Apuntes Completos Biologia IB SL

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Downloaded by Mauricio Ochoa (Student) (mauricio.ochoa@eton.edu.mx)

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Topic 1.1: Cell Theory

Cell Theory Functions of Life
According to the cell theory: Organisms consisting of only one cell carry
out all the life functions in that single cell
1.  Living organisms are composed of cells (or cell products)
2.  The cell is the smallest unit of independent life
•  Metabolism
3.  Cells can only arise from pre-existing cells
•  Reproduction
•  Sensitivity
Caveats to the cell theory include:
•  Homeostasis
•  Striated muscle – composed of fused cells that are multinucleated •  Excretion
•  Giant algae – unicellular organisms that are very large in size (~7 cm) •  Nutrition
•  Aseptate hyphae – lack partitioning and have a continuous cytoplasm •  Growth
Cell Size
Surface area to volume ratio is important in the limitation of cell size Small SA:Vol Ratio
Cells need to exchange materials with the environment in order to produce ︎ metabolic rate
the chemical energy required for survival (via metabolism) ➡︎ material exchange
•  The rate of metabolism is a function of a cell’s mass / volume Low survival chances
•  The rate of material exchange is a function of a cell’s surface area
Large SA:Vol Ratio
As a cell grows, volume (units3) increases faster than surface area (units2) ➡︎ metabolic rate
•  If metabolic requirements exceed material exchange, a cell will die ︎ material exchange
•  Hence, cells must stay small or increase their SA:Vol ratio to survive High survival chances
Magnification Microscopes
Calculating Magnification (MIA): Light microscopes use lenses to bend light

Magnification = Image Size ÷ Actual Size •  Can view living specimens in natural colour
•  Have lower magnification and resolution
Calculating Actual Size (AIM):
Electron microscopes use electromagnets to focus electrons
Actual Size = Image Size ÷ Magnification
•  Can only view dead specimens in monochrome
•  Have higher magnification and resolution
Cellular Organization
•  Can show cross-sections (TEM) or surface renderings (SEM)
In multicellular organisms:
•  Cells may be grouped together to form tissues Emergent Properties
•  Tissues may interact to form functional organs
An emergent property is a function that is present in multicellular
•  Organs may combine to form body systems
organisms, but is not present in its individual component cells
Emergent properties arise from synergistic interactions between

the individual cells to produce entirely new aggregate functions
An example of an emergent property is the increased levels of
antibiotic resistance that can be seen in bacterial biofilms
Muscle Cardiac Heart Vascular
(Cell) (Tissue) (Organ) (System) ‘The whole is greater than the sum of its parts’ – Aristotle

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Topic 1.1: Cell SPECIALIZATION

Stem Cells
Stem cells are unspecialised cells that have two key qualities:
Embryonic Totipotent
1.  Self-Renewal – They can continuously divide and replicate Stem Cells
2.  Potency – They have the capacity to differentiate
Pluripotent
Fetal
There are four main types of stem cells during human development: Stem Cells Multipotent
•  Totipotent – Can form any cell type, as well as extra-embryonic tissue
Adult Unipotent
•  Pluripotent – Can form any cell type (e.g. embryonic stem cells)
Stem Cells
•  Multipotent – Can differentiate into closely related cell types
•  Unipotent – Cannot differentiate, but are capable of self-renewal Types of Stem Cells
Stem Cell Therapy Therapeutic Examples
Stem cells can replace damaged or diseased cells with healthy ones Example Condition Treatment
The therapeutic use of stem cells involves: Stargardt’s Macular Replace defective
disease degeneration retinal cells
•  Harvesting stem cells from appropriate sources
•  Using biochemical solutions to trigger cell differentiation Parkinson’s Death of Replace damaged
•  Surgically implanting new cells into patient's own tissue disease nerve tissue nerve cells
•  Suppressing the host immune system to prevent rejection
Cancer of Replacement of
•  Monitoring new cells to ensure they do not become cancerous Leukemia
the blood bone marrow
Ethics of Stem Cell Use
Source Growth Potential Tumour Risk Harvesting Disadvantages
Can be generated Requires destruction of the embryo

Embryo High (pluripotent) Higher risk
artificially by SCNT (results in the loss of a potential life)
Umbilical Easily obtained and Cells must be stored from birth at cost
Low (multipotent) Lower risk
Cord Blood stored / preserved (raises issues of financial accessibility)
Adult Tissue Low (multipotent) Lower risk Invasive to extract May be restrictions in scope / availability
Differentiation Gene Packaging
All cells of an organism contain an identical genome – each cell Within the nuclei of eukaryotic cells, gene instructions
contains the entire set of genetic instructions for that organism (DNA) are packaged with proteins as chromatin
Differentiation involves the expression of some genes and not •  Active genes are loosely packed as euchromatin
others in the cell’s genome (i.e. selective gene expression) •  Inactive genes are packed tight as heterochromatin
The activation of different genes within a given cell will cause it Nucleus Micrograph:
to develop differently from other cells (i.e. cell specialisation)
Heterochromatin (inactive)
Red cell (gene A)
Green cell (gene B) Euchromatin (active)

Single cell

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Topic 1.2: PRokAryotic Cells

Prokaryotic Cell Structure
Prokaryotes are organisms whose cells lack a nucleus

•  They belong to the kingdom Monera (i.e. bacteria) Pilus
Cytoplasm
Prokaryotic cells share the following structures: Genophore Cell wall
•  A single, circular DNA molecule (genophore)
•  A peptidoglycan cell wall and 70S ribosomes Cell membrane
70S Ribosome
Prokaryotic cells may also contain the following:
•  Pili (for attachment or bacterial conjugation) Plasmid
Flagellum
•  Flagella (a long whip-like tail for movement)
•  Plasmids (autonomous DNA molecules) Glycocalyx
Prokaryote Micrographs
Nucleoid (yellow) Bacterial Conjugation (pili = red) Cell Wall (purple) Flagella (white)
Prokaryotic versus Eukaryotic Cells Bacterial Cell Division
Prokaryotic and eukaryotic cells differ Prokaryotes divide via a process of asexual
according to a number of key features: reproduction known as binary fission
•  DNA (composition and structure)
•  Organelles (types present and sizes) In this process
•  Reproduction (mode of cell division) •  The circular DNA is copied
•  Average Size (exceptions may exist) •  The DNA loops attach to the membrane
•  The cell elongates, separating the loops
Prokaryote Eukaryote •  Cytokinesis occurs to form two cells
DNA is naked DNA bound to protein

DNA DNA is circular DNA is linear
Usually no introns Usually contains introns DNA replication
No nucleus Has a nucleus

Organelles Cell growth
70S ribosomes 80S ribosomes
Via binary fission Via mitosis and meiosis

Reproduction Cytokinesis
Single chromosome Paired chromosomes
Average Size Smaller (~1 – 5 µM) Larger (~10 – 100 µM)

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Topic 1.2: EuKAryotic Cells

Eukaryotic Cell Structure
Golgi body Smooth ER Nucleus Rough ER

Lysosome
Mitochondrion
Rough ER Cytosol
Smooth ER
Nucleolus Ribosome
Cytosol
(80S)
Nucleus
Membrane
Golgi body Membrane
80S Ribosome
Mitochondrion Vacuole Chloroplast Cell wall
Animal Cell Plant Cell
Eukaryote Micrographs
Golgi complex Chloroplast
Animal Cell (exocrine gland cell) ER (rough) Mitochondrion Plant Cell (palisade mesophyll)
Organelles Animal versus Plant Cells
Organelles are compartmentalised structures that serve specific purposes Animal Cells Plant Cells
Examples of eukaryotic organelles include: ︎No chloroplast Have chloroplast

•  80S ribosomes – Responsible for protein synthesis (translation)
•  Nucleus – Stores genetic information (site of transcription) No cell wall Cell wall (cellulose)
•  Mitochondria – Site of aerobic respiration (ATP production)
•  Endoplasmic reticulum – Transports materials between organelles No plasmodesmata Plasmodesmata
•  Golgi complex – Sorts, stores, modifies & exports secretory products
•  Centrosomes – Involved in cell division (mitosis and meiosis) Temporary vacuoles Large central vacuole
Organelles found only in specific cell types include: Cholesterol present No cholesterol in
•  Chloroplasts – Site of photosynthesis (plant cells only) in the cell membrane the cell membrane
•  Lysosomes – Breakdown of macromolecules (animal cells)
Glucose glycogen Glucose starch
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Topic 1.3: membrAne Structure

Phospholipid Bilayer
Structure of Phospholipids:
•  Contain a polar (hydrophilic) head composed of phosphate (+ glycerol) Polar head
Hydrophilic
•  Contain two non-polar (hydrophobic) tails, each composed of a fatty acid chain
•  Hence, phospholipids are amphipathic (have hydrophilic and hydrophobic parts) Non-polar tail
Hydrophobic
Arrangement in Membranes:
•  Phospholipids spontaneously arrange into a bilayer Phospholipid
•  The hydrophilic phosphate heads face out into the surrounding solution, while
the hydrophobic fatty acid tails face inwards and are shielded from the polar fluids
Properties of the Phospholipid Bilayer:

•  The bilayer is held together by weak hydrophobic interactions between the tails
•  Individual phospholipids can move within the bilayer (fluidity and flexibility)
•  Amphipathic properties restrict passage of certain substances (semi-permeable) Bilayer
Cholesterol Membrane Proteins
Cholesterol is a fundamental component of animal cell membranes Membrane proteins are diverse in terms of
•  It is not present in plant cell membranes (as they have a rigid cell wall) their structure and position in a membrane
Cholesterol reduces membrane fluidity and permeability to some solutes Membrane proteins serve many functions:
•  It also anchors certain peripheral proteins and prevents crystallization
•  Junctions
•  Enzymes
•  Transport
•  Recognition
Cholesterol •  Anchorage
(amphipathic) •  Transduction
Fluid Mosaic Model Membrane Models
Cell membranes are represented as a fluid-mosaic model Membranes appear trilaminar when viewed with an electron
•  Fluid – membrane components can move position microscope (trilaminar = three distinct layers)
•  Mosaic – phospholipid bilayer is embedded with protein
Davson-Danielli proposed a model whereby a phospholipid
This model was proposed by Singer-Nicolson in 1972, bilayer was flanked by two protein layers (sandwich model)
following the falsification of the Davson-Danielli model
This model was falsified based on the following findings:
integral protein •  Fluorescent tagging showed the proteins are mobile
cholesterol
•  Not all membranes have a constant lipid : protein ratio
•  Freeze fracturing identified transmembrane proteins
phospholipid
peripheral protein Trilaminar appearance Sandwich Model

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Topic 1.4: membrAne TrAnsport

Properties of Membranes Types of Membrane Transport
Cell membranes have two key properties Membrane transport can either be:
•  Semi-permeable (only certain things can cross) •  Passive (along concentration gradient, no ATP expenditure)
•  Selective (membranes can regulate material passage) •  Active (against concentration gradient, ATP is required)
Passive Transport
Simple Diffusion Facilitated Diffusion

The net movement of particles from a region of higher The passive movement of molecules across a cell membrane
concentration to a region of lower concentration (i.e. along via the aid of a membrane protein (carrier / channel protein)
the gradient) until equilibrium is reached •  Involves large / charged molecules (e.g. ions, glucose, etc.)
•  Involves small / lipophilic molecules (e.g. O2, CO2, steroids) •  E.g. Voltage-gated channels control the flow of ions in neurons
High [ ] Low [ ] Protein Channel Carrier Protein
Osmosis Osmolarity
The net movement of water molecules across a semi-permeable Osmolarity is a measure of solute concentration
membrane from a region of low solute concentration to a region
Solutions can be measured as:
of higher solute concentration (diffusion of free water molecules)
•  Hypertonic: High solute concentration (gains water)
Low solute concentration High solute concentration •  Hypotonic: Low solute concentration (loses water)
12 H2O total ; 12 H20 free 12 H2O total ; 0 H2O free •  Isotonic: Same solute concentration (no net flow)
net
Hypertonic Isotonic Hypotonic
Active Transport Vesicular Transport
Active transport uses energy (ATP) to move molecules The fluidity of the plasma membrane allows it to break and
against a concentration gradient (i.e. from low to high) reform around certain materials (this process requires ATP)
•  Molecule binds to a transmembrane protein pump •  Exocytosis: Materials released from a cell via vesicles
•  Hydrolysis of ATP causes a conformational change, •  Endocytosis: Materials internalised within a vesicle
translocating the molecule across the membrane
•  E.g. Sodium-potassium pumps move ions in neuron Intracellular vesicles can move materials between cell organelles
•  E.g. rough ER Golgi complex plasma membrane
Sometimes molecules are passively coupled to an
actively transported molecule (co-transport)
•  Symport: Both molecules move the same direction
•  Antiport: Molecules move in opposite directions
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Topic 1.5: Origin of Cells

Abiogenesis
The formation of living cells from non-living materials

(abiogenesis) is theorised to involve 4 four key processes:
Inorganic Organic Polymer
•  Non-living synthesis of simple organic molecules compounds monomers
•  Assembly of organic molecules into complex polymers
•  Formation of polymers that can self-replicate
•  Packaging of molecules into membranes to create an
internal chemistry different from the surroundings
Self-replication
The Miller-Urey experiment replicated the conditions of a
pre-biotic Earth in order to synthesize organic molecules Formation of cell
Biogenesis
Abiogenesis requires specific conditions in order to proceed Methodology Control Results Experimental
•  Including a reducing atmosphere (no oxygen) and either
high temperatures (>100ºC) or electrical discharges
As these conditions no longer commonly exist on Earth,

cells can only be formed from division of pre-existing cells
heat no growth growth
This law of biogenesis was demonstrated by Louis Pasteur
Broth boiled to Condensation Break to expose
•  Broths were stored in sealed vessels that were sterilised
kill organisms seals the flask contaminants
•  Bacterial growth occurred if vessel was unsealed, but
did not occur if vessel stayed sealed (no contamination) Conclusion: Cells only arise from pre-existing cells
Endosymbiosis Oxygenation of Earth
Eukaryotic cells are believed to have evolved from aerobic The appearance of photosynthetic organisms lead to the
prokaryotes that were engulfed by endocytosis rapidly increasing oxygenation of the Earth’s environment
The engulfed cell remained undigested and contributed new Oceans

functionality to the engulfing cell (i.e. it became an organelle) •  Originally, Earth’s oceans had high levels of dissolved
iron (released from crust by underwater volcanic vents)
•  Oxygen chemically reacted with the iron to form an
insoluble precipitate (iron oxide)
Ancestral Endosymbiosis Ancestral Rock Deposition

Prokaryote Eukaryote •  Insoluble iron formed banded iron formations (BIFs)
•  These deposits are not commonly found in rock that is
Chloroplasts and mitochondria arose via endosymbiosis: younger than 1.8 billion years (hence, identifies when
•  Membranes (have a double membrane) photosynthetic organisms first evolved)
•  Antibiotics (show susceptibility)
•  DNA (have naked and circular DNA) Atmosphere
•  Division (occurs via a fission-like process) •  When dissolved iron was completely consumed, oxygen
•  Ribosomes (have 70S ribosomes) started accumulating in the anoxic atmosphere

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Topic 1.6: Cell Division

Cell Cycle
The cell cycle is an ordered set of events that culminates in cell division
M phase
C Interphase
T
A G1
An active phase of the cell cycle where many metabolic reactions occur
M Growth and
•  Consists of G1, S and G2 stages
metabolism
P
G2 S M phase
and
Growth Replication The period of a cell cycle in which the cell and contents divide
preparation of DNA
•  Consists of mitosis (P, M, A, T) and cytokinesis
Interphase
Some cells may also enter a non-proliferative quiescent phase (G0)
Interphase Supercoiling
Normal metabolism cannot occur during M phase, so key During mitosis, chromatin condenses via supercoiling to
events must occur during interphase to prepare for division: become tightly packed chromosomes
•  Due to replication (S phase), chromosomes consist of
•  DNA replication (during S phase)
identical sister chromatids (joined at a centromere)
•  Organelle duplication
•  Cell growth
•  Transcription / translation S phase Mitosis
•  Obtaining nutrients
•  Respiration (cellular)
Mitosis Cytokinesis
Mitosis is the division of a diploid nucleus Cytokinesis is the process of cytoplasm division, whereby a cell splits in two
into two genetically identical diploid nuclei •  It occurs concurrently with telophase and differs in plants and animals
This process of cell cloning is needed for Animals:

many important processes: •  Microtubules form a concentric ring and
contract towards the centre (centripetal)
•  Tissue repair
•  Organism growth Plants:
•  Asexual reproduction •  Vesicles form at the cell centre and fuse
•  Development of embryos outwards to form a cell plate (centrifugal)
Mitotic Index Mitosis Micrographs
The mitotic index is a measure of the proliferative

Prophase Metaphase Anaphase Telophase
status of a cell population (i.e. number of dividing cells)
The mitotic index will be elevated during growth and

repair processes and acts as a prognostic tool for cancer
Cells in mitosis*
Mitotic Index =
Total number of cells
*Mitotic cells have no nucleus and have visible chromosomes
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Topic 1.6: STAGES of miTosis

Stage Diagram Key Events
•  DNA is uncondensed (chromatin)

Before: After:
Interphase
•  DNA is replicated (S phase) to form
(2n) S phase
genetically identical sister chromatids
•  Cell grows in size and organelles are

duplicated (G1 and G2)
Nuclear •  DNA supercoils and condenses

membrane (forms visible chromosomes)
Prophase dissolves
•  Nuclear membrane dissolves
(2n)
Centrosomes
move to poles •  Centrosomes move to poles and
begin to produce spindle fibres
•  Centrosome spindle fibres attach to

Spindle fibres
the centromere of each chromosome
Metaphase •  Spindle fibres contract and move the

(2n) chromosomes towards the cell centre
•  Chromosomes form a line along the
M = Middle
equator (middle) of the cell
Chromatids
•  Spindle fibres continue to contract
•  Sister chromatids separate and move
Anaphase
to opposite sides of the cell
(2n 4n)
•  Sister chromatids are now regarded as
A = Apart two separate chromosomes
Nuclear
membranes •  Chromosomes decondense
reform (DNA forms chromatin)
Telophase
•  Nuclear membranes form around the
(4n)
two identical chromosome sets
•  Cytokinesis occurs concurrently
•  Cytoplasmic division occurs to divide

the cell into two daughter cells
Cytokinesis
•  Each daughter cell contains one copy
(2n × 2)
of each identical sister chromatid
•  Daughter cells are genetically identical

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Topic 1.6: Cell cycle RegulAtion

Cell Cycle Checkpoints Cyclins
A cell cycle contains numerous checkpoints that ensure Cyclins are proteins that control progression of the cell cycle
the fidelity and viability of continued cell divisions
•  Cyclins bind to cyclin dependent kinases (CDKs)
G1 checkpoint •  The activated complex phosphorylates proteins involved

•  Monitors potential growth conditions (nutrients, etc.) in specific cell cycle events (e.g. centrosome duplication)
•  Assesses level of DNA damage (from UV, etc.) •  After the event has occurred, the cyclin is degraded and
the cyclin dependent kinase is rendered inactive
G2 checkpoint
•  Monitors state of pre-mitotic cell (suitable size, etc.) Cyclin Cyclin active
Cyclin
•  Identifies and repairs any DNA replication errors P P
CDK CDK
Metaphase checkpoint CDK
•  Ensures proper alignment (prevents aneuploidy) Target protein
Cancer Cancer Development
Cancers are diseases caused by uncontrolled cell division Cancers can be caused by many different factors:
•  The resulting abnormal cell growths are called tumors
Mutagens
Tumor cells may remain in their original location (benign) Mutagens are agents that change the genetic material of cells
or spread and invade neighboring tissues (malignant) •  These agents may be either physical (e.g. UV), chemical
(e.g. arsenic) or biological in origin (e.g. certain viruses)
Metastasis is the spread of cancer from an original site to •  Mutagens that cause cancer are classified as carcinogens
a new body location (forming a secondary tumor)
Genetics
Most cancers are caused by mutations to two classes of genes:
•  Proto-oncogenes stimulate cell growth and proliferation
•  Tumor suppressor genes repress cell cycle progression
normal cancer
uncontrolled
cell cell tumor Proto-oncogene mutations create cancer-causing oncogenes
divisions
Cell Death Smoking
The death of a cell may occur by one of two mechanisms: There is a strong positive correlation between the
frequency of smoking and the incidence of cancer
Necrosis (uncontrolled ‘cell homicide’)
•  Cigarette smoke contains >60 known carcinogens
•  The cell loses functional control due to injury, toxins, etc.
•  There is a destabilization of the membranes, leading to swelling
500
•  The cell bursts and releases its contents (causing inflammation)
400
Incidence of cancer
Apoptosis (programmed ‘cell suicide’)

(per 100,000 men)
•  It is a controlled event triggered by mitochondrial proteins 300
•  Cell contents are packaged in membranous protrusions (blebs) 200

•  The cell fragments into apoptotic bodies which are recycled
100
Disintegration Fragmentation
0
10 20 30 40
NECROSIS APOPTOSIS Cigarettes per day

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Topic 2.1: moleculAR biology

Metabolism
Metabolism describes the totality of chemical processes that occur within a living organism in order to maintain life
•  It is the web of all enzyme–catalysed reactions that occur within a particular cell or organism
Molecular biology explains these biological processes in terms of the chemical substances (molecules) involved
Organic Compounds Biomacromolecules
Organic compounds are molecules that contain carbon There are four main groups of organic compounds in cells:
and are found in living things •  Carbohydrates, lipids, proteins and nucleic acids
•  Exceptions include carbonates and oxides of carbon
Carbohydrates, proteins and nucleic acids are all made up of
Carbon atoms form the basis of organic life due to their recurring subunits (monomers)
capacity to form four covalent bonds
•  This allows a diversity of stable compounds to exist CLASS MONOMER POLYMER
Carbohydrate Monosaccharide Polysaccharide
Protein Amino acid Polypeptide
4 valence 4 empty
Nucleic Acid Nucleotide DNA / RNA
electrons slots
Lipids are not composed of repeating monomers, but may

contain smaller subunits (e.g. triglycerides)
CARBON ATOM CLASS SUBUNITS
CONFIGURATION
6 ELECTRONS 1s2 2s2 2px1 2py1 2pz0 Triglyceride Glycerol + Fatty Acid (×3)
Types of Reactions
Anabolism Catabolism
•  The synthesis of complex molecules from simpler ones •  The breakdown of complex molecules into simpler ones
•  Involves condensation reactions (water is produced) •  Involves hydrolysis reactions (water is consumed)
•  An example of an anabolic reaction is photosynthesis •  An example of a catabolic reaction is cellular respiration
ANABOLISM via CONDENSATION CATABOLISM via HYDROLYSIS
Small molecules join into Large︎ molecule Large molecule breaks to Small︎ molecules
Water produced ✓ H2O H2O H2O H2O H2O H2O ✗ Water consumed
Vitalism
Theory of Vitalism Falsification of Vitalism

Vitalism was a doctrine that dictated that organic molecules In 1828, Frederick Woehler disproved the theory of vitalism
could only be synthesized by living systems by artificially synthesizing an organic molecule
•  Living organisms were thought to possess a “vital force” •  He heated an inorganic salt (ammonium cyanate) under
that was required to manufacture organic molecules laboratory conditions to produce urea (organic)

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Topic 2.2: WATER

Water Structure Hydrogen Bonding
Water is made up of two hydrogen atoms covalently The dipolarity of the water molecule enables it to form polar
bonded to an oxygen atom (molecular formula: H2O) associations with other charged molecules (polar or ionic)
Oxygen has a higher electronegativity and attracts the Water molecules can also form hydrogen bonds with other
shared electrons more strongly, resulting in polarity water molecules (between an δ+ hydrogen and an δ– oxygen)
δ–
O O
H H δ+ H H δ+
Water Structure Water Polarity Hydrogen bonds
Cohesive Properties Solvent Properties
Water can form intermolecular associations with other Water is commonly referred to as the universal solvent due to its
molecules that share common properties (e.g. polarity) capacity to dissolve a large number of substances (ionic / polar)
•  Large quantities of water molecules can sufficiently weaken
•  Water can form hydrogen bonds with other water
forces (e.g. ionic bonds) and form dispersive hydration shells
molecules (cohesion: like molecules stick together)
•  Water can form polar associations with charged Substances that can dissolve in water are called hydrophilic
molecules (adhesion: unlike molecules stick together) •  Includes glucose, amino acids, sodium chloride, oxygen (low)
The cohesive properties of water results in a relatively Substances that cannot dissolve in water are called hydrophobic
high surface tension (can resist low level external forces) •  Includes lipids (fats and cholesterol)
The adhesive properties of water allow for potential These solvent properties make water an important medium for
capillary action (e.g. transpiration stream in plants) metabolic reactions, as well as a necessary transport medium
Thermal Properties Water versus Methane
Water has the capacity to absorb large amounts of heat Water and methane differ in thermal properties despite having
energy before undergoing a resultant change in state similar structures (comparable weight, size, valence structure)
•  Extensive hydrogen bonding must first be broken
The differences are due to the polarity of water and its capacity
Water therefore has a very high specific heat capacity to form intermolecular hydrogen bonds
•  Energy required to raise temperature of 1g by 1ºC
METHANE WATER
These properties make water a very effective coolant
•  Evaporation of sweat requires absorption of heat δ+

δ+
δ–
Other Properties
Formula CH4 H2O

Water is transparent, allowing light to pass through it
•  Important for photosynthesis and also for vision Polarity Non-polar Polar
Heat Capacity
Water expands when frozen, becoming less dense (J.g–1.ºC–1) 2.20 4.186
•  Important for life on Earth as it means ice floats and
the oceans underneath don’t automatically freeze Boiling Point (ºC) –161 100

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Topic 2.3: CARBOHyDRATES

Monosaccharides Polysaccharides
The monomer of a carbohydrate is called a monosaccharide Monosaccharides are covalently joined by glycosidic linkages
•  Monosaccharides primarily function as an energy source to form polymers (requires condensation reactions)
Examples of monosaccharides include glucose and ribose Monosaccharides may be joined into disaccharides for ease
of transport, or may form more complex polysaccharides
CH2OH
O HOCH2 O OH
Polysaccharides may be used for a variety of cell functions:
•  Short term energy storage (e.g. glycogen, starch)
OH •  Structural components (e.g. cellulose)
HO OH •  Recognition / receptors (e.g. glycoproteins)
OH OH OH
The carbohydrate formed depends on the monosaccharide
Glucose Ribose subunits used and the bonding arrangement between them
Types of Polysaccharides
Cellulose (component of plant cell wall) Cellulose Amylose

•  Linear molecule made of β-glucose subunits
•  Subunits bound in a 1-4 arrangement
Starch (energy storage in plants)

•  Composed of α-glucose subunits and exists in two forms
•  Amylose is linear (helical) and bound in 1-4 arrangements Glycogen Amylopectin
•  Amylopectin is branched (bound in 1-4 and 1-6 arrangements)
Glycogen (energy storage in animals)

•  Branched molecule composed of α-glucose subunits
•  Is like amylopectin but with more frequent 1-6 bonding
Energy Storage Body Mass Index
Carbohydrates and lipids are both used as energy storage While carbohydrates (and lipids) are important components
molecules, however they differ in certain key aspects: of a healthy diet, excess intake can affect body mass
•  Storage (lipids used for long term storage)
The body mass index (BMI) can be calculated as follows:
•  Osmotic pressure (lipids easier to store)
•  BMI = Mass in kg ÷ (Height in m)2
•  Digestion (carbohydrates easier to utilise)
•  ATP yield (lipids store more energy per gram) BMI can be calculated with an alignment chart (nomogram)
•  Solubility (lipids insoluble / harder to transport)
150
Carbohydrate Lipid Obese

Weight (kilograms)
130
Storage Short term Long term 110

a l
Osmolality More effect Less effect 90 Nor m
Digestion Easier to digest Harder to digest 70
Underweight
ATP Yield Smaller Larger (~2×)
50
1.5 1.6 1.7 1.8 1.9 2.0 2.1 2.2
Solubility Soluble (mono-/dimer) Insoluble in water Height (metres)

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Topic 2.3: LIPIDS

Functions of Lipids Triglycerides
Lipids are a class of non-polar organic molecules Triglycerides are lipids used for long-term energy storage
•  Include triglyceride (adipose tissue), phospholipid (bilayer),
They are composed of a glycerol molecule covalently linked
cholesterol (animal cell membrane), steroids (hormones)
to three fatty acid chains (via condensation reactions)
Lipids may serve a variety of cellular functions, including: H O
FATTY ACIDS
•  Storage of energy (triglycerides) H C O
GLYCEROL
O
•  Hormonal roles (steroids)
H C O O
•  Insulation (thermal)
•  Protection of organs H C O
•  Structural roles (cholesterol) ×3
H
Fatty Acids
Fatty acids are long hydrocarbon chains found in certain lipids Unsaturated fatty acids occur in two distinct configurations
•  Principally found in triglycerides and phospholipids
Cis Isomer Trans Isomer
Saturated Fatty Acids
•  Possess no double bonds in the hydrocarbon chain
•  Are generally solid at room temperatures (e.g. animal fat)
Unsaturated Fatty Acids

•  Possess double bonds (mono = one ; poly = many) H atoms on the same side H atoms on different sides
•  Are generally liquid at room temperature (e.g. plant oils) Double bond creates Double bond does not
kink in fatty acid chain create kink (linear chain)
O Are loosely packed and Are tightly packed and
Carboxylic
Hydrocarbon H3C (CH2 )n C usually liquid usually solid
group
OH
Occur commonly in nature Occurs in processed food
General Structure of a Saturated Fatty Acid Generally good for health Generally bad for health
Lipid Health Risks
Fats and cholesterol cannot dissolve in the blood and so are

Saturated and
packaged with proteins (as lipoproteins) for transport “BAD” trans fats raise
•  Low density lipoproteins (LDLs) transport cholesterol cholesterol
from the liver to the rest of the body (bad for health) Cholesterol ✗
LDL
•  High density lipoproteins (HDLs) scavenge excess
cholesterol and return it to the liver for disposal (good) deposits
Fatty acids can influence the levels of lipoproteins:

•  Cis fats raise levels of HDL (➡ blood cholesterol) removes
Liver
•  Saturated fats raise levels of LDL ( ︎︎ blood cholesterol) Artery
•  Trans fats raise levels of LDL and lower levels of HDL
✓
Cholesterol HDL
High levels of blood cholesterol can cause atherosclerosis Cis fats lower
Breakdown
and lead to health issues like coronary heart disease (CHD) “GOOD” cholesterol

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Topic 2.4: PROTEINS

Amino Acids Peptide Bonds
The monomer of a protein is called an amino acid Amino acids are covalently joined by peptide bonds to form
•  Amino acids are linked together to form polypeptides polypeptide chains (requires condensation reactions)
There are 20 different amino acids that form polypeptides The sequence of amino acids is encoded by genes and the
•  These can be linked in any sequence to create variation assembly of a polypeptide chain occurs at the ribosome
H H H
H O H O H O
Amine Carboxyl
group C group H N C C N C C OH
H N C OH
R Variable side chain R Peptide R

bond
Structure of a Generalised Amino Acid Structure of a Dipeptide
Protein Structure
Primary Structure
•  Order of amino acid sequence 1º A1 A2 A3 A4 A5
•  Formed by covalent peptide bonds
Secondary Structure
•  Folding into repeat patterns (α-helix or β-pleated sheet)
2º OR
•  By hydrogen bonds between amine and carboxyl groups
-helix -sheet
Tertiary Structure
•  Overall three-dimensional arrangement of a polypeptide
•  Determined by interactions between variable side chains
3º 4º
Quaternary Structure (optional)
•  Presence of multiple polypeptides or prosthetic groups
Functions of Proteins Denaturation
Proteins are a very diverse class of compounds that may Denaturation is a structural change in a protein that results
serve a wide range of functions within the cell, including: in the loss (usually permanent) of its biological properties
•  Structure (collagen, spider silk)
Denaturation can be caused by certain conditions:
•  Hormonal (insulin, glucagon)
•  Temperature (heat may break structural bonds)
•  Immunity (immunoglobulins)
•  pH (alters protein charge ︎ changes solubility & shape)
•  Transport (haemoglobin)
•  Sensation (rhodopsin)
•  Movement (actin, myosin)
•  Enzymatic (Rubisco, catalase)
The totality of all proteins that are expressed within a cell,

tissue or organism at a certain time is called the proteome
•  The proteome of any given individual will be unique as
protein expression patterns are influenced by a genome Folded Protein Unfolded (Denatured)

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Topic 2.5: EnzymES

Catalysis
An enzyme is a globular protein which speeds up the rate of a chemical

equation by lowering the activation energy (i.e. it is a biological catalyst)
•  Enzymes are not consumed by the reactions and can be re-used Active site
The molecule(s) the enzyme reacts with is called the substrate, which Substrate
binds to a complementary region on the enzyme’s surface (active site) Enzyme
Specificity
Lock and Key Model Induced Fit Model

•  Enzyme and substrate complement each other precisely •  Active site is not a rigid fit for the substrate and changes
in terms of both their shape and chemical properties its conformation to better accommodate the substrate
•  The active site and the substrate will share specificity •  This stresses the substrate bonds and induces catalysis
Substrate Products Substrate Products
Catalysis Catalysis
Factors Affecting Enzyme Activity Enzyme Kinetics
Temperature The rate of enzyme catalysis can be increased by increasing

•  Increases enzyme activity (more kinetic energy = more collisions) the frequency of enzyme-substrate collisions (molecular motion)
•  Enzyme activity peaks at an optimal temperature
The rate of enzyme catalysis is decreased by denaturation
•  Higher temperatures decrease activity (causes denaturation)
pH
•  Enzyme activity is highest at an optimal pH range Denatured
•  Activity decreases outside of this range (due to denaturation) Specificity
Substrate Concentration
•  Increases enzyme activity (more particles = more collisions) Industrial Enzymes
•  At a certain point, activity plateaus (saturation of active sites)
Immobilised enzymes are often used in industrial practices
•  They are fixed to a static surface to prevent enzyme loss
•  This improves separation of product and purity of yield
Rate
Rate
One application for immobilised enzymes is the production

of lactose-free milk and associated dairy products
•  Lactase (enzyme) digests lactose into glucose / galactose
Graph 1 Graph 2
•  Lactase is fixed to an inert surface (e.g. alginate beads)
•  Milk is passed over this surface to become lactose free
Key:
Graph 1 – Temperature There are several benefits associated with lactose-free milk:
Rate
Graph 2 – pH level •  Provides a source of dairy for lactose-intolerant people

•  Increases sweetness of milk (less need for sweeteners)
Graph 3 – Substrate level
Graph 3 •  Reduces crystallization and production times for cheese

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Topic 2.6: nuCLEIC ACIDS

Nucleotides Nitrogenous Bases
The monomer of a nucleic acid is called a nucleotide Each nucleotide possesses one of five different nitrogenous bases
•  Adenine, Guanine, Cytosine, Thymine or Uracil
Each nucleotide consists of three basic components:
•  A pentose sugar Bases may either be purines (A, G) or pyrimidines (C, T, U)
•  A phosphate group •  T is present in DNA, whereas U is present in RNA
•  A nitrogenous base
H2N
N H
H NH3 Cytosine
Phosphate H N
PYRIMIDINES
N N
PURINES
N O H
Base N
O
CH2 H Adenine
O Uracil H NH
5 N
O H N
4 1 H3C O O
HN N H NH
Sugar 3 2
H2N N Guanine HN O Thymine
Polynucleotide Formation
Nucleotides are linked together into a single strand via condensation reactions C G
5’
(between a 5’-phosphate and a 3’-hydroxyl group of adjacent nucleotides)
3’
3’
This polynucleotide arrangement results in the formation of a sugar-phosphate A T
backbone that is covalently linked together by phosphodiester bonds
5’
DNA Structure
Two complementary strands line up in opposite directions (anti-parallel) with the
bases facing inwards and connected by hydrogen bonds (G ≡ C and A = T)
The double stranded molecule then twists in order to adopt a more stable energy
configuration – a double helix
RNA Structure
The polynucleotide chain remains single stranded, but may fold upon itself to
form double stranded motifs (e.g. the cloverleaf shape of a tRNA molecule) DNA Ladder Double Helix
DNA versus RNA Watson and Crick
DNA and RNA are both polymers of nucleotides, The structure of DNA was elucidated by Watson and Crick in 1953
however they differ in a few key structural aspects
Using data from previous scientific experiments (plus trial and error),
DNA RNA Watson and Crick developed a DNA model that demonstrated:
•  A double helix structure composed of antiparallel DNA strands
Sugar is deoxyribose Sugar is ribose •  Internally facing bases with complementary pairing (A=T, G≡C)
Has thymine (T) Has uracil (U)
James Francis
(along with A, C and G) (along with A, C and G)
Watson Crick
Is double stranded
Is single stranded
(forms a double helix)
Model

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Topic 2.7: DNA REPLICATION

Semi-Conservative
DNA replication is semi-conservative – one strand is from an original template molecule and one strand is newly synthesised
•  This occurs because each base will only pair with its complementary partner and thus ensure the sequence is conserved
Original strand
Newly synthesised
DNA Replication
Helicase: DNA Polymerase III

•  Unwinds and separates the double stranded DNA •  Free nucleotides line up opposite complementary partners
•  Breaks the hydrogen bonds between the base pairs •  DNA Pol III covalently joins the free nucleotides together
5’ 3’
DNA Pol III
Helicase
3’ 5’
Meselson-Stahl Experiment Polymerase Chain Reaction
The Meselson-Stahl experiment supported the theory that The polymerase chain reaction (PCR) is an artificial method
DNA replication occurred via a semi-conservative process of DNA replication that is used to rapidly copy sequences
They incorporated radioactive nitrogen isotopes into DNA PCR occurs in a thermal cycler over three repeating steps:
•  Templates were prepared with heavier 15N •  Denaturation: DNA heated in order to separate strands
•  New sequences were replicated with lighter 14N •  Annealing: Primers attach to ends of a target sequence
•  Elongation: A heat-tolerant polymerase copies strands
The DNA was then separated via centrifugation in order to
determine its composition of radioisotopes A standard reaction of 30 cycles would generate 230 copies
•  1st division: DNA had 15N and 14N (i.e. mixed) of the target DNA sequence (i.e. >1 billion copies of DNA)
•  2nd division: DNA is mixed or has 14N only
The results were consistent with a semi-conservative model 1. Denaturing
Strands separate
ACTUAL RESULT SEMI-CONSERVATIVE (95°C)
1st Division
2. Annealing
N-15 / N-14 Primers bind

N-15 Mix (×2) (55°C)
3. Extension
2nd Division
N-14 only
Taq polymerase
N-15 / N-14 (72°C)
Mix Mix N-14

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Topic 2.7: TRAnSCRIPTIOn & TRAnSLATIOn

Transcription Types of RNA
Transcription is the synthesis of an RNA sequence from a DNA template Three main types of RNA may be produced:
•  This process occurs within the nucleus of a cell •  mRNA – Transcript used to make protein
•  tRNA – Transfers amino acid to ribosome
Transcription is mediated by the enzyme RNA polymerase, which:
•  rRNA – Catalytic component of ribosome
•  Separates the DNA strands (breaks H bonds between base pairs)
•  Covalently joins free complementary RNA nucleotides together
After transcription, the RNA is released to the cytoplasm (for translation)

and the DNA remains within the nucleus and reforms a double helix mRNA tRNA rRNA
Genetic Code
The genetic code is the set of rules by which information encoded in UUU UCU UAU UGU
Phe Tyr Cys
mRNA sequences is converted into a polypeptide sequence UUC UCC
Ser
UAC UGC
UUA UCA UAA STOP UGA STOP
Leu
UUG UCG UAG STOP UGG Trp
Codons: Triplets of bases which correspond to a particular amino acid CUU CCU CAU CGU
His
CUC CCC CAC CGC
Leu Pro Arg
The order of the codons determines the amino acid sequence for a protein CUA CCA CAA CGA
Gln
CUG CCG CAG CGG
•  A coding sequence always begins with a start codon (AUG) AUU ACU AAU AGU
Asn Ser
•  A coding sequence is terminated with a stop codon AUC Ile ACC AAC AGC
Thr
AUA ACA AAA AGA
Lys Arg
AUG Met ACG AAG AGG
The genetic code has two key features: GUU GCU GAU GGU
Asp
GUC GCC GAC GGC
•  Universality – All organisms use the same genetic code Val Ala Gly
GUA GCA GAA GGA
Glu
•  Degeneracy – Multiple codons may code for the same amino acid GUG GCG GAG GGG
Translation
Translation is the process of polypeptide synthesis by the ribosome tRNA polypeptide amino acid
•  Messenger RNA (mRNA) is transported to the ribosome
•  A ribosome reads an mRNA sequence in base triplets called codons
•  Each codon codes for a specific amino acid (as per the genetic code)
•  Amino acids are transported to ribosomes by transfer RNA (tRNA)
•  Each tRNA aligns opposite a codon via a complementary anticodon anticodon codon
•  The ribosome moves along the mRNA sequence (5’ 3’) and joins
amino acids together with peptide bonds (condensation reaction)
•  The synthesis of a polypeptide is initiated at a start codon (AUG)
and is completed when the ribosome reaches a STOP codon ribosome
mRNA
Gene Protein
A gene is a sequence of DNA which encodes a polypeptide sequence

DNA (gene)
•  One gene = one polypeptide (proteins may have multiple polypeptides)
transcription
There are exceptions to this fundamental relationship:
•  Genes may be alternatively spliced (one gene = many polypeptides) mRNA
•  Genes encoding tRNA or rRNA are transcribed but not translated translation
•  Genes may be mutated to alter the original polypeptide product polypeptide

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Topic 2.8: CELL RESPIRATIOn

Cell Respiration ATP
Cell respiration is the controlled release of energy ATP (adenosine triphosphate) is a molecule that functions as an
from organic compounds to produce ATP immediate source of energy when hydrolysed (to form ADP)
The main organic compounds used are carbohydrates Pi

(i.e. glucose), but lipids or proteins may also be used +
ATP ADP
•  Different organic compounds will have distinct
breakdown pathways and so have varied ATP yields High-energy bond Free energy
Glycolysis Anaerobic versus Aerobic Respiration
Cell respiration begins with the break down of glucose Pyruvate (from glycolysis) will follow one of two pathways:
via a process called glycolysis (occurs in the cytosol)
Anaerobic Respiration
•  Glucose is broken down into pyruvate (×2)
•  Occurs in the cytosol and does not require oxygen
•  There is a small ATP yield (net gain = 2 ATP)
•  Results in a small energy yield (2 ATP from glycolysis)
•  Requires the reduction of NAD+ (to form NADH)
•  Forms lactic acid (animals) or ethanol and CO2 (plants / yeast)
•  Also known as fermentation and is reversible
2× ATP NAD+ ADP
Aerobic Respiration
•  Occurs in the mitochondria and requires oxygen
Pyruvate •  Results in a large energy yield (~36 ATP per glucose)
Glucose ADP NADH 4× ATP
(×2) •  Forms carbon dioxide and water
INVEST PAYOFF •  Uses hydrogen carriers to make ATP (oxidative phosphorylation)
Fermentation Respirometry
Fermentation is a reversible anaerobic process that allows A respirometer determines an organism’s respiration rate by
ATP production to continue in the absence of oxygen measuring either carbon dioxide production or oxygen uptake
•  Commonly used for invertebrates or germinating seeds
Fermentation restores NAD+ stocks (needed in glycolysis)
to ensure a continued production of ATP (by glycolysis) A simple respirometer may involve the use of a manometer:
•  An organism is sealed in a container with a CO2 absorbant
Fermentation in animals produces lactic acid, and is used
•  Oxygen uptake creates a pressure change which displaces
to maximise muscle contractions when oxygen is limited
the fluid in the manometer (allowing for quantitation)
•  This reaction can be reversed when oxygen is restored
Fermentation in plants and yeast produce ethanol and

CO2 gas which can be used in baking (leavening dough)
•  Also for the production of alcohol, yogurts and cheese
GLYCOLYSIS FERMENTATION
glucose lactate ethanol + CO2

NAD+
ATP
NADH Platform A: Manometer Platform B:
Specimen and pressure change Equivalent
pyruvate CO2 absorbant moves the water volume / mass

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Topic 2.9: PHOTOSynTHESIS

Photosynthesis Light Spectrum
Photosynthesis involves the use of light energy to synthesise Visible light has a range of wavelengths (~ 400 – 700 nm)
organic compounds from inorganic molecules •  Violet has the shortest wavelength, red has the longest
Light The Visible Spectrum

6 CO2 + 12 H2O C6H12O6 + 6 O2 + 6 H2O
Chlorophyll
Carbon Water Glucose Oxygen Water
dioxide 700 nm 400 nm
Light Absorption
Pigments are required for the conversion of light energy into chemical energy in photosynthetic organisms
Chlorophyll is the main photosynthetic pigment, although other accessory pigments also exist (e.g. carotenoids)
•  Chlorophyll absorbs red light and blue light most effectively and reflects green light more than other colours
An absorption spectrum (left) indicates the wavelengths of light absorbed by each photosynthetic pigment (e.g. chlorophyll)
An action spectrum (right) indicates the overall rate of photosynthetic activity at each wavelength of light
Relative absorption
Photosynthetic rate
carotenoid
chlorophyll a
chlorophyll b
400 500 600 700 400 500 600 700

Wavelength of light (nm) Wavelength of light (nm)
Stages of Photosynthesis
Light Dependent Reactions Light Independent Reactions

Light energy is converted into chemical energy Carbon compounds are made from the chemical energy
•  Light is absorbed by chlorophyll to produce ATP •  ATP and hydrogen are fixed with carbon dioxide
•  The photolysis of water forms oxygen and hydrogen •  This results in the formation of organic molecules
Light energy Carbon dioxide NADPH ATP
Water Chlorophyll Chemical energy

Carbon fixation
e–
Oxygen Hydrogen NADPH ATP Organic compounds Cell Processes
Chromatography Limiting Factors
Pigments can be separated by chromatography When a process depends on more than one condition, the
•  Pigments are dissolved in fluid rate will be limited by the factor nearest its minimum value
•  The fluid is passed through a static material
Limiting factors in photosynthesis include:
•  Pigments are separated according to size
•  Temperature (influences photosynthetic enzymes)
A retardation factor (Rf value) is calculated: •  Light intensity (required for chlorophyll photoactivation)
Rf = distance of pigment ÷ distance of solvent •  Carbon dioxide concentrations (CO2 is a core substrate)

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Topic 3.1: GENES

Genes versus Alleles Genetics Comparisons
A gene is a heritable factor that consists of a sequence of There is no clear correlation between genetic complexity and
DNA and influences a specific trait chromosome numbers, genome size or the number of genes
•  The position of a gene on a chromosome is the locus
Diploid Genome Gene
Species
Alleles are the alternate forms of a gene that code for the Number Size (Mb) Count
different variations of a specific trait Virus n/a 0.17 280
•  Alleles for a specific gene will differ by only a few bases T4 Phage
Bacteria n/a 4.6 4200

New alleles may be formed as a result of gene mutations E. coli
Fruit Fly 8 130 13,000

D. melanogaster
Genome
Roundworm 4 185 14,000
A genome describes the totality of the genetic information P. equorum
in an organism Rice 24 470 38,000

•  It includes all genes and non-coding sequences O. sativa
Canopy Plant 40 150,000 ?

The Human Genome Project was completed in 2003 and P. japonica
mapped the entire base sequence of human genes Dog 78 2,900 20,000
•  Human cells typically have 46 chromosomes C. familiaris
•  The human genome consists of ~3 billion base pairs Chimpanzee 48 3,300 22,000
P. troglodytes
•  It contains roughly 21,000 genes (although estimates vary)
Human 46 3,200 21,000
The genomes of other organisms are now being sequenced H. sapiens
Mutations Sickle Cell Anemia
A gene mutation is a change in the base sequence of a Cause of Sickle Cell Anemia:
section of DNA coding for a particular characteristic Base substitution: GAG GUG (6th codon: hemoglobin beta)
•  Gene mutations may be beneficial, detrimental or neutral Amino acid change: Glutamic acid Valine (Glu Val)
Gene mutations may be described as either: Consequences of Sickle Cell Anemia:

•  Somatic – Occurs in a body cell and affects a tissue •  Alters haemoglobin structure (forms insoluble strands)
•  Germline – Occurs in a gamete and affects offspring •  Cannot transport oxygen effectively (causing fatigue)
•  Red blood cells adopt a sickle shape (may form clots)
Point mutations may include either: •  Sickle cells are destroyed at a higher rate (causes anemia)
•  Substitutions (either silent, missense or nonsense)
Heterozygous Advantage:
•  Frameshifts (insertions or deletions)
•  Sickle cell anemia is a codominant trait and heterozygous
Mutations can arise spontaneously as copying errors during individuals demonstrate an increased resistance to malaria
DNA replication or can be induced by mutagenic agents
Point Mutation
Original Sequence Silent Missense Nonsense
DNA TTC TTT TCC ATC
RNA AAG AAA AGG UAG
Protein Lys Lys Arg STOP Normal Blood Cell Sickle Blood Cell
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Topic 3.2: CHROmOSOmES

Chromosomes Autoradiography
Prokaryotes John Cairn pioneered a technique for measuring the length

•  Have a single circular molecule made of naked DNA of DNA molecules while uncoiled (via autoradiography)
•  May have additional plasmids (autonomous DNA units) •  Radioactive thymidine is incorporated into a cell’s DNA
•  Chromosomes were fixed to a photographic surface and
Eukaryotes treated with silver bromide (AgBr)
•  Multiple linear DNA molecules packaged with histones •  Radiation converts silver ions into insoluble grains that is
•  Do not have plasmids (unless genetically modified) visible via electron microscopy when a film is developed
Prokaryotic DNA Eukaryotic DNA Autoradiograph Interpretation
Diploid versus Haploid Sex Determination
Sexually reproducing organisms receive genetic material from both parents Humans have 23 pairs of chromosomes
•  Diploid = 2 sets of chromosomes (i.e. body cells) •  Diploid number (2n) = 46 chromosomes
To reproduce, these organisms only pass on half their genetic material 22 pairs are homologous autosomes
•  Haploid = 1 set of chromosomes (i.e. sex cells / gametes) •  Each pair has identical genes and loci
•  Alleles may differ (one from each parent)
When haploid sex cells fuse, the diploid cell can grow into a new organism
The 23rd pair are the sex chromosomes
Homologous Chromosomes •  Females have two X chromosomes (XX)
•  Males have X and Y chromosomes (XY)
Homologous chromosomes are the paired chromosomes inherited from
both parents (maternal and paternal) in sexually reproducing animals The Y chromosome is responsible for the
development of male sex characteristics
Homologous chromosomes have the same genes at identical loci positions
•  Hence, the father always determines sex
•  However the specific alleles for each gene may be different
Karyotyping Karyograms
Chromosome number is a characteristic feature of members of a species A karyogram shows the chromosomes of a
•  Karyotypes identify the number and types of chromosomes in a cell cell in homologous pairs of decreasing length
Karyotyping is performed pre-natally to identify the sex of offspring or Female: Down Syndrome (Trisomy 21)
diagnose potential chromosome abnormalities (e.g. aneuploidies)
Amniocentesis 1 2 3 4 5
•  Cells are collected from the amniotic fluid of the pregnant mother
•  Conducted at ~16 weeks with a slight risk of miscarriage (~0.5%) 6 7 8 9 10 11 12
Chorionic Villi Sampling 13 14 15 16 17 18

•  Cells are collected directly from the placental tissue
•  Conducted at ~11 weeks with a higher risk of miscarriage (~1%) 19 20 21 22 X X

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Topic 3.3: mEIOSIS

Meiosis Mitosis versus Meiosis
Meiosis is the reduction division of a diploid cell to produce Hint: Disco Pug Mitosis Meiosis
four haploid cells (gametes) that are genetically distinct
Divisions One Two
It involves two divisions:
Independent
•  Meiosis I separates homologous chromosomes No Yes (Metaphase I)
Assortment
•  Meiosis II separates sister chromatids
Yes
Synapsis No
(bivalents / tetrads)
Crossing Over No Yes (Prophase I)
Outcome Two cells Four cells
Ploidy Diploid Diploid Diploid Haploid
Use Body cells Sex cells (gametes)

Interphase Meiosis I Meiosis II
Genetics Identical (clones) Genetic variation
Genetic Variation
Crossing Over Random Assortment

•  Crossing over occurs via synapsis in Prophase I •  The homologous pairs orient randomly in Metaphase I
•  Homologous chromosomes form bivalents (or tetrads) •  This means there is an equal chance of a resulting gamete
•  Chiasmata represent the points where genetic information containing either the maternal or paternal chromosome
has been exchanged between the homologous pair •  As humans have a haploid number of 23, consequently
•  The non-sister chromatids that have exchanged DNA are there are 223 potential gamete combinations (>8 million)
called recombinants
Homologous Bivalent
chromosomes (+ chiasma) Recombinants Parent Cell Potential Gamete Combinations
Sexual Life Cycle Non-Disjunction
The halving of chromosome number by meiosis allows Non-disjunction refers to chromosomes failing to separate,
for a sexual life cycle with the fusion of gametes resulting in gametes with extra or missing chromosomes
•  This acts as a further source of genetic variation
The failure to separate may involve the homologous pairs in
Fertilisation Anaphase I or the sister chromatids in Anaphase II
Egg If a gamete with an extra chromosome fuses with a normal

(n = 23) gamete, the resulting zygote will have three copies
•  E.g. Trisomy 21 (Down Syndrome)
Zygote Embryo
(2n = 46) (2n = 46)
Sperm Studies show parental age influences chances of non-disjunction
(n = 23) •  Older parents are at a higher risk of non-disjunction events

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Topic 3.3: STAGES OF mEIOSIS

Stage Diagram Diagram Stage
Interphase (S phase)
Before After
(1 × 2n) (4 × n)
Cytokinesis
(2n n) × 4
Prophase I
(2n) Telophase II
(2n) × 2
Metaphase I Anaphase II
(2n) (n 2n) × 2
Anaphase I Metaphase II
(2n) (n) × 2
Telophase I
(2n) Prophase II
(n) × 2
Cytokinesis
(2n n) × 2
Meiosis I Summary Meiosis II Summary

•  Is a reduction division (diploid haploid) •  Is akin to a mitotic division (but of haploid cells)
•  Separates the homologous chromosomes •  Separates the sister chromatids
•  Crossing over may occur during Prophase I to create •  Occurs because DNA is replicated in interphase to create
genetically divergent sister chromatids chromosomes with sister chromatids

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Topic 3.4: InHERITAnCE PATTERnS

Monohybrid Crosses Sex Linkage
A monohybrid cross determines the allele combinations for Sex linkage refers to when a gene is on a sex chromosome
potential offspring for one gene only •  I.e. X or Y (all other chromosomes are autosomal)
•  Crosses can be represented via the use of Punnett grids
Sex chromosomes (X/Y)
Monohybrid crosses are calculated via the following steps: •  Y chromosome is short X
•  Designate letters to represent alleles (e.g. A, a)
and has few genes (<100)
•  Identify genotype / phenotype of parents (P generation)
•  Determine genotype of gametes (haploid) •  X chromosome is large
•  Work out gamete combinations with a Punnett grid with many genes (~2000) Y
•  Identify ratios of offspring (F1 generation)
Sex-Linked Traits
Bb Bb
Sex-linked traits have altered inheritance patterns:
•  Males have a higher rate of X-linked recessive conditions
P Gametes B b B b
as they cannot mask the recessive allele (are hemizygous)
B •  Females can be carriers for X-linked recessive conditions
B
b BB b (heterozygotes can carry the allele but not express it)
Bb Bb
For X-linked conditions:
bb
•  Recessive: Affected mothers must have affected sons
•  Dominant: Affected fathers must have affected daughters
BB Bb Bb bb
Examples of X-linked recessive traits include:
•  Haemophilia (cannot clot blood properly)
F1 B B B b B b b b
•  Red-green colour blindness
Modes of Inheritance
A pedigree is a chart of genetic history over several generations

AUTOSOMAL DOMINANT
In a typical pedigree chart:
•  Males are represented as squares, while females as circles
•  Shaded symbols denote individual has a specified condition
•  A horizontal line between man and woman represents mating
•  Offspring numbered from left to right according to age PROOF
Not recessive as two affected parents

Autosomal Dominance: could not have an unaffected offspring
•  If both parents are affected by a trait and any offspring is
not, the trait must be dominant (parents must be heterozygous) AUTOSOMAL RECESSIVE
Autosomal Recessive:
•  If neither parents is affected by a trait but any offspring is,
the trait must be recessive (parents must be heterozygous)
PROOF
Sex-Linked Traits:
•  No way to conclusively prove sex-linkage with a pedigree Not dominant as two unaffected parents
could not have an affected offspring
chart, but certain patterns may suggest the possibility
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Topic 3.4: mODES oF InHERITAnCE

Principles of Inheritance Genotype versus Phenotype
Gregor Mendel established the principles of inheritance via A genotype is the allele combination for a specific trait
experimentation (he crossed large numbers of pea plants)
There are three possible types of allele combinations:
His findings pioneered current scientific understanding: •  Homozygous – Both alleles are the same (e.g. AA)
•  Organisms have heritable factors (genes) •  Heterozygous – Alleles are different (e.g. Aa)
•  Parents contribute equally to inheritance by supplying •  Hemizygous – Only one allele (e.g. X/Y genes in males)
one version of the gene each (alleles)
•  Gametes contain only one allele of each gene (haploid) A phenotype is the physical expression of a specific trait
•  Fusion of gametes results in zygotes with two alleles of •  It is determined by genotype and environmental factors
each gene (diploid)
A B
It is now known that the separation of the two alleles of Homo Hetero
each gene into separate haploid gametes occurs via meiosis A b
Modes of Inheritance
Complete Dominance Codominance

One allele is expressed over another Both alleles are equally expressed in the phenotype
•  Dominant allele is expressed in heterozygote (capital letter) •  Heterozygotes have a distinct phenotype (superscript letter)
•  Recessive allele is masked in heterozygote (lower case letter) •  An example of codominance is the ABO blood system
A recessive phenotype can only be expressed in homozygotes Blood Type Genotype Phenotypes
•  Heterozygotes will display the dominant phenotype
A IA IA or IA i
A B
B IB IB or IB i
AB IA I B
Phenotype Black Black Brown AB O
Genotype BB Bb bb O ii
Genetic Diseases Radiation Exposure
Genetic diseases can be due to recessive, dominant or codominant alleles Radiation and mutagenic chemicals increase
•  Recessive conditions are most common, as heterozygotes are carriers mutation rates and can cause genetic diseases
•  Most genetic diseases in humans are rare
Autosomal Recessive
•  Cystic fibrosis is caused by a mutated CFTR gene (chromosome 7) Two examples of radiation exposure are:
•  Produces thick mucus that clogs airways and causes respiratory issues •  Nuclear bombing of Hiroshima (1945)
•  Accident / meltdown in Chernobyl (1986)
Autosomal Dominant
Some long-term consequences included:
•  Huntington’s disease is caused by a mutated HTT gene (chromosome 4)
•  An amplification of CAG repeats (>40) leads to neurodegeneration •  An increased incidence of cancer
•  Reduced immunity (➡︎ T cell count)
Autosomal Codominant •  Congenital abnormalities (Chernobyl only)
•  Sickle cell anemia is caused by a mutated HBB gene (chromosome 11) •  A variety of organ-specific health effects
•  Sickling of blood cells leads to anemia and other complications (e.g. liver cirrhosis, cataract induction, etc)

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Topic 3.5: GEnETIC mODIFICATIOn

Gel Electrophoresis DNA Profiling
Gel electrophoresis is a technique that separates proteins or DNA profiling is a technique by which individuals can be
fragments of DNA according to size identified and compared by their genetic sequences
•  Samples placed in a block of gel and current is applied •  Individuals have different lengths of particular DNA
•  Smaller samples move faster through the gel (➡ resistance) segments called short tandem repeats (STR)
•  These segments are amplified by PCR and then separated
Samples will move towards the positive terminus (anode) by gel electrophoresis for comparison
•  DNA is negatively charged (due to phosphate group) •  Unique profiles appear when multiple loci are compared
•  Proteins are treated with an anionic detergent in order to
impart a uniform negative charge on all molecules DNA profiling is commonly used for:
•  Forensic investigations (matching suspect to the crime scene)
LARGE •  Paternity tests (offspring STRs are a combination of parents)
MEDIUM Sample Paternity Test
SMALL
Mother Child ‘Dad’ 1 ‘Dad’ 2 ‘Dad’ 3

Gene Transfer
Gene transfer can occur because the genetic code is universal
Step 1: DNA Extraction

•  Gene of interest isolated from organism
•  Gene is amplified using PCR (along with a plasmid)
Step 2: Digestion and Ligation

•  Plasmid and gene cut with a specific restriction enzyme GMO Debate
•  Gene is spliced into plasmid vector by DNA ligase
Benefits of GM Crops:
Step 3: Transformation and Expression •  Could be used to improve nutritional standards
•  Recombinant plasmid is inserted into a host cell •  Can grow in a wide range of environments ( yields)
•  Antibiotic selection may be used to select for successful •  Could reduce farming costs and associated deforestation
transgenic cells (if plasmid has an antibiotic resistance gene) •  Can be used to reduce spoilage (longer shelf life)
•  Transgenic cells express new protein (for extraction / use)
Risks of GM Crops:
Example: Production of Human Insulin in Bacteria •  Could trigger unexpected health issues (e.g. allergies)
•  Patent protections could restrict access (equity issues)
•  Possible cross-pollination with weeds (hard to contain)
Insulin Transgenic •  Could compete with native plants (reduce biodiversity)
gene bacteria
Human
Example of GM Crop:
Cell
•  Bt corn is a transgenic crop that produces an insecticide
Selection
(B. thuringiensis toxin kills European corn borer insect)
•  Bt corn may be impacting survival of monarch butterflies
•  In lab conditions, butterfly mortality is higher when fed
Bacteria plants dusted with Bt pollen, however there is insufficient
Plasmid Extract field evidence to support this (diet not naturally restricted)

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Topic 3.5: CLONING

Clones
Clones are groups of genetically identical organisms, derived from a single original parent cell
•  Various methods of cloning exists for animals and plants, while humans can also clone organisms or tissues artificially
Animal Cloning Human Cloning
Binary Fission Humans can also produce clones via natural mechanisms
•  The parental organism divides equally into two clones •  Identical twins (monozygotic) are created when fertilised
•  Occurs in flatworms (also used by bacteria and protists) eggs split in two, forming two identical embryos
Budding
MONOZYGOTIC TWINS
•  Cells split off from parent, generating smaller clones
•  Occurs in Hydra, but is also common to yeast
Fragmentation
•  New organisms grow from separated fragment of parent
•  Common to starfish and some species of annelid worm Zygote
splits
Parthenogenesis Genetically Shared
•  Embryos formed from an unfertilised (diploid) ova identical placentas
•  Occurs in some species of fish, insect, reptile, amphibian
Plant Cloning
Plants have the capacity for vegetative propagation, whereby small pieces of plant can be induced to grow independently
•  This is because adult plants possess totipotent meristematic tissue capable of cellular differentiation
A stem cutting is a separated portion of a plant stem that is used to regrow a new clone via vegetative propagation
Artificial Cloning
Embryo Cloning Adult Cloning

•  Animals can be cloned from an embryo by separating the •  Adults can be cloned via the process of somatic cell
embryonic cells into groups nuclear transfer (SCNT)
•  As embryonic stem cells are pluripotent, each cell can •  The nucleus is removed from an adult body cell (diploid)
potentially form a cloned offspring and fused with an enucleated egg cell
•  As this method occurs after random fertilization, it is not •  An electric shock stimulates division of the egg cell and
possible to control the genetic features of potential clones the growing embryo is implanted into a surrogate
UV
Early embryo
(identical cells)
Egg cell
enucleated
Clone
Adult cells Nuclei
Clone Clone cultured removed
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Topic 4.1: SPECIES ECOSystems

Ecological Organisation Modes of Nutrition
Species: Living organisms can obtain chemical energy by one of two

A group of organisms that can interbreed methods of nutrition (a few species can use both methods):
and produce fertile, viable offspring
Autotrophs
Population: Autotrophs synthesise organic molecules from inorganic
Group of organisms of the same species, nutrients within the environment, using energy from either:
living in the same area at the same time •  Light (photoautotrophs)
•  Oxidation reactions (chemoautotophs)
Community:
A group of different populations living Heterotrophs
together and interacting in a given area Heterotrophs obtain their organic molecules from other
organisms via a variety of feeding methods and food sources
Habitat: •  Consumers ingest other living organisms
The environment in which a species lives •  Detritivores ingest detritus (decomposing matter and faeces)
or the normal location of an organism •  Saprotrophs externally digest dead organisms (decomposers)
Ecosystem: Autotrophs are commonly referred to as producers, as they

A community and also its environment are responsible for the production of organic molecules
(all biotic and abiotic factors) •  Heterotrophs could not survive without autotrophs
Nutrient Cycling Mesocosms
Nutrients are materials required by organisms for survival Ecosystems have the potential to be sustainable over long
periods of time, however this requires three conditions:
The supply of inorganic nutrients within the environment is
•  Energy availability (e.g. light source)
finite and therefore must be constantly recycled:
•  Nutrient availability (e.g. decomposers)
•  Autotrophs convert inorganic nutrients into organic
molecules (i.e. they are producers) •  Waste recycling (e.g. detoxifying bacteria)
•  Heterotrophs ingest organic molecules and may release
Mesocosms are enclosed environments
inorganic byproducts (e.g. carbon dioxide)
with controlled conditions (e.g. terrariums)
•  Saprotrophs break down the nutrients in dead organisms
and return them to the soil (i.e. they are decomposers) •  They can be used to study sustainability
Species Associations Quadrat Sampling
The presence of species in a habitat may be dependent on The presence of a species in a given area can be determined
the interactions between them (either positive or negative) via quadrat sampling (to assess sessile/non-motile species)
•  Rectangular frame placed in an area (+ repeat sampling)
If species are always found in the same habitat, this suggests •  Species numbers within the frame are counted/estimated
a positive association (such as):
•  Predator / prey relationships
•  Symbiotic interaction (mutualism, commensalism, parasitism)
If species do not share the same habitat, this suggests there

is a negative association (such as):
•  Competition (niche partitioning or competitive exclusion)

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Topic 4.1: CHI-SquARED TesT

Worked Example
A chi-squared test can be applied to quadrat sampling data to determine if there

QUEEN
is a statistically significant association between the distribution of two species
Present Absent Total
Case Study: Scallops on a Rocky Shore
The presence / absence of two scallop species is recorded in 50 quadrats (1m2) Present 6 15 21
KING
The following distribution was found: Absent 20 9 29
• 6 quadrats = both species • 15 quadrats = king scallop only
Total 26 24 50
• 20 quadrats = queen scallop only • 9 quadrats = neither species
Step 1: Identify Expected Frequencies
There are two distinct possibilities regarding associations between the two species:
•  Null Hypothesis (H0) – There is no association (i.e. distribution is random)
QUEEN
•  Alternative Hypothesis (H1) – There is an association (positive or negative) Present Absent Total
A table must be constructed that identifies expected frequencies of distribution 21 × 26 21 × 24

Present 21
50 50
•  This data will be compared against the observed values previously identified
KING
29 × 26 29 × 24
Absent 29
50 50
The expected frequencies can be calculated using the following formula:
•  Expected frequency = (Row total × Column total) ÷ Grand total Total 26 24 50
Step 2: Apply the Chi-Squared Formula
The chi-squared (!2) formula calculates a value based on a comparison of the

QUEEN
observed frequencies (O) and the expected frequencies (E)
2 Present Absent
!2 = ∑ (O – E)
E O 6 15
Present
Based on the worked example, the value calculated by the chi-squared test is: E 10.9 10.1
•  !2 = 2.20 + 2.38 + 1.59 + 1.73 = 7.90 (O – E)2
2.20 2.38
KING
E
A degree of freedom (df) will also be required to determine statistical significance O 20 9
Absent
•  df = (number of rows – 1) × (number of columns – 1) E 15.1 13.9

(O – E)2
Raw data table had two rows and two columns, so degree of freedom equals one 1.59 1.73
E
Step 3: Determine Significance
The chi-squared value is used to determine statistical significance (p value) Values that
df
•  p<0.05 is considered significant (less than 5% likelihood results due to chance) are greater
1 than this are
Based on the worked example, a value of 7.90 lies above a p value of 0.01 statistically
•  This means results are significant (less than 1% probability it is due to chance) 0.01 6.635 significant
p value
The null hypothesis can be rejected and the alternative hypothesis accepted 0.05 3.841
Because the species do not tend to co-exist, we might infer a negative association 0.1 2.706

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Topic 4.2: EnERGy FLOW

Energy Flow Trophic Levels
Energy Source An organism’s trophic level refers to the position it occupies

Light is the initial energy source for almost all communities within a feeding sequence
•  Some producers derive energy from chemical processes •  Producers always occupy the first trophic level
Light energy is converted into chemical energy (i.e. organic

Trophic Level Organism
compounds) via the process of photosynthesis
1 Producer
Energy Transfer 2 Primary Consumer
Heterotrophs obtain their chemical energy by feeding
3 Secondary Consumer
•  The energy stored in organic molecules is released via
cellular respiration (in heterotrophs and autotrophs) 4 Tertiary Consumer
Feeding Patterns
Food Chains Food Webs

Food chains show linear feeding patterns between the Food webs show interrelated feeding patterns
species in a community •  Most species have multiple food sources and hence will
•  Arrows indicate the direction of energy flow occupy multiple trophic levels
Producer Primary Secondary Tertiary

Consumer Consumer Consumer
Energy Loss Pyramids of Energy
Not all the stored energy is transferred upon feeding – most Pyramids of energy are representations of the amount of
of the energy released via cell respiration is lost as heat energy available at each trophic level
•  Organisms cannot convert heat into other energy forms •  Measured in energy units per area per time (kJ m2 year–1)
and hence the heat is lost from the ecosystem
Pyramids of energy can never be inverted and their levels
Only ~10% of energy is transferred from one trophic level should differ by a factor of ~10
to the next (90% is lost as heat or is unconsumed) •  Because energy transformations are ~10% efficient
•  These energy losses restrict the length of food chains
and limit the biomass of higher trophic levels
10 J
SIMPLE FOOD CHAIN
100 J
1,000 J
10,000 J
100 L 10 L 1L 100 mL 1,000,000 J of sunlight

ENERGY FLOW OVERVIEW
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Topic 4.3: CARBON CyCLING

Carbon Cycle Organic Conversions
Autotrophs convert atmospheric carbon dioxide into organic

CO2 compounds via the process of photosynthesis
Photo-
synthesis •  Equation (balanced): 6CO2 + 6H2O C6H12O6 + 6O2
Respiration
Feeding Heterotrophs obtain organic compounds via feeding
The breakdown of organic compounds via cell respiration

MACHINES ANIMALS PLANTS OCEAN (to produce ATP) releases carbon dioxide as a by-product
•  Equation (balanced): C6H12O6 + 6O2 6CO2 + 6H2O
Combustion
Decomposition
CO2 CO2
FUELS FOSSILS CaCO3 CARBON

COMPOUNDS
Fossil Fuels
PHOTO- CELL
In aerobic conditions, saprotrophic bacteria will break down SYNTHESIS RESPIRATION
organic material and return it to the soil (i.e. decomposition)
In anaerobic conditions, decomposition is prevented as the Aquatic Conversions

saprotrophic bacteria cannot function effectively
In aquatic ecosystems, carbon dioxide may remain dissolved
•  Anaerobic respiration will produce organic acids (➡ ph)
in water or alternatively form hydrogen carbonate ions
Peat / Coal
Animals may combine the carbonate ions with calcium to
•  Organic matter that is not fully decomposed in anoxic or
form hard shells (e.g. mollusca) and exoskeletons (e.g. coral)
acidic soils will become peat
•  When peat is compressed under layers of sediment, heat Carbonate ions may also interact with rock and sediment to
and pressure remove moisture to transform it into coal form limestone
Oil / Natural Gas

•  When marine organisms are buried under sediment on Methane Production
the ocean floor, compaction and anaerobic conditions
Methane (CH4) is produced from organic compounds by
transform the organic matter into oil and natural gas
methanogenic archaeans
Combustion This requires anaerobic conditions (commonly found in

wetlands, marine sediments or digestive tract of ruminants)
Hydrocarbons undergo combustion in the presence of O2
•  The reaction is exergonic and CO2 and H2O is produced Methane diffuses into the air or forms deposits underground
•  In the air, methane is oxidised to form CO2 and H2O
Sources of hydrocarbons include:
•  Fossilised organic matter (i.e. coal, oil and gas) H O
•  Biomass (e.g. bioethanol and biofuels) H H
H C H OXYGEN C O
The energy produced by combustion reactions is typically H O
used to power industrial processes
•  The combustion of fossil fuels is responsible for a Methane Carbon Water
significant increase in atmospheric CO2 concentrations Dioxide (vapor)

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Topic 4.4: CLImATE CHAnGE

Greenhouse Effect
Greenhouse gases include carbon dioxide, water vapor, methane & nitrogen oxides
•  Their impact depends on their concentration and ability to absorb IR radiation Long
wavelength
•  Water vapor and carbon dioxide are the most significant greenhouse gases
The greenhouse effect is a natural process that increases average temperatures: Short
•  Incoming radiation from the sun includes short-wave ultraviolet (UV) radiation wavelength
•  This radiation may be emitted by the Earth as long-wave infrared (IR) radiation
•  Greenhouse gases absorb and re-emit this infrared radiation as heat
Carbon Dioxide Concentrations
Carbon fluxes describe the amount of carbon transferred

390
between various carbon pools (e.g. lithosphere atmosphere)
Carbon dioxide concentration (ppmv)

Atmospheric Carbon Dioxide 380
Measured at Mauna Loa, Hawaii
Carbon dioxide concentrations are increasing within the
370
atmosphere due to a number of human-induced activities:
360
•  Industrial practices (i.e. combustion of fossil fuels)
•  Deforestation (less CO2 transferred to the biosphere) 350
•  Agriculture (land clearing and methane production) Annual Cycle 340
330
As global temperatures and climate patterns are influenced
by greenhouse gases, increasing CO2 concentrations may be 320
Jan Apr Jul Oct Jan
causing global climate change (enhanced greenhouse effect) 310
1960 1970 1980 1990 2000
•  There is a positive correlation between rising CO2 levels
Year
(since industrial revolution) and average global temperature
Ocean Acidification
The oceans are a major carbon sink (i.e. stores CO2 from the atmosphere)
NORMAL
•  Some of the CO2 remains dissolved, but most of it is chemically converted

•  CO2 is converted into carbonic acid, which dissociates to release H+ ions
This conversion impacts marine organisms (such as coral) in a number of ways:

BLEACH
•  It increases ocean acidity, which can stress coral survival ( H+ = ➡ pH)

•  It lowers carbonate levels, which is required for shells and exoskeletons
•  These conditions can cause coral to expel mutualistic algae (coral bleaching)
Climate Change Debate
Is current climate change natural? Are greenhouse gases the cause? Are climate models reliable?
Claim: Claim: Claim:

Historical data show temperature cycles Changes could be caused by sunspots Models may make varying predictions
Counter: Counter: Counter:

Past changes were not as abrupt Climate changes don’t match sun activity All the climate models are predicting a
Ocean levels are rising, pH decreasing CO2 levels are highest ever recorded temperature increase by 2100 (~2–6ºC)

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Topic 5.1: EvOLuTIOn

Evolution
Evolution is the cumulative change in the heritable characteristic of a population (i.e. biological change over time)
•  These characteristics are encoded by genes and transferred between generations as alleles
Hence, evolution is a change in the allele frequency of a population’s gene pool over successive generations
Theories of Evolution
Lamarck Darwin (and Wallace)

Proposed that species change via habitual use and disuse Proposed that species change via natural selection
•  A giraffe stretches it neck to reach leaves in tall trees •  A giraffe with a longer neck can reach leaves in tall trees
•  The giraffe’s neck becomes extended from constant use •  The giraffe will get enough food to survive and reproduce
•  The giraffe’s offspring inherit its long neck •  The giraffe has more offspring (that inherit a long neck)
This theory has been rejected because these acquired traits Darwin’s theory has been reinforced by our understanding
do not have a genetic basis (and thus cannot be inherited) of modern genetics (incorporated as neo-Darwinism)
Mechanisms of Change
Fundamental to the process of evolution is the presence of There are two mechanisms by which population variety can
variation within populations upon which selective forces act be altered (➡ biodiversity):
•  Random chance (genetic drift)
There are three main mechanisms by which genetic variation
•  Directed intervention (natural or artificial selection)
within a population is maintained:
•  Mutations – changes to the gene sequence The impact of a change is greater if the population is small
•  Sexual reproduction – new gene combinations (this may occur via population bottlenecks or founder effect)
•  Gene flow – immigration and emigration
chance selection
event pressure
Mutation Sex Gene Flow Genetic Drift Natural Selection
Speciation
If populations become isolated, the level of genetic divergence

gradually increases the longer the populations remain separated
•  Continuous variation across a geographical range of related
populations matches this concept of gradual divergence
Speciation will occur when populations diverge to the extent that

they can no longer interbreed and produce fertile, viable offspring

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Topic 5.1: EvIDEnCE FOR EvOLuTIOn

Fossil Record Comparative Anatomy
A fossil is the preserved remain or trace of a past organism Homologous structures are anatomical features that share a
•  The totality of all fossils is called the fossil record common basic structure despite having distinct functions
Law of Fossil Succession The rapid diversification of an anatomical feature is a result

The fossil record shows that changes have occurred in of adaptive radiation (organisms adapt to different niches)
organisms and these changes have occurred in a consistent •  Closely related species demonstrate greater homology
sequence of development (the law of fossil succession)
•  Example: Ferns always appear before flowering plants The pentadactyl limb is a prime example of a homologous
structure (different appendages, yet same bone structure)
Transitional Fossils
Transitional fossils represent intermediary forms within the Homologous Structures – Pentadactyl Limb
evolution of a genus and demonstrate species connections
•  Example: The archaeopteryx links the evolution of
birds (wings and feathers) to dinosaurs (jaws and claws)
Selective Breeding
Selective breeding involves the mating of animals with

desired characteristics (it is a form of artificial selection)
As human intervention drives selection, changes will occur

over fewer generations as phenotype extremes are promoted
Comparative Embryology
Examples of selective breeding include:
Comparing embryonic development in animals demonstrates
•  Draft horses (power) versus racing horses (speed)
similarities that suggest a common evolutionary pathway
•  Large variation in types of dog breeds
•  All terrestrial animals have non-functioning gill slits
•  Many vertebrate have a primitive tail in early stages
Molecular Evidence
Closely related species share a greater degree of similarity in

their DNA and protein sequences (due to common ancestry)
If a particular gene has a stable mutation rate, the time of

evolutionary divergence can be estimated (‘molecular clock’) Chicken Tuna fish Human Dolphin
Vestigial Structures Biogeography
Some species show the presence of functionless or reduced Biogeography is the distribution of species across an area
remnants of organs that were once present in ancestors •  Related species will usually be found in close proximity
•  E.g. Whales have a pelvic bone (ancestors were terrestrial) •  E.g. Monotremes are exclusive to Australia/New Guinea
Exceptions may be explained via continental drift

•  E.g. The ratites (flightless birds) are globally
distributed over continents that were once
part of a single land mass (Gwondanaland)

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Topic 5.2: nAturAL SELECTIOn

Natural Selection
The process of natural selection occurs in response to certain conditions:

•  There is genetic (inheritable) variation within a population (caused by mutations, meiosis and sexual reproduction)
•  There is competition for survival (species tend to produce more offspring than the environment can support)
•  Environmental selection pressures give rise to differential rates of reproduction
•  Organisms with beneficial traits are likely to survive and reproduce, while those less well adapted produce less offspring
•  Over generations, these beneficial traits become more common (evolution = a change in allele frequency in a gene pool)
bright dull
Variation Competition Adaptations Selection
Overview Selection Pressures
The key components to the process of natural selection are: Examples of environmental selection pressures include:
•  Inherited variation •  Predator / prey dynamics
•  Competition •  Abiotic factors (e.g. climate)
•  Environmental selection •  Nutrient supply (food source)
•  Adaptations •  Diseases / pathogens
•  Genotype frequency changes •  Available resources (e.g. light)
•  Evolution occurs •  Space requirements (habitat)
Adaptations
Adaptations are traits that make an individual suited to its environment and way of life
•  Adaptations can be structural, behavioural, physiological, biochemical or developmental
insects
Populations will evolve different adaptations according to environmental conditions
leaves nectar
•  The functional position of an organism in the environment is its ecological niche
seeds grubs
Ancestor
When members of a species occupy a variety of different ecological niches, it will lead to
tool use
the rapid diversification of the original ancestral line (this is called adaptive radiation)
•  An example of this can be seen in the changes in beaks of finches on Daphne Major
Examples of Evolution
Certain types of bacteria have developed antibiotic resistance The peppered moth displays two distinct melanic forms
•  These strains are more prevalent where antibiotics are •  The frequency of these forms has evolved with pollution
commonly used (e.g. hospitals) levels (dark colors thrive when trees are covered in soot)
1 2 3 4
Both strains Antibiotics kills Resistant Conjugation may Industrial period Post-Industrial period
exist normally susceptible strains strains thrive transfer trait (black moths more common) (white moths more common)

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Topic 5.3: CLASSIFICATIOn

Binomial Nomenclature Domains of Life
The binomial system of naming is a globally recognised All living organisms are classified into one of three domains:
classification scheme developed at a series of congresses •  Eukarya (all eukaryotic organisms)
•  It was first proposed by Carl Linnaeus in 1735 •  Archaea (prokaryotic extremophiles)
•  Eubacteria (common pathogenic bacteria)
According to the binomial system, every organism has a
two-part scientific name: Originally, the two prokaryotic domains (Archaea and Eubacteria)
•  Genus is written first and is capitalised (e.g. Homo) were considered part of a single kingdom (Monera)
•  Species follows in lower case (e.g. Homo sapiens) •  However, biochemical differences prompted a reclassification
Hierarchy of Taxa Eukarya Archaea Eubacteria

Histones Present Present Absent
Taxonomy is the science of classifying organisms based
on shared characteristics (or taxa) Introns Present Present Absent
•  More taxa shared = more closely related organisms Nucleus Present Absent Absent
Taxa Animal Plant Hint: Ribosome 80S 70S 70S
Kingdom Animalia Plantae Katy

Natural Classification
Phylum Chordata Angiosperm Perry
Class Mammalia Eudicotidae Comes Natural classification involves grouping organisms according to
common ancestry rather than by common characteristics
Order Primate Ranunculales Over
•  This allows for species to be identified by their evolutionary
Family Hominidae Ranunculacae For
pathways and enables the prediction of traits within a group
Genus Homo Ranunculus Grape
A disadvantage of natural classification is that taxonomists may
Species sapiens acris Soda
need to reclassify groups if new phylogenetic evidence emerges
•  Gorillas and chimps were included in a Homininae sub-family
Common Human Buttercup
•  The figwort family was reclassified based on cladistics data
Dichotomous Keys
A dichotomous key involves sequentially dividing organisms into two categories until every organism is individually identified
Example of a Dichotomous Key: Diagrammatic Representation:

1.  Organism is asymmetrical .................................... Porifera Invertebrate Phyla
Organism is symmetrical ................................... Go to Q2
Asymmetrical Symmetrical
2.  Has radial symmetry ............................................ Cnidaria
Bilateral Radial
Has bilateral symmetry ...................................... Go to Q3
Porifera
3.  Has no separate anus ................................. Platyhelmintha Anus No anus
Cnidaria
Has a separate anus ........................................... Go to Q4 Not visible Segmentation
4.  Has visible body segmentation .......................... Go to Q5 Platyhelmintha

Segmentation not clearly visible .......................... Mollusca Mollusca None Exoskeleton
5.  Has an exoskeleton ........................................ Arthropoda

Has no exoskeleton ............................................ Annelida Annelida Arthropoda

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Topic 5.3: BIODIvERSITy

Plant Phyla
Bryophyta (e.g. liverworts and mosses) Coniferophyta (e.g. conifers)

•  No vascularisation (lacks xylem / phloem) •  Have vascularisation (xylem and phloem)
•  Reproduce via spores released by stalks •  Reproduce via seeds (found in cones)
•  No ‘true’ leaves, roots or stems •  Narrow leaves with a thick, waxy cuticle
Filicinophyta (e.g. ferns) Angiospermophyta (e.g. flowering plants)

•  Have vascularisation (xylem and phloem) •  Have vascularisation (xylem and phloem)
•  Reproduce via spores in sporangia •  Reproduce via seeds (found in fruits)
•  Have large fronds divided into leaflets •  Have flowers as reproductive organs
Invertebrate Phyla
Porifera (e.g. sponges) Annelida (e.g. earthworms and leeches)

•  Have an asymmetrical body plan •  Possess bilateral symmetry
•  Have no mouth or anus (have pores) •  Have a separate mouth and anus
•  May have spicules for structural support •  Body composed of ringed segments
Cnidaria (e.g. jellyfish and anemones) Mollusca (e.g. squids, slugs, snails, bivalves)
•  Possess radial symmetry •  Possess bilateral symmetry
•  Have a mouth but no anus (single opening) •  Have a separate mouth and anus
•  Has tentacles and stinging cells (cnidocytes) •  Has non-visible segments (may have a shell)
Platyhelmintha (e.g. flatworms, tapeworms) Arthropoda (e.g. insects, spiders, crustaceans)

•  Possess bilateral symmetry •  Possess bilateral symmetry
•  Have a mouth but no anus (single opening) •  Have a separate mouth and anus
•  Has a flattened body (increases SA:Vol ratio) •  Have jointed appendages and exoskeleton
Vertebrate Classes
Phylum Chordata (i.e. vertebrates) Reptiles

•  Possess bilateral symmetry •  Covered in scales (made of keratin)
•  Have a separate mouth and anus •  Have internal fertilisation (lays soft eggs)
•  Have a notochord (may form a backbone) •  Breathe via lungs and are ectothermic
Fish Birds
•  Covered in scales (bony plates of skin) •  Covered in feathers (made of keratin)
•  Reproduce via external fertilisation •  Have internal fertilisation (lays hard eggs)
•  Breathe through gills and are ectothermic •  Breathe via lungs and are endothermic
Amphibians Mammals
•  Have a moist skin (permeable to gases) •  Covered in skin (and keratin hair follicles)
•  Reproduce via external fertilisation •  Have internal fertilisation (and lactation)
•  Breathe through skin and are ectothermic •  Breathe via lungs and are endothermic

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Topic 5.4: CLADISTICS

Clades
Cladistics involve classifying organisms into groups of species (clades)

CLADE NOT A CLADE
•  A clade consists of a single common ancestor and all descendants
Cladograms are tree diagrams where each branch point represent the
splitting of two new species groups from a common ancestral species
•  Each branch point (node) represents a speciation event
•  The more nodes between groups, the less related the groups are
Structural Evidence Molecular Evidence
Historically, cladograms have been constructed based on Cladograms are now being generated via a comparison of
structural characteristics, however this not always a reliable biochemical evidence (i.e. DNA or amino acid sequences)
method for establishing evolutionary connections •  Related species will have sequences with more similarities
•  Related species may have distinctive (homologous) features •  Amino acid sequences will accumulate differences at a
•  Unrelated species may have similar (analogous) features slower rate to DNA sequences (due to degeneracy)
If a sequence accumulates mutations at a constant rate, the

HOMOLOGOUS ANALOGOUS time of divergence can be calculated based on the number
Structures look different Structures look similar of mutations between the two species (molecular clock)
Due to different Due to common

selection pressures selection pressures
Species do share a Species do not share

common ancestry a common ancestry
Evidence of Evidence of
divergent evolution convergent evolution Human Monkey Dog Bird Fish
E.g. Pentadactyl limb E.g. Fins (whale vs shark) Haemoglobin -chain: Similarities Differences
Cladograms
Structural Data: Compare characteristics via a table Example: Humans and Other Primates
Lungs Endothermic Hair / skin

Fish – – –
Lizard – – Gibbon Orangutan Gorilla Chimp Man
Bird – 0
Rodent
5
Millions of years ago
Molecular Data: Compare sequences via multiple alignment 10

Mutations
fish F A A A A F Q F G F T I 4
15
lizard F S T A A F R P P H T V 3
bird F S T A A F R G G H T I 1
20
rodent F S T A A F R F G H T I 0
Consensus F S T A A F R F G H T I 25

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Topic 6.1: DIGESTIOn

Purpose of Digestion
The main purpose of the digestive system is to break large molecules down into smaller subunits due to the fact that:
•  Large molecules are typically chemically inert and need to be broken down and reassembled into usable products
•  Large molecules are typically insoluble and cannot be easily absorbed into cells, whereas smaller subunits are soluble
Digestive System Structure Digestive System Components
The digestive system is composed of the alimentary canal

and a variety of supporting accessory organs
Salivary
Glands
Oesophagus Alimentary Canal (directly transfers food)
•  Oesophagus – Food tract from mouth to stomach
Liver •  Stomach – Storage tank with low pH (protein digestion)
Stomach •  Small intestine – Site of nutrient absorption
Gall •  Large intestine – Absorbs water and dissolved minerals
Bladder
Pancreas Accessory Organs (supports digestive processes)
Small •  Salivary glands – Moistens food bolus (starch digestion)
Intestine •  Pancreas – Secretes key enzymes into small intestine
Large
•  Liver – Metabolises absorbed nutrients (produces bile)
Intestine
Rectum •  Gall bladder – Stores and secretes bile (emulsifies fats)
Digestive Movement
Peristalsis Segmentation
•  Unidirectional movement of food along alimentary canal •  Bidirectional mixing of food within the small intestine
•  Caused by contraction of sequential longitudinal muscles •  Caused by contraction of non-sequential circular muscles
Types of Digestion Starch Hydrolysis
Food can be digested by one of two ways: Starch is composed of glucose monomers Liver
•  Is linear (amylose) or branched (amylopectin) Mouth
Mechanical Digestion
The breakdown of food via physical actions Amylase (salivary or pancreatic) digests starch
•  Chewing (grinding food using teeth) •  It digests amylose into maltose disaccharides
•  Churning (squeezing stomach contents) •  It digests amylopectin into dextrin chains
•  Segmentation (intestinal contractions)
The pancreas regulates the uptake of glucose Stomach
Chemical Digestion •  Insulin increases glucose uptake by cells
The breakdown of food via chemical agents •  Glucagon decreases glucose uptake by cells
•  Stomach acids (low pH environment)
The liver is responsible for glucose storage Pancreas
•  Bile (emulsification of fats into droplets)
•  Enzymes (catalyse hydrolysis reactions) •  Glucose is stored as glycogen (polysaccharide) Small Intestine
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Topic 6.1: ABSORPTIOn

Purpose of Absorption
Absorption involves the movement of fluids or dissolved substances (such as nutrients) across a cellular membrane
•  The absorbed components then undergo assimilation within the cell in order to become fluid or solid parts of an organism
Nutrient absorption occurs within the small intestine, while water and mineral ions are absorbed within the large intestine
Membrane Transport Mechanisms
Secondary Active Transport Endocytosis

•  Glucose and amino acids are co-transported across the •  Dissolved materials may be rapidly absorbed en masse via
epithelial membrane with sodium ions (Na+) the process of pinocytosis (cell ‘drinking’)
Facilitated Diffusion Extracellular Fluid

•  Certain monosaccharides, vitamins and some minerals
may be transported by epithelial channel proteins
Simple Diffusion
•  Hydrophobic materials (e.g. lipids) are capable of freely
Cytoplasm Vesicle
diffusing across the epithelial membrane
Small Intestine Structure
Transverse Cross-Section Longitudinal Cross-Section
Serosa
Villi
Longitudinal muscle
Circular muscle
Mucosa
Submucosa
Muscle
Mucosa layers
Villi Modelling Absorption
Villi are finger-like mucosal projections that Dialysis tubing can be used to model the Sample Experiment:
increase the surface area of epithelium over size-specific permeability of a membrane
which absorption is carried out •  Large molecules cannot cross (e.g. starch)
•  Smaller molecules can cross (e.g. glucose)
Key features of villi include:
•  Microvilli ( ︎ SA:Vol) If large molecules are digested with enzymes,
•  Rich blood network the absorption of the smaller subunits can
•  Single layer epithelium then be measured in a number of ways:
•  Lacteals (absorb lipids) •  Via a change in fluid / meniscus levels Control Digestion
•  Intestinal crypts (exocrine) •  Via the presence of specific materials Starch in Maltose exits
•  Membrane proteins (identified via treatment with a reagent) Water in Water exits

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Topic 6.2: THE BLOOD SySTEm

Circulation
William Harvey proposed the modern understanding of the circulatory system

Vena Cava Pulmonary
According to Harvey: Vein
•  The major blood vessels (arteries & veins) are connected by a single network
ORGAN LUNG
•  Blood flow is unidirectional (due to the presence of one-way valves)
•  The heart is a central pump (arteries = from heart ; veins = to heart) Pulmonary
Aorta Artery
•  Blood flows continuously and is not consumed by the body
It has further been dicovered that: RIGHT SIDE LEFT SIDE

•  Arteries and veins are connected by capillaries (via arterioles & venules) Body Lungs Lungs Body
•  There is a separate circulation for the lungs (pulmonary versus systemic) (Deoxygenated) (Oxygenated)
Blood Vessels
Arteries Veins Capillaries

•  Transport blood from the heart •  Transport blood to the heart •  Facilitate material exchange
•  Blood at high pressure (80-120 mmHg) •  Blood at low pressure (<15 mmHg) •  Blood at low pressure (~10 mmHg)
•  Walls are thick (muscle and elastin) •  Walls are thin (with wider lumen) •  Walls made of single layer of cells
•  Walls stretch or contract with pulse •  Have valves to prevent pooling •  Extremely narrow lumen (~10 µm)
Capillaries may be categorised as:

•  Continuous (intact basement membrane)
•  Fenestrated (have endothelial pores)
•  Sinusoidal (discontinuous membrane)
endothelium basement
collagen muscle/elastic fibres collagen muscle/elastic fibres (single layer) membrane
Blood Blood Flow
Blood contains three main elements: A heart pumps blood around the body via two distinct circulatory pathways
•  Red blood cells (transport oxygen)
Right Side (of heart):
•  White blood cells (fight infections)
•  Deoxygenated blood (from tissues) enters right atrium via the vena cava
•  Platelets (responsible for clotting)
•  Blood in the right ventricle is pumped to lungs via the pulmonary artery
The blood fluid (plasma) transports: •  Gas exchange at the lungs (capillaries ⟷ alveoli) oxygenates the blood
•  Nutrients (e.g. glucose)
Left Side (of heart):
•  Antibodies
•  Oxygenated blood (from lungs) enters left atrium via the pulmonary vein
•  Carbon dioxide •  Blood in the left ventricle is pumped to the body tissues via the aorta
•  Hormones
•  Material exchange occurs at the respiring tissue (deoxygenates the blood)
•  Oxygen
•  Urea Valves in veins ensure proper circulation by preventing backflow of blood
•  Heat NACHO-UH! •  Contraction of skeletal muscles may compress veins to aid blood flow

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Topic 6.2: THE HEART

Heart Structure Mechanism of Heart Beat
Superior Pulmonary A heart beat is myogenic (contraction initiated by the heart)

Vena Cava Artery •  Electrical signals are initiated by a sinoatrial (SA) node
Aorta
•  This pacemaker stimulates the atria to contract and also
relays signals to an atrioventricular (AV) node
Pulmonary •  The AV node sends signals to ventricular Purkinje fibres
Left Vein
Atrium (via a Bundle of His within the wall of the septum)
Right 2 •  The Purkinje fibres cause the ventricular walls to contract
Atrium
3 Left
4 Ventricle The SA node maintains a normal sinus rhythm (60-100 bpm)
Inferior •  The pacemaker is regulated by the medulla oblongata
Vena Cava 1 Right •  Sympathetic nerves release noradrenaline ( ︎ heart rate)
Ventricle
•  Parasympathetic nerves release acetylcholine (➡ heart rate)
•  Heart rate may also be increased via hormonal action
Valves: (via the release of adrenaline / epinephrine)
1.  Tricuspid valve (right) 3.  Pulmonary valve (right) •  Adrenaline will cause a more sustained elevation in heart
2.  Bicuspid valve (left) 4.  Aortic valve (left) rate than that achieved by the action of the brainstem
Cardiac Cycle
The cardiac cycle describes the events of a heart beat

Atrial Ventricular Systole Diastole
Systole (contraction)
•  As atria contract, atrial pressure exceeds ventricular 120 Aortic valve Aortic valve
pressure (AV valves open blood flows to ventricles) opens closes
•  As ventricles contract, ventricular pressure exceeds
atrial pressure (AV valves close 1st heart sound) 90
•  Pressure builds (isovolumetric contraction) until the Aorta

ventricular pressure exceeds the arterial pressure Ventricle
60
•  Semilunar valves open and blood flows into arteries
Diastole (relaxation) Atrium AV valve AV valve

30 opens
closes
•  As blood flows into arteries, ventricular pressure drops
•  Backflow closes semilunar valves 2nd heart sound
0
•  When ventricular pressure drops below atrial pressure, 0 100 200 300 400 500 600
the AV valves will open and cardiac cycle is repeated Pressure (mm Hg) Time (ms)
Coronary Heart Disease Risk Factors
Coronary thrombosis is caused by clots within the coronary arteries Risk factors for CHD include:
•  Vessels are damaged by cholesterol deposition (atherosclerosis) •  Genetics (e.g. hypertension)
•  The deposits reduce vessel diameter and increase blood pressure •  Obesity (overweight = risk)
•  The stress damages arterial walls (and is repaired with fibrous tissue) •  Diseases (e.g. diabetes)
•  The vessel wall loses elasticity and forms atherosclerotic plaques •  Diet (e.g. ︎ trans fats)
•  If a plaque ruptures, blood clotting is triggered, forming a thrombus •  Exercise (inactivity = risk)
•  If the thrombus blocks blood flow, a myocardial infarction results •  Smoking ( ︎ blood pressure)
•  These events are collectively described as coronary heart disease •  Sex (males = higher risk)
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Topic 6.3: DEFEnCE AGAInST DISEASE

Pathogens Antibiotics
Pathogens are disease-causing agent that disrupt the normal Antibiotics are compounds that target prokaryotic features
physiology of infected organisms (i.e. homeostatic imbalance) but don’t harm eukaryotic cells (i.e. don’t affect host organism)
•  May target structures (e.g. cell wall) or metabolic processes
Pathogens may be species-specific or cross species barriers
•  Diseases that can be naturally transmitted between Some strains of bacteria have evolved with genes that confer
animals and humans are called zoonotic diseases resistance to antibiotics (some even have multiple resistance)
•  Antibiotics can’t be used to treat viruses (no metabolism)
LIVING (CELLULAR) NON-LIVING
The first antibiotic identified was penicillin (Fleming – 1928)
•  Its treatment use was demonstrated by Florey and Chain
Experiment: Mice infected with pathogenic bacteria

Parasite Protozoa Fungi Bacteria Virus Prion Control: No treatment Treatment: Penicillin
Lines of Defense
Immune system can be divided into three lines of defense:

•  1st line of defense – Surface barriers (skin / mucus)
Result: All mice died Result: All survived
•  2nd line of defense – Innate immunity (non-specific)
•  3rd line of defense – Adaptive immunity (specific) Conclusion: Penicillin has antibiotic properties
Surface Barriers Clotting
The first line of defense against infectious disease is the Clotting seals damaged vessels to prevent pathogenic entry
surface barriers that function to prevent pathogenic entry •  Injured cells and platelets release clotting factors
•  These factors convert prothrombin into thrombin
Skin •  Thrombin converts fibrinogen (soluble) into fibrin (insoluble)
•  Protects external structures (i.e. outside the body) •  Fibrin forms a mesh of fibres that block the injured site
•  Thick, dry and composed predominantly of dead cells •  Clotting factors also cause platelets to become sticky and
•  Glands secrete chemicals to restrict bacterial growth form a solid plug (called a clot), sealing the wound
•  This process of events is called a coagulation cascade
Mucous Membranes
•  Clot formation in coronary arteries lead to heart attacks
•  Protects internal structures and cavities (inside body)
•  Thin region composed of living cells that secrete fluid
(mucus) to trap pathogens (which may then be removed) Clotting Factors
Lysozyme Prothrombin Thrombin

Cilia within in tears
nasopharynx
Fibrinogen Fibrin
Mucus lining
Intact skin trachea
Commensals pH change
(normal flora) in the gut
Vaginal acids Flushing of

(in females) urinary tract Damaged Vessel Clot Formation

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Topic 6.3: InnATE ImmunITy

Innate Immunity
The innate immune responses share two key characteristics:

•  They are non-specific (i.e. they do not differentiate between different types of pathogens)
•  They are non-adaptive (i.e. they produce the same response to every infection – there is no immunological memory)
Lymphatic System Phagocytosis
The lymphatic system is a secondary transport system that Macrophages and dendritic cells migrate via the blood to
protects the body by producing and filtering lymph sites of infection (damaged cells release chemotactic agents)
•  Lymph is a clear fluid rich in white blood cells that arises
The pathogens are surrounded by extensions (pseudopodia)
from the drainage of interstitial fluid from the tissues
and are then internalised within a vesicle (via phagocytosis)
•  Lymph is filtered at lymph nodes, whereby pathogens are
removed and the fluid is returned to venous circulation The vesicle may fuse with a lysosome to digest the pathogen
•  Fragments (antigens) are presented on the surface of the
Inflammation cell in order to activate the third line of defense (adaptive)
Tissue damage causes mast cells to release histamine, which antigen presentation
triggers vasodilation and increased capillary permeability
•  This improves the recruitment of white blood cells
An inflammatory response, while necessary, has side effects:

•  Vasodilation = localised redness & heat ( ︎ blood flow)
•  Capillary permeability = swelling & tenderness ( ︎ fluid) pathogen
Inflammation can be short-term (acute) or long-term (chronic)
Fever Complement System
Fever is an abnormally high body temperature (due to infection) Inactive complement proteins are produced by white blood
•  It increases metabolism and activates heat shock proteins cells and certain body cells (particularly the liver)
•  It reduces the growth rate of infectious pathogens
In response to immune activation, they trigger a cascade of
Fever occurs when white blood cells release cytokines reactions that help protect the body from infection:
•  This causes the hypothalamus to produce prostaglandin •  Opsonisation (increase pathogen recognition by phagocytes)
•  Prostaglandin increases the temperature of the body •  Chemotaxis (recruitment of phagocytes to the infection site)
•  Membrane attack (forms a complex that ruptures cell walls)
While a fever may initially strengthen an immune response,
beyond tolerable limits it will cause damage to the body
Natural Killer Cells
Pathogens Hypothalamus Prostaglandin
Natural killer cells are a class of non-specific lymphocytes
that can target and destroy infected body cells or tumor cells
•  Infected cells release chemicals called interferons, which
function to promote the activation of natural killer cell
•  Natural killer cells induce apoptosis in the infected cell
Natural killer cells are part of the innate immune response

Leukocytes Cytokines Fever because they do not rely on antigen recognition to function

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Topic 6.3: ADAPTIvE ImmunITy

Adaptive Immunity
The adaptive immune responses share two key characteristics:

•  They are specific (i.e. they can differentiate between different types of pathogens and respond accordingly)
•  They are adaptive (i.e. they produce a heightened response upon re-exposure – there is immunological memory)
Antigen Recognition Antibodies
Antigens are substances that the body recognise as foreign Antibodies are proteins produced by B lymphocytes that are
and that can elicit an immune response specific to a given antigen (they are also called immunoglobulins)
Antigens are presented to lymphocytes via identification

Variable region
markers on the surface of native cells (MHC molecules) (binds to the antigen)
•  MHC I markers are found on all body cells (except RBCs)
and present endogenous antigens (cell-mediated response) Heavy chain (×2)
Light chain Constant region
•  MHC II markers are on innate immune cells (macrophages) (site for opsonisation)
(×2)
and present exogenous antigens (humoral response)
Role of Lymphocytes
Humoral Immunity (targets ‘non-self ’) Cell Mediated Immunity (targets ‘self ’)

•  B cells each produce one specific type of antibody •  Infected cells present antigens on their MHC I markers
•  Macrophages or dendritic cells present antigen fragments •  Antigens are recognised by cytotoxic T cells (and TH cells)
(via MHC II markers) to helper T lymphocytes (TH cells) •  Cytotoxic T lymphocytes (TC cells) bind to the infected
•  TH cells release cytokines and activate the antigen-specific cell and trigger its destruction (via perforating enzymes)
B cells (which rapidly divide to form many plasma cells) •  TH cells stimulate the formation of memory TC cells
•  The plasma cells make antibodies specific to the antigen •  TC cells can target virus-infected cells and tumor cells
•  A small proportion of B cell clones differentiate into •  Suppressor T cells regulate the action of TC cells in order
long-lasting memory B cells (for long-term immunity) to prevent sustained T cell activation (i.e. autoreactivity)
B Cell
Pathogen Virus
Macrophage + TH Cell Infected cell + TC cell Lysed cell
antibodies
Immune System Disorders
Immunodeficiency Hypersensitivity
•  HIV is a retrovirus that infects helper T cells (TH cells) •  Allergens are substances that trigger an immune response
•  It is usually transmitted via the exchange of bodily fluids despite not being inherently harmful (e.g. peanut allergy)
(e.g. sex, breastfeeding, transfusions, injections, etc.) •  When a B cell is activated by an allergen, it makes large
•  HIV is integrated into the genome of infected TH cells quantities of allergen-specific antibodies (IgE)
•  After a prolonged period of inactivity, it becomes active •  These IgE antibodies bind to mast cells and ‘prime’ them
and lyses the TH cell as it begins to spread •  Upon re-exposure to the allergen, the sensitised mast cells
•  This results in an inability to produce antibodies and a release large quantities of histamine (causes inflammation)
general loss of immunity (disease is called AIDS) •  This inflammatory response is called an allergic reaction

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Topic 6.4: GAS ExCHAnGE

Ventilation Lung Structure
Ventilation is the exchange of gases between the lungs and

larynx
the atmosphere (achieved by the physical act of breathing) trachea
These gases are integral to the process of cell respiration alveolus

intercostal
•  Oxygen is an input, carbon dioxide is a by-product muscles
bronchus
Ventilation maintains the concentration gradient necessary rib
for passive diffusion (O2 = into lungs, CO2 = out of lungs)
bronchiole
lung
Ventilation rates will change with exercise and can be
measured via spirometry (measures amount / rate of air) diaphragm
Mechanism of Breathing Pneumocytes
Breathing utilises antagonistic sets of respiratory muscles in Pneumocytes (alveolar cells) line the alveoli and comprise
order to facilitate the passage of air (inhalation / exhalation) the majority of the inner surface of the lungs
•  Muscles change lung volume to create negative pressure
•  Negative pressure is equalised by air from atmosphere Type I pneumocytes:
•  Air flows in / out according to the volume of the thorax •  Involved in gas exchange between alveoli and capillaries
•  Are extremely thin (minimises gas diffusion distances)
Inhalation
•  Diaphragm muscles contract (diaphragm flattens) Type II pneumocytes:
•  External intercostal muscles pull ribs up (outwards) •  Responsible for the secretion of pulmonary surfactant
•  This increases the volume of the thoracic cavity •  This creates a moist surface that reduces surface tension
•  Pressure in lungs decreases below atmospheric pressure (prevents sides of alveoli from adhering to each other)
•  Air flows into the lungs in order to equalise the pressure
Lung Disorders
Exhalation
•  Diaphragm muscles relax (diaphragm curves upwards) Lung Cancer
•  Internal intercostal muscles pull the ribs down (inwards) Cancer is uncontrolled cell proliferation, leading to tumors
•  Abdominal muscles contract to push diaphragm upwards •  Lungs possess a rich blood supply (for gas exchange),
•  This decreases the volume of the thoracic cavity increasing the chances of metastasis (spread of cancer)
•  Pressure in lungs increases above atmospheric pressure
There are many factors that contribute to lung cancer:
•  Air flows out of the lungs to equalise the pressure
•  Intrinsic: Genetics, age, certain diseases / infections
•  Extrinsic: Smoking, asbestos, radiation exposure
Emphysema
Air in Air out
Emphysema is the abnormal enlargement of the alveoli
Ribs move Ribs move •  These form air spaces and lower the overall surface area
outwards inwards
Emphysema is most commonly caused by smoking
•  Chemicals in the cigarettes damage the alveoli
Diaphragm Diaphragm •  Phagocytes release elastase as part of immune response
flattens rises
•  Elastase destroys the elastic fibres in the alveolar walls
•  Huge air spaces (pulmonary bullae) develop in the lungs
INHALATION EXHALATION

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Topic 6.5: nEuROnS & SynAPSES

Nervous System Structure of a Motor Neuron
The nervous system consists of two main divisions: Soma

Dendrite
•  Central nervous system (CNS) = brain and spinal cord (cell body) Axon terminal
•  Peripheral nervous system (PNS) = peripheral nerves
Axon
The nervous system is composed of specialised cells called
neurons that function to transmit electrical signals
The CNS coordinates sensory & motor signals from the PNS Myelin
sheath
•  Sensory neurons send signals to the CNS (afferent pathway)
•  Motor neurons send signals from the CNS (efferent pathway)
•  Relay neurons (interneurons) send signals within the CNS Direction electrical impulse travels
Membrane Potentials Myelination
Neurons have a difference in charge across their membranes Nerve impulses are action potentials propagated via axons
due to the distribution of positively-charged ions (Na+ / K+) •  Action potentials are ‘all or none’ and are only propagated
if a certain threshold potential is reached (~ -55mV)
Electrical signals are created by changing membrane polarity
•  Polarity of a neuron at rest is the resting potential (-70mV) In certain neurons, the axon is covered by a myelin sheath
•  Polarity of a firing neuron is the action potential (+30mV) •  This enables saltatory conduction ( transmission speed)
•  The action potential ‘hops’ between gaps in the myelin
sheath (called nodes of Ranvier) for faster transmission
Nerve Impulses
The resting potential is maintained by a Na+/K+ pump Synaptic Transfer

•  It exchange sodium ions (3 out) and potassium ions (2 in)
so that the membrane potential becomes slightly negative Synapses are the physical junctions between two neurons
•  Electrical impulses cannot cross these physical gaps
An action potential changes the resting membrane potential
•  The opening of sodium channels causes a sodium influx Neurons release neurotransmitters into the synapse cleft
•  This creates a positive membrane potential (depolarisation) •  Depolarisation in axon terminals opens Ca2+ channels
•  Opening potassium channels causes a potassium efflux •  Ca2+ influx causes vesicles containing neurotransmitters
to release their contents into the synapse (via exocytosis)
•  This restores a negative membrane potential (repolarisation)
•  Neurotransmitters bind receptors on post-synaptic cells
The ion distribution must be restored to original conditions and generate graded potentials (excitatory or inhibitory)
before a neuron can fire again (this is the refractory period) •  The summation of these graded potentials determines if
the post-synaptic neuron (or effector cell) is activated
30
Membrane Potential (mV)
20
10
0
Neonicotinoid Pesticides
- 10
- 20 Acetylcholine is a neurotransmitter used in CNS and PNS
- 30 •  It is broken down in synapses by acetylcholinesterase
Threshold
- 40
- 50 Potential •  This prevents the overstimulation of the receptors
- 60
- 70 Neonicotinoid pesticides irreversibly bind to acetylcholine
- 80
receptors and cannot be digested by acetylcholinesterase
Resting Potential Depolarisation •  Insects have higher levels of these types of receptors
Repolarisation Refractory Period •  This makes neonicotinoids highly effective pesticides

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Topic 6.6: HoRmonES & HomEOSTAsIS

Homeostasis Endocrine System
Homeostasis is the maintenance of a constant internal The endocrine system releases chemical messengers called
environment within physiological tolerance limits hormones into the blood to act on distant target cells
•  A disease ensues if a factor deviates from its normal range •  Hormones only act on the cells with a specific receptor
Physiological processes are regulated by negative feedback The endocrine system works in tandem with the nervous
•  An effect is antagonistic (opposite) to the stimulus system to maintain physiological balance (homeostasis)
•  This means the detected change is reversed •  Hormones initiate slower responses (longer durations)
Thermoregulation Blood Glucose Regulation
Body temperature is regulated by the hormone thyroxin Blood sugar levels are regulated by insulin and glucagon
•  Thermoreceptors (skin) send signals to the hypothalamus •  These hormones are secreted by cells in the pancreas
•  Thyroxin is released from the thyroid gland when body
temperature is low and increases metabolism (generates heat) Insulin is secreted by β-cells to lower blood sugar levels
•  Stimulates glucose uptake by the liver and adipose cells
Thyroxin production requires iodine and a deficiency will •  Increases the rate of glucose metabolism ( ︎ respiration)
result in goitre (enlargement of the thyroid gland)
Glucagon is secreted by α-cells to raise blood sugar levels
Skin Brain Thyroxin Heat •  Stimulates glycogen breakdown within the liver
•  Decreases the rate of glucose metabolism (➡︎︎ respiration)
Adipose cells insulin -cells release

Thermoreceptor Hypothalamus Thyroid Gland Metabolic Rate take up glucose insulin
Circadian Rhythms After Eating

➡ blood sugar levels ︎
Circadian rhythms are regulated by the hormone melatonin
•  Photoreceptors (eyes) send signals to the hypothalamus After Exercise
•  Melatonin is secreted by the pineal gland (in the brain)

•  Melatonin release is inhibited by light (levels high at night)
α-cells release glucagon Liver cells
•  High levels of melatonin promote sleep in diurnal animals glucagon release glucose
Changing time zones can disrupt melatonin release (jet lag)

•  Melatonin supplements can recalibrate sleep patterns Diabetes
Diabetes is a disorder that prevents blood sugar regulation

Appetite Control •  It can be either type I (IDDM) or type II (NIDDM)
Appetite suppression is regulated by the hormone leptin
Type I Type II
•  Adipose cells secrete leptin to suppress appetite (➡ hunger)
•  Leptin binds to receptors located in the hypothalamus Onset Early (childhood) Late (adulthood)
Body does not Body does not
Over-eating causes more fat cells to be produced (obesity) Effect
produce insulin respond to insulin
•  Over time, obese people become desensitized to leptin
β-cells destroyed Insulin receptors
and therefore are more likely to continue to over-eat Cause
(autoimmune?) down-regulated
•  Hence, leptin treatments for obese people are ineffective
(obesity linked to leptin unresponsiveness – not a deficiency) Treatment Insulin injections Diet management

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Topic 6.6: ReProduCTIve SySTEmS

Human Reproductive Systems
Male System: Female System:

Ureter Uterus
Vas
Deferens Bladder
Seminal
Prostate Vesicle
Gland
Urethra Erectile Endometrium Ovary

Tissue
Epididymis Fimbria
Fallopian Tube
Penis Testis (Oviduct) Vagina
Menstrual Cycle
The menstrual cycle involves four key hormones and describes Follicular Phase Luteal Phase
the recurring changes that occur to enable pregnancy
Pituitary
LH
FSH
Pituitary Hormones (FSH and LH):
•  Stimulate follicular growth within the ovaries
Follicle
•  Stimulate estrogen secretion (from the ovarian follicles)

•  Stimulate progesterone secretion (from corpus luteum) Maturing Follicle Corpus Luteum
•  A mid-cycle surge in LH triggers ovulation (egg release)
Ovarian
Estrogen
Ovarian Hormones (estrogen and progesterone): Progesterone
•  Promote development / thickening of the endometrium
Uterus
•  Promote FSH / LH secretion during the follicular phase

•  Inhibit FSH / LH secretion during the luteal phase
Day 1 5 10 15 20 25 28
Reproductive Theories
One of the earliest theories involving how human reproduction occurs was the ‘soil and seed’ theory proposed by Aristotle
•  Males provide all the information for life in a ‘seed’, which forms an egg when mixed with menstrual blood (the ‘soil’)
William Harvey dissected deer after the mating season and was unable to identify embryos until several months after mating
•  He concluded that the ‘soil and seed’ theory was incorrect and that menstrual blood did not contribute to fetal growth
Sex Development In Vitro Fertilisation
Fertilisation requires a combination of male and female ‘seeds’ •  Stop normal menstrual cycle with drugs
•  Hormone treatments to induce ovulation
Male sex is determined by a gene on the Y chromosome which
•  Extract multiple eggs from female
causes gonads to develop as testes and secrete testosterone
•  Sperm sample is collected from male
•  Testosterone produces sperm and male sex characteristics
•  Fertilisation occurs externally (in vitro)
Female reproductive organs develop in the absence of this gene •  Implantation of embryos into surrogate
•  Estrogen and progesterone develop female sex characteristics •  Test for pregnancy to determine success

Apuntes Completos Biologia IB SL

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lOMoARcPSD|16195808

Downloaded by Mauricio Ochoa (Student) (mauricio.ochoa@eton.edu.mx)

Topic 1.1: Cell Theory

Calculating Magnification (MIA): Light microscopes use lenses to bend light

Emergent properties arise from synergistic interactions between

Downloaded by Mauricio Ochoa (Student) (mauricio.ochoa@eton.edu.mx)

Topic 1.1: Cell SPECIALIZATION

Stem Cell Therapy Therapeutic Examples

Ethics of Stem Cell Use

Source Growth Potential Tumour Risk Harvesting Disadvantages

Can be generated Requires destruction of the embryo

Differentiation Gene Packaging

Green cell (gene B) Euchromatin (active)

Downloaded by Mauricio Ochoa (Student) (mauricio.ochoa@eton.edu.mx)

Topic 1.2: PRokAryotic Cells

Prokaryotes are organisms whose cells lack a nucleus

Prokaryotic versus Eukaryotic Cells Bacterial Cell Division

DNA is naked DNA bound to protein

No nucleus Has a nucleus

Via binary fission Via mitosis and meiosis

Average Size Smaller (~1 – 5 µM) Larger (~10 – 100 µM)

Downloaded by Mauricio Ochoa (Student) (mauricio.ochoa@eton.edu.mx)

Topic 1.2: EuKAryotic Cells

Golgi body Smooth ER Nucleus Rough ER

Animal Cell Plant Cell

Golgi complex Chloroplast

Organelles Animal versus Plant Cells

Examples of eukaryotic organelles include: ︎No chloroplast Have chloroplast

Topic 1.3: membrAne Structure

Properties of the Phospholipid Bilayer:

Cholesterol Membrane Proteins

Fluid Mosaic Model Membrane Models

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Topic 1.4: membrAne TrAnsport

Simple Diffusion Facilitated Diffusion

High [ ] Low [ ] Protein Channel Carrier Protein

Hypertonic Isotonic Hypotonic

Active Transport Vesicular Transport

Topic 1.5: Origin of Cells

The formation of living cells from non-living materials

As these conditions no longer commonly exist on Earth,

Endosymbiosis Oxygenation of Earth

The engulfed cell remained undigested and contributed new Oceans

Ancestral Endosymbiosis Ancestral Rock Deposition

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Topic 1.6: Cell Division

This process of cell cloning is needed for Animals:

Mitotic Index Mitosis Micrographs

The mitotic index is a measure of the proliferative

The mitotic index will be elevated during growth and

Topic 1.6: STAGES of miTosis

• DNA is uncondensed (chromatin)

• Cell grows in size and organelles are

Nuclear • DNA supercoils and condenses

• Centrosome spindle fibres attach to

Metaphase • Spindle fibres contract and move the

• Cytoplasmic division occurs to divide

•  DNA is uncondensed (chromatin)

•  Cell grows in size and organelles are

Nuclear •  DNA supercoils and condenses

•  Centrosome spindle fibres attach to

Metaphase •  Spindle fibres contract and move the

•  Cytoplasmic division occurs to divide

G1 checkpoint •  The activated complex phosphorylates proteins involved

•  It is a controlled event triggered by mitochondrial proteins 300

•  Cell contents are packaged in membranous protrusions (blebs) 200

Graph 2 – pH level •  Provides a source of dairy for lactose-intolerant people