chemical properties of water - part 1

©1998 by Alberts, Bray, Johnson, Lewis, Raff, Roberts, Walter. http://www.essentialcellbiology.com Published by Garland Publishing, a member of the Taylor & Francis Group.

Chemical Properties of Water - Part 1

HYDROGEN BONDS

hydrogen bond

d +Because they are polarized, twoadjacent H2O molecules can forma linkage known as a hydrogenbond. Hydrogen bonds have only about 1/20 the strengthof a covalent bond.

Hydrogen bonds are strongest whenthe three atoms lie in a straight line. d +

d +2d _

d +

2 d _

H

H

H

H

O O

H

H

HO

0.10 nmcovalent bond

bond lengths

hydrogen bond0.27 nm

H

O

H

WATER

Two atoms, connected by a covalent bond, may exert different attractions forthe electrons of the bond. In such cases the bond is polar, with one end slightly negatively charged ( d _

) and the other slightly positively charged ( d +).

Although a water molecule has an overall neutral charge (having the same number of electrons and protons), the electrons are asymmetrically distributed, which makes the molecule polar. The oxygen nucleus draws electrons away from the hydrogen nuclei, leaving these nuclei with a small net positive charge. The excess of electron density on the oxygen atom creates weakly negative regions at the other two corners of an imaginary tetrahedron.

Molecules of water join together transientlyin a hydrogen-bonded lattice. Even at 37oC,15% of the water molecules are joined tofour others in a short-lived assembly knownas a “flickering cluster.”

The cohesive nature of water isresponsible for many of its unusualproperties, such as high surface tension,specific heat, and heat of vaporization.

WATER STRUCTURE

electropositiveregion

electronegativeregion

d +

d _

d _

d _

d _

d _

d _

d _

d +

d +

d +

d +d +

d +

H

H O

Na+

O

H

H

H

H

H

H

O

O

O

H

H

O

O

H

HH

H

O

H

H

OH

H

OH H

Cl_

O

O

H H

H

H O

H

H

O

H

H

O

H

C

N

N

OH

H

H H

H

H

OH

Substances that dissolve readily in water are termed hydrophilic. They arecomposed of ions or polar molecules that attract water molecules throughelectrical charge effects. Water molecules surround each ion or polar moleculeon the surface of a solid substance and carry it into solution.

Ionic substances such as sodium chloride dissolve because water molecules are attracted to the positive (Na+) or negative (Cl

_) charge of each ion.

Polar substances such as urea dissolve because their moleculesform hydrogen bonds with the surrounding water molecules

HYDROPHILIC MOLECULES HYDROPHOBIC MOLECULESMolecules that contain a preponderance of non-polar bonds are usually insoluble in water and are termed hydrophobic. This is true, especially, of hydrocarbons, which contain many C–H bonds. Water molecules are not attracted to such molecules and so have little tendency to surround them and carry them into solution.

H

O

O

HO

HO

H

H

H

H

O

H

H

H O

H

HH

C

H H

C

H H

H

C

O

H

H

O


Chemical Properties of Water - Part 2

WATER AS A SOLVENT

ACIDS

10_1

10_2

10_3

10_4

10_5

10_6

10_7

10_8

10_9

10_10

10_11

10_12

10_13

10_14

1

2

3

4

5

6

78

9

10

11

12

13

14

pHH+

conc.moles/liter

ALK

ALI

NE

AC

IDIC

The acidity of asolution is definedby the concentration of H+ ions it possesses.For convenience weuse the pH scale, where

pH = _log10[H+]

For pure water

[H+] = 10_7 moles/liter

Substances that release hydrogen ions into solutionare called acids.

Many of the acids important in the cell are only partially dissociated, and they are therefore weak acids—for example,the carboxyl group (–COOH), which dissociates to give ahydrogen ion in solution

Note that this is a reversible reaction.

Many substances, such as household sugar, dissolve in water. That is, theirmolecules separate from each other, each becoming surrounded by water molecules.

When a substance dissolves in a liquid, the mixture is termed a solution. The dissolved substance (in this case sugar) is the solute, and the liquid thatdoes the dissolving (in this case water) is the solvent. Water is an excellentsolvent for many substances becauseof its polar bonds.

pH

HYDROGEN ION EXCHANGE

Substances that reduce the number of hydrogen ions insolution are called bases. Some bases, such as ammonia,combine directly with hydrogen ions.

Other bases, such as sodium hydroxide, reduce the number of H+ ions indirectly, by making OH– ions that then combine directly with H+ ions to make H2O.

Many bases found in cells are partially dissociated and are termed weak bases. This is true of compounds that contain an amino group (–NH2), which has a weak tendency to reversibly accept an H+ ion from water, increasing the quantity of free OH– ions.

Positively charged hydrogen ions (H+) can spontaneouslymove from one water molecule to another, thereby creatingtwo ionic species.

often written as:

Since the process is rapidly reversible, hydrogen ions arecontinually shuttling between water molecules. Pure water contains a steady state concentration of hydrogen ions andhydroxyl ions (both 10–7 M).

BASES

water molecule

sugar crystal sugar molecule

sugardissolves

hydronium ion(water acting as

a weak base)

hydroxyl ion(water acting as

a weak acid)

H2O H+ OH–+

hydrogenion

hydroxylion

HClhydrochloric acid

(strong acid)

H+

hydrogen ionCl–

chloride ion+

H+

hydrogen ionNH3

ammoniaNH4

+

ammonium ion+

OH–Na+NaOH +

–NH2 + H+ –NH3

+

H+ +

(weak acid)

C

O

OH

C

O

O–

H H

H

HO

H

H

OO

H

OH ++

sodium hydroxide(strong base)

sodiumion

hydroxylion


Chemical Bonds and Groups - Part 1

CARBON SKELETONS

C

C

C

C

C

C

C

C

C

C

C

C

C

C

C

C

C

C

also written as also written as

or rings

Carbon has a unique role in the cell because of itsability to form strong covalent bonds with othercarbon atoms. Thus carbon atoms can join to formchains.

or branched trees

C

C

C

C

C

C

also written as

C

C

C

C C

C C C

C C

C

C

C

C C

C C C

C C

H

H

H

H

H

H

H

H

H

H

H

H

often written as

The carbon chain can include doublebonds. If these are on alternate carbonatoms, the bonding electrons movewithin the molecule, stabilizing thestructure by a phenomenon calledresonance.

Alternating double bonds in a ringcan generate a very stable structure.

the truth is somewhere betweenthese two structures

C H

H

H

H C

H

H

H

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

H2C

CH2

H3C

CH2

Carbon and hydrogen togethermake stable compounds (orgroups) called hydrocarbons. These are nonpolar, do not form hydrogen bonds, and aregenerally insoluble in water.

methane methyl group

part of the hydrocarbon “tail”of a fatty acid molecule

C–H COMPOUNDS

ALTERNATING DOUBLE BONDS

C N O

C N O

Double bonds exist and have a different spatial arrangement.

A covalent bond forms when two atoms come very close together and share one or more of their electrons. In a single bond one electron from each of the two atoms is shared; in a double bond a total of four electrons are shared. Each atom forms a fixed number of covalent bonds in a defined spatial arrangement. For example, carbon forms four single bonds arranged tetrahedrally, whereas nitrogen formsthree single bonds and oxygen forms two single bonds arranged as shown below.

COVALENT BONDS

Atoms joined by twoor more covalent bondscannot rotate freely around the bond axis.This restriction is amajor influence on thethree-dimensional shape of many macromolecules.

benzene


Chemical Bonds and Groups - Part 2

C–O COMPOUNDS

H

H

C OH

C

H

OC

O

C

OH

O

C C

OH

O

HO C C

O

CO

H2O

Many biological compounds contain a carbonbonded to an oxygen. For example,

The –OH is called ahydroxyl group.

The C—O is called acarbonyl group.

The –COOH is called acarboxyl group. In waterthis loses an H+ ion tobecome –COO

_.

Esters are formed by combining anacid and an alcohol.

esters

carboxylic acid

ketone

aldehyde

alcohol

acid alcohol ester

C–N COMPOUNDS

Amines and amides are two important examples ofcompounds containing a carbon linked to a nitrogen.

Amines in water combine with an H+ ion to becomepositively charged.

Amides are formed by combining an acid and anamine. Unlike amines, amides are uncharged in water.An example is the peptide bond that joins amino acidsin a protein.

Nitrogen also occurs in several ring compounds, includingimportant constituents of nucleic acids: purines and pyrimidines.

cytosine (a pyrimidine)

C N

H

H

H+ C N

H

H

H+

C

OH

O

CH2N

C

C

N

O

H

H2O

C C

CN

O

H

H

H

N

NH2

PHOSPHATES

P O_

O_

HO

O

Inorganic phosphate is a stable ion formed fromphosphoric acid, H3PO4. It is often written as Pi.

—

C

C

P

C OH P O_

HO

O

C P O_

O

O

O_

O_ C O

H2O

alsowritten as

Phosphate esters can form between a phosphate and a free hydroxyl group.Phosphate groups are often attached to proteins in this way.

high-energy acyl phosphatebond (carboxylic–phosphoricacid anhydride) found insome metabolites

phosphoanhydride—a high-energy bond found inmolecules such as ATP

The combination of a phosphate and a carboxyl group, or two or more phosphate groups, gives an acid anhydride.

C

OH

O

P O_

HO

O

O_

C

O

P O_

O

O

O_

C

O

O P

also written as

P

O_

OH

O

P O_

O

O

O_

HO P

O

O_

O P O_

O

O_

OP

also written as

PO

H2O

H2O

H2O

H2O

C

acid amideamine


Types of Weak Non-covalent Bonds - Part 1

At very short distances any two atoms show a weak bonding interaction due to their fluctuating electrical charges. If the two atoms are too close together, however, they repel each other very strongly.

VAN DER WAALS FORCES

attr

acti

on

r

epu

lsio

n

distance between centers of atoms

0

van der Waals contact distance

Each atom has a characteristic “size,” or van der Waalsradius: the contact distance between any two atoms isthe sum of their van der Waals radii.

Two atoms will be attracted to each other by van der Waals forcesuntil the distance between them equals the sum of their van der Waals radii. Although they are individually very weak, vander Waals attractions can become important when two macromolecular surfaces fit very close together.

0.2 nm0.12 nm 0.15 nm 0.14 nm

ONCH

Organic molecules can interact withother molecules through short-rangenoncovalent forces.

WEAK CHEMICAL BONDS

Weak chemical bonds have less than 1/20 the strength of astrong covalent bond. They are strong enough to providetight binding only when many of them are formedsimultaneously.

weakbond

As already described for water (see Panel 2–2, pp. 50–51) hydrogen bonds form when a hydrogen atom is “sandwiched” between two electron-attracting atoms (usually oxygen or nitrogen).

HYDROGEN BONDS

Hydrogen bonds are strongest when the three atoms are in a straight line:

Examples in macromolecules:

Amino acids in polypeptide chains hydrogen-bonded together.

O H O N H O

R C

HC O

R C H

C O

H

N

H

H C R

N

C

C

C

C

N

NH

H

O

NH

O

C

CN

N

CCN

C

N

H

H

NH

H

H

Two bases, G and C, hydrogen-bonded in DNA or RNA.

Any molecules that can form hydrogen bonds to each othercan alternatively form hydrogen bonds to water molecules.Because of this competition with water molecules, thehydrogen bonds formed between two molecules dissolvedin water are relatively weak.

HYDROGEN BONDS IN WATER

C CC

O

N

H

O

H HO

H

H

C CC

O

N

H

C CC

O

N

H

C CC

O

N

H

2H2O

2H2O

peptidebond

EN

ER

GY


Types of Weak Non-covalent Bonds - Part 2

HYDROPHOBIC FORCES

C

H

HH

CH

HH

C

HH

H

HH

H

C

Water forces hydrophobic groups togetherin order to minimize their disruptiveeffects on the hydrogen-bonded waternetwork. Hydrophobic groups heldtogether in this way are sometimes saidto be held together by “hydrophobicbonds,” even though the attraction isactually caused by a repulsion from thewater.

Charged groups are shielded by theirinteractions with water molecules.Ionic bonds are therefore quite weakin water.

IONIC BONDS IN AQUEOUS SOLUTIONS

C

O

O

O

OO

O

P

O

O

H

H

H

OH

H

H O

H

H

O

H H

H

OH

H

OH

H

Mg

Similarly, other ions in solution can cluster aroundcharged groups and further weaken ionic bonds.

Despite being weakened by water andsalt, ionic bonds are very importantin biological systems; an enzyme thatbinds a positively charged substratewill often have a negatively charged amino acid side chain at theappropriate place.

–

+

substrate

enzyme

Ionic interactions occur either between fully charged groups (ionic bond) or between partially charged groups.

IONIC BONDS

d + d –

The force of attraction between the twocharges, d + and d –, falls off rapidly as the distance between the charges increases.

In the absence of water, ionic forcesare very strong. They are responsiblefor the strength of such minerals asmarble and agate.

a crystal ofsalt, NaCl

Cl–

Na+

H N

H

H

hand drawnfig 2.105/2.07

++

OHOH

H

Na

+

Na

Na

Na Na

+

+

+

+ + Cl

Cl

Cl

ClCl


Outline of Sugar Types Found in Cells - Part 1

Monosaccharides usually have the general formula (CH2O) n , where n can be 3, 4, 5, 6, 7, or 8, and have two or more hydroxyl groups. They either contain an aldehyde group ( ) and are called aldoses or a ketone group ( ) and are called ketoses.

MONOSACCHARIDES

Note that each carbon atom has a number.

Many monosaccharides differ only in the spatial arrangement of atoms—that is, they are isomers. For example, glucose, galactose, and mannose have the same formula (C6H12O6) but differ in the arrangement of groups around one or two carbon atoms.

These small differences make only minor changes in the chemical properties of the sugars. But they are recognized by enzymes and other proteins and therefore can have important biological effects.

RING FORMATION ISOMERS

C

C

H

HHO

OH

CH OH

CH OH

CH

H

OH

C

H

H

HO

OH

CH OH

CH OH

CH

H

OH

CH OH

CH OH

CH OH

CH

H

OH

CH OH

CH

H

OH

3-carbon (TRIOSES) 5-carbon (PENTOSES) 6-carbon (HEXOSES)

ALD

OS

ES

KE

TO

SE

S

C

OH

C

OHC

OH

glyceraldehyde ribose glucose

fructose

H

H

OH

CH OH

CH OH

CH

H

OH

ribulose

H

H

OH

CH

H

OH

dihydroxyacetone

O

C

C

O

C

C

O

C

C

CH

CH2OH

CH2OH

OH

CH OH

CHO H

CH

H

H

HH

H

H H

HH

H

HO

OH

OH

OH

OH

OH

OHOH

CO

O

CH2OH

CH

CH2OH

OH

CH OH

CH OH

1

2

3

4

4

4

5

5

6

3

3

2

2

1

CH2OH

HH

H

H

H

HOOH

OH

OH

O

1

5

1

2

3

4

5

6

glucose

CH2OH

H

H

H

H

H

HOOH

OH

OH

O

mannose

CH2OH

HH

H

H

H

HO

OH

OH

OHgalactose

O

O

CO

C OH

glucose

ribose

In aqueous solution, the aldehyde or ketone group of a sugarmolecule tends to react with a hydroxyl group of the samemolecule, thereby closing the molecule into a ring.

HC

O


Outline of Sugar Types Found in Cells - Part 2

CH2OH

HO

O

OH

OH

CH2OH

OH

CH2OH

NH

HOCH2

HO

CH2OH

HO

O

OH

OH

O H CH2OH

OH

HOCH2

HO

HO

+

O

CH2OH

O CH2OH

O

OH

O

HO

OH

HO

O OH

NH

OO

HO

CH3

O

In many cases a sugar sequence is nonrepetitive. Many different molecules are possible. Such complex oligosaccharides are usually linked to proteins or to lipids, as is this oligosaccharide, which is part of a cell-surface moleculethat defines a particular blood group.

COMPLEX OLIGOSACCHARIDES

OLIGOSACCHARIDES AND POLYSACCHARIDESLarge linear and branched molecules can be made from simple repeating units.Short chains are called oligosaccharides, while long chains are calledpolysaccharides. Glycogen, for example, is a polysaccharide made entirely ofglucose units joined together.

branch points glycogen

sucrose

a glucose b fructoseDISACCHARIDES The carbon that carries the aldehyde or the ketone can react with any hydroxyl group on a second sugar molecule to form a disaccharide. Three common disaccharides are

maltose (glucose + glucose) lactose (galactose + glucose) sucrose (glucose + fructose)

The reaction forming sucrose is shown here.

a AND b LINKS SUGAR DERIVATIVESThe hydroxyl group on the carbon that carries the aldehyde or ketone can rapidly change from one position to the other. These two positions are called a and b .

As soon as one sugar is linked to another, the a or b form is frozen.

The hydroxyl groups of a simple monosaccharide can be replaced by other groups. For example,

C O

CH3

C O

CH3

OHO

OH

O

b hydroxyl a hydroxyl

C

O

OH

OH

OH

HO

OH

CH2OH

CH2OHNH2

H

O

OH

OH

HO

O

OH

OH

HO

CH3

O

NH

C

Hglucosamine

N-acetylglucosamineglucuronic acid

O

H2O

O

O

O


Fatty Acids and Other Lipids - Part 1

These are carboxylic acids withlong hydrocarbon tails.

COOH

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH3

COOH

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

COOH

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH

CH

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH3

CH3

stearicacid(C18)

palmiticacid(C16)

oleicacid(C18)

–O O

C

O

C

Hundreds of different kinds of fatty acids exist. Some have one or more double bonds in theirhydrocarbon tail and are said to be unsaturated. Fatty acids with no double bonds are saturated.

oleicacid

stearicacid

This double bondis rigid and createsa kink in the chain. The rest of the chain is free to rotateabout the other C–Cbonds.

space-filling model carbon skeleton

Fatty acids are stored as an energy reserve (fats and oils) through an ester linkage to glycerol to form triacylglycerols.

H2C OC

O

HC OC

O

H2C OC

O

H2C OH

HC OH

H2C OH

glycerol

COMMON FATTY ACIDS

TRIACYLGLYCEROLS

CARBOXYL GROUP

O_

O

C

O

O

C

N

O

C

C

H

If free, the carboxyl group of afatty acid will be ionized.

But more usually it is linked toother groups to form either esters

or amides.

PHOSPHOLIPIDS

CH2 CH CH2

P O_

O

O

O

hydrophilicgroup

Phospholipids are the major constituents of cell membranes.

hydrophobicfatty acid tails

In phospholipids two of the –OH groups in glycerol are linked to fatty acids, while the third –OH group is linked to phosphoric acid. The phosphate is further linked to one of a variety of small polar groups (alcohols).

space-filling model ofthe phospholipidphosphatidylcholine

general structure ofa phospholipid

–O

UNSATURATED SATURATED

choline


Fatty Acids and Other Lipids - Part 2

LIPID AGGREGATES

Fatty acids have a hydrophilic headand a hydrophobic tail.

In water they can form a surface filmor form small micelles.

Their derivatives can form larger aggregates held together by hydrophobic forces:

Triglycerides form large spherical fatdroplets in the cell cytoplasm.

Phospholipids and glycolipids form self-sealing lipidbilayers that are the basis for all cellular membranes.

200 nmor more

4 nm

OTHER LIPIDS Lipids are defined as the water-insoluble molecules in cells that are soluble in organic solvents. Two other common types of lipidsare steroids and polyisoprenoids. Both are made from isoprene units.

CH3

C CH

CH2

CH2

isoprene

STEROIDS

HO O

OH

cholesterol—found in many membranes testosterone—male steroid hormone

Steroids have a common multiple-ring structure.

GLYCOLIPIDS

Like phospholipids, these compounds are composed of a hydrophobicregion, containing two long hydrocarbon tails, and a polar region, which, however, contains one or more sugar residues and no phosphate.

CC

CC

CH2

HH

NH

OHH

O

galactose

C

Ohydrocarbon tails

sugarresidue

a simpleglycolipid

POLYISOPRENOIDS

long chain polymers of isoprene

O–

O–O

O

P

dolichol phosphate—used to carry activated sugars in the membrane-associated synthesis of glycoproteins and some polysaccharides

H

micelle


Amino Acids Found in Proteins - Part 1

THE AMINO ACID

The general formula of an amino acid is

+

H

H2N COOH

R

C

R is commonly one of 20 different side chains.At pH 7 both the amino and carboxyl groupsare ionized.

H

H3N COO

R

C

a -carbon atom

carboxyl group

side-chain group

OPTICAL ISOMERSThe a -carbon atom is asymmetric, which allows for two mirror image (or stereo-) isomers, L and D.

H

NH3+ COO–

R

C a

COO–

R H

NH3+

Proteins consist exclusively of L-amino acids.

C aL D

PEPTIDE BONDS

Amino acids are commonly joined together by an amide linkage, called a peptide bond.

HH

H OH

O

CCN

R H

H

H OH

O

CCN

R HH

H

CN

R H

C

R

OH

O

CC

O

N

H

H2O

Peptide bond: The four atoms in each gray box form a rigidplanar unit. There is no rotation around the C–N bond.

H

C

CH2

CC

O

N

H

H3N

CH2

SH

C

CH

CC

O

N

H H

COO–

CH

NH+

HN

HC

CH3 CH3

Proteins are long polymers of amino acids linked bypeptide bonds, and they are always written with theN-terminus toward the left. The sequence of this tripeptide is histidine-cysteine-valine. These two single bonds allow rotation, so that long chains of

amino acids are very flexible.

amino, orN-, terminus

+

carboxyl, orC-, terminus

FAMILIES OFAMINO ACIDS

The common amino acidsare grouped according towhether their side chainsare

acidic basic uncharged polar nonpolar

These 20 amino acidsare given both three-letterand one-letter abbreviations.

Thus: alanine = Ala = A

BASIC SIDE CHAINS

H

C C

O

N

H

CH2

CH2

CH2

CH2

NH3

lysine

(Lys, or K)

H

C C

O

N

H

CH2

CH2

CH2

NH

C

arginine

(Arg, or R)

H

C C

O

N

H CH2

histidine

(His, or H)

C

CH

NH+

HN

HC

+H2N NH2

This group isvery basicbecause itspositive chargeis stabilized byresonance.

These nitrogens have a relatively weak affinity for anH+ and are only partly positiveat neutral pH.

+

amino group


Amino Acids Found in Proteins - Part 2

ACIDIC SIDE CHAINS

H

C C

O

N

H CH2

aspartic acid

(Asp, or D)

C

O O–

H

C C

O

N

H

CH2

glutamic acid

(Glu, or E)

C

O O–

CH2

UNCHARGED POLAR SIDE CHAINS

H

C C

O

N

H CH2

asparagine

(Asn, or N)

C

O NH2

H

C C

O

N

H

CH2

glutamine

(Gln, or Q)

C

O

CH2

NH2

Although the amide N is not charged at neutral pH, it is polar.

H

C C

O

N

H CH2

serine

(Ser, or S)

OH

H

C C

O

N

H CH

threonine

(Thr, or T)

OH

H

C C

O

N

H CH2

tyrosine

(Tyr, or Y)

CH3

OH

The –OH group is polar.

NONPOLAR SIDE CHAINS

glycine

(Gly, or G)

H

C C

O

N

H H

H

C C

O

N

H

alanine

(Ala, or A)

CH3

H

C C

O

N

H

valine

(Val, or V)

CH3CH3

CH

H

C C

O

N

H

leucine

(Leu, or L)

CH2

CH

CH3CH3

H

C C

O

N

H

isoleucine

(Ile, or I)

CH2CH3

CH

CH3

H

C C

O

N

H

phenylalanine

(Phe, or F)

CH2

H

C C

O

N

H

methionine

(Met, or M)

CH2

CH2

S CH3

H

C C

O

N

proline

(Pro, or P)

CH2

CH2

CH2

(actually animino acid)

H

C C

O

N

H

cysteine

(Cys, or C)

CH2

SH

Disulfide bonds can form between two cysteine side chains in proteins.

S S CH2CH2

H

C C

O

N

H

tryptophan

(Trp, or W)

NH

CH2


Survey of Nucleotides - Part 1

BASES

The bases are nitrogen-containing ring compounds, either pyrimidines or purines.

C

C

CHC

NH

NH

O

O

C

CHC

NH

N

O

NH2

H3C

C

CHC

NH

NH

O

O

HC

HC

U

C

T

uracil

cytosine

thymine

N

N1

2

34

5

6

N

N

1

23

4

56N

N

7

8

9

O

N

NH

C

C

C

CN

NH

NH2

HC

N

NH

C

C

C

CHN

N

HC

NH2

adenine

guanine

A

G

PYRIMIDINE PURINE

PHOSPHATES

The phosphates are normally joined tothe C5 hydroxyl of the ribose ordeoxyribose sugar (designated 5'). Mono-, di-, and triphosphates are common.

O

O

O–

–O P CH2

O

O–

–O P

O

O

O–

P CH2O

O

O–

–O P

O

O–

PO

O

O

O–

P CH2O

as inAMP

as inADP

as inATP

The phosphate makes a nucleotide negatively charged.

NUCLEOTIDES

A nucleotide consists of a nitrogen-containingbase, a five-carbon sugar, and one or more phosphate groups.

N

N

O

NH2

O

O

O–

–O P CH2

OH OH

O

BASE

PHOSPHATE

SUGAR

Nucleotides are thesubunits ofthe nucleic acids.

BASIC SUGARLINKAGE

N

O

C

H

SUGAR

BASE

1

23

4

5

N-glycosidicbond

The base is linked tothe same carbon (C1)used in sugar-sugarbonds.

SUGARS

Each numbered carbon on the sugar of a nucleotide is followed by a prime mark; therefore, one speaks of the“5-prime carbon,” etc.

OH OH

O

H H

HOCH2 OH

H H

OH H

O

H H

HOCH2 OH

H H

PENTOSE

a five-carbon sugar

O

4’3’ 2’

1’

C 5’

two kinds are used

b -D-riboseused in ribonucleic acid

b -D-2-deoxyriboseused in deoxyribonucleic acid


Survey of Nucleotides - Part 2

NUCLEIC ACIDS

Nucleotides are joined together by aphosphodiester linkage between 5’ and3’ carbon atoms to form nucleic acids.The linear sequence of nucleotides in anucleic acid chain is commonly abbreviated by a one-letter code,A—G—C—T—T—A—C—A, with the 5’end of the chain at the left. O

O–

–O P

O

O–

PO

O

O

O–

PO

NOMENCLATURE The names can be confusing, but the abbreviations are clear.

BASE

adenine

guanine

cytosine

uracil

thymine

NUCLEOSIDE

adenosine

guanosine

cytidine

uridine

thymidine

ABBR.

A

G

C

U

T

Nucleotides are abbreviated bythree capital letters. Some examplesfollow:

AMPdAMPUDPATP

= adenosine monophosphate= deoxyadenosine monophosphate= uridine diphosphate= adenosine triphosphate

sugar

base

sugar

base

P

BASE + SUGAR = NUCLEOSIDE

BASE + SUGAR + PHOSPHATE = NUCLEOTIDE

O

OH

sugar

base

CH2

O

O–

–O P O

+

O

OH

sugar

base

CH2

O

O–

–O P O

O

sugar

base

CH2

O

O–

–O P O

O

sugar

base

CH2

P

O

–O O

O

5’

OH3’3’ end of chain

3’

5’

phosphodiester linkage

5’ end of chain

example: DNA

NUCLEOTIDES HAVE MANY OTHER FUNCTIONS

OCH2

N

N N

N

NH2

OH OH

1 They carry chemical energy in their easily hydrolyzed phosphoanhydride bonds.

O

O

O–

PO

CH2

N

NN

N

NH2

OH

2 They combine with other groups to form coenzymes.

O

O–

PO OCCCCNCCCNCCHS

OO

H

H

H

H

HH

H

H

H

H H

HH

HO CH3

example: coenzyme A (CoA)

CH3

3 They are used as specific signaling molecules in the cell.

O

O

O–

P

OCH2

N

N N

N

NH2

O OH

example: cyclic AMP (cAMP)

phosphoanhydride bonds

example: ATP (or )ATP

O

P O–

O–

O

P

ATP ADP

CH2OH

O

OH

OH

OHHO

glucose

CH2O

H+

O

OH

OH

OHHO

glucose 6-phosphate

+ + +

hexokinase

P

P

CH2O

O

OH

OH

OHHO

glucose 6-phosphate fructose 6-phosphate

(ring form) (ring form)

(open-chain form)

1

1

2

2

3

4

56

6

O H

C

CH OH

CHO H

CH OH

CH OH

CH2O

3

4

5

P

P

(open-chain form)

1

1

2

2

6

C

CHO H

CH OH

CH OH

CH2O

CH2OH

3

34 4

5

5

phosphoglucoseisomerase OH2C CH2OHO

HO

OH

OH

6

ATP+ ADP H++ +phosphofructokinaseP OH2C CH2OHO

HO

OH

OH

P POH2C CH2OO

HO

OH

OH

Glucose is phosphorylated by ATP to form a sugar phosphate. The negative charge of the phosphate prevents passage of the sugarphosphate through the plasma membrane, trapping glucose inside the cell.

Step 1

The six-carbon sugar is cleaved to produce two three-carbon molecules. Only the glyceraldehyde3-phosphate can proceed immediately through glycolysis.

Step 4

The other product of step 4, dihydroxyacetone phosphate, is isomerized to form glyceraldehyde 3-phosphate.

Step 5

A readily reversible rearrangement of the chemical structure (isomerization) moves the carbonyl oxygen from carbon 1 to carbon 2, forming a ketose from an aldose sugar. (See Panel 2–3, pp. 70–71.)

Step 2

The new hydroxyl group on carbon 1 is phosphorylated by ATP, in preparation for the formation of two three-carbon sugar phosphates. The entry of sugars into glycolysis is controlled at this step, through regulation of the enzyme phosphofructokinase.

Step 3

fructose 6-phosphate fructose 1,6-bisphosphate

+

(ring form)

OH

C

CH OH

aldolase

P

P

(open-chain form)

C

CHO H

CH OH

CH OH

CH2O

CH2O

O

P

C

CHO H

H

CH2O

PCH2O

O

P POH2C CH2OO

HO

OH

OH

fructose 1,6-bisphosphatedihydroxyacetone

phosphateglyceraldehyde

3-phosphate

O

P

C

CH2O

CH2OH triose phosphate isomerase

OH

C

CH OH

PCH2O

glyceraldehyde3-phosphate

dihydroxyacetonephosphate

O

For each step, the part of the molecule that undergoes a change is shadowed in blue,and the name of the enzyme that catalyzes the reaction is in a yellow box.

Panel 13–1 Details of the 10 steps of glycolysis

+ +ADP

enolase

phosphoglycerate mutase

+

O O–

C

CH OH

PCH2O

3-phosphoglycerate

O O–

C

CH O P

CH2OH

2-phosphoglycerate

O O–

C

CH O P

CH2OH

2-phosphoglycerate

O O–

C

C O P

CH2

H2O

phosphoenolpyruvate

O O–

C

C O P

CH2

phosphoenolpyruvate

O O–

C

C O

CH3

pyruvate

O O–

C

C O

CH3

O O–

C

C O

CH3

ATP+ ADP

phosphoglycerate kinaseO O

C

CH OH

P

P

CH2O

1,3-bisphosphoglycerate

+

O O–

C

CH OH

PCH2O

3-phosphoglycerate

The two molecules of glyceraldehyde 3-phosphate are oxidized. The energy-generation phase of glycolysis begins, as NADH and a new high-energy anhydride linkage to phosphate are formed (see Figure 13–5).

Step 6

H+

+ ++

glyceraldehyde 3-phosphatedehydrogenaseO H

C

CH OH

PCH2O

glyceraldehyde3-phosphate

O O

C

CH OH

P

P

CH2O

1,3-bisphosphoglycerate

NADH

NADH

H++

The transfer to ADP of the high-energy phosphate group that was generated in step 6 forms ATP.

Step 7

The remaining phosphate ester linkage in 3-phosphoglycerate, which has a relatively low free energy of hydrolysis, is moved from carbon 3 to carbon 2 to form 2-phosphoglycerate.

Step 8

The removal of water from 2-phosphoglycerate creates a high-energy enol phosphate linkage.

Step 9

The transfer to ADP of the high-energy phosphate group that was generated in step 9 forms ATP, completing glycolysis.

Step 10

NET RESULT OF GLYCOLYSIS

ATP

ATP

+pyruvate kinase

CH2OH

O

OH

OH

OHHO

glucosetwo molecules

of pyruvate

ATP

ATP

NADH ATP

ATP

ATP

In addition to the pyruvate, the net products aretwo molecules of ATP and two molecules of NADH.

1

2

3

PiNAD+

After the enzyme removes a proton from the CH3 group on acetyl CoA, the negatively charged CH2

– forms a bond to a carbonyl carbon of oxaloacetate. The subsequent loss by hydrolysis of the coenzyme A (CoA) drives the reaction strongly forward.

Step 1

An isomerization reaction, in which water is first removed and then added back, moves the hydroxyl group from one carbon atom to its neighbor.

Step 2

COO–

COO–

COO–HO

H H

H H

C

C

C

COO–

COO–

COO–

HO

H H

H

H

C

C

C

COO–

COO–

COO–

H H

H

C

C

C

citrate cis-aconitateintermediate

isocitrate

aconitase

H2O

H2O

H2O

H2O

acetyl CoA S-citryl-CoAintermediate

citrateoxaloacetate

COO–

COO–

O OCC S CoA

citratesynthase

CH3 CH2

H2OO C S CoA

CH2

COO–

COO–CHO

CH2

HS H+CoA

CH2

COO–

COO–

COO–

CHO

CH2

+ + +

Details of the eight steps are shown below. For each step, the part of the molecule that undergoes a change is shadowed in blue,and the name of the enzyme that catalyzes the reaction is in a yellow box.

CH2

COO–

COO–

COO–

CHO

CH2

H2O

H2O

H2O

CH2

CO2

CO2

CO2

COO–

COO–

COO–

HC

CHHO

CH2

COO–

COO–

C O

CH2

CH2

COO–

COO–

CH2

CH

COO–

COO–

CH

H OHC

COO–

COO–

CH2

COO–

C O

CH2

S CoA

O

CH3 S CoA

acetyl CoA

HS CoA

HS CoA

HS CoA

HS CoA

CH2

OC

COO–

COO–

CH2

O

O

C

COO–

COO–

COO–

CH2

CH3 C

next cycle

Pi

GTPGDP

+

Step 1 Step 2

Step 3

Step 4Step 6

Step 7

Step 8

Step 5

citrate (6C) isocitrate (6C)

succinyl CoA (4C)succinate (4C)

fumarate (4C)

malate (4C)

oxaloacetate (4C)

oxaloacetate (4C)

pyruvate

α-ketoglutarate (5C)+ H+

NADH

+ H+NADH

+ H+NADH

NAD+

NAD+

NAD+

+ H+NADHNAD+

FADH2

FAD

(2C)

CITRIC ACID CYCLE

The complete citric acid cycle. The two carbons from acetyl CoA that enter this turn of the cycle (shadowed in red ) will be converted to CO2 in subsequent turns of the cycle: it is the two carbons shadowed in blue that are converted to CO2 in this cycle.

C

Panel 13–2 The complete citric acid cycle

Banques de données et outilsBanques de données et outils

• ExPASy (http://expasy org/)ExPASy (http://expasy.org/)• BRENDA (http://www.brenda‐enzymes.org/)

GG (h // j /k /)• KEGG (http://www.genome.jp/kegg/)• SBML (http://sbml.org/Main_Page)• System Biology Research Group (http://gcrg.ucsd.edu/)( p //g g /)

chemical properties of water - part 1

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