Biology - Unit 4

Pearson Edexcel International Advanced Subsidiary/Advanced Level in Biology Topic 5 and 6

photosynthesis

requiring energy from light to split apart the strong bonds in water molecules, storing the hydrogen in a fuel (glucose) by combining it with carbon dioxide and releasing oxygen into the atmosphere

photophosphorylation of ADP

requires energy and the hydrolysis of ATP provides an immediate supply of energy for biological reasons

light-dependent reaction

light energy is trapped by exciting electrons in chlorophyll, which jump from PSII to PSI via ETC. Photolysis happens and the hydrogen concentration increases (oxygen is released as waste gas). Chemiosmosis is the increase of H+ ions that create a pH and concentration gradient. The H+ ions are passed through the ATP Synthase, which starts reduction (ADP+Pi→ATP). The H+ ions start another reduction reaction (NADP++H+→NADPH+e-). The extra electron is sent back to PSII for the reaction to start again.

light-independent reaction

• Calvin Cycle: fixation of carbon dioxide using the products of the LDR.

• C02+RuBP with the enzyme RUBISCO → two molecules of 3GP. ATP is added and 3GP is activated. NADPH is added and it’s reduced into G3P.

• Two G3P are needed to form glucose but out of the 6 products 5 are used to replace RuBP. Two cycles are needed to synthesise new biological molecules.

Chloroplasts

• Thylakoid

• Grana

• Photosystems

• Stroma

• Lamellae

Absorption spectrum

used to determine the wavelengths absorbed by specific pigments, showing the percentage of light absorbed at each wavelength

Action spectrum

helps to show the relationship between the rate of photosynthesis for a given wavelength

NPP = GPP - R

• NPP - net primary productivity, gpp - the rate of energy loss to metabolism and mantainance

• GPP - gross primary productivity, the amount of chemical energy created from light energy at a specific time

• R - respiration

Population

all the members of one species in a habitat at one time

Community

all the organisms in a particular habitat at one time

Habitat

geographical area occupied by an ecosystem

Ecosystem

all biotic and abiotic factors in a particular area, which interact and are interdependent. They make up a self-contained system which is self-supporting in terms of energy flow

numbers and distribution of organisms in a habitat

controlled by biotic (predators) and abiotic factors (temperature)

Niche

role of a species within an ecosystem

Primary succession

area previously inhabited → pioneer community (lichens, mosses and weeds) will colonise it (little diversity, low biomass and simple food web) → over time nutrient-rich soil will form and other plants will be able to grow → Intermediate communities (grasses and shrubs) will give way to more complex plants (more biomass, more diversity and a bigger food web) → climax community will develop with a stable and complex ecosystem

records of carbon dioxide levels

• CO2 levels have been rising for all of history, but had a significant increase after the Industrial Revolution.

• We know CO2 is a greenhouse gas, and the records see a correlation between high CO2 levels and increasing temperatures.

pollen in peat bogs

• Made of partly decomposed plant material, mainly mosses. They’re acidic, cool and anaerobic, which helps peat preserve pollen grains, moss spores and even plant tissue.

• As it builds in layers, we can determine the type of vegetation growing around that specific time.

• Some mosses indicate wet conditions, and some dry; warmer and cooler, etc.

temperature records

• Scientists drill down into the Antarctic and Greenlandic ice cores and analyse the air trapped in them.

• Oxygen isotope ratios show the temperature of the air when the ice formed.

• CO2 can also be analysed to measure its levels.

dendrochronology

• The dating of past events using tree ring growth can tell us about the climate past. Large cells in spring and small cells in autumn give the illusion of rings.

• The growth depends on many factors, which can help determining changes in the climate.

anthropogenic climate change

• humans have increased the release of greenhouse gasses significantly since the Industrial Revolution, and this has enhanced the greenhouse effect.

• The release of CO2, methane and the burning of fossil fuels

Carbon cycle

• There are carbon sinks in nature, through which carbon fluctuates and ragulates naturally.

• Humans have altered this balance by burning fossil fuels.

• Planting more trees, or limiting industries would be some solutions

Climate change models

scientists use data to create reliable models to predict how climate change will affect the future

Climat change models limitations

• models can’t perfectly predict everything as there will be sudden changes and events that have no warning

• trends in society can also affect the climate and those can’t be predicted either

effects of climate change

• warm season become longer and cold ones shorter as temperatures increase

• precipitation patterns will change, extreme precipitation events will increase in serverity and frequency, blizzards will be worse

• the atmosphere will hold onto more moisture

• more extreme heat waves and cold

effects of climate change on animals

• breeding seasons/coming out of hibernation is earlier

• mismatched prey-predator habits

• less food

• surviving young decrease

• some species will have no food/shelter and will disappear

temperature

• warmer temperatures mean higher enzyme rate but also more chances of them denaturing

• if it rises too much they might stop working and the organisms would die

temperature coefficient

Q₁₀ = (R₂/R₁)^{10/ (T₂-T₁)}

Evolution

• Natural selection → Individuals with a specific characteristic are the only ones to reproduce

• Genetic mutation → some individuals have better chances of survival because of a mutation fitted for their life

Speciation

a group within a species separates from other members of its species and develops its own unique characteristics. The demands of a different environment or the characteristics of the members of the new group will differentiate the new species from their ancestors.

Allopatric speciation

geographical speciation. The difference in environmental factors causes the change in allopatric speciation.

Sympatric speciation

evolution of new species takes place from a single ancestral species without geographical interference

how decisions about controversial things (climate change) can have different results depending on who takes it

• politicians usually make these decisions and can be influenced by groups

• many look at short term benefit

• the action needed can negatively affect many of those who are in charge of deciding

Human needs and conservation

a middle ground is needed:

• reforestation

• biofuels

• limiting certain industries

• sustainable resources

Thylakoid

flattened discs that have small internal volume to maximise the hydrogen gradient

Grana

thylakoid arranged into stacks to increase SA:Vol of the membrane

Photosystems

pigments are organised to maximise light absorption

Stroma

central cavity with appropriate enzymes and pH for the reactions to take place

Lamellae

connects and separates grana, maximising photosynthetic efficiency

pioneer community

(lichens, mosses and weeds)

Intermediate communities

(grasses and shrubs)

climax community

Oaks

photosynthesis equation

6CO₂ + 6H₂O → C₆H₁₂O₆ + 6O₂

aseptic technique

when an organism is grown, we must avoid cross-contaminating. Methods of handling sterile equipment and microorganisms are used so cultures are made without unwanted organisms

aseptic method 1

1. sterilise the inoculating loop in a blue flame

2. dip the loop in the suspension of the bacteria

3. streak the loop across the agar dish’s surface

4. replace the lid, tape it close and turn in upside down

aseptic method 2

1. sterilise the inoculating loop in a blue flame

2. dip the inoculating loop across the agar dish or wherever the culture is

3. swirl the loop in the serialised liquid medium in a conical flask

4. remove the loop and seal the flask with a sterilised cotton wool

methods of measuring the growth of microorganisms

• cell counts

• dilution plating

• mass

• optical methods (turbidity)

phases of bacterial growth curve

• lag (time it takes for bacteria to reach a state where they can grow and divide quickly)

• exponential/log (when cells divide by binary fission and the doubling of each generation creates the exponential growth)

• stationary (time where population size is constant following the log phase due to limiting factors like a lack of available nutrients)

• death (decrease in the number of bacteria caused by the depletion of nutrients or other unfavourable conditions)

bacteria

• living organisms

• bigger

• single cell organism

• can reproduce outside host

• microscopic

• limited to a part of the body

• pneumonia, tuberculosis, tetanus, food poisoning

types of bacteria

• spherical - cocci

• rod-shaped - bacilli

• spiral - spirilla

virus

• not living organisms

• smaller

• can only reproduce in host (dormant otherwise)

• submicroscopic

• infection is systemic

• influenza, measles, polio, aids, covid-19

lytic cycle

viral replication cycle

virus takes over a host cell’s genetic material and uses the cell’s structure to replicate until the cell bursts

lysogenic (latency) cycle

viral replication cycle

virus’ nucleic acid is integrated into host cell’s chromosomes, a provirus is formed and replicates everytime the cell reproduces, cell survives until the virus is activated and the cycle begins

ebola virus

• severe and often fatal fever

• unexplained bleeding

• fatigue

• vomiting and diarrhea

• headaches

• transferred through bodily fluids

• genetic material - RNA

tobacco mosaic virus (TMV)

• plant virus → affects the chloroplasts

• turns leaves yellow/white forming a mosaic pattern

• spread naturally or through contact from farmers

• reduces surface area and ability to photosynthesise

• lytic virus

• genetic material → RNA

human immunodeficiency virus (HIV)

• targets T-helper cells

• once they are activated the virus replicates and bursts the cell

• causes a weakened immune system and leads to AIDs

• AIDs is when the body can’t defend itself against basic infections

• symptoms → weight loss, diarrhoea, dementia, cancers and oportunistic infections (TB)

• latent virus (lysogenic)

• gentic material - RNA

lambda phage

• bacteriophage - infects bacterial cells

• lambda phage infects E. coli

• found in intestines, normally harmless but can cause food poisoning

• head, tail, tail fibres

• can alternate between life cycles

• genetic material → DNA

tuberculosis (TB)

• bacterial disease (Mycobacterium tuberculosis)

• infects phagocytes in the lungs

• first infection is symptomless as the infected phagocyted are sealed in tubercules as a result of inflamatory response

• bacteria lie dormant in the tubercules as they are covered by a thick waxy layer that protects them

• activated when the immune system is weak

• symptoms → breathing problems, coughing (blood), weight loss, fever, fatigue

• genetic material → DNA

virus structure

• protein capsid

• lipid envelope

• spikes

• genome (RNA)

bacteria structure

• flagellum

• plasmid

• cell wall

• nucleoid (DNA)

• cytoplasm

• ribosomes

• cell membrane

major routes pathogens take

• inhalation - coughing, sneezing and talking

• ingestion - contaminated food

• direct contact - skin to skin or bodily fluids

• vector - organisms that carry the pathogen

• fomites - inanimate objects that carry the pathogen

physical and chemical barriers

• skin

• stomach acid

• gut and skin flora

• cough reflex

• mucus

skin

• physical

• epidermal cells

• keratinised cells

• strong barrier

stomach acid

• chemical

• gastrointestinal tract

• low pH kills the pathogens

• quick change in pH guarantees no pathogen has survived

gut and skin flora

• chemical

• skin - sebum is produced

• gut - they compete with the pathogens for food and space

mucus

• physical

• produced in the goblet cells

• mucus traps the pathogens and the cilia pushes them back out of the system

non-specific immune response (innate)

• inflammation

• lysozyme

• interferon

• phagocytosis

• fever

inflammation

1. tissue gets damaged

2. platelets and basophils release histamine

3. histamine causes blood vasodilation and the increased permeability of blood vessels

4. result; more blood flow to that area (looks red) and more antibodies, white blood cells and plasma are leaked out into the damaged tissue

lysozyme

• enzyme found in secretions like tears and mucus which kills bacteria by damaging their cell walls

interferon

• produced by the infected cell

• anti-viral protein

• they stimulate inflammation

• inhibit translation of viral proteins

• activate T-killer cells

phagocytosis

• process through which a white blood cell called a phagocyte engulfs the pathogen

• pathogen is in a phagocytic vessel in which lysosomes release lysozyme

• the pathogen is digested

• digested pathogen will be removed through exocytosis

• some antigen molecules will be kept and presented on the surface of their cells

types of white blood cells

• Neutrophil - first responders

• Lymphocytes - adaptive immunity

• Monocyte - antigen presentation

• Eosinophil - multicellular parasites

• Basophil - inflammatory response

specific response

1. after the pathogen is digested some molecules are presented on the outside of the phagocyte’s cell wall

2. it becomes an antigen-presenting cell (macrophage)

3. macrophages activate other types of immune systems

   • B cells

   • T cell

T lymphocytes

• white blood cells with specific receptors on their cell surface

• when it binds to its complementary antigen (macrophage/pathogen) it’s activated (clonal selection)

• when activated it divides by mitosis (clonal expansion)

  • T helper cells

  • T killer cells

  • T memory cells

T helper cells

• activate B lymphocytes

• activate T killer cells

T killer cells

• destroy any cells that have been infected by the pathogen

memory cells

• kept in low levels in the bloodstream

• if activated they replicate to create an immune response

• when there is another infection the response is much quicker

• allow for longterm immunity

B lymphocytes

• white blood cells with specific antibodies (membrane-bound) on their cell surface

• activate when T helper cells release chemicals or when a complimentary antigen binds to it

• when activated they divide by mitosis and differentiate

  • B effector cells (plasma cells) - secrete antibodies

  • B memory cells

• can also digest the pathogen, present its antigen and activate T cells

B effector cell / plasma cell

produce complementary antibodies for the antigen

antibodies

structure

• four polypeptide chains held together by disulphide bridges

• variable site (specific) → antigen-binding site

• constant region (non-specific) → binding site for the immune system

• hinge region → flexibility

functioning

• agglutination - antibodies bind to two pathogens simultaneously so they are clumped together

• neutralising →bind to toxins released to neutralise their effects

• blocking access to human cells

how do individuals develop immunity

ways

• natural

• artificial

types

• active

• passive

natural

active → individual has an infection and develops the antibodies for it

passive → mother passes on antibodies to their baby/foetus via body fluids (placenta, breast milk)

artificial

active → vaccine

passive → injected antibodies from another organism

evolution of pathogens

• bacteria and viruses replicate very quickly

• this allows them to quickly develop adaptations to evade the immune system

• this means new infections may need new responses as memory cells don’t recognise it

• advantageous alleles are passed on quickly, creating a resisting strain

antibiotics

• chemicals that are used to fight infection

  • bactericidal

  • bacteriostatic

bactericidal

kill the bacteria by bursting open their cell walls

bacteriostatic

inhibit the growth of bacteria by stopping protein synthesis and production of nucleic acid so they can’t divide

pathogens and evolution

• they evolve to evade the immune system

• high mutation rate means every infection needs a new primary immune response; eg. HIV

• memory cells from previous responses don’t recognise the new antigen

• evolution could make them resistant to antibiotics

resistant strain

• bacteria that have had mutations that make them immune to antibiotics as they are a selection pressure

• those with a resistant mutation will survive and reproduce passing on the advantageous allele

• this could happen very quickly as viruses and bacteria reproduce fast

nosocomial infections

• resistance to antibiotics can cause infections in hospitals

• there are some guidelines to stop this from happening

preventing nosocomial infections

• new patients are screened, isolated and treated if it’s an infectious disease

• antibiotics are only used when needed and their course if completed so no resistant strains form

• staff must follow the code of practice

  • strict hygiene

  • washing hands with alcohol-based gels

  • wearing suitable clothing

energy units

kJ m-2 year-1

microorganisms in decomposition and recycling of carbon

• break down tissue, forming gas and decomp. fluid, which leaves through orifices

• inorganic ions are returned to the soil → assimilated by plants

• carbon → taken in by microorganisms and released into the atmosphere when they respire

• CO2 is taken in through photosynthesis → turned into biomass → die

• decomposition cycle begins again

decomposition

• autolysis → body’s own enzymes digest and break down tissue

• putrefaction → microorganisms (bacteria/fungi) break down the remaining dead tissue

estimating time of death (ToD)

• stage of succession

• body temperature

• degree of muscle contraction

• forensic entomology

• extent of decomposition

stage of succession

• fresh

• putrefaction

• fermentation

• dry decay

• skeletonization

each stage attracts different organisms and happen during different periods in a specific order

body temperature

• decreases in a sigmoid curve over the first 24 hours

• 1.5 - 2ºC per hour

• stops when it reaches ambient temperature

• factors that affect it: weather, body fat, body size, clothes, water, air movement, cover

degree of muscle contraction

rigor mortis is the process where ethe body muscles contract after death

• 4-6 hours muscles will stiffen

• no oxygen → anaerobic respiration → accumulation of lactic acid

• lactic acid has a low pH so enzymes denature

• ATP can’t be used to unbind muscle proteins (actin and myosin) which causes the muscles to stiffen

• smaller muscles → bigger muscles → bigger muscles → smaller muscles

• 36 hours post-mortem muscles begin to relax

• factors that affect it: muscle development, temperature

forensic entomology

study of insects found in the body

• blow flies → flesh flies →beetles (decomposed fats) → pyralid moths (flesh and clothes —better if natural fibers) → cheese skippers (digested and remaining food) → burying beetles (dead flesh)

• they lay eggs in warm and moist places (orifices)

• identifying the species can help understand the extent of the decomposition as they have different life cycles and times of appearance

• letting maggots develop to identify which species it is is sometimes needed

extent of decomposition

appearance of the body

• up to a few days → skin turns green

• few days to few weeks → body becomes bloated, skin falls off

• after several weeks → tissues liquefy and seep out of the body

• few months to a few years → all tissues are broken down and only bones remain

• after several decades → bones disintegrate