Biology sem1- chap3

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    TOPIC 3

    MOLECULES OF LIFE

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    LEARNING OUTCOMES3.1 WATER

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    WATER

    Structure of a water

    molecule

    A water moleculeconsist of an oxygen

    atom and two

    hydrogen atoms

    The two hydrogen

    atoms are combined

    with the oxygen atom

    by sharing of electrons

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    The three atomsform a triangle,

    not a straight line

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    The water molecule

    is electricallyneutral, but there is

    a net negative

    charge on theoxygen atom and a

    net positive charge

    on both hydrogen

    atoms.

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    A molecule carrying such an unequal

    distribution of electrical charge is called apolar molecule.

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    The positively

    charged hydrogenatoms of one water

    molecule are

    attracted to the

    negatively chargedoxygen atoms of

    nearby water

    molecules byforces called

    hydrogen bonds.

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    Hydrogen bonds are weaker than covalentbonds.

    But there are strong enough to hold watermolecules together.

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    Because of their hydrogen bonds,

    water molecules are attracted tocharged particles or charged

    surfaces.

    In fact, hydrogen bonds largely

    account for the unique properties

    of water.

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    Properties of water as vital

    constituent of life

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    powerful solvent for polar substances.

    These include ionic substances like

    sodium chloride (Na+ and Cl-), and also

    organic molecules with ionized groups(such as the carboxyl group COO- , and

    amino group NH3+).

    Water as a universal solvent

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    These cations (negatively charged ions)

    and anions (positively charged ions)

    become surrounded by a shell of

    orientated water molecules.

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    Soluble organic molecules like sugars

    dissolve in water due to the formation ofhydrogen bonds between the water

    molecules and the slightly charged

    hydroxyl (-OH) groups in these organic

    molecules.

    Once dissolve, the molecules of a

    substance are free to move around.

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    This makes them more reactive chemically

    than when they form part of an undissolve

    solid.

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    At the same time, non-polar substances

    are repelled by water, as in the case of oil

    on the surface of water. Non-polar

    substances are hydrophobic.

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    Viscosity of water

    It has a low viscosity

    This unique property makes it suitablemedium of transportation in living

    organisms.

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    Specific heat capacity

    A lot of energy is required to raise the

    temperature of water.

    This is because, much energy is needed

    to break the hydrogen bonds that restrict

    the movement of water molecules.

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    This property of water is known as its specific

    heat capacity.

    The specific heat capacity of water is the highest

    of any known substance.

    Consequently, aquatic environments like stream

    and rivers, ponds, lakes and seas are all very

    slow to change temperature when thesurrounding air temperature changes.

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    Aquatic environments have more stable

    temperatures than terrestrial environments do.

    Another consequence is that cells and the

    bodies of organisms do not change temperature

    readily.

    Bulky organisms particularly tend to have a

    stable body temperature in the face of a

    fluctuating surrounding temperature, whether in

    extremes of heat or cold.

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    Latent heat of vaporization of water

    The hydrogen bonds between water

    molecules make it difficult for them to be

    separated and vaporized.

    This means that much energy is needed to

    turn liquid water into water vapor.

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    This amount of energy known as the

    latent heat of vaporization, and forwater it is very high.

    Consequently, the evaporation ofwater in sweat on the skin, or in

    transpiration from green leaves,

    causes marked cooling because theescaping molecules take a lot of

    energy with them.

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    And since a great deal of heat is lost

    within the evaporation of a small

    amount of water, cooling byevaporation of water is also

    economical on water.

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    The amount of heat energy needed tomelt ice is very high, and the amount

    of heat that must be removed from

    water to turn into ice is also great.

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    This amount of heat energy is known as

    the latent heat of fusion.

    Again, it is very high for water. This means

    that both the contents of cells and thewater in the environment are slow to

    freeze when it very cold.

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    Effect of temperature on water

    density

    Most liquids contract on cooling, reaching their

    maximum density at their freezing point.

    Water is unusually reaching its maximum density

    at 4C.

    As water freezes, the ice formed is less densethan the cold water around it. The ice floats on

    top. The floating layer of ice insulates the water

    below.

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    This is why the bulk of ponds, lakes or the

    sea rarely freeze solid.

    Aquatic life can generally survive a freeze-

    up.

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    Surface tension- adhesive and

    cohesive forces

    Water adheres strongly to most surfaces

    and can be drown up into long columns

    through narrow tubes like the xylem

    vessels of plant stems, without the water

    column breaking.

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    Compared with other liquids, water has

    extremely strong adhesive and cohesive

    properties that prevent the column

    breaking under tension.

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    The outermost molecules of water form

    hydrogen bonds with water molecules belowthem.

    This gives a very high surface tension to water-

    higher than that of any other liquid exceptmercury. Surface skate.

    The insects waxy cuticle prevents wetting of itsbody, and the mass of the insect is not great

    enough to break through the surface.

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    pH as measure of hydrogen ion in

    aqueous solution

    pH scale which ranger from 0 -14

    compress the range of H+ and OH-

    concentration by employing logarithms.

    The pH of a solution is defined as the

    negative logarithms (base 10) of the

    hydrogen ion concentration:

    pH = - log [ H+ ]

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    pH declines as H+ concentration

    increases.

    An acid is a substance that increases the

    hydrogen ion concentration of a solution.

    A base is a substance that reduces the

    hydrogen ion concentration of a solution,

    therefore it has a higher concentration of

    hydroxyl ions.

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    CARBOHYDRATE

    carbohydrates

    monosaccharides disaccharides polysaccarides

    carbonyl group hydroxyl group starch glycogen cellulose

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    Use of carbohydrates:

    Source of energy

    Storage of energy

    Structural component of cell membranes

    and cell walls

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    Three main groups

    1. Monosaccharides single sugars

    2. Disaccharides double sugars

    3. Polysaccharides- many sugars

    All are composed of carbon, hydrogen andoxygen atoms.

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    MONOSACCHARIDES

    Characteristic:1. Small

    2. Sweet

    3. Readily soluble in water

    General formula : ( CH2O)n

    (glucose C6H12O6)

    Carbonyl group and hydroxyl group

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    TYPE

    1. Triosa sugar contains 3 carbon atoms(glyceraldehydes)

    2. Pentose sugar contains 5 carbonatoms (ribose)

    3. Hexose sugar contains 6 carbon atoms(glucose)

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    FUNCTIONAL GROUP

    i. Ketose , e.g fructose

    ii. Aldose, e.g glucose

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    Two types of glucose

    E - glucose and F- glucose

    With six carbon atoms numbered

    Are said to be isomers (different

    compounds with the same molecularformula.

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    DISACCHARIDES

    Small, sweet and soluble.

    Monosaccharides may join together togive a double sugar molecule a

    disaccharide.

    Joined together to form it by a

    condensation reaction.

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    The bond between two carbon atoms is

    called a glycosidic bond.

    All condensation reactions can be

    reversed by adding water to the glycosidic

    bond this is known as hydrolysis.

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    POLYSACCHARIDES

    Are formed when many hundreds ofmonosaccharides condense (join) to formchains.

    The chains formed may be:

    1. Variable in length

    2. Branched or unbranched3. Folded ideal for energy storage

    4. Straight or coiled

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    Characteristic of polysaccharides:

    1. large,2. not sweet

    3. Insoluble in water

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    Starch

    Used as storage of glucose in plants.

    1. Amylose2. Amylopectin

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    Amylose

    Made from -glucose molecules

    Forming unbranched helical chain of 300units in length.

    Each -glucose is joined by a glycosidic

    bond between neighbouring C1 and C4atoms.

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    Amylopectin

    Made from -glucose molecules

    Forming branched chains of up to 1500 units

    Branches occur every 30 units and are formed

    between neighbouring C1 and C6 atoms which

    are then held together by glycosidic bond.

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    Glycogen

    Is the only carbohydrate energy store

    found in animals.

    Found in liver and muscle tissue and

    made up of short branched chains of -

    glucose units.

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    Cellulose

    Important structural materials in plants

    Long chains of -glucose units which areunbranched but parallel strands of

    cellulose are linked by means of hydrogen

    bonds, making the cell wall a very stable

    structure.

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    LIPIDSLIPIDS

    General term for any water-insoluble organic

    molecules that can be extracted from cellsby ethers, benzene, or other nonpolar

    solvents.

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    1. TRIGLYCERISESe.g. Fat & oil

    2. PHOSPHOLIPIDSe.g. Lecithin

    3. STEROIDS

    e.g. Cholesterol & Testosterone

    3 MAJORCLASSESOFLIPIDS3 MAJORCLASSESOFLIPIDS

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    FORMATION VIA CONDENSATIONFORMATION VIA CONDENSATION

    Breakdown By Hydrolysis

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    IMPORTANCEOFLIPIDSIMPORTANCEOFLIPIDS

    1. Energy storage

    2. Component of cell membrane

    3. Insulation : blubber

    4. Emulsifiers

    5. Important carriers or precursors ofimportant flavor and odor compounds.

    6. Transports fat-soluble vitamins7. Immune system

    8. Contributes to obesity, coronary heartdisease and other health problems.

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    TRYGLYCERIDETRYGLYCERIDE

    Composed of 3 fatty acid molecules attachedto a glycerol backbone

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    FATTYACIDSFATTYACIDS Long linear hydrocarbon chains

    One end - contains a carboxylic acid group

    The other end is the methyl, "n" or omega end.

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    Classification of fats based on fatty acids

    1. Saturated fat : saturated fatty acid

    2. Unsaturated fat : unsaturated fatty acid

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    Classification fatty acidsClassification fatty acids

    Based on the number of double bonds at the

    hydrocarbon chain :

    1.Saturated fatty acid [ CnH2O2 ] .E.g. Stearic acid.

    2. Unsaturated fatty acid [ CnH2nO2].E.g. Oleic acid.

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    PHOSPHOLIPIDS

    Example : Lecithin (in cell membrane structure).

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    Importance of lecithin in cell membrane

    structure:-

    1. Polarization leads to solubility in water. It act

    as a permeability barrier, so that exchanges

    across this membrane are very limited and

    very slow.

    2. Permeable to water molecules, but not to

    ions such as Na+, K+, and Cl-.

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    STEROIDSExamples : Cholesterol & Testosterone.

    Structure ofSteroids.

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    Structure ofCholesterol.

    S f

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    Structure of testosterone.

    Testosterone :

    Male sex hormone

    that stimulates sperm

    formation, promotes

    the development ofthe male duct system

    in the fetus, and is

    responsible for

    secondary sexcharacteristics such

    as facial hair growth.

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    Steroid abusesSteroid abuses

    Effect of anabolic steroids abuses :

    1. Impotent

    2. Liver tumors

    3. Renal failure

    Effect of topical corticosteroids: clinicalexamples of abuses.

    1. Iatrogenic Cushing syndrome

    2. Ichthyosiform scaling.

    3. Itchy skin lesion

    Oth ff t f t id b

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    Other effects of steroids abuses :

    Cardiovascular disease : heart attack & stroke.

    Cause male-pattern baldness, cysts, acne, and oily hair

    and skin.

    Affect your mood - angry &hostile for no reason.

    There are recorded cases of murder attributed to intense

    anger from steroid use.

    Increase the risk of infection from sharing needles orusing dirty needles to inject steroids puts you at risk for

    diseases such as HIV/AIDS & hepatitis.

    IMPORTANCE OF

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    IMPORTANCEOF

    CHOLESTEROLINHEALTH

    Increase the membrane permeability

    of non-polar solutes. The presence of

    the steroids moves the polar headsfurther apart, giving greater access of

    non-polar substances to the lipid

    layers, plus these materials also tend

    to be soluble in the steroidsthemselves.

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    PROTEIN

    Are always composed of nitrogen, carbon,

    hydrogen and oxygen and sometimes sulphur

    and phosphorus.

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    Function of protein:

    1. Nutrition digestive enzymes.

    2. Transport of respiratory gases

    haemoglobin.

    3. Immunity antibodies.

    4. Co-ordination hormomes.

    5. Growth and repair membrane proteins.6. Support and movement myosin/actin,

    keratin.

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    Protein molecule

    Each different proteins molecule is made under the direction ofits own gene and performs its precise function.

    The shape of it is determined by its amino acids sequence.

    Amino acids are the building blocks from which protein aremade.

    There are about 20 commonly occuring amino acids in protein.

    All have the same basic structure but differ in theirRESIDUAL CHAIN ( R ).

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    Formation of Polypeptides

    Two amino acids can be joined by a condensationreaction to form a dipeptide.

    If any amino acids are joined together by peptidebonds then a polypeptide is formed.

    A polypeptide usually contains hundreds of amino

    acids.

    The repeated sequence (-N-C-C-N-) is the

    polypeptide backbone.

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    Structure of proteins

    A typical protein consists of one or more polypeptidechains which may be folded, branched and cross-linked at intervals.

    Each proteins has a specific three-dimensional shape.

    In describing the structure of a protein, it is usual to

    refer to four separate levels of organization.

    Primary, secondary, tertiary and quaternary.

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    Secondary structure

    Once a linear chain of amino acids is formed it

    spontaneously folds to form a helix or a

    pleated sheet.

    Hydrogen bonds holds the secondary structure

    together.

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    Tertiary structure

    Once they have been folded by hydrogen

    bonds, polypeptides may then fold into a

    globular shape which is maintained by

    hydrogen bonds, ionic bonds and covalentbonds between sulphur atoms in the residual

    chains of the amino acids.

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    Quaternary structure

    Some proteins consists of more than one

    polypeptide chain.

    Human haemoglobin is an example.

    It consists of four chains (two -polypeptide

    chains and two -polypeptide chains) wrapped

    around an iron haem group.

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    NUCLEIC ACID

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    NUCLEIC ACID

    Nucleic Acids are very Large and Complex OrganicMolecules that STORE Important Information in the Cell.(Genetic or Heredity Information)

    Nucleic Acids use a System of FOUR Compounds tostore Heredity Information. A Sequence of the fourcompounds arranged in a certain order acts as a Codefor Genetic Instructions of the Cell.

    DEOXYRIBONUCLEICACID, ORDNA, containsinformation that is essential for almost all Cell Activities,Including Cell Division.

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    RIBONUCLEICACID, ORRNA, Stores

    and Transfers Information essential for the

    Manufacturing of Proteins.

    Both DNA and RNA are Polymers,

    composed of thousands of linked

    Monomers called NUCLEOTIDES.

    STRUCTURE OF DNA AND RNA

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    STRUCTUREOFDNAANDRNA

    Each Nucleotide is made ofTHREEMain

    Components:

    APHOSPHATE GROUP,

    AFIVE-CARBONSUGAR,

    ARING SHAPEDNITROGEN BASE

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    Pentose

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    Pentose

    The sugar found in the nucleotides of DNA isdeoxyribose.

    Ribose is found in RNA.

    Deoxyribose and ribose are pentose sugars(containing 5 carbon atoms).

    The carbon atoms are numbered for orientationand "primes" are used to distinguish the atomsof the sugars from the atoms of the nitrogenousbases in nucleotides.

    Pentose

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    Pentose

    Note that the 5' ("five prime") carbon atom is nota part of the ring.

    The fifth atom of the ring is an oxygen.

    The only difference between deoxyribose andribose is that deoxyribose lacks a hydroxyl groupat the 2' position.

    Thus, the deoxyribose found in nucleic acids ismore properly known as 2'-deoxyribose.

    PENTOSE SUGAR

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    PENTOSE SUGAR

    Bases

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    The nitrogenous bases of nucleotides are ring structuresof nitrogen and carbon with other organic side chains

    attached at specific locations.

    Bases classified as purines have a double structure and,depending on the organic side chains attached, may beeither adenine or guanine.

    Bases classified as pyrimidines have a single ringstructure and may be cytosine, uracil, or thymine.

    The numbering shown around the generalized structures

    in these figures are used for orientation.

    Purines are adenine and guanine

    Pyrimidines are thymine, cytosine and uracil

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    Formation of n cleotide

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    Formation of nucleotide

    Pentose, phosphate group and bases link up toform a nucleotide via condensation reaction.

    Base is joined to carbon atom 1 of the pentose

    molecule.

    Phosphate group attached to the sugar moleculeat atom 5.

    Two molecules of water are removed in theprocess.

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    Formation of polynucleotide

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    Formation of polynucleotide

    Nucleotides are combinded end-to-end to form asingle strand of nucleic acid.

    In a single strand, nucleotides are linked by a

    phosphodiester bond, a covalent bond, betweenthe alpha phosphate of one nucleotide to the 3'carbon of the adjacent nucleotide.

    At one end of the stand, a free (unattached)5'

    phosphate group from the terminal nucleotide isfound.

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    Polynucleotide sequences are referenced

    in the 5' to 3' direction.

    Typically, polynucleotides will contain a 5'

    phosphate and 3' hydroxyl terminal groups.

    The common representation of polynucleotides

    is as an arrow with the 5' end at the left and

    the 3' end at the right.

    Structure of DNA

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    Structure ofDNA

    In most living organisms (except for viruses), geneticinformation is stored in the molecule deoxyribonucleicacid, or DNA.

    DNA is made and resides in the nucleus of living cells.

    DNA gets its name from the sugar molecule contained inits backbone(deoxyribose); however, it gets itssignificance from its unique structure.

    Four different nucleotide bases occur in DNA: adenine(A), cytosine (C), guanine (G), and thymine (T).

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    The DNA molecule is a double helix, as

    shown at right.

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    Th t t d h ld t th b

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    The two strands are held together by

    hydrogen bonds that form between thenitrogenous bases of opposite strands.

    E.g; adenine pairs with thymine and formtwo hydrogen bonds, cytosine pairs with

    guanine and form three hydrogen bonds.

    This known as complementary base

    pairing.

    Structure of RNA

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    Structure ofRNA

    Single strand-stranded molecule.

    Sugar ribose is found in the nucleotide.

    Adenine, guanine, cytosine and uracil.

    Three types; mRNA, rRNA and tRNA.

    Functions of RNA:

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    Functions of RNA:

    mRNA directs the translation of proteins,

    RNAs of ribosomes (1/3 protein and 2/3 RNA)

    probably have functional as well as structural

    roles,

    tRNA delivers amino acids to the ribosomes

    during translation,

    Features DNA RNA

    Basic unit Deoxyribonucleotide Ribonucleotide

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    Basic unit Deoxyribonucleotide Ribonucleotide

    Pentose Deoxyribose Ribose

    Nitrogenous base Adenine, Guanine,

    Cytosine, Thymine

    Adenine, Guanine,

    Cytosine, Uracil

    Structure double helix consisting of two chains (STRANDS)

    of nucleotides coiled

    around each other

    single strand

    Size Large molecule Relatively small

    molecule

    Location In the nucleus In the nucleus and

    cytoplasm

    Type One Three

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    End of this topic