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Sam Stafford

on 5 January 2014

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Transcript of Biology

Animal Behavior
Plant Responses
Respiration is the process whereby energy stored in complex organic molecules (carbohydrates, fats and proteins) is used to make ATP. It occurs in living cells.
Covered So Far...
Photosynthesis is the process whereby light energy from the sun is transformed into chemical energy and used to synthesise large organic molecules from inorganic substances.

Organisms that are able to photosynthesise are known as photoautotrophs.
An autotroph is an organism that uses light energy or chemical energy and inorganic molecules (Carbon Dioxide and water) to synthesise complex organic molecules. In the case of photoautotrophs sunlight is their energy source and the raw materials are carbon dioxide and water.

Takes place in specialised organelles called Chloroplasts.
Photsynthesis takes place in two main stages:
Sam Stafford
Structure to function
Light Dependent Stage
Light Independent Stage
- Each chloroplast are between 2-10 micrometers long.
- They are surrounded by a double membrane (an envelope).
- There is an intermembrane space in between the inner and outer membrane.
- Outer membrane is permeable to many small ions.
- Inner membrane less permeable, has transport proteins embedded into it. It is folded into lamellae (thin plates) which are stacked up. Each stack of lamellae is called a granum (grana for plural).
- Grana are connected by intergranal lamellae.

Two distinct regions within a chloroplast: Stroma and Grana, both visible under a light microscope.

- Stroma: Fluid-filled matrix. Light-independent reactions take place here as the necessary enzymes are located here. Starch grains, oil droplets as well as DNA and prokaryote-type ribosomes are located here also.

- Grana: Stacks of flattened membrane compartments, called thylakoids. These are the sites of light absorption and ATPsynthesis during the light-dependent stage. Thylakoids are visible using an electron microscope.
- Inner membrane, with its transport proteins can control entry and exit of substances between the cytoplasm and the stroma inside the chloroplasts.
- The many grana, consisting of up to 100 thylakoid stacks provide a large surface area for the photosynthetic pigments, electron carriers and ATP synthase enzymes, all of which are involved in the light-dependent reaction.
- Photosynthetic pigments arranged into photosystem to allow maximum absorption of light energy.
- Proteins embedded in grana hold photosystems in place.
- Fluid-filled stroma contains enzymes necessary for the light-independent stage.
- Grana surrounded by the stroma so the products of the light-dependent reactions which are needed in the light-independent reactions can readily pass into the stroma.
- Chloroplasts can make some proteins needed for photosynthesis, using genetic instructions in the chloroplast DNA, and the ribosomes to assemble the proteins.
The Light-dependent stage of photosynthesis takes place on the thylakoid membranes. The photosystems with the photosynthetic pigments are embedded in these membranes. There are two photosystems, Photosystem 1 (PSI) and Photosystem 2 (PSII), PSI occurs mainly on the intergranal lamellae and PSII occurs almost exclusively on the granal lamellae. It is these pigments that trap light energy from sunlight so that it can be converted into chemical energy in the from of ATP.
The first stage of the light dependent stage of photosynthesis is the photolysis of water. This is the splitting of a water molecule using photons of light. In photolysis 2 molecules of water are split into 4 electrons, 4 protons and 2 oxygen atoms. This occurs inPSII which is actually the first photosystem used. The oxygen that is produced is actually a waste product and is mostly released through the stomata of the leaves, although some remains in the plant to be used in aerobic respiration.
However the electrons are accepted by PSII, and are excited by the light energy, which causes them to move between pigments until they are accepted by an electron carrier. (a cytochrome) This passes the electrons through the membrane from carrier-to-carrier until one of the carriers pass the electrons to PSI. The movement of the electrons between carriers releases energy which is used to actively pump protons (hydrogen atoms) across the membrane against the gradient.
The electrons however continue to move between carriers in PSI until they reach the enzyme NADP-reductase which in turn reduces a coenzyme called NADP
The protons remain in the thylakoid space creating a concentration gradient from the thylakoid space into the stroma. Meaning that whenever protons are pumped into the thylakoid space due to the release of energy from electron carriers (a process called chemiosmosis) the protons always flow back across the membrane down these set up gradients, but they do this via specialised channel proteins known as ATP synthase. As this happens the ATP synthase enzyme is activated and it joins an inorganic phosphate group to an ADP molecule, creating ATP, this is known as photophosphorylation (there are actually two types, cyclic and non-cyclic).
As Hydrogen ions flow back across the membrane they join with NADP and the electrons received from the electron carriers. The electrons and protons (2 of each) electrons combine with protons to form 2 Hydrogen atoms, and NADP reductase catalyses the reaction between NADP and Hydrogen to produce reduced NADP (NADPH). This is a product at this stage and goes on to be used in the second stage of photosynthesis.
Cyclic Photophosphorylation
- Uses only PSI.
- Excited electrons pass to electron acceptor and then back to the chlorophyll molecule from which they were lost.
- No photolysis of water.
- No NADPH produced.
- Small amounts of ATP made.
- May be used in the light-independent reaction.
- Could be used in guard cells as they only contain PSI.
Non-cyclic photophosphorylation
- Uses PSI and PSII.
- Light strikes PSII, electrons excited.
- Pair of electrons leave chlorophyll from the primary pigment reaction centre.
- Electrons pass along a chain of electron carriers.
- Energy released is used to synthesise ATP.
- Light also strikes PSI and a apri of electrons have been lost.
- These electrons along with protons (created in the photolysis of water) join with NADP to form NADPH.
- Electrons from oxidised PSII replace electrons lost from PSI.
Electrons from photolysis replace those lost in PSII.
Protons from photolysis take part in chemiosmosis to make ATP, and are then captured by NADP in the stroma, they will be used in the light-independent stage.
This stage does not need light to function. However it does need the products from the light-dependent stage: NADPH and ATP. These reactions take place in the stroma of the chloroplast.
The ATP and NADPH is already present here. Carbon Dioxide is the only thing needed. This enters the leaf through diffusion through the stomata. It then enters the leaf via the spongy mesophyll to the palisade layer, then through the cellulose cell wall, the cell surface membrane, the cellular cytoplasm and then the chloroplast double membrane into the stroma. The series of reactions that take place here are known as the Calvin cycle and they are as follows:
- A molcule of Ribulose bisphosphate (RuBP), a five carbon compound has carbon dioxide added to it by enzyme RuBisCO.
- Unstable 6 carbon compound formed which splits into 2 molecules of glycerate phosphate (GP).
- 2 molecules of GP are phosphorylated (phosphate group added, from ATP) and reduced 0using hydrogen from NADPH). Forms triose phosphate (3 carbon compound).
- 10 of every 12 TP molecules produced are phosphorylated again and recycled into 6 molecules of RuBP. The other 2 go onto be made into other biological molecules, such as glucose.
TP can also be converted to glycerol, which combined with fatty acids can form lipids, another respiratory substrate. Also molecules of GP can be used to create amino acids and fatty acids when combined with the glycerol from TP.
In summary photosynthesis can be expressed as:
6CO2 + 6H2O  C6H12O6 + 6O2
Plants respond to both biotic and a biotic components of their environment which means they respond to both living and non-living components. They do this in order to survive as it helps them avoid stress and predation, meaning they are able to survive long enough to reproduce.
There are two types of movements that plants do, they are either: nastic movements or tropic movements.
A nastic movement is a non-directional response to stimuli. For example a flower opening and closing due to light levels.
A tropic response is a directional growth response in which the direction of the response is determined by the direction of the external stimulus.
Examples include:
chemo: response to chemicals
photo: response to light
thermo: response to temperature
thigmo: response to touch
hydro: response to water
These can either be nastic or tropic responses.
What controls plant responses:
Plant hormones (or growth substances) are what coordinate plant responses to environmental stimuli. They are chemical messengers similar to animal hormones and they are able to be transported away from their production site and sent to act in other areas, where they are first detected by receptors on target cells or target tissues.
Hormones are able to move around the plant via: active transport, diffusion, mass flow in the phloem sap, or in xylem vessels.
How do plants grow:
Due to the cell wall present in plant cells they are limited in their ability to expand and divide unlike animal cells, which lack a cell wall. Due to this growth in plants only happen in certain areas where there are groups of immature cells which are still capable of division; these regions are known as meristems.
There are three types of meristems:
- apical meristems: located at the tips of roots and shoots (responsible for growth in these areas).
- lateral meristems (cambium strip) cylindrical chunk of meristem cells around the stem or trunk.
- lateral bud meristems at the 'nodes' in the stem where the shoots derive

Cell division occurs in the meristems but plant growth is due to both cellular division and cell elongation. Certain hormones in the plant trigger cell division while others trigger cell elongation.
An example of plant growth due to an environmental response is phototropism. This is where the shoot of a plant bends towards a light stimulus. This happens because the shaded side of the shoot elongates much faster than the illuminated side, causing the end of the shoot to lean towards the light.
This is evidence for phototropism.
Plant hormones
Auxins (indole-3-acetic acid) - Promotoes cell elongation; inhibits growth of side-shoots; inhibits leaf abscission.
Cytokinins - promotes cell division
Gibberellins - promotes seed germination and growth of stems
Abscisic acid - Inhibits seed germination and growth; causes stomatal closure when the plant is stressed by low water availability
Ethene - promotes fruit ripening
Effects and uses of Plant hormones
Leaf abscission
Cytokinins stop the leaves of deciduous trees ageing making sure the leaf acts as a sink for phloem transport meaning it gets a good supply of nutrients.
However if cytokinin production drops, that supply of nutrients dwindles and senescence begins, this is usually followed by leaves being shed (abscission).
Usually auxins inhibit abscission by acting on cells in the abscission zone, however:
- Leaf senescence causes auxin production at the tip of the leaf to drop.
- This makes cells in the abscission zone more sensitive to another growth substance called ethene.
- A drop in auxin concentration also causes an increase in ethene production.
- this in turn increases production of the enzyme cellulase, which digests the walls of the cells in the abscission zone, eventually separating the petiole from the stem.
Apical dominance
This is when the growing apical bud at the tip of the shoot inhibits growth of lateral buds further down the shoot.
If you break the shoot tip off a plant, the plant starts to grow side branches from lateral buds that were previously dormant. Researches suggested that the explanation for this was that auxins usually prevent lateral buds from growing. This is apical dominance. When the tip is removed the auxin concentration in the shoot drops and the buds grow.
To test this researches applied a paste containing auxins to the cut end of the shoot, and the lateral buds did not grow. However this can not be accepted as the only reason straight away. This is due to the fact that there may be some other factors that may produce the effect, for example:

Upon exposure to oxygen, cells on the cut end of the stem could have produced a hormone that promoted lateral bud growth. Due to this Ken Thimann and Folke Skoog applied a ring of auxin transport inhibitor below the apex of the shoot. The lateral buds grew. Based on this result they suggested that normal auxin concentrations and growth inhibition confirms that the hormone directly causes the pattern of growth.
However it was later further proved that abscisic acid inhibits bud growth. Higlh concentrations of auxin in the shoot may keep abscisic acid levels high in the bud. When the tip is removed which is the source of the auxin, the abscisic acid concentrations drop and the bud starts to grow.
Also cytokinins promote bud growth, applying these directly to buds can overide apical dominance. When the auxin source is removed, cytokinins spread around the plant promoting frowth in the buds.
These increase cell division and cell elongation. Most associated with stem elongation, although they are involved in a number of plant processes. It was research in Japan on the disease Bakanae which sparked interest into gibberellins. This disease was caused by a fungus which made rice plants grow very tall. Studies isolated the chemical which caused it (gibberellins).
The above experiment shows how evidence of the effect of gibberellins can be shown experimentally. The importance of this experiment over using artificial gibberellin is that this proves the growth has occured due to natural production of the hormone and natural processes in the grafted plant. Had gibberellins been artificially inserted, the results would have been less convincing.
Respiration releases energy which is used to phosphorylate (add an inorganic phosphate to) ADP, making ATP. This phosphorylation also transfers energy to the ATP molecule.
ATP is a phosphorylated nuckeotide. It is a high energy intermediate compound that is found in both prokaryotic and eukaryotic cells. Each molecule consists of adenosine (which is adenine and a ribose molecue) plus three phosphate molecules. It can be hydrolysed to ADP which in turn releases 30.6kJ of energy per mol. This means energy is immediately available for the cell in small manageable amounts.

Respiration occurs in 4 main stages:
Happens in 4 stages: (In the cytoplasm)

One ATP molecule is hydrolysed and the phosphate group released is attached to the glucose molecule at carbon 6.
Glucose 6 phosphate is changed to fructose 6-phosphate.
Another ATP is hydrolysed and the phosphate group is attached to the fructose 6-phosphate at carbon 1. This activated hexose sugar is now known as fructose 1,6-bisphosphate.
The energy from the hydrolysed ATP molecules activates the hexose sugar and prevents it from being transported out of the cell.

Splitting of hexose 1,6-bisphosphate:
Each molecule of hexose 1,6-bisphosphate is split into two molecules of triose phosphate molecules.

Oxidation of triose phosphate:
Two hydrogen atoms are removed from each triose phosphate molecule.This involves dehydrogenase enzymes.
These are aided by the coenzyme NAD which is a hydrogen acceptor. NAD combines with the hydrogen atoms, becoming reduced NAD.
So: 2 molecules of NAD reduced per molecule of glucose.
Also 2 molecules of ATP produced at this stage. (substrate-level phosphorylation).

Conversion of triose phosphate to pyruvate:
Four enzyme-catalysed reactions convert each triose phosphate molecule to a molecule of pyruvate. (Also a 3 carbon compound).
In this process another 2 molecules of ADP are phosphorylated to 2 molecules of ATP.

So overall the products of glycolysis are: 2 ATP molecules (4 created, 2 used).
2 molecules of reduced NAD.
2 molecules of pyruvate.

The link reaction and Krebs cycle:
Happen in the mitochondrial matrix)
The link reaction:
Pyruvate dehydrogenase removes hydrogen atoms from pyruvate.
Pyruvate decarboxylase removes a carboxyl group, which eventually becomes carbon dioxide, from pyruvate.
The coenzyme NAD accepts the hydrogen atoms.
Coenzyme A accepts acetate to become acetyl coenzyme A. The function of CoA is to carry acetate to the Krebs cycle.

The Krebs Cycle:
The acetate is offloaded from CoA and joins with a 4-carbon compound called oxaloacetate, to form a 6-carbon compound called citrate.
Citrate is decarboxylated and dehydrogenated to form a 5-carbon compound. The pair of hydrogen atoms is accepted by a molecule of NAD, which becomes reduced.
The 5-carbon compound is decarboxylated and dehydrogenated to form a 4-carbon compound and another molecule of NAD is reduced.
The 4-carbon compound is changed into another 4-carbon compound. During this reaction a molecule of ADP is phosphorylated to produce a molecule of ATP. This is substrate-level phosphorylation.
The second 4-carbon compound is changed into another 4-carbon compound. A pair of hydrogen atoms is removed and accepted by the coenzyme FAD which is reduced.
The third 4-carbon compound is further dehydrogenated and regenerates oxaloacetate. Another moelcule of NAD is reduced.

Oxidative phosphorylation and chemiosmosis.
The final stage of respiration involves eletron carriers embedded in the inner mitochondrial membranes.
These membranes are folded into cristae, increasing the surface area for electron carriers and ATP synthase enzymes.
Recuded NAD and FAD are reoxidised when they donate hydrogen atoms which are split into protons and electrons, to the electron carriers.
The first electron carrier to accept electrons from reduced NAD is a protein complex, complex I called NADH - coenzyme Q reductase. (NADH dehydrogenase).
The protons go into solution in the matrix.

The electron transport chain:
The electrons are passed along a chain of electron carriers and then donated to molecular oxygen, the final electron acceptor.

As electrons flow along the electron transport chain, energy is released and used, by coenymes associated with some of the electron carriers complexes I, III and IV to pump protons across to the intermembrane space.
This builds up a proton gradient, which is also a pH gradient and an electrochemical gradient.
Thus potential energy builds up in the intermembrane space.
The hydrogen ions cannot diffuse through the lipid part of the inner membrane but can diffuse through ion channrls. These channels are associated with the enzyme ATP synthase. This flow of hydrogen ions is chemiosmosis.

Oxidative phosphorylation:
This is the formation of ATP by the addition of an inorganic phsophate group to a molecule of ADP in the presence of oxygen.
As protons flow through an ATP synthase enzyme they drive the rotation of part of the enzyme which joins ADP with an inorganic phosphate group, forming ATP.
The electrons are passed from the last electron carrier in the chain to a molecular oxygen, which is the final electron acceptor.
Hydrogen ions also join with the oxygen, so it is reduced to water.

So: so far there has been 2 molecules of ATP produced in gycolysis and 2 in the krebs cycle.
In oxidative phosphorylation: reduced NAD also provides hydrogen ions that contribute to the proton gradient. The 10 molecues of NAD can theoretically produce 26 molecules of ATP during oxidative phosphorylation.
So overall a total of 30 molecules of ATP should be made, however this is not so as some protons leak across the mitochondrial membrane reducing the number of protons to generate the proton motive force. Some ATP produced is used to actively transport pyruvate into the mitochondria. Some ATP is used for the shuttle to bring hydrogen from reduced NAD made during glycolysis in the cytoplasm, into the mitochondria.
Anaerobic respiration
Anaerobic respiration is the release of energy from substrates, such as glucose, in the absence of oxygen. There are two types: lactate fermentation and alcoholic fermentation. Each depends on how NAD is reoxidised.
Lactate fermentation:
This occurs in mammalian muscle tissue. It happens by:
Reduced NAD must be reoxidised to NAD+.
Pyruvate is the hydrogen acceptor.
It accepts hydrogen atoms from reduced NAD.
NAD is now reoxidised and is available to accept more hydrogen atoms from glucose.
Glycolysis can continue, generating enough ATP to sustain muscle contraction.
The enzyme lactate dehydrogenase catalyses the oxidation of reduced NAD, together with the reduction of pyruvate to lactate. This can be carried away in the blood away from the muscles, to the liver. When more oxygen is available the lactate can be converted back to pyruvate, which may enter the krebs cycle via the link reaction or recycled to glucose and glycogen.
Alcoholic fermentation:
This occurs in yeast cells.
Each pyruvate molecule loses a carbon dioxide molecule; it is decarboxylated. and becomes ethanal.
This reaction is catalysed by the enzyme pyruvate decarboxylase which has a coenzyme (thiamine diphosphate) bound to it.
Ethanal accepts hydrogen atoms from reduced NAD, which becomes reoxidised as ethanal is reduced to ethanol catalysed by ethanol dehydrogenase.
The reoxidised NAD can now accept more hydrogen atoms from glucose, during glycolysis.
Animals show two different types of behaviour. There is Innate and Learned behaviour.

Innate behaviour are those that offsrping are born with, and naturally occur, they are genetically encoded within the organisms DNA, where the patterns of behaviour are the same throughout the species.
Learned behaviour are determined by genetic makeup of the organism and their interaction with and influences of the environment, these are learnt through conditioning, imprinting and habituation and are not passed onto offspring genetically, but may be taught to offspring by learning.

Innate behaviour
These are described as being stereotyped as they are always reproduced the same way and are same throughout the entire species. Innate behaviour such as breathing, feeding and recognising danger and being afraid of this danger are all ways of helping an organism survive and so therefore play a part in their evolutionary theory.

One example of innate behaviour is a reflex action. This is a fast stereotyped response the most commonly known is the escape reflex common to many invertebrates, such as fish and shrimp, who use the reflex to escape predation. For example with a fish a change in water pressure around them causes their tails to flick which darts them away from the area in a certain direction. These are involuntary responses.

Second type is the taxis. These are not immediate like reflexes, they are more gradual but still innate. They are directional movement responses (can be positive or negative). Examples can be that of ants, where positive chemotaxis describes the responses in their antennae which direct them to move towards the stimulus' chemical. Second example is a maggot with negative phototaxis which describes the maggots detecting a light stimulus and moving away from it.

Third and final type is kinesis. These are non-directional movement responses, whereby a particular direction is not indicated but the response of the organism is to change their direction. This response involves an increase in movement when the organism is in unfavourable conditions. An example of this is within woodlice, who prefer dark damp conditions to avoid predation so when in bright and dry conditions they move brightly and do not turn frequently. This is until they find an area that suits them and has favourable conditions and they they move slowly and turn often.

A more complex type of innate behaviour is a Fixed Action Patter or FAP. This is where behaviours always follow the same set of rules, but this is a set of responses to a non-immediate stimulus. A good example is the waggle dance in worker honey bees, whereby a bee is able to indicate the distance and direction to a food source based on the angle and duration of its dance.
Learned Behaviour
Described as that which shows adaptation in response to experience. This type of behaviour is of greatest survival benefit to animal:
- with a longer life span, and so time to learn.
- with an element of parental care of the young, which involves learning from parents.
- living for a part of the time at least with other members of the species in order to learn from them.

The main advantage of learned behaviour over innate behaviour is that it is adapted in response to changing circumstances or environments. There are six major areas of learned behaviour:

These are able to delay leaf senescence (ageing) due to this reason they are sometimes used to prevent yellowing of lettuce leaves after they have been picked.
They are also used in tissue culture to help mass-produce plants. They promote bud and shoot growth from mall pieces of tissue taken from a parent plant. This produces a short shoot with a lot of side branches, which can be split into lots of small plants. Each of these is then grown separately.
Because ethene is a gas and is not able to be sprayed directly scientists have developed 2-chloroethylphosphonic acid, which can be sprayed in solution, is easily absorbed and slowly releases ethene inside the plant.Commercial uses of ethene include:

- speeding up fruit ripening in apples, tomatoes and citrus fruits.
- promoting fruit drop in cotton,cherry and walnut.
- promoting female sex expression in cucumbers, reducing the chance of self pollination (pollination makes cucumbers taste bitter)and also increasing the yield.
- promoting lateral growth in some plants, yielding compact flowering stems.

Restricting ethene's effects can also be useful. Storing fruit in a low temperature iwith little oxygen and high carbon dioxide concentration prevents ethene synthesis and thus prevents fruit from ripening. This means that fruit is able to be stored for longer period of times. This is essential when shipping the likes of unripe bananas from the Caribbean. Other inhibitors of ethene synthesis, such as silver salts, can increase the shelf life of cut flowers.
Commercial uses
These delay senescence in citrus fruits, extending the time the fruits can be left unpicked, and making them available for longer in the shops.
Gibberellins acting with cytokinins can make apples elongate to improve their shape.
Without Gibberellins bunches of grapes are very compact; this restricts the growth of individual grapes. With gibberellins the grape stalks elongate, they are less compacted and the grapes get bigger.
Gibberellins can be used to speed up the process of brewing.

Sugar Production:
Gibberellins can be used to increase the sugar yield by up to 4.5 tonnes per hectare.

Plant breeding:
Gibberellins can help speed up selective breeding by inducing seed formation in young trees,
They can also increase growing speed making it able to harvest some plants sooner.
Animal Responses
Animals must be able to respond to their environment if they are to stay alive. This could vary fro, the coordinated voluntary muscle actions required in order to run away from a predator, to the fine control of balance, posture and temperature regulation. These coordinated responses are organised in animals using nerves and hormones. Here we are going to look at the brain and nervous system and how these are arranged in order to send messages and coordinate responses.
The Brain
Four of the main regions in the brain are the cerebrum, the cerebellum, the hypothalamus and the medulla oblongata, each have their own function and they are as follows:

Cerebrum: largest part of the brain. Divided into two hemispheres left and right. These are connected via the corpus callosum. Outermost layer, which has a surface area of around 2.5 metres squared is folded and consists of a thin layer of nerve cell bodies known as the cerbral cortex. This region is more highly developed in humans than any other organism. It is in control of 'higher brain functions' including: conscious and emotional responses, the ability to override some reflexes and features associated with intelligence, such as reasoning and judgement,
Medulla Oblongata
The cerebral cortex i subdivided into areas responsible for specific activities and body regions. There are three areas these are the sensory area which receives impulses indirectly from receptors. The association areas which compare input with previous experience in order to interpret what the input means and judge an appropriate response. And then finally there is the motor area which sends impulses to effectors e.g muscles and glands.
The motor areas on the left side of the cerebral cortex control the muscular movements on the right hand side of the body and vice versa.
The cerebellum is involved with coordinated motor responses. These may involved the likes of muscular activities associated with responding o changes in body position to remain balanced and upright.
Sensory activities such as judging the position of objects and limbs. The tensioning of muscles in order to manipulate tools/instruments effectively. Feedback information on muscle position, tension and fine movements. Operation of antagonistic muscles to coordinate contraction and relaxation.
Neurones of the cerebellum carry impulses to the motor areas motor output to the effectors can be adjusted appropriately in relation to these requirements. Explaining why we go on 'auto-pilot' when carrying out such activities, as they are said to become programmed into the cerebellum. Also explains how we can catch a ball by judging its speed and trajectory and close out fingers around it.

The cerebellum contains over half of all nerve cells in the brain. It plays a key role in coordinating balance and fine movement. To do this it process sensory information from:
the retina; the balance organs in the inner ear (the vestibular system); specialised fibres in muscles called 'spindle' fibres which give information about muscle tension; and also the joints.
The medulla oblongata controls non-skeletal muscles e.g cardiac and involuntary muscles. This means that it is effectively in control of the autonomic nervous system.
Regulatory centres for a number of vital processes are found in the medulla oblongata including: the cardiac centre, which regulates heart rate; and the respiratory centre, which controls breathing and regulates the rate and depth of breathing. It is also involved with blood vessel function, sneezing and swallowing.
It is a cone-shaped neuronal mass in the hind brain and is located in the brain stem, anterior of the cerebellum.
The medulla oblongata contains both myelinated and non-myelinated neurones. (Or white matter and grey matter respectively).
The hypothalamus controls most of the body's homeostatic mechanisms. Sensory input from temperature receptors and osmoreceptors is received by the hypothalamus and leads to initiation of automatic responses that regulate body temperature and blood water potential. The hypothalamus also controls much of the endocrine function of the body because it regulates the pituitary gland.
The hypothalamus also helps regulate complex behaviours such as appetite, thirst, sleep general arousal, and reproductive behaviours. It also plays a role in emotional reactions, including anger and aggression.
The Nervous System
The Nervous system coordinates the actions of the body through electrical impulses. However it also works in conjunction with the endocrine system. Both of which are essential for maintaining life in humans. Structurally and functionally it is divided into subsystems, helping us describe nervous actions and understand coordination processes.
There is the
central nervous system
) which consists of the
brain and spinal cord
. It consists of
grey matter
white matter
(which are billions of
non-myelinated nerve cells
and longer
myelinated axons and dendrons
that carry impulses respectively). The presence of myelin makes the long fibres appear white. Following on from the CNS there is the
peripheral nervous system
which is made up of neurones that carry impulses into and out of the CNS.

The peripheral nervous system is further divided into
motor systems
. Sensory neurones can carry impulses from the many receptors in and around the body, to the CNS. Whereas the motor neurones are responsible for transmitting signals from the CNS to the
organs. Many neurones are bundled together and covered in connective tissue to from nerves. The motor system is further subdivided into
The somatic motor neurones carry impulses from the CNS to
skeletal muscles
, which are under
control. Whereas the autonomic motor neurones carry impulses from the CNS to
cardiac muscle
smooth muscle
in the
and to
of which are under
The autonomic nervous system operates largely independent of conscious control. It is responsible for controlling the majority of homeostatic mechanisms and so plays a vital role in regulating the internal environment of the body within set parameters. The system is also capable of controlling the heightened responses associated with the stress response. The autonomic nervous system varies from the somatic in a number of ways, such as: most autonomic neurones are non-myelinated whereas somatic ones are. Autonomic connections to effectors always consist of at least two neurones whereas somatic connections to effectors only consist of one. The two neurones connect at a swelling known as a
. Also autonomic motor neurones occur in two types either
Sympathetic and parasympathetic subsystems vary both in structure and action. Often both referred to as antagonistic systems as in many cases the action of one system opposes the action of the other. Under normal conditions impulses are passing along the neurones of both systems t a relatively low rate. This is altered by a change in internal conditions or stimulation of the stress response, as it leads to an altered balance of stimulation between the two systems, which leads to an appropriate response. The balance of stimulation is controlled by subconscious parts of the brain.
The parasympathetic nervous system is part of the autonomic nervous system and is the division of the nervous system that is involved with automatic process such as digestion, respiration and heart rate,
It acts in concert with the sympathetic nervous system and is in control of conserving the body's energy by ringing bodily functions back to homeostasis, particularly after the fight or flight response is activated by the sympathetic nervous system.
Parasympathetic nerves originate in the middle of the spinal column arising from the spinal nerves of the CNS. Axons of this system are usually quite long and extend into ganglia in the rest of the body. These ganglia are usually located in or near organs allowing the parasympathetic to rapidly receive and emit signals throughout the body. Due to the fact that the parasympathetic nervous system originates from the spinal column it does not typically require conscious thought to stimulate a reaction.
The parasympathetic system is often referred to as the rest and digest part of the body as it is involved with regulating processes that are vital for the maintenance of normal life. The functions of this system include:
regulating digestion including urination and defecation; regulating sexual arousal; slowing heart rate and lowering blood pressure after the fight or flight response; pupil constriction; decreased ventilation rate after the fight or flight response.
The parasympathetic nervous system is most active during sleep and relaxation. The neurones of a pathway are linked at a ganglion within the target tissue. So pre-ganglionic neurones vary considerably in length. Post-ganglionic neurones secrete acetylcholine as the neurotransmitter at the synapse between neurone and effector.
The sympathetic nervous system is a component of the autonomic nervous system. It is commonly regarded as the part of the nervous system involved with the fight or flight response, the sympathetic also plays a constant role in regulating homeostasis.
The sympathetic nervous system originates within the spinal cord meaning many of its functions are automatic and unconscious. Neurones in the spinal cord usually regulate functions that do not require conscious thought. The neurones of the sympathetic nervous system are located towards the middle of the spinal and are attached to long axons.
These axons in turn are connected to ganglia on either side of the spine. Peripheral sympathetic neurones are located here and carry signals to and from neurones throughout the body including to the organs.
The sympathetic nervous systems two main functions are instigating the fight or flight response and maintaining homeostasis. During times of stress the sympathetic nervous system is able to dilate the pupils, elevate heart rate, increase ventilation, increase sweating, elevate blood pressure and orgasm. It is most active during times of stress. The neurones of a pathway are linked at a ganglion just outside of the spinal so pre-ganglionic neurones are very short. Post-ganglionic neurones secrete the neurotransmitter noradrenaline at the synapse between neurone and effector.
During normal bodily functions the sympathetic nervous system maintains homeostasis by maintaining a relatively consistent heart rate and blood pressure.
People suffering from prolonged stress may experience constant activation of the sympathetic nervous system. This can lead to health problems such as depressed immunity and prolonged illness.
It may also contribute to the development of mental health issues such as anxiety, depression, post traumatic stress and hyper-reactivity.
Coordinated movement
Coordinated movements require the action of the brain in sending impulses along motor neurones to voluntary muscles. Voluntary muscles are attached to bones of the skeleton by tendons, such that contraction of the muscles moves the bones at the joints.
Tendons are made of of tough, inelastic collagen which is continuous with the muscle and the periosteum (which is the connective tissues covering the bone).
Muscles are only capable of producing force when they contract. So the movements of any bone a joint requires the coordinated action of at least two muscles. As one muscle is stimulated and contracts the other muscle of the pair must relax to allow for smooth movement. Muscles which work in pairs opposite each other are known as antagonistic. However the movement of bones at many joints require a wider range of actions and is under the control of groups of muscles called synergists.
The elbow is an example of a synovial joint. These joints occur where a large degree of movement is required. The synovial fluid is a lubricant which eases the movement of bones at the joint. The biceps and triceps muscles act antagonistically in order to move the forearm at the elbow.
The nervous system controls muscle action because motor neurones re connected to muscle cells at a neuromuscular junction. Impulses arriving at the neuromuscular junction stimulate contraction. A neuromuscular junction is very similar in structure and operation to a synapse between neurones.
Some muscular movements require a stronger contraction than others
Such as the differences between the contraction of leg muscles for walking and the contraction of the leg muscles while running, or the difference between holding an egg and crushing a can.
The brain controls the strength pf contraction because many motor neurones stimulate a single muscle. Each one branches to neuromuscular junctions, causing the contraction of a cluster of muscle cells known as a
motor unit. The more motor units stimulated the greater the force of contraction. This is known as gradation of response.
Types of muscle
Muscles are composed of cells that are elongated to form fibres. Muscle cells have the ability to relax and contract. All muscle cells produce a force on contraction because they contain filaments made up of the proteins myosin and actin.
There are three types of muscle, these are: involuntary muscle which is also known as smooth muscle; cardiac muscle; and voluntary muscle also known as striated or skeletal muscle. These three types of muscle have distinctly different structures and functions.
Involuntary (smooth) muscle
Cardiac muscle
Voluntary (skeletal or striated) muscle
Smooth muscle is innervated by neurones of the autonomic nervous system. This means that contractions of this type of muscle are not under voluntary control.
Under microscopic examination, involuntary muscles does not appear striated like voluntary and cardiac muscle. Muscle cells are referred to as being 'spindle-shaped'. They contain small bundles of actin and myosin, and a single nucleus.
Cells in in the relaxed state are around 500 micrometers long and 5 micrometers wide. Contraction is relatively slow, but this muscle also tires very slowly.
Examples of smooth muscles are as follows:
Cardiac muscle forms the muscular part of the heart. There are three types: artial muscle; ventricular muscle and specialised excitatory and conductive muscle fibres.
Artial and ventricular muscle contract and in a way similar to that of skeletal muscle but with a longer duration of contraction. The excitatory and conducive fibres contract feebly but conduct electrical impulses and control the rhythmic heartbeat.

Some cardiac muscle fibres are capable of stimulating a contraction without an impulse, this type of contraction is known as myogenic. However neurones of the autonomic system carry impulses to the heart to regulate the rate of contraction.
Sympathetic stimulation increases its rate, whereas parasympathetic decreases its rate. The sinoatrial node in the wall of the right atrium, is made of specialised excitatory and conducive fibres. It has the greatest ability for self-excitation and the electrical activity stimulated there spreads immediately into the atrial wall. A layer of non-conducting fibres separate the ventricles and atria, so the electrical activity can only spread to the atria via the atrioventricular node. This node conducts the activity to the ventricle tips via the Purkyne fibres.
Cardiac muscle fibres are made of many individual cells connected in rows. There is a dark area which is known as intercalated discs, which are cell membranes. These membranes fuse in such a way that there are gap junctions with free diffusion ions and so action potentials pass very easily and quickly between cardiac muscle fibres through the latticework of interconnections. Cardiac muscle, when viewed under a microscope, is striated. Contraction and relaxation of cardiac muscle is continuous throughout life. This type of muscle contracts powerfully and without fatigue.
The action of voluntary muscles leads to movement of the skeleton at the joints. This moves the limbs.
Muscle cells form fibres of about 100 micrometres in diameter, containing nuceli. Each fibre is surrounded by a cell surface membrane called the sarcolemma.
Muscle cell cytoplasm is known as sarcoplasm and contains organelles including: many mitochondria; an extensive sacroplasmic reticulum (which is just a specialised endoplasmic reticulum); a number of myofibrils. These are the contractile elements and each consists of a smaller contractile units called sarcomeres. Within the myofibrils there are two types of protein myofilaments and these are thin actin and thick myosin which run the length of the cell.
Microscopic examination of voluntary muscle shows a striped or banded pattern. The bands are given names as shown in the picture. This type of muscle contracts quickly and powerfully, but it fatigues quickly, unlike involuntary and cardiac muscle.
How skeletal muscles contract
The sliding filament model
As mentioned each contractile unit of a skeletal muscle is known as a sarcomere. This is made up of thin and thick filaments. The striped appearance of voluntary muscle under the microscope is different when the muscles are relaxed and when they are contracted.
The span from one Z-line to the next is known as the sarcomere, and in a relaxed state is around 2.5 micrometers in length. Z-lines are closer together during contraction because lengths of the I-band and H-zone are reduced. The A-band does not change in length during contraction.
There are two types of protein filaments that are found in muscle cells, these are:
thin filaments
which are two strands made mainly of actin coiled around each other like a twisted double string of beads. Each strand is composed of actin subunits, tropomyosin which is a rod-shaped protein, this is coiled around the actin reinforcing it. A troponin complex is attached to each tropomyosin molecule. Each troponin complex consists of three polypeptides. One binds to actin, one to tropomyosin (so this keeps tropomyosin in place around the actin filaments) and one to calcium ions.
Thick filaments
which are bundles of the protein myosin. Each one consists of a tale and two protruding heads. Each thick filament consists of many myosin molecules whoes heads stick out from opposite ends of the filament.
The power stroke
This is how muscle contraction occurs:
Myosin head groups attach to surrounding actin filaments forming a cross-bridge.
The head group then bends, causing the filament to be pulled along and so overlap more with the thick filament. This is the power stroke.
ADP and Pi are released. The cross-bridge is then broken as new ATP attaches to the myosin head. The head group moves backwards as the ATP is hydrolysed to ADP and Pi. It can then form a cross-bridge with the thin filaments further along and bend.
In a contracting muscle, several million cross-bridges are continuously being made and broken, causing thin filaments to slide past the thick filaments and so shorten the sarcomere. This shortens the whole length of the muscle.
Calcium ions allow muscles to contract. The binding sites for the myosin head group on the actin fibre are covered by the tropomyosin subunits. This means that a myosin head group cannot attach to any such binding site, this means that cross-bridges can not form and thus muscle contractions cannot occur. When an action potential arrives via a neurone
at the neuromuscular junction calcium ions are released from the sacroplasmic reticulum in the sarcomeres. These calcium ions diffuse through the sarcoplasm and bind to troponin molecules.
This binding changes the shape of the troponin which moves the tropomyosin away from the binding sites on the actin. The actin-myosin binding sites are uncovered and so cross bridges can form. This allows the power strike and muscle contraction to occur.
How is ATP involved?
The role of ATP in the power stroke:
When the myosin head group attaches to the actin binding site and 'bends', the molecules are in their most stable form.
Energy from ATP is required in order to break the cross bridge connection and re-set the myosin head forwards. The myosin head group can then attach to the next binding site along the actin molecule and bend again.
Maintenance of ATP:
Sufficient ATP in muscle cells for about 1-2 seconds worth of contraction. Therefore for continued contraction more ATP must be regenerated as quickly as it is used up. This is done by either:
Aerobic respiration in muscle cells mitochondria. The ATP production of this type is dependent on the amount of oxygen available for the muscle cells as a respiratory substrate.
Anaerobic respiration in the muscle cell sarcoplasm, this process is quite quick but lactic acid is produced, this enters the blood and increases blood flow to the muscles.
Transfer from creatine phosphate in the muscle cell sarcoplasm, the phosphate from the creatine phosphate can be transferred to ADP to form ATP, this can be done very quickly by the enzyme creatine phospotransferase. The supply of creatine phosphate is sufficient enough to support muscular contractions for a further 2-4 seconds.
Sensory Receptors
These are specialised cells that can detect changes in our surroundings. They are energy transducers which means they convert different forms of energy into nerve impulses. There are different types of energy sensory receptors and each one is a transducer, and each type is adapted to detect changes in a particular form of energy. This could be a change in light levels, pressure on the skin, or many other other energy changes. It is these changes in energy that are known as stimuli (stimulus for singular) Whatever the stimulus is the sensory receptor converts it in to an electrical energy which is known as a nerve impulse.
Examples of sensory receptors
Light-sensitive cells (rod and cones) in the retina of the eye. These detect light intensity and a range of wavelengths (colours).
Olfactory cells lining the inner surface in the nasal cavity. These detect the presence of volatile chemicals.
Taste buds in the tongue, hard palate, epiglottis, and the first part of the oesophagus are responsible for detecting the presence of soluble chemicals.
Pressure receptors in the skin known as Pacinian corpuscles detect pressure on the skin.
Sound receptors in the inner ear known as cochlea detect vibrations in the air.
Muscle spindles called proprioreceptors detect the length of muscle fibres.
Once these sensory receptors have detected a stimulus they need to relay the message to the brain in order for action to be take.This is done by the signal being transmitted through a series of neurones. The first in the series being a sensory neurone, and these impulses are transmitted along these neurones as action potentials. There are however a number of different types of neurones, these include: as aforementioned a sensory neurone which is responsible for carrying the action potential from a sensory receptor to the Central Nervous System(CNS); there are motor neurones that carry an action potential from the CNS to an effector such as a muscle or gland; there is then also relay neurones which are responsible for connecting sensory and motor neurones.
The function of the neurone is to transmit the action potentials from one part of the body to another. Most neurones have a very similar basic structure that enables them to carry out this function.They are very specialised cells and have the following features:
Many are very long so they are able to transmit action potentials over a very long distance.
The cells curface membrane (plasma membrane) has many gated ion channels that control the entry or exit of sodium, potassium and calcium ions.
They have sodium/potassium ion pumps that use ATP to actively transport sodium ions out of the cell and potassium ions into the cell.
They maintain a potential difference across their cell surface membrane.
They are surrounded by a sheath called the myelin sheath which is actually a series of schwann cells which insulate the nurones from electrical activity in nearby cells. There are gaps between each Scwhann cell known as the nodes of Ranvier.
They have a cell body that contains the nucleus, many mitochondria and ribosomes.
Motor neurones have their cell body in the CNS and have a long axon that carries the action potential out to the effector.
Sensory neurones have a long dendron carrying the action potential from asensory receptor to the cell body which is positioned just outsideof the CNS. They then have a short axon carrying the action potential into the CNS.
Both sensory and motor neurones have numerous dendrites connected to other neurones.
Action potentials
Action potentials as mentioned before are what nerve impulses actually are.
All cell surface membranes contain proteins. Some protein sare channels that allow the movement of ions, which are charged particles.
If the channels are open permanently then ions are able to diffuse across the membrane and will do so until there is an equal concentration of ions on either side of the membrane.
Neurones have more specialised channel proteins that are specific either to sodium ions or potassium ions. They also posses a gate that can open or close the channel. When open the membrane becomes more permeable to that particular ion, and when it is closed it becomes less permeable. The channels are usually kept closed.
Nerve cell membranes also contain carrier proteins that actively transport sodium ions out of the cell and potassium ions into the cell. Due to this the inside of the cell is negatively charged in respects with the outside of the cell. The cell membrane is said to be polarised.
A nerve impulse or action potential is created by altering the permeability of the nerve cell membrane to sodium ions. As the sodium ion channels open the membrane permeability to sodium is increased and sodium ions can move across the membrane down their concentration gradients and into the cell. The movement of ions across the membrane creates a change in the potential difference across the membrane. The inside of the cell becomes less negative in comparison to outside of the cell than usual.This is called depolarisation.
Generator potential
Receptor cells respond to changes in the environment. The gated sodium ion channels open, allowing sodium ions to diffuse across the membrane into the cell.

A small change in potential caused by one or two sodium ion channels opening is known as a generator potential. The larger the stiumulus meaning the greater the change in environmental conditions, the more sodium ion channels that will be opened.
If enough open then this will result in the potential difference of the cell changing significantly and will result in the depolarisation of the cell membrane hence causing an action potential (impulse).
This is also known as the all-or-nothing principal, in the sense that a generator potential in the sensory receptors are depolarisations of the cell membrane. A small deoplarisation will have no effect on the voltage-gated channels. However if the depolarisation is large enough to reach the threshold potential it will result in nearby voltage-gated sodium ion channels opening. This will resultin a large influx of sodium ions and the depolarisation reaches +40mV which is an action potential and is the same every time regardless of the size of the stimuli, the only thing that will change is the frequency of the action potentials, the larger the stimuli the larger the frequency of action potentials. This is how the brain differentiates between large and small stimuli by the strength of the frequency.
However once the value of +40mV is reached the neurone willtransmit the action potential because many voltage-gated sodium ion channels open. The action potential is self-perpetuating meaning that once it starts at one point in the neurone it will continue along to the end of the neurone.
Steps in action potentials
Firstly before an action potential is generated the neurone is at resting potential. This is when the neurone is not transmitting an action potential so it is said to be at rest.

However even while the neurone is not transmitting an action potential it is still actively transporting ions across its cell surface membrane. Sodium/potassium ion pumps use ATP to actively pump out 3 sodium ions out of the cell for every 2 potassium ions that are actively pumped into the cell.
However the plasma membrane is more permeable to potassium ions than it is to sodium ions and as a result many diffuse out again. The cell cytoplasm also contains large organic anions which are negatively charged ions. Hence the interior of the cell is maintained at a negative potential when compared to outside of the cell. The cell membrane is said to be polarised. The potential difference across the cell membrane is about -60mV and this is called resting potential.
Now there is then the action potential itself, this consists of a set of ionic movements. These ions move across the cell membrane when the correct ion channel is open. The action potential consists of these following stages:
Membrane starts in its resting potential - polarised with inside of cell being around -60mV compared to outside of the cell.
Generator potential causes sodium ion channels to open and sodium ions diffuse into cell.
The membrane depolarises, it becomes less negative compared with outside of the cell and reaches the threshold value of -50mV.
Voltage-gated sodium ion channels open causing an influx of sodium ions. As more sodium ions enter the cell the inside of the cell becomes positively charged compared with outside of the cell.
Potential difference across plasma membrane reaches +40mV, the inside of the cell is positive compared with outside.
Sodium ion channels close potassium ion channels open,
Potassium ions diffuse out of cell bringing potential difference back negative inside compared with outside. This is called repolarisation.
Potential difference overshoots slight and cell becomes hyperpolarised. The original potential difference is restored so that the cell returns to its resting potential.
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