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The Chemistry of the Cell

Can be structured around 5 principles:

1. The importance of carbon2. The importance of water

3. The importance of selectively permeable membranes4. The importance of synthesis by polymerization of small

molecules5. The importance of self-assembly

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Chemistry of Cells

Cells composed of water, inorganic ions

and carbon-containing (organic)molecules

Review:Atoms- smallest unit of the chemical elements

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Ionic bondsthere is transfer of es from one atom to a second atom

Na + Cl Na+ + Cl NaCl

Symbol Atomic # Atomic mass # of ChemicalBonds

Hydrogen H 1 1 1

Carbon C 6 12 4Nitrogen N 7 14 3Oxygen O 8 16 2Sulfur S 16 32 2

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Covalent Bonds- formed when atoms share their valence e s

a. Nonpolar - eg. O2; H2b. Polar - eg. H2O

Nonpolar CB> Polar CB> Ionic Bond>WanderWaals

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c. Organic molecules 80-90% of the dry weight of most cells- carbohydrates, lipids, proteins, and nucleic acids

Biomolecules Simple forms

Carbohydrates monosaccharidesProteins amino acidsNucleic acids nucleotidesLipid fatty acid and glycerol

Molecular Composition of Cells:a. Water abundant molecule ( 70% of total cell mass)

- it is polar and it can form H-bonds with eachother or with polar molecules

b. Inorganic ions Na, K, Mg2, Ca2 , phosphate(HPO42 , Cl and bicarbonate (HCO3)- 1% or less of the cell mass

- these ions are involved in number of aspects ofcell metabolism

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Water Molecules are Polar

-This accounts for its

cohesiveness, temperature-stabilizing capacityand

solvent properties of water.

The Importance of Synthesis by Polymerization

Macromolecules Are Responsible for Most of the Formand Function in Living Systems

-

Cells contain Three different Kinds of Macromolecules informational storage and structural

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Biological PolymerProteins Nucleic

AcidsPolysaccharides

Kind of

macromolecule

Information

al

Information

al

Storage Structural

Examples Enzymes, DNA, RNA Starch,Glycogen

Cellulose

Hormones,

Antibodies

Repeatingmonomers

Amino Acids Nucleotides Monosaccharides Monosaccharides

Number ofkinds of

20 4 in DNA;4 in RNA

One or a few One or a few

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Carbohydrates

-the most abundant class of organic compounds found in living

organisms.- include simple sugars and polysaccharides

-They fill numerous roles in living things, such as thestorage and

transport ofenergy (eg: starch, glycogen) and structurcomponents(eg: cellulose in plants and chitin).

General Formula: (CH2O)nSugars:

3 C= trioses 6 C= hexoses4 C= tetroses 7 C= heptoses5 C= pentoses

http://en.wikipedia.org/wiki/Energyhttp://en.wikipedia.org/wiki/Starchhttp://en.wikipedia.org/wiki/Glycogenhttp://en.wikipedia.org/wiki/Cellulosehttp://en.wikipedia.org/wiki/Chitinhttp://en.wikipedia.org/wiki/Chitinhttp://en.wikipedia.org/wiki/Cellulosehttp://en.wikipedia.org/wiki/Glycogenhttp://en.wikipedia.org/wiki/Starchhttp://en.wikipedia.org/wiki/Energy

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Aldoses and Ketoses

OR O

R

D-glucosean aldose

analdohexose

D-fructose

a ketosea

ketohexose

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Fig. 2-4: Stereoisomers (chirality):Mirror images depends on an asymmetricatom.

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Number ofCarbons CategoryName Examples

4 TetroseErythrose,

Threose

5 Pentose

Arabinose,Ribose,Ribulose,Xylose,Xylulose,

Lyxose

Allose,Altrose,Fructose,

Galactose,

Monosaccharide classifications based on the number of carbons

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D-Erythrose D-Threose

Tetros

es

Pentos

es

D-Ribose D-Arabinose D-Xylose D-Lyxose

The ring form of ribose is a component ofribonucleic acid (RNA). Deoxyribose, which is

missing an oxygen at position 2, is acomponent ofdeoxyribonucleic acid (DNA). Innucleic acids, the hydroxyl group attached tocarbon number 1 is replaced withnucleotide bases.

Ribose Deoxyribose

http://www.scientificpsychic.com/fitness/aminoacids1.htmlhttp://www.scientificpsychic.com/fitness/aminoacids1.html

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Hexose

s

Hexoses, such as the ones illustrated here, have the

molecular formula C6H12O6.German chemist Emil Fischer (1852-1919) Identified thestereoisomers for these aldohexoses in 1894. He receivedthe 1902 Nobel Prize for

chemistry for his work.

D-Glucose D-Mannose D-Galactose

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Glucose is by far the most common carbohydrate andclassified as a monosaccharide, an aldose, a hexose, andis a reducing sugar. It is also known as dextrose .

-also called blood sugar as it circulates in the blood at aconcentration of 65-110 mg/mL of blood.

Fructose is more commonly found together with glucoseand sucrose in honey and fruit juices. Fructose, alongwith glucose are the monosaccharides found indisaccharide, sucrose.

-the most important ketose sugar- common name for fructose is levulose

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Disaccharide DescriptionComponent

monosaccharides

sucrose common table sugar glucose 12fructose

maltoseproduct of starch

hydrolysis

glucose 14

glucose

lactose main sugar in milk

galactose 14

glucose

Disaccharide descriptions and components

Disaccharides consist of two simplesugars

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Sucrose Lactose Maltose

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Oligosaccharide- a saccharide polymer containing a small number

(typically three to ten) simple sugars- commonly found on the plasma membrane of

animal cells where they can play a role in cell-cellrecognition.

Polysaccharides are polymers of simplesugars

Many polysaccharides, unlike sugars, are insoluble in

water.Dietary fiber includes polysaccharides andoligosaccharides that are resistant to digestion andabsorption in the human small intestine but which are

completely or partially fermented by microorganismsin the lar e intestine.

http://en.wikipedia.org/wiki/Saccharidehttp://en.wikipedia.org/wiki/Simple_sugarshttp://en.wikipedia.org/wiki/Simple_sugarshttp://en.wikipedia.org/wiki/Saccharide

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Starch

Starch is the major form of stored carbohydrate in plants. Starch iscomposed of a mixture of two substances:

amylose, an essentially linear polysaccharide,and amylopectin, a highly branched polysaccharide.

Both forms of starch are polymers of-D-Glucose.

Natural starches contain 10-20% amylose and 80-90%amylopectin. Amylose forms a colloidal dispersion in hot water

(which helps to thicken gravies) whereas amylopectin is completelyinsoluble.

Amylosemolecules consist typically of 200 to 20,000 glucoseunits which form a helix as a result of the bond angles betweenthe glucose units.

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Amylose

Amylopectin differs from amylose in being highly branched. Short sidechains of about 30 glucose units are attached with 16 linkagesapproximately every twenty to thirty glucose units along the chain.

Amylopectin molecules may contain up to two million glucose units.

Amylopectin The side branching chains are

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Glucose is stored as glycogen in animal tissues by the process

of glycogenesis. When glucose cannot be stored as glycogen orused immediately for energy, it is converted to fat. Glycogen is a

polymer of -D-Glucose identical to amylopectin, but the branchesin glycogen tend to be shorter (about 13 glucose units) and more

frequent. The glucose chains are organized globularly like branches

of a tree originating from a pair of molecules ofglycogenin, aprotein with a molecular weight of 38,000 that acts as a primer at

the core of the structure. Glycogen is easily converted back to

glucose to provide energy.

Glyco

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Cellulose

Cellulose is a polymer of-D-Glucose, which in contrast to

starch, is oriented with -CH2OH groups alternating above andbelow the plane of the cellulose molecule thus producing long,

unbranched chains. The absence of side chains allows cellulosemolecules to lie close together and form rigid structures.

Cellulose is the major structural material of plants. Wood islargely cellulose, and cotton is almost pure cellulose. Cellulose

can be hydrolyzed to its constituent glucose units bymicroorganisms that inhabit the digestive tract of termites and

ruminants.

Cellulose

Chiti

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Chitin

Chitin is an unbranched polymer of N-Acetyl-D-glucosamine. It is found in fungi and is the principal

component of arthropod and lower animalexoskeletons, e.g., insect, crab, and shrimp shells. Itmay be regarded as a derivative of cellulose, in whichthe hydroxyl groups of the second carbon of each

glucose unit have been replaced with acetamido (-NH(C=O)CH3) groups.

Chitin

Gl cosaminogl cans

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Glycosaminoglycans

Glycosaminoglycans are found in the

lubricating fluid of the joints and ascomponents of cartilage, synovial fluid, vitreoushumor, bone,and heart valves.

- are long unbranched polysaccharides

containing repeating disaccharide units thatcontain either of two amino sugar compounds-- N- acetylgalactosamine or N-acetylglucosamine, and a uronic acid such as

glucuronate (glucose where carbon six forms acarboxyl group).

- are negatively charged, highly viscous

molecules sometimes calledmuco ol saccharides. He a

ChondroitinSulfate

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II. Lipids- diverse group of non-polar biomolecules

- have the ability to dissolve in organic solvents (chloroformor benzene but not in water.

Three Major Roles in Cells

1. provide an important form of energy storage2. as major component of cell membrane (great

importance in cell biol3. play important role in cell signaling as

a. steroid hormones (eg. Estrogen and testosterone)b. messenger molecules convey signals from cell

surface receptors to targets within the cell.

TRIGLYCERIDES/FATS

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TRIGLYCERIDES/FATS-consist of three fatty acids linked to a glycerol molecule- insoluble in water and therefore accumulate as fat droplets in

the cytoplasm.- can be broken down for use in energy-yielding reactions( more

efficient formof energy storage than carbohydrates, yielding more than twice

as muchenergy per weight of material broken down.

Fatty acids- consist of long

hydrocarbon chains,most frequently containing 16or 18carbon atoms, with a carboxyl

group(COO-) at one end

-maybesaturated or

unsaturatedfatty acids

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Saturated fatty Acids - lack double bonds (eg.Stearic acid)

- common component of animal fats

(solid at room T)Unsaturated fatty acids - possesing double bonds- double bonds create kinks in the

molecules- found in vegetable fats(liquid at

roomT)

Phospholipids-principalcomponents of cell membrane

- are amphipathic

molecules (part water-solubleand part water-insoluble )

Figure 2.7. Structure of phospholipidsGlycerol phospholipids contain two fatty acids

joined to glycerol. The fatty acids may bedifferent from each other and are designated R1and R2. The third carbon of glycerol is joined toa phosphate group (forming phosphatidic acid),which in turn is frequently joined to anothersmall polar molecule (formingphosphatidylethanolamine, phosphatidylcholine,phosphatidylserine, or phosphatidylinositol). Insphingomyelin, two hydrocarbon chains are

bound to a polar head group formed from serineinstead of glycerol.

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886

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Figure 2.9.Cholesterol andsteroid hormonesCholesterol, an

importantcomponent of cellmembranes, is anamphipathicmolecule because ofits polar hydroxylgroup. Cholesterol isalso a precursor tothe steroid

hormones, such as

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Nucleic Acids

DNA and RNA- the principal informational molecules of the cell

DNA - Deoxyribonucleic acid (has a unique role as the genetic material)- a double-stranded molecule consisting of two polynucleotide chains

running in opposite directions- contains two purines (adenine and guanine) and two pyrimidines (

cytosine and thymine).- 2-deoxyribose sugar

RNA- Ribonucleic acid- single-stranded- Adenine, guanine, and cytosine are also present in RNA,

but RNA contains uracil in place of thymine- ribose sugar- different types ofRNA participate in a number of cellular activities

a. Messenger RNA (mRNA) -carries information from DNA to theribosomes, where it serves as a template for protein

synthesis

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886

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b. Ribosomal RNA(rRNA) involves in protein synthesisc. Transfer RNA(tRNA)

*polymerization of nucleotides to form nucleic acids involves theformation ofphosphodiesterbonds between the 5 phosphate of onenucleotide and the 3 hydroxyl of another

oligonucleotide - a short polymer of only a few nucleotides

the large polynucleotides that make up cellular RNA and DNA maycontain thousands or millions of nucleotides, respectively.

Polynucleotides are always synthesized in the 5 to 3 direction,with a free nucleotide being added to the 3 OH group of a growingchain.

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886

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Figure 2.10.Componentsof nucleic

acids Nucleicacids containpurine andpyrimidine

bases linked tophosphorylatedsugars. Anucleic acidbase linked to a

sugar alone is a

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Figure 2.12. Complementary pairingbetween nucleic acid bases

Figure 2.11.Polymerization ofnucleotides Aphosphodiester bond is

formed between the 3hydroxyl group of onenucleotide and the 5phosphate group ofanother. A polynucleotide

chain has a sense of

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Proteins -primary responsibility is to execute the tasks directed by

that information in nucleic acids

-the most diverse of all macromolecules (each cell containsseveral thousand different proteins, which perform a widevariety of functions)

1. serving as structural components of cells and tissues2. acting in the transport and storage of small

molecules (e.g., the transport of oxygen byhemoglobin

3. transmitting information between cells (e.g., proteinhormones)

4. and providing a defense against infection (e.g.,antibodies)

-the most fundamental property of proteins is their abilityto act as enzymes-direct virtually all activities of the cell.-polymers of 20 different amino acids

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886

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Figure 2.13. Structure ofamino acids Each aminoacid consists of a centralcarbon atom (the carbon)bonded to a hydrogen atom,

a carboxyl group, an aminogroup, and a specific sidechain (designated R). Atphysiological pH, both thecarboxyl and amino groupsare ionized, as shown.

Figure 2.14. Theamino acids Thethree-letter and one-letter abbreviations foreach amino acid are

indicated. The amino

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Figure 2.15.Formation of apeptide bond Thecarboxyl group of one

amino acid is linked to

Proteinstructure1. primary structure

2. secondary structure

3. tertiary structure4. quaternary structure

Primary Structure -thesequence of amino acids

in itspolypeptide chain

Figure 2.16. Amino acid

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886

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Secondary structure- theregular arrangement ofamino acids within

localized regions of thepolypeptide.

Figure 2.19. Secondarystructure of proteins

Tertiary structure-thefolding of thepolypeptide chain as a

result of interactionsbetween the side chainsof amino acids that lie indifferent regions of theprimary sequence

Figure 2.20.Tertiary structureofribonuclease

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Quaternary structure- consists of the interactions betweendifferent polypeptide chains in proteins composed of morethan one polypeptide.

Figure 2.21.Quaternarystructure ofhemoglobin

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Bioenergetics, Enzymes and Metabolism

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Bioenergetics: The Flow of Energy inthe

Cell-the study of the various types of energytrans-

formations that occur in living organisms

-the prodn of energy, its storage and its useare

central to the economy of the cell

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- the capacity to do work (the capacity to changeor move something).

-cell require energy to do all their work, includingthe synthesis of sugars from CO2 and H2O inphotosynthesis, the contraction of muscles and thereplication of DNA

POTENTIAL ENERGY- several forms of PE are biologically significant

1. stored in the bonds connecting atoms inmolecules

2. concentration gradient3. electric potential (the energy of charge

separation)

Energy

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Cells Need Energy to Cause Six Different Kinds ofBiological Work

1. Synthetic Work -changes in chemical bonds (formationand generation of new molecules)e.g. process of photosynthesis

2. Mechanical Work- physical change in the position ororientation of a cell or some part of ite.g. Contraction of weightlifters muscleor movement of cell thru its flagella

3. Concentration Work - movement of molecules across amembrane against a concentrationgradiente.g. Na+-K+ pumps across plasmamembrane

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4. Electrical Work - movement of ions across a membraneagainst an electrochemical gradiente.g. Membrane potential of mitochondrion

(generated by active proton transport)

5. Heat - an increase in temperature that is useful towarm blooded animalse.g. Use to maintain body T near 37oC where

metabolism is most efficient by warm-bloodedanimals

6. Bioluminescence production of light

e.g.Seen during courtship of fireflies, in dino-flagellates, luminous toadstools, deep-sea fish

M t i bt i ith f li ht f

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Most organisms obtain energy either from sunlight or fromorganic food molecules:

a. Phototrophs light-feeders (plants, algae,cyanobacteria and photosynthesizingbacteria).

b. Chemotrophs- chemical-feeders (all animals,fungi,protists and most bacteria)

Energy flows through the biospherecontinuously

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System -By convention, the restricted portion of the

universe

under consideratione.g. Reaction/process occurring in a beaker of

chemicals or in a cellSurroundings - referred to all the rest of the universe

2 types of System:1. Open System - can exchange energy with its

surroundings

- can use incoming energy to increaseits orderliness thus decreasing its entropy.2. Closed System can not exchange energy w/ its

surroundings- tends toward equilibrium and

increases its entropy

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*All living organisms areopensystems, exchanging

energy

freely with theirsurroundings.

Th d i

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-the study of the changes in energy that accompanyevents in the universe.

1st Law of thermodynamics(Law of conservation of Energy)

- E is neither created nor destroyed but can be

converted from one form to another

energy stored = energy in energy out or

E = Eproducts - Ereactants (chemical reactions)

In the case of biological rxns and processes, we aremore interested in the change in enthalpy or heatconstant (H)

Thermodynamics

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H = E + (PV) =E

H = Hproducts -Hreactants*if the heat content of the products is less than that ofthereactants, H will be negative and the rxn is said to be

ExothermicIf the heat content of the products is greater than that ofreactants, H will be positive and the rxn is endothermic

-energy can be expressed in the same units of measurementsuch as cal or kilocalorie

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2nd Law of thermodynamics- the universe and its parts (including living

systems) become increasingly disorganized (Entropy)

Energy transformations thus increased the amount ofentropy of a system.

*only E that is in an organized state-called free energy-

can be used to do work

Free energy or G- a measure of the potential energy ofa system which is a function of the enthalpy (H) and

entropy (S)

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Enthalpy(H)Heat-in a chemical rxn, the E of thereactants or products is equal to their total bondenergies (heat released or absorbed during achemical reaction)

Entropy(S)- a measure of the degree of disorder orrandomness in a system; the higher the entropy, the

greater the disorder resulting frm a rxn

-thus determines its chemical equilibrium andpredicts in which direction the reaction will proceedunder any given set of conditions

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*many biological rxns (such as synthesis of macromolecules) arethermodynamically unfavorable under cellular conditions(G>0or-)(for the reaction to proceed an additional source of energy is

required)A B G=+10kcal/mol

How?: by coupling the conversion of A to B with an energeticallyfavorable

reactionC D G= -20kcal/molTHUS:

A + C B + D G= -10kcal/mol

* Enzymes are responsible for carrying out such coupledreactions in a coordinated manner

*the cell uses this basic mechanism to drive manyenergetically unfavorable reactions that must take place inbiological system

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At constant T & P, it is possible to predict the direction of a chemicalrxnby using G.

G =H-TS where T= K

-the change in Free Energy(G) determines the direction of achemical

reaction

Free Energy change, G = G products G reactantsifG(-) for a chemical reaction, forward rxn occursifG(+) reverse reaction occursifG = 0, both forward and reverse rxns occur at equal

rates; the rxn is at equilibrium

A B

Standard Free-Energy Change (G )

G = -RTln K where K= [B]/[A]

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Endergonic Reactions chemical reactions that require input of E.eg. CO2 + H2O CH2O + O2

Exergonic Reactions-rxns that convert molecules with morefree energy to molecules with less- and, therefore, thatrelease energy as they proceed.eg. C6H12 O6 + O2 CO2 + H2O

Equilibrium vs Steady StateMetabolism

At equilibrium: 1. reaction has stopped (no net reaction are possible)2. no energy can be released

3. no work can be done and order of living state can notbe maintained

*The continual flow of oxygen and other materials into and out ofcells allows cellular metabolism to exist in a Steady state. ( thus lifeis possible because living cells maintain this state).

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Coupled Reactions: ATP

-Energy liberating reactions are thus coupled toenergy-requiring reactions.

-Adenosine 5-triphosphate (ATP) plays a central role in

this process by acting as a store of free energy withinthe cell

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Figure 2-24. Inadenosine triphosphate(ATP), two high-energyphosphoanhydride

bonds (red) link thethree phosphategroups.-The bonds between the phosphates in ATP (HIGH- ENERGY BONDS)

-large amount of free energy is released when hydrolyzed withinthe cell (G approx = 12kcal/mol)from ATP to ADP and Pi

-energy released from the breakdown of ATP is used to power theenergy-requiring processes in cells.-known as the universal energy carrier,ATP serves to more

efficiently couple the E released by the breakdown of food molecules to theE required by the diverse endergonic processes in the cell.

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Figure 2-25. The ATP cycle. ATP is formed from ADP and Piby photosynthesis in plants and by the metabolism of energy-rich compounds in most cells. The hydrolysis of ATP to ADPand Pi is linked to many key cellular functions; the free energyreleased by the breaking of the phosphoanhydride bond is

trapped as usable energy.

Coupled Reactions: Oxidation-Reduction

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p-involve the transfer of hydrogen atoms- a molecule is said to be oxidized when it loses electrons and it issaid to be reduced when it gains electrons

- a reducing agent is thus an electron donor; an oxidizing agent isan electron acceptor-although oxygen is the final electron acceptor in the cell, othermolecules can act as oxidizing agents-a single molecule can be an electron acceptor in one reactionand an electron donor in another.

1. NAD and FAD can become reduced by acceptingelectrons from hydrogen atoms removed from othermolecules

2. NADH + H+ and FADH2 in turn, donate these electronsto other molecules in other locations within the cells

3. Oxygen is the final electron acceptor (oxidizing agent)in a chain of oxidation-reduction reactions that provideenergy for ATP production.

Rxnit HH

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Nicotinamide adeninedinucleotide

site

+2H

N

H

+H

H

NAD+(Oxidized state)

NADH(Reduced state)

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Flavin Adenine Dinucleotide(FAD) (Oxidized

Form)

+2H

H3

C

H3C

N

N N

N

H

O

H

H

O

FADH2(Reduced form)

The Central Role of Enzymes

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The Central Role of Enzymesas Biological Catalysts

Enzymescatalysts that increase the rate ofvirtually all the chemical reactions within cells.

2 Fundamental Properties:1. they increase the rate of chemical reactions

without themselves being consumed orpermanently altered by the reaction.

2. they increase reaction rates without alteringthe chemical equilibrium between reactants and

products.

Active site

-a specific region of the enzyme where

the

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Figure 2.23. Enzymaticcatalysis of a reaction betweentwo substrates The enzymeprovides a template upon which

the two substrates are broughttogether in the proper position andorientation to react with eachother.Figure 2.22.

Energydiagrams forcatalyzed anduncatalyzedreactions

Figure 2.24. Models ofenzyme-substrateinteraction (A) In the lock-and-key model, the substratefits precisely into the activesite of the enzyme. (B) In theinduced-fit model, substratebinding distorts theconformations of bothsubstrate and enzyme. Thisdistortion brings the substratecloser to the conformation ofthe transition state, therebyaccelerating the reaction.

Prosthetic groupsare small molecules bound to proteins inwhich they play critical functional roles

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.glossary.2886

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Coenzymes -molecules that work together with enzymes to enhancereaction rates.-are not irreversibly altered by the reactions in which theyare involved but are recycled and can participate inmultiple enzymatic reactions.

which they play critical functional roles-either small organic molecules (coenzymes) or

inorganic like metal ions (cofactors)

Coenzyme Related vitamin Chemical reaction

NAD+, NADP+ Niacin Oxidation-reductionFAD Riboflavin (B2) Oxidation-reductionThiamine pyrophosphate Thiamine (B1) Aldehyde group transfer Coenzyme A Pantothenate Acyl group transfer Tetrahydrofolate Folate Transfer of one-carbon

groups

Biotin Biotin CarboxylationP ridoxal hos hate P ridoxal B6 Transamination

Table 2.1. Examples of Coenzymes andVitamins

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Figure 2.29. Allosteric regulation

In this example, enzyme activity isinhibited by the binding of aregulatory molecule to an allostericsite. In the absence of inhibitor, thesubstrate binds to the active site of

the enzyme and the reaction

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Metabolism

Metabolism

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Metabolism-all of the reactions in the body that involve energy

transformation

2 Categories:1. Anabolism reactions require the input of energy andinclude the synthesis of large energy-storage

molecules, including glycogen, fat and protein.2. Catabolism reactions release energy, usually by thebreakdown of larger organic molecules into

smaller molecules.*The catabolic reactions that break down glucose, fatty acid,

and amino acids serve as the primary source s of energy forthe synthesis of ATP.

*Some of the chemical-bond energy in glucose is transferred tothe chemical-bond energy in ATP.

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Fig.3 Three Stages of

Metabolism

The Generation of ATP from Glucose

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The Generation of ATP from Glucose-breakdown of glucose (major source of cellular energy)

2 Stages:

1. Glycolysis2. Tricarboxylic acid (TCA) cycle

Glycolysis- initial stage in the breakdown of glucose (aerobic cells)

- common to all cells (occurs in the cytosol)-occurs in the absence of O2 (can provide all themetabolic

energy of anaerobic organisms)- conversion of glucose to pyruvate with the net gain of2 molecules of ATP

Glu + 2ADP + 2Pi + 2NAD+ 2 Pyruvate + 2ATP +2NADH + 2H+ +2H2O

Enzymes: (important regulatory points of glycolyticpathway)

1. Hexokinase-

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Figure 2.32. Reactions of glycolysis Glucoseis broken down to pyruvate, with the netformation of two molecules each of ATP andNADH. Under anaerobic conditions, the NADH isreoxidized by the conversion of pyruvate toethanol or lactate. Under aerobic conditions,pyruvate is further metabolized by the citric acid

cycle. Note that a single molecule of glucoseyields two molecules each (shadow boxes) of the

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Glycogenesis the formation of glycogen from glucose

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Glycogenesis the formation of glycogen from glucose(see fig. enzyme=glycogen synthase)

Glycogenolysis- the conversion of glycogen to glucose -6-P(enzyme= glycogen phosphorylase)

Gluconeogenesis- the conversion of noncarbohydratemolecules (not just lactic acid but also amino

acids and glycerol) through pyruvic acid to glucose

Cori Cycle

- gluconeogenesis in the liver allows depletedskeletal muscle glycogen to be restored w/in 48 hrs.- it is a two-way traffic between skeletal muscles andthe liver

In the liver are enzymes: glu-6-phosphatase & lactic

dehydrogenase

The CoriCycle

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Glycogen

Glu-6-

phosphate

Pyruvicacid

Lacticacid

Glycogen

Glu-6-

phosphate

Pyruvicacid

Lacticacid

CycleSkeletalMuscles

Liver

Exercise

1

Rest9 Gluc

ose

Blood

Blood

2

3

4

5

8

7

6

TCA or Krebs cycle

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TCA or Krebs cycle- occurs in the mitochondria (matrix)- leads to the final oxidation of the carbon atom s to carbon

dioxide

Figure 2.33. Oxidativedecarboxylation ofpyruvate .Pyruvate isconverted to CO2 and acetylCoA, and one molecule of

NADH is produced in theprocess. Coenzyme A (CoA-SH) is a general carrier ofactivated acyl groups in a

variety of reactions.

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Figure 2.34. Thecitric acid cycle Atwo-carbon acetylgroup is transferred

from acetyl CoA tooxaloacetate,forming citrate. Twocarbons of citrateare then oxidized toCO2 andoxaloacetate isregenerated. Eachturn of the cycle

yields one molecule

Electron Transport and Oxidative

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Phosphorylation

-built into the foldings, cristae of the innermitochondrial membrane are a series of molecules thatserve as electron transport system during aerobicrespiration

-the molecules of electron transport system are fixed

in position within the inner mitochondrial membrane insuch a way that they can pick up electrons from NADHand FADH2 and transport them in a definite sequenceand direction.

-the electron transport chain thus act as an oxidizingagent for NAD and FAD.

Oxidative Phosphorylation- the production of ATP thru the coupling of the

electron-transport system with the phosphorylation of

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Figure 2.35. Theelectron transportchain Electronsfrom NADH and

FADH2 aretransferred to O2through a series ofcarriers organizedinto four proteincomplexes in themitochondrialmembrane. The freeenergy derived from

electron transport

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ATP Balance SheetS Th ti l ATP i ld 36 t 38 ATP l

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Summary:Theoretical ATP yield =36 to 38 ATP per glucose Actual ATP yield = 30 to 32 ATP per glucose (allowing

for the costs of transport)

Phases of

Respiration

Subsrate-

level

phosphorylat

ion

Reduced Coenzymes ATP Made by

Oxidative

Phosphorylation*

Glucose to pyruvate

(in cytoplasm)

2 ATP (net

gain)

2 NADH, but usually goes

into mitochondria as 2FADH2

1.5 ATP per FADH2 X 2

= 3ATP

Pyruvate to acetyl

CoA(x2 bec one glu

yields 2 pyruvates)

None 1 NADH (X2) = 2NADH 2.5ATP per NADH x 2 =

5ATP

Krebs cycle (x2 bec

one glucose yields 2Krebs cycles)

1 ATP (X2) = 2

ATP

3 NADH (X2) 2.5ATP per NADH x 3

=7.5 ATP X 2 = 15 ATP1.5 ATP per FADH2 X 2

= 3ATP

SUBTOTALS 4 ATP 26 ATP

GRAND TOTAL 30 ATP

Table 3. ATP Yield per Glucose inAerobic Respiration

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*Theoretical estimates of ATP production fromoxidation phosphorylation are 2 ATP per FADH2 and 3

ATP per NADH. If these numbers are used, a total of32 ATP will be calculated as arising from oxidativephosphorylation. This is increased to 34 ATP IF thecytoplasmic NADH remains as NADH when it is

shuttled into the mitochondrion. Adding thesenumbers to the ATP made directly gives a total of 38ATP produced from a molecule of glucose.Estimatesof the actual number of ATP obtained by the cell arelower because of the costs of transporting ATP out of

the mitochondria.

Glyco

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gen

Gluco

se

Phosphoglyceraldehyde

Pyruvic Acid

AcetylCoA

C

6C

5

C

4

TCAcycl

e

Glycerol

Lacticacid

Fatty

Acids

FATS

Ketone

bodie

s

Amino

acids

Protein

Urea

Figure 5.17 The interconversion of glycogen, fat androtein

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Figure 2.36. Oxidation offatty acids The fatty acid(e.g., the 16-carbonsaturated fatty acid

palmitate) is initially joinedto coenzyme A at the cost ofone molecule of ATP.Oxidation of the fatty acidthen proceeds by stepwiseremoval of two-carbon unitsas acetyl CoA, coupled to theformation of one moleculeeach of NADH and FADH2.

ATP Produced: 108 ATP

Amino Acid Metabolism

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Transamination- type of reaction in which the amine groupis

transferred from one amino acid to form another

Oxidative Deamination- the metabolic pathway thatremoves

amine groups from amino acidsleaving a keto acidand ammonia (which is converted to urea).Essential amino acids- can not be produced by the bodyandmust be obtained in the diet (lysine, tryptophan,phenylalanine, threonine, valine, methionine, leucine,isoleucine & histidine(children))

Nonessential amino acids- the body can produce them ifprovided with a sufficient amount of carbohydratesand the essential aas (aspartic acid glutamic acid