Genetic variation, diversity. ( :

All members of the same species have the same genes. Organisms differ in their alleles. It's the combination of alleles that the organism has that makes indivaiduals within a speicies, different from one and other. The greater the number of alleles all the memebers of that species have, the greater the genetic diversity.

Factors that influemce genetic diversity:

• Selective breeding
• The founder effect
• Genetic bottlenecks

Selective Breeding - Deliberatley picking out offspring with desired characteristics, and using them to parents the next generation so that these alleles are more likely to be passed forward. Members of the species without these characteristics are made unable to continue breeding so that only the desired characteristics are carried forward.

Genetic diversity: Caused in differences in alleles.

Genotype: The alleles you have for a particular gene.

Factors that reduce genetic diversity: Selective Breeding, The founder effect, genetic bottlenecks.

Factors that increase genetic diversity: Mutations, different alleles being introduced by migration.

Selective breeding, unwanted alleles bred out of population. Reduced genetic variation.

The founder effect: Part of the population colonises elsewhere, only certain alleles go, therefore, genetic diversity decreases, due to the changed frequency of alleles.
Can eventually create completely different species.

Genetic bottlenecks: Something reduces the population to a really small number. Some alleles, are, therefore not carried on. This means that some trait s are lost, and genetic diversity is lost.

Variation: continuous, discontinuous. In continuous, it is controlled by multiple genes, affected by the environment, and there are a large range of phenotypes. With discontinuous, it is controlled by a single gene, it is less affected by the environment, and there is a small range of phenotypes.

DNA shizzz.

Every cell in body is identically, genetically. When they specialise, some of the genes are switched on, and some switched off. Different genes produce different proteins and enzymes and therefore, different characteristics.

Sequence of bases in protein synthesis of amino acids wihch makes up the proteins.

DNA Strands are held together by H bonds. Double structure: support, protects bases.

Semi conservative replication: New DNA molecules after replication has one strand on old DNA, one new.

What is meant by specific base pairing? When each base only pairs with one other base known as complimentary. E.G. Guanine and Cytosine.

Why is specific base pairing important? It allows identical/exact copies of DNA to be made, both strands act as templates, and complimentary bases pair alongside both strands.

2 Features of DNA that make it stable are: The large number of Hydrogen bonds, there is a strong sugar phosphate backbone, and the coiling and two strands reduce the chance of damage to the bases.

DNA Polymerase joins the bases. Replication takes place in INTERPHASE.

Semiconservative Replication: Both strands acts as template to make two complimentary copies, the daughter DNA is one new strand, (free nucleotides), and one original.

Differences in DNA and RNA: DNA has Deoxyribose, RNA has Ribose. DNA contains the bases T, A, C and G. RNA Contains the bases A, U, G and C.

The DNA strands separate then the hydrogen bonds between them are broken. Each strand forms a template, and a new strand is built alongside it from free nucleotides, depending on the solution it is in. If, for instance, it contained radioactive thymine (the solution), it would be complimentary to the adenine on the the old, non radioactive strand, and would form bonds with it. This means the new strands in the new DNA molecules are radioactive.

A random note I found on mitosis.

What is a clone?
A genetically identical offspring.

After replication of DNA, a chromosome appears as a double structure, consisting of two chromatids, held at a region called a centromere.

Interphase = A growth phase.

• Mitosis is always preceeded by interphase, a period when the cell is not dividing.
• The cell is very active: growing + synthesising proteins.
  
• The cell copies it's DNA, DNA replication takes place.
  

Metal Extraction Equations.

Aluminium

Al3+ + 3e- => Al
2O- => O2 + 4e-

Molten aluminium oxide, Cryolite, High temperature+current.


Copper

CuCO3 => CuO + CO2
2Cuo + 2C => 2Cu + 2CO

High temperatures.


Iron

C + O2 => CO2
CO2 + C => 2CO
Fe2O3 + 3CO => 2Fe + 3CO2

Blast furnace, Coke is burnt, produces CO2 (first equation). This is exothermic, causes temperatures of 2000K. The CO2 reacts with more carbon to form carbon monoxide, which acts as a reducing agent to the Iron Oxide.


Tungusten

WO3 + 3H2 => W + 3H2O

High temperatures. Risk: Using hydrogen gas in reaction, very reactive/volatile.


Titanium

TiO2 + 2C + 2Cl2 => TiCl4 + 2CO (1713K)
TiCl4 + 4Na => Ti + 4NaCl (1300K, Inert argon atmosphere.)

Correct me if I'm wrong. (:

Mitosis/Meiosis and that.

Mitosis takes place for growth, repair, and in mitosis, a diploid cell produces two haploid cells. The diploid number in humans is 46, the haploid number is 23. Also, in meiosis, cells produced are genetically different.

Diploid = Homogulous pair of chromosomes.
Haploid = One Chromosome.

Stage of meiosis: PMAT
P - Prophase
M - Metaphase
A - Anaphase
T - Telephase.

Homogulous pairs are the same size, shape and carry genes controlling the same characteristic within the same locus.

A cell with pairs of homogulous chromosomes is called a diploid.
A cell with one chromosome from each homogulous pair is a haploid.

Haploid -> Haploid = Mitosis
Diploid -> Diplois = Mitosis
Diploid -> Haploid = Meiosis.

Meiosis increases variability of genes.

Independant segregation causes different combinations in humans. 23 Chromosomes, Two to the power of twenty three different chromosomes = how many different combos there are.

Chemotherapy drugs interfere with metaphase, mess up spindle formation.

Genetic Variation in BACTERIA ^__^

The genetic material in bacteria is the same as in other organisms: DNA. They increase their speicies diversity via mutation, ad conjugation.

Mutations result in different characteristics. Bases can be deleted, replaced, or added. Three bases code for one amino acid, (the triplet code) and therefore, any change in this sequence of bases will change what amino acids are sythesized. Since animo acids make polypeptide chains, and from there, proteins, and proteins define characteristics, characteristics can be changed.

Conjugation takesplace between bacterial cells. One cell produces a thin projection that meets the oher cell, and a conjugation tube forms. The cell donating replicates a plasmid of DNA, The circle shape of the plasmid breaks, and it passes along the conjugation tube. Contact between the cell is brief, and only a portion is exchanged, which means the recipient cell gets new characteristics.

So, wait, let me get the hang of that one. :P

First, the small projection is made from one of the cells, which connects to another cell and forms a conjugation tube. The cell donatiing then replicates it's plasmid of DNA, the circle shape is borken so it is linear, and it then passes through the conjugation tube. This connection is only for a limited time so only a portion of DNA is given. The receiving cell gains new characteristics.

(One thing I've learnt from almost a year of AS Biology, is that I really rathher dislike the word 'characteristics', much sorrys if there about 41 different spellings of it throughout. xP)

Annnnnd again.

1) Cell produces projections, which connects to other cell. This forms a conjugation tube.
2) The donating cell replicates a plasmid of DNA.
3) The circle shape is broken, and it becomes linear, and passes through the conjugation tube.
4) The connection is only for a limited amount of time, and therefore, only a portion of DNA is given.
5) The receiving cell gets new characteristics.

You may also hear about 'Horizontal' and 'Vertical'. Horizontal is Conjugation. Where characteristics are passed from species to species (across ways). Vertical is characteristics being passed via generation (down ways).

Hiiii ^_________^

So, the next couple of posts down are all the notes I have on my laptop involving unit 1 biology.

If any of you are retaking, I'd recommmend reading through them, as they're fairly thorough, and they cover the textbook questions too. I basically just went through each nelson and thornes chapter. It was from the time I was revising for them myself, and they helped me come out with an A, so hopefully, they'll help you lot out too.

^_^ <3

Cholera

Cholera:
A prokaryotic cell is a cell with no true nucleus and no membrane bound organelles. It is different from a eukaryotic cell, as the eukaryotic cell does have a nucleus, and contains membrane bound organelles. Prokaryotic have circular DNA, whereas eukaryotic have chromosomes.
When cholera bacteria (taken in through water) get to the small intestine.

Active Transport

Active Transport:
Active Transport is the movement of molecules or ions in or out of a cell against a concentration gradient using energy and carrier molecules.
Active transport requires ATP, to directly move molecules, as opposed to relying on their kinetic energy like in passive transport. It also requires a concentration gradient; otherwise the molecule will not move from an area of low concentration to high.
1) State one similarity and one difference between active and passive transport: Active transport requires ATP whereas passive does not. Both active transport and passive involve getting molecules or ions in or out of cells.
2) The presence of mitochondria in cells that carry out active transport is necessary, because the mitochondria produce ATP, which is energy, and energy is required in active transport, as molecule need to be moved directly, and not by their own kinetic energy. So cells that use this process, would therefore need lot of mitochondria as they need lots of energy.

Absorption in the Small Intestine:
The villi and microvilli increase the surface area, and an increased surface area is a factor that increases the rate of diffusion. They are very thin walled, which makes a shorter diffusion distance, which also increases the rate of diffusion; they are well supplied with blood vessels so they can transport absorbed materials away.
The products or carbohydrate digestion are absorbed in the small intestine… As they are being digested constantly, there is normally a greater concentration of glucose in the small intestine then in the blood. There is therefore, a concentration gradient, which glucose diffuses from the small intestine to the blood. The blood is always being circulated by the heat, and so the glucose is removed by the cells on it’s way round, and this helps to maintain the concentration gradient.
Sodium ions are actively transported out by a sodium potassium pump, into the blood and the potassium comes in. There is then a higher concentration of Sodium in the lumen of the gut then in the epithelial cells, which creates a concentration gradient. They pass into the epithelial cells through co-transport proteins, and couple with a glucose molecule on the way. The glucose then goes into the blood via facilitated diffusion.

1) A glucose concentration gradient is maintained, as carbohydrates are constantly being digested, and this means there will always be a high concentration of glucose in the lumen of the small intestine. The heart is also always circulating blood, which means that the blood rich with glucose will be being pumped round and the glucose will be getting used in cells for respiration, keeping the concentration of it in the blood low.
2) Co-transport is used to describe the transport of glucose into cells as it relies on the Sodium ions going from the lumen of the gut to the cell for it to be able to pass into the cell, it wouldn’t do it on its own.
3) Sodium moving out of the epithelial cell is active. Sodium moving into the cell is passive. Glucose moving into the cell is passive.

Osmosis

Osmosis:
Osmosis is the passage of water from a region of higher water potential to a region of lower water potential through a partially permeable membrane.
The water potential of pure water is zero.
Water potential affects movement, as it will cause water to move from an area of high water potential (the highest being zero) to an area of lower water potential (the more negative value).
With an animal cell, if the water potential outside is higher, then water will enter the cell and it will swell and burst. If the water potential is the same, no water will move in or out. If the water potential outside is lower, water leaves, and the animal cell shrinks.
With a plant cell, the cell wall makes it slightly different. When the water potential outside is higher, the water enters the cell, the protoplast (inside bit) swell, and pushes up against the cell wall. The cell is said to be turgid. If it is the same, no water enters or leaves, but the protoplast is slightly pulled away from the wall. If the water potential outside the cell is lower, then water will leave the plant cell, and the protoplast will shrink and become plasmolyzed.

Diffusion

Diffusion:
It is the net movement of molecules or ions from a region where they are more highly concentrated, to a region where they are less concentrated.
It occurs when there is a high concentration of molecules/ions in one place and less in another, and, through random movement, the particles spread out evenly over time, under the concentration is in equilibrium.
The factors that affect the rate of diffusion are: Concentration Gradient (The greater the difference, the faster the rate), Area over which the diffusion takes place (The larger the area of an exchange surface, the faster it can take place), and the thickness of the exchange surface (the thinner the exchange surface, the faster the rate of diffusion.)
The nature of the plasma membrane can also affect it. How many pores it has and how it is composed, etc. The size and nature of the molecule diffusing affects it too. Smaller ones go through quicker, and lipid soluble ones go through faster then the water soluble ones, as they can pass straight through the membrane, and not a protein.
Facilitated diffusion differs from simple diffusion in that it only occurs at specific points down the membrane, where there are special protein molecules. They are filled with water and allow water soluble molecule and ions to pass through. These channels only open to specific molecules. If that substance is not present, it remains closed. This means there is control over what goes in. Carrier proteins can also be used. When the right proteins show up, it bind to the carrier protein, and changes its shape in a way that releases it to the inside.

1) Three factors that affect diffusion are: Surface area (if there’s a large surface area, the rate of diffusion is quicker.) The thickness of the membrane/diffusion distance (the thinner it is, the quicker the rate of diffusion.) Also, there is the difference is concentration. The greater the distance, the faster the rate of diffusion.
2) Facilitated diffusion differs from diffusion in that it only occurs at certain points along the membrane, and involves proteins, whereas simple diffusion only uses the phospholipids.
3) Facilitated diffusion is passive because it only uses the kinetic energy of the molecules involved; it doesn’t involve anymore being produced then what it already has.

Lipids, Cell surface membrane, etc.

Lipids:
Triglycerides are formed by a condensation reaction. Each fatty acid forms a bond with glycerol, and a water molecule in taken away on each, (Condensation reaction.) Hydrolysing a triglyceride is therefore, going to form glycerol and three fatty acids.
Fatty acids can vary by how saturated they are. If there are no double bonds it’s described as saturated as all of the carbons are linked to the maximum possible number of hydrogen atoms. If there is a single double bond it is mono-unsaturated, and if there is more then one double bond it is poly-unsaturated.
The structure of phospholipids is similar to lipids, except one fatty acid is replaced by a phosphate molecule. The fatty acids repel water (hydrophobic) but the phosphate molecules attract water (hydrophilic). Therefore, the phospholipids are made up of a hydrophilic head and a hydrophobic tail. This makes them polar, which means the have two ends that behave differently. In water, the hydrophilic end gets as close to the water as possible and attracts it, and the hydrophobic end goes as far from it as possible.
A presence of lipids is identified by the lipid emulsion test, and this is carried out by putting 2cm3 of the sample in a test tube with 5cm3 of ethanol, and shaking, to dissolve any lipid in the sample. You then add water and shake, and if a cloudy white emulsion is formed, then a lipid is present.
1) Fats and oils make up a group of lipids called triglycerides which, when hydrolysed, form glycerol and fatty acids. A fatty acid with more then one carbon –carbon double bond is called poly-unsaturated. In a phospholipid, the number of fatty acids is two, and these are described as hydrophobic because they repel water.
2) State two differences between a triglyceride and a phospholipid: a triglyceride has three fatty acids, whereas a phospholipid has two. The phospholipid is polar, and contains a phosphate molecule, whereas the triglyceride is not, and does not do either.
3) Because when oxidised, lipids produce almost twice the amount of energy the same amount of carbohydrate would, and if something is moving, it needs more energy released, so lipids are more efficient.

The Cell Surface Membrane:
The structure of the cell surface membrane is a bi-layer of phospholipids. One layer has all the hydrophilic heads pointing inwards, the other has them pointing outwards. The hydrophobic tails point inwards on both, protected from the water on both sides. It also contains proteins, intrinsic and extrinsic.
The function of the phospholipids in the membrane are to are to allow lipid soluble substances access to the cell, and to prevent water soluble molecules from having access. It also makes it flexible.
The proteins are there it add strength to the cell, and to act as carriers for water soluble molecules across the membrane. They form ion channels so active transport for sodium/potassium, etc, can take place. They form recognition sites by identifying cells, and act as receptors, for example, for hormones.
The fluid mosaic model is the way of explaining how all of the components of a membrane come together. It is fluid, because the individual phospholipid molecules can move, relative to each other. This makes the membrane flexible and constantly changing in shape. It is mosaic, because the proteins embedded in the bi-layer can vary in size and shape, much like the stones in a mosaic.

1) The overall function of cell surface membrane is to control the movement of substances and the conditions in and out of a cell.
2) The hydrophobic end of the phospholipid molecule towards the inside of the cell surface membrane.
3) A molecule that is soluble in lipids is likely to pass the phospholipids to get in and out of the cell. A mineral ion is water soluble, so it is likely to enter and exit the cell via an intrinsic protein (carrier).
4) It should be small and lipids soluble if a drug water to get through a cell surface membrane quickly.

Structure of an Epithelial cell.

Structure of an Epithelial Cell:
Nucleus: The function of a nucleus is to act as the control centre of the cell, by producing mRNA, and therefore, protein synthesis. Also, to produce ribosomal RNA and ribosomes, and retain the cell’s genetic material in the form of DNA and chromosomes.
Its structure aids this, as it has the nuclear envelope, which is a double membrane, where all the reaction take place in the nucleus, it controls what goes in and out of the nucleus, and it connected with the endoplasmic reticulum, and has ribosomes on it. It has nuclear pores, to allow large molecules out, such as messenger RNA. It has nucleoplasm, the material that makes up the bulk of it, jelly like. It contains Chromatin (the nucleoplasm) which contains DNA, as it is the diffuse form that chromosomes take when the cell is not dividing. The nucleolus is a spherical body within the nucleoplasm which makes ribosomal RNA and ribosomes.
Mitochondrion: Function is to produce ATP for respiration from carbohydrates. The structure applies to this function as it has a double membrane, the outer controls what goes in and out, and the inner is folded to from Cristae, which increase the surface area, so more can be taken in, and provide a large surface area for the attachment of enzymes. The enzymes involved in respiration are found in the matrix of the mitochondria, and this is where they produce their own proteins (control it).
Endoplasmic Reticulum: Function of the rough one is to provide a large surface area for the synthesis of proteins and glycoproteins, and to provide a pathway for the transport of materials through the cell. The smooth one store and transport lipids, and store and transport carbohydrates.
It spreads through the cytoplasm of the cell and is continuous with the nuclear membrane. Large sheet like membranes = large surface areas for storage. Often have larger ER’s in cells like secretory cells which contain and store large amounts of carbohydrates, proteins, and lipids.
Golgi Apparatus: Add carbohydrates to proteins to form glycoproteins. They produce secretory enzymes, such as those secreted by the pancreas (pancreatic amylase,) to secrete carbohydrates, to transport, modify, and store lipids, and to form Lysosomes. The structure relates to this because: It’s made up of stacks of flattened sacs, or cisternae, with small rounded structures called vesicles. Proteins and lipids produced by the endoplasmic reticulum pass through in a sequence, and the golgi modifies them, then ‘labels’ them, so they can be accurately sorted and sent to the right places. Once sorted, they are put into vesicles and transported the vesicles can move to the cell surface where they can release their contents to the outside.
Lysosomes form when the vesicles of the Golgi apparatus contain enzymes like lipase and protease. Up to 50 enzymes can be in a lysosome. They isolate them and either releases them outside, or in a phagocytic vessel. They break down cells after they die, break down worn out organelles release enzymes to the outside of the cell to destroy material around it, and break down materials ingested by phagocytic cells.
Microvilli: finger like projections that increase surface area.
You can relate the cell ultra structure to the function by indications such as how many of a certain organelle it contain, like if there is a lot of mitochondria, as they produce ATP, it would be thought that, needing a lot of it, that cell has a high metabolic rate.
1) Ribosomes are important in protein synthesis.
2) Three carbohydrates absorbed by the epithelial cell of the small intestine are Glucose, Galactose, and Fructose.
3) A) It posses structures called Cristae = Mitochondria. B) It contains chromatin = nucleus. C) Rough Endoplasmic Reticulum. D) It digests worn out organelles = Lysosome.
4) A sperm cell would have a well developed nucleus, as, to fertilise, it give DNA in the form of chromosomes, which is in chromatin in the nucleus, so this would have to be developed. Also, it would need mitochondria, as it moves using a flagellum, and the beating of this pushes it forward, but it would need an energy source, which mitochondria have, in the form of ATP, so it would have a lot of these, as it is almost in constant motion.
5) It would have a developed golgi apparatus, as these are what produce Lysosomes, and it needs lots of Lysosomes, as Lysosomes break down the material that phagocytic cells such as white blood cells, ingest.
6) Liver cells that manufacture proteins and lipids at a rapid rate would need a developed endoplasmic reticulum, as the rough deals with synthesising proteins, and the smooth synthesises lipids, and it would also need a developed Golgi Apparatus, as the golgi apparatus stores, modifies and transports proteins and lipids.

Electron Microscopes and all that jazz.

The electron microscope:
Electron microscopes work by using a beam of electrons, instead of light, as they have a shorter wavelength and with will give them a higher resolving power.
Differences between Scanning Electron Microscope and Transmission Electron Microscope are the TEM sends a beam of electrons through a thin section of the specimen. Parts of it absorb the electrons and appear dark, and parts of it appear light, as they allow the electrons to pass through and an image is produced. With the SEM, A thin section is not needed, as the electrons are not made to penetrate the sample. Instead, the electrons are directed onto the surface, and go over the surface in a pattern, gaining a 3D image, because of the way the electrons end up scattered over the contours of the surface. The SEM, however, has a lower resolution then the TEM.
The limitations of the TEM are that you have to have a thin sample, and it must be in vacuum, so no living specimens can be used. The image may contain artefacts, things that enter through the prep process, which wouldn’t be in the real cell. Also, there is a complex staining process, but the image is still only in black and white.
The limitations of the SEM are the same as the limitations of the TEM, (staining process, artefacts, in a vacuum), but it doesn’t have to be extremely thin, as the electrons are on the surface and don’t penetrate the sample.

1) The electron microscope is able to resolve objects better then a light microscope, as it has a shorter wavelength, which means it have a greater resolving power.
2) The specimens in an electron microscope must be in near vacuum to be viewed effectively, as the electrons can be absorbed my molecules in the air, and without the electrons, a picture could not be created.
3) A light microscopes resolution isn’t very good, therefore it could probably see a bacterium or a plant cell, the TEM has a resolution on 0.1nm, so you could see all of them with it (Plant cell, DNA Molecule, Virus, Actin Molecule, and a Bacterium.) The SEM has a resolving power 20nm, so you could see the plant cell, the virus and the bacterium.
4) The resolving power of an electron microscope cannot always be achieved as the preparation process of the sample can be quite problematic, and can cause difficulties.
5) Image = 25mm, Actual = 5um, Magnification =25000/5 = x5000

Resolution and stuff

Resolution is (resolving power) refers to microscopes, and is the minimum distance two objects can be apart for them to appear as separate objects.
Cell Fractionation is when cells are broken up and the different organelles they contain are separated out.
The tissue being separated must be put in a solution that is cold, isotonic, and buffered. It is cold so that any enzyme activity that could damage the organelles is stopped. It is isotonic to keep the water potential equal, to stop any organelles from bursting or becoming plasmolyzed when water is osmosed in. It is buffered to maintain a constant pH.
Ultracentrifugation is the process of how the fragments (after the solution has been homogenised [chopped up]), are filtered and separated. The ultracentrifuge (machine) spins test tubes of homogenate (chopped up tissue) at high speeds. This means the heaviest organelles are forced to the bottom of the test tube, and they form a sediment. The supernatant (fluid above this bit), it removed, and spun again at a faster speed, so the next heaviest are forced to the bottom of the tube. This is carried on until all the organelles are separated, always increasing in speed.
Cold: To stop any enzymes from working that could damage the organelles. Isotonic: To keep equal water potential, to prevent organelles from becoming turgid, or plasmolyzed. Buffered: To maintain a constant pH.
1) Magnification is increasing the size or an image, whereas resolution is the minimum distance apart two objects can be for them to be seen as separate under a microscope.
2) Magnification= Image / Actual. Therefore, Magnification = 1000 / 5 = x200
3) Image= Actual x Magnification = 25 x 400000 = 10000000, convert into mm = 10mm
4) Actual = Image/Magnification = 6 / 12000 = 0.0005mm or 0.5 um or 500nm
5) To get a sample of chloroplasts from a plant cell you would have to spin it for ten minutes, but at a gravitational force in-between 1000 and 3500, so probably around 2150.
6) Magnification = 10000, Image= 20mm, therefore, actual size is 20/10000, or 0.002mm. If magnification was 1000000 and the image was 25mm the actual size would be 25/1000000, or 0.000025 mm
7) A) Nuclei. B) Lysosomes. C) Mitochondria, Lysosomes, Ribosomes. D) Ribosomes.

Magnification

Investigating the Structure of Cells:
Magnification is how many times bigger an image is then the actual object it is capturing. IAM, I=A times by M. You can put this into a triangle. I is Image, A is Actual Size, and M is Magnification.
Magnification = Size of an image, divided by the size of object.

I = image, A= Actual Size, M= Magnification.

Always convert the units so that they are the same, usually
change the bigger unit into the smaller one.

Enzyme Inhibitors

Enzyme Inhibition:
Competitive inhibitors bind to the active site of the enzyme. They have a shape similar to that of the substrate, which allows them to fit the active site of the enzyme. If the amount of substrate is higher then the amount of inhibitor though, as the inhibitor doesn’t stay there, it when it goes, the active site it leaves empty has to be filled, and if the substrate concentration is higher, the active site is more likely to be filled by a substrate as opposed to an inhibitor. Therefore, competitive inhibition can be overcome.
Non-competitive inhibitors attach to the inhibitor at a site other then the active site. When it attaches to the enzyme, it changes the shape of it, and the shape of the active site, so a substrate cannot occupy it, therefore, the enzyme can’t function. The substrate and inhibitor are not competing for the same site, so an increase is substrate will not affect it, so it cannot be overcome.
Enzyme inhibition is when substances directly or indirectly interfere with the functioning of the active site of an enzyme and thus, reduce its activity.
1) A competitive inhibitor enters the active site, as it is about the same shape as the substrate, and it blocks a substrate from entering. It can be over come, though, if the substrate concentration is increased. A non competitive inhibitor enters the enzyme at a site other then the active one and therefore, the substrate concentration cannot affect it, as they aren’t competing for the same site and they can’t be over come. By enter at another site, they change the shape of the enzyme, and therefore, the active site, so no more enzyme substrate complexes could be formed and no more products would be made.
2) You could tell if a inhibitor was competitive or non competitive by increasing the amount of substrate, as an increase in substrate only affects competitive inhibitors, so they would be non competitive if nothing happened.

Factors Affecting Enzyme Action

Factors affecting enzyme action:
An enzyme controlled reaction is measured by it’s time course. The time it takes for a certain event to happen. There are two common events usually measured, the formation of the products of the reaction, or the disappearance of the substrate in the reaction.
Temperature affects the rate of an enzyme controlled reaction as it increases the kinetic energy, which makes the molecules move around more and collide more rapidly. This means the enzyme and substrate come together more frequently to form enzyme substrate complexes, and therefore, the rate of reaction increases. Although, at around sixty degrees Celsius, the enzyme would denature, as they are biological catalysts, which means they work at human body temperature, after this they would cease to work, so only a limited temperature rise increases the rate in an enzyme controlled reaction.
pH affects the rate in an enzyme controlled reaction, each enzyme has an optimum pH, and the further away from that optimum pH the pH gets, the less effective the enzyme is, and the lower the rate of the enzyme controlled reaction. It can alter the charge on the amino acids around the active site, which means bonds (of opposite charges) could not be formed between enzyme and substrate, and the complex would not be formed, making not products (lower rate), and it could cause some similar bonds holding the tertiary structure together, which means the enzyme would change shape, and the active site could change, and no products would be formed.
The substrate concentration can also affect this. With lower amount of substrate there is less for the enzymes to collide with, so the rate is lower. As this increases there is more to collide with, until there is the same amount of enzymes and substrates. This is the optimum rate of reaction, any excess substrate added after this are unable to find an active site, as they would all be occupied at that time, and no more complexes, and therefore products, could be made.
1) Enzymes function less well at lower temperatures, because there is less kinetic energy, and the enzymes and substrates are colliding less, so less enzyme substrate complexes are being made in that period of time.
2) Enzymes are biological catalysts, so they work at human body temperatures, of around 37 degrees Celsius. When the temperature gets higher then this the enzyme will then denature. Meaning that less or no complexes will be formed, as they won’t keep their shape, as bonds will break, and if they don’t have their shape, the active site will change and enzymes won’t fit. Therefore, no products will be made.
3) A) Food is heated to a high temperature before being canned to allow the enzymes that produce the harmful micro organisms to denature, as they are biological catalysts, and work at human body temperature, so temperatures high then this would make them denature and not work, so they can’t produce the micro organisms. B) Onions are preserved in vinegar as vinegar is acidic, and if it is acidic, which means the pH is 6 or below. This means that it must be in vinegar as the pH is no-where near the optimum of the enzyme, and it will cause bonds in either the active site, or the tertiary structure to break, changing the structure, so the substrate won’t fit, making the enzyme inactive, so no micro organisms.

Enzyme Action

Nicola Eld 18 May at 19:05

Proteins:
Amino acids are the monomer units that are linked to from polymer units called polypeptides. Polypeptides can be combined to form proteins. Amino acids are linked by peptide bonds.
Two monomers can be joined together to form dipeptides. The process is pretty much the same as a monosaccharide making a disaccharide; a condensation reaction, where a water molecule is taken out between them, only it is joined by the carbon and nitrogen joining together, and this is called a dipeptide bond.
After a series of condensation reactions, a polypeptide chain is formed. (100’s of amino acids joined up together.)
The amino acid sequence defines the shape, so a change in this could stop it carrying out it’s function.
The secondary structure is formed by hydrogen bonds forming between the N-H, and C-O as they have opposite charges. This twists the chain into a 3D shape; such as the alpha helix.
The tertiary structure is formed by the bending and twisting of the polypeptide helix into a more compact shape, all three types of bonding, disulfide, hydrogen and ionic, take part in holding the shape together.
The quaternary structure is formed by several polypeptide chains and prosthetic groups joining together into one complex molecule.
The test for proteins is the Biuret test. You place a sample of the solution with equal volumes of Sodium Hydroxide into a test tube. You then add a few drops of copper sulphate, and mix. A purple colouration indicates the presence of peptide bonds, and therefore, a protein. Without, it stays blue.
1) Dipeptide bonds link amino acids together.
2) A condensation reaction is involved in linking amino acids together.
3) The four different components of an amino acid are: An amino group, a carboxyl group, a hydrogen atom, and a functional ‘R’ group.




Enzyme Action:
Enzymes speed up chemical reactions by lowering the activation energy of the reaction. In this way, the reactions can take place at a lower temperature then what they usually would. So, in other words, the reaction can that would take far longer at a lower temperature, would be made quicker with a catalyst, as what they spend the time overcoming has been lowered.
The structure of enzyme molecules related to their function in that they are globular proteins, and therefore, have a specific 3D shape (which is a result of their sequence of amino acids.) Although enzymes are large, only the active site really takes part in anything. It forms a hollow depression within the much larger enzyme molecule. When the substrate & active site form an enzyme substrate complex, the substrate is held there by bonds that temporarily form between the amino acids of the active site and groups on the substrate molecule.
The lock and key model of enzyme action proposes that enzyme s work in the same way as a lock and key; only shape of key will fit one specific lock, which applies, as a substrate would be the key, which only fits one specific enzyme, the lock.
The induced fit model shows how the enzyme is not rigid, but flexible. It compares the enzyme to more of a glove then a lock. A glove has a complimentary shape to a hand, and when a hand (like the substrate) fits into it, it sort of ‘moulds’ around it.
As the enzyme changes shape it puts a strain on a particular bond, which makes the activation energy needed to break that bond lower, which is how enzymes work.

1) A Catalyst is a globular protein that speeds up a reaction, by lowering the activation energy, but doesn’t directly take part and can be re-used.
2) Enzymes are effective in tiny quantities as they can be reused repeatedly.
3) By changing one of the amino acids that make up the active site, it would change the primary structure, (sequence) which would affect the tertiary structure, and the shape that it makes, and therefore change the shape of the active site, meaning the substrate that was meant to fit there would no longer fit, and the enzyme would not me able to produce products from the substrate as it would not fit, and it would therefore, not be active.
4) Because changing amino acids not near the active site would change the primary structure, and in turn, change the tertiary, which would change the shape, and this 3D shape that is made is important as it makes each protein distinctive so it can be recognised and recognise (by) other molecules, and if this is changed, it won’t be recognised, so the substrate will not locate the enzyme, and that way, no products will be made.

Proteins

Proteins:
Amino acids are the monomer units that are linked to from polymer units called polypeptides. Polypeptides can be combined to form proteins. Amino acids are linked by peptide bonds.
Two monomers can be joined together to form dipeptides. The process is pretty much the same as a monosaccharide making a disaccharide; a condensation reaction, where a water molecule is taken out between them, only it is joined by the carbon and nitrogen joining together, and this is called a dipeptide bond.
After a series of condensation reactions, a polypeptide chain is formed. (100’s of amino acids joined up together.)
The amino acid sequence defines the shape, so a change in this could stop it carrying out it’s function.
The secondary structure is formed by hydrogen bonds forming between the N-H, and C-O as they have opposite charges. This twists the chain into a 3D shape; such as the alpha helix.
The tertiary structure is formed by the bending and twisting of the polypeptide helix into a more compact shape, all three types of bonding, disulfide, hydrogen and ionic, take part in holding the shape together.
The quaternary structure is formed by several polypeptide chains and prosthetic groups joining together into one complex molecule.
The test for proteins is the Biuret test. You place a sample of the solution with equal volumes of Sodium Hydroxide into a test tube. You then add a few drops of copper sulphate, and mix. A purple colouration indicates the presence of peptide bonds, and therefore, a protein. Without, it stays blue.
1) Dipeptide bonds link amino acids together.
2) A condensation reaction is involved in linking amino acids together.
3) The four different components of an amino acid are: An amino group, a carboxyl group, a hydrogen atom, and a functional ‘R’ group.

Carbohydrate Digestion

Carbohydrate Digestion:
To hydrolyse starch, salivary amylase breaks down any of the starch in the food with the amylase to maltose by breaking the glycocydic bonds. Maltose is a disaccharide, which can therefore be broken down further.
Starch Digestion is finished in the small intestine by the pancreas producing pancreatic amylase and secreting this into the small intestine, where this breaks down any remaining starch into maltose. Then, muscles in the intestine wall push the food along, while the epithelial lining of the small intestine secretes the enzyme maltase, which breaks the maltose down into alpha glucose.
Disaccharides are digested by enzymes being secreted by the small intestine’s epithelial lining, which break the disaccharides down into monosaccharides, such as sucrase (fructose and glucose), lactase (Galactose and glucose), or maltase (glucose and glucose).
Lactose intolerance is when a human produces little or none of the enzyme lactase, and lactose stays undigested. When this undigested lactose reaches the large intestine, micro-organisms break it down, making large volumes of gas, which can result in bloating, nausea, diarrhoea, and cramps. Lactose intolerance is not life threatening, and can be managed by an adapted diet.
1) The final product of starch digestion in the gut is alpha glucose.
2) Three enzymes produced by the epithelium of the small intestine are Sucrase, Lactase, and Maltase.

Carbohydrates

Carbohydrate – disaccharides and polysacchairdes:
Monosaccharides join together in pairs to for disaccharides. They join by a molecule of water being removed from between them, which is called a condensation reaction, and leaves the two monosaccharides joined by oxygen, which is a glycocydic bond.
The test for non-reducing sugars is to do the Benedict’s reagent test (put 2cm3 in test tube, add equal volumes of Benedict’s, and then boil for five minutes.) If this remains blue, however, then, add another 2cm3 of the sample to 2cm3 of dilute hydrochloric acid and boil for five minutes, to hydrolyse the disaccharide into monosaccharides, and then add sodium hydrogen carbonate, to neutralise the HCl, as the Benedict’s won’t work in acidic conditions. You then re-test the solution with Benedict’s (add equal volumes, boil for five minutes), and if the precipitate goes brown, a non reducing sugar was present, due to the reducing sugars made in hydrolysis.
1) Lactose is made up of Glucose and Galactose
Sucrose is made up of Glucose and Fructose
Starch is made from Alpha glucose and Alpha Glucose.
2) Formula of sucrose = C12H22O5

The test for starch is using Potassium Iodide solution from a change in colour from yellow to blue-black when 2 drops of potassium iodide is added to 2cm3 of a sample.

Enzymes and Digestion

Enzymes and Digestion:
The major parts of the digestive system are:
• The oesophagus, long digestive tract that carries the food from the mouth to the stomach. Adapted for transport, in ways such as being made up of a thick muscular wall.
• The stomach, a muscular sac with an enzyme producing inner layer. Function is to store and digest food. Has glands which produce enzymes to break down proteins, and also has glands that produce mucus, so it doesn’t digest itself.
• The small intestine, a long muscular tube where food is further digested by enzymes that are produced by it’s walls and by glands that secrete into it. The inner walls are folded into villi and these villi have even tinier projections called microvilli, which increase the small intestine’s surface area, which adapts it for it’s purpose of the absorption of the products of digestion into the bloodstream.
• The large intestine, is designed to absorb water, which makes the food in the large intestine more solid in consistency, and therefore, forming faeces.
• The rectum is the last section in the system. The faeces are stored in it before being removed by the anus the egestion (pooing.)
• The salivary glands, pass their secretions via a duct in the mouth, it contains amylase (salivary amylase) which breaks down starch into maltose.
• The pancreas, is a gland below the stomach, which makes pancreatic juice, it secretes into the stomach. It contains amylase to digest starch, protease to digest proteins, and lipase to digest lipids.

The digestive system breaks down food physically by, (if it is large), broken down into smaller chunks my structures such as teeth, this breaks it down into a larger surface area for chemical digestion. It is also churned by muscles into the stomach walls, which breaks it up more.
It is broken down chemically by enzymes, which break down large insoluble molecules into smaller soluble molecules.
The role of enzymes in digestion is by hydrolysis. The molecules are split up by adding water to the chemical bonds which breaks them. Enzymes are very specific, so more then one is needed to break down a large molecule. One enzyme splits a large molecule into sections, and these molecules are then hydrolysed into smaller molecules by one or more enzymes. Carbohydrases, Lipases, and Proteases, are the most important types of enzyme. After being broken down they are absorbed into the bloodstream, and carried around the body to the pats where they are needed.

1) a) The stomach is adapted for churning food by having muscles in the stomach wall, as when these contract, the food gets moved around. B) It is adapted to prevent the enzymes it produces from digesting the surface of the stomach by having glands that produce mucus to layer the surface.
2) Hydrolysis is the splitting of molecules into smaller ones by adding water to the chemical bonds that hold them together, which causes them to break.
3) The two structures that produce amylase is the salivary glands, and the pancreas.
4) The stomach does not have villi or microvilli as the stomach wall does not absorb anything, so an increase in surface area is not needed. Also, the food particles already have an increased surface area for chemical digestion from being churned.

Lifestyle and Health

Lifestyle and Health:
Risk is the probability that damage to health will occur as a result of a given hazard.
Risk is measured in percentage, although a timescale needs to be taken into account.
The risk factors that affect your chances of contracting cancer are: Smoking (lung cancer, passive smoking including, CO damage to lungs), Diet, (less salt, high fibre, low fat.), Obesity, (increases risk), Physical Activity, (more makes lower risk), Sunlight (more, greatens chance of skin cancer. UV.)

Pathogens

Pathogens:
Include bacteria, virus and fungi.
Pathogens are micro-organisms that cause disease.
They cause disease by penetrating or going through one of the interfaces with the environment, e.g. skin, gas exchange system (mouth, nose, lungs are ideal for bacterial growth/culture), the digestive system (food and water carrying the pathogens in.)
Pathogens cause disease by either damaging host tissues (Number of pathogens causes damage, like preventing them from functioning properly, many pathogens can break down membranes, for example.) Or, by producing toxins, which most bacterial pathogens do, such as the cholera bacterium (vibiro cholorae) that leads to water loss for the intestines.

1) A pathogen is a micro-organism that causes disease
2) The digestive system and respiratory system is often a site of entry for pathogens, as they are richly supplied with blood vessels. Also, the body linings at these points are thin, moist (sticky) and have a large surface area. So, overall, Blood vessels, large surface area, thin, and moist (sticky.)
3) The two ways pathogens cause disease are through, firstly, causing damage to the host tissue. The sheer numbers of the pathogen could stop the cell from functioning properly, such as breaking down the membrane. And, secondly, by producing toxins, these could have an effect such as the cholera bacterium, which causes water loss in the lining of the intestines.
4) A reason why gastroenteritis/diarrhoea are not treated with oral antibiotics, is because the main symptoms are diarrhoea and vomiting, which would mean the antibiotic would be digested properly, and therefore, wouldn’t have the desired effect.

More Group Seven Metals ... Again

Just so I really get the hang of it. (:

The Halogens are diatomic molecules: F2, Cl2, Br2, I2... At2

At room temperature, Fluorine => Pale yellow gas.
Chlorine => Greenish gas.
Bromine => Red-brown liquid
Iodene => Black solid.

The size of atoms increase as you go down the group, because as you go down the group, you go down a period, which means each has one more shell of electrons then the next, making the atomic radius larger. (As you go down the group.)

Electronegativity: is the ability an atom has to pull electrons towards itself within a covalent bond. The trend is that as you go down the group, it gets less electronegative. This is because as you go down the group you get one more outer shell, as you go down a period, and this means the distance between the outer shell and the nucleus is further, and also, there are more electrons as you go down the group, and this means there is more shielding, making the electrostatic forces lower, and therefore, a lower electronegativity as you go down the group.

The melting point increases as you go down the group, as there are more electrons as you go down the group, and therefore, great Van Der Waals forces holding the compound together. The melting point relies on the energy you need to put in to break the bonds and with stonger bonds, you need to put in more energy to break them. And therefore, the melting point will be higher.

Astetine would be expected to be darker and denser then all of the others in the group.

Group 7, Halogens.

The atomic radius of group 7 atoms increases as you go down the group. as each element as you go down the group has one more shell of electrons compared to the one above.

Electronegativity is the measure of an atom's ability to pull elecrons towrds itself, within a covalent bond. Factors that affect it are the atraction between the nucleus and the electrons in the outer shell, also, the distance between the nuclues and the outer electrons, and the shielding between them. This means, that as you go /down/ the group, the atoms will get less electronegative, as the atoms are bigger as you go down the group, meaning there are more shells, and there is therefore, a further distance, and more shielding taking place.

The oxidising ability of the group 7 elements increases as you go up the group. So, fluorine is the most powerful oxiding agent. You can tell this from displacement reactions, as none of the other hallides can displace from fluorine, and only fluroine can displace from chlorine, and so on.

Infra Red Spectroscopy.

The absorbption of infra-red radiation can be used to indicate the presence of certain functional groups in a molecule because each bond has it's own frequency. Each particular bond can only absorb radiation of the same frequency as that of what it contains naturally. So, when radiation is shined through it, you can ideantify the bond by what emerges, as what absorbed will be the same frequency as the bond, so you can tell that that is in it.

The fingerprint region is a unique area of the spectrum which is different in each chemical. It's is under the wavenumber 1500 and has many small peaks. The finger print region can be used to confirm a compound's indentity, as it is unique to each one.

Infra red spectra can show impurities too, because they will show up peaks that are not supposed to be there.

Analytical Techniques - Mass spec.

Spectrometry is used to mesure the relative atomic masses of atoms, and also, is a frequent method of measuring the relative atomic masses of compounds too. As a recap: the compound enters as a Vapour. It is then Ionised by at electron gun that bombards it with high speed electrons. After this the compound is Acclereated through the spectrometer as a beam of ionoised molecules, and then they are deflected into the scanner by altering the strength of the magnetic. This depends on the mass and charge of the compound. The compounds are then detected via their mass and charge.

When compounds are in a mass spec, they get ionised, as I said above. The ion that they form at this point is the molecular ion. The molecular ions are really unstable and can break down into fragments. When it goes through the spectrometer, a spectrum is produced. Generally, the largest peak is the molecular ion (as it is the biggest thing going into the detctor (not having broken down [FRAGMENTATION]). This is how you can tell the molecular formula. As, it will be the same as the molecule's relative mass, and the molecule is the highest peak.

There are lots of peaks in the mass spec of a compound, because of the fragmentation taking place. They break down into smaller parts, and these smaller molecules are also detected, and, obviously, they will have different masses, and therefore, different readings as it is relative to m/z ratio.

High resolution mass spec tells us the Mr to 3 decimal places. This means that by adding up the atoms (to three decimal places) we can work out the molecular formula.