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Notes and
Unit 4: Environment
Survival
Topic 5: On the wild side
4.5.1
Kingdom
Phylum There are 5 kingdoms Animals, Plants, Fungi,
Class Protoctists, Prokaryotes
Order
Family You need to know the main characteristics of
Genus each kingdom
Species
Prokaryotes
Protoctists
The Proctoctist’s kingdom tends to be full of organisms that do not fit into any
other Kingdom e.g. algae and yeast
Fungi
Plants
Animals
1. Independent Assortment
2. Mutation
3. Random fusion
4. Crossing Over
Independent Assortment = which allele of each pair goes into
which gamete. This is caused by the orientation of homologous
pairs of chromosomes during metaphase 2 of meiosis
Gametes:
AD Ad AD Ad
aD ad aD ad
F1 Genotype:
AD Ad aD ad
Purple & Big : Purple & Little : Green & Big : Green & Little
4.5.4 Ecological Sampling Techniques
Biotic Factor: A living variable within the ecosystem, which affects the survival
of organisms. Examples include predation, competition, and pollution from
excreted waste.
Abiotic Factor: A non-living variable within the ecosystem, which affects the
survival of organisms. Examples include temperature, light, and water.
Line Transect:
• Used where time is limited
• Used to visually illustrate how species change along a line
Belt Transect:
• Produces more data, gives detail about species abundance down the line
as well as range
• Shows species dominance down the line
Transects can either be continuous with the whole length of the line being
sampled, or samples can be taken at particular points along the line
For both line and belt transects, the interval at which samples are taken will
depend on the individual habitat, as well as on the time and effort which can be
allocated to the survey.
• Too great an interval may mean that many species actually present are
not noted, as well as obscuring zonation patterns for lack of observations.
• Too small an interval can make the sampling time consuming, as well as
4.5.5 yielding more data than is needed.
An example of a Named Environment
Is the British Rocky Seashore
Upper Shore: Black Tar Lichen – can survive long periods without water, grows
slowly, but is less tolerant to dessication than lichen.
Middle Shore: Eggwrack – More water availability, less temp range, but more
predation from herbivores and carnivores
Lower Shore: Kelp – constant environment, usually submerged, lower light levels,
intense competition from same and other species
Don’t learn this case study if your teacher gave you notes
on a different habitat. Learn this study if you’re desperate
4.5.6
Limpet:
Micro-algae (Bladderwrack):
Dogwhelk:
Common Shore Crab:
1. Has a adapted radula that bores through
1. Has antennal glands, which allows it to
barnacle shells
osmoregulate (it can cope with varying
2. Has a grove in its shell that allows it to
salinity)
breath whilst boring
2. Can bubble air through its gills and
3. Vary in colour across species
breathe out of water
4. Has a very muscular foot to stop the effect
3. Strong claws for snapping open dogwhelk
of wave action
shells
4. Carries eggs to be released in optimum
conditions
Blenny:
The purpose of the light dependent step is to produce ATP and NADPH.
ATP provides the energy for converting CO2 into glucose and NADPH
provides the H for glucose.
CO2
RuBP GP
GALP
Glucose
There are three steps in the Calvin Cycle;
4.5.9
4.5.10
Thylakoid membrane = location of photosystems & electron transport chain
Stroma = site of Calvin Cycle & photolysis of water
NPP = GPP – R
NPP = Net Primary Productivity (amount of stored chemical energy the
plant has to use for growth. This is directly proportional to biomass)
Best analogy is a salary. GPP is the amount of stored chemical energy the
plant earns through photosynthesis. R is like income tax. The plant has to
pay “respiration tax” because it can’t photosynthesis at night & not all
parts of the plant are capable of photosynthesis. NPP = disposable
income: what the plant has to spend after paying tax.
4.5.11
Lost energy
NPP in plant
Lost energy
Energy in
Sunlight
Energy is lost between trophic levels. Energy is lost in the following ways;
in respiration (mostly lost through heat), energy still present in egested
food, through movement, through digestion, energy still present in
excreted materials etc
Of the 100% sunlight energy that reaches plants, ~3% is converted into
NPP. Energy is lost in the following ways; reflected light, light of
wavelengths not useful to plants, passes through leaves, lost in
respiration, lost as heat etc
4.5.12
Evolution: the idea that one species changes into another over time
4. The fittest survive long enough to reproduce and pass their alleles
onto the next generation.
6. Soon all / most individuals have the “fit” phenotype and the “unfit”
phenotype is eradicated
8. Over this time new mutations occur, which give new even better
alleles
9. Over time the mutations accumulate in the phenotype until the
organism is unable to reproduce (i.e. produce fertile offspring) with
the original organisms. At this point a new species has been
produced (speciation)
This process is speeded up by isolation (see 4.5.14) because this stops the
influx of alleles from outside and allows new mutations to accumulate in
the genotype more quickly
4.5.13
Law 1: Organs / structures grow if they are used. This means that the
environment determines the phenotype of an organism
So a blacksmith, who uses his muscles all day, will grow bigger muscles.
This works! But, will the bigger muscles be passed onto his children? No,
so Lamarck’s theory is easy to falsify.
4.5.15
Evolution is a theory, not a fact. Many people believe that species were
created (creationism). Other people believe in evolution, but by
mechanisms other than Natural Selection. You should respect the opinions
of other people, even if you do not necessarily agree with them.
4.5.16
4.5.17
Gametes:
1. Conducting research
4. Educating people
F1 Phenotype: 9:3:3:1
A_B_ : A_bb : aaB_ : aabb
Purple & Big : Purple & Little : Green & Big : Green & Little
R r R r
If the parents only have 2 children and they are both Red (RR) then the r
allele has been lost. This is genetic drift and is a big cause of the loss of
genetic diversity in an endangered species.
To avoid this studbooks are kept (basically, a family tree for the captive
animals) so that only non-related animals are bred with each other. This
decreases the change of genetic drift and also decreases the change of
genetic disease.
Reintroducing species into the wild has some success, but depends
greatly on the species. As a general rule of thumb, the more advanced the
species the more difficult reintroduction is. This is because animals need
to learn specific behaviours e.g. how to hunt, how to reproduce, how /
where to find shelter, group behaviours. Breeding animals in captive
environments that mimic the wild has more success because it allows some
of these behaviours to be learned in captivity. Feeding the animals in the
wild also helps survival rates.
4.5.18
If you get a question on this in the exam you’ll need to think. There are no
set facts to learn.
4.5.19
If you get a question on this in the exam you’ll need to think. There are no
set facts to learn.
SNAB A2 Revision
Notes
Unit 4: Environment and
Survival
Topic 6: Infection, Immunity & Forensics
4.6.1
o Body temperature
o Extent of rigor mortis
o Level of decomposition
o Forensic entomology
Body temperature:
A body cools following an S-shaped
(sigmoid) curve. The initial plateau at
37˚C lasts 30 – 60 min, then the body
cools quickly to ambient temperature.
Rigor mortis is the stiffening of joints and muscles. Small muscles stiffen
first and unstiffen last.
Muscles stiffen because they run out of ATP, causing the actin and
myosin muscle fibres to stick permanently to each other. Muscles
unstiffen because the muscle fibres begin to break down.
On page 80 of your text book is a little more detail about the sequence of
events that causes muscles to run out of ATP.
Level of decomposition:
Autolysis is the break down of body tissues using the body’s own enzymes
from the digestive system and from lysosomes
After this, bacteria from the gut invade tissues and release more
enzymes. This tends to happen in anaerobic conditions, which favours the
growth of anaerobic bacteria
The presence of wounds, the clothing the person was wearing and the
combination of gases released during decomposition also have an effect.
Forensic entomology:
The insects found in a dead body can help identify time of death in 3
ways;
Corpse succession:
e.g. a maggot 3mm long found growing at 28˚C will be roughly 0.3 days (8
hrs old)
3. If maggots are taken from the body, allowed to grow and the time
taken to pupate is recorded; it is sometimes possible to work
backwards from the pupation date and work out hold the maggots
must have been when they were taken from the body. This works
because maggots of different species usually take a fixed number
of days to pupate.
4.6.2
1. Identity papers
2. Fingerprints
3. Dental records
4. Genetic Fingerprint
Fingerprinting process:
4.6.3
Succession on corpses:
Succession and forensic entomology also show if the body has been
moved.
4.6.4
A typical prokaryote
Ribosomes. Same function as eukaryotic cells (protein synthesis),
but are smaller (70s rather than 80s).
A typical virus
Viruses have a wide range of different structures. Some viruses are
about 100nm in diameter, whilst others can range from 20 –
3000nm.
All viruses have a protein coat (the capsid), which contains genetic
material. The genetic material is either DNA or RNA, and can be
single or double-stranded.
The virus genetic material (the viral genome) contains only a few
genes, from about 20 in the polio virus to more than 200 in the
herpes virus (human genome contains ~80,000 genes). The viral
genome codes for the proteins required to manufacture the virus.
(ligands)
Viruses that have a DNA code instead of an RNA code often insert
their viral DNA into the host cell’s DNA. Other RNA viruses inject
the enzyme Reverse Transcriptase, which makes a cDNA copy of
the viral RNA. The cDNA copy is then inserted into the host cell’s
DNA. Other viruses (e.g. HIV) also inject the enzyme integrase,
which helps insert the viral cDNA into the host’s DNA
DNA Polymerase:
RNA Transcriptase:
Integrase:
BUT
2. The chronic phase. This can last for many years. The virus
continues to replicate, but the Killer T cells keep the numbers
in check. However, because the immune system is weakened
other bacteria and viruses are more likely to infect the
person (TB may reactivate at this point)
The huge problem with HIV is that it mutates very quickly. Once
inside the body the viral antigens change and the (already
damaged ) immune system can’t keep pace with the changes.
Another problem is that HIV attacks Helper T cells, which are
crucial for activating the B cells and also play a role in activating
Killer T cells. With low numbers of Helper T cell, the immune system
cannot communicate effectively and this increases the ability of
HIV to survive in the body.
4.6.7
Antigen-binding site
Variable
Region
Disulphde
Bridges
Constant
Region
Antibody
Pathogen
Antigen
4.6.9
Killer T Cells: attach to the infected / foreign cell and release the
enzyme Perforin, which makes holes in the pathogen’s cell membrane
causing it to die
d) An antigen-antibody complex is
formed
4.6.10
E.g.
1. High [glucose] in blood causes insulin release
2. insulin stimulates liver to take up glucose & convert it into
glycogen stores
3. [glucose] falls
4.6.11
Body Temperature:
Exercise
All white blood cells communicate with each other and the rest of
the immune system using a class of hormones called cytokines. The
cytokines have hundreds of different roles and many more are yet
to be discovered. One class of cytokine is the hormone interleukin,
which causes fever.
4.6.12
Barrier Mechanisms include;
• Skin
• Stomach Acid
• Normal Flora
• Epithelial cells
Stomach Acid:
Normal Flora:
The skin, respiratory tract and gut are covered with commensual
bacteria, which are part of the normal flora of the body.
Commensual bacteria are adapted to live the environment of the
skin and the gut and the and compete with invading pathogens for
the limited supply of nutrients.
4.6.13
4.6.14
3. It does not kill immediately. This means that it has a large window
of opportunity to spread to others
5. It can survive inside macrophages and lie dormant until the immune
system is weakened, when it can re-infect.
4.6.15
4.6.16
4.6.17
5. Humans have been reckless with use of antibiotics. They are often
given to people who don’t need them (i.e. they have viral infections)
or to people who don’t bother to complete the course of antibiotic.
4.6.18
SNAB A2 Revision
Notes
structures without damaging eukaryotic ones) there may well be a
global pandemic of resistant bacteria.
5.7.1
Cartilage: a tissue made from collagen, which protects bone ends
A muscle: an organ that produces movement by contraction
A joint: the junction between two bones
A tendon: joins muscle to bone
A ligament: joins bone to bone to stabilise a joint
A Synovial Joint
Bone
Ligament
Muscle
Cartilage
Synovial Fluid
Synovial membrane
Tendon
5.7.2
Muscles are made from muscle fibres arranged into bundles. Each
fibre is made from bundles of myofibrils, which are extremely long,
cylindrical muscle cells.
The8. sarcomere
ATP (alreadycontains overlapping
bound to the myosin
actin and
head)myosin. The myosin
is hydrolysed causingisthe
often
called myosin
the thick
headfilament because inthe
to pivot forwards
myosintheheads
powerstroke
make it appear thick.
The9. actin
As the is,
headtherefore, the thin
pivots the thick
Cross-Bridge Cycling:
filament
filament moves across the thin
filament – muscle contraction
The process by which the thin filaments are pulled in towards each other by
occurs
the myosin is called cross-bridge cycling. It is how muscles contract.
10. ADP diffuses away from the
myosin head leaving the ATP-
binding site empty
Ribose
The energy used in all cellular reactions comes from ATP. By
breaking the 3rd phosphate from the ATP molecule energy is
released, which can be used to power intracellular reactions. The
ATP is then regenerated by recombining the phosphate and ADP in
respiration (or another process e.g. photosynthesis).
The recycling of ATP is crucial for life. For example a runner uses
~84kg of ATP in a marathon (more than their total body weight),
yet there are only 50g of ATP in the entire body! This means each
that each molecule of ATP has been recycled 1676 times during the
race!
ATP = one adenosine
molecule with 3
Adenosine P phosphate groups
attached
“Energy rich bond”
Less energy rich bond(30.6kJ/mol)
“Energy rich bond”
(13.8kJ/mol) ATP + H2O → ADP + Pi
(30.6kJ/mol)
How the energy in ATP is liberated:
Energy
P + H2O → AMP + Pi
Adenosine ADP
Energy
Adenosine P
AMP + H2O → Adenosine + Pi
Energy
Adenosine
Glucose
2ATPs are required
Glyceraldehyde Glyceraldehyde
Phosphate Phosphate
2ATPs are made (4 overall)
Overall; 4ATP are made, 2NADH are made and 2ATPs are used.
In anaerobic conditions [H+] rises in the mitochondria as there are no available oxygen
molecules to mop it up with and form water. This leads to saturation of the electron
transport chain and a build-up of NADH and FADH2. This means [NAD] falls, which stops
the Krebs’ Cycle. Acetyl CoA levels build-up, [CoA] falls and the Link Reaction stops.
Pyruvate levels start to rise…
Muscle cells turn pyruvate into lactate to stop rising [pyruvate] from stopping Glycolysis
(remember, enzyme controlled reactions are reversible and depend on [reactants] and
[products]).
Pyruvate Lactate
NADH NAD
In the liver the lactate is converted back into pyruvate. This requires
oxygen, which is the basis of the “Oxygen Debt”
Pyruvate
CoA enzyme
2 NADH are made (4 overall)
Respiration:
Overall; Step 24
4NADH, 2FADH – Oxidative
, 2CO Phosphorylation
2 and 2ATP are made.
NADH
H2O
NAD ½ O2 + 2H+
Hydrogen atoms from the NADH and the reduced FADH2 are
passed onto 2 the first 2 enzymes of the Electron Transport
Chain. These enzymes are Hydrogen Carriers and they accept
the H atoms from the NADH and the FADH2.
Chemiosmosis of H+ ions
from the mitochondrial
envelope into the matrix
through ATP Synthetase
proteins is what actually
generates the ATP in
respiration
The electron transport chain uses the process of chemiosmosis
(the diffusion of ions across a membrane). H+ ions are actively
pumped into the mitochondrial envelope. This is done by the
proteins in the electron transport chain, using the energy
stored in NADH and FADH2.
The [H+] builds up to very high levels in the envelope. However,
H+ cannot escape because it is charged (hydrophilic) and
therefore cannot move through the phospholipid bilayer in the
envelope membranes.
In summary;
5.7.7
c h e m o r e c e p t o r s in
c h e m o r e c e p st o t rr es t ci n h r e c e p t oc r o s r t e x
a o r t ic a n d c a r o t i d
m e d u l la in m u s c l e s( v o l u n t a r y c o n t r o l)
b o d ie s
R E S P I R A T O R Y
C E N T R E
in m e d u l la o f b r a in
in t e r c o s t a l
p h r e n i nc e r v e
n e r v e v a g u s
n e r v e
s t r e t ci n h t e r c o s t a l
r e c e p m t o u r ss c l e s
d ia p h r a g m
p r e s s u r e
c h e m o r e c e p t o t er s m i pn e r a t u r e
r e c e p t o r s i n a o r t ic s t r e t c h r e c e p t o
a o r t ic a n d c a r r o e t ci d e p t o r s i n
a n d c a r o t id in m u s c le s
b o d ie s m u s c le s
b o d ie s
C A R D I O V A S C U L A R
C E N T R E
in m e d u l la o f b r a in
p a r a s y m p a t h e t ic
s y m p a t h e t i c
n e r v e n e r v e
( in h ib it o r )
( a c c e le r a t o r )
v a s o c o n s t r ic t io n
a n d
s in o a t r ia l v a s o d il a t io n
n o d e
5.7.9
TV
You are not expected to know how the spirometer works… although its not
very difficult to understand.
5.7.12
5.7.13
Increased BMR
1. Decreased blood pressure
2. Increased HDL
3. Decreased LDL
4. Maintaining healthy BMI
5. Decreased risk of diabetes
6. Increased bone density
7. Improved well being
8. Decreased adrenaline levels
9. Less stress
10.Decreased risk of CHD
11. Moderate exercise increases levels of Natural Killer cells,
which secrete apoptosis-inducing chemicals in response to
non-specific viral or cancerous threat
5.7.14
5.7.15
• Dangerous (obviously)
• May be pushed onto athletes by trainers
• Effects are permanent
• Not used under doctor’s supervision
• Often cut with other drugs
• Exposes athletes to criminals (danger of using other drugs)
The list goes on, just think for yourself in the context of the
question. You can argue the toss either way, but make sure you can
back up your opinion with some sensible, logical arguments.
SNAB A2 Revision
Notes
Unit 5: Energy, Exercise and
Coordination
Topic 8: Grey matter
5.8.1
Schwann cells: wrap around the axon of the long nerves, creating
a thick layer of membrane, which insulates the
nerve and allows for much faster conduction
speed. The thick layer of membrane has gaps in it
between adjacent Schwann cells, these are called
Nodes of Ranvier.
5.8.2
High light intensity Low light intensity
5.8.3
Voltage-Gated K+
Channels open
Voltage-Gated Na+
Channels open
Nerve is
hyperpolarised and
inactive (refractory
period)
As one part of the nerve fires off, Na+ diffuses into the next
section of the nerve, which depolarises the nerve to threshold. This
sequence is repeated like a tiny Mexican wave down the axon of the
nerve.
Nodes of Ranvier speed this conduction process up. When one node
depolarises it induces the next section of the nerve to depolarise
by forming a mini-circuit between nodes. This causes the action
potential to “jump” between nodes of ranvier, making conduction
speed much faster.
5.8.4
6
7
In the dark retinal is in the cis form, but when it absorbs a photon
of light it quickly switches to the trans form. This changes its shape
and therefore the shape of the opsin protein as well. This process is
called bleaching. The reverse reaction (trans to cis retinal) requires
an enzyme reaction and is very slow, taking a few minutes. This
explains why you are initially blind when you walk from sunlight to a
dark room: in the light almost all your retinal was in the trans form,
and it takes some time to form enough cis retinal to respond to the
light indoors.
Cones work in exactly the same way, except that they contain the
pigment Iodopsin, which is found in 3 different forms; red-
sensitive, blue-sensitive and green-sensitive. This gives us colour
vision.
5.8.6
5.8.7
Midbrain
Cerebrum
Cerebellum
Medulla Brainstem
Hindbrain
Brainstem – Uppermost part of the spine, where the spine joins the
brain
Midbrain:
Forebrain:
This is the part of the brain that actually “thinks.” The cortex is
very large in humans and is folded to increase the surface area
further. Other animals have roughly similar size hind- and
midbrains. However, their cortex is much, much smaller.
Premotor
Somatosensory
(Speech
Auditory
motor Visual
area)association area association area
Technique How it works What it allows us to see
During brain surgery a local The patient can tell the doctor
anaesthetic is often used. This what he/she is feeling as the
allows the surgeon to ask the doctor stimulates parts of
Surgery
patient questions as he his/her brain. This can tell us a
operates on their brain lot about the function of the
brain.
Thousands of narrow-beam X- CT Scans(Understanding
show brain structures,
language)
rays pass through the patient’s not brain activity. They also only
head
Occipital from
lobe a rotating& source.
- processes giveinformation
interprets “frozen” from
still theimages.
eyes The rays are collected on the However, they are very useful
other side of the head and for picking up diseases, such as
their strength measured. The cancer, stroke and oedema.
Temporal lobe - processes & interprets information from the
C T Scan
density of the tissue the Xray
ears and processes language and the meaning of words
passes through decreases the
strength of the signal, and
Parietaltherefore,
lobe – processes
lets us workand interprets
out information about
touch, taste,
what typepressure, pain,isheat
of tissue and cold. Also initiates motor
in the
commands.
brain.
Magnetic fields are used to By recording the energy given
Frontalalign
lobeprotons
- plans and organises
in water molecules thought, is involved
out by protons we canwith build up a
in thememory
short term patientsandbrain.
putsWhen thetogether.
speech sequence of thin pictures of the
fields are switched off, the types of tissues inside the brain.
MRI Scan
5.8.8 protons give out a little energy, This can be fed into a computer,
which can be detected. which uses the picture to build up
a 3D image of the inside of the
head
Very similar to above, except As above, but the doctor not only
that the magnetic fields are knows what the tissues look like,
tuned to excite deoxygenated but whether they are active.
fMRI Scan
haemoglobin. This shows up all This is the only technique, that
the areas in the brain where shows brain activity.
oxygen is being used
5.8.9
5.8.10
Lines A and B are the same length, yet look different – why? The
answer is that you have learned to process this kind of stimuli in a
certain way. We live in a “carpentered world” of straight lines and
we interpret line B as a corner (therefore larger than it appears,
because it must be far away) and line A as a corner (therefore,
smaller than it appears, because it must be close).
5.8.11
US → UR (Food → Salivation)
Over time, if a neutral stimulus (CR) is played with the US, it
becomes associated with the US and begins to elicit the same
response. Eventually, the animal learns
CS → CR (Bell → Salivation)
Operant Conditioning:
Habituation:
Insight Learning:
5.8.12
Pavlov’s Dogs
US → UR
US + CS → UR
Eventually, CS → CR
3. Test the monkeys to see whether they can see using each eye
The results:
You need to know about these experiments because they all use
animals
5.8.15
MDMA:
L-Dopa:
5.8.16
5.8.17