Biology Chapter 3

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The building blocks of life

Atoms create molecules that make up cellular components. Different types of atoms are called elements. Each element has a differnent number of protons in the nucleus. 

Bonding- atoms can bond to create molecules. These can be joined with covalent bonds, where they share electrons. 

-Carbon can form 3 bonds

-Nitrogen can form 3 bonds

-Oxygen can form 2 bonds

-Hydrogen can form 1 bond. 

This helps create fundamental molecules e.g H2, H2O, CO2, CH4 (methane) and NH3 (ammonia)

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Ions

This is where an atoms donates an electron to another atom. This creates two ions that are now held together by the attraction of opposite charges. A negavite ion is called an anion and a cation is a positive ion. 

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Water

Water is a polar molecule as the oxygen is slightly negatively charged as it contains a greater share of the electrons in the covalant bond. This means that both of the hydrogen atoms are slightly negatively charged, making it polar. This creates weak hydrogen bonds between the water molecules but they aren't permenant as they break and reform constantly as the water is moving. 

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Characteristics of water

Water has a high boiling point. This is because the hydrogen bonds between the individual molecules are difficult to break with heat so they stay as a liquid at room temp. 

Water also has the property of adhesion as is attracts to other molecules. This is because water is a polar molecule and attracts to other materials. It also has cohesive properties for the same reason. There is an attraction between the water molecules themselves because the oxygen and hydrogen atoms of other molecules attract. They are more cohesive to each other than they are adhesive to air so this gives water surface tension. 

Also when water gets cooled to 4*C it creates a tetrahedral arrangement of the molecules with the oxygen atoms in the centre of each. The hydrogen bonds are slightly more distanced in this structure meaning when it freezes it has a lower density that the water and so gives it the proprty of floating. 

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Water for life

Water is a good solvent because it is a polar molecule. Things can be dissolved in it as the charged molecules attract to the othe polar solutes and separate the molecules from each other. This also makes it a good medium for chemical reactions and is why the cytosol of prokaryotic and eukaryotic cells are mostly water. 

Water is also good as a transport medium as the water has the properties of adhesion and cohesion that together make it exhibit capillary action that means that the water can rise up a narrow tube against the force or gravity.

Water is also good as a coolant in the body as it requires so much energy to break the hydrogen bonds between the water molecules. This is used to keep enzymes ect at a perfect temperature. 

As Ice is less dense that the water, it floats. This means that it becomes more habitable as it protects the water beneath it from freezing as it is above it rather that sinking and cooling the water around it. This means in colder parts of the world/year fish can still survive easily. 

Some creatures also live on the water such as pond skaters as they use the waterssurface tension to stay on top of the water. 

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Glucose

Glucose is a monomer (sugar) so is a monosaccharide. This means that it is just one molecule and there isnt a chain of them. Glucose is C6H12O6 meaning that it a hexose sugar as it has 6 carbon atoms. There are two variation of glucose, alpha and beta. 

Glucose is soluble in water as there are hydrogen bonds between the water molecules and the hydroxyl groups of the glucose. 

When two glucose molecules bond, it makes a condensation reaction as a water molecule is released. This bond that is formed between the two glucose molecules is known as a glycosidic bond. If the bond is between two alpha glucose molecules, it is a 1-4 glycosidic bond and creates maltose, a disaccharide. 

To break this bond a hydrolysis reaction takes place. This is useful in plants and animals to access the stored glucose that is in a polysaccharide molecule. 

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Other Sugars

Fructose and galactose are also hexose sugars, fructose sweeter than glucose and galactose less sweet. Sucrose is a dissaccharide sugar created from one glucose and one fructose. This is common sugar/cane sugar. 

Galactose and glucose make the sugar lactose which is in milk and milk products. 

Pentose sugars 5 carbon atoms in the monosaccharide, one example being ribose. 

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Starch

It is the energy store for plants. Starch can be in one of two forms, Amylose or Amylopectin. They are both chains of alphaglycose so they both spiral. Amylose however has no extra branching off it. It is one straight chain of glucose. Amylopectin has branching every 25ish subunits. these branches are between c1 and c6 so its a 1-6 glycosidic bond. This makes more free ends to be used for respiration.

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Glycogen

This is essensially the same as Amylopectic however has much more branching meaning it is has more free ends. This is usefull as it is the store of energy for animals and they are more active than plants so need the ability to easily remove and add glucose. It is also more compact because of the extra branching meaning that it is useful for animals as they move around a lot. 

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Cellulose

Beta glucose molecules can't join in the same way that alpha glucose can because of their structure so need to be alterately swapped in direction so that it creates a polymer chain. This chain is straight because of the alternate directions of the beta glucose. For cellulose this is usefull as it stops coils forming. This allows hydrogen bonds to form between the strands of cellulose to form microfibrils. These microfibrils join together to create macrofibrils that join to create one cellulose fibre. This fibre is strong and insoluble in water so is hard to break down by the body but is important for the digestive system. Cellulose is used in cell walls as it is insoluble in water so doesnt dissolve and it's strong. 

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Testing for Carbohydrates

Reducing Sugars - The sample to be tested needs to be placed in a boiling tube, either groud up and blended with water or already as a liquid. Then the benedicts solution (copper(II) Sulphate) is added. This is then slowly heated in a water bath for 5 minutes. If a reducing sugar is present then the Cu2+ ions in the benedicts solution are reduced to Cu+ ions. The Cu2+ is blue and the Cu+ is brick-red so the result is a qualitive analysis of the colour. Somewhere inbetween the red and blue would indicate a small amount or the reducing sugar. 

Non-reducing sugar test- First test for reducing sugars, if it is a negative result then boil it with dilute hydrochloric acid to break down the disaccharides into the monosaccharides. This makes it into reducing sugars that can be tested in the same way as reducing sugars. 

Testing for starch- The iodine test is used. A few drops of iodine are added to a potassium iodide solution that is then mixed with the sample. If the colour changes from yellow/brown to purpla/black then the starch is present and if there is no change it isnt present. 

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Lipids

They are fats/oils. They are non-polar so they aren't soluble in water. They are a large complex known as macromolecules which arent built from repeating units like polymers.

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Triglycerides

These are made from one glycerol molecule (an alcohol) and 3 fatty acids (carboxylic acids that contain a carboxyl group and a hydrocarbon chain. The hydrogen atoms from the glycerol and the hydroxyl groupd from the fatty acid chains interact in a condensation reaction to from the triglyceride, releasing water and creating an ester bond. Water is added to break these bonds.

Saturated / unsaturated

If a triglyceride is saturated then there are no double bonds between the carbon atoms in the hydrocarbon chains in the fatty acids. If the triglyceride is un-saturated, it contains a double bond or more between the carbon atoms. Poly-unsaturated means that there is more than one double bond, mono-unsaturated means there is only one double bond in the chain. The double bonds cause kinks in the chains meaning that they dont stack so oils (unsaturated triglycerides) are liquid at room temperature. The fats (saturated) are solid as no kinks in the chains mean they stack. Some evidence shows saturated fats are worse for the body as they stack but the evidence is inconclusive. 

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Phospholipids

These are modified triglycerides that have a phosphate head containing phosphorous. The phosphate ions are negatively charged and so are polar so are soluble in water. Because of this, with a fatty acid chain, a molecule with a polar end and a non-polar end (hydrophyllic and hydrphobic). This means that they have an end that is attracted to the water and an end that repells the water. 

Because of this, when in water, the head points into the water with the tails on the outside. This is then known as a surface active agent or surfactant for short. They can also form bilayers like this as they arrange themselves to have the tails pointing the centre and the heads on the outside. This is what creates the membrane of the cell as there is an aqueous environment on the outside and inside of the cell. 

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Sterols

This is part of the lipid group and is known as a sterol alcohol. They contain a 4 carbon ring that is non-polar and a hydroxyl group (OH) that is polar. They are not a fat or oil and have very little in common with them structurally.

Cholesterol is an example of a sterol and is found in membranes. They are made in the liver and intestines to be used in the cell membranes. The cholesterol provides stability of the cell memebrane and control the fluidity of the membrane by keepig it at a low temperature. They are located between phospholids in the membrane with the hydroxyl group on the peripheral of the membrane.  

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Roles of lipids

-Membrane formation

-Hormone production

-Electrical insulation for nerve impulse transmissions

-Waterproofing on birds and leaves.

-Thermal insulation to reduce heat loss

-Cusioning to protect organs

-Buoyancy in aquatic animals

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Testing for Lipids + Health advice

The emulsion test is used. This is when ethanol is added, then water and is shaken. If a white precitate appears then a lipid is present. 

The changing health advice on topics like what amount of types of lipids should be consumed mostly come about because of the system by which the information is distributed. This is mostly because the information has not been validated fully before it is published in the media or because the technology used to test the effects of different nutrients is improving constantly.

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Amino Acids

Amino acids all have the same basic structure with the difference between each amino acid being the R group attahed to it. There are 20 different amino acids found in the body, 5 of which aren't considered essential as the body can make them using the other amino acids. 9 are considered essential as they are always needed and the other 6 are only needed during the years of development.

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Synthesis of peptides

The amino acids join when the carboxyl group of one amino acid and the hydrogen from the amine group of another amino acid react. This is a condensation reaction that creates a peptide bond. Many of these amino acids creates a polypeptide chain (protein). The reaction is catalysed by the enzyme peptidyl transferase present in the ribosomes. 

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Levels of protein structure

Primary structure- This is the sequence of amino acids determined by the DNA information

Secondary structure- This is the structure that is created based on the primary structure. Weak hydrogen bonds form between the amino acids pulling it into either an alpha helix or a beta pleated sheet. 

Tertiary structure- This is the folding of the protein into its final shape. It happens due to the interactions between the R groups of the amino acids. The interations include hydrophobic and hydrophylic, weak hydrogen bonds, disulphide bridges and ionic bonding, if the R groups are oppositely charged. 

Quartenary structure- This is the same as tertiary except it's interactions between different protein chains rather than reactions in the same one. 

The way that the proteins fold is decided by the r groups. If the R group is hydrophylic, it stays on the outside of the protein, if it is hydrophobic, it stays on the inside. This creates the folding of the protein. It does this because it is aqueous inside the cytoplasm. 

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Globular proteins

Globular proteins are proteins that have been formed into a roughly spherical shape that was created by the hydrophylic R groups staying on the outside, keeping it together. This means that they are soluble in water so comes in useful for life as they need to be used in many ways to regulate processes to life. These include chemical reactions, immunity and muscle contractions. 

Insulin

Insulin is an example of a globular protein so is soluble in water which is useful for a hormone as it needs to dissolve into the bloodstream to be taken around the body. It also needs to have a very precise shape so that it can be detected by the recpetors on the exterior of cells. 

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Conjugated proteins

Conjugated proteins are globular proteins that contain a prostheic group.

A prothetic group is attached to the protein and is a non-protein material. They can be lipids or carbohydrates, forming lipoproteins or glycoproteins or metal ions and molecules derived from vitamins. these are known as cofactors and are neccessary for the fuction of the protein.

Haemoglobin

It is formed from 4 polypeptides. There is two alpha and beta subunits, each containing a haem group. These haem groups are what contain Iron II and and so helps to pick up oxygen as the heamoglobin is within the redblood cells to carry oxygen as the Iron can combine with an oxygen molecule reversibly. This allows it to carry oxygen around the body. 

Catalase

Catalase is an enzyme that is made up of 4 polypeptide chains, each with a haem group. The presence of Iron allows it to breakdown the hydrogenperoxide made through metabolism as a biproduct. 

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Fibrous proteins

These are quite repetitive chains of protein that are insoluble as there is a majority of hydrophobic R groups that repel the water. They have an organised structure due to its repetitive sequence.

Keratin

This has a high presence of the sulphur containing amino acid cysteine. this results in more disulphide bridges which are strong making it a strong protein. More disulphide bridges are found in the keretin in nails than hair as it is stronger. 

Elastin

This is a fibrous protein that is in the walls of arteries to give them flexibility. It is a quarternary protein made from molecules called tropoelastin. 

Collagen

This is a long rope-like connective tissue that is found in tendons, ligments and the nervous system. It is made from 3 polypetides wound around each other giving it strength and flexibilty. 

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Nucleic acids and Nucleotides

One nucleotide is made from a pentose monosaccharide, a phosphate group (an inoganic molecule that is acidic and negatively charged) and a nitrogenous base that contains 1-2 carbon rings and nitrogen. 

They are joined to each other with condensation reactions between the hydroxyl group on the carbon 3 and the phosphate group on the carbon 5. This creates a phosphodiester bond and forms the sugar-phosphate backbone with a base on each sugar. They are broken with hydrolysis reactions.

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Deoxyribonucleic acid (DNA)

This is the nucleic acid of a deoxyribose sugar (a ribose sugar with one less oxygen). There are 4 different types as they can have 4 different bases. they are divided into two groups:

-Pyrimidines - These are the smaller bases that contain only one carbon ring in the structure. Cytosine (C) and Thymine (T)

-Purines - These are larger and have 2 carbon rings in their structure.  Adenine (A) and Guanine (G)

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The double helix + base pairing rules

The DNA is coiled into a helix as there are two antiparrallel strands of DNA attatched by the interactions of the opposite bases. The pairing allows them to be transcribed. 

Gyanine and Cytosine can both form 3 hydrogen bonds so they are comlimentary and Thymine and Adenine can bond with each other. This means that the amount of Adenine abd Thymine is equal same with C+G. It also means that there is one large base attaching with one small base, keeping the distance between them constant. 

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Ribonucleic acid

This is essential as the DNA strands are too large to leave the nucleus so they need to be transcribed before leaving the nucleus. This information is condensed down into the (m) RNA as it can fit through the nulear pores. These are much shorter but contain the information to code for a protein.

RNA nucletides are composed of the ribose sugar rather than the deoxyribose sugar and contain the base Uracil rather that Thymine. Uracil is also a pyramidine that can form 2 hydrogen bonds so it still keeps the complimentary base pairning rules.

Once the RNA is used, the phosphodiester bonds are broken down in the aqueous cytoplasm for the nucleotides to be reused. 

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DNA replication

The strand of DNA to be replicated unwinds. Then the enzyme DNA helicase separates the two strands of DNA. This continues to do so as the free nucleotides match up with the complimentary base pairs. Once they are lined up, they are joined by DNA polymerase (bottom 3 nucleotides) the rest attract to their complimentary base pairs. DNA polymerase contines to join them together until there are two new molecules both containing half of the old strand and half of the new one- semiconservative replication. Any changes in the DNA is known as a mutation. This can happen as an error during the replication. 

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Genetic code

DNA was found to be in the form of a code as the different proteins created have different proterties and the DNA carries the information to synthesise these proteins, therefore the DNA must be a genetic code for the order of the amino acids. 

A triplet code is the 3 bases (codon) that code for a single amino acid. A section of DNA codes for an entire protein. This is known as a gene. The gentic code is the same for all organisms. 

A degenerate code means that multiple combinations of bases can code for the same amino acid. Also there are codons that start the synthesis and some that end the sequence. These help to stop mutations. The start codon allows it to start on the 1st base and not a different one. 

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Transcription

The DNA helix is too large to leave the nucleus so it needs to be transcribed onto (m)RNA to leave the nuclear pores in the nuclear envelope. This is done by unzipping the part of the DNA where the gene is (with DNA helicase) that needs to be used to code for the protein. 

On the DNA, the sense strand (5' to 3') is the part is the strand that needs to be copied and the antisense strand is the opposite that pairs with it. The antisense strand (3' to 5') is used as a template as the complimentary base pairs will match up to create the replica of the DNA strand. The differences however are that this is RNA, not DNA and contains Urasil in the place of Thymine so that it can leave the nuclear pores. 

Free RNA nucleotides match up with complimentary base pairs to create the RNA strand that is formed with phosphodiester bonds keeping it together but with U in place of T. Then the mRNA detaches from the DNA and leaves the nucleus. Then the DNA is coiled back up. The mRNA makes its way to the ribosomes for Translation. 

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Translation

The ribosome is made of two subunits, large and small. They both contain equal amounts of protein and rRNA (ribosomal RNA). rRNA plays a role in the structural stability of the synthesis of the protein and has a role in catalysing the reactions. 

The mRNA binds to the small unit and is translated into a sequence of amino acids.

The tRNA (transfer RNA) is an RNA molecule that has 3 folds with the middle one containing an anitcodon (3 bases that correspond to a codon). This anticodon joins onto codons and leaves behind an amino acid to make the protein. It doesnt all happen at once as the ribosome is needed to act as a binding site for the mRNA and tRNA. Further modifications may be added at the golgi apparatus. Also multiple identical proteins can be coded for by the same mRNA strand that will feed through multiple ribosomes. 

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ATP structure

Cells require energy for 3 main things:

Synthesis-e.g. protein synthesis

Movement-e.g. contracting muscle cells

Transport-e.g. moving ions across the cell membranes by active transport.

Stands for adenosine triphosphate as it is 3 phosphate groups and one adenosine (one ribose and one adenine). Adenine is a nitrogenous base and ribose is a pentose sugar. 

It releases energy (around 30.6kJ/mol) when the bonds between the phosphate groups are broken and release energy in formation reactions. This gives the equation:

ATP + H2O --> ADP + P + energy

ATP is hydrolysed into ADP, a phosphate ion and energy

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ATP properties

It is not good at storing energy for a long time as they are unstable, carbs and fats are better for this so they are broken down to give energy for the creation of the ATP from the ADP which requires energy in the condensation reaction. This is called phosphorylation.

ATP is also small so it can move in and out of cells.

It is water soluble as the reactions take place is an aqueous environment

The bonds between the phosphate groups has an intermediate amount of energy so there is enough for cellular reactions but not too much to have any wasted as heat energy. 

They are also easily regenerated with energy.

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