nucleotides & enzymes

7/30/2019 Nucleotides & Enzymes

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Nucleotides Nucleic Acids (DNA and RNA) are polymers and their monomers are Nucleotides .

Each nucleotide is composed of o a Pentose Sugar (Deoxyribose in DNA and Ribose in RNA)o an Organic Nitrogenous Base o a Phosphate Group

Nucleotides are joined together by a Condensation Reaction between thePhosphate Group of one and the Sugar Group of another. The bond between the twomonomers is called a Phosphodiester Bond . Many nucleotides joined together inthis way make a repeating Sugar-Phosphate 'backbone' out of which the organic bases project.


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There are five possible organic bases that can form nucleotides, and as two mean thesame in terms of genetic code, there are only really four different nucleotides thatcode for DNA.

The organic bases are grouped into Pyrimidines and Purines . Pyrimidines are

smaller as they contain a single ringed structure , whereas Purines are larger asthey contain a double ring structure . The Pyrimidines are:o Thymine o Uracil o Cytosine

The Purines are:

o Adenine o Guanine

If one has too much Nucleic Acid, especially in one's extremities, one may develop acondition known as Gout . In the liver, excess Purines are broken down in Uric Acid, which is then excreted in the urine. However, if one's blood contains too much of this Uric Acid, it may form crystals that are deposited in the joints, which can beparticularly painful.

The Structure of DNA DNA (Deoxyribonucleic Acid) is composed of two Polynucleotide

Strands (the polymers of nucleotides ), which form what looks like a ladder.The Nitrogenous Bases in DNA store the instructions for making polypeptide chains ,essentially coding for every feature of the entire organism.

The two polynucleotide strands run ' antiparallel ' to each other, with Nitrogenous Basesprojecting inwards. The term 'antiparallel' means that the strands run in oppositedirections, parallel to one another. The antiparallel strands twist in a complete DNA structure, forming a Double Helix .

The strands are held together by Hydrogen Bonds between the Nitrogenous Bases thatare opposite each other. Bases bonded together are termed ' paired ', and are very specific as to which Base they will join to. A Purine will only pair with a Pyrimidine .

Not only that, but the Adenine Purine will only pair with the Thymine Pyrimidine ( A-


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T), and the Guanine Purine will only pair with the Cytosine Pyrimidine (G-C ). These base pairings are termed Complementary Base Pairings .

The reason that Purines will only bond with Pyrimidines is that Purines are largermolecules (composed of a double ring structure), so in order to ensure that thepolynucleotide strands are equally spaced apart , the larger Bases must pair with thesmaller bases. The root for the specific Complementary Base Pairings is the number of Hydrogen bonding sites available . Adenine and Thymine have two sites each , whereas Guanine and Cytosine have three sites each .


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Replication DNA must be copied when cells divide. This is called Replication . This process takes

place during Interphase .

The Double Helix is untwisted and the antiparallel strands are unzipped -the Hydrogen bonds between the bases are broken . Free floating Nucleotides join with the exposed Nitrogenous Bases, forming Hydrogen bonds - this part of the 'reason'for Complementary Base Pairing. The new Nucleotides are bonded together by theenzyme DNA Polymerase , which form complete strands opposite the original strands.The two new DNA molecules form Double Helices .

The new molecules contain one strand of the original an one new strand, and so this typeof replication is called Semi-Conservative Replication .


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RNA and Protein Synthesis RNA (Ribonucleic Acid) is a polynucleotide , similar to DNA, one of whose roles

is protein synthesis . RNA is structurally different from DNA, in thato It is usually single stranded .o It contains the Nitrogenous Base Uracil instead of Thymine.o Its Nucleotides contain Ribose sugar, as opposed to Deoxyribose sugar.

DNA contains Genes , which code for specific Polypeptide Chains .RNA reads the instructions ( Transcription ) and assembles the PolypeptideChain ( Translation ).

During Transcription , the DNA molecule ' opens up ', exposing the gene to beread. Free RNA nucleotides , which are complementary using the base paringrules C-G and A-U (since Uracil is similar to Thymine) bond to the exposed baseson the Template Strand .

The RNA backbone then forms creating an mRNA (messenger RNA) molecule which is identical to the Coding Stand (opposite to the Template Strand). ThemRNA then ' peels away ' from the DNA strand.

The mRNA strand leaves the nucleus through a nuclear pore and attaches toa Ribosome , which is composed of rRNA (ribosomal RNA).

tRNA (Transfer RNA) carries amino acids . When the tRNA carrying the correctamino acid in the sequence collides with the Ribosome, the amino acid joins withthe previous amino acid, forming a Peptide Bond .

This produces a polypeptide chain , whose Primary Structure is dictated by the sequence of bases in the gene. Primary Structure gives riseto Secondary and Tertiary Structures .


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Enzymes Enzymes are Biological Catalysts . They increase the rate of Metabolic reactions .

Almost all Biological Reactions involve Enzymes. All enzymes are Globular Proteins witha specific Tertiary Shape . They are usually specific to only one reaction.

The part of the Enzyme that acts a Catalyst is called the Active Site . The rest of theEnzyme is much larger and is involved in maintaining the specific shape of of theEnzyme.

When a reaction involving an Enzyme occurs, a Substrate is turned into a Product . TheSubstrate can be one or more molecules. The Active Site of an Enzymeis Complementary to the Substrate is catalyses.

Some examples of Enzymes are:o Lactase : Breaks down Lactose into Glucose and Galactose.o Catalase : Breaks Hydrogen Peroxide down into Water and Oxygen.o Glycogen Synthase : Catalyses the formation of Glycosidic Bonds between Glucose

molecules.o ATP-ase : Breaks down ATP into ADP, producing energy.

Enzymes in the Real World Since Enzymes are Proteins, which are effected by their environment , organisms that live

in varying conditions have adapted by producing Enzymes more suitable to theirenvironments. Endotherms (animals that maintain their body temperature) keepthe temperature of the Enzymes within their bodies constant to ensure optimumrates of reaction .

Enzymes are used for a wide variety of purposes, such as in digestion . The action of anEnzyme may be Intracellular (the Enzymes are attached to the cell membrane or are in


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the Cytoplasm , and reactions occur inside the cell) or Extracellular (Enzymes work outside cells , and their products may be absorbed into the cell)

Enzymes are also used in protection against Pathogens . They can be usedto destroy invading Microorgansims. For example, Phagocytes engulf Pathogens and the Endocytosed Vesicle then fuses with Lysosomes which contain enzymes that destroy the Pathogen's cell membrane.

How Enzymes Work Most reactions in a cell require very high temperatures to get going, which

would destroy the cell. Enzymes work by lowering the Activation Energy of a reaction.

The Activation Energy of a reaction is lowered by putting stress on the bonds within amolecule, or by holding molecules close together. This increases the likelihood of areaction, and so lowers the energy required to begin it.

The Lock-and-key Hypothesis The Lock-and-key Hypothesis is a model of how Enzymes catalyse Substrate

reactions. It states that the shape of the Active Sites of Enzymes are exactly Complementary to the shape of the Substrate.

When a substrate molecule collides with an enzyme whose Active Site shape iscomplementary, the substrate will fit into the Active Site and an Enzyme-SubstrateComplex will form.


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The enzyme will catalyse the reaction, and the products , together with the enzyme, willform an Enzyme-Product Complex . According to this model, it is possible for anenzyme to catalyse a reverse reaction.

The Induced-Fit Hypothesis

A more recent model, which is backed up by evidence and is widely accepted asdescribing the way enzymes work is the Induced-Fit Hypothesis . It states that the shapeof Active Sites are not exactly Complementary , but change shape in the presence of a specific substrate to become Complementary .

When a substrate molecule collides with an enzyme, if its composition isspecifically correct, the shape of the enzyme's Active Site willchange so that the substrate fits into it and an Enzyme-Substrate Complex can form.The reaction is then catalysed and an Enzyme-Product Complex forms.


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Factors affecting Enzyme Activity The activit y of an Enzyme is affected by its environmental conditions . Changing

these alter the rate of reaction caused by the enzyme. In nature,organisms adjust the conditions of their enzymes to produce an Optimum rate of reaction , where necessary , or they may have enzymes which are adapted to function

well in extreme conditions where they live.

Temperature Increasing temperature increases the Kinetic Energy that molecules possess. In

a fluid , this means that there are more random collisions between molecules.

Since enzymes catalyse reactions be randomly colliding with Substratemolecules , increasing temperature increases the rate of reaction , forming moreproduct.

However, increasing temperature also increases the Vibrational Energy thatmolecules have, specifically in this case enzyme molecules , which puts strain onthe bonds that hold them together.

As temperature increases, more bonds , especially the weaker Hydrogen and Ionic bonds, will break as a result of this strain. Breaking bonds within the enzyme will cause the Active Site to change shape .


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This change in shape means that the Active Site is less Complementary tothe shape of the Substrate , so that it is less likely to catalyse the reaction. Eventually,the enzyme will become Denatured and will no longer function .

As temperature increases , more enzymes molecules' Active Sites' shapes will be less Complementary to the shape of their Substrate , and more enzymes will be Denatured . This will decrease the rate of reaction .

In summary, as temperature increases , initially the rate of reaction will increase , because of increased Kinetic Energy . However, the effect of bond breaking will become greater and greater , and the rate of reaction will begin to decrease .

The temperature at which the maximum rate of reaction occurs is called theenzyme's Optimum Temperature . This is different for different enzymes . Most enzymes in the human body have an Optimum Temperature of around 37.0 C.

pH - Acidity and Basicity pH measures the Acidity and Basicity of a solution. It is a measure of the Hydrogen

Ion (H +) concentration , and therefore a good indicator of the Hydroxide Ion (OH -)concentration. It ranges from pH1 to pH14 . Lower pH values mean higherH + concentrations and lower OH - concentrations.

Acid solutions have pH values below 7 , and Basic solutions (alkalis are bases) have pH values above 7 . Deionised water is pH7 , which is termed ' neutral '.

H + and OH - Ions are charged and therefore interfere with Hydrogen and Ionic bondsthat hold together an enzyme, since they will be attracted or repelled by the charges created by the bonds. This interference causes a change in shape of the enzyme , and importantly, its Active Site .

Different enzymes have different pH values at which the bonds within them areinterfered with in such a way that the shape of their Active Site is the mostComplementary to the shape of their Substrate . At the pH, the rate of reaction is atan Optimum , so this is the Optimum pH .

Any change in pH above or below the Optimum will quickly cause a decrease inthe rate of reaction, since more of the enzyme molecules will have Active


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Sites whose shapes are not, or at least less, Complementary to the shape of their Substrate .

Small changes in pH above or below the Optimum do not cause a permanentchange to the enzyme, since the bonds can be reformed . However, extremechanges in pH can cause enzymes to Denature and permanently loose their function.

Enzymes in different locations have different Optimum pH values sincetheir environmental conditions may be different. For example, the enzyme Pepsin functions best at around pH2 and is found in the stomach, which contains Hydrochloric Acid (pH2).

Concentration Changing the Enzyme and Substrate concentrations affect the rate of reaction of an

enzyme catalysed reaction. Controlling these factors in a cell is one way that anorganism regulates its enzyme activity and so its Metabolism .

Changing the concentration of a substance only affects the rate of reaction if it isthe limiting factor : that is, it the factor that is stopping a reaction from preceding ata higher rate .

If it is the limiting factor , increasing concentration will increase the rate of

reaction up to a point , after which any increase will not affect the rate of reaction. Thisis because it will no longer be the limiting factor and another factor will be limiting the maximum rate of reaction.

As a reaction proceeds , the rate of reaction will decrease , since the Substrate willget used up . The highest rate of reaction, known as the Initial Reaction Rate isthe maximum reaction rate for an enzyme in an experimental situation .


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Substrate Concentration Increasing Substrate Concentration increases the rate of reaction. This is

because more substrate molecules will be colliding with enzyme molecules ,so more product will be formed.

However, after a certain concentration , any increase will have no effect on the rate of reaction, since Substrate Concentration will no longer be the limiting factor .The enzymes will effectively become saturated , and will be working at their maximumpossible rate .

Enzyme Concentration Increasing Enzyme Concentration will increase the rate of reaction, as more

enzymes will be colliding with substrate molecules.

However, this too will only have an effect up to a certain concentration , where theEnzyme Concentration is no longer the limiting factor .


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Enzyme Inhibitors Enzyme Inhibitors reduce the rate of reaction of an enzyme catalysed reaction

by interfering with the enzyme in some way. This effect may bepermanent or temporary .

Competitive Enzyme Inhibitors work by preventing the formation of Enzyme-Substrate Complexes because they have a similar shape to the substrate molecule.

This means that they fit into the Active Site , but remain unreacted since they havea different structure to the substrate. Therefore less substrate molecules can bind to theenzymes so the reaction rate is decreased .

Competitive Inhibition is usually temporary , and the Inhibitor eventually leaves theenzyme. This means that the level of inhibition depends on the relative

concentrations of substrate and Inhibitor , since they are competing for places inenzyme Active Sites.

Non-competitive Enzyme Inhibitors work not by preventing the formation of Enzyme-Substrate Complexes, but by preventing the formation of Enzyme-Product

Complexes . So they prevent the substrate from reacting to form product. Usually, Non-competitive Inhibitors bind to a site other than the Active Site, called

an Allosteric Site . Doing so distorts the 3D Tertiary structure of the enzyme, suchthat it can no longer catalyse a reaction.

Since they do not compete with substrate molecules, Non-competitive Inhibitors are notaffected by substrate concentration .


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Many Non-competitive Inhibitors are irreversible and permanent , andeffectively denature the enzymes which they inhibit. However, there are a lot of non-permanent and reversible Non-competitive Inhibitors are vital in controllingMetabolic functions in organisms.

Enzyme Inhibitors as Metabolic Poisons Many poisons work by inhibiting the action of enzymes involved in Metabolic

processes , which disturbs an organism.

For example, Potassium Cyanide is an irreversible Inhibitor of the enzyme Cytochrome C Oxidase, which takes part in respiration reactions in cells. If this enzyme is inhibited, ATP cannot be made since Oxygen use is decreased. This means that cells can only respire Anaerobically, leading to a build up of Lactic Acid in the blood. This is potentially fatal.

The poison Malonate binds to the Active Site of the enzyme Succinate Dehydrogenase,competing with Succinate, with is important in respiration.

Enzyme Inhibitors as Medicines Some Enzyme Inhibitors can be used as Medicines in the treatment of conditions .

For example, infection by viruses can be treated by Inhibitors to the viral enzyme Protease, often competitive Inhibitors. This means that viruses cannot build new proteincoats and therefore cannot replicate.


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Penicillin works by Inhibiting a bacterial enzyme that is responsible for forming cross-

links in bacteria cell walls. This therefore halts reproduction.

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