Biological molecules

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  • Created by: Elliew176
  • Created on: 04-04-17 14:23

biological elements and bonding rules

  • Elements – different types of atoms are called elements. They are distinguished by the number of protons in their atomic nuclei. All living things are made primarily from four key elements – carbon (C), hydrogen (H), oxygen (O) and nitrogen (N).
  • Bonding – atoms connect with each other by forming bonds. When two or more atoms bond together the complex is called a molecule. A covalent bondis when atoms share a pair of electrons.

Bonding rules-

  • Carbon atoms can form four bonds with other atoms.
  • Nitrogen atoms can for three bonds with other atoms.
  • Oxygen atoms can form two bonds with other atoms.
  • Hydrogen atoms can only form one bond with another atom

Ions – an atom or molecule in which the total number of electrons is not equal to the total number of protons is called an ion. When an atom loses an electron is has a positive charge and is called a cation. If an atom gains electrons it has a negative charge and is called an anion.  In ionic bonds, one atom in the pair donates an electron and the other receives it. They are held together by the attraction of opposite charges. Ions in solutions are called electrolytes.

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Elements

  • Carbohydrates – carbon, hydrogen and oxygen usually in the ration Cx(H2O)X
  • Lipids – carbon, hydrogen and oxygen.
  • Proteins – carbon, hydrogen, oxygen, nitrogen and sulphur.
  • Nucleic acids – carbon, hydrogen, oxygen, nitrogen and phosphorus.

Polymers – biological molecules are often polymers. Polymers are long chain molecules made up by the linking of multiple individual molecules called monomers in a repeating pattern. In carbohydrates the monomers are sugars (saccharides) and in proteins the monomers are amino acids.

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Water

Covalent bonds occur when atoms share electrons. However, the negative electrons are not always shared equally by the atoms of different elements. In many covalent bonds, the electrons will spend more time closer to one of the atoms than the other. The atom with the greater share of negative electrons will be slightly negative and the other will be slightly positive.

Molecules in which this happens are said to be polar – they have regions of negativity and regions of positivity.

Polar molecules, including water, interact with each other as the positive and negative regions of the molecule attract each other and form bonds called hydrogen bonds. Hydrogen bonds are relatively weak interactions which break and reform between the constantly moving water molecules. Even though hydrogen bonds are weak, they occur in high numbers

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characteristics of water

  • Water has an unusually high boiling point. It is also liquid at room temperature and this is because of the hydrogen bonding between water molecules. It takes a lot of energy to increase the temperature of water and cause water to evaporate.
  • When water freezes, it turns to ice. Unlike other substances, water is less dense when it is ice. Usually, most substances are more dense when they are solid than when they are liquid. However, water is less dense in its solid state because of the hydrogen bonds formed. As the water cools below four degrees Celsius the hydrogen bonds fix the positions of the polar molecules slightly further apart than the average distance in the liquid state. This produces a giant, rigid but open structure, with every oxygen atom at the centre of a tetrahedral arrangement of hydrogen atoms resulting in a solid that is less dense than liquid water. For this reason, ice floats.
  • Therefore, water has cohesive properties. It moves as one mass because the molecules are attracted to each other (cohesion).
  • Water has adhesive properties – this is where water molecules are attracted to other materials.
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Water for life

  • Because water is a polar molecule, it acts as a solvent in which many organisms can be dissolved. The cytosol of prokaryotes (bacterial) and eukaryotes is mainly water.
  • Water acts as a medium for chemical reactions and also helps transport dissolved compounds into and out of cells.
  • Water makes a very efficient transport medium within living things. Cohesion between water molecules means that when water is transported through the body, molecules will stick together.
  • Adhesion occurs between water molecules and other polar molecules.The effects of adhesion and cohesion result in water exhibiting capillary action. This is the process by which water can rise up a narrow tube against the force of gravity.
  • Water acts as a coolant, helping to buffer temperature changes during chemical reactions in prokaryotic and eukaryotic cells because of the large amounts of energy required to overcome hydrogen bonding. Maintaining constant temperatures in cellular environments is important as enzymes are often only active in a narrow temperature range.
  • Many organisms, such as fish, lie in water and cannot survive out of it. Water is stable – it does not change or become a gas easily, therefore providing a constant environment. Because ice floats, it forms on the surface or ponds and lakes, rather than from the bottom up. This forms an insulating layer above the water below.
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carbohydrates

Carbohydrates are molecules that contain the elements carbon, hydrogen and oxygen. The word ‘carbohydrate’ means hydrated carbon (carbon and water).

The general formula for carbohydrates is Cx(H2O)y.

· Carbohydrates are also known as saccharides or sugars. A simple sugar unit is known as a monosaccharide. Examples of this include glucose, fructose and ribose.

· When two monosaccharaides join together they form a disaccharide. Examples of this include lactose and sucrose.

· When two or more (usually many more) monosaccharides are linked together they form a polymer called polysaccharide. Examples of this include glycogen, cellulose and starch.

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Glucose (carbohydrate)

  • The building blocks, or monomers, of some biologically important large carbohydrates are glucose molecules which has the formula C6H12O6. Glucose is a monosaccharide composed of six carbons. It is therefore a hexose monosaccharide (hexose sugar).
  • In molecular structure diagrams, carbons are numbered clockwise beginning with the carbon to the right (clockwise) of the oxygen atom within the ring.
  • There are two structural variations of the glucose molecule, alpha (α) and beta (β) glucose, in which the OH (hydroxyl) group on carbon 1 is in opposite positions.
  • α-glucose is when the H is above the ring.
  • β-glucose is when the H is below the ring.
  • Alpha – above
  • Beta – below
  • Glucose molecules are polar and soluble in water. This is due to the hydrogen bonds that form between the hydroxyl groups and water molecules.  The solubility in water is important because it means glucose is dissolved in the cytosol of the cell.
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condensation and hydrolysis reactions

Condensation:

When two alpha molecules are side by side, two hydroxyl groups react. When this happens, bonds are broken down and bonds are reformed in different places making new molecules.

Two hydrogen atoms and an oxygen atom are removed from the glucose monomer and joined to form a water molecule. A bond forms between carbon 1 and 4 on the glucose molecules and the molecules are now joined. A covalent bond called a glycosidic bond is formed between the two glucose molecules. This is called a condensation reaction as water is formed as one of the products of the reaction. In this reaction, carbon 1 of one glucose molecule is joined to carbon 4 of the other glucose molecule. This is called a 1,4 glycosidic bond. The new molecule is maltose which is a monosaccharide which is made up of two monosaccharide’s.

Hydrolysis:

To release glucose for respiration, starch or glycogen undergoes hydrolysis reactions. This requires the addition of water molecules. These are the reverse of condensation reactions that form the glycosidic bonds. The reactions are catalysed by enzymes.

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types of carbohydratyes - cellulose

Beta glucose molecules are unable to join together in the same way that alpha glucose molecules can.

The hydroxyl groups on carbon 1 and carbon 4 of the two glucose molecules are too far from each other to react. The only way that beta glucose molecules can join together and form a polymer is if alternate beta glucose molecules are turned upside down.

When a polysaccharide is formed from glucose in this way it is unable to coil and form branches. A straight chain molecule is formed called cellulose.

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cellulose - structure, bonding, properties and rol

Structure and bonding:

  • Structural polysaccharide
  • Formed from thousands of beta glucose molecules linked by beta 1-4 glycosidic bonds.
  • Hydrogen bond formation between neighbouring strands produces bundles of molecules lying side by side to form fibrils which associate together forming fibres.
  • Straight chain polysaccharide.

Properties of molecule:

  • Fully permeable to water and dissolved solutes
  • Metabolically inactive
  • High tensile strength
  • Flexible

Role of this molecule in organisms:

  • Major component of plant cell walls maintaining structure and form of the cell. Provides the opposing force preventing the rupturing of the cell membrane and creating turgor pressure in plant cells
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Testing for carbohydrates

Monosaccarhides and some disaccarides, such as maltose and lactose, are reducing sugars. This means that they can donate electrons. In the chemical test for a reducing sugar, the chemical is called benedict's reagent - an alkaline solution of coppor sulphate.

The test is carried out as follows: Place the sample to be tested in a boiling tube. If it is not in liquid form, grind it up or blend it in water. Add an equal volume of benedict's reagent. Heat the mixture gently in a boiling water bath for five minutes.

Reducing sugars will react with the copper ions in Benedict's reagent. This results in the addition of electrons to the blue Cu2+ ions, reducing them to brick red Cu2+ ions. When a reducing sugar is mixed with Benedict's reagent and warmed, a brick red precipitate is formed indicating a positive result. The more reducing sugar present, the more precipitate formed and the less blue Cu2+ ions are left in solution so the actual colour seen will be a mixture of brick red (precipitate) and blue (unchanged copper ions) and will depend on the concentration of ther reducing sugar present. This makes the test qualitative. 

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Testing for carbohydrates

Using Benedict's test for non-reducing sugars:

Non-reducing sugars do not react with Benedict's solution and the solution will remain blue after warming, indicating a negative result. Sucrose is the most common non-reducing sugar. If sucrose is first boiled with dilute hydrochloric acid it will then give a positive result when warmed with Benedict's solution. This is because the sucrose has been hydrolysed by the acid to glucose and fructose, both reducing sugars.

Iodine test for starch:

The iodine test is used to detect the presence of starch. To carry out the test, a few drops of iodine dissolved in potassium iodide solution are mixede with a sample. If the solution changes colour from yellow/brown to purple/black, starch is present in the sample. If the iodine solution remains yellow/brown it is a negative result and starch is not present.

Reagent strips:

Can be used to test for the presence of reducing sugars, most commonly glucose. The advantage is that the concentrate of the sugar can be determined.

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Lipids and triglycerides

Commonly known as fats and oils. Lipids are molecules containing the elements carbon, hydrogen and oxygen. Generally, fats are lipids that are solid at room temperature whereas oils are lipids that are liquid at room temperature.

Lipids are non-polar molecules as the electrons in the outer orbitals are more evenly distributed than in polar molecules. There are no positive and negative areas in the molecule which means lipids are not soluble in water - water and oil do not mix. Lipids are large complex molecules known as macromolecules which are not built from repeating units, or monomers, like polysaccharides.

A triglyceride is made my combining one glycerol molecule with three fatty acids. Glycerol is a member of a group called alcohols. Fatty acids belong to a group called carboxylic acid – they consist of a carboxyl group (-COOH) with a hydrocarbon chain attached

The hydroxyl groups interact leading to the formation of three water molecules and bonds between the glycerol and fatty acid molecules. These are called ester bonds and the process is called esterification. This is an example of a condensation reaction.

When triglyceride molecules need to be broken down, three water molecules need to be added to reverse the reaction that formed the triglyceride. This is an example of a hydrolysis reaction.

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Saturated and unsaturated bonds

Saturated acids are fatty chains that have no double bonds between the carbon atoms because all of the carbon atoms form the maximum number of bonds with hydrogen atoms.

Unsaturated acids are fatty acids with double bonds between some of the carbon atoms.

If there is just one double bond, it is called monounsaturated.

If there are two or more double bonds, it is called polyunsaturated.

The presence of double bonds causes the molecules to kink and bend so they cannot pack so closely together. This makes them liquid at room temperature rather than solid so they are described as oils rather than fats.

Plants contain unsaturated triglycerides which normally occur as oils and tend to be healthy in the human diet than saturated triglycerides, or (solid) fats. There has been evidence that in excess, saturated fats can lead to coronary heart disease

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Phospholipids

Phospholipds are modified triglycerides and contain the element phosphorus along with carbon, hydrogen and oxygen. Inorganic phosphate ions are found in the cytoplasm of evry cell. The phosphate ions have extra electrons and so are negatively charged, making them soluble in water.

One of the fatty acid chains in a triglyceride molecule is replaced with a phosphate group to make a phopholipid.

Phospholips are unusual because due to their length, they have a non-polar end or tail (the fatty acids chains) and a charged end or head (the phosphate group). The non-polar tails are repelled by water but mix readilly with fat. They are hydrophobic. The charged heads will interact with and are attracted to water. They are hydrophillic.

Due to the hydrophobic and hydrophillic structure, phospholipds behave in an interesting way when they interact with water. They form a layer on the surface of the water with the phosphate heads in the water and the fatty acid tails sticking out of the water. Because of this they are called surface active agents or surfactants. They also form structures called a bilayer with all the hydrophobic tails pointing towards the centre of the sheet, protected from the water by the hydrophillic head. As a result of the bilayer, phospholipids play a key role in forming cell membranes.

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Sterols

Another type of lipid found in cells. They are not fats or oils and have little in common with them structurally. They are complex alchol molecules based on a four ring structure with a hydroxyl (OH) group at one end. Like phospholipids they have duel hydrophobic/hydrophillic characteristics. The hydroxyl group is polar and therefore hydrophillic and the res of the molecule is hydrophobic.

Cholesterol is a sterol. It has an important role in the formation of cell membranes, becoming positioned between the phospholipids with the hydroxyl group at the periphery of the membrane. This adds stability to cell membranes and regulates their fluidity by keeping membranes fluid at low temperatures and stopping them becoming to fluid at high temperatures.

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Roles of lipids

Lipids have many biological roles due to their non-polar nature: membrane formation and the creation of hydrophobic barriers, hormone production, electircal insulation necessary for impulse transmission, waterproofing, for example in birds' feathers.

Lipids (triglycerides in particular) have an important role in long term energy storage. They are stored under the skin and around vital organs where they also provide thermal inulation to reduce heat loss, cushioning to protect vital organs such as the heart and kidneys, buoyancy for aquatic animals like whales.

Identification of lipids:

Lipids can be identified in a test called the emulsion test. First the sample is mixed with ethanol. The resulting solution is mixed with water and shaked. If a white emulsion forms as a layer on top of the solution this indicates the presence of a lipid. If the solution remains clear the text is negative.

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Structure of proteins

Peptides are polymers made up of amino acid molecules.

Amino acids: all amino acids have the same basic structure. Different R-groups result in different amino acids. Twenty different amino acids are commonly found in cells. Five of these are said to be not essential as our bodies can form other amino acids. Nine are essential and can only be obtained from what we eat. 

Synthesis of peptides: amino acids join when the amine and carboxylic acid groups connected to the central carbon atoms react. The R-groups are not involved at this point. The hydroxyl in the carboxylic acid group of one amino acid. A peptide bond is formed between the amino acids and water is produced. The resulting compound is a dipeptide.

when many amino acids are joined together by peptide bonds a polypeptide is formed. This reaction is catalysed by an enzyme present in ribosomes, the sites of protein synthesis.

The different R-groups of the amino acids making up a protein are able to interact with each other forming different types of bonds. The bonds lead to the long chains of amino acids (polypeptides) folding into complex structures (proteins). This presence of different sequences of amino acids leads to different structures with different shapes being produced. The very specific shapes of proteins are vital for the many functions proteins have.

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Levels of protein structure

Primary structure: this is the sequence in which the amino acids are joined. It is directed by information carried within DNA. The particular amino acids in the sequence will influence how the polypeptide folds to give the protein's final shape. This in turn determines its function. The only bonds involved in the primary structure of a protein are peptide bonds.

Secondary structure: the oxygen, hydrogen and nitrogen atoms of the basic, repeating structure of the amino acids interact. Hydrogen bonds may form within the amino acid chain, pulling it into a coil shape called an alpha helix.

Polypeptide chains can also lie parallel to one another joined by hydrogen bonds, forming sheet like structures. The pattern formed by the individual amino acids causes the structure to appear pleated, known as a beta pleated sheet.

Tertiary structure: this is the folding of a protein into its final shape. It often includes sections of secondary structure. The coiling or folding of sections of proteins into their secondary structures brings R-groups of different amino acids closer together to they are close enough to interact and further folding of these sections will occur. 

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Levels of protein structure

The following interactions occur between the R-groups:

  • hydrophobic and hydrophilic interactions - weak interactions between polar and non-polar R-groups
  • hydrogen bonds - these are weakest of the bonds formed
  • ionic bonds - these are stronger than hydrogen bonds and from between oppositely charged R-groups.
  • disulfide bonds - these are covalen an the strongest of the bonds but only form between R-groups that contain sulfur atoms.

This produces a variety of complex-shaped proteins, with specialised characteristics and functions.

Quaternary structure - this results from the association of two or more individual proteins called subunits. The interactions between the subunits are the same as in the tertiary structure except that they are between different protein molecules rather than within one molecule.

The protein subunits can be identical or different. Enzymes often consist of two identical subunits where insulin has two different subunits. Haemoglobin, a protein required for oxygen transport in the blood, has four subunits, made up of two sets of two identical subunits.

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Hydrophilic and hydrophobic interactions

Hydrophilic and hydrophobic interactions

Proteins are assembled in the aqueous environmentof the cytoplasm. The way in which a protein folds will also depend on whether the R-groups are hydrophilic or hydrophobic. Hydrophilic groups are on the outside of the protein while hydrophobic groups are on the inside of the molecule shielded from the water in the cytoplasm.

Breakdown of peptides

Peptides are created by amino acids linking together in condensation reactions reactions to form peptide bonds. Proteases are enzymes that catalyse the reverse reaction turning peptides back into their amino acids. A water molecule is used to break the peptide bond in a hydrolysis reaction, reforming the the amine and carboxylic acid groups.

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Types of proteins - globular proteins

Globular proteins: 

Compats, water soluble and usually roughlyu spherical in shape. Form when proteins fold into their tertiary structure so that the hydrophobic R-groups on the amino acids are kept away from the aqueous environment. The hydrophillic R-groups are on the outside of the protein - makes the proteins soluble in water. The solubility is important for the many functions of globular proteins. They are essential for regulating many processes necessary to life. The include processes such as chemical reactions, immunity and muscle contraction.

Insulin:

Insulin is a globular protein. A hormone involved in the regulation of blood glucose concentration. Hormones are transported in the blood so they need to be soluble.

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Types of proteins - conjugated proteins

Conjugated proteins are globular proteins that contain a non-protein component called a prosthetic group. There are different types of prosthetic groups. Lipids or carbohydrates can combine with proteins forming lipoproteins or glycoproteins. Metal ions and molceules derived from vitamins also form prosthetic groups which are called cofactors when they are necessary for the proteins to carry out their functions. Haem groups are examples of prosthetic groups and contain an iron II ion. Catalase and haemoglobin both contain haem groups.

Haemoglobin:

Is a red, oxygen-carrying pigment found in red blood cells. A quaternary protein made from four polypeptides, two alpha and two beta subunits. Each subunit contains a prosthetic group. The iron II ions present in the haem groups are able to combine reversibly with an oxygen molecule which is what enables haemoglobin to transport oxygen arond the body. It can pick oxygen up in the lungs and transport it to the cells that need it, where it is released.

 

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Types of proteins - conjugated proteins

Catalase:

An enzyme. Enzymes catalase reactions so they increase reaction rates. It is a quaternary protein containing four haem prosthetic groups. The presence of the iron II ions in the prosthetic groups allow catalse to interact with hydrogen peroxide (a common byproduct of metabolism but is damaging to cells if it accumulates) and speed up its breakdown. Catalase makes sure this doesn't happen.

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Types of proteins - fibrous proteins

Formed from long, insoluble molecules due to the presence of a hgih proportion of amino acids with hydrophobic R-groups in their primary structures. The amino acid sequence in the primary structure is usually quite repetitive. This leads to very organised structures reflected in their roles.

Keratin:

A group of fibrous proteins present in hair, skin and nails. Has a large proportion of the sulfur-containing amino acid, cysteine. This results in many strong disulfide bonds forming stong, inflexible and insoluble materials. Hair contains fewer bonds making it more flexile than nails which has more bonds.

Elastin:

Found in elastic fibres present in the walls of blood vessels and alveoli of the lungs and give these tructures the flexibility to expnad and return to their normal size.

 

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Types of proteins - fibrous proteins

Collagen:

A connective tissue found in skin, tendons, ligaments and the nervous system.  All are made up of three polypeptides wound together in a long and strong rope-like structure. It has flexibility.

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Nucleotides and nucleic acids

There are two types of nucleic acid – DNA and RNA and they both have roles in the storage and transfer of genetic information and the synthesis of polypeptides (proteins). They are the basis of heredity.

Nucleic acids contain the elements carbon, hydrogen, oxygen, nitrogen and phosphorus. They are large polymers formed from many nucleotides (the monomers) linked together in a chain.

 An individual nucleotide is made up of three components:

  • A pentose monosaccharide (sugar) containing five carbon atoms.
  • A phosphate group, –PO42-, an inorganic molecule that is acidic and negatively charged.
  • A nitrogenous base – a complex organic molecule containing one or two carbon rings in its structure as well as nitrogen.
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Nucleotides and nucleic acids

Nucleotides are linked together by condensation reactions to form a polymer called a polynucleotide. The phosphate group at the fifth carbon of the pentose sugar of one nucleotide forms a covalent bond with the hydroxyl (OH) group at the third carbon of the pentose sugar of an adjacent nucleotide. These bonds are called phosphodiester bonds. This forms a long, strong-phosphate ‘back bone’ with a base attached to each sugar. The phosphodiester bonds are broken by hydrolysis, the reverse of condensation, releasing the individual nucleotides.

  • Deoxyribonucleic acid (DNA) – deoxyribonucleic acid (DNA) is deoxyribose – a sugar with one fewer atoms than ribose. The nucleotides in DNA each have one of four different bases. This means there are four different DNA nucleotides. The four bases can be divided into two groups:
  • Pyrimidines – the smaller bases, which contain single carbon ring structures – thymine (T) and cytosine (C).
  • Purines the larger bases, which contain double carbon ring structures – adenine (A) and guanine (G).
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Nucleotides and nucleic acids

The double helix – the DNA molecule varies in length from a few nucleotides to millions of nucleotides. It is made up of two strands of polynucleotides coiled into a helix.

The two stands of the double helix are held together by hydrogen bonds between the bases (like a ladder). Each strand has a phosphate group (5’) at one end and a hydroxyl group at the other end. The two parallel strands are arranged so that they run in opposite directions – they are said to be antiparallel.

The pairing between the bases allows DNA to be copied and transcribed – key properties required of the molecule of heredity. 

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Base pairing rules

Base pairing rules – the bases bind in a very specific way. Adenine and the thymine are both able to form two hydrogen bonds and always join with each other. Cytosine and guanine form three hydrogen bonds and so also only bind to each other. This is known as complementary base pairing.

These rules mean that a small pyrimidine base always binds to a large purine base. This arrangement maintains a constant distance between the DNA ‘backbones’, resulting in parallel polynucleotide chains.

Complementary base pairing means that DNA always has equal amounts of adenine and thymine and equal amounts of cytosine and guanine. This was known long before the detailed structure of DNA was determined by Watson and Crick 1953.

It is the sequence of bases along a DNA strand that carries the genetic information of an organism in the form of code.

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RNA

Ribonucleic acid (RNA) – ribonucleic acid (RNA) plays an essential role in the transfer of genetic information from DNA to the proteins that make up the enzymes and tissues of the body. DNA stores all of the genetic information needed by an organism, which is passes on from generation to generation. However, the DNA of each eukaryotic chromosome is a very long molecule, comprising many hundreds of genes and is unable to leave the nucleus in order to supply the information directly to the sites of protein synthesis.

To get around this problem, the relatively short section of the long DNA molecule corresponding to a single gene is transcribed into a similarly short messenger RNA (mRNA) molecule. Each individual mRNA is therefore much shorter than the whole chromosome of DNA. It is a polymer composed of many nucleotide monomers.

RNA nucleotides are different to DNA nucleotides as the pentose sugar is ribose rather than deoxyribose and the thymine base is replaced with the base uracil (U). Like thymine, uracil is a pyramidine that forms two hydrogen bonds with adenine. Therefore the base pairing rules still apply when RNA nucleotides bind to DNA to make copies of particular sections of DNA.

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RNA

The RNA nucleotides form polymers in the same way as DNA nucleotides – by the formation of phosphodiester bonds in condensation reactions. The RNA polymers formed are small enough to leave the nucleus and travel to the ribosomes, where they are central in the process of protein synthesis.

After protein synthesis the RNA molecules are degraded in the cytoplasm. The phosphodiester bonds are hydrolysed and the RNA nucleotides are released and reused.

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DNA replication and genetic code

DNA replication and genetic code – cells divide to produce more cells needed for growth and repair of tissues. The two daughter cells produced as a result of cell division are genetically identical to the parent cell and to each other (the DNA sequence is identical to the original parent cell).

When a cell prepares to divide, two strands of DNA double helix separate and each strand serves as a template for the creation of a new double-stranded DNA molecule. The complementary base pairing rules ensure that the two new strands are identical to the original. This process is called DNA replication.

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Semi-conservative replication

Semi–conservative replication – for DNA to replicate, the double helix structure has to unwind and then separate into two strands. The hydrogen bonds holding the complementary bases together must be broken. Free DNA nucleotides will then pair with their complementary bases, which have been exposed as the strands separate. Hydrogen bonds are formed between them. Finally the new nucleotides join to their adjacent nucleotides with phosphodiester bonds.

In this way, two new molecules of DNA are produced. Each one consists of one old strand of DNA and one new strand. This is known as semi-conservative (meaning half the same) replication.

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Roles of enzymes in replication

Roles of enzymes in replication – DNA replication is controlled by enzymes, a class of proteins that act as catalysts for biochemical reactions. Enzymes are only able to carry out their function by recognising and attaching to specific molecules or particular parts of the molecules.

Before replication can occur, the unwinding and separating of the two strands of the DNA double helix is carried out by the enzyme DNA helicase. It travels along the DNA backbone, catalysing reactions that break the hydrogen bonds between complementary base pairs as it reaches them. This can be thought as the strand unzipping.

Free nucleotides pair with the newly exposed bases on the template strands during the unzipping process. A second enzyme called DNA polymerase catalyses the formation of phosphodiester bonds between these nucleotides.

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Replication errors and genetic code

Replication errors – sequences of bases are not always matched exactly, and an incorrect sequence may occur in the newly-copied strand. These errors occur randomly and spontaneously and lead to change in the sequence of bases, known as a mutation.

Genetic code – DNA is contained within the cells of all organisms. Scientists understood that DNA must carry the instructions or blueprints needed to synthesis the many different proteins needed by other organisms. Proteins are made up of a sequence of amino acids, folded into complex structures.  Therefore, DNA must code for a sequence of amino acids. This is called the genetic code.

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Triplet code

A triplet code – the instructions that DNA carries are contained in the sequence of bases along the chain of nucleotides that make up the two strands of DNA.  The code in the base sequences is a simple triplet code. It is a sequence of three bases called codon. Each codon codes for an amino acid.

A section of DNA that contains the complete sequence of bases (codons) to code for an entire protein called a gene.

 A genetic code s universal – all organisms use the same code although the sequences of bases coding for each individual protein will be different.

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Degenerate code

Degenerate code – there are four different bases which means there are 64 different base triplets or codons possible. This includes one codon that acts as the start codon when it comes at the beginning of a gene, signalling the start of a sequence that codes for a protein. If it is the middle of a gene, it codes for the amino acid methionine. There are also three stop codons that do not code for an amino acids and signal the end of the sequence.

Having a single codon to signal the start of a sequence ensures that the triplets of bases (codons) are read in frame. In other words the DNA base sequence is read from base 1, rather than base 2or 3. So the genetic code is non-overlapping.

As there are only 20 different amino acids that regularly occur in biological proteins, there are a lot more codons than amino acids. Therefore, many acids can be coded for by more than one codon. Due to this the code is known as degenerate.

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Transcription

Protein synthesis occurs in the in the cytoplasm at ribosomes, but a chromosomal DNA molecule is too large to leave the nucleus to supply the coding information needed to determine the protein's amino acid sequence. To get around this problem, the base sequence of genes have to be copied and trnasported to the site of protein synthesis, a ribosome. This process is called transcription and produces shorter molecules of RNA.

Has many similarities with DNA replication . The section of DNA that contains the gene unwinds and unzips under the controle of DNA helicase, beginning at a start codon. This involves the breaking of hydrogen bonds between the bases.

Only one of tghe two strands of DNA contains the code for the protein to be synthesised. This is the sense strand. The other strand is a complementary copy of the sense strand and does not code for a protein. This is the sntisense strand and it acts as the template during transcription, so that the complementary RNA strand formed carries the same base sequence as the sense strand.

Free RNA nucleotides will base pair with complementary bases exposed on the antisense strand when the DNA unzips. The thymine base in RNA nucleotides is replaced with the base uracil. Uracil binds to adenine on the DNA template strand.

Phosphodiester bonds are formed between the RNA nucleotides by the enzyme RNA polymerase.  The completed short strand of RNA is called messenger RNA. 

The mRNA then detatches from the DNA template and leaves the nucleus through a nuclear pore. The DNA double helix reforms. This mRNA molecule then travels to a ribosome in the cell cytoplasm for the next step in protein synthesis.

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Translation

After leaving the nucleus, the mRNA binds to a specific site on the small subunit of a ribsome. The ribosome holds mRNA in position while it is decoded/translated into a sequence of amino acids. This process is called translation.

Transfer RNA (tRNA) is another form of RNA which is necessary for translation of the mRNA. It is composed of a strand of RNA folded in such a way that three bases, called the anticodon, are at one end of the molecule. This anticodon will bind to a complementary codon on mRNA following the normal base pairing rules. The tRNA molecules carry an amino acid corresponding to that codon.

When the tRNA anticodons bind to complementary codons along the mRNA, the amino acids are brought together in the correct sequence to form the primary structure of the protein coded for by the mRNA.

This cannot happen all at once. Instead amino acids are added one at a time and the polypeptide chain (protein) grows as this happens. Ribosomes act as the binding site for mRNA and tRNA and catalyse the assembly of the protein.

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Summary of translation

1) the mRNA bonds to the small subunit of the ribosome at its start codon.

2) a tRNA with the complementary anticodon binds to the mRNA start codon. 

3) another tRNA with the anticodon UGC and carrying the corresponding amino acid then binds to the next codon on the mRNA. A maximum of two tRNAs can be bound at the same time..

4) the first amino acid is transferred to the amino acid on the second tRNA by the formation of a peptide bond. This is catalysed by the enzyme peptidyl transferase, which is an rRNA component of the ribosome.

5) the ribosome then  moves alonf he mRNA, releasing the first tRNA. The secon tRNA becomes the first.

Stages 3-5 are repeated, with another amino acid added to the chain each time. The process keeps repeating until the ribbosome reaches the end of the mRNA at a stop codon and rhe polypeptide is released.

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