VCE Biology 3/4 Notes

TERMS:

Procedure - The set of processes used to define the scientific method typically including a hypothesis, experiment, observation, analysis, conclusion and evaluation

Hypothesis - If the (DV) then the (IV)  

Independent variable - Variable that is manipulated and has a direct effect on the DV 

Dependent variable - the measured variable that is observed/recorded

Repeatability - The ability of the experiment to be repeated identically in the same environment

Precision - The degree to which the results are consistent 

Accuracy - The degree to which the results are close to the true value

Reproducibility - The ability of the experiment to be repeated with the same materials and method in a different environment

Validity - The experiment is measuring what it's supposed to be measuring

Bar Graphs - Different groups of data 

Line graphs - Ranged set or continuous data 

Control set up - The experiment without the independent variable 

Controlled variables - Variables that are used to keep the experiment and control set up the same except for the independent variable.

Scientific Method: 

Terms:

• Procedure - The set of processes used to define the scientific method typically including a hypothesis, experiment, observation, analysis, conclusion and evaluation

• Hypothesis - If the (DV) then the (IV)  

• Experiment 

• Observation 

• Analysis

• Conclusion 

• Method

• Investigation

• Independent variable - what is manipulated and has a direct effect on the DV 

•  dependent variable - the measured variable that is observed/recorded

• Experimental Set-up - To test the hypothesis, will have the independent variable

• Control Set-up - Used to compare and confirm findings in experimental set-up, Does not have the IV, 

• Controlled Variable - Factors that are applied in both setups. Constant factor. purpose is to ensure that only one variable is tested at a time in an investigation: To make it valid. Eg. how much water you drink, weather, light, etc. 

• Repeatability 

• Precision 

• Accuracy 

• Reproducibility 

Notes: 

• Set of procedures to gain knowledge 

• 6 key steps

  • Question 

  • Hypothesis: educated guess or prediction, must be testable, states variables, “if, then”

  • Experiment 

  • Observation 

  • Analysis 

  • Conclusion: statement of whether the original hypothesis was supported or refuted

• Steps are not always linear but systematic 

• To make a hypothesis: ask a research question then change that into hypothesis 

• VCAA formula: If (DV) (relationship to IV) then (trend/effect on DV) and (IV whatever) 

• Controlled variable ≠ control set up 

• An investigation should only have ONE independent variable 

• Two setups only: Experimental Set-Up + Control Set-up

• Results will be in graphs or tables. 

• RULES: 

  • Title your table, including IV and DV

  • Column headings - Units included in Headings

  • Left column must be the IV

  • Data entry must have the same number of decimal places

  • Keep things neat and aligned 

• TAILS

  • Title 

  • Axis 

  • Interval 

  • Label 

  • Scale

• Bar graphs are for different groups of data 

• Line graphs are a ranged set of data/ continuous data 

• Don’t forget repeatability 

Example

Observation: Mice that are given Vitamin D increase the Calcium Absorption 

Independent Variable: Vitamin D being given to mice 

Dependent Variable: The Calcium absorption in the mice blood

Hypothesis: If Mice are given Vitamin D then the Calcium absorption in their blood will be increased. 

 OR

If mice are given Vitamin D then the Calcium levels in the blood will be less than the mice not given Vitamin D

Experimental set-up

• 100 Mice given Vitamin D 

• Vitamin D 

Controlled Set up

• 100 Mice not given vitamin D but instead a placebo 

Controlled Variables:

• Amount of Vitamin D and placebo 

• Duration  

• Species of mice

• Age of Mice 

• Same period of testing

• Same food

• Same water 

• Mice Sex 

Results to support hypothesis:

A greater % of mice in the experimental group will have less calcium the blood while the control group show no increase of calcium absorption 

Results to refute hypothesis: 

A greater % of mice in the experimental group show no change in calcium levels

Accuracy

• Not a quantity

• How close to the true value

• Bottle weighing 3kg measuring at 2kg is inaccurate

• More trials does not increase accuracy 

Precision

• How closely two of more measurements agree with each other 

• Little spread among the values 

• If true value is 2.4 and results are 2.3, 2.3, 2.4, 2.4 then accurate and precise

• 5.6, 5.7, 5.9, 5.8 precise not accurate

• Lack of accuracy but precision is systematic errors 

• Lack of precision could mean random errors 

• More trials can increase precision 

Repeatability

• Same method on identical materials with the same condition 

• The exact same experiment with the same person who did the experiment or operator

• To obtain same results

• Provides evidence of validity and reliability

Reproducibility:

• Same method, same materials but different conditions 

• The exact same experiment in different environment  with possibly a different operator 

• Identifying random or systematic errors 

• To obtain the same results

Validity 

• A measurement is valid if what is being measured is exactly what was claimed 

• Data is valid if the independent variable is the ONLY variable 

• Similar to accuracy 

Reliability

• Similar to precision 

Random Errors

• Random errors are unpredictable events or mistakes that affect the results 

• Outliers 

• Mistakes etc. 

• Affects accuracy and precision 

Systematic Errors

• Occurring the measuring system and affects every single measurement 

• Does not necessarily affect precision, affects accuracy

• Re-calibrate machines

U3AOS2 

• Enzymes → P1

• Photosynthesis → P2

• Respiration → P3

Enzymes

Terms: 

• Catalyst

• Proteins

• Enzymes

• Enzyme functions

• Catalyse

• Substrates

• Coenzymes

• Active Site

• Enzyme substrate complex

• Enzyme product complex  

• Anabolic - building up, 1 + 1 → 2, always requiring energy, (endergonic)

• Catabolic - breaking down, 2 → 1 + 1, reduce complexity, always releasing energy (exergonic)

• Endergonic - Requires energy, uphill reaction, energy requiring 

• Exergonic - Releases energy, downhill reaction, energy release

• Activation energy 

• Denature - Active site has changed and thus the enzyme becomes useless

• Optimum temperature 

• Saturation point

• Substrate concentration

• Cofactors

• Metal ions

Key Knowledge:

• Enzymes and coenzymes are catalysts that assist with photosynthesis and cellular respiration 

• Factors that impact on enzyme function

• Enzymes are proteins made from amino acids

• Reusable

• Speeding up chemical reactions by lowering the activation energy 

Notes

• Usually have the suffix ‘ase’ or ‘in’ (Eg. sudcrase, lipase, trypsin, pepsin)

• Names can identify the substrate 

  • Sucrase catalyses sucrose

  • Lipase catalyses lipids

• Describes what the enzyme does or what fits in it

• Substrates are substances that ‘fit’ into the active site of an enzyme. 

• Bonds are formed between the substrate, energy → water released and peptide

• Active site is the region where only specific substrates are able to bind and undergo a chemical reaction 

• Substrate is the substance that can bind to the active site in an enzyme, 

• Enzyme specificity  is based on the specific shape of the active site 

• When an enzyme binds to a substrate its called an enzyme substrate complex 

• Becomes enzyme product complex after catalysis 

Theories:

• Substrate and enzyme are directly complementary 

• Lock and Key Model

• Perfect fits designed for each other 

• The active site and substrate are complementary 

• Induced Fit, the enzyme conforms for the substrate 

• The active site becomes complementary

• Enzymes ARE proteins and are made of amino acids 

• Biological catalysts → speeds up processes 

• Not permanently changed in processes 

• Reusable

• NOT reactants → written on the arrow in reaction equations 

Catabolic Reactions

• Large molecules to small molecules 

• Breaks down

• Exergonic, releases energy

• Needs water

Anabolic Reactions

• Small molecules to large molecules 

• Builds

• Requires intake of energy 

• Endergonic

• Produces water

Activation energy:

Energy needed for any chemical reaction, any reaction will occur with enough energy. Enzymes work by lowering the required activation energy. 

Factors affecting enzyme activity: 

Temperature 

• Heat energy means more collisions between enzymes and substrates however enzymes denature so the rate of reaction falls

• Optimum temperature is 37.5 degrees celsius

• When there is low temperatures there is less kinetic energy

• The enzyme is NOT denatured at low temperatures but it IS denatured at high temperatures 

• 

• Low kinetic energy low molecule collisions less enzymes substrate complexes forming etc.

pH

• pHs have an optimum pH for enzymes but enzymes can denature on both sides of pH, if it’s too low or too high. 

• Works only within a small pH range

• pH disruption generally results in complete loss of activity

• Identical parabola

Substrate concentration

• Substrate graph optimum is the point of saturation

• Point of saturation means all active sites have been occupied and the enzymes must produce at a stable reaction rate. 

• More enzymes = Increasing reaction rate

• Increasing then plateau

Enzyme concentration 

• Rate of reaction can increase as long as there is enough substrate 

• If there is an overabundance of enzymes and not enough substrate no reaction will occur 

• Constant line

Cofactors & Coenzymes

• Cofactors can either be metal ions or coenzymes

• Metal ions bridge enzymes + substrate together, combined with the catalyst

• Coenzymes, non-proteins, organic complex

• makes the substrate fit better

• All coenzymes are cofactors not all cofactors are coenzymes

• Activate the enzyme

Inhibitors

• Competitive and noncompetitive inhibitor 

• Competitive is COMPETING with the active site and binding to the active site

• Non competitive inhibitors are not trying to bind to the active site, they bind to the enzyme changing the active site inhibiting the substrate from binding 

• More substrates can overcome competitive inhibition but cannot overcome noncompetitive inhibitors

• Competitive Inhibitors are TEMPORARY and REVERSIBLE, because they can eventually leave the enzyme 

• Allosteric = not the active site 

• Non competitive inhibitors force the enzyme to change PERMANENTLY and are IRREVERSIBLE 

Stirring/Agitation

• Increases collision and increases reaction rate 

• Increases the substrate and enzyme collision 

Biochemical Pathways

Terms:

• Feedback inhibition

• Metabolic pathway

• Dephosphorylation

• Phosphorylation

Notes:

• Large molecules need to be broken down slowly over multiple stages 

• The last product made in a process can be an inhibitor for enzyme one which stops too much product being made. 

• Feedback inhibition

• Metabolic pathway

• Each pathway requires a specific enzyme 

• The pathway is stopped by feedback inhibition 

• If the gene coding for an enzyme is messed up then the lack of feedback inhibition will cause a build up of a certain substrate and there will be no product 

• Exergonic

• Dephosphorylation - Losing a phosphate 

• Phosphorylation - gaining a phosphate 

ATP, ADP, energy and other coenzymes

Terms:

• ATP

• ADP

• Phosphate

• Metabolic Reactions

• Mechanic work 

• Nucleotide

• Hydrolysis 

• Hydrolyse

• Loaded - Fully energised (ATP)

• Unloaded - Not fully energised (ADP)

• Inorganic phosphate (Pi)

• Organic - molecule with carbon

• Inorganic - molecule without carbon

Notes:

• Cells need energy to make muscles work, carry out chemical reactions, the growth and repair of cells, making larger molecules, maintaining body temperature

• Enzymes are important in cellular respiration

• Mechanical reactions, metabolic reactions

• Adenine Triphosphate  

• 1 Adenine (N-Base) + 1 Ribose Sugar + 3 Phosphates 

• Linked by hydrogen bonds

• ATP breaks down and releases a lot of energy and becomes ADP and phosphate 

• ATP → ADP → ATP (reversible)

• ATP is a nucleotide

• Hydrolysis - To split ATP

• Water is needed to split ATP into ADP

• ATP is a loaded molecule

• Enzyme used to catalyse ATP is called ATPase

• Reaction type is Exergonic, Hydrolysis, Catabolic, Dephosphorylation 

• ADP is an unloaded molecule

• ATP can act as a coenzyme and assist other enzymes 

• It is an energy carrying molecule

• Provides enough energy to support reactions through the breaking of phosphate bonds. 

• ATP’s third phosphate is weakly bonded and has high energy 

ATP SYNTHESIS 

• ATP is synthesised through cellular respiration

• ATP synthase is enzyme to create ATP from ADP

• Located in the mitochondria’s membrane and in chloroplasts 

• Found where ATP is needed to be made ie: mitochondria, chloroplast etc. 

• Dehydration/Condensation reaction = water being produced (ADP→ATP)

• Endergonic, Anabolic

OTHER COENZYMEs: 

• Coenzymes are not specifically for substrates they are carriers to the reaction products 

• Coenzymes are regenerated to be reused 

• H+ (electrons)

• NAD+ (+) H+ (+) 2e- (Unloaded → NADH (Reduction) (Loaded)

• The other way round is Oxidation

• FAD (Unloaded) → FADH2 (Loaded)

• NADP→ NADPH 

Workbook 20-21

CELLULAR RESPIRATION

AEROBIC RESPIRATION

Term

• Reactants

• Cellular resp

• Glycolysis

• Krebs cycle - Takes place in the mitochondrial matrix

• ATP yield (NOT NUMBER IN TEXTBOOK) 

• Electron transport chain - Set of reactions in the mitochondria

• inputs/outputs

• Locations of glycolysis 

• Coenzymes 

• Pyruvate/Pyruvic Acid (3 Carbon molecule, break down of glucose)

• Intermediate reaction

• Cristae - Mitochondrial inner membrane, most ATP is made

• Mitochondrial matrix is the fluid in the mitochondria

Notes

• Glucose + Oxygen ⇒ 30-32 ATP + (Water) + (Carbon Dioxide)

• CO2 and Water are byproducts the intention is for ATP

• 

• 1 glucose makes 30-32 Total ATP which is too much energy to be produced at once

• All cells respire

• Respiration is a set of metabolic reactions

• Purpose: To convert glucose to ATP

• Mitochondria is the powerhouse of the cell

• Wherever ATP is being made there is ATPsynthase

• When glucose enters a cell it breaks down with glycolysis, taking place in the cytoplasm

• The glucose breaks into Pyruvate x 2which breaks down into CO2 x 2 and Acetyl CoA x 2

• Pyruvate to CO2 and Acetyl CoA is an intermediate reaction

• Acetyl CoA then goes to the mitochondria’s matrix which is a fluid where the Krebs cycle occurs

• When glucose → pyruvate → acetyl CoA is made Hydrogen ions are released which would disrupt the pH of the cell, NAD + FAD pick up the hydrogen ions and become NADH or FADH2 which are reduced, loaded molecules and are used to transport to the cristae 

• NAD and FAD are electron carriers/coenzymes

• NAD  is an important coenzyme that is used to activate lactic dehydrogenase enzyme 

• Intermediate reaction = link reaction = transition reaction

• Glycolysis → Intermediate reaction → Krebs cycle → Chemiosmosis

• Glycolysis produces 2 ATP and Krebs produces 2 ATP and Electron transport chain produces 26-28 ATP so in TOTAL 30-32

• Glycolysis - Cytosol

• Matrix - Kreb cycle

• Cristae - ETC

Mitochondria has;

• Two membranes, Outer and Inner (Cristae)

• Shaped for maximum efficiency

Glycolysis

• Requires 2ATP and ATPase 

• Breaks down into Pyruvate or Pyruvic acid

• NAD+ come and collect the hydrogen ions 

• 2 ATP is produced from both ‘breakdowns’ 

• Total of 4 ATP produced but net 2ATP because there is an investment of ATP

• 

Krebs Cycle/Citric Acid Cycle

• Input 2 acetyl coa 2 Adp 6 NAD+ 2 FAD+

• Output 4CO2 2 ATP 6 NADH 2 FADH2

• Only 2ATP are produced 

• Oxygen is NOT involved

• More electrons are picked up by NAD and FAD

• All co2s have been released

• Made in the MATRIX

Electron Transport 

• NADH is oxidised and GIVE UP its hydrogen ions

• Made in the Inner mitochondrial membrane or the cristae

• The hydrogen ions cross the cristae membrane

• All the hydrogen ions then go through ATP synthase and make ADP into ATP

• 26-28 ATP

• Facilitated diffusion through ATP synthase 

• Electron transport chain = oxidation phosphorylation

• H+ cross membrane → proton gradient (concentration) increases outside membrane → H+ is then facilitated diffusion-ed through ATP synthase → ATP made

• Oxygen is the final electron acceptor, water is made as oxygen + H+ + electrons

10 mill ATP is produced per second by one cell 

ANAEROBIC RESPIRATION

Terms

• Fermentation

• Alcohol Fermentation 

• Lactic Acid Fermentation

• Anaerobic Respiration

• Muscle Fatigue

• O2 Debt

• Ethanol

• Lactic Acid 

Notes

• When oxygen is not present in the cells, the process of fermentation occurs

• Glycolysis → Fermentation

• NADH returns the H ion and the pyruvate becomes lactate or ethanol 

• Reversible once oxygen becomes available

• Lactic acid in animals, bacteria and some fungal cells

• Alcohol/Ethanol produced in plants and yeast

• 2(C3H6O3)

• Lactic acid is poisonous to the body and builds up creating muscle cramps, it is broken up by oxygen

• Ethanol is 2C2H5OH created by plant and yeast fermentation

• Lactate dehydrogenase and Alcohol dehydrogenase 

• Glucose → ethanol + carbon dioxide + energy (2ATP

• Glucose → Lactic  acid + energy (2ATP)

• When animals run out of O2, pyruvate becomes lactic acid creating muscle fatigue and O2 debt

• Provides rapid bursts of ATP in muscle cells 

• But is incredibly toxic 

FACTORS AFFECTING CELLULAR RESPIRATION

• Oxygen concentration

• Temperature 

• Glucose availability

• Hydration, light, age, activity level

OXYGEN CONCENTRATION

• Respirometer is a device that determines an organisms respiration rate by measuring the rate of exchange of O2 and CO2 

• Living specimens enclosed in sealed container

• Pressure changes affect the manometer

• Increasing Co2 levels or decreasing oxygen levels → Increases respiratory rate

• **RATE OVER TIME (over time must be included) 

• Temperature denatures enzymes therefore pathways cannot continue 

• Oxygen measured by the amount of CO2 produced 

• Increase O2 —> increase resp. Rate until point of saturation 

• Anaerobic respiration is measured by lactic acid of alcohol produced, aerobic respiration measured by Co2 levels

GLUCOSE CONCENTRATION 

• Glucose and oxygen are substrates

• Glucose conc increases 

BIOMASS +  BIOFUELS

Terms

• Biofuels - reducing the amount of greenhouse gases by being renewable and recyclable fuel made from recently living organisms such as plants and algae 

• Fossil Fuel

• Biomass 

• Fermentation

• Renewable 

Notes

• Burning biofuels releases carbon dioxide but they are carbon neutral because they cancel out the amount they release by holding that amount of carbon dioxide when being grown. 

• Needs to be easy to make, transport and able to mix with fossil fuels

• Places to grow this. 

• Processes requiring energy

• Two main types of biofuels, bioethanol and biodiesel 

• Bioethanol/Ethanol 

  • Fermenting sugarcane /starchy plant materials 

  • Blended with petrol

• Biodiesel 

  • Made from lipids/fatty acids

Photosynthesis

Key Knowledge:

• Inputs, outputs

• Roles of enzymes and coenzymes in facilitation 

• Locations of light dependent and light independent stages 

• Rate of photosynthesis and factors that affect rate

• Factors: light, water, temperature, carbon dioxide

Terms

• Photosynthesis

• Light dependent 

• Light independent

• Autotrophs, producers

• Heterotrophs 

• Palisade layer - generally the more photosynthetic cells 

• Epidermal layer

• Spongy layer

• Mesophyll - all the in between bits (palisade and spongey)

• Bundle Sheath cells 

• Stomata/Stomate

• Guard Cells around the stomata - close at night, open day  which allows for the diffusion of Co² 

• Oxidation

• Reduction 

• Xylem tubes - Carry water

• Phloem tubes - Carry food

• Veins

• Granum is the pile of discs or Thylakoids

• Thylakoid, the membrane of the discs in a chloroplast, is the disc

• Stroma 

• Inner Membrane

• Outer Membrane

• NADP and NADPH 

• Calvin cycle 

• Limiting Factor 

• G3P

• PG3 - Phosphoglycerate 

• Glucose 

• C3

• C4

• CAM

• Turgid

• Flaccid

Notes:

• Sunlight is needed because it is the initial energy source 

• Plants make glucose during daylight, as long as there is sunlight

• They require glucose because they are autotrophs, they make their own food

• 

• Water is diffused by osmosis

• Inputs: Water + Carbon Dioxide 

• Outputs: Sugar + Oxygen 

• Include light and chlorophyll on the →

•  Cuticle protects plant 

• Epidermal Layer is made of epidermal cells

• Palisade Layer, made of palisade cells

• Sponge layer, made of sponge cells and air

• Stomata used for co2 diffusion and water transpired out

• Photosynthesis takes place in the chloroplast 

• Chlorophyll, containing ATP synthase 

• 6CO2 + 6H2O → C6H12O6 + O2

• 6CO2 + 12H2O→ C6H12O6 + 6O2 + 6H2O 

• Reduction is gain of electrons

• Oxidation is loss of electrons

• H2O is oxidised, CO2 is reduced

• NADP comes and picks up the hydrogen ions released from the reaction and split of H2O and comes and picks up the ions and becomes NADPH

• Oxidation reaction = water being oxidised to oxygen through NADP

• Reduction reaction = Carbon Dioxide is reduced to glucose

• Glucose is made for cellular respiration 

• Xylem tubes carry water from roots to leaves and parts of the plant through veins

• Phloem tubes carry food to all parts of the plant body for all cells to respire 

• 

• Made up of granums which are discs filled with chlorophyll and membrane known as Thylakoids 

• Water is trapped in the Thylakoids and is split releasing Oxygen to be diffused out of the cell, some may be used in respiration but the rest will diffuse into the atmosphere

• NADP comes and collects the hydrogen from the split H20 becoming NADPH 

• The H+ is used to synthesise glucose 

• Light dependent stage, splitting of H20 takes place in the Thylakoid

• The Calvin Cyle or the synthesis of glucose and the reduction of Co2 doesn’t require light and is the light independent stage

• ADP + Pi becomes 18ATP

• Photosynthesis is photo, then synthesis

• Photo - light dependent

  • Thylakoid/Granum 

  • Chlorophyll traps the light to split water and produces 18 ATP and O2

• Synthesis - light independent 

  • Stroma 

  • Calvin cycle 

  • Using 18 ATP from light dependent reaction

• Photosystems 1 and 2 are photosynthetic pigments that absorb light energy 

• Calvin cycle: CO2 + NADPH + 18ATP → NADP + 18ADP + GLUCOSE

• Occurs in the stroma and doesn’t require light but depends on products of light dependent stage

• Uses ATP and NADPH to synthesise glucose

• Endergonic and Anabolic 

• NADPH → NADP

• Enzyme rubisco is required

  • It fixes RUBP (sugar with 5 Carbon) to CO2 and turns it into a 6 Carbon molecule 

  • Which becomes 2 x G3P

  • One G3P will leave as an output of SUGAR

  • The other will continue in the cycle and become RUBP 

  • A higher concentration of CO2 means more reaction

• 

• 

• Calvin cycle runs 6 times before producing glucose 

• Rubisco is an enzyme for Carbon Dioxide but when there is a high concentration of Oxygen, oxygen will bind to Rubisco instead. 

Factors Affecting Photosynthesis

External Factors include:

• Light

• Temperature

• CO2

• Water

Internal factors

• Chlorophyll - affects the amount of light being absorbed - is a limiting factor 

• Limiting factors are factors that limit the reaction such as limited by temperature being too low or temperature being too high etc. 

Photorespiration

• When there is no CO2 entering due to closed stomata and increase in O2 concentration then photorespiration occurs

• Rubisco picks up O2, high temp, stomata closed, when oxygen is more concentrated than co2 and creates CO2 by binding O2 to Rubisco

Rubisco, C3, C4 & CAM 

• Stomata/Stomate - openings guarded by the guard cells 

• Guard cells turgid/Stoma Open 

• Turgid = Full

• Cells flaccid/Stoma closed 

• Guard cells use osmosis to open and close by the concentration of sugars 

• C3 plants have thin bundle sheath cells 

• C3 make up most plants 

• Occurs only in mesophyll cells 

C4

• Pep Carboxylase ( PEPCase) always binds to CO2 to produce C4 Acid Oxaloacetate

• More efficient than Rubisco because it will always collect Co2 

• PepCase makes Malate and CO2 in the Mesophyll cells from Co2 and PEP Carboxylase 

• Co2 Increases, Rubisco picks up Co2 to fix to RUBP and continue the calvin Cycle

• Occurs in Bundle sheath then Mesophyll

CAM

• Closes stomata during the hottest part of the day 

• Traps Co2 at night time 

• Making sugar with trapped CO2 

• Similar to C4 plants uses PEP carboxylase to malate fixation of CO2 and then to the Calvin Cycle 

• Occurs in Mesophyll all the time however the different processes are at night vs day

AOS1: Proteins

Introduction to Proteins

Terms:

• Proteins

• Hormones

• Structural proteins 

• Biomacromolecules 

• Carbohydrates

• Lipids

• Nucleic Acid 

• Monomers

• Polymers 

• Polymerisation - Making polymers from monomers, a reaction that combines monomers to make polymers

• Oligomers 

• Alpha helix

• Beta Pleated sheet 

• Polypeptide

• Peptide bond

• Primary, secondary, tertiary, quaternary protein structures

• Globular Protein 

• Filament 

• Protofilament

• Fibrous Protein

• Proteomics - Study of proteome

• Proteome - the complete array of proteins produced by a single cell/organism in a particular environment is called the proteome of the cell/organism

• Purines - A & G

• Pyrimidines - T & C

• Chromatins

• Messenger RNA 

• Transport RNA 

• Ribosomal RNA 

• Transcription - Occurs in nucleus, copying Dna code onto mRNA 

• Translation - Translating mRNA (Decoding)

Notes

• Proteins are used for everything such as contraction, reception, hormones, protection, transport, storage, enzymes, structural, identification, signal etc. 

• They are coded from Amino acids which are building blocks 

• Contain C, O, H, N & S

• Proteins are building blocks. They have a wide range of functions

• Monomers are the basic building block 

• Amino acids are the monomers for proteins 

• Nucleotides are monomers for nucleic acids 

• Monosaccharides are monomers for carbohydrates

• All amino acids have 

  • An amino group

  • A carboxyl group 0=C-OH

  • A unique side chain (often depicted as R) H-C-R

• Amino Acid 1 + Amino Acid 2 → Dipeptide + Water 

• Condensation/Dehydration reaction because production/loss of water 

• Amino acids combine and peptide bonds form from amino acids to become a polypeptide. 

• The covalent bond between the amino acids is the peptide bond

• Polypeptide chains can be broken down via hydrolysis reactions which splits the chain.

• 4 levels of protein structure 

• Primary protein structure - Linear sequence of a chain of amino acids 

• Secondary protein structure - an alpha helix + a beta-pleated sheet which is the folding of polypeptide chains into helices or sheets

• Tertiary protein structure - 3D folding pattern of a protein due to side chain interactions - Globular protein, very specific shape being formed 

• Some proteins only continue to Tertiary structure but some combine into more than one amino acid chain

• Quaternary Protein structure - Protein consisting of more than one amino acid chain

• Linear sequence will provide information on how the protein folds, function or no function, evolutionary relatedness between species. 

• Hydrogen bonds hold alpha helix, peptide bonds form between amino acids 

SECONDARY PROTEIN STRUCTURE 

1. Alpha helix 

2. Beta Pleated sheets 

3. Random Coils

TERTIARY STRUCTURE

• Total irregular folding and bending of chain

• Causes amino acids to become close 

• Function depends on shape

• 3D protein 

• Disulphide bonds only existing in tertiary structure

• Hydrogen bonds 

QUATERNARY

• Fibrous or globular 

• Some are conjugate containing inorganic compounds 

• Eg. Haemoglobin 

NUCLEIC ACIDS 

• The two types of nucleic acids

• DNA + RNA 

• Made of a sugar, phosphate and nitrogenous base (ATGC or AGCU)

• RNA is single stranded

• DNA is double stranded and also has no oxygen - Antiparallel double stranded helix 

• AT are double bonded 

• GC are triple bonded

• The phosphate makes DNA negatively charged

• The units of DNA inside the nucleus are Chromatins which when needed to split become Chromosomes. 

• 5’ and 3’ Antiparallel structure (‘ = prime)

• Three types of RNA

  • Messenger RNA - Carries instructions for polypeptide synthesis 

  • Ribosome - Structural subunits of the ribosome

  • Transfer RNA - Carries amino acids to ribosome

• DNA are the instructions the RNA are the messengers

• RNA copies a strand of DNA and then this is used to go to the ribosome which codes 3 bases at a time using amino acids taken from food and the breakdown of proteins 

• DNA is in the mitochondria, chloroplast and some in the mitochondria only 1 type

• RNA in the nucleus and cytoplasm has at least 3 types

• Made in 3s in the ribosome 

• Transcription occurs in the nucleus - the copying of DNA onto mRNA 

• Translation in the ribosome - decoding of mRNA into the ribosome  

• Gene Expression = Protein Synthesis 

Protein Synthesis

Terms

• Transcription

• Translation

• Ribosome

• Protein Synthesis 

• Sense/Antisense strand

• Template/Non-template strand 

• Amino acids 

• Non-Coding/Coding

• Pre-RNA
  Elongation

• Binding 

• Initiation 

• Promoter region

• Methylated Capping 

• Introns

• Exons 

• Gene sequence 

• Exon juggling 

Notes:

• DNA codes the instruction for protein synthesis but

• Ribosome is the site of protein synthesis which is in the endoplasmic reticulum

• DNA cannot leave nucleus but Ribosomes cannot enter the nucleus 

• A copy of DNA is made as RNA through transcription 

• At the ribosomes, the copy is translated by tRNA and the necessary amino acids will be produced 

• Template strand/Antisense Strand/Non-coding strand

• Sense/Non-template/Coding strand 

• 

• Gene sequence = correct order of nucelotides 

• Steps of Transcription

  • 1.Initiation: Initiation factors (proteins) bind to DNA stand to switch on the gene 

  • 2. Binding: RNA polymerase binds to the promoter region of the template strand

  • 3. Elongation: RNA polymerase moves along the template stand, preliminary to RNA 

• Methylated Capping and poly-deniylation tail for Transcription

• Introns and Exons 

• Base pairs are read by tRNA three base pairs at a time

• tRNA structure consists of a structure of amino acid and anti-codon 

TRANSLATION STEPS

1. mRNA attaches to a ribosome

2. tRNA (anticodon) attaches to mRNA (codon) (base pairing)

3. A specific amino acid is detatched to form either a polypetide or a peptide bond with an amino acid 

• Stop Codons are codons that literally stop the process of forming the polypeptide chain etc. 

• The stop codons are UAA, UAG, UGA

• All living organisms have the same amino acids 

• There are more than one codon for each amino acid to allow for error

Gene Regulation

Terms:

• Gene Regulation - when a gene is switched on

• Structural gene - gene that encodes for a specific protein

• Regulatory gene  - A gene that encodes for protein that regulates the structural gene ie activators or repressors to switch the genes on and off, codes for regulatory proteins

• Activator proteins - turns genes on to start transcription

• Repressor proteins - turns the gene off to prevent transcription 

• Promoter region - where RNA polymerase binds

• Operator region - where regulatory proteins binds

• Operons - only occurring in prokaryotic cells, a functional unit of transcription that regulates gene expression in bacteria

• TRP Operon 

• Tryptophan

• Anti-termination loops

• Termination Loop/Attenuator stem loop

• Hairpin loops

• Attenuation

• Attenuator

• Lead mRNA

• trpL 

• Leader region 

Notes:

• Genes need to be regulated because not all cells can make every single protein all the time so certain cells are made to produce certain proteins and certain genes are on or off

• The controlling of gene expression 

• Structural gene 

• Regulatory gene 

• The regulatory protein (activators or repressors) binds to the Operator region

Prokaryotic Gene Regulation

• Does not have introns or exons or gene capping

• Can combine multiple structural genes to create an operon 

• Occurs in the cytoplasm

• 

• 

TRP OPERON 

• The TRP operon is an operon in bacteria 

• Made by bacteria by the TRP Operon

• Tryptophan - Amino Acid

• The TRP operon codes for enzymes that catalyse the creation of Tryptophan

• When TRP is high - Operon turns on 

• When TRP is low - Operon turns off

• The TRP can regulate the levels 

• Only in prokaryotes 

• An Operon is a cluster of genes under the control of a single promoter

• 

• Transcribed and then Translated

• 

• When the operon needs to lower the amount of trp enzymes the regulatory region will make regulatory proteins that switch structural genes on and off 

• Tryptophan levels high → Tryptophan binds to the Repressor, and RNA polymerase cannot bind

ATTENUATION

• Alternative method of reducing the expression of the trp Operon in prokaryotic cells

• It relied on the capacity for prokaryotes to be both transcribing and translating SIMULTANEOUSLY

• It prevents transcription from being completed 

• It can occur when tryptophan levels are high as a backup to terminate transcription when the repressor detaches from the operator

• Stops further synthesis of the creation of tryptophan 

• In the trpL (lead protein) 

• The leader region of the operon is the trpL leader + Attenuator

• trpL codes for the leader mRNA

• Four regions that can form base pairs to form 3 hairpin loops

• When there are low levels of tryptophan, the antiterminator loop occurs and blocks the formation of the termination loop (attenuator) it pauses the protein synthesis

• The attenuator is like a stop codon and will stop transcription, the termination loop will cause the ribosome to stop translation

• there are trp codons on the trpL when the tryptophan levels are high and it will pause the ribosome at the stop codons which covers the 2 and stops 2 and 3 from binding and then allowing the termination loop

• When the 3rd loop forms stuff don't work 

Protein Packaging

Terms: 

• Vesicles - membrane bound packages 

• Transport Vesicles 

• Secretion Vesicles

• Synthesis

• Exocytosis - leaving the cell

• Lysosomes - vesicles with digestive enzymes

• Golgi apparatus

• Smooth ER

• Rough ER 

Notes:

• Proteins are transported in vesicles from the Rough ER to the golgi apparatus and are then transported to be secreted from the cell membrane or used around the cell

• Smooth ER for hormones and lipids

• Rough ER usually for proteins

REVISION QUESTIONS:

Tryp Operon

1. What is the role of the trp operon in regulating the synthesis of tryptophan?

The TRP operon regulates the production of the enzymes for the  biosynthesis of tryptophan. 

2. What type of gene regulation is involved in the regulation of the trp operon?

Negative regulation. 

3. How does the presence of tryptophan affect the expression of the trp operon?

HIgh levels of TRP make the trp repressor fall off the operator region by binding to the repressor, in low levels, the repressor falls off. If the repressor falls off while trp levels are high then attenuation is used.  

4. What is the role of the trp repressor in regulating the trp operon?

It prevents RNA polymerase from transcribing the leader genes and the structure genes so that the enzymes for the biosynthesis of tryptophan cannot occur. 

5. How does attenuation regulate the expression of the trp operon?

It acts as an emergency in case the repressor is not bound to the operator region of the operon when tryptophan levels are high. By not pausing RNA polymerase when it reaches region 1 and pausing at region 2 it allows regions 3 and 4 to bind creating a hairpin loop that forces the ribosome to fall off.

Gene Regulation

1. What is gene regulation and why is it important for an organism?

Gene regulation is the control of the production of proteins based on gene expression and it is important for specialised cell functions and proper cellular development. 

2. What are the different types of gene regulation mechanisms?

Negative and positive regulation, splicing, attenuation, feedback inhibition, transcriptional regulation, translational regulation

3. What is the role of transcription factors in gene regulation?

4. How do epigenetic modifications affect gene expression?

5. What is the difference between positive and negative gene regulation?

Protein Packaging

1. What is protein packaging and why is it important?

2. What is the structure of a nucleosome and how does it package DNA?

3. How are histones involved in protein packaging?

4. What is chromatin and how does it affect gene expression?

5. How does the packaging of DNA affect the accessibility of genes for transcription?

Protein Synthesis

1. What is protein synthesis and what are the two main stages involved in it?

2. What is the role of messenger RNA (mRNA) in protein synthesis?

3. What is the function of ribosomes in protein synthesis?

4. How is the genetic code translated into a specific amino acid sequence?

5. What is the role of transfer RNA (tRNA) in protein synthesis?

Nucleic Acids

1. What are nucleic acids and what is their function in cells?

2. What is the structure of a nucleotide and how are nucleotides joined together to form a nucleic acid?

3. What is the difference between DNA and RNA?

4. What is the function of DNA in cells?

5. What is the central dogma of molecular biology and how do nucleic acids play a role in it?

Proteins

1. What are proteins and what is their function in cells?

2. What is the structure of an amino acid and how are amino acids joined together to form a protein?

3. What is the difference between a primary, secondary, tertiary, and quaternary structure of a protein?

4. What is denaturation and how does it affect the function of a protein?

5. What is the role of chaperone proteins in protein folding and quality control?

Dna Manipulation (Enzymes)

Terms:

• Biotechnology - use of an organism or organism component to make a product or process (ie: COVID vaccine)

• DNA technology - sequencing, analysis and cut & paste of DNA

• Meiosis

• Genetic Recombination - Exchange of info between 2 DNA segments 

• rDNA - recombinant DNA technology

• Vectors

• Plasmid

• Cloning Factor

• Amplified Gene

• Amplified Protein

• Recognition sequence - identifies if something needs to be cut 

• Restriction enzymes 

• Reverse transcriptase 

• Ligase

• Polymerase

• Sticky ends

• Blunt ends 

• Ligation 

Notes:

• VCAA Knowledge: The use of enzymes to manipulate DNA including polymerase to synthesise DNA 

• Majority of Biotechnology relies on DNA manipulation

• DNA technology is the sequencing, analysis and cut & paste of DNA sequences

• Genetic Recombination which uses or occurs in meiosis and exchanges info between 2 DNA segments (like homologous chromosomes)

  • Occurs b/w same species 

  • Makes a recombinant chromatid (or non-recombinant) 

• DNA manipulation literally manipulates genomes/genes to introduce or take away specific objectives. 

• rDNA is recombinant DNA technology

  • Genetic engineering, recombinant biotechnology, DNA manipulation 

  • Gene technology includes manipulation and analysis of DNA 

  • DNA manipulation alters DNA by adding or editing DNA 

• Bacteria is often used as vectors

• To reproduce an edited gene a cloning vector is needed such as a plasmid from Bacteria to create a recombinant plasmid

• Protein or Gene can be amplified 

• In order to → Tools used

  • cut DNA: Restriction enzymes (Endonuclease)

  • Stick DNA fragments: DNA ligase

  • Copy of DNA: Polymerase 

  • Make multiple copies of DNA: Polymerase Chain reaction (PCR)

  • Separate DNA fragments: Electrophoresis

  • Edit Genes: CRISPR 

POLYMERASE (DNA or RNA makes the respective thing) 

• To synthesise DNA, replicate or repair

• Copy DNA and make copies 

• Example: Taq polymerase used in PCR

• DNA Polymerase creates DNA by asembling 749 (approx) nucelotides per second

• Synthesis from 5’ to 3’ 

• Taq Polymerase is a DNA polymerase used on PCR (chain reaction) 

LIGASE (Glue/Attaches)

• Joins different pieces of DNA

• Used to make recombinant DNA

• Recombines the DNA 

• Ligase closes the ‘nicks’ in the phosphodiester bonds + close the gaps and seals the newly transferred dna segment 

• Same Restriction enzymes cut gene of interest and plasmid /cloning vector

• Plasmid and gene fragments connect and anneal

• Ligase used to anneal the recombinant plasmid and seal it 

• Ligation

ENDONUCLEASE or RESTRICTION ENZYMES

• Cuts DNA and creates fragments

• Examples: BamH1 (Bam = bacteria, H = Strain, 1 = Order of discovery)

• EcoR1 and Taq1 

• EcoR1 - GAATTC (recognition sequence) will cut between the G and A so long as there is an AATTC following. 

• Sticky ends and blunt ends when one is overhanging or when there is a clean cut 

REVERSE Transcriptase

• Obtaining DNA from RNA

• Reversing the transcription

Polymerase Chain Reaction (PCR)

Terms

• PCR

• Heating and Cooling Cycles

• Amplify

• DNA segment

• Target DNA sequence

• Primers - complementary segments that will attach to the 3’ prime end of a chain, extend the DNA through complementary base pairing 

• Buffer Mix - Maintains pH

• Taq polymerase - 

Notes

• PCR is a technique to amplify or produce copies of a DNA segment 

• Using heating and cooling cycles

• Replication at an exponential Rate

3 Steps

1. Denature

• Separating the hydrogen bonds (94-95^o)

2. Anneal

• Primers bind to template (50-56^o)

• ‘Annealing of the primer when it ‘cools’ 

3. Extension

• Increases in temperature to 72

• Synthesising a new strand

• PCR can be used for;

  • consumer genomics

  • Food and agriculture

  • Forensic science

  • Genetic research 

  • Medicine

  • Phylogenetics 

  • Environmental biology

• State purpose of PCR

  • To replicate specific DNA segments

• Identify components

  • Primer

  • Nucelotide

  • Heat 

  • Buffer

  • DNA sample

  • PCR Tube

• Draw Steps to illustrate basic process 

1. Heat stuff up and break hydrogen bonds

2. Anneal stuff with primers at the 3’ ends

3. Synthesise new strand

• Identify Two applications

Gel Electrophoresis

Terms

• Gel Electrophoresis - used for sorting dna fragments

• Agarose Gel - Jelly (containing buffer solution to maintain pH)

• Buffer

• Gel Matrix

• Cathode

• Standard - Kind of like a ruler used to compare dna sizes

• Loading Dye

• Ethidium Bromide - Fluorescent dye, binds to dna, mutagen

Notes:

• DNA fragments put into gel, and has positive and negative charges on each side, DNA is negative charged cos Phosphates so is drawn to positive charge. 

• Gel/matrix traps larger fragments and therefore separates dna fragments by size 

  • Separate mixtures

  • Calculate size 

• Components

  • Electric current

  • Agarose Gel - traps dna allowing small fragments to move further down

  • Loading Dye

  • Standar - to calculate sizes

  • Ethidium Bromide - Fluorescent dye, binds to DNA

  • Buffer solution

  • Combs - to create wells to load DNA

  • Positive and negative terminal

• STEPS

  • DNA fragments loaded in neg side

  • Electric current

  • Dna fragments migrate towards pos side

• Small fragments move easily and travel far distance/larger fragments are trapped and travel less

• Unit, Size (bp or Base Pairs) , Quantity (ng)

• Sometimes known as a ladder (the standard) 

DNA profiling

Terms

• DNA profile

• Polymorphic regions - regions that have more than one change

• Polymorphisms - differences in these region

• Probable Origin

• Microsatellites - they are STRS

• STRs/Short tandem repeats

• Non-coding DNA

• Repeating code

• Genetic loci (location)

• Heterozygous genotype

• Combined DNA index System or CODIS

Notes

• Can be used to identify probable origin

  • Reveal family relationships

  • Identify Victims in disasters

  • Paternity Tests

  • Find Evolutionary relationships between species 

• Small sections in DNA vary, everything else is identical, these small sections identify individuals

• Everyone inherits unique combination of polymorphisms

• Process: Collecting DNA then cutting with endonuclease and then using gel electrophoresis to separate and identify.

• STRS are regions of non coding DNA that contain repeats of the same nucleotide sequence

• Short → 1-9 base pairs long

• Tandem → Repeating Code

• STRS are found in different places/genetic loci 

• Microsatellites (1-9bp), Minisatellites (10-100bp), Macrosatellites (>100bp)

• Minisatellites for fingerprinting

• STRS/Microsatellites for DNA profile

• STR-XX (x,y)

• If it’s different length, then its heterozygous

• If same length, homozygous

ETHIC ISSUES

• Limits of testing 

Bacterial Transformation

Terms

• Plasmids

• Bacterial Chromosome

• Recombinant 

• Colony

• Vector 

• Antibiotic plate

• Transgenic organisms (TGO)

• Genetically modified organisms (GMO)

• Cloning Vector

• Gene of interest

• Foreign gene

• Foreign cell

Notes

• Bacteria have both Plasmid DNA and Bacterial DNA 

• Plasmids are used as cloning vectors in rDNA technology because they can

  • Replicate

  • transfer genes from one cell to another.

• Bacterial transformation is when foreign DNA is transferred

• Bacteria are able to take up new DNA very quickly, coming from other cells

• Changing the Genome/DNA transfer = Bacterial Transformation

• pGLO is a plasmid from a jellyfish that glows

• They can put the plasmid in via Heat shock and Electric shock

• 

• Heatshock: By putting bacteria into very cold solution, plasmids are added, then in hot water the plasmid and bacteria combine, then in ice bath again.

• pGLO, ampicillan etc. has an antibiotic resistance gene

• Some of the bacteria will take up the plasmid but some will not

• To find the recombinant plasmid, they use an antibiotic plate and the antibiotic resistant plasmid will form a colony and show that the plasmid has affected it. 

• A vector is a molecule used as a vehicle to carry genes of interest to foreign cell. 

• Bacterial plasmids are commonly used because of self replication etc.

• These plasmids can be modified for specific usage. 

PLASMID VECTORS

• Multiple Cloning site - contains numerous recognition sites to allow gene insertion

• Promoter - Initiates transcription

• Origin of replication - for plasmid synthesis

• Antibiotic resistance -  selects modified cells

• Reporter gene - makes products that attach to the protein to enable detection 

STEPS IN PLASMID CLONING

• Restriction enzymes to digest DNA sample and DNA plasmid 

• DNA ligase to seal

• Transformation of recombinant plasmid into bacteria

• Agar plates with selection antibiotic resistance allow bacteria with the resistance and gene of interest is cloned. 

ANTIBIOTIC PLATE

• The antibiotic plate is used to see if the transformation has occurred, as the antibiotic plate will kill any bacteria that has not been transformed, and transformed bacteria will grow because they have the antibiotic resistance and therefore show what has and has not been transformed. 

• 

• Can be used to increase gene pool

DNA Manipulation Production of human insulin

Terms

• Humilin

• Insulin

• Cloning Vector 

• A Chain  - 21 Amino acids

• B Chain - 30 amino acids

• cDNA - copy DNA 

• ‘S’ - suppression not resistant

• ‘R’ - resistant, immune

• Fusion protein - A protein made from a fusion gene which is created by joining parts of two different genes. 

Notes

• Has 51 amino acids

• Is a hormone produced by beta cells

• Lowers blood glucose

• Has a quaternary protein structure consisting of 2 peptide chains held together by  disulphide bonds between cysteines

• Chain A - 21 amino acids long

• Chain B - 30 amino acids long

• A plasmid vector and insulin gene are isolated from E.coli then it is cut open by the same restriction enzyme. 

• 1 bacteria is used to make Chain A and a different bacteria is used to make chain B so that we have complete control over when chain A and B are together and manufactured. 

• Insulin will only become functional when its taken from the two cells. 

• When DNA is transcribe into mRNA then reverse transcription occurs its a DNA (single), polymerase is needed to make it double stranded. 

Synthesis of Chain A/B

1. Obtain copy of the insulin A gene that is double stranded without introns

• It must not have introns because bacteria do not have introns and cannot function with such. 

• Double stranded to anneal to the double stranded plasmid.

• cDNA is copy DNA 

• pBR322 has ampicilin resistance and TET resistance. It will be used to insert the insulin A gene which will make the CHAIN A protein. 

• pBR322 is the cloning plasmid.

• When only one restriction enzyme is used, the sticky ends may stick back together, so two restriction enzymes are used. EcoRI and BamHI 

  • Decrease the risk/chance of the plasmid coming back together.

• Now a recombinant plasmid that has ‘Insulin A gene’ and loses its TET resistance 

• TET is interupted 

• WHen rplasmid mix with E.coli, some of the rplasmid will be transferred to E.coli to make them transformed, but not all will be transformed.

• Rplasmid - AMP(r) + InsulinA gene + Interrupted TET gene

• 3 POSSIBLE OUTCOMES 

  • Bacteria with NO pBR322

    • Untransformed

    • NO resistance to tetracycline or ampicillin

  •  Bacteria WITH pBR322

    • Transformed bacteria by plasmid

    • Resistance to Tetracycline and ampicillin

  • Bacteria with Recombinant pBR322 containing the insulin Gene: 

    • Transformed bacteria by rplasmid

    • ONLY resistant to ampicillin. 

• Method 2 uses Beta - galactosidase gene that codes for B-galactosidase enzyme which breaks down lactose and glucose and galactose 

• It’s used as a marker to identify the plasmids that have the insulin A/B gene, by changing colour

• B-gal is to next to the Insulin A gene and goes into. 

• Gene expression of this plasmid 

  • Beta galactose

  • Insulin A gene

  • Resistance to ampicillin

• 3 POSSIBLE OUTCOMES: 

  • Untransformed bacteria 

    • Did not take any plasmid 

    • Not resistant to ampicilin

  • Transformed bacteria

    • Resistant to ampicillin 

    • Insulin Gene

    • No Beta Galactosidase gene → No fusion protein made

  • Transformed bacteria

    • Resistant to ampicillin

    • Insulin gene

    • Beta galactosidase gene - Fusion protein made. 

• To identify which colonies have functional insulin gene (ie: Beta-galactosidase gene) bacteria will be grown on agar plate with X gal. 

• X-Gal detects the presence of Beta galactosidase and insulin gene by causing bacteria; colonies to have a blue or white colour.

  • BLUE colony: Beta galactosidase & Insulin Gene present

  • WHITE colony: NO Beta Galactosidase and Insulin gene. 

 BIOETHICS

Terms

• Ethics

• Bioethics

• Moral principles

• Human rights

• Welfare of people

• Informed Consent

Notes:

• Ethics: A system of moral principles, right v wrong 

• Bioethics: Moral principles specific to biological science 

• Beneficence - must not hurt others, maximising benefits and minimise harm

• People welfare is prioritised over interests of science 

• Informed Consent

• Holding healthcare institutions accountable and reviewing scientist works 

Unethical things; 

• Plagiarism 

• False reports 

• Dishonesty 

• Breaches in integrity 

• Strict guidelines for evaluation, publication and follow up 

Ethical Approaches to Bioethics: 

1. Consequence bases

• Places central importance on the consideration of the consequences of an action (the ends)

• Aims to achieve the maximisation of positive results, with the minimisation of negative results.

• The focus is on the eventual outcome as opposed to the process taken to reach it 

• What is the end result? Does it outweigh the negatives of the process?

• Does the ends justify the means?

2. Duty/rule base

• Duty of Care

• concerned with how people act (the means) and the process taken to get to the result.

• places central importance on the idea that people have a duty to act in a particular way,

• •and/or that certain ethical rules must be followed, regardless of the consequences that may be produced. 

• Ie: it is not acceptable to cause immediate or temporary harm in the pursuit of a potential ‘greater good’

3. Virtues based

• Is person-based rather than action-based. 

• Consideration is given to the virtue or moral character of the person carrying out the action.

• Providing guidance about the characteristics and behaviours a good person would seek to achieve to then be able to act in the right way.

• Things that are self-seeking are unethical 

• Use keywords: Outcome, good virtues, process, means, etc. 

• Ethical concepts are used when identifying bioethical issues and are used to inform ethical guidelines

• When deciding the extent to which the outcome of something or the course of action is ethically applicable

INTEGRITY: 

• The commitment to searching for knowledge and understanding. 

• Honest reporting of results, sources, in ways that permit scrutiny and contribute to public knowledge and understanding

• Regardless of favourable or unfavourable results

• Must be transparent 

JUSTICE

• The moral obligation to ensure fair consideration of competing claims 

• No unfair burden on a particular group from an action. Fair distribution and access to the benefits of an action. 

BENEFICENCE 

• Maximising benefits

• Minimising risks and harms in taking a particular course of action or position. 

• ‘Zero harm’

NON MALEFICENCE 

• Avoiding causation of harm 

• The harm must be less than the benefits of the courses of action and outcomes.

• Harm/Risk can be a little as long as it is outweighed

RESPECT:

• Consideration of the intrinsic value of all living things 

• Regarding welfare, liberty, autonomy, beliefs, perceptions. Customs. Culture 

• Considerations for agency 

• When living things have diminished capacity to make their own decisions ensuring they are protected and empowered. 

CRISPR

Terms

• Photosynthetic efficiencies

• Crop yields

• CRISPR-Cas9

• Bacteriophage

• gRNA - guide rNA

• sgRNA - single guide RNA 

Notes

• CRISPR is used for Gene editing to ‘find and replace’ 

•  CRISPR Cas-9 is an Endonuclease complex that naturally exists in bacteria to edit virus DNA (bacteriophage)

• Clustered Regularly Interspaced Short Palindromic Repeats

• CRISPR has two important features:

1. Palindromic repeats : short palindromic repeats 

2. The spacers are segments of viral DNA (bacteriophages) that allow the bacteria to recognise the same virus in the event of subsequent invasions. 

• CRISPR can: 

  • Repair the damaged DNA by using a template with the correct sequence.  

  • Silence a faulty gene: The DNA can ‘self repair’ when cas9 cuts it; however, mutations can occur to introduce the ‘STOP’ codon. 

  • Replace faulty gene sequence with the correct sequence, by using cas9 to introduce enzymes that would replace faulty bases with the correct bases.

  • Increase transcription of a gene by deactivating cas9 and adding activators.

EVERYTHING I DON’T KNOW: 

Notes:

• Complement proteins do three things, 

1. Stimulate phagocytes to increase phagocytosis

2.  Highlight/Tag invaders for phagocytosis
3. Cytolysis the lysis of a pathogen forming Membrane Attack Complex (splitting of a cell)

• Cytokines are signalling molecules

• Peptide, protein or glycoproteins 

• A chemical signal for cells to carrry out immunologic responses

• Released in response to cell damage or to indicate presence of pathogen

• Crucial in controlling growth and activity of other immune system cells and blood cells

• Trigger cells to;

  • Proliferate (reproduce)

  • Induce inflammation

  • Promote antibody response

  • Activate macrophage

• Interferons (IF) are cytokines, protein and signalling molecules 

• Act as a warning signal from infected cells to all other cells

• Viral host cell is triggered to synthesise interferon which targets neighbouring cells 

• Allergens are harmless substances NOT harmful substances

ANTIGENS & MHC

• Antigen = Antibody Generator

• An antigen is a unique molecule (eg. protein) that triggers the production of antibodies and the immune system

• Could be part of a microbe or foreign substance (does not have to be whole pathogen); bacteria, pollen, protein

• Immune response may be

  • Antigen non-specific → innate immune response

  • Antigen specific → adaptive immune response

• The presence of antigens classify blood type on Red Blood Cells

• 

• Antibodies? 

• Antigens are foreign to organisms and stimulate antibodies that are specific to that antigen

• One antibody will generally bind to one antigen 

• Antigens are non-self/foreign molecules that the immune system recognises as enemies. 

• Cells are self or non-self, non-self cells have antigens.

• Self Markers (MHC) label the body’s cells as a friend and are tolerated by the immune system. 

• MHC = Major Histocompatibility complex 

• If MHC is present, immune cells will not be activated to respond. 

• MHCs are a group of venus that code for proteins found on the surface of cells that help the immune cells distinguish between self and non-self cells

• Two main types in vertebrates: Class I and Class II 

• Class I markers are found on body cells, somatic cells NOT red blood cells. 

• Class II markers are found on immune cells, macrophages, dendritic cells, monocytes, B cells, antigen presenting cells.  

• Class I: All nucleated cells eg. Body cells

• Act to identify cells self antigens from non-self antigens

• Class II: Primarily on professional APC [Antigen presenting cells]

• These cells present Antigen fragments on their class markers to T lymphocytes and other immune cells. Immune cells will have both classes EXCEPT RED BLOOD CELLS. 

• Professional antigen-presenting cells - APC, identify antigens as non-self and process antigens 

• Present the antigen on a MHC marker, so that immune cells lymphocytes so that they can identify and destroy/respond to invaders. 

• ANTIGEN PROCESSING: 

  • Cell engulfs an antigen bearing particle

  • LYSOSOME FUSES WITH ENDOCYTIC VESICLE

  • Endocytic vesicle forms 

  • Particle is digested nto bit

  • MHC markers bind fragments of particle

  • ANTIGEN MHC complex becomes displayed on cell surface. 

• 

• 

• Cytotoxic T Cells will target intracellular pathogens, cells that have been infected INSIDE the cell and if it is a body cell then the Cytotoxic T Cell will release cytotoxins and destroy the cell. 

• MHC I - Are from inside the cell

• MHC II - Outside the cell/body, external. 

ADAPTIVE IMMUNE RESPONSE 

• Third line of defence are the lymphocytes

• Specialised Lymphocytes 

  • B Cells 

  • T Cells

• 

• Depending on where the stem cell lymphocytes are matured, (T cells in thymus and B cells in bone marrow) they will become T/B cells 

• Pre-T cells leave the bone marrow and go into the lymphatic system/ circulation and then go to the lymph nodes, which is where they wait for antigens

• 

• Two types of adaptive immunity: Antibody mediated immunity/Humoural Immunity and Cell mediated Immunity 

• B cells → Humoral Immunity/Antibody Mediated Immunity → Plasma Cell which makes Antibodies, B CELLS do not make antibodies only the plasma cells. 

• T Cells → Cell Mediated Immunity → matures in the Thymus glance

• Cytotoxic cells/CD8+ - will release cytotoxins

• Helper T cells/CD4+  - will release cytokines

• T Memory - A memory cell that will become either cytotoxic or helper T cells, for future infections

• Regulatory Cell - T Supressor, stops the fighting

• Natural Killer Cells - Lymphocytes - Not part of the adaptive immunity response, part of the innate immunity

• B Memory - A memory cell that will become a plasma cell again

• 

• Cytotoxic cells have the CD8 glycoprotein and are activated by APC’s (antigen presenting cells) 

• They defend against intracellular bacteria, viruses, cancerous cells, transplanted foreign tissue, protozoa, fungi and worms. 

• Activated by MHC Class 1, releases cytotoxins such as perforin, granzymes to induce apoptosis. 

• Helper T Cells are not cytotoxic or phagocytic 

• They activate humoral immunity: B cells to make plasma cells to make specific antibodies

• Cell mediated immunity: TC cells to release cytokines 

• Innate immunity: macrophages to initiate phagocytosis. 

• 

• A naive Th-Cell means it hasn’t come in contact with that specific antigen before 

• Plasma b cells contain LOTS of rough er and undergo apoptosis 

• They make antibodies and antibodies are proteins so they need rough ER because ribosomes make proteins 

• Antibody Structure: Globular glycoproteins, quaternary structure

• They are immunoglobulin 

• Two heavy and two light polypeptide chains (4 in total)

• Chains are held together by disulphide bridges with Variable and Constant regions. 

• 

• Order of amino acids determines the shape of the variable region binding site 

• Antibodies can neutralise antigens, agglutination (clumping bateria up), precipitation, assist in complement protein, enhance phagocytosis, inflammation, cell lysis

• 

• 5 immunoglobulin isotypes

• Humoural immunity 

• 

• B cell receptor is the antibody 

• 

• A naive B cell that has just processed the same antigen will present the antigen on its receptor 

• 

• 

Lymphatic System

Terms:

• Lymphocytes

• Circulatory system 

• Lymph nodes

• Lymphatic vessels 

• Lymph fluid 

• Capillaries 

Notes:

• The lymphatic system protects from infection and disease

• Part of the immune system 

• Lymph fluid pass through lymph nodes

• Network of lymph vessels connects the lymph nodes together 

• Lymphatic system acts as a one way drainage system, transports fluid from body tissue, houses lymphocytes and filters cellular waste

• Capillaries are necessary so that all cells have access to oxygen and to get rid of CO2

• Lymph Nodes, small structures that work as filters for harmful substances, located in strategic points 

Acquired Immunity

Terms:

• Immunity 

• Symptoms 

• Innate Immunity

• Humoral Immunity

• Cellular Immunity

• Immunisation - harmless part of microbes are introduced to trigger the body’s immune response

• Herd immunity

• Vaccine - A suspension of antigens that are deliberately introduced into the body

Notes:

• Immunity can be

  • Innate or Adaptive

  • Natural or Artificial 

  • Active or Passive

• Natural Immunity occurs through contact with a disease causing agent, it is not deliberate; by chance

• Artificially acquired immunity develops only through deliberate actions such as immunisation. 

• Both natural and artificial immunisation have the same result of activating adaptive immune response 

• Passive immunity is acquired through the transfer of antibodies, their immune system has not been activated, they are NOT receiving antigens, but instead antibodies. Memory cells are not made, they only have antibodies. Immunity only lasts as long as the antibodies are present. 

• Active immunity is the adaptive immune system activated. Delivery of antigens.

• 

• ACTIVE-NATURAL IMMUNITY

  • Pathogen/Antigen enters body (illness)

  • Adaptive immune system is activated

  • Memory cells are made 

  • Long Term Immunity

• ACTIVE-ARTIFICIAL IMMUNITY

  • About immunisation (vaccines)

  • Herd immunity

  • Active, deliberate process

  • Antigens are introduced and memory cells are made

  • Long term immunity 

  • Types of Vaccines: Subunit or Whole agent vaccines

    • Subunit - contains some part or product

    • Whole-agent - contains whole, non virulent microorganism which can be inactivated (killed) or attenuated (weakened)

  • 

  • Herd Immunity, the resistance to the spread of a contagious disease within a population that result if a sufficiently high proportion of individuals are immune to the disease especially through vaccination

  • 

  • Minimisation of an epidemic 

• PASSIVE ARTIFICIAL

  • Antibodies injected

  • Used when a very rapid immune response is needed like antivenom 

  • Human antibodies are injected 

  • ANtibodies come from blood donors who recently had vaccination

  • Only provides short term protection

  • No memory cells

• PASSIVE NATURAL

  • Mother’s antibodies pass across the placenta to the foetus 

  • Colostrum (the first breast milk) contains lots of IgA which remain on the surface of the baby’s gut wall and pass into blood.

Immunotherapy

Terms

• Immunotherapy

• Metastases 

• Benign

• Malignant 

• Cancer

Notes:

• Cancer is a group of diseases involving abnormal cell growth, with the ability to spread throughout the body

• Benign or Malignant tumours

• Beninghn cannot spread by invasion or metastasis

• Malignant can spread through the body via the bloodstream

• Immunotherapy uses Vaccines and monoclonal antibodies (mAbs) 

• Tumour cells thrive because they are able to hide from the immune system by expressive defective class-1 MHC

• Immunotherapy uses the host system

SPECIFIC:

• Marks cancer cells so immune system can find and destroy

• Triggers response

• B&T lymphocytes are stimulated to target cancer cells

• Contain: Peptides, antigens or whole proteins of cancer cells and adjuvants 

• Adjuvants: substances that enhance the effect of a vaccine or other treatments

• No side effects

• Classified: Preventive or Therapeutic and personalised 

• Preventative, harmless virus-like particles containing viral DNA trigger immune response to create antibodies and memory cells etc. 

• Therapeutic: For the treatment of someone experiencing cancer. The tumour is not yet recognised by the immune system so immune cells are trained to recognise antigens and injected into individuals so the adaptive response is activated to be able to recognise and attack the tumour. 

• 

• 

• Monoclonal Antibodies are made to treat diseases

• mAbs target specific antigens found on diseased or cancerous cells

• mAbs can act directly when binding to cancer specific antigens to ;

  • Induce immunological response: apoptosis

  • Highlight cancer cells to immune cells

  • Block growth signals

  • Deliver toxins 

•  

NON SPECIFIC:

• Boot immune system to work better

• Trigger innate response, cytokines et: interleukin and interferon

AUTOIMMUNE DISEASES:

• Diseases that have the immune cells targeting self-cells

• Cytotoxic T cells, B cells activating, mast cells→ histamines and inflammation 

• 

• No cure

• Immune suppression that can help control overactive immune response and decreasing pain 

• Anti-inflammatory

• 

• Alongside immune suppressive medication

• Acts as competitive inhibitor signals.

• Interleukin competitive inhibitor, stops signals for immune system to work 

• Can stop the b cells, and t cells etc. Targets the immune system that will be targeting self-cells 

Genetic Changes in a population over time

Terms:

• Bacterial resistance 

• Antigenic shift

• Pathogens

• Population

• Evolution

• Reservoir

• Novel Strain

• Rational Drug Design - Targeted approach to designing new drugs, involves analysing the structure of a pathogen

• Gram-positive - thick cell wall of peptidoglycan

• Gram-negative - thin cell wall of peptidoglycan

• Broad spectrum antibiotics - targets wide range of bacterial species 

• Narrow spectrum antibiotics - targets one or two bacterial species

• Bacteriostatic

• Bactericidal

• Microevolution 

• Antigenic Drift

• Antibiotics

• Bottleneck Effect

• Predation

Notes:

• Evolution = Change 

• Outbreak:  the occurrence of one or several cases of a disease in an area in which it is not normally present

• Epidemic: an uncontrolled outbreak that is the infection of many people simultaneously

• Pandemic: An epidemic on a global scale, disease spread worldwide 

• Endemic: A disease that exists permanently in a particular region/population

• Outbreaks require identification of cause, treatment, prevention of spreading and another outbreak

Condition for a pandemic

• New pathogen/Novel strain - there is a lack of interaction with antigens and cannot be protected against because there is no immunity, no vaccine   

•  Pathogen infects people and non-human hosts providing a ‘reservoir’

• Pathogen is easily transmitted through direct contact, air or vector

• Infected individuals are not isolated

• No vaccination or preventative measures are in place

• No control measures (masks, quarantine)

Influenza virus Structure

• Two spike proteins, neuraminidase/sialidase and hemagglutinin

• Nucleoprotein - RNA

• Neuraminidase - enzyme, viral exit - cuts out

• Hemagglutinin - viral entry, receptor - goes in

• The virus enters and undergoes endocytosis, the nucleus is usesd for mRNA synthesis and RNA replication so now the virus has taken over the cell and will be used to make the virus while the virus exits and infects more cells

• Subtypes of Influenza A are differentiated on the basis of the two surface antigens 

• Three Subtypes of H (Hemagglutinin) (H1,H2,H3)

• Two of N (N1 and N2) generally cause the annual epidemics

• Influenza A viruses are classified by A,B,C

• Influenza A can cross species

• A&B are main causes of epidemics/pandemics Type C cause mild versions 

• 

ANTIGENIC DRIFITING

• There can be gradual minor changes in HA/NA caused by point mutation

• Occurs in A&B

• Vaccines are annually updated

ANTIGENIC SHIFT

• Sudden Major Change, genetic reassortment of genes caused, when two subtypes infect a host, direct transmission from other animal to human introduces a NEW novel strain

• Explosive Spread

• Only in Influenza A

• Creates a pandemic/epidemic 

What are the scientific and social challenges presented in terms of the treatment strategies and vaccine programs (caused by viral antigenic drift and shift)? 

Scientific: Vaccines created in response to viruses would have to change dramatically to accommodate for major changes due to antigenic shifts in the virus’s structure. Identification of mutation would be difficult and the difficult within identifying antigenic shift or drift. 

Social: Immune responses of the population are naive and there is no immunity to a novel strain as the antigenic shift has drastically changed the virus’s structure. Vaccination development can be expensive and time-consuming as well as how measures will be implemented such as quarantines, lockdowns, masks, vaccinations etc. 

CONTROL: 

• Antiviral drugs that prevent viral entry by binding to receptors 

• Inhibition of enzymes that catalyse reproduction of virus genome 

• Blocking transcription and translation 

• Prevents viruses form leaving cells to prevent further infection

RATIONAL DRUG DESIGN: 

• Rational Drug Design - Targeted approach to designing new drugs, involves analysing the structure of a pathogen

• Uses this information to design a drug that will mimic or block the action of the disease-causing agent.

• Produces drugs that have complementary shapes to the active sites of the pathogen or molecule they are targeting.

• 

• 

OTHER CHEMICALS TO CONTROL PATHOGENS:

• Disinfectants - Non specific, 

• Antiseptics - Non specific, against bacteria, viruses and fungi

• Antibiotics

Antibiotics:

• Substances produced by microorganism or artificially that in low concentrations inhibits the growth or kills microorganisms

• Broad spectrum antibiotics - targets wide range of bacterial species

  • Negative: Unnecessary introduction of antibiotics that may cause harm

• Narrow spectrum antibiotics - targets one or two bacterial species

  • Better but takes time

• 

• Bacteriostatic - slows growth of bacteria by interfering with synthesis processes, like DNA replication, enzyme activity or protein synthesis

• Bactericidal - kills bacteria, as an example may prevent the growth of cell walls to kill the bacteria. 

• Antibiotics only for bacteria because viruses hide in body cells and also they don’t have cell walls so bacteriostatic can’t target them, bactericidal can’t destroy the cell wall; they have different structures to bacteria

• 

• 

• 

• Four types of antibiotic resistance

• Impermeable barrier, target modification, antibiotic modification, efflux pump mechanism 

• Evolution = Change in allele frequencies

• 

• Bacteria transfer genes easily and go into plasmids/DNA, high reproduction rate, exponential growth of population 

Population: A population is the number of all the organisms of the same group or species, which live in a particular geographical area, and have the capability of interbreeding to produce fertile offspring.

Species: A group of living organisms consisting of similar individuals capable of exchanging genes or interbreeding.

Alleles: Alternate forms of a gene, two alleles is 1 genotype 

Allele pool/Gene pool: The sum total of allele for all genes present ina  population at one time

• Large gene pool indicates genetic diversity and biological fitness

• Small gene pool indicates low genetic diversity and biological fitness → Increasing chances of extinction 

• Used to determine allele frequency proportion of a particular allele within a population

Biological Fitness: The level of fitness a species has for surviving changes in environment based on the ability to adapt to new situations

• Evolution change in allele frequencies over time

Mechanisms of Change:

1. Mutation

• Random change in the genetic composition due to changes in the DNA base sequence or chromosome

• Point mutation 

2. Gene Flow

• Movement of alleles into or out of populations due to immigration/emigration

• Gene flow keeps separate populations similar

3. Sexual Reproduction

• Sex can introduce new gene combinations

• Alter allele frequencies if mating is assortative

• Random mating

• Non-random mating

  • Assortative Mating - Preference for similar genotypes/phenotypes

  • Disassortative Mating- Preference for different genotypes/phenotypes

4. Genetic Drift 

• Completely random/chance

• Causes the allele frequencies to drift from one generation to the next

• No selective agents 

• May cause gene variants to completely disappear

• Genetic drift has a greater effect on small populations (5/100 vs 5/10) 

• Population bottlenecks and Founder Effects

• 

• Bottleneck → Catastrophic event reduces population and reduces genetic diversity by chance

• Founder Effect → Small group moves and reproduces in a new location, genetic variation is low

5. Natural Selection/Selection Pressure 

• Change in gene pool composition as a result of differentially selective environmental pressures 

• Predation, Abiotic factors, Nutrition, Disasters, Finding a mate

• Selective pressures are biotic and abiotic factors that select for certain characteristics in a population to be passed on and selected against other characteristics that will not be passed on

• Eg. Dark bug camouflaging on a dark tree doesn’t get eaten by bird, bright coloured bug gets eaten

  • 1. Variation: Intraspecies differences

  • 2. Selection Pressure: A struggle is applied to population

  • 3. Adaptations: Survival of the fittest

  • 4. Reproduction: Adaptive quality is passed onto offspring

  • 5. Change in population: Allele frequency/microevolution

• Increase offspring of a certain trait due to survival of the fittest (organisms most capable of reproducing produce more offspring with whatever trait they have that has enabled them to survive and reproduce)

• If there is no selective pressure, different traits do not matter

• There needs to be a struggle to live (selective pressure)

Selective pressures:

• Just because a phenotype has been wiped out does not mean the allele has disappeared/genotype may still have the alleles that will trigger the recessive allele

• The allele cannot be dominant because then even a single allele will trigger the phenotype thus, if the allele IS dominant it has gone extinct 

• NO SELECTIVE PRESSURE NO CHANGE! 

• Things that mean NO change to allele frequencies: Large population, no mutation, no migration, random mating (organisms choose partners randomly), no selection (no traits can be favoured) 

Mutation:

Terms:

• Point mutation

• Block mutation

• Chromosome

• Meiosis

• Allele

• Gene sequence

• Mutation

• Substitution

• Deletion

• Addition

• Non-disjunction 

Notes:

• Adds a new allele to increase gene pool

• A mutation is a change in the gene sequence or chromosome. 

• Gene mutations (point mutation) localised changes to DNA base sequence ie: substitution, deletion or addition

• Chromosomal Mutations (Block mutation) large scale mutations occurring during meiosis that can change chromosome structure and number

Gene mutation: 

Missense substitution

• Type of mutation is a change in one DNA base pair resulting in amino acid subbing in for another in the protein made by a gene

• Eg. Sickle Cell Anaemia

Nonsense Substitution

• Accidental mutation codes for STOP codon resulting in a shortened protein/junk protein

Insertion (Frame Shift)

• An insertion changes number of DNA bases, protein may not function properly as point mutation has caused a frame shift

Silent mutation: 

Nothing is changed, redundancy allows for the same amino acid to be produced

Deletion (Frame Shift)

• Changes number of DNA bases, frame shift because protein will be changed sequence

Frameshift Mutation

• Can change every amino acid that follows point of mutation and alters a protein so much 

• Changes the sequence, shifts reading frame

Chromosomal Mutations [Block Mutation]

Block mutations can cause polyploidy, changes in chromosome number and structure. 

Duplication

• Alleles are duplicated/added

Inversion

• Positions are swapped, frequency doesn’t change but sequence does

Deletion

• Removed segments of chromosome

Insertion

• New alleles introduced

Translocation

• Also swaps but with a different chromosome 

Meiosis:

• Meiosis can stuff up and nondisjunction may occur, Main cause for aneuploidy

• Aneuploidy, incorrect chromosome number

• (Chromosomes do not separate properly)

• Variation is introduced because random alignment and crossing over/random assortment when there is exchanging of whatever 

• Polyploidy cells are organisms containing three or more times the haploid number of chromosomes like 3N or 4N, uncommon in animals, common in plants 

• Occurs through allopolyploidy and autopolyploidy

• Allopolyploidy - An individual or strain whose chromosomes are composed from two different species to produce hybrids 

• Can have the full chromosome set of two different species

• Autopolyploidy - resulting in offspring with two sets of chromosomes from it’s own species 

Artificial Selection / Selective Breeding

Terms:

Notes:

• Criteria: variation in a population and heritable traits

• Humans select

1. Determine desired trait

2. Interbreed parents with desired trait

3. Select offspring with desired trait and interbreed them

4. Process continues until reliable reproduction of desired trait is achieved

Problems with selective breeding

• Gene pool has been reduced and alleles are lost therefore reduced resistance to environmental change

• Reduced Biodiversity Genetic diversity decreases, ability for adaptation is decreased

• Increased genetic abnormalities, Genetic defects can be selected for with favourable traits

Geological Change

Terms:

• Stratigraphy 

• Geologic Time Scale 

• Palaeontology - the study of fossils

• Body fossil

• Trace fossil

• Impression fossil

• Mineralised fossil

• Intermediate 

• Transitional fossil

• Permineralisation

• Index fossil

• Sedimentary

• Strata

Notes:

• Geologic Time Scale (GTS) is a system of chronological dating that relates geo strata (stratigraphy) to time

• First prokaryotic life form - Cyanobacteria

• Fossils preserved in rock, soil or amber

• Remains of organisms 

• Palaeontology is the study of fossils

• Lowest rock layers are older

• Rock layers formed later contain more complex organisms

• Variety also increases

• Body Fossils - fossilised remains of an organism eg: bones, leaves

• Trace Fossils - No parts of an organisms, impressions of activity eg: footprints

• Impression Fossils -  Organism decays and leaves an impression the rock/earth

• Mineralised fossil -  minerals replace the organism structure

• Fossilization requires 

  • Rapid burial: protection against scavengers, erosion and damage

  • Low oxygen: protection of oxygen damage and lack of decomposition

  • High pressure: to promote mineralisation of remains

  • Remains undisturbed: To allow for permineralization

  • Hard body parts: eg. teeth, shell

1. Death and decay: Soft body parts decay, leaving only hard body remains

2. Deposition/rapid burial - hard remains are rapidly covered with silt and sand and layers build over time

3. Permineralization - pressure from layers od dirt and rock cause hard organic material to be replaced by minerals

4. Erosion/ exposure - movement of earth plates may displace the fossil and return to discovery

• Soft body fossils are less likely because they have more water and are more likely to decompose, more likely to create impression fossils (ie: jellyfish)

• Transitional fossils: Fossil that can link two different lifeforms, remains of a pre-existing organism that shows a progression/transitions

• Should show transitional/intermediate characteristics 

Dating Fossils: 

REMINDER: GO THROUGH PRESENTATION 6. FOSSILS WE LOST TIME AND GO THRU IT BETTER

• Absolute dating: anything that gives exact dates and numbers, numerical dating, determined by radiometric dating, estimates the age in years by measuring certain radioactive isotopes the object contains. 

• Relative dating: estimates the age of fossils found within strata, cannot tell the actual age of the fossil, using index fossil/stratigraphy, older than this/that, MUST COMPARE SOMETHING

• Sedimentary rocks

• Some of these layers may be laid down by water (Sedimentary) or volcanic activity (igneous)

• Importance of the sequence in which is was deposited etc. 

• Relative dating is important to figure out index fossils

• Index fossils are organisms that were geographically widespread and abundant but only existed for a limited span of time. 

• Must be distinctive, globally widespread and recognizable, became extinct quickly to pinpoint precise time periods 

ABSOLUTE DATING

Radiometric:

• Using the isotopes of carbon to determine age 

• Isotopes: Variation in neutrons

• The presence of Carbon-13 and Carbon-14 indicate how long something has been around and the decay of that isotope 

• Isotopes go through radioactive decay 

• Parent Isotope is unstable

• Daughter Isotope is stable

• Radioactive decay is when the parent isotope becomes stable

• When half of parent isotopes have decayed/become stable becomes 1 half life and so forth

• 

• 

• Carbon-14 is not old enough for REALLY OLD shit

• Carbon 14 takes 5730 years for half of the isotopes to become stable and become N14

• 

Process of C-14 → N-14

1. Cosmic radiation heat N-14 

2. N-14 loses a proton → C-14

3. C-14 + C-12 are in the atmosphere and get absorbed by living organisms

4. When those organisms die, bones lose C-14 as it becomes N-14 via beta decay (gains a proton) 

• Maximum limit of this method is 60 000 years

LIMITATIONS OF FOSSIL RECORDS

• Organisms decompose rapidly

• Are eaten 

• Soft-bodies organisms do not fossilise easily due to water

• Small fraction of organisms die in conditions favourable to fossilisation

• Fossils are still unearthed 

Speciation

Terms:

• Macroevolution

• Speciation - the evolution by which new biological species arise over time

• Species - Organisms that can produce fertile offspring with one another excluding asexual reproducing organisms

• Ancestral population

• Allopatric Speciation

• Prezygotic Barrier

• Postzygotic barrier

• Geographical isolating mechanism

• Isolating mechanism

• Reproductive mechanism

• Adaptive radiation - divergence of a large number of related species from a common ancestor 

Notes:

• Speciation is MACROevolution - the evolutionary process by which new biological species arise over time

• Ancestral populations are divided then isolated preventing gene flow

• Different selective pressures will create differences in population

Allopatric speciation

1. Ancestral population: There is gene flow and variations

2. Isolating Mechanism: prevents gene flow (the movement of genes between populations)

• Geographical isolation

• Reproductive/Genetic isolating 

3. Mutation creates new variants in different areas

4. Natural Selection: different selection [pressures select for new vairants 

5. Speciation: individuals from each population can no longer produce fertile offspring with each other or the original ancestral population.

Reproductive Isolation

Mechanisms that prevent mating and reproduction, ie: individuals not responding to courtship

• No gene flow

• No exchange of alleles between populations

• Prezygotic isolation

  • No fertilisation → No zygote

• Postzygotic isolation

  • Zygote is formed but it is inviable or infertile (dies or can not reproduce) 

• Pre-Zygotic 

• 

• Post Zygotic:

• 

• Adaptive radiation - divergence of a large number of related species from a common ancestor 

CHARLES DARWIN'S GALAPAGOS ISLAND FINCHES:

• Finches with different features found on Galapagos islands all descendants of the mainland ancestral species. 

• Geological Isolation

Sympatric Speciation

• Species share the SAME geographical area but are reproductively isolated

• Isolation comes from within the group

• Assortative mating

Determining Relatedness

Terms:

• Relatedness

• Relation

• Divergence - Speciation

• Homologous Structures

• Adaptive radiation

• Vestigiality

• Molecular homology - sameness on a molecular level

Notes:

• Comparing anatomical structure, Mitochondrial DNA, genetic sequences

• Structural vs Molecular 

Homologous Structures:

• Homologous Structures 

  • Evolved from the same structure in an ancestral species

  • Different functions

  • Immediate common ancestors

  • Organisms show divergent evolution

  • Adaptive radiation

• Eg. Pentadactyl limb

• 

• Vestigial - Describes homologous characters of organisms which have seemingly lost all or most of their original function in a species

• Vestigiality can be structures, behaviours and biochemical pathways

• Changes to the environment have rendered these structures redundant and so over time they have lost their functionality

Analogous structures: 

• Same function

• Different structure

• No immediate common ancestor

• Organisms develop the same structure due to convergent evolution

• 

Molecular Homology

• Molecular clock hypothesis is:

  • Changes in DNA and proteins are constant over evolutionary time and across different lineages

  • The amount of molecular change between two species measures how long ago they shared a common ancestor

• Molecular clock calculations are carried out on DNA or amino acid sequences btw species to establish relatedness

• Comparison of DNA sequences and amino acid sequences 

• If divergence has occurred further back in time, there will be less similarity/less molecular homology

Mutation Rate:

• Change in DNA over time

• Can be expressed as the number of nucleotide changes over a million years

• Molecular clock uses the rate of accumulation of mutations of DNA to determine how long ago divergence occurred.

Less Related Species:

• More mutations

• Greater differences

• Divergence occurred further back in time

Closely related species

• Less mutations

• Less differences

• Divergence occurred more ‘recently’

Amino acid:

• Differences in amino acid sequence reflect changes in DNA sequence

• Changes in the gene nucleotide should build over time

DNA comparison:

• Direct Comparison of DNA base sequences

• Comparing whole genome

• DNA hybridisation

• Comparing karyotype

• Mitochondrial DNA

  • Mitochondrial DNA

  •  

  • Only inherited from mother

  • 

  • Mostly for recent (20 mil)

  • Can be recovered from teeth and bones

  • There’s a lack of recombination of mtDNA, remains the same

  • Higher mutation rate: Contains non-coding regions known as the D-loop that mutates at a higher rate

  • High copy number - cells have lots of mitochondria 

  • Maternal inheritance: mtDNA is inherited from the mother only, to establish ancestry • It is used as a molecular clock.

  • Mitochondrial Molecular Clock: rate at which mutations have been accumulating in the mitochondrial genome of hominids during the course of human evolution. 

• Closely related species will show more similarities in base sequences, genome, DNA, Chromosomes, mtDNA

Phylogenetic Trees

Terms:

• Lineage

• Phylogenetic

• Ancestor

• Ancestral lineage

• Descendant 

• Relatedness - determined by comparison of aa sequences or DNA to establish phylogeny, how recently species diverged

• Phylogeny - refers to an evolutionary line of descent, can be determined by comparing sequences in different species.

Notes:

• 

• Phylogenetic trees act as evidence for relatedness

• Phylogeny refers to the evolutionary line of descent, determined by comparison

• Phylogenetic tree: 

  • Hypothesis relatedness

  • Phylogram

  • Compares sequences that have a constant rate of mutation (evolutionary clocks)

  • Mitochondrial DNA is a useful source as it is maternally derived has a known mutation rate and lacks recombination

  • Difference → mutation in either nucleotide of amino acid sequences.

• Evolutionary trees can evolve to alter hypotheses if new evidence alters understanding

• All living organisms have Cytochrome B

Human Change Over Time

Terms:

• Hominidae

• Genus

• Family

• Order

• Species

• Hominoid

• Primate

Notes:

• Primary ancestors would have had

  • Arboreal

  • Grasping hands

  • Long, mobile limbs

  • Quadrupedal locomotion

  • Binocular vision

  • Upright sitting position

  • Nails instead of claws

  • Large eyes to improve eyesight, colour vision 

  • Large highly developed area associated for vision 

  • Reduced development for smell 

  • Different types of teeth for wider variety of food sources

  • Singular birth: Longer parental care, increased infant dependency

  • Tails

• Hominoidea - superfamily that includes apes and humans

• Hominoids - members of the superfamily hominoidae

• Hominids - all modern and extinct great apes. Gorillas chimps etc. and Immedieate ancestors

• Hominins - any species of early human that is more closely related to humans that chimpanzees including modern humans

• 

• 

• 

• Pre-Hominins - Arboreal lifestyle, food resources were readily available in near-continuous forest

• Cooling climate —> Trees became scarce

• As trees became scarce, pre-hominins were forced to leave trees in order to seek out food sources

Bipedal Walking

1. S-curved spine

2. Inward femur angle

3. Pelvis shape

4. Foot shape/structure

5. Reduced Canines (Not related to walking)

6. Foramen Magnum - hole in skull

7. Brain size/Skull 

• 

• Bipedal motion through S-shaped, flexible spine for balance 

• Femur/tibia angled inwardly for centre of gravity and allow for balance and walking 

• Short broad pelvis to allow for attachment of large powerful muscle

• Bow shaped to support torso organs

• Chimpanzee feet has opposable thumbs

• Human feet has an arch, acts a spring, loss of big thumb, slightly larger toe

• Transverse Arch - Converts foot into a spring allowing for transmission of stresses and improving walking efficiency ef

• Foramen Magnum is the hole at the base of the skull thru which the spinal cord passes 

• If the foramen magnum is positioned towards the back (posterior) - quadruped

• Foramen is more centred/to the front – Bipedal

• Larger brain size, reduced brow ridge and flatter face 

• Cranium Capacity - Mass of brain that can fit into a human

Trends in Skull Anatomy

1. Shape and slope of forehead

2. Brow ridge

3. Facial Angle

4. Size of teeth

5. Protrusion of mouth

6. Position of foramen magnum

7. Size and shape of zygomatic arch

8. Brain case - size and shape

9. Size of mandible

10. Sagittal crest present? (Humans, not present)

11. Shape of occipital region

Differences between skulls of Australopithecus Afarensis and Homo Sapiens

Why was Bipedalism Selected for/Adapatations!

1. Enabling a more proficient use of tools by freeing hands when upright

2. Bipedalism is more energy efficient

3. Thermoregulation: Lowers body temperature as solar radiation is retatined

4. Greater view of surroundings therefore able to escape predators more effectievly

5. Greater ability to disperse and cover more ground leading to habitat variability 

6. More effective mating strategies leading to successful reproduction

7. Reduced canines was also selected for

8. Ability to carry food and weapons when walking

9. Carrying offspring while moving and eating

10. Hair loss 

    1. Retention of head hair for reflection of heat

    2. Easier to control parasites 

    3. Thermoregulation - Less trapped heat, Greater heat loss, well developed sweat glands

• Early Hominins

• Australopithecus 

• Homo genus

• Environment, what they looked like, how they moved etc. 

Homo Erectus

• First human emigrant 

• Left Africa 

• Founder effect, some remained in Africa

• Larger brains and advanced toolmaking

• Left btw 100 000 and 1.6 million years ago 

• Wore skins enabling travel from Africa into china and south East Asia 

• 

Homo Floresiensis

• ‘Hobbit’ 

• Small stature

• Wide pelvis and hunched shoulders

• Lived in Asia between 100,000-60,000

• Flat face’

Theories

• Smaller body possibly due to surviving with constrained resources, island dwarfism 

• Descendants of homo habilisi 

• Has a pathological condition in modern humans (microcephaly)

Homo Neanderthalensis 

• Complex species 

• Bigger brain than humans 

• Similar but they have a bigger brow ridge 

• Shorter

• Had a more robust skeleton and muscular 

• Cousins NOT direct ancestors, shared a common ancestor

• Co-existed with modern humans 

• Went extinct 28000 years ago 

• Shows many single base differences however DNA is very very similar

• Neanderthals did not contribute any mitochondrial DNA to any homosapiens living today 

• Human females and Neanderthal males 

• 0% of Neanderthal DNA in African populations

• 1-4% in people of European or Asian descent

• Did not migrate to Africa, only came in contact in Eurasia 

• Possibly went extinct due to transmission of disease, pressure of incoming migrant humans, or being slaughtered by modern humans (killer ape theory)

Homo Denisovans

• Diverged from modern humans about 500 000 y.a., related to neanderthals 

• Diverged from neanderthals about 300 000 years ago

• Possibly resembled neanderthals

Epigenetics:

adding methyl groups, not actually altering DNA etc

Working out pattern of methl or whatever could see gene expression and effects on appearance.

Archaic Human 

• Includes neanderthals, H. Floresiensis and H. Denisova

• Mainly differed in skull

• Backward sloping forehead

• Big brow ridge

• Long elongated skull

Why did they leave Africa:

• Depletion of resources

• Competition for resources

• Climate change - droughts leading to starvation

• Curiosity

Human Migration Evidence

• DNA Evidence to support the hypothesis that early hominins migrated out of Africa around 150 000 ya

• DNA evidence suggests interbreeding btw modern homninins and nanderthals in Europe and the Middle East

• Reached australia 35-60 000 ya

• The Pleistocene Ice Age created a land bridge that connected Asia and Alaska over 13,000 years ago. 

• DNA suggests that modern humans reached australia continent approx 55 000 ya

• 

• Out of Africa = Replacement theory 

• H. Erectus left, evolved into Archaic humans

• H. Sapiens left 200 00 years later and replaced archaic humans

• Out of Africa model II = Assimilation theory 

• Same as A except some H. erectus survived and interbred and joined H. Sapiens

• Multiregional - Continuity theory

• • Significant migration of H.erectus across Africa, Asia and Europe for the last 1.8my. • Isolation of the populations à divergence of gene pools, traits & behaviour. • interbreeding btw populations could have occurred • genetic drift led to the DNA of the other species being lost from the H.sapien genome.

• 

• Multiregional theory 2

• 

• 

Haplogroup

• Group who share common ancestor on paternal or maternal line

• Inherited Y chromosome

• Inherited mtDNA

Indigenous Migration

• Single migration from Africa to Australia 60 000

• 42 000 ya, extinction of megafauna

• Aboriginal people have strong sense of country and place

• Place- space mapped by intangible boundaries that individuals or groups of Torrest Strait Islander peoples occupy and regard as their own via spiritual and emotional connections

Connections:

• Connection via Maternal and paternal lines of descent • Clan group • Language groups • Spiritual connection