Year 12s: what will be the first way you research your future options? >>

AQA BIOL5 Biology Unit 5 Exam - 22nd June 2011

Scroll to see replies

ATP

Adenosine triphosphate (ATP) is a nucleotide that is used as a coenzyme in cells. It transports chemical energy within cells for metabolism. This complex molecule is comprised mainly of three phosphate groups that are attached to a pentose sugar. In essence , ATP is critical for all life, from the simplest to the most complex of entity. An intricate nanomachine, ATP is at the epicentre of the design and biological functioning of the natural world we live in today.
Nearly all living organisms produce ATP through respiration. In humans, muscle and liver cells require a lot of energy in the form of ATP to function properly. Firstly, glucose is phosphorylated in the cytoplasm by the addition of two phosphate ions that are provided by the hydrolysis of two ATP molecules by ATPase during its glycolysis. This phosphorylation makes the glucose more reactive by lowering the activation energy for the enzyme-controlled reactions that follow. Phosphoryalted glucose undergoes several steps until pyruvate is formed. This enters the mitochondrion and is decarboxylated, and oxidised. During oxidation by dehydrogenase enzymes, pyruvate transfers its hydrogen ions and electrons to electron carriers, NAD and FAD. These carriers transfer electrons to the electron transport chain, thus providing energy for hydrogen ions are pumped into the inter-membrane spaces of the cristae via chemiosmois. This is used to create an electrochemical gradient that drives the proton motive force of the axial on ATP Synthase to form ATP as part of oxidative phosphorylation.
In the absence of oxygen, glycolysis continues to produce 2 net ATP molecules per glucose. This is not as efficient as aerobic respiration, and so more carbohydrate stores need to be broken down to provide enough ATP to meet the organism metabolic and physical needs. During anaerobic respiration, reduced NAD oxidises pyruvate to lactate in animals and ethanol (& CO2) in plants and fungi.
Contraction of muscles requires ATP. When a muscle is stimulated by an action potential, calcium ions bind to troponin, which causes tropomyosin to move away from the binding site on actin filaments. This allows the myosin heads to attach to the actin, forming cross bridges. The myosin heads change angle, causing the actin to move over the myosin. ATP attaches to the myosin head, causing it to become detached from the actin filaments. Calcium ions activate ATPase to hydrolyse ATP to ADP and phosphate ions, a process that releases energy for myosin heads to resume normal position and so, the reformation of cross bridges. When muscle stimulation ceases, calcium ions are actively transported back into the sarcoplasmic reticulum against their concentration gradient, using energy from the hydrolysis of ATP by ATPase. Contraction of the muscle sarcomere allows the contraction of skeletal muscle, allowing the animal to move.
In a very active muscle, oxygen is rapidly used up in respiration to produce ATP for contraction. It takes time for the blood to supply more oxygen quickly. Therefore, there needs to be a means of providing energy to maintain efficiency of muscles; particularly important if an organism escaping from predation. A molecule known as phosphocreatine is one that can rapidly generate ATP from ADP and inorganic phosphate in aerobic conditions. This molecule is in plentiful supply within fast-twitch fibres that produce powerful contractions over short periods.
On use of ATP is in the formation of a resting potential in nerve cells. Hydrolysis of ATP provides energy that is used to pump out three sodium ions and pump in two potassium ions into the axon of a neurone through a NA+/K+ATPase pump by active transport. A reduction of the membrane permeability to sodium ions maintains a resting potential of -70mV on the inside of the axon. This ATP is provided by respiring shwann cells that are densely packed with mitochondria. These cells span the length of a myelinated axon, except at the nodes of ranvier. Moreover, ATP provides the energy to move and fuse vesicles containing the neurotransmitter, acetylcholine with the pre-synaptic membrane (exocytosis) as well as providing energy for the re-synthesis of acetylcholine from ethanoic acid and choline.

Autotrophic organisms produce ATP during photosynthesis to produce their own chemical energy. The photolysis of water yields hydrogen ions and electrons. Together with the electrons, the hydrogen ions are used to reduce NADP in the light-dependent reaction in the thylakoid. This reduced NADP is used to reduce glycerate-3-phosphate, using energy from the hydrolysis of ATP, to form triose phosphate and then glucose in the stroma of the chloroplast. Hydrogen ions also play a role in the production of ATP in the electron transport chains. They are pumped into the inter-membrane space and generate an electrochemical gradient that provides energy for the activation of ATPase, which combines ADP and inorganic phosphate ions to form ATP by photo-phosphorylation.
Mutualistic nitrogen fixing bacteria in the roots of leguminous plants reduce atmospheric nitrogen to ammonium containing compounds such as protein, using energy from ATP. These compounds are taken-up by the plant, to which the bacteria has a mutualistic relation with, in exchange for carbohydrates.
All organisms use ATP as an immediate energy source for processes such as active transport. In plants, root hair cells have specific channels for ions such as nitrate and potassium. These channels have the enzyme ATPase which hydrolyses ATP and releases energy to absorb the ions against a concentration gradient into the cell. This movement into the cell from the soil lowers the water potential of the roots hair cells allowing water to enter by osmosis. Movement of this water then takes place via the symplast pathways and apoplast pathways. Active transport of the mineral ions into the xylem allows the water to enter the xylem by osmosis, generating a hydrostatic pressure called the root pressure. This creates a push, which together with the cohesion-tension, pulls water up the xylem in a column through the hollow lignified xylem vessels.

In this essay, I have outlined how ATP is mainly produced in organisms and some of its uses. There is no doubt that ATP is essential for the survival of organisms. It really intrigues me that with every keystroke I am taking of this computer, ATP is acting in wondrous ways to keep me functioning; from providing energy to help muscles in my hand contract and so allow me to type, to providing me with the energy to think of what word I am going to type next. The overwhelming application of ATP amazes me and I am proud to have been given the knowledge to understand the theory behind such a vital component to the finite mechanism that is life.

Reply 1881

kingsmod1

sorri guys but i do not understand why they use the sanger method and how that helps locate the bases they are lookin got, i mean if they didnt kno the bases they lookin for so then why are primers complemantary to it

many thanks!!!! :P

Reply 1882

Stirlo

Original post by cor_fortis

And I found that the question about IAA on the specimen paper was actually pulled from a 2003 paper of either the old spec or a different exam board. blasphemy

Yup, I found a unit 4 question where 2 marks were based solely on knowledge from the CGP revision guide, the stuff that you needed to say to get the marks wasn't even mentioned in Nelson Thornes

Reply 1883

AVERAGEJOE123

Original post by strawberry_cake

For the essay, if, say, we mention 3-4 topics from units 1,2 and 4, do we still 'have' to mention something from unit 5? Or does that not matter, since its synoptic? Thanks :smile:

Use information from the units that are relevant, they mark you on breadth so the more units you cover the better I guess. If you have mentioned from 1 2 and 4, you wouldn't HAVE to mention unit 5, but if there is relevant information in it then it would be advisable to put it in

Reply 1884

*QueenBeee

Original post by appleschnapps

Stem cells aw yeah.

They are unspecialised (which means you can bring them into an essay on specialised cells for contrast), they are constantly replacing themselves, and embryonic stem cells are totipotent. (This means they can mature into any type of body cell.) Adult stem cells, which are found in bone marrow, are multipotent - this means they can only mature into a few types of cells, and thus narrows their usage.

How they become specialised: certain genes are expressed, others are switched off, which means when transcription occurs only the mRNA from the expressed genes is transcribed, so only those selected proteins are produced - these proteins determine the cell's structure and its processes which make it suited for its function.

In plants, totipotent stem cells can be taken from the root or the shoot (hurray rhyming!), and will produce a genetically identical plant if the stem cell is placed in growth medium that contains growth factors and necessary nutrients, and kept in the right conditions (e.g. not too hot).

Stem cells can treat disease as they can be used to replace diseased or damaged cells, and has already been used to treat lymphoma and leukaemia. However, this is an application-y area as you need to consider the ethical viewpoints surrounding stem cell treatment.

+ Can save lives.
+ Improve quality of life.
+ embryos produced for IVF would otherwise be destroyed.
- Does an embryo have a right to life?
- Shouldn't use humans as a means to an end.
- Respect for human life - will human cloning etc. follow if we allow stem cell research?

Adult stem cells don't get as much criticism, but can't develop into as many types of cell as embryonic.

you my friend are a life saviour!! Amazzzing!
I understand it now - could you help me on muscles?? Its just the sliding filament theory - if youre busy then its fine
but seriously big big thanks!!!

Reply 1885

NRican

Original post by Reccoshai

Can someone please explain to me the use of reverse transcriptase and how it synthesisis cDNA from RNA? (any conditions please include) :smile:

Cells that produce required protein isolated, mRNA extracted for said protein, Reverse transcriptase attaches complimentary nucleotides to form a single strand of cDNA (c - complimentary) DNA Polymerase makes it double stranded DNA by attaching complimentary nucleotides.

Reply 1886

Sparkly-Star

Original post by rootcanal

I'm pretty sure we don't. Its not on the specification

*Phew* I was just reading over it thinking I will never remember that... :p:

Reply 1887

Jin3011

This is the first essay I ever did. Its rubbish but it may help =]

Importance of water!

Water is a simple molecule that is a vital entity in sustaining life on earth. It covers two-thirds of our planet and for millions of years has played an integral role in the biological process and ecology of organisms; from the first photosynthesising body to the weird and wonderful that roam the planet today.
Water (H2O) is a polar molecule. Its polarity is brought about by the electronegativity of oxygen, that is, its affinity to draw electrons away from hydrogen atoms in a in a covalent bond within the molecule. This results in hydrogen being electropositive, possessing a small positive charge. The electronegative oxygen and electropositive hydrogen of adjacent water molecules therefore attract one another, forming weak hydrogen bonds.
This polar nature of water makes it a good universal solvent. This is important for transport in an organism. In humans, blood is used to transport material around the body whereas sap is used to transport substances in plants. Blood is vital in transporting oxygen, glucose, vitamins and minerals to the tissues and carbon dioxide (and other waste products) from the tissues. It also facilitates the transport of hormones, to control various organs and acts as a buffering agent to regulate pH of body fluids. Both these mediums of transport are mainly composed of water: as this is the solvent that can dissolve the products to be transported.
During sexual fertilisation, a male sperm cell must reach a female sex cell, the ovum, in order to fuse to produce a zygote, which will develop into a new individual. The sperm is often transported in a fluid medium known as semen, which contains mostly water. The many rich complex inorganic and organic substances are dissolved in the water, the semen constituent, which provide nutrients to the spermatozoa and allow it to move. The foetus also develops in a water-filled sack, which provides thermal stability.
Water evaporates from the sea and condenses back to the earth as rain. Plants can absorb the water from the soil by actively transporting mineral ions into their root hair cells against a concentration gradient, , using energy supplied by ATP, to lower water potential. The lower water potential in the root hair cells now draws in water, which moves towards the endodermis through the apoplast and symplast pathways. The water is forced up the xylem through the generation of a root pressure by the pumping of ions into the xylem to lower water potential. Evaporation of water through, the stomata on the underside of the leaf draws water up the xylem by cohesion-tension creating a transpiration stream that returns the water to the atmosphere.
Xerophytes are specialised plants that are adapted to survive in harsh drought-stricken conditions and so, are at a selective advantage. They do this by limiting water loss by transpiration. A cacti for e.g is a xerophytes that has needle-like leaves that provide a reduced surface area to volume ratio. According to flick’s law this slows down the rate of diffusion and so the loss of water is considerable reduced.
In addition, plant cells have a strong cellulose cell wall. This prevents the cell bursting by the osmotic entry of water. It does this by exerting an inward pressure that stops further influx of water, causing living plant cells to become turgid: making herbaceous parts of a plant semi-rigid. This helps maintain stems, and leaves in a turgid state so that they can provide the maximum surface area for photosynthesis.
Moreover, water absorbed is essential for plants and several other autotrophic organisms to carry out photosynthesis; therefore, limiting supplies of water will limit the rate of photosynthesis and hence productivity, although only small amount are needed. The equation for photosynthesis: h20 + co2 -> c6h12o6 + o2. In the light dependant reaction that occurs in the tylakoid of chloroplast, water is split into oxygen, hydrogen ions and electrons. These electrons replace those lost to the electron-transport system by chlorophyll molecules in photosystem II. The hydrogen ions reduce the coenzyme NADP to NADPH2, which is used in the Calvin cycle to reduce glycerate 3 phosphate into triose phosphate using energy from the ATP that is also synthesised in the light reaction. Glucose, a photosynthetic product, can be used as a respiratory substrate for autotrophs. Consequently, enzymes can condense sugars to more complex polysaccharides that incorporate into autotrophic biomass, which in turn can be broken down by digestive enzymes to provide chemical energy to primary consumers that feed on them. The oxygen released in photolysis of water is also vital to life, as it is required for all organisms that respire aerobically.

Animals also use the water they drink to transport hydrophilic substances such as glucose through their blood. Inevitably, although water is lost to the environment by animals, this loss comes with physical benefits (providing that an organism has enough water left within them to sustain life). Water is lost as sweat when used to regulate body temperature through the evaporation from the skin. This temperature maintenance helps optimise enzyme activity and thereby regulate metabolism. Loss is also through excretion of water from the bladder as concentrated urine; produced by the kidneys to remove the metabolic waste product, urea. Moreover, water is lost through the exchange surface of the lungs when exhaling (Co2 is also lost to the atmosphere at the exchange surface).
Insects also lose water through spiracles that are gas exchange pores in their rigid outer skeleton. Insects such as woodlice display a behaviour called kinesis that ensures they spend a greater amount of time in dark, moist conditions that aid in their survival. Conditions need to be moist in order to reduce the diffusion gradient of water between the atmosphere and their body surface, so that less water evaporates. If they are exposed to high temperatures, they randomly move and turn direction rapidly until they can identify an optimum environment. Kinesis prevents them dying from desiccation and predation.
Marine and freshwater ecosystems provide habitats for a diverse range of organisms. Water freezes at low temperatures to form ice. At low temperature, water molecules have less kinetic energy and therefore the molecules move less and expand to accommodate more hydrogen bond formation, thereby producing the ice structure. Ice is less dense than water and so floats. As water freezes from the top down, it provides a habitat, above and below the ice, thereby allowing organisms that are adapted for this type of environment to survive.
Human activities such as the burning of fossil fuels and deforestation over the past few decades have led to an increase in atmospheric carbon dioxide concentrations. Co2 is a greenhouse gas and therefore traps infrared radiation from the sun, which ultimately leads to an increase in the average earth temperature. The consequences of this global phenomenon are diverse in that polar ice caps are melting, changing the environment for organisms that are adapted for arctic conditions. The increased sea levels may cause flooding of low-lying coastal land, increasing the salination of soil, but decreasing the concentration of salt in sea. These changes will act as selection pressures on organisms, forcing the process of natural selection. Those members of a given species that are best adapted to survive the changes are more likely to survive and pass on their beneficial alleles to their offspring. In this way, the allele frequencies may change, ultimately altering the phenotypes. For example, salination of soil causes by coastal flooding would favour xerophytically adapted plants, as the reduced water potential in the soil would make it hard for the plant to take up enough water for its needs.
Having outlined several principles, showing how vital water is to life, has really increased the nervous impulses being signalled around my brain. I am enthralled by the limitless application of such a simple molecule composed of 3 atoms. Water, with its intricate complexities, has infinite value in biology. Being an organism, I can say I am proud to understand what I am fundamentally composed of. I am confident that for years to come, scientists will put forward more theories, in an attempt to unravel greater mysteries, far beyond our current comprehension, of the pandoras box that is the h20 molecule.

Reply 1888

shirin123

why u writinnngg so biggggggggg

Reply 1889

Tericon

Original post by flowerscat

Restriction mapping: using Fig 4 and 5 on page 269 of NT book.

Aim: Trying to find out how the DNA fragments are linked to each other, and what restriction sites separate them (imagine you are sequencing a chromosome and want to find out how the pieces of the DNA go back together once you have cut it with restriction enzymes for sequencing).

Method: Cut the DNA with each of the individual enzymes - run on a gel - this tells you how many restriction recognition sites there for each enzyme in the DNA.

Take 3 restriction enzymes. Start mixing them together in pairs, then using them for digest. Run on a gel.

Now using the first combination of enzymes, lay out the pieces that you get (90 kb + 10 kb). One cut must be due to BamH1 and the other due to HindIII. Since one of the fragments they generate is 10kb, then two sites must be quiet close to each other.

Look at the way the DNA has been cut by the set combination of enzymes - they will overlap with the first sample, but the "cuts" will be in different sections. (60 kb + 40 kb) As these fragments are smaller than 90 kb, Not I must be between BamH1 and HindIII

Do the same with the third. (70kb and 30 kb). Because of the 30 kb fragment, the only way the jigsaw will fit is if Not1 is closer to BamH1 than HindIII.

The easiest way to figure this out if you draw a circular loop of DNA and try and account for all the bands in the gel. You will see that there is no other way the jigsaw can fit together.

Thanks

That helped a lot, I like the whole metaphor of a jigsaw :smile:

I don't have that book, just CGP revision guide, and our college don't use it either because our teacher co-wrote the Collins book and wouldn't want us using anything other than that :rolleyes:

Reply 1890

angel1992

can someone explain the difference between a dna probe and primer? they both are the same things>> so cant one do the job of the other

Reply 1891

flowerscat

Original post by Sparkly-Star

Very likely, it's the biggest chapter of all. I really hate it too. :frown:

Just a question, do we need to know about cystic fibrosis and the CFTR gene annd adenoviruses?

I think you would need to understand cystic fibrosis and what damage it causes to the cells and possible routes of treatment i.e. how gene therapy can help since it is an inherited condition.

Reply 1892

Tericon

For gene sequencing, how do you know what primers to add to the mixture if you don't know the sequence of bases?

Reply 1893

Sparkly-Star

Original post by flowerscat

I think you would need to understand cystic fibrosis and what damage it causes to the cells and possible routes of treatment i.e. how gene therapy can help since it is an inherited condition.

I know about the gene therapy but not the specific bits of cystic fibrosis and SCID too actually.

-----

Those are huge essays. I could never do that!

Reply 1894

Jin3011

Original post by angel1992

can someone explain the difference between a dna probe and primer? they both are the same things>> so cant one do the job of the other

Dna probe is a short radioactively/fluorescently labelled single standed section of DNA that has complementary bases to those of the gene we are trying to locate.

Primes are short single stranded sections of DNA that have complementary bases to those at one end of each of the two DNA fragments. They start the process of DNA synthesis as DNA polymenrase can only act on double stranded DNA. They also prevent DNA fragments from rejoining.
(I think)

(edited 12 years ago)

Reply 1895

stressedatschool

im not really sure about the difference, our teacher just mentions you use primers with PCR but not what they do. DNA probe is used to find a specific sequence of DNA, it identifies it because the probe is labelled with fluoresence or radioacitve. What do you think a primer is?

Reply 1896

Sparkly-Star

Original post by Tericon

For gene sequencing, how do you know what primers to add to the mixture if you don't know the sequence of bases?

You just need to know that a primer is added, I don't think you need to know why. They probably know the end and begin of a DNA strand cos that's where the primers anneal and all that.

Reply 1897

Tericon

Original post by angel1992

can someone explain the difference between a dna probe and primer? they both are the same things>> so cant one do the job of the other

Yes they are essentially the same, but probes are labelled, (so you can identify if the hybirdisation has taken place) whereas primers aren't. Another difference is in their function, Probes = looking for a target gene, Primers = triggering hybirdisation in gene technology.

Reply 1898

Jin3011

Original post by Tericon

For gene sequencing, how do you know what primers to add to the mixture if you don't know the sequence of bases?

lol don't think about that too much. I spent ages trying to get my head around it but then figured that they may have done other sciency sort of things to determine the base sequence initially.

Reply 1899

flowerscat

Original post by stressedatschool

That my problem, with all the gene technology stuff, why do you used restriction endonucleases to 'cut' the fragment when you are going to sequence it, how do you know what restriction endonucleases to use?!
Also, are neurotransmitter's hormones?
Thanks guys! So nervous!
xxx

- because larger fragments are harder to sequence, and lead to more errors

what restriction endonucleases
- trial and error - you want it cut to reasonably-sized chunks, but not into really small fragments or they will be hard to put back together. Think of it like a jigsaw, the smaller the pieces the harder it is to figure out how they go back together.