a nucleus

what structures do all prokaryotes have

• cell membrane

• cytoplasm

• ribosomes

• DNA in a nucleoid region ( not a nucleus)

what do most bacteria have outside the cell membrane

• a cell wall outside the plasma membrane made of peptidoglycan for support and protection

what is a bacterial capsule

a sticky outer layer made of polysaccharides, helps with protection and attachment

what is a flagellum

• movement (helps bacteria swim or move towards nutrients)

• more complex in eukaryotes

what are pili

• help with attachment to surfaces

• transfer of DNA between bacteria

what are ribosomes

• small cellular structure made of ribosomal RNA and proteins that carry out protein synthesis

what do ribosomes do

site of protein synthesis, where amino acids are joined to form proteins

prokaryotic ribosomes vs eukaryotic ribosomes

prokaryotic:

• smaller and simpler

• less complex structure

eukaryotic:

• larger and more complex

• have extra structural components (extensions) thus can make more proteins

atomic structure

the whole universe is made of 2 catergories

• matter

• energy

matter

• anything that has mass and takes up space/volume

• the fundamental unit of matter = the atom

Atoms structure

• have a central nucleus made of protons (positive charge) and neutrons (no charge)

• surrounded by a cloud of electrons (negative charge)

• atoms are mostly empty space (vacuum) between the nucleus and electrons

what is electronegativity

a measure of an atom’s ability to attract its bonding (outer) electrons (-) towards its nucleus (+)

how does number of protons effect electronegativity

more protons → more positive nucleus → higher electronegativity

how does electronegativity change across the period

it increases from left to right because nuclear charges increases while shielding stays similar.

how does electronegativity change down a group?

it decreases down a group because electrons are further from the nucleus and more shielded

nuclear charge

the total positive charge of an atom’s nucleus, determined by the number of protons. (Z)

how does number of electron shells nucleus affect electronegativity

more electron shells → greater distance → less attraction → less electronegativity

two main factors that control electronegativity

1. nuclear charge (no. of protons)

2. distance/shielding (number of electron shells)

what are bonds

when 2 atoms together they can share outer electrons, forming a bond

intramolecular bond types

• ionic, polar covalent, non-polar covalent

ionic bonds

• electronegativity difference > 1.9

• more electronegative atom steals electrons from another atom

• creates permanently charged cation (+) and anion (-)

polar covalent

• electronegativity difference → 0.4-1.9

• two atoms unevenly share a pair of electrons

• the electrons are closer to more electronegative atom

non-polar covalent

• electronegativity difference < 0.4

• two atoms evenly share a pair of electrons

• electrons are equidistant between nuclei

carbon

• the primary component of all known life

• has 4 electrons in its outshell and can form up to 4 covalent bonds

what are macromolecules

• large molecules (polymers) container thousands or more atoms

• made of smaller repeating subunits called monomers

• carbohydrates, proteins, nucleic acids, lipids

• but lipids are not polymers → subunits are fatty acids and glycerol

intermolecular forces

• electrostatic forces between atoms, molecules or ions

• ion-dipole, dipole-dipole, London disperson force, hydrogen bonding

London dispersion forces

• weakest intermolecular attraction, caused by temporary fluctuations in electron distribution, creating instantaneous dipoles

• exist in all molecules, but is the only force present in non polar molecules

• the larger the atom, the more electrons ad greater surface area = stronger London dispersion force

dipole-dipole forces

• intermolecular attraction between the positive end of one polar molecule and the negative end of another

• the molecule must have an asymmetrical distribution of charges

• meaning molecules have 1 positive side and 1 negative side

• also called hydrophilic interactions

hydrogen bonding

• strong type of dipole-dipole interaction, involves hydrogen bonded to highly electro negative atoms (N, O, F)

• the bond is extremely polar, causing the hydrogen electron to be pulled away and expose the hydrogen nucleus, leaving a naked positive charge (H+ proton)

• the hydrogen forms a bond to other electron rich atoms given that it is a lone pair of electrons (generally another N, O, F)

ion-dipole forces

• strong intermolecular attractions between an ion and a polar molecule

• occur when ionic compounds dissolve in polar solvents (like water)

• between an ion (cation or anion) and a polar molecule (dipole)

order of strength for intermolecular forces

hydrogen < dipole-dipole < hydrogen < ion-dipole

how do water molecules interact with each other

• properties explained through hydrogen bonding

• water molecules form a dynamic network of hydrogen bonds that are constantly breaking and reforming

water properties

• high melting point

• high specific heat capacity

• high heat of vaporisation

• cohesion

• adhesion

high specific heat capacity of water

• water can absorb large amounts of energy before changing temperatures

• because energy has to be used to break down the strong hydrogen bonds instead of just increasing kinetic energy and molecular movement

• limits the rise in temperature, slows temperature change

• stabilises environmental temperature, preventing rapid heating or cooling that can damage aquatic organisms

high melting point of water

water’s hydrogen bonding creates strong intermolecular forces that require significant energy to overcome before transitioning from solid ice to water

high heat of vaporisation

water requires large amount to completely break hydrogen bonds so water molecules can escape into gas phase, makes evaporation energetically costly

cohesion in water

• attraction between water molecules, caused by hydrogen bonding

• holds water molecules together and contributes to surface tension where water holds together at the surface

• surface tension → resistance of the surface of water to being broken/stretched because water molecules have a strong cohesion to neighbouring water

adhesion in water

• attraction between water molecules and other substances

• water’s polarity allows it to form hydrogen bonds or electrostatic interactions with other polar or charged surfaces

• seen in water sticking to glass or plant cell walls

what makes a molecule polar

• when a molecule has one or more polar bonds, where the electronegativity differences are big enough to consider it a polar bond

• must be asymmetrical (one side is positive, one side negative)

water’s polarity

• water is a polar molecule because of an uneven distribution of electron density, creating bent asymmetrical shape

• has a partial negative charge near the oxygen and a partial positive charge near the hydrogen atoms

• arises from oxygen’s high electronegativity, which pulls shared electrons closer, allowing hydrogen bonds and acts as a universal solvent

hydrophilic

• water loving, substances interact readily with water

• polar or charged molecules

hydrophobic

• water fearing, substances that do not interact well with water and tend to repel it

• non-polar molecules

water as a medium for chemical reactions in living organisms

• most biochemical reacts occur in aqueous solutions

• because water dissolves many polar and ionic substances

• molecules can move freely in it as hydrogen bonds in water are constantly breaking and reforming

water as an acid or base

• amphiprotic behaviour

• water can donate H+ (acid) = hydroxide OH^-

water can accept H+ (base behaviour) = hydronium H₃O+

• water can react with itself to make hydroxide and hydronium

• 2H2​O(l)⇌H3​O+(aq)+OH−(aq)

water acting as an acid

• H₂O→OH^-+H⁺

• water donates H+ to become hydroxide

water acting as a base

• H₂O+H²→H₃O⁺

• water uses a lone pair on an oxygen and donates a proton H+

• forms hydronium

hydrolysis

• reaction where water is added and a covalent bond is broken

• large molecules are split into smaller monomers

condensation

• builds polymers and produces water, covalent bond is formed

• reverse reaction of hydrolysis

carbohydrates

• general formula = (CH₂O)_n → for polysaccharides

• n = number of carbon atoms

• basic unit → monosaccharides (basic sugars)

types of carbohydrates

• 1 subunit → monosaccharide (glucose, ribose, deoxyribose)

• 2 subunits → disaccharide (sucrose, maltose, lactose)

• 3-10 subunits oligosaccharide (often a receptor signal on end of proteins)

• 100s or 1000 subunits → polysaccharides (CH₂O)_n (starch, glycogen, cellulose)

glycosidic bonds

• a covalent bond formed when two monosaccharides (sugars) join via condensation making a disaccharide

• water is released

• also called ether linkage in carbohydrates

• each sugar has multiple hydroxyl (-OH) groups

• one sugar provides a H from an -OH

• one sugar provides an -OH

• combine to H₂O

• sugar-OH + HO-sugar → sugar-O-sugar + H₂O

• sugar and O bridge is the glycosidic bond

alpha and beta glucose

• alpha glucose = OH below the ring at the carbon 1

• beta glucose = OH above the ring at the carbon 1 (a glucose must flip upside down to form glycosidic bond)

why can humans digest starch but not cellulose

• humans have enzymes for alpha 1,4 bonds (starch) but not beta 1,4 bonds (cellulose)

1,4 bond for carbon

• carbon 1 of one glucose is joined to the carbon 4 of another glucose

• linked by a glycosidic bond by a condensation reaction

glycogen

animal storage polysaccharide made of alpha-glucose, highly branched for rapid energy release (glucose does not need to flipped when forming glycosidic bond, branches easily and can form a coiled helix, more surface area)

starch

• plant energy storage polysaccharide made of alpha-glucose

• easily degraded by enzymes (amylases)

• primary energy storage compound in plants

• alpha glucoses condense together, form an alpha 1,4 glycosidic link, a straight chain of glucoses

• ends between branches can be digested and glucose can be taken off to access energy

• can form coiled helix, similar to glycogen

cellulose

• a structural polysaccharide in plant cell walls made of beta-glucose linked by beta-1,4 bonds

• the chain forms hydrogen bonds, cellulose chains are grouped together as microfibrils

• a straight rigid structure, cannot branch, more chemically stable than starch

• humans cannot digest

cellulose chains into microfibrils

• because of hydrogen bonding and London dispersion force (they’re large macromolecules)

• cellulose fibrils maintain shape through hydrogen bonding between neighbouring hydroxyl group

• condensation reactions form the chains, extensive hydrogen bonding links the chains together

Lipids

• group of macromolecules mainly used for energy storage, membrane structure and signalling

• non polar molecules (no charge) and cannot form hydrogen bonds, are insoluble

• mainly held together by LDF, weak force individually but significant when many are together

fatty acids

• a long hydrocarbon chain with a carboxyl group (-COOH) at the end

• saturated: only single bonds (C) between carbons, bonds can spin (flexible shape, and straight chains pack tightly together→ high LDF, decrease membrane fluidity and diffusion

• unsaturated: one or more double bonds (C=C) in the carbon chain, bonds cannot spin and cause kinks, decreased packing, inflexible rigid structure → lower LDF, increase membrane fluidity and diffusion

triglyceride

• a type of lipid that is used for long-term energy storage, the oil and fat in our diet that gets stored within fat cells (adipose)

• your body converts the extra calories into triglycerides, releasing them for energy during movement between meals

• triglyceride synthesis: combine glycerol (a 3 carbon molecule with three hydroxyl groups) linked (via ester bond, condensation reaction) to 3 fatty acids (each has a carboxyl group at one end)

steroids

• four fused carbon rings (the rings share carbons) from 17 carbons

• three 6-membered rings (hexagon), one 5-membered rings (pentagon)

• no fatty acid, a rigid ring structure

• mostly non-polar but may have small polar groups attached

• cell signalling

phospholipids

• two fatty acid tails → form hydrophobic tails, very non polar

• one phosphate group → hydrophilic head, very polar

• allows both non polar and polar things to interact with it → called a surfactant

phospholipid bilayer

• double later of phospholipid that forms basic structure of cell membranes

• hydrophilic heads face outward towards water

• hydrophobic tail faces inward cell away from water

• inside the two layers of the bilayer are the fatty acid tails, forming a non polar interior

• the heads can do ion bonding, dipole bonding, hydrogen bonding

• tails can only do LDF (how the 2 layers are being held together)

• this creates compartmentalisation, forming closed vesicles in water

nucleotides

the monomer of nucleic acids

consists of:

• a nitrogenous base

• pentose sugar (ribose or deoxyribose)

• phospate group

nucleoside

nitrogenous base + pentose sugar

nucleic acids

• how we transfer and store info in living things

• form long linear chains of receptive nucleotide units formed by phosphodiester bonds, making polynucleotides, that never branch

• DNA: deoxyribonucleic acid

• RNA: ribonucleic acid

DNA

• deoxyribonucleic acid

• 4 nucleotides:

→ adenine

→ cytosine

→ guanine

→ thymine

• has a double helix, 2 linear strands joined together by hydrogen bonds at the bases, antiparallel strands

• stores genetic information in cells, is the template for RNA synthesis