Chapter 2 Basic Plant Chemistry

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Basic Plant ChemistryChapter 2


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Atoms want to fill their outer shells with electrons!

Chemical reactions enable atoms to give up oracquire electrons in order to complete their outer

shells

Chemical Bonding and Molecules

These interactions usually result in atoms stayingclose together

Interactions between outer shells of atoms= chemical bonds


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When an atom losesor gains electrons, itbecomes electricallycharged

1) Ionic Bonds

Charged atoms arecalled ions

Ionic bonds are

formed betweenoppositely chargedions (transferofelectrons)

Sodium atom (Na) Chlorine atom (Cl)

Completeouter shells

Sodium ion (Na) Chloride ion (Cl)

Sodium chloride (NaCl)


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2) Covalent Bonds

A covalent bond forms when two atoms shareone or more pairs of outer-shell electrons


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The number of covalent bonds an atom canpotentially form = number of additional electrons

needed to fill its outer shell.


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Carbohydrates Of the macromolecules that we will cover in

this class, those involving carbohydrates arethe most abundant in nature.

Via photosynthesis, over 100 billion metrictons of CO2and H2O are converted intocellulose and other plant products.

The term carbohydrate is a generic one thatrefers primarily to carbon-containingcompounds that contain hydroxyl, keto, oraldehydic functionalities.

Carbohydrates can range in sizes, fromsimple monosaccharides (sugars) tooligosaccharides, to polysaccharides.


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Carbohydrates Carbohydrates constitute more than 1/2 of organic molecules

Main role of carbos in nature Storage of energy

Structural support

Lipid and protein modification:

membranes asymmetry, recognition by IgG/fertilization/virus

recognition/cell cell communication

Definition: Carbohydrates, Sugars and Saccharides- are all polyhydroxy

(at least 2 OH) Cn(H20)n= hydrate of carbon

Notice that there are two distinct types of monosaccharides, ketoses andaldoses.

The number of carbons is important in general nomenclature (triose = 3, pentose= 5, hexose =6,


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Basic factsMonosaccharides - Simple sugars

Single polyhydroxyl

Cant be hydrolyzed to simpler form

Trioses- Smallest monosaccharides have three carbon atoms

Tetroses (4C) Pentose(5C) Hexoses(6C) Heptoses (7C) etc

Disaccharide- two sugars linked together. Can be the same moleculeor two different sugars. Attached together via a glycosidic linkage

Oligosaccharide- 2 to 6 monosaccharides

Polysaccharides - straight or branched long chain monosaccharides.Bonded together by glycosidic linkages


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The functional groups

Aldehyde:

Consists of a carbon atombonded to a hydrogen atom and double-bonded to an oxygen atom. Polar. Oxygen, more electronegative than carbon, pulls the

electrons in the carbon-oxygen bond towards itself,creating an electron deficiency at the carbon atom.

Ketone:Characterized by a carbonyl group (O=C)linked to two other carbon atoms or a chemical

compound that contains a carbonyl group A carbonyl carbon bonded to two carbon atoms

distinguishes ketones from carboxylic acids, aldehydes,esters, amides, and other oxygen-containing compounds
http://en.wikipedia.org/wiki/Image:Ketone-displayed.pnghttp://en.wikipedia.org/wiki/Image:Aldehyde2.png


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Classification of monosaccharides Monosaccharides are classified according to

three different characteristics: the placement of its carbonyl group, the number of carbon atoms it contains its chiral handedness.

If the carbonyl group is an aldehyde, themonosaccharide is an aldose

if the carbonyl group is a ketone, themonosaccharide is a ketose.

Monosaccharides with three carbon atoms

are called trioses, those with four arecalled tetroses, five are called pentoses, sixare hexoses, and so on.

These two systems of classification areoften combined.

For example, glucose is an aldohexose (asix-carbon aldehyde)


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carbonyl group

A functional group composed ofa carbon atom double-bonded toan oxygen atom: C=O.

The term carbonyl can alsorefer to carbon monoxide asa ligand in

an inorganic or organometalliccomplex.


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Classification of monosaccharides

D-glucose

is an aldohexose with the formula(CH2O)6.

The red atoms highlight thealdehyde group

the blue atoms highlight the

asymmetric center furthest from thealdehyde; because this -OH is on theright of the Fischer projection, thisis a D sugar.


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Classification of monosaccharides The aand banomers of glucose.

Note the position of the hydroxylgroup (red or green) on the anomericcarbon relative to the CH2OH group

bound to carbon 5:

Either on the opposite sides (a)

Or the same side (b).


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Important disaccharides Sucrose The osmotic effect of a substance

is tied to the number of particlesin solution, so a millilitre ofsucrose solution with the sameosmolarity as glucose will behave twice the number carbon

atoms and therefore about twicethe energy. Thus, for the same osmolarity,

twice the energy can betransported per ml.

As a non-reducing sugar, sucroseis less reactiveand more likely tosurvive the journey in the phloem.

Invertase (sucrase) is the onlyenzyme that will touch it and

this is unlikely to be present inthe phloem sieve tubes.


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Important disaccharides Maltose Malt sugar or corn sugar consists

of two glucose molecules linkedby an a-1,4-glycosidic bond

It comes from partial hydrolysisof starch by the enzyme amylase,which is in saliva and also in grains(like barley)

Maltose is an importantintermediate in the digestion ofstarch. Starch is usedby plants as a way tostore glucose. After cellulose,starch is the most abundant

polysaccharide in plant cells.


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Important plant saccharides Raffinoseis a trisaccharide composed

ofgalactose, fructose, and glucose.

Raffinose can be hydrolyzed to D-galactose and sucrose by the enzyme -galactosidase (a-GAL), an enzyme notfound in the human digestive tract. a-GALalso hydrolyzes other a-galactosides suchasstachyose, verbascose, and galactinol, ifpresent. The enzyme does not cleave -linked galactose, as in lactose.

The raffinose familyof oligosaccharides (RFOs) are alpha-galactosyl derivatives of sucrose, and the

most common are raffinose, stachyose,verbascose. RFOs are almost ubiquitous in

the plant kingdom, being found in a largevariety of seeds from many differentfamilies, and they rank second only tosucrose in abundance as solublecarbohydrates.


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Carbohydrates-make up 16-25% of sap. The major organic transport

materials are sucrose, stachyose

(sucrose-gal), raffinose (stachyose-gal).

These are excellent choices fortransport materials for two reasons:

(a) they are non-reducing sugars (thehydroxyl group on the anomericcarbon, the number one carbon, istied up) which means that they areless reactive and more chemicallystable.

(b) the linkage between sucrose andfructose is a "high-energy" linkagesimilar to that of ATP. Thus, sucroseis a good transport form thatprovides a high energy, yet stable

packet of energy;


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Important Polysaccharides:

Starch - energy reservoirin plants - made of twopolysaccharides

Amylose-long unbranchedglucose a(1,4) withopen reducing end largetight helicalforms.

Test by iodination..


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Important Polysaccharides:Starch - energy reservoir in plants - made of two polysaccharides

Amylose -long unbranched glucose a(1,4) with open reducing end large tight

helicalforms. Test by iodination. Amylopectin- polymer of a(1,4) and a(1,6) branches. Not helical.


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Plant Starch (Amylose and Amylopectin) Starchcontains a mixture of amylose and amylopectin

Amyloseis an unbranched polymer (forms a-helix) of D-glucose molecules linked by a-1,4-glycosidic bonds

Amylopectinis like amylose, but has extensive branching, with the branches using a-1,6-glycosidic bonds


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Cellulose

This means that cellobiose, and not glucose, is the basicrepeating unit of the cellulose molecule. Groups of 30 to 40of these chains laterally hydrogen-bond to form crystallineor para-crystalline microfibrils.


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Proteins

Basic facts

Ami id


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Amino acids -20 common amino acids there are others

found naturally but much less frequently

Common structure for amino acid

COOH, -NH2, H and R functional groups allattached to the alpha carbon


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Proteins: Three-dimensional structure Background on protein composition: Two general classes of proteins

Fibrous -long rod-shaped, insoluble proteins.These proteins are strong (high tensile strength).

Globular- compact spherical shaped proteinsusually water-soluble. Most hydrophobic amino

acids found in the interior away from the water.Nearly all enzymes are globular

Proteins can be simple-no added groups or modifications, justamino acids

Or proteins can be conjugated. Additional groupscovalently bound to the amino acids. The nakedprotein is called the apoprotein and the added group isthe prosthetic group. Together the protein and

prosthetic group is called the holoprotein. Ex.chlorophyll


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Four levels of protein structure Primary structure:amino acid only. The actual amino

acid sequence is specified by the DNA sequence. Theprimary structure is used to determine geneticrelationships with other proteins - AKA homology. Amino

acids that are not changed are consideredinvariant orconserved.

Primarysequence is alsoused todetermine

importantregions andfunctions ofproteins -domains.


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Four levels of protein structure Secondary structure:This level is only concerned with the

local or close in structures on the protein - peptidebackbone. The side chains are not considered here,even though they have an affect on the secondary

structure.Two commonsecondarystructures - alphahelix and betapleated sheetNon- regular

repeating structureis called a randomcoil.- no specificrepeatable pattern


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Four levels of protein structure


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Four levels of protein structureTertiary structure- the overall three-dimensional shapethat a protein assumes. This includes all of the secondary

structures and the side groups as well as any prostheticgroups. This level is also where one looks for native vs.denatured state. The hydrophobic effect, salt bridges

And other

molecularforces areresponsiblefor

maintainingthe tertiarystructure


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Four levels of protein structure Quaternary structure:The overall interactions of

more than one peptide chain. Called subunits.Each of the sub units

can be different oridentical subunits,hetero or homo x

mers (ex.Heterodimer is aprotein composed oftwo differentsubunits).


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LipidsLipids fats oils. Greasy molecules, mmmmm donuts.

Several levels of complexity: Simple lipids - a lipid that cannot be broken down to smaller

constituents by hydrolysis. Fatty acids, waxes and cholesterol

Complex lipids - a lipid composed of different molecules held

together mostly by ester linkages and susceptible to cleavagereactions. acylglycerols - mono, di and triacyl glycerols ( fatty acids and

glycerol)phospholipids(also known asglycerophospholipids) - lipids which

are made of fatty acids, glycerol, a phosphoryl group and analcohol. Many also contain nitrogen glycolipids (also known as glycosphingolipids): Lipids which have

a spingosine and different backbone than the phospholipids


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General Structure- The longer the fatty acids the higher

the melting point.

- Again the more hydrophobicinteractions effects the more theenergy it takes to break the order.Decreases in the packing efficiency

decreases the mp

- The van der Waals forces then comeapart more easily at lowertemperatures.

- Animal alter the length and unsaturatedlevel of the fatty acids in lipids(cholesterol too) to deal with the coldtemps


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Saturated or not the power of H The terms saturated, mono-

unsaturated, and poly-unsaturatedrefer to the number of hydrogensattached to the hydrocarbon tails ofthe fatty acids as compared to thenumber of double bonds betweencarbon atoms in the tail.

Oils, mostly from plant sources, havesome double bonds between some ofthe carbons in the hydrocarbon tail,

causing bends or kinks in the shape ofthe molecules.

Because some of the carbons sharedouble bonds, theyre not bonded to asmany hydrogens as they could if they

werent double bonded to each other.


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Trans and Cis In unsaturated fatty acids, there are two

ways the pieces of the hydrocarbon tail canbe arranged around a C=C double bond.

TRANS

The two pieces of the molecule are on

opposite sides of the double bond, that is,one up and one down across from eachother.

CIS

the two pieces of the carbon chain oneither side of the double bond are eitherboth up or both down, such that bothare on the same side of the molecule


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Trans and Cis Naturally-occurring unsaturated vegetable

oils have almost all cis bonds but using oil for frying causes some of the

cis bonds to convert to trans bonds.

If oil is used only once like when you fry an

egg, only a few of the bonds do this so its nottoo bad.

However, if oil is constantly reused, like infast food French fry machines, more andmore of the cis bonds are changed to transuntil significant numbers of fatty acids withtrans bonds build up.

The reason this is of concern is that fattyacids with trans bonds are carcinogenic!

Phospholipids:


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Phospholipids Two fatty acids covalently

linked to aglycerol, whichis linked to aphosphate.

All attached to a headgroup, such as choline, anamino acid.

Head group POLAR sohydrophilic(loves water)

Tail is non-polar hydrophobic

The tail varies in lengthfrom 14 to 28 carbons.


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Nucleic Acids


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Nucleic Acids Composed of 4

nucleotide bases, 5

carbon sugar andphosphate.

Base pair = rungs of aladder.

Edges = sugar-

phosphate backbone.

Double Helix

Anti-Parallel


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The bases

Chargaffs Rules

A=T

G=C

led to suggestion of a

double helix structurefor DNA


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The Bases

Adenine(A) always base pairs with thymine(T)

Guanine(G) always base pairs with Cytosine(C)


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The Bases

The C#T pairing on the left suffers from carbonyl dipolerepulsion, as well as steric crowding of the oxygens. TheG#A pairing on the right is also destabilized by stericcrowding (circled hydrogens).


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DNA Replication

Adenine(A) always base pairs with thymine(T) Guanine(G) always base pairs with Cytosine(C)

ALL Down to HYDROGENBonding

Requires steps: H bonds break as enzymes unwind molecule

New nucleotides (always in nucleus) fit into placebeside old strand in a process called ComplementaryBase Pairing.

New nucleotides joined together by enzyme calledDNA Polymerase


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Central Dogma of Molecular

Biology DNA holds the code

DNA makes RNA

RNA makes Protein

DNA to DNA is called REPLICATION

DNA to RNA is calledTRANSCRIPTION

RNA to Protein is called

TRANSLATION


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Central Dogma of Molecular

Biology DNA holds the code

DNA makes RNA

RNA makes Protein

DNA to DNA is called REPLICATION

DNA to RNA is calledTRANSCRIPTION

RNA to Protein is called

TRANSLATION


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RNA Formed from 4

nucleotides, 5 carbonsugar, phosphate.

Uracil is used in RNA.

It replaces Thymine

The 5 carbon sugar hasan extra oxygen.

RNA is single stranded.


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Chapter 2 Basic Plant Chemistry

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