UNIT 1 - Chapters 4,5UNIT 1 - Chapters 4,5

THE CHEMISTRY OF LIFETHE CHEMISTRY OF LIFE

Carbon and its role in life

• Although living cells are made up of 70% - 90% water, most of the “meat and potatoes” is made up of carbon based compounds

• Carbon is a solid in its natural state

• The study of carbon compounds is called Organic Chemistry

• Carbon can form 4 covalent bonds

• The simplest organic molecule is CH4 or methane

Hydrocarbons

• A carbon backbone surrounded with hydrogen• Hydrocarbons can exist as straight chains, rings, and

several other structural forms• A simple chain of carbons with its full complement of

hydrogens (single C-C bonds) is said to be saturated. These saturated, simple, straight chain hydrocarbons are known as alkanes.

• Hydrocarbons with double bonds in them are said to be unsaturated. Their molecules contain at least one double bond.

• Hydrocarbons containing double C-C covalent bonds are called alkenes and those with triple bonds are alkynes

Alkanes

Straight-chain alkanes Ring-form alkanes

Alkenes

Can you name these alkenes?

Ethene or ethylene

Propene or propylene Butene or butylene

Alkynes

Can you name these alkynes?

Ethyne Propyne

Butyne

IsomersIsomers

• Sometimes two hydrocarbon molecules Sometimes two hydrocarbon molecules can have the same numbers of the same can have the same numbers of the same atoms but have different arrangements of atoms but have different arrangements of these atoms. These are called these atoms. These are called isomersisomers

• There are 3 major types of isomers: There are 3 major types of isomers: Structural, Geometric and enantiomersStructural, Geometric and enantiomers

Structural Isomers

• Have the same molecular formula, but different covalent arrangement of their atoms – so different chemical properties

Butane vs. isobutane

Geometric Isomers•Involve molecules with double bonds that prevent free rotation•The inflexibility of the double bonds allows for different shapes and hence different properties

cis ethylene dibromide vs. trans ethylene dibromide

cis-2-butene vs. trans-2-butene

Enantiomers•Different molecular arrangements around an asymmetric Carbon •An asymmetric carbon is one with 4 different atoms or groups of atoms around it•They are mirror images and cannot be superimposed (Chiral)•They have right-hand (D - for dextrorotatory ) and left-hand (L – for levorotatory) versions•There are many enantiomers in a living cell, but usually only one of the two is active (the cell can distinguish between the two)

Enantiomers, cont’d.

• For example, S-caravone ("left-handed") is the flavor of caraway, while R-carvone ("right-handed") is the flavor of spearmint.

• An example of this is thalidomide which is racemic — that is, it contains both left and right handed isomers in equal amounts. One enantiomer is effective against morning sickness, and the other is teratogenic. It should be noted that the enantiomers are converted to each other in vivo. That is, if a human is given D-thalidomide or L-thalidomide, both isomers can be found in the serum. Hence, administering only one enantiomer will not prevent the teratogenic effect in humans.

SpearmintCaraway

Functional GroupsFunctional Groups

• These are the parts of a molecule that give These are the parts of a molecule that give the molecules its “personality”the molecules its “personality”

• Functional groups are the parts of a Functional groups are the parts of a molecule that are molecule that are most involvedmost involved in in chemical reactionschemical reactions

• Functional groups have specific behaviors, Functional groups have specific behaviors, regardless of which molecule they are regardless of which molecule they are found in (although the molecules found in (although the molecules themselves have unique properties)themselves have unique properties)

Functional groups

commonly found in living cells

The Hydroxyl Group

• -OH • The hydroxyl group is polar because of the

oxygen atom and makes a compound soluble

• Organic compounds containing OH groups as the prominent functional group are called alcohols

• Most alcoholic compounds end with “ol” as in ethanol, methanol, glycerol, etc.

The Carbonyl GroupThe Carbonyl Group

• -C=O (Carbon and oxygen sharing a double -C=O (Carbon and oxygen sharing a double covalent bond)covalent bond)

• If the carbonyl group is at the end of a If the carbonyl group is at the end of a hydrocarbon chain (terminal), the compound is hydrocarbon chain (terminal), the compound is considered an considered an aldehydealdehyde; these compounds ; these compounds usually contain an “al” as in usually contain an “al” as in PropanalPropanal or or FormaldehydeFormaldehyde

• If the carbonyl group is not terminal, the If the carbonyl group is not terminal, the compound is considered acompound is considered a ketone ketone; these ; these compounds usually contain an compounds usually contain an “one”“one” as in as in AcetoneAcetone or or PropanonePropanone

The Carboxyl Group

• Compounds with this functional group are called carboxylic acids, because they tend to give up the H from the –OH group (This is because the 2 oxygen atoms in the carboxyl group pull the shared electrons away from the H)

• If the –OH was alone or far away from the C=O, the H would not dissociate as easily

+ H+

Acetic Acid Acetate Ion Proton

The Amine Group• A nitrogen atom bonded to 2 Hydrogens• Acts as a base, because the –NH2 or NH3

can pick up protons (H+) from their surroundings; remember nitrogen’s lone pair of electrons that attract H+ ions?

Ammonium ion

Amino Acids• These compounds have both: a carboxyl group as well as an amino group• Sometimes both the carboxyl end and the amino end are in the ionized state

– these are now called zwitterions

Zwitterion

The Phosphate Group• PO4

• Derived from phosphoric acid• The Hydrogens tend to dissociate easily due to the

number and proximity of oxygen atoms • So phosphoric acid becomes a phosphate ion• Very important component of the DNA backbone

P

O

O-

O

O-

-Phosphate ion

The Sulfhydryl Group

• S-H• Sulfur is under Oxygen in the

periodic table, both can form 2 covalent bonds

• Organic compounds containing sulfhydryl groups are called Thiols

• Sulfhydryl groups are found in certain amino acids like cysteine and methionine and are extremely important in the tertiary structure of proteins

The Structure and Function of Macromolecules

Polymers

• Large compounds made of repeating subunits of a smaller compound called monomers

• Formed by dehydration synthesis (Condensation reaction)

• Dissociated by hydrolysis

Four Biological MacromoleculesFour Biological Macromolecules

• CarbohydratesCarbohydrates – Range from simple sugars, – Range from simple sugars, to complex carbs like starch.to complex carbs like starch.

• LipidsLipids – Include oils, fats, waxes and steroids. – Include oils, fats, waxes and steroids. They are the only macromolecules that are not They are the only macromolecules that are not considered polymersconsidered polymers

• ProteinProtein – made up of repeating units of amino – made up of repeating units of amino acidsacids

• Nucleic AcidsNucleic Acids – DNA, tRNA, mRNA, rRNA– DNA, tRNA, mRNA, rRNA

CARBOHYDRATES• The building blocks are simple “single” sugars called

monosaccharides• Sugars contain a hydrocarbon backbone, with 2

important functional groups: - multiple hydroxyl groups and a- carbonyl group

• Monosaccharides can bond to each other and form disaccharide (2), oligosaccharides (~10) or polysaccharides (100s or 1000s)

• Sugars are named according to:- the number of carbons in their backbone- and the location of the carbonyl group

• Another characteristic of monosaccharides is that they can act as mild reducing agents. This is because the aldehyde group (Carbonyl) that is present can be oxidized to form a carboxylic acid group, or in the presence of a base, a carboxylate ion group.

Structure of some Monosaccharides

(also known as dextrose)

Sugars end in “ose”

Linear versus Ring forms

Sugars tend to change into ring forms when placed in an aqueous solution. Here is an example of straight chain glucose changing into its ring form. But while in solution, the molecules can keep changing back-and-forth from chain to ring, ring to chain.

α and β forms of glucose

When the glucose molecule takes on a ring form, it can form one of 2 isomers. The tiny difference between these two isomers of the same molecule means that the polysaccharide that they form is different. The 2 isomers, α and β forms of glucose is evident in the diagrams above.

OH group on top

OH group on the bottom

Making Disaccharides• 2 glucose molecules bond covalently to form maltose• 1 fructose and 1 glucose bond to form sucrose (table sugar)• 1 glucose and 1 galactose bond to form lactose (found in milk

and dairy products)

People who are lactose intolerant, do not make lactase, an intestinal enzyme that hydrolyzes lactose into its constituent monosaccharides, glucose and galactose which can then be easily absorbed into the blood, across the intestinal lining. When lactose cannot be broken down, it ferments in the gut and causes bloating, diarrhea, flatulence, etc.

70% of the world population is lactose intolerant. However, only 10% of Europeans are.

Making Polysaccharides

• Multiple monosaccharides form chains by forming covalent bonds through dehydration synthesis. These covalent bonds are called glycosidic linkages.

• Polysaccharides can be considered either “storage polysaccharides” or “structural polysaccharides”, based on their structure and role in cells.

Storage Polysaccharides•Plants store their polysaccharides as starch. So starch = stored energy.•Starch s made up of 2 types of polysaccharides - amylose and amylopectin•Amylose is α-glucose molecules in 1-4 glycosidic linkages•Amylopectin is α-glucose molecules in 1-4 as well as 1-6 glycosidic linkages. This makes amylopectin more highly branched.•Starch is stored in plant cellular organelles called plastids, including amyloplasts and chloroplasts.

Storage Polysaccharides, cont’d.• Animals store their polysaccharides as glycogen. Glycogen = stored energy• Glycogen is made up of a-glucose molecules in 1-4 as well as 1-6 glycosidic

linkages. It is similar to amylopectin, but more highly branched.• Animals store glycogen in muscle and liver cells, in cellular organelles called

mitochondria. Here it is hydrolyzed into glucose molecules, for cellular respiration.

• Animals derive glucose from food – mainly starch from plants, which is hydrolyzed by the enzyme amylase, into glucose, absorbed into the blood stream and the excess is converted into glycogen for storage.

Starch - α-glucose moleculesPlant-storage polysaccharide

•α-glucose molecules combine in 1-4 glycosidic linkages to form amylose, the simplest form of starch. The fact that in α-glucose both hydroxide groups are on the bottom of the ring means that all of the monosaccharide rings are in the same plane. This polysaccharide is easily metabolized by the human digestive system; in fact, it is the principal source of energy for most people.

•Starch also consists of another more complex form called amylopectin. The only difference between amylose and amylopectin is that amylopectin is branched – it has 1-4 as well as 1-6 glycosidic linkages.

Cellulose – β-glucose moleculesPlant structural polysaccharide

β-glucose molecules combine to form cellulose. Because of the structure of β-glucose, in cellulose every other sugar molecule is upside-down to accommodate 1-4 linkages. Cellulose is mainly found in plant cell walls.

Cellulose is also known as dietary fiber. This polysaccharide cannot be broken down by the human digestive system. Instead, it passes unaffected through the intestine, with no nutritional value. Grass-eating animals cannot break it down either, but rely on bacteria in their guts to break it down for them. Termites do not produce cellulase, but share a symbiotic relationship with protozoans in their gut who do produce the enzyme.

Chitin – β-glucose moleculesAnimal structural polysaccharide

Chitin is almost identical to cellulose, except that its glucose monomers contain a nitrogen-containing side chain. Chitin is found in the cell walls of fungi and arthropod exoskeletons (insects, crustaceans, arachnids).

Cellulose, chitin, and starch are the three most abundant

organic compounds in nature.

Reducing Sugars• Another characteristic of monosaccharides is that they can act as mild

reducing agents. This is because the aldehyde group that is present can be oxidized to form a carboxylic acid group, or in the presence of a base, a carboxylate ion group.

• Fructose can also act as a reducing sugar, even though it has a ketone group instead of an aldehyde group. Under basic conditions, the fructose molecules can, essentially, have the location of the carbonyl bond switched to convert them into a glucose molecule. This occurs in a number of steps involving removing hydrogens from the #1-C and its oxygen and moving them to the #2-C and its oxygen.

• In one sense, monosaccharides that are in the ring form are not reducing sugars because they don't have the aldehyde group that can be oxidized. However, because they're in equilibrium with the open form, any monosaccharide molecule that's in a ring form will, within a fraction of a second, be in the open form and, thus, be able to react with the oxidizing agent and reduce it.

LaboratoryDetecting reducing sugars in solution

• What is Benedict’s Solution?

It is a deep-blue alkaline solution used to test for the presence of the aldehyde functional group, -CHO.

The substance to be tested is heated with Benedict's solution; formation of a brick-red precipitate indicates presence of the aldehyde group.

Simple sugars (e.g., glucose) give a positive test,

One liter of Benedict's solution contains 173 grams sodium citrate, 100 grams sodium carbonate, and 17.3 grams cupric sulfate pentahydrate. Benedict's solution contains copper(II) ions complexed with citrate ions in sodium carbonate solution. The cupric ion (complexed with citrate ions) is reduced to cuprous ion by the aldehyde group (which is oxidized), and precipitates as cuprous oxide, Cu2O, which is a deep brick red.

RCHO + 2 Cu 2+ (in complex) + 5OH- RCOO- + Cu2O + 3H2O

Benedict’s Test Results

5 50 23

Detecting starch in solutionAmylose and amylopectin

• When starch is mixed with iodine in water, an intensely colored starch / iodine complex is formed. Starch consists of two types of molecules, amylose (normally 20-30%) and amylopectin (normally 70-80%). The unbranched amylose is a chain of glucose molecules bounded together. The chain is coiled in the shape of a helix. The iodine (in the form of KI5) inserts itself into the helix making it rigid. This changes the color to blue. Helix amylose possesses a relatively hydrophobic inner surface that holds a spiral of water molecules. It is responsible for the characteristic binding of amylose to chains of charged iodine moleclues (polyiodides formed from neutral iodine molecules in aqueous solution). The blue color is due to donor acceptor interactions between water and the electron deficient polyiodides. When heat is applied, the complex is destroyed. When the solution has cooled the 'blue' of the amylose/iodine combination appears.

• Starch from different sources contains different proportions of amylose and amylopectin. Waxy rice consists of 100% amylopectin and no amylose. Amylopectin having a branching structure does not form a helix. It reacts with iodine to form red-brown color.

Iodine Test Results

0 2 0 1

Lipids

• Lipids are the only major biological macromolecules that are not polymers (no repeating units)

• The lipid family consists of fats, oils, waxes, phospholipids and steroids.

• All lipids are hydrophobic (completely or partially)

Fats - Triglycerides

• If they contain only single bonds, they are considered saturated (carrying their full complement of Hydrogen atoms.

• If they contain double or triple bonds, they are considered either mono or poly unsaturated

•Fats or triglycerides are composed of 3 fatty acids and one glycerol molecule.•Fatty acids are long hydrocarbon chains with a terminal carboxyl group

•The “tail” of a fatty acid is a long hydrocarbon chain, making it hydrophobic. The “head” of the molecule is a carboxyl group which is hydrophilic.

•They have varying lengths and may contain double or triple bonds

Fats – Triglycerides, cont’d.

• Fats and oils are made from two kinds of molecules: glycerol (a type of alcohol with a hydroxyl group on each of its three carbons) and three fatty acids joined by dehydration synthesis. Since there are three fatty acids attached, these are known as triglycerides.

• Although fatty acids are part hydrophilic, when the head end is attached to glycerol to form a fat, the whole fat molecule is hydrophobic.

Is this a saturated or unsaturated fat?

Fat = 1 glycerol + 3 fatty acidsFat = 1 glycerol + 3 fatty acids

3 ester linkages (OH + COOH) are formed through dehydration synthesis, 3 ester linkages (OH + COOH) are formed through dehydration synthesis, releasing 3 water molecules.releasing 3 water molecules.

Fats vs. Oils• Saturated fats tend to have a high melting

point, because their fatty acid chains are straight and the fat molecules can pack closely together making them solid at room temperature. Saturated fats are found in animals (lard) and are to blame for clogging arteries!

• Unsaturated fats have kinks in their tails, so they cannot pack closely. This gives them a low melting point and the tendency to be liquid at room temperature and are called oils. Oils are found in plants and fish. Much better for your arteries!

What are Hydrogenated Fats?

• Oils tend to have a shorter shelf life because they become rancid – oxidized through exposure to air and light

• Oils are therefore often “artificially saturated” or hydrogenated, so they become solid at room temperature and more stable

Trans-Fatty acids

• The body utilizes the curved structure of unsaturated fats to

a) form pathways in and out of cells,

b) to transmit electric impulses. Double bonds (cis) have a slight charge where single bonds and straightened (trans) double bonds do not. This makes the passage of cis-fatty acids across membranes easier.Omega-3 oils, which are healthy unsaturated

oils, are simply oils that contain a double bond after the 3rd carbon atom. Omega-6 oils contain a double bond after the 6th carbon atom. A healthy diet should contain a balance of both omega-3 and omega-6 oils.

Wax

• Wax has traditionally referred to a substance that is secreted by bees (beeswax) and used by them in constructing their honeycombs.

• In modern terms, wax is an imprecisely defined term generally understood to be a substance with properties similar to beeswax, namely

• plastic (malleable) at normal ambient temperatures • a melting point above approximately 45 °C (which differentiates

waxes from fats and oils) • a relatively low viscosity when melted (unlike many plastics) • insoluble in water • hydrophobic • Waxes may be natural or artificial. In addition to beeswax, carnauba (a

vegetable wax) and paraffin (a mineral wax) are commonly encountered waxes which occur naturally. Ear wax is a sticky substance found in the human ear. Some artificial materials that exhibit similar properties are also described as wax or waxy.

• Chemically, a wax may be an ester of ethylene glycol (ethan-1,2-diol) and two fatty acids, as opposed to a fat which is an ester of glycerin (propan-1,2,3-triol) and three fatty acids. It is a type of lipid.

Eeeeewww! Ear Wax!

• Cerumen is produced in the outer third of the cartilaginous portion of the human ear canal. It is a mixture of viscous secretions from sebaceous glands and less-viscous ones from modified apocrine sweat glands (Alvord & Farmer, 1997). Cerumen is genetically determined – Asians and Native Americans are more likely to have the dry type of cerumen (grey and flaky), whereas Caucasians and Africans are more likely to have the wet type (honey-brown to dark-brown and moist; Overfield, 1985). In fact, cerumen type has been used by anthropologists to track human migratory patterns, such as those of the Inuit (Bass & Jackson, 1977).

Phospholipids• Phospholipids are diglycerides that are covalently bonded

to a phosphate group by an ester linkage • In many cells the phospholipids are further modified by

the covalent bonding of additional compounds the phosphate.

Phospholipids, cont’d.

• Phospholipids are amphipathic• When phospholipids are

suspended in water they can form a variety of structures. In all cases the hydrophilic phosphate region interacts with water and the hydrophobic fatty acid regions are excluded from water and form hydrophobic interactions.

How do detergents work?

1. Made up of phospholipids

2. The hydrophobic tails surround greasy dirt particles

3. Hydrophilic heads face water and lift the grease to the surface

4. Water washes off trapped grease particle

Phospholipid Bilayers • One structure that can result when phospholipids are suspended in

water is shown below. A bilayer of phospholipids forms a sphere in which water is trapped inside. The hydrophilic phosphate regions interact with the water inside and outside of the sphere. The fatty acids of the phospholipids interact and form a hydrophobic center of the bilayer.

PL bilayers form plasma (cell) membranesPL bilayers form plasma (cell) membranes

Steroids• Another major class of lipids is

steroids, which have structures totally different from the other classes of lipids. The main feature of steroids is the ring system of three cyclohexanes and one cyclopentane in a fused ring system as shown below. There are a variety of functional groups that may be attached. The main feature, as in all lipids, is the large number of carbon-hydrogens which make steroids non-polar.

• Steroids include such well known compounds as cholesterol, sex hormones, birth control pills, cortisone, and anabolic steroids.

Proteins

• Proteins can be categorized into several different families, depending on their role in a living organism

• Amino acids are the building blocks of proteins

• There are over 100 amino acids, only 20 of which are used in protein building, by all organisms

Collagen

Catalase, Amylase

DNA Polymerase

An amino acid

2 is in the Zwitterion state – when a compound can exist as an anion and a cation at the same time

The 20 Amino

acids used for protein synthesis

These amino acids have been separated according to the chemical properties of their side chains

Source of amino acids• Unlike by plants, most amino acids cannot be synthesized by

animals. Those that cannot be synthesized are called essential amino acids (EAA) and animals have to rely on obtaining them through their diet (either from plants or from other animals which already contain them) or on their synthesis by gut bacteria.

The Essential Amino Acids

Histidine

Isoleucine

Leucine

Lysine

Methionine (and/or cysteine)

Phenylalanine (and/or tyrosine)

Threonine

Tryptophan

Valine

Dipeptides, Polypeptides

• Amino acids are joined end – to –end by enzymes through dehydration synthesis, to form polypeptides (releasing a water molecules as a by product)

• The covalent bond that forms between the carbon of one amino acids and the nitrogen of another is called a peptide bond.

Polypeptides• All polypeptides have a carboxyl end (C-

terminus) and an amino end (N-terminus)

N-terminus

C-terminus

Protein structureProtein structure

• Once a polypeptide forms, it tends to fold Once a polypeptide forms, it tends to fold into several possible structuresinto several possible structures

• These structures form due to various types These structures form due to various types of bonding and chemical interactions of bonding and chemical interactions between the amino acids in the chainbetween the amino acids in the chain

Primary Structure

• The first level of structure is called primary structure. The primary structure of a peptide or protein is simply the sequence of amino acids. The sequence of amino acids determines the structural and functional characteristics of the protein. Proteins with very different sequences of amino acids (different primary structures) will have very different properties.

• The primary structure is held together by peptide (covalent) bonds

Secondary Protein StructureSecondary Protein Structure-Helix and -Helix and -pleated sheets-pleated sheets

•Depending on the sequence of amino acids, a Depending on the sequence of amino acids, a polypeptide chain can fold in a number of ways. This polypeptide chain can fold in a number of ways. This folding will be driven in part by the tendency of folding will be driven in part by the tendency of hydrophobic side chains to minimize their contact with hydrophobic side chains to minimize their contact with water and hydrophilic side chains to maximize their water and hydrophilic side chains to maximize their contact with water. contact with water.

•In an In an - helix, hydrogen bonding between every fourth - helix, hydrogen bonding between every fourth amino acid maintains the structureamino acid maintains the structure•In In -pleated sheets, the hydrogen bonding is between -pleated sheets, the hydrogen bonding is between adjacent amino acidsadjacent amino acids

Secondary Protein Structure-Helix and -pleated sheets

•Depending on the sequence of amino acids, a polypeptide chain can fold in a number of ways. This folding will be driven in part by the tendency of hydrophobic side chains to minimize their contact with water and hydrophilic side chains to maximize their contact with water. •In an - helix, hydrogen bonding between every fourth amino acid maintains the structure•In -pleated sheets, the hydrogen bonding is between adjacent amino acids

Tertiary StructureTertiary Structure• This occurs when the protein folds into a This occurs when the protein folds into a

complex 3-dimensional shapecomplex 3-dimensional shape• It involves many different kinds of bonds and It involves many different kinds of bonds and

interactions between amino acids side chains interactions between amino acids side chains such as: Hydrogen bonds, Hydrophobic such as: Hydrogen bonds, Hydrophobic interactions, Van der Waals forces, disulfide interactions, Van der Waals forces, disulfide bridges and ionic bonds.bridges and ionic bonds.

• These proteins are usually called globular and These proteins are usually called globular and are soluble in waterare soluble in water

• Enzymes are examples of globular proteinsEnzymes are examples of globular proteins

Tertiary Structure

Quaternary Structure• When multiple tertiary

structures interact to form a more complex globular protein, it is called a quaternary structure

• Hemoglobin is a protein made up of 4 tertiary protein chains

• The quaternary structure is usually held together by hydrogen bonds between the chains

Protein Structure Summary, cont’d.

Protein Denaturation

• When a protein loses its tertiary or secondary structure, it also loses its function – it is denatured

• A change in pH (treatment with an acid or base), or temperature (freezing or boiling) can cause a protein to denature

• Occasionally, if the denatured protein remains dissolved, it can return to its original conformation when the denaturing agent is removed.

Protein Manufacture

• Polypeptides are assembled at the ribosomes

• They are then folded into their native configuration either in the endoplasmic reticulum, or in the cell cytoplasm

• This folding is “supervised” by many proteins called Chaperone proteins.

Biuret Reagent for protein detection

Nucleic Acids• Category consists of DNA and RNA• DNA = Deoxyribonucleic Acid, RNA = Ribonucleic Acid• DNA is double stranded, contains the sugar deoxyribose and

the nitrogenous bases Thymine, Adenine, Guanine and Cytosine

• RNA is single stranded (usually), contains the sugar ribose and the nitrogenous bases Uracil, Adenine, Guanine and Cytosine

Nucleotide triphosphates• A nucleotide is the building block of DNA or RNA• It consists of a 5-Carbon sugar (either ribose or deoxyribose), 1

Phosphate groups and a Nitrogenous base• A nucleotide that has not been incorporated into DNA starts out with 3

phosphates instead of 1• 2 of the 3 phosphates are hydrolyzed by enzymes. This gives the

enzyme energy to incorporated the nucleotide into the DNA

Deoxyribonucleotide triphosphate (dNTP)

Enzymatic hydrolysis of high Energy bond between 2nd and 3rd

Phosphates

Deoxyribonucleotide monophosphate (dNMP)

Pyrophosphate released( Inorganic phosphate (PPi) )

Incorporation of Nucleotides into DNA

The Nitrogenous Bases• They are Nitrogen-containing

compounds that are basic in nature – but overall, DNA is mildly acidic

• Divided into Purines and Pyrimidines

• Purines are larger in structure than pyrimidines

• Adenine and Guanine are purines

• Cytosine, Thymine and Uracil are pyrimidines

• A and T or A and U can form 2 Hydrogen bonds

• G and C form 3 Hydrogen bonds (a stronger alliance than A-T)

Guanine and Cytosine

Adenine and Thymine

DNA is antiparallel. DNA is antiparallel. One strand runs 5’ to One strand runs 5’ to 3’ and the other 3’ to 3’ and the other 3’ to 5’. This is the only 5’. This is the only

configuration that will configuration that will allow proper H bond allow proper H bond

formation and formation and distances between distances between

the bases.the bases.

Su

gar

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osp

hat

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ackb

on

e

Su

gar-p

ho

sph

ate backb

on

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5’ t

o 3

’ dir

ecti

on

3’ to 5’ d

irection

DNA in a nutshell• 2 antiparallel strands• Sugar-Phosphate backbone held together

by phosphodiester bonds • Right-handed • One full turn every 3.4 nm or 10 base pairs • Sugar phosphate backbones on the outside • Bases stacked on the inside • Purine-pyrimidine pairing, stabilized by H

bonds (G=C) and (A=T) • B-DNA form is most common in organisms• Major groove and minor groove – major

groove is where enzymes that replicate DNA bind to the molecule

Maj

or

gro

ove

Min

or

gro

ov

e

DNA - View from the top

DNA gets packaged into a chromosome

Types of RNA