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AQA Categories Archives: 3.1 Biological molecules

Inorganic ions

Biological molecules (AQA AS Biology) PART 8 of 8 TOPICS

 

 

TOPICS: Carbohydrates  Lipids  Proteins  Many proteins are enzymes  Nucleic acids  ATP  Water  Inorganic Ions

Inorganic ions:

Inorganic ions can either occur in high concentrations or low concentrations in the cytoplasm and body fluids.

H+ ions regulate how acidic a solution is where the more protons there are the more acidic a solution is.

Iron ions in haemoglobin bind to oxygen so that oxygen can be released to respiring cells (more on this in a later module in AS, check it out).

Sodium ions are used for the transfer of glucose to the cells by co transport:

  • Sodium ions are pumped out of the cell into the blood by the sodium-potassium pump powered by Pi. (Potassium ions come in from the blood also but have no relevance to co transport)
  • This causes the concentration of sodium ions in the cell to drop so the sodium ions from the lumen comes into the cell down its concentration gradient along with glucose going up its concentration gradient by facilitated diffusion through the coupled transport protein. This is called a symport.

NB: Sodium-potassium pump is on the opposite side to the coupled transport protein of the cell when glucose is transported which is described above. When it comes to amino acids the sodium-potassium pump is on the same side to the coupled transport protein of the cell. Sodium ions are actively transported into the ileum from the epithelial cells instead of into the blood. Then the sodium ions diffuse back in along with amino acids into the epithelial cells.

Phosphate ions are used to make nucleotides, ATP and making bones strong by reacting with calcium to make calcium phosphate [Ca3(PO4)2]

] That is all that you need to know about inorganic ions [

 

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Nucleic acids

Biological molecules (AQA AS Biology) PART 5 of 8 TOPICS: Nucleic acids

 

 

TOPICS: Carbohydrates  Lipids  Proteins  Many proteins are enzymes  Nucleic acids  ATP  Water  Inorganic Ions

Nucleic acids:

Two types of nucleic acids needs to be known for this module and they are DNA (deoxyribose nucleic acid) and RNA (ribonucleic acid). These are important information carrying molecules where DNA holds genetic information and RNA transfers the genetic information to the ribosomes. The structures of DNA and RNA should be known:

 

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ATP

Biological molecules (AQA AS Biology) PART 6 of 8 TOPICS

 

 

TOPICS: Carbohydrates  Lipids  Proteins  Many proteins are enzymes  Nucleic acids  ATP  Water  Inorganic Ions

ATP:

ATP (Adenosine triphosphate) is a single molecule made up of adenine, ribose and three inorganic phosphate groups.

ATP is made in a condensation reaction between ADP (Adenosine diphosphate) and and inorganic phosphate group (Pi) and is catalysed by the enzyme ATP synthase. The reverse reaction is hydrolysis is catalysed by the enzyme ATP hydrolase. NB: A tip on remembering what each enzyme does to avoid confusion; Synthase sounds like synthesis which means to make something therefore ATP Synthase helps to make ATP. As one enzyme makes ATP the other breaks it.

Hydrolysis can be coupled to energy required reactions such as respiration within cells which is covered in a powerpoint made for A2 AQA Biology.

The inorganic phosphates can be used to phosphorylate other compounds often to make them more reactive.

] As you can see, ATP is quite a small topic at AQA. This is all based on the exam boards spec which is explained in a little more detail to help you understand the points which are only said briefly on the specification [

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Many proteins are enzymes

Biological molecules (AQA AS Biology) PART 4 of 8 TOPICS: Many proteins are enzymes

 

 

Many proteins are enzymes:

TOPICS: Carbohydrates  Lipids  Proteins  Many proteins are enzymes  Nucleic acids  ATP  Water  Inorganic Ions

At GCSE, the lock and key model was the method that had to be known where the substrate could fit into the active site of the enzyme to make the products. At A Level, this is not the only method that is performed. The induced fit model is another method that should be known alongside the lock and key model. This follows the same procedure as the lock and key model however, the active site of the enzyme is not complementary to the substrate (complementary just means that the active site and the substrate are similar shape as they are not identical. NB: Remember that they are not the same because you will lose a mark). Therefore when the substrate needs to bind to the active site, the active site changes shape so the substrate can fit inside. This fitting when the substrate is in the active site is called enzyme-substrate complexes. Then the products are made as usual like the lock and key model.

As an enzyme is a biological catalyst, there are factors that will affect the rate of enzyme activity. Simple factors such as just increasing the number of enzymes will increase the rate of reaction and just increasing the number of substrates will decrease the rate of reaction. Typical  factors such as temperature and pH can change how fast the enzyme works. If temperature is low, there will be a slow rate of reaction. As the temperature will start increasing, so would the rate of reaction until reaching the optimum temperature where the enzyme is working at its fastest rate. Once the temperature goes over the optimum temperature, the enzyme will start to denature, meaning it will no longer be able to work as an enzyme as the bonds that held the quaternary structure will break causing fewer enzyme-substrate complexes forming therefore a low yield in products. Different enzymes require different temperatures and also pH levels. pH levels will also have the same effect on the enzyme if the pH is not right or at the optimum.

There are two complicated factors that will be explained that affects the enzymes’ activity and they are competitive inhibitors and non-competitive inhibitors. Inhibitors as a whole means that they invade the site at which reactions occur – being the active site. This is known as a competitive inhibitor because they compete with the substrate for the active site therefore reducing the number of enzyme-substrate complexes. However not all inhibitors invade the enzyme in this way such as non-competitive inhibitors. These invade at a place other than the active site known as allosteric site where they are not competing with the substrate for a site on the enzyme. This behaviour reduces the number of enzyme-substrate complexes because once the non-competitive inhibitor is in, the active site changes shape and stays changed whilst the non-competitive inhibitor is in. The effects are seen on the graphs illustrated.

 

You may well be asked to calculate a value for the hydrogen concentration of a solution with enzymes The equation is:

[H+] = 10-pH where

[H+] = hydrogen concentration (needs to be square brackets as it a concentration value)

If a pH is given and you need to find the concentration, you would do 10 to the power negative of the pH value to give the hydrogen ion concentration. E.g. if the pH of a solution was 7 then the hydrogen ion concentration would be 10-7 which equals 1 x 10 -7.

If a hydrogen ion concentration is given and you need to find the pH, you would do the negative of log([H+]) to give the pH. E.g. if the hydrogen ion concentration is 1 x 10-7 then the pH would be log((1×10-7)) which equals 7. Incase if log is not clear what it is, it is just a function to know what the power would be to give a known answer ([H+]) to a known base (10). It is on your standard Casio calculator shown as ‘log’ as well as on other makes such as Sharp. 

 

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Lipids

 

TOPICS: Carbohydrates  Lipids  Proteins  Many proteins are enzymes  Nucleic acids  ATP  Water  Inorganic Ions

Lipids:

Triglycerides are formed by the condensation reactions of one molecule of glycerol and 3 molecules of fatty acids to create ester bonds:

Triglycerides have fatty acids with double bonds which increase solubility. Triglycerides that are liquids at room temperatures are classed as oils and any that are solids are classed as fats. Phospholipids are used in the bilayer of cell membranes where it is impermeable (only allows water and gases to diffuse in or out and not large molecules) as it has a hydrophilic head and hydrophobic tails:

Knowing the test for lipids has to be known for the exam:

Lipids:

·         Add ethanol and shake

·         Add an equal amount of cold water

RESULT

·         A cloudy white suspension should be observed

 

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Proteins

 

Proteins:

TOPICS: Carbohydrates  Lipids  Proteins  Many proteins are enzymes  Nucleic acids  ATP  Water  Inorganic Ions

Amino acids are the monomers of proteins. The structure of these molecules should be known:

A condensation reaction between two of these amino acids will remove a water molecule and form a peptide bond to create a Dipeptide. Polypeptides are chains of many amino acids joined by the same reaction where this chain is referred to as a primary structure. Secondary structure is where the primary structure is folded into an alpha helix or a beta pleated sheet. Tertiary structure is the further folding of the structure which is held by hydrogen bonds, ionic bonds and disulphide bridges. Quaternary structure is where there is more than one polypeptide chain.

Some proteins are functional and can be primary, secondary, tertiary or quaternary structures. The functions involved are as an energy source, for structure (hair), as enzymes and carrier proteins, hormones, antibodies and are used as a buffer.

 

 

Knowing the tests for proteins needs to be known for the exam

Proteins

  • Add KOH and mix (quantities do not need to be known)
  • Add copper sulphate solution and mix (quantities do not need to be known)

RESULT

  • Purple is colour is observed
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Many proteins are enzymes

 

TOPICS: Carbohydrates  Lipids  Proteins  Many proteins are enzymes  Nucleic acids  ATP  Water  Inorganic Ions

Many proteins are enzymes:

At GCSE, the lock and key model was the method that had to be known where the substrate could fit into the active site of the enzyme to make the products. At A Level, this is not the only method that is performed. The induced fit model is another method that should be known alongside the lock and key model. This follows the same procedure as the lock and key model however, the active site of the enzyme is not complementary to the substrate (complementary just means that the active site and the substrate are similar shape as they are not identical. NB: Remember that they are not the same because you will lose a mark). Therefore when the substrate needs to bind to the active site, the active site changes shape so the substrate can fit inside. This fitting when the substrate is in the active site is called enzyme-substrate complexes. Then the products are made as usual like the lock and key model.

As an enzyme is a biological catalyst, there are factors that will affect the rate of enzyme activity. Simple factors such as just increasing the number of enzymes will increase the rate of reaction and just increasing the number of substrates will decrease the rate of reaction. Typical  factors such as temperature and pH can change how fast the enzyme works. If temperature is low, there will be a slow rate of reaction. As the temperature will start increasing, so would the rate of reaction until reaching the optimum temperature where the enzyme is working at its fastest rate. Once the temperature goes over the optimum temperature, the enzyme will start to denature, meaning it will no longer be able to work as an enzyme as the bonds that held the quaternary structure will break causing fewer enzyme-substrate complexes forming therefore a low yield in products. Different enzymes require different temperatures and also pH levels. pH levels will also have the same effect on the enzyme if the pH is not right or at the optimum.

You may well be asked to calculate a value for the hydrogen concentration of a solution with enzymes The equation is:

[H+] = 10-pH where

[H+] = hydrogen concentration (needs to be square brackets as it a concentration value)

If a pH is given and you need to find the concentration, you would do 10 to the power negative of the pH value to give the hydrogen ion concentration. E.g. if the pH of a solution was 7 then the hydrogen ion concentration would be 10-7 which equals 1 x 10 -7.

If a hydrogen ion concentration is given and you need to find the pH, you would do the negative of log([H+]) to give the pH. E.g. if the hydrogen ion concentration is 1 x 10-7 then the pH would be log((1×10-7)) which equals 7. Incase if log is not clear what it is, it is just a function to know what the power would be to give a known answer ([H+]) to a known base (10). It is on your standard Casio calculator shown as ‘log’ as well as on other makes such as Sharp. 

There are two complicated factors that will be explained that affects the enzymes’ activity and they are competitive inhibitors and non-competitive inhibitors. Inhibitors as a whole means that they invade the site at which reactions occur – being the active site. This is known as a competitive inhibitor because they compete with the substrate for the active site therefore reducing the number of enzyme-substrate complexes. However not all inhibitors invade the enzyme in this way such as non-competitive inhibitors. These invade at a place other than the active site known as allosteric site where they are not competing with the substrate for a site on the enzyme. This behaviour reduces the number of enzyme-substrate complexes because once the non-competitive inhibitor is in, the active site changes shape and stays changed whilst the non-competitive inhibitor is in. The effects are seen on the graphs illustrated.

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Carbohydrates

TOPICS: Carbohydrates  Lipids  Proteins  Many proteins are enzymes  Nucleic acids  ATP  Water  Inorganic Ions

Carbohydrates:

Monosaccharides are the monomers from which larger carbohydrates are made. These include glucose, fructose and galactose. Only the structure of glucose needs to be known for the whole of a level which is illustrated as follows on either side. Notice the OH group and the hydrogen are on opposite sides on carbon number 1 (there is no particular way of counting the carbons however exam questions will refer to this particular carbon as carbon 1. Number 4 is always the carbon opposite carbon number 4).

Two monosaccharides form a disaccharide in any combination where glucose is always one of the reactants –

Glucose + Glucose = Maltose

Glucose + Fructose = Sucrose

Glucose + Galactose = Lactose

 

Polysaccharides are made by the condensation reactions of many monosaccharides. Glycogen and starch are made from many alpha glucose molecules and cellulose is formed from many beta glucose molecules. As part of AQA, you need to know the characteristics of these three polysaccharides:

Starch:  Is insoluble so it does not draw water in by osmosis. Starch will not diffuse easily out and is stored in a tight place because it is compact due to the coils it has. It can easily be hydrolysed into alpha glucose molecules which can used in respiration. Starch is found in plants.

Glycogen: Is shorter and is more branched than starch. It is more readily hydrolysed than starch.

Cellulose: Is made up of many straight unbranched chains of beta glucose molecules that run parallel to one another. Hydrogen bonds link these chains together which gives cellulose its strength which we are familiar with when talking about cell walls.

Knowing the tests for the sugars and for starch has to be known for the exam:

Reducing sugars (includes glucose, fructose, galactose, maltose and lactose):

  • Add Benedict’s reagent and heat

RESULT

  • Blue to brick red precipitate

Non-reducing sugar (sucrose):

  • Add HCl (hydrochloric acid) and boil
  • Add NaOH (sodium hydroxide) to neutralise
  • Add Benedict’s reagent

RESULT

  • Blue to brick red precipitate

Starch:

  • Add Iodine Potassium solution

RESULT

  • Blue-black colourisation

 

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