biology FINAL

radiocarbon dating

• known that Carbon 14 decays to form nitrogen 14 with a half-life of 5730 years.

• Radiocarbon dating is a technique in which scientists compare the proportion of parent (C14) to daughter (N14) isotopes to calculate how many half lives have passed

fossilisation

1. Rapid burial after death = organisms dies and is buried quickly (hidden from scavengers)

2. Undisturbed = so that remains are intact and not broken up from scavenging animals/weather

3. Decomposition prevented = conditions must be such that bacteria (and fungi) that normally decompose dead tissue cannot survive

   1. constant cold temperatures, dehydration, high acidity, lack of oxygen, darkness

4. Downward pressure = from layers of sediments above

symptoms of inflammation

redness - vasodilation of blood vessels, leading to red blood cells released into tissue

pain - swelling causes pressure on the surrounding tissue, which stimulates pain receptors and contributes to the pain

heat - increased blood flow

swelling - increased movement of fluid (blood & lymph) into tissues (due to increased capillary permeability) after vasodilation

function of antibodies

Agglutionation: form antigen-antibody complexes, causing the antigens to clump together and make them more recognisable to phagocytes

Neutralization: prevent binding of pathogen to self-cells to neutralise harmful effects

Opsonisation: tag pathogens for destruction (by binding to surface antigens on pathogens to form antigen-antibody complexes), activating phagocytes and complement proteins - leading the destruction of the pathogen

epidemic

sudden increase in occurrence of a disease among a specific population in a given area at a particular time

pandemic

an epidemic that has spread across multiple countries in different regions of the world

endemic

disease that is constantly present at a stable, predictable baseline level within a specific geographic area or population

relative dating

dates relative to the position of the fossil or relative to an index fossil of known age

Based on statigraphy; states that the oldest stratum is at the bottom and younger layers lie above

Faunal selection = fossils contained in sedimentary rock strata succeed one another in a predictable order, even when they are found in different places

consequence based approach

central importance on consideration of the consequences/effects of an action, aims to achieve maximization of positive outcomes/benefits and minimization of negative effects

• may allow an individual to break the rules to achieve the greatest good

duty/rule based

concerned with how people act; some actions are essentially good/bad, dependent on their nature and a clear set of rules

• humans have an obligation/duty to follow these ethical rules regardless of consequences that may be produced

virtue-based

- individual should be driven by their character, rather than by any fundamental rules or consequences; action can be justified simply for its virtues

- which action would a good person choose (is it of moral character to be…)

integrity/justice/beneficence/non-maleficence

honest reporting of all sources of information and communication of results, whether favorable or unfavorable

ensure that there is 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 -  regardless of socioeconomic status

commitment to maximizing benefits and minimizing the risks/harms involved in taking a particular position or course of action.

involves avoiding the causations of harm so that the harm resulting from any position or course of action should not be disproportionate to the benefits from any position or course of action

respect

consideration of the extent to which living things have an (inherent/functional worth) intrinsic value and/or instrumental value;

• valuing the differences between people in terms of their beliefs, values and freedoms.

• consideration of the capacity of living things to make their own decision

biochemical pathway

series of steps (which may occur at different locations within a cell or different cells) from initial reactants to a final product and that each step is facilitated by specific enzymes and coenzymes

allows for the efficeint & controlled production of complex molecules (ATP)

enzymes

organic, protein, biological catalyst, that lowers activation energy to increase the rate of reaction within living cells without being consumed in the process

alltrostic site

a binding site (outside of the active site) on the enzyme where OTHER molecules that are not the substrate can bind

coenzymes

non-protein organic molecules that facilitate reactions by cycling as loaded or unloaded forms moving energy, protons and electrons between reactions in the cell.

• Type of organic cofactor

• ATP - energy transfer (carry from one site to another)

  NADH/FADH2 - transfer of electrons and protons

LI stage of PS

1. CO2 is taken in (powered by ATP)

2. ATP breaks apart CO2 and NADPH unloads H+ ions

3. C’s, O’s, and H’s recombine into C6H12O6 (Glucose)

1. additional oxygen molecules from CO2 and hydrogen ions from NADPH bind together to create water

• Doesn’t require light, but requires light-dependent stage

base addition/deletion

causes the reading panel of codons to change

shifting the frame either forwards or backwards by a base. Causes all subsequent codons to change.

more codons you change the more likely they code for a new amino acid and thus produce a different protein (or none at all)

genetic code

sequence of nucleotides in DNA/RNA that determines the sequence of amino acids in a protein

control group

= condition where these is the absence of the IV

• acts as a point of comparison

• changes in the DV can be attributed to changes in the IV and not other variables

• improves validity

amino acid strucutre

sticky vs blunt ends

Sticky ends: cuts overlap (staggered cuts/not directly opposite each other) and provide complementary bases for inserting fragments in the correct position and direction.

Blunt ends: used for digesting DNA in gel electrophoresis where end sequences do not matter. If rejoined, would be randomly joined (via ligases). cuts the 2 strands at points directly opposite each other

Gel Electrophoresis:

used to separate large molecules on the basis of their size, electric charge, separates depending on

•  concentration of ionic buffer (conducts electricity thus higher concentration, faster moving)

• Viscous - thick, resistant to flow

• voltage applied (higher = faster moving)

Small fragements in gel electrophoresis

= able to better move and weave through the porous agarose gel

Vector:

 

a self-replicating vehicle (plasmid/viral DNA) used to transfer a gene (DNA) from one cell/organism into another

• able to replicate inside their host organism (self-replicate)

• 1 or more recognition sites (where restriction enzyme can cut)

• some kind of genetic marker - allows them to be easily identified

• Small in size (easier to insert/uptake into target cell)

Recombinant plasmids:

plasmids that carry foreign DNA

Bacterial transformation:

process of inserting foreign DNA (ie. a gene of interest) into bacteria

genetically modified organism (GMO):

organism whose genetic make-up has been artificially changed, using genetic engineering

Transgenic organisms (TGOs):

any organism that possesses a ‘foreign’ gene or (segment of ‘foreign’ DNA) from another species in their genome as a result of human experimentation

Why GMO?

create pest/disease resistant plants, larger fruits, increase affinity of rubisco to carbon dioxide, and increase yield in crops and farm animals

GMO pro = Better crop productivity (more yield - more profits), more food grown w/ less land, reducing habitat loss due to land clearing + better food security

GMO con = Lose effectivness if weed or pests evolve resistance & Widespread use could result in loss of genetic diversity in crop population

Non-competitve inhibitor

• increasing substrate concentration will not change this

• maximum rate of reaction is decreased, when compared to inhibitor being present.

role of rubisco

enzyme that catalyzes the entry of carbon dioxide into the photosynthetic metabolism

• Fixes inorganic carbon (atmospheric CO2) into organic molecules that a plant can use to produce gluscose (occurs in LI stage)

  • combining CO₂ with RuBP, a five-carbon molecule, to form an unstable six-carbon intermediate that splits into two molecules of GP (PGA)

  • 
    

• Problems:

  • uses up already fixed carbon

  • wastes energy (consumes ATP)

  • Produces no glucose, only CO2

  • Reduces rate of photosynthesis IN HOT DRY CONDITIONS

Measuring rates of photosynthesis

= bubbles produced, pH change, gas displacement method

label mitochondria

improvement of photosynthetic efficiencies?

allows for the maximisation of the production of organic compounds (such as glucose)

 improve the efficiency of Rubisco in carbon dioxide fixation by reducing its ability to bind to oxygen and undergo photorespiration,

advantages & disadvantages of biofuel

advantages

• Carbon neutral biomass as a part of the carbon cycle. Carbon from the atmosphere is absorbed into plants during photosynthesis and when the plant decays or is burnt that carbon goes back into the atmosphere.

• Biomass is cost-effective. Energy harnessed from biomass is inexpensive compared to coal and oil. Typically, its cost about one-third less than fossil fuels doing the same job.

Disadvanatges:

• Requires space: big areas are required for all the different processes involved in harnessing energy from biomass. Large areas are required for storage.

• balance between increased production of biofuels and food availability. Biofuels will need to be made using waste products from plants, such as corn leaves, stalks and cobs

physical barrier

• intact skin is a barrier to entry of pathogens as the epidermis of the skin is composed of many layers of cells, making it difficult for pathogens to penetrate

Mucus – forms a protective layer and traps bacteria

• Mucus membrane in the mouth cavity traps microorganisms

  • Also in lining of the nasal cavity

chemical barrier

• Skin = produces chemical secretions (fatty acids/oils and sweat) that inhibit the growth of bacteria and fungi

  • Stomach acid = breaks down bacteria (low pH in the stomach)

    • stomachs acid & digestive enzymes kill pathogens that enter the digestive tract in food or water

• Lysozymes (enzyme that destroys pathogens in sweat, mucus, tears, saliva)

--> destroy bacterial cell walls

phagocytosis

1. Pathogen englufed

2. Fusion with lysosome

3. Lysozymes start to digest and destroy pathogen - broken into small fragments

4. Fragments of antigens presented on cell surface, some released via exocytosis

degranulation

in NKCs & Tc cells

Release granules via degranulation, containing perforins (polymerize & form hole in the enemy cell membrane) and granzymes (enter perforin hole & degrade enemy cell enzymes) which induce apoptosis in the abnormal cell

complement proteins

= assist phagocytes to recognise foreign material

direct killing of extracellular pathogens when a MAC forms on the plasma membrane of the pathogen, which inserts into the plasma membrane of the pathogen and produces a pore that allows fluid to enter, causing the pathogen cell to swell and burst

opsonisation

interferons

type of cytokine secreted by virally infected cells into its surroundings --> induce resistance to viral infection by acting as a warning signal from the cell already infected

• bind to receptors on neighboring cells, producing signals that stimulate infected and surrounding cells to produce defensive proteins (viral RNA cleaving enzymes) that inhibit translation and prevent viral protein synthesis & replication.

• make the plasma membrane less fluid, making its fusion with viral particles more difficult and reducing chance of viral infection in these cells

Capillary permeability & Vasodilation of blood vessels

= access the area of infection more easily

= increase in the number of white blood cells able to access

the area infected

antigen, self vs non-self

Antigen: molecules that assist in distinguishing a substance as non-self and may trigger/elicit an immune response

Self-antigens: located on the surface of cells and mark cells of an organism as ‘self’ so that the immune system does not attack them.

Non-self-antigens: a molecule from outside the body - foreign

• does not possess the MHC markers specific to self-cells, such as surface proteins - MHC I - of transplanted organs ) that is recognized by the immune system and initiates an immune response

MHCI vs MHCII

MHC I: Proteins expressed on the surface of all nucleated cells in the body, allowing cells to be recognised as 'self' to avoid attack by NKCs etc.

• (excludes red blood cells which have no nucleus)

MHC II: Found on the surface of specialized cells of the immune system (specific WBCs)

• APC & helper T cells --> present antigen fragments on their MHC Class II markers to T lymphocytes and other immune cells

pathogen

Pathogen = causative agent of disease

allergens.

Allergens (non-pathogenic) = an antigen that causes the immune system to produce an abnormal and inappropriate overreaction when a person is exposed to it (allergic reaction/trigger immune response)

• allergic reactions = hypersensitive immune reaction to a substance that normally would be harmless and not cause an immune response (malfunction of the immune system)

  • allergen binds to IgE antibodies that are already bound to receptors on mast cells.

  • inflammatory response due to histamine release from mast cells which can vary in severity.

  • symptoms like inflammation/swelling, rash, sneezing, shortness of breath.

Primary lymphoid organs & examples

= provides a location for lymphocytes to be produced and mature

• Bone marrow (hips, pelvis, humorous bones)

  • Cells of the immune system are made here from stem cells

  • B Lymphocytes mature here

• Thymus (center of chest)

  • Site of T cell maturation after being released from the bone marrow

Secondary lymphoid organs & examples

= provides a site for antigen recognition by lymphocytes to trigger adaptive immune response

--> where mature B cells and T cells are activated by meeting their complementary antigens and developing into effector cells

• Spleen (behind the stomach, upper left)

  • Filters blood passing through it, clearing it of pathogens 

    • Contains T & B cells that detect and respond to infectious agents in the blood

    • Contains other immune cells, including macrophages & dendritic cells

• Lymph nodes (armpit, groin, neck and abs)

  • site of antigen recognition, in which T and B lymphocytes come into contact with their specific antigens

  • Swell when infection occurs due to production of more lymphocytes (clonal expansion)

  • bean-shaped structure located along lymphatic vessels

Adaptive immunity =

specific response against a specific pathogen (unique receptors complementary to a specific antigen), with memory retained for future infection.

draw antibody

regions on antibody

• Constant region: does not vary between antibodies of the same class

• Variable region: differs between antibodies and is the antigen binding site

  • same on each side of a single antibody & specific antigen

natural/artifical & passive/active

Active immunity: antibodies are produced by a person’s own, memory

Passive immunity = transfer of antibodies directly to a person from an external source

• advantage: immediate protection to the person receiving the antibodies

• disadvantage: short-term as antibody levels decline quickly (2-3 weeks) and no long-lasting immunity to the receiver (less effective, no memory)

• Natural = without deliberate/artificial intervention

Infectious (communicable diseases)

= can be transmitted from one individual to another; these diseases are caused by pathogenic agents.

re-emerging disease

= reappears after a significant decline in its incidence

--> were once controlled but have increased to a level that causes significant health issues

Herd immunity

Vaccination reduces the number of susceptible hosts in a population, which establishes herd immunity. This decreases the probability of contact between an infected person and a susceptible individual, thereby interrupting chains of transmission. Consequently, this leads to fewer cases and limits the spread of the pathogen

Autoimmune disease

= when lymphocytes fail to recognise self-markers and end up inducing an immune response against self-cells

for autoimmue

1. Antibody-dependent cell-mediated cytotoxicity (ADCC): monoclonal antibodies bind to cancer cells and interact with cells of the immune system, particularly NKCs, causing them to recognise the antibody-coated cancer cell as foreign and kill it

2. Conjugated monoclonal antibodies – with molecules (chemotherapy drugs or radioisotopes) attached to them

   • due to their specificity for cancer cell antigens, they can specifically deliver these molecules to cancer cells killing them directly and not harming other healthy cells

Suppression immunotherapies:

aim to prevent or reduce an immune response

• Cytokine inhibition – Monoclonal antibodies can bind to and inhibit cytokines to reduce the immune response

• B and T cell depletion and inhibition – monoclonal antibodies can bind to autoreactive B and T cells and either inhibit them or stimulate other immune cells to destroy them

Gene pool =

total sum of all the genetic information (genes & their alleles) present in a population at any one time

Mutation

= permanent alterations in the DNA of chromosomes, the source of all new alleles

nonsense vs missense

• Nonsense codes for a STOP codon, producing a shorter polypeptide (hence desired protein not produced

• missense changes the amino acid being added and therefore the amino acid sequence (altering shape/function of the protein)

 result in small numbers of amino acids being different between species for the protein, with the remaining amino acids unaffected,

genetic drift

= random events that can change allele frequencies (and a populations overall diversity), particularly in small populations (larger change in allele frequencies)

Population bottleneck

= a sharp reduction in the size of a population due to random environmental events, disasters or human activities

• small number of individuals remaining in the gene pool often not representative of the original, larger gene pool

Founder effect

= small # of individuals become isolated from their original population and are not genetically representative of the parental population

• small sample of alleles from the parent population’s gene pool

• evolve in a different direction than parent population due to different selection pressures in new environment

gene flow

= the movement of alleles between populations (immigration and emigration) by interbreeding

Genetic diversity

= the level of genetic variation within a gene pool, is integral for survival & evolution of a species

antigenic drift vs shift

Antigenic shift is the process that leads to the formation of a new viral subtype. It occurs through the reassortment of genetic material when two or more different strains of a virus infect the same host cell and combine, resulting in sudden, major changes in surface antigens

antigenic drift involves small, gradual point mutations in the viral genome that result in new 'strains' - changes to antgien

Transitional fossil

= provide evidence for an intermediate evolutionary form between an ancestor and its descendants (link b/w 2 species)

• Exhibits common traits between ancestral group and descendant group, often providing a link between related species that appear to be very different

index fossils

= absolute age determined, used to define and identify geological periods

• date relative to a known date

  • physically distinctive (hence, easily recognisable)

  • have had a large population

  • have existed in many geographical areas

  • only lived within a known short period of time

• presence of index fossils in rock strata in widely separated regions of the world can identify these rocks as having the same age

mtDNA vs nuclear DNA

advantage = mutation rate in mtDNA higher than in nuclear DNA; closely related species, ensures that there are enough differences in DNA

advantage = mtDNA is only inherited from the mother, thus it remains unchanged across generations; no recombination (crossing over)--> change due to mutation --> measure # of base changes to identify point of divergenece --> more differences --> more time since recent common ancestor, easier to trace past ancestors 

disadvantage = mtDNA only provides information about one lineage (the maternal line), meaning it cannot provide a complete picture of an organism’s ancestry. In contrast, nuclear DNA can trace ancestry from both parents, providing more information about evolutionary relationships.

 

Researchers can track unbroken female lineages (haplogroups) and definitively trace populations back to a common ancestor due to inheritance of mtDNA from the mother. Because mtDNA accumulates mutations at a relatively constant rate, it functions as a molecular clock, enabling scientists to estimate the time elapsed since the divergence of populations. Therefore we can use the timing of the major dispersal events to map migration routes

amino acid vs nucleotide sequencing

• closely related species --> share very similar sequences for certain protein; nucleotide sequences, looking for silent mutations that may have accumulated without altering the amino acid sequence as the genetic code is degenerate

• amino acid sequences are easier to interpret (due to less data); relatedness in more distantly related species

analogous structures

= structures that serve similar functions but are not derived from a common ancestor

vestigial structures

= degenerate structures that have lost all or most of their usefulness as a result of evolution by natural selection

Inherited from an ancestor

Homologues structures

= features present in two or more species that may look and function differently in each species, but are derived from a recent common ancestor

• Physical evidence of divergent evolution (the process where 2 or more populations diverge into different species)

• evidence of evolution because they indicate that the species possessing these structures inherited them from a common ancestor. The structures then evolved independently in each species fter they diverged.

mammal

1. Mammal classification (distinguishing mammals from other vertebrates)

   • Milk–producing mammary glands = mammals use the milk produced by these glands to feed their offspring

   • Hair/fur = whilst some adult mammals have lost their hair/fur, all mammals at some stage of their life have various amounts of hair/fur on their bodies

   • Three bones in the middle ear = all mammals have three bones in their middle ear to help with hearing.

   • One lower jawbone = the lower jawbone is one single bone that attaches directly to the skull, giving them an extremely powerful bite

primmate

Primate

• Highly developed, colour, binocular vision with enclosed eye sockets in the skull

• Mobile, sensitive fingers and toes with flat nails instead of claws

  • Opposable thumbs

• Large brain relative to body size

• Full rotating shoulder - arm rotation

Hominoids

Hominoids - the apes

--> orangutan, gorilla, chimpanzee, gibbons

• Lack of a prehensile tail

• Flattened nose (no snout)

• Bony eye ridges

• Brachiating (swing underneath branches)

• Mainly ground dwelling and quadrupedal

• Arms longer than legs (except humans)

• Sensitive hands

• Large brains

 

hominins

• Bipedal with modified feet

  • walks with a bipedal locomotion

• Large cerebral cortex (forebrain)

• Position of foramen magnum is centered under the skull

• Smaller jaws and teeth

• Less hair (finer and shorter)

• Curved lower spine

• Shorter, broader pelvis

• Prominent nose and chin

• Reduced eye ridges (more brain space, don’t need protection from branches)

• Highly sensitive skin (sense danger, etc. hot temperatures)

homo sapiens to austrolopithecus

big toe = opposable & splayed to aligned with the other toes	improving forward propulsion during bipedal walking as push off when walking - imrpoves efficieny and balance
cranial capacity increased; indicating size of brain also increased	increased brain capacity, along w/ the greater cognitive capabilities it provides
lengths of legs in hominins became longer in comparison to their arms	better assists with bipedal motion, preventing knuckle dragging
Pelvis shape shorter & more bowl shaper (larger surface area for muscle attachment) Used to be long & narrow shape	Supports internal organs that stablise the body when upright
Leg attaches to the pelvis more angled inward, (whereas earlier species had legs attached in more of a straight line) positioning knees/feet underneath the body	walk upright more easily - before had to swing their legs wide when walking which made them slower) Improved balance and more efficient gait
Brow ridge decreased over time due to increasing size of the cranium
Foramen magnum: further under the skull in its position (centered), more upright the stance of the hominin	supports head (balance on top of spine) → efficen,t banalnce uprjgith walk
Dental arch changed from a U-shape to a shorter V-shape
transverse arch	converts the foot into a spring allowing it to transmit the stresses of walking and improve walking efficiency

country

= is an area traditionally owned and looked after by an Aboriginal group

Songlines =

trace the journey of ancestors of abroginial people, removes such an area of cultural improtance, forcing songlines to be modifed/altered --> preventing future generations from learning about their ancestors

Respect (rio)

= considering the cultural heritage of the individual & collective - disregarded as destroyed ancient aterfects of cultural significance to the abo people

Rio tinto destoryed = area not preserved (country define), connection more spiritual than physical

fossil record

Fossil scarcity: Hominin fossils are extremely rare, and those found are often

incomplete or highly fragmented. (1 mark) This makes precise species identification,

reliable dating, and clear tracing of evolutionary relationships difficult (and subject to

different interpretations by experts). (1 mark)

Dating challenges: Archaeological sites, especially very old ones, often have

disturbed layers or lack suitable material for accurate dating techniques (like

radiocarbon or luminescence), (1 mark) leading to wide date ranges and conflicting

results across different sites

function of CRISPR in Prokaryotes

• immune defense to protect bacteria from reinfection from bacteriophage

• Spacer - created using viral genome & integrated into the CRISPRE genome, acting as memory of past infection

• Repeats - used to separate each viral genome (spacer)

types of bonds

Hydrogen bonds	b/w complementary nitrogenous base of 2 secondary structure (b/w amine & carboxyl group) Broken in denaturation
Phosphodiester (covalent)	join nucleotides (sugar of one & phosphate group of another) = strong
peptide	b/w amino acids - primary structure
Disulfide	b/w R groups - Tertiary & quaternary structure

Plants physical defenses

• waxy cuticle forms a waterproof physical barrier over the leaf surface, preventing entry

• Thick bark is an external layer of dead cells preventing entry

• stomata closed to prevent entery OR sunken and sit lower down

plants chemical defenses

• Defensins are antimicrobial proteins produced by plants that interfere with fungal cell membranes, inhibiting fungal growth

• Saponins are plant proteins that disrupt bacterial and fungal cell membranes, inhibiting their growth

allergic reaction steps

• Damaged or infected cells release cytokines to attract immune cells

• Mast cells bind to release histamine, this triggers:

  • Vasodilation = increased blood flow

    • Causing redness and heat

  • Increased permeability of capillary walls = migration of phagocytes to site of infection

    • Causing swelling and pain

• Return to pre-infection conditions

Zoonotic disease

Infectious diseases that are transmitted from animals to humans

CO2 affect on pH + alkaline enviorement?

lowers pH by increasing acidity

Alkaline environment = high pH (low acidity)

Cas9 vs restriction enzymes

Cas9 is guided by a gRNA (sgRNA), which determines the target sequence, whereas a restriction endonuclease cuts at a specific, fixed DNA sequence known as a restriction site.

enzyme avalibility for PS/CR…how changed?

amount of enzyme can be raised or lowered through gene regulation

affect of inhibitors? on graph

case study

Investigating a real or hypothetical situation that reflects what would be expected to happen in a real-world scenario

classification and identification

Classification = arrangement of objects, events or phenomena into specific sets

Identification = exploring of OEP belonging to particular sets or a new set.

correlation study

Conducting investigations to understand the associations that exist between variables without manipulation by the investigator

fieldwork

Making observations external to a classroom environment through the use of sampling, observations and surveys

literature review

Exploration and analysis of secondary data that usually relate to the findings and viewpoints of others