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Function;
➔ Site of photosynthesis
◆ Thylakoid highly folded + many grana to provide large SA for reactions
◆ Thylakoid membrane contains photosystems and stroma contains enzymes
crucial to light-dependent and light-independent reactions respectively
◆ Arrangment of different photosynthetic pigments1 in the photosystems allows for
the maximum absorption of light energy
◆ Chloroplasts contain DNA and ribosomes to make proteins needed for
photosynthesis
◆ Phtosystems rich in light absorbing photosynthtic pigments such as Chlorophyll
Photosynthesis
The use of energy from the sun to split the bonds in water molecules2, store hydrogen in a fuel
by combining it with carbon dioxide and release oxygen into the atmosphere.
1
Which absorb different wavelengths (thus colours) of light
2
By photolysis
Photosynthesis: 6CO2 + 6H2O → C6H12O6 + 6O2
3
Energy absorbed by chlorophyll triggering the release of excited electrons
4
Their energy levels rise and fall
5
Which contains chlorophyll a, b and accessory pigments
6
Present in the thylakoid membrane
2. Light-independent reactions:
This is the process that produces glucose7 from carbon dioxide using energy from ATP and
NADPH. This hexose sugar is then used to produce amino acids and other carbohydrates.
1. Rubisco catalyses the reaction which combines CO2 and RuBP to make GP
2. Using ATP and NADPH, GP is reduced to make GALP
3. 2 of the GALP molecules are used to synthesize organic compounds
7
Carbon fixation: Process by which atmospheric carbon is converted to energy-rich molecules such as
glucose
4. The other 10 GALP molecules are recycled and use energy from ATP to make 6
RuBP
molecules.
8
By giving off CO2
Gross Primary Productivity: Total chemical energy in the form of biomass made by
primary producers including plant respiration.
Net primary productivity: The rate at which energy is incorporated into biomass or
organic matter in green plants.
R: The rate at which organic compounds made during GPP are lost (respiration).
NPP= GPP - R
dendrochronology.
Carbon sink: A forest, ocean or other natural environment that has the ability to absorb
and store atmospheric carbon dioxide.
The numbers and distribution of organisms in a habitat are controlled by biotic and abiotic
factors.
-Abiotic factors: Non-living chemical and physical parts of the envirnoment which affect
living organims.
-i.e; Water availability, sunlight, humidity, edaphic factors9
● To measure oxygen concentration: take a sample of soil of water and use an
oxygen meter/probe
● To measure light: use a light metre/probe held at ground level
● To measure water calculate mass of soil sample before and after drying
-Biotic factors: Living factors which affect living organisms and their distribution in a
habitat.
-i.e; Mates, predators, prey, competition
-to measure numbers in rivers, collect water sample or use a net.
Concept of Niche
A niche is the specific role or function of an organism in its habitat which is a result of its
physical, anatomical and physiological adaptations.
Adaptations:
➔ Behavioral; The ways an organism acts
◆ I.e: bird calls, migration
➔ Physiological: processes that take place inside an organism’s body
◆ I.e: Making venom, secreting slime
➔ Anatomical: Structural features of an organism
◆ I.e: long beaks, sharp claws
Sucession is the gradual change in the species structure of an ecological community over time.
● Primary sucession:
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To do with soil
○ starting point is bare ground --there is no soil to begin with
● I.e; formation of a new island by a volcanic eruption, retreat of
glacier
●Secondary succession: Occurs following a less destructive disturbance in which the soil
is left intact. Same process as primary succession beyond that point.
*Ecological communities are ever changing, however, following disturbances, or when new,
bare ground is revealed, communities tend to take the same steps towards climax community.
Global warming
Increase in the average global temperature over time.
Causes
-Increased GHG10 emmissions due to
10
Carbondioxide, methane, water vapour
-Fossil fuel combustion
-Deforestation
-Massive increase in cattle rearing
-Intensive rice farming
Effects
-Melting of ice caps and glaciers
-Rising sea levels and subsequent flooding
-Increased natural disasters
-changing rainfall patterns
*Predictions can be made on future global temperatures using extrapolated data from graphs
and computer models. At times relationships show correlation only as there is no proof of
causation.
Evolution
Evolution is the theory that all living organisms are related through descent with
modification from common ancestoral stock. It is the gradual change in allele
frequency due to random gene mutations and in turn, natural selection or speciation.
1. Geographical isolation of a population
2. New selection pressures
3. Random gene mutations --some are advantageous
4. Individuals with advantageous alelles11 are more likely to survive and reproduce
5. Alelle frequency (of advantageous alelle) in gene pool increases over
generations leading to the change in the heritable traits of a species → evolution.
11
From random gene mutations → these are heritable
12
Fertilised cell
○ Offspring has high mortality rate and cannot grow into a mature adult
● Hybrid sterility:
○ Offspring can grow into a mature adult but it will be infertile
■ I.e; Mules
If populations can no longer mate with each other (could be following a long period of
geographical isolation), genetic differences accumulate and give rise to a new species
(speciation).
Nitrogenous bases:
➔ Adenine (pairs with Thymine, or Uracil in RNA)
➔ Cytosine (pairs with Guanine)
➔ Guanine (pairs with Cytosine)
➔ Thymine (pairs with Adenine)
DNA is a polynucleotide
composed of mononucleotides.
Adjacent mononucleotides are
joined by phosphodiester
bonds13 forming the sugar phosphate backbone and two strands are joined by hydrogen
bonds formed by complimentary base pairing.
*One mononucleotide is made of a phosphate joined to a deoxyribose and a nitrogenous base
Protein synthesis:
13
Condensation reaction
Transcription:
1. DNA helix in the nucleus unwinds and is unzipped by DNA Helicase
2. RNA polymerase catalyses the addition of RNA nucleotides based on the
template DNA strand by complementary base pairing
3. The new single stranded mRNA detaches from the template strand and moves
out of the nucleus through a nucleopore
Translation:
1. mRNA binds to, or associates with ribosome sub units in the cytoplasm
2. Anti codons in tRNA form temporary base pairs with complementary codons on
mRNA
3. Two tRNA14 molecules can bind to a ribosome at once, the (specific) amino acids
on adjacent tRNA molecules form peptide bonds
4. The ribosome slides and a new tRNA binds to the next codon on mRNA, another
peptide bond forms adding to the growing polypeptide chain
5. A stop codon stops the process of
translation and releases the newly formed
polypeptide
14
Each tRNA molecule carries a single amino acid
Amino acids are connected by peptide bonds. This forms the primary structure of
proteins15. The secondary structure is the hydrogen bonding which takes place that
results in the formation of either an alpha helix or a beta sheet. The tertiary structure
forms the three dimensional shape of the protein. It is determined by the bonds which
take place including; disulfide bridges and ionic interactions between r groups.
Hydrophobic parts of the protein will be on the inside and the hydrophyllic on the
outside. The bonds that take place depend on the R groups in the primary structure.
Globular proteins: Spherical shaped proteins which are water soluble16. The have
primary, secondary, tertiary structures and, occasionally, quaternary structures.
Fibrous proteins: elongated strand-like proteins which are insoluble in water and weak
acids. They only have primary and secondary structures. I.e; collagen and keratin
*enzymes are globular structures. Extremes of pH can lead to denaturation as the shape of the
active site is altered due to ionization of R groups. Affects enzyme-controlled reactions such as
respiration.
In most eukaryotic genes, coding regions (exons) are interrupted by noncoding regions
(introns). During transcription, the entire gene is copied into a pre-mRNA, which
includes exons and introns. During the process of RNA splicing17, introns are
removed by the splicesome and exons are joined to form a contiguous coding
sequence. Thus, a variety of different protein structures can be formed from
polypeptides synthesised using the same genes.
Post mRNA is different form Pre-mRNA.
Proteins present in a cell may be different from genes of cells because of this reason as
well as:
● Proteins may have been secreted out of the cell
● The cell may not actively be synthesizing protein
● There may have been a mistake during trnscription
15
Sequence of amino acids in a polypeptide chain
16
Hydrophobic parts on the inside, hydrophillic on the outside.
17
Post-transcriptional changes to mRNA
DNA Profiling:
Used to distinguish between individuals of the same species using only samples
of their DNA. It is also used in forensics to identify criminals.
DNA fingerprinting:
*Sources of DNA: Blood, saliva, semen hair roots and skin cells.
1. Restriction endonucleases cut strands of DNA into fragments at recognition sites
2. Gel electrophoresis19:
a. Fragments placed in agarose gel medium with a buffering solution
b. A dye which binds to DNA is added to the gel
c. An electric current is applied to it
d. Fragments of DNA move towards positive anode. The smaller fragments
travel faster
e. To compare two or more different DNA fingerprints the different DNA
samples are run side-by-side on the same electrophoresis gel20.
18
Primers work at lower temperatures
19
Form of chromotography
20
DNA ladders form
Analysing DNA fingerprints:21
Structure of Bacteria:
Structure of
Viruses:
● Stran
d of nucleic
22
Made of peptidoglycan
23
Localised but not contained
24
Some bacteria exchange genetic material
acid: DNA or RNA
● Capsid; protective protein coat
● Spikes: glycoprotein molecules; used in cell recognition, bind to receptors on
host cells
● Some have: envelope; lipid bilayer made from lipids/phospholipds derived from
host cell membrane
● Some have enzymes: i.e; Retroviruses have reverse transcriptase
Similar
ities to
bacteri
a:
➔ N
o
nucleu
s
➔ N
o
membr
ane
bound
organe
lles
Differences:
➔ Viruses do not have cytoplasm
➔ Bacteria have DNA, viruses can have DNA or RNA25
➔ Bacteria have cricular DNA whereas viral DNA/RNA is straight
➔ Viruses are considered non-living as they do not carry out life process and
depend on host cells to replicate
➔ Viruses do not have cell walls, plasma membranes, plasmids, mesosomes or
flagella
25
Retroviruses such as HIV have RNA
HIV structure:
HIV
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Mainly in areas with many sebacious glands
HIV gradually destroys the immune system by attacking and killing a type of white blood cell
called a CD4 cell. The HIV virus is a retrovirus. A retrovirus is one that inserts its own genome
into the hosts genome. In this way, it becomes part of your cells.
Their virions contains a protein called reverse transcriptase that converts their RNA genome
into DNA under the process of reverse transcription.27
27
Body cells do not differentiate between viral genome and its own genome during protein
transcription and translation.
Tuberculosis:
Infection:
● Infection is intitiated following inhalation of myobacteria in aerosol droplets
Stages of infection:
1. Primary infection:
a. Macrophages engulf the bacteria
b. Bacteria manage to survive
c. Inflammatory response brings other defensive cells to the area
d. The cells form a granuloma (core of infected macrophages inclosed by other cells
of the immune system)
2. Latent (dormant) infection28:
a. Macrophages are killed while bacteria become dormant
b. Chronic asymptomatic stage
c. Non-contagious
28
If not diagnosed early enough or patient is old or suffers from HIV or is taking immunosupressant
drugs, they are more likely to progress to the next stage and potentially, die.
29
Opportunistic infections such as pneumonia arise
Immunity
Types of immunity:
● Active immunity:
○ Natural: Through the specific immune response triggered by infections
○ Artificial: Vaccination
■ Safely exposes individuals to weakened or dead strains of bacteria or
viruses which stimulates a primary response against the antigens without
causing symptoms of the disease.
● Passive immunity:
○ Natural: Through breast milk or during pregnancy
■ Certain antibodies are passed on from the maternal bloodstream to the
fetal bloodstream (via placenta).
● Important as it provides temporary protection until the new
born’s immune system develops
○ Artificial: Injection of antibodies
■ This type of immunization is short-lived
Interferons:
1. Cell invaded by virus
2. Infected cell produces interferons
3. Interferons bind to uninfected cell’s interferon receptors on membrane surface
4. Production of anti-viral proteins is signalled
5. Cells switch to a virus resistant state in the event of viral invasion → virus cannot
infect host cells and in turn, replicate
6. Virus can more easily by destroyed by phagocytosis
*Chemicals can also interfere with viral replication by inhibiting viral enzymes.
Phagocytosis:
1. Antibodies produced by lymphocytes mark bacteria by attaching to antigens30
2. Phagocytes engulf the bacteria
3. Ingested bacteria (phagosome) fuses with lysosome which contains the enzyme
lyzosyme which destroys bacterial cell walls
4. Bacteria is digested and waste materials are discharged by exocytosis
*Unlike macrophages, neutrophils self-destruct following phagocytosis and form pus
Cell mediated response: (recognizes infected body cells and destroys them)
T killer cells bind to infected body cells and release perforin causing lysis and, in turn,
apoptosis, as pores form allowing water to enter the cell.
Antibodies:
❖ Opsonisation: antibodies’ ability to enhance phagocytosis
❖ Agglutination: Antibodies combine with the surfaces of microorganisms and
cause them to clump together, reducing the number of infectious units and
easing phagocytosis.
❖ Toxin neutralization: Antitoxin antibodies block toxin interactions with target
cells
Pathogens such as the Myobacterium tuberculosis are known to have evolved into drug
resistant strains. When tb patients do not take the full course of antibiotics as is
prescribed, some of the more resistant bacteria survive and produce offspring that are
resitant to the prescribed drugs. This raises a major issue as resistant strains of serious
infectious disease develop and spread across communities making antibiotics
ineffective.
Moreover, HIV-1 has evolved to utilize a number of strategies to overcome the antiviral
effects of the host innate immune system. “One possible mechanism by which HIV-1
manages to avoid immune encounter of the host is that HIV-1 can modify its PAMPs by
altering or hiding its nucleic acids in the viral capsid in order to mimic the cellular
proteins. The ability of genetic variability of HIV-1 is one of the major immune evasion
strategies for the virus.”
“Superbugs' are commonly found in places where antibiotic use is highest and during
surgery where the protective layer of the skin is breached (like hospitals) and are known
as hospital-acquired infections. MRSA and C. difficile are two of the most common
hospital-acquired infections in the UK.
2. Hygiene measures: washing hards, using alcohol-based gels between patients and
not wearing long ties or white coats can prevent cross-infection.
4. Prevention of infection coming into the hospital: all patients coming in to the hospital
for any procedure should be tested or screened for common infections.
Initially, the body’s own enzymes break it down. Then microgorganisms such as
bacteria and fungi begin to digest the body resulting in the production of gases and
decomposition fluids31. The body becomes bloated due to the gases released.
Decomposers feed off dead tissue and obtain energy from proteins, fats and nucleic
acids and respire anaerobically and aerobically. They do this by releasing digestive
enzymes on to dead matter and absorbing the soluble products of this extracellular
digestion.
Decomposition is a major part of the carbon cycle. As decomposers respire, they relase
large amounts of CO2 into the environment. Microorganisms also improve the quality of
soil and add humus to it.
Key words
Accuracy: The difference between the measurement and the part's actual value
Reliability: is the degree to which an assessment tool produces stable and consistent
results. → can be ensued by repeating an investigation and obtaining means
Precision: The variation you see when you measure the same part repeatedly with the
same device
Validity: How well a scientific test or piece of research actually measures what it sets
out to, or how well it reflects the reality it claims to represent. → can be ensured by
controlling other variables
Ecology
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Affected by ambient temperature, physical activity of person before death, body fat, body cover...
● Habitat: Where an organism lives.
● Environment: Biotic and abiotic factors which make up an area or habitat.
● Biome: Large community of flora and fauna occupying a distinct region defined
by its unique climate and vegetation.
● Ecosystem: Biological community of interacting organisms and their physical
environment.
● Community: An interacting group of various species in a common location.
● Population: A group of organisms of the same species which interbreed and
living in an area.
● Species richness: The number of different species in an area.
● Species evenness: Looks at how close in number different species are in an
area.
● Species abundance: Number of individuals per species.