ch3 chemistry of life

8/10/2019 Ch3 Chemistry of Life

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Ch 3.1. Chemical elements and water

(taken from assessment statements)

3. 1. 1. State that the most frequently occurring chemical elements in living things are

carbon, hydrogen and nitrogen.

+ 3. 1. 2. State that a variety of other elements are needed by living systems, including

sulfur, calcium, phosphorus, iron and sodium.

+ 3. 1. 3. State the role for each of the elements mentioned in 3. 1. 2.

Symbol Name Abundance (%) (Wikipedia) Uses

O Oxygen 65 carbohydrates, fats,

water

C Carbon 18 all organic compoundsH Hydrogen 10 water, all organic

compounds

Ca Calcium 1.5 bones, muscle

Fe Iron H2O

A hydrogen bond can only form when hydrogen is bonded

to an atom with a very high electronegativity, thus

generating a partial charge (oxygen, nitrogen and fluorine).

3. 1. 5. Outline the thermal, cohesive and solventpro per ti es of wat er .

+ 3. 1. 6. Explain the relationship between the properties of water and its uses in living

organisms as a coolant, medium for metabolic reactions and transport medium


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Thermal:

because of hydrogen bonds, a lot of energy needs to be invested to increase the kinetic energy of water

molecules => it takes a lot of energy to change the temperature

high thermal capacity / high specific heat (can take in a lot of energy without changing temperature greatly)

=> used in homeostasis

high heat of vaporization (absorbs a lot of energy in vaporization) => used by perspiration

Cohesive:

Cohesion:molecules of the same type are attracted to one another.

Hydrogen bonding holds molecules closer together => used in transpiration

When solid, hydrogen bonds form a crystal structure => ice is less dense than liquid water => stays floating

on top of lakes; turnover effect

Adhesion: molecules of a different kind sticking to one another.

Solvent:

excellent solvent => reactions of polar molecules can occur in it

hydrogen bonds can form with other molecules (ie. ethanol)

polar solvent solves polar solute (many organic molecules, apart from fats are polar)

The fact that water is polar and cytosol etc. is water-based affects the folding of proteins and thus the

functionality of enzymes etc.

Aqueous solution Location Common reactions

cytosol from the nuclear membrane to

the cellular membrane (apart

from organelles)

glycolysis, translation, many

reactions

nucleoplasm inside nuclear membrane transcription, DNA replicationstroma inside chloroplast (outside

grana)

light-independent reactions of

photosynthesis

matrix mitochondria cytosol Krebs cycle of respiration

blood plasma fluid in blood transport of respiratory gases,

nutrients and antibodies;

clotting

xylem fluid fluid in plant xylem water transport in plants

sap fluid in plant phloem sugar transport in plants


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Ch 3.2 Carbohydrates, lipids and proteins

3. 2. 1. Distinguish between organic and inorganic compounds.

Organic compounds are defined by the presence of carbon.

They often include catenation of carbon. This means that carbon forms long molecules with chains of carbon

3. 2. 2. Identify amino acids, glucose, ribose and fatty acids from diagrams showing their

structures:

Name Structure

Amino acid

Glucosesee next

Ribose

Fatty acid

3. 2. 3. List three examples each of monosaccharides, disaccharides and polysaccharides

+ 3. 2. 4. State one function of glucose, lactose and glycogen in animals, and of fructose,

sucrose and cellulose in plants.

MonosaccharidesName Structure Use

Ribose (D)

/ beta D ribofuranose

present in RNA


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Deoxyribose (beta D)

/ beta-D-ribofuranose

present in DNA

Glucose (D)

/ Alpha-D- glucopyranose

blood sugar, utilized

in glycolysis to

obtain ATP

Fructose (D)

/ Alpha-D-fructofuranose

isomer of glucose,

one of the

monomers of

sucrose

Galactose (D)

/ Beta-D-galactopyranose

monomer of lactose

Disaccharides

Name Structure UseLactose

(Galactose must be beta-D, glucose can be

beta-D or alpha-D)

linked through beta1->4 glycosidic linkage

Milk sugar (8-10% of milk)

Sucrose

alpha-D-glucopyranose and beta-D-

fructofuranose with alpha 1->2 glycosidic

energy source


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linkage

Maltose

(Two alpha D glucopyranoses linked through

alpha 1->4 glycosidic linkage

Malt sugar

Constituent of starch

Polysaccharides

Name Structure Use

Amylose

(alpha D glucopyranoses with alpha 1->4 glycosidic

linkages)

~20% of starch, soluble in

water, plant energy

storage

Amylopectin

(like amylose, but additional alpha 1->6 bonds linking

individual chains)

~80& of starch, insoluble

in water, plant energy

storage

Glycogen

(very similar to amylopectin, but it is impossible to tell,

what chain is main)

storage in animals

Cellulose (hydrogen bonds between chains provide more stability) Cell walls, structural

Chitin You do not need to know this! Structural, cell walls of

fungi, exoskeletons of

insects

3. 2. 5. Outline the role of condensation and hydrolysis in the relationships between fatty

acids, glycerol and triglycerides; and between amino acids and polypeptides.


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Condensation reaction in triglycerides

3. 2. 6. State three functions of lipids:

1. Thermoregulation

2.

Energy storage

3. Protection

4. Membranes

3. 2. 7. Compare the use of carbohydrates and lipids in energy storage.

Carbohydrates Lipids better for short-term

faster utilization (breaking up by enzymes)

undergo glycolysis and acetyl CoA step

same mass can result in of the energy a lipid

could provide

better for long-term

slower utilization

go straight into Krebs cycle

same mass can result in 2x much energy as

carbohydrate


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Ch 3.3 DNA structure

3. 3. 1. Outline DNA nucleotide structure in terms of sugar, base and phosphate.

+ 3. 3. 2. State the names of the four bases in DNA.

In RNA, theres uracil:

3. 3. 3. Outline how DNA nucleotides are linked together by covalent bonds into a single

strand.

+ 3. 3. 4. Explain how a DNA double helix is formed using complementary base pairing and

hydrogen bonds.

+ 3. 3. 5. Draw and label a simple

diagram of the molecular structure of

DNA.


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Ch 3.4 DNA replication

3. 4. 1. Explain DNA replication in terms of unwinding the double helix and separation of

the strands by helicase, followed by formation of the new complementary strands by DNA

poly me ras e.


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3. 4. 2. Explain the significance of complementary base pairing in the conservation of the

base sequence of DNA.

Because base pairing is complementary, the DNA strands are also fully complementary. This means that since DNAreplication is semi-conservative, the daughter strands (newly synthesised) will be complementary to the original.

Why? Well, if base pairing is complementary, only one base can hydrogen bond to any other base of the parent

strand, and only the one that bonds can then be polymerized into the newly synthesised DNA strand. So, the DNA

sequence will be conserved. (Of course, mutations can occur)

3. 4. 3. State that DNA replication is semiconservative.

DNA replication is semiconservative. This means, that after replication, the two DNA molecules will each contain a

new DNA strand and an old one.


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Ch 3.5 Transcription and translation

3. 5. 1. Compare the structure of RNA and DNA.

DNA RNA

sugar 2-deoxyribose ribose

nucleotides thymine uracil3D structure usually double helix usually single stranded

3. 5. 2. Outline DNA transcription in terms of the formation of an RNA strand

complementary to the DNA strand by RNA polymerase.

This occurs in the nucleus.

1. The sequence to be transcribed is recognized by

TRANSCRIPTION FACTORS, which bind to it, changing

conformation.

2. RNA polymerase binds to the promoter

sequencewith the help of the already bound

transcription factor.

3.

RNA polymerase breaks the hydrogen bonds

holding the two strands together.

4.

RNA polymerase synthesises pre-mRNA

(direction 5->3).

5. Upon recognition of the terminator, RNA

synthesis is terminated.

6.

The RNA transcript is released and travels out of

the nucleus through nuclear pores.

The DNA strand read is the antisense strandand the

mRNA sequence corresponds to that of the sense strand.


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3. 5. 3. Describe the genetic code in terms of codons composed of triplets of bases.

The DNA, and thus mRNA, triplets can be

translated into amino-acids. These triplets are

called codons.

The genetic code is specific, but degenerate.

Specific:one codon can only be translated to

one amino acid only.

Degenerate:Multiple codons can be translated

into the same amino acid.

It is also conservedthroughout evolution

(there can be some exceptions , but the vast

majority is the same).

3. 5. 4. Explain the process of translation, leading to polypeptide formation.

Translation involves the reading of an mRNA template and the synthesis of a polypeptide strand based on the

genetic code.

INITIATION

1. Small ribosomal

subunit scans the mRNA

strand.

2. First tRNA with the

anticodon to AUG becomes

activated with Methionine.

(Met-tRNA-Met).

3. Small ribosomal

subunit (40S) recognizes

mRNA binding site.

4. Met-tRNA-Met

recognizes start codon

(AUG) on mRNA and binds

(with hydrogen bonds.

5.

Large ribosomal subunit (60S) arrives and ribosome assembles.

ELONGATION / PROPAGATION and TRANSLOCATION

6. Met-tRNA-Met is currently at the P site of the ribosome.

7.

Another activated tRNA arrives at the A site (the one with the appropriate anti-codon) and binds via h-

bonds.

8.

A peptide bond is formed between the Methionine and the next amino acid.

9. Ribosome translocates along mRNA and the Met-tRNA is currently at the E site, stops bonding and leaves the

ribosome. A new activated tRNA arrives at the A site.


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TERMINATION

10.

Stop codon is not matched to any tRNA, but to the termination factor.

11.

Peptide is released.

12.Ribosome disassembles.

3. 5. 5. Discuss the relationship between one gene and one polypeptide.

One polypeptide is coded for by one gene.

Note that it is not true, that one protein = one gene. This is because one protein can be composed of multiple

subunits.


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Ch 3.6 Enzymes

3. 6. 1. Define enzyme and active site.

Enzymesare globular proteins acting as biological catalysts(a catalyst decreases the activation energy of a reaction

and is not used up in the reaction).

There are 3 main types of enzymes:

catabolic-> catalyse the breaking up of polymers and large molecules (ie. AMYLASE -> amylose into maltose,

LACTASE -> lactose into glucose and galactose)

anabolic -> catalyse the synthesis of polymers and large molecules (ie. RUBISCO in photosynthesis)

isomerases-> catalyse isomerization ( ie. from fructose to glucose)

The active siteis an area within the 3D structure of the protein that will match the shape of the substrate and where

reactions occur.

3. 6. 2. Explain enzyme-substrate specificity.

Enzymes are generally specific for substrates and reactions. This is because of the 3D shape of the enzymes active

site, into which only the specific substrate(s) will fit.

Lock and key model

This model describes that an enzyme is like a lock and the substrate is the key. That is, their shapes fit completely

and no other substrate will click no other reaction can occur. It also states that the shape of the active site is

complementary to the shape of the substrate at all times, even when no reactions are occurring.

This is an older and too simplified model, though.

Induced fit model

Unlike the lock and key model, the induced fit model does not say that the active site is perfectly fitting the substrate

at all times. Rather, it proposes that the active site changes shape to acquire complementary to the substrate due to

electrostatic forces etc. upon contact with the substrate. Of course, the specificity still applies.

This model expresses reality significantly better and is presently used.

3. 6. 3. Explain the effects of temperature, pH and substrate concentration on enzyme

activity.

The factor which results in lower enzyme activity (and when removed, the enzyme activity grows) is called the

limited factor.

Temperature

An increase in energy means an increase in kinetic energy of the molecules.


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pH

(Negative logarithm of H+)

Thus, pH is indirectly proportional to the concentration of H+

ions (in acids, there are many H+ions and thus the pH is

very low).

Substrate concentration

With growing substrate concentration, the reaction can occur

faster (more product over same time), because the enzymes

available will be able to catalyse the reaction of more substrates

at the same time.

The kinetic energy is so high

that the enzyme is shaken so

much, that its 3D structuregets distrupted.

The kinetic energy makes all

the molecules move more

and thus it will be more likely

for an enzyme and substrate

to collide and meet.

The enzyme will be more acidic than its

environment and will therefore start

losing hydrogens. This will break it up.

With falling pH, there will be many

hydrogen ions in the environment. These

will interact with the enzyme via their

charge (electrostatic interactions) and

change its conformation.


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In this graph, enzyme concentration is the limiting factor, because at a certain substrate concentration, not enough

active sites will be available for catalysis of the reaction.

3. 6. 4. Define denaturation.

In denaturation, the 3D structure of an enzyme is permanently disrupted to the extent that it cannot function at all.

3. 6. 5. Explain the use of lactase in the production of lactose-free milk.

Lactose is a disaccharide naturally occurring in milk. Most adults on Earth (mostly of other races than Caucasian) are

not able to digest it. Lactase is an enzyme that can digest lactose into glucose and galactose, its two constituents. If

lactose is pre-digested by lactase prior to consumption, even lactose-intolerant people will be able to drink milk,

because no lactose (only glucose and galactose) will be present.


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Ch 3.7 Cell respiration

3. 7. 1. Define cell respiration.

Respiration is the controlled and slow series of catabolic redox reactions through which organisms extract the energy

stored in complex molecules and use it to generate ATP (adenosine triphosphate).

A slow and controlled oxidation of glucose occurs.

3. 7. 2. State that, in cell respiration, glucose in the cytoplasm is broken down by glycolysis

into pyruvate with a small yield of ATP.

The first step of respiration is called glycolysis. This does not require oxygen and is universal in nature.

FEEBACK INHIBITION (occurs when a high concentration of a product inhibits one of the previous steps in the

metabolic pathway):

glucose-6-phosphate inhibits glucoseglucose-6-phosphate

ATP inhibits fructose-6-phosphatefructose-1,6-bisphosphate

YIELD:

-2ATP+4ATP = 2ATP

2NADH+H+

2 pyruvate

3. 7. 3. Explain that, during anaerobic cell respiration, pyruvate can be converted in thecytoplasm with no further yield of ATP.

Anaerobic respiration occurs when the cell lacks oxygen or the organism is anaerobic. No oxygen is needed for it.

glucose (6C)kinase

glucose -6-phosphate(6C) fructose -6-phosphate(6C)isomerasekinase

fructose -1,6-bisphosphate(6C)

ATP ADP

ATP ADP

dihydroxyacetone

phosphate (3C)

glyceraldehyde-3-phosphate (3C) 2 1,3-bisphosphoglycerate

(3C)

NAD+ NADH+H

+

2 pyruvate (3D)

4ADP 4ATP

PREPARATORY

PHASE

PAY-OFF PHASE

2Pi


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The first step is glycolysis, the second step is fermentation. There are 2 types of fermentation:

ETHANOLIC FERMENTATION

Occurs in yeast

( http://upload.wikimedia.org/wikipedia/commons/thumb/0/08/Ethanol_fermentation-1.svg/495px-

Ethanol_fermentation-1.svg.png)

LACTIC FERMENTATION

Occurs in bacteria and animal cells deprived of

oxygen

(http://chsweb.lr.k12.nj.us/mstanley/outlines/respiration/image

156.gif)

3. 7. 4. Explain that, during aerobic cell respiration, pyruvate can be broken down in the

mitochondrion into carbon dioxide and water with a large yield of ATP.

In aerobic organisms, aerobic respiration can occur when there is enough oxygen in the environment. This also

begins with glycolysis, but continues with the link reaction (acetyl-CoA step), the Krebs cycle and the electron

transport chain.

In the presence of oxygen, pyruvate produced in glycolysis may enter the mitochondrion, where the rest occurs.

Note that for 1 molecule of glucose, all of the following steps must be doubled (because a pyruvate has the

carbons of a glucose).

LINK REACTION: (in matrix)

Yield for 1 pyruvate:

1 NADH+H+

1 acetyl-CoA

KREBS CYCLE/CITRIC ACID CYCLE: (in matrix)

pyruvate 3C acetyl-CoA

NAD+ NADH+H+

CoA CO2
http://upload.wikimedia.org/wikipedia/commons/thumb/0/08/Ethanol_fermentation-1.svg/495px-Ethanol_fermentation-1.svg.pnghttp://upload.wikimedia.org/wikipedia/commons/thumb/0/08/Ethanol_fermentation-1.svg/495px-Ethanol_fermentation-1.svg.pnghttp://upload.wikimedia.org/wikipedia/commons/thumb/0/08/Ethanol_fermentation-1.svg/495px-Ethanol_fermentation-1.svg.pnghttp://upload.wikimedia.org/wikipedia/commons/thumb/0/08/Ethanol_fermentation-1.svg/495px-Ethanol_fermentation-1.svg.pnghttp://chsweb.lr.k12.nj.us/mstanley/outlines/respiration/image156.gifhttp://chsweb.lr.k12.nj.us/mstanley/outlines/respiration/image156.gifhttp://chsweb.lr.k12.nj.us/mstanley/outlines/respiration/image156.gifhttp://chsweb.lr.k12.nj.us/mstanley/outlines/respiration/image156.gifhttp://chsweb.lr.k12.nj.us/mstanley/outlines/respiration/image156.gifhttp://chsweb.lr.k12.nj.us/mstanley/outlines/respiration/image156.gifhttp://upload.wikimedia.org/wikipedia/commons/thumb/0/08/Ethanol_fermentation-1.svg/495px-Ethanol_fermentation-1.svg.pnghttp://upload.wikimedia.org/wikipedia/commons/thumb/0/08/Ethanol_fermentation-1.svg/495px-Ethanol_fermentation-1.svg.png


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Yield for 1 pyruvate:

1 ATP

1 FADH2

3 NADH+H+

2 CO2

ELECTRON TRANSPORT CHAIN: (on

cristae)

Oxidative phosphorylationis the

process of ATP synthesis via redox

processes in the electron transport

chain.

Remember, that NADH+H+means

that only one H is bound covalently;

the other is floating in the cytosol.

The electron transport chain is a

series of membrane proteins

including proton (H+) channels. The

first membrane protein is

energetically highest and each

following is lower in energy.

Reduced coenzymesproduced in

previous steps have their electronand proton removed by the first

membrane protein. As the electrons are then passed between the membrane proteins (gradually to a lower energy

each time), the energy released can be used to pump proteinsof the coenzymes and from the cytosol across the

citrate (6C)

oxaloacetate (4C)

acetyl-CoA CoA

(5C)

CO2

NAD+

NADH+H+

several compounds (4C)

NAD+

NADH+H+

CO2

NAD+

NADH+H+

FADH2

FAD+

ATP

ADP


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membrane. This results in more protons in the intermembrane space and thus a negative charge of the matrix

relative to the intermembrane space (an electrical potential, like in a battery). On the last protein (cytochrome c

oxidase), the electrons are passed to the final electron acceptoroxygen (this is the only reason oxygen is needed

in aerobic respiration!), along with two protons from the cytosol:

() () () ()

The water produced becomes a part of the matrix. The energy released in this reaction is enough to pump 1 more

proton across the membrane.

The electrical potential can be used as a source of energy. The membrane protein ATP synthaseis capable of

utilizing this energy for ATP synthesis.Chemiosmosisis the movement of ions across a semipermeable membrane

down their electrochemical gradient. Chemiosmosis of protons through the ATP synthase results in a loss of

potential energy of these ions; this energy is used for ATP synthesis.

FADH2has electrons with a lower energy than NADH+H+and so it enters the ETC later (at an energetically lower

membrane protein) than the latter.

ATP Yield from ETC:

http://upload.wikimedia.org/wikipedia/commons/thumb/8/89/Mitochondrial_electron_transport_chain%E2%80%94Etc4.svg/600px-Mitochondrial_electron_transport_chain%E2%80%94Etc4.svg.png

Note: you do not need to know other names than ATP synthase and cytochrome c oxidase (IV on picture).

OVERALL ENERGY YIELD OF RESPIRATION

watch this:https://www.youtube.com/watch?v=OXgOsy8yQuk

for 1 glucose molecule

ATP NADH+H+ FADH2

glycolysis 2 2

link reaction 2

Krebs cycle 2 6 2

total 4 10 2

4 protons are necessary to form 1 molecule of ATP:

1 NADH+H+10H

+pumped2.5ATP

1 FADH26H+pumped1.5ATP

(Note that the result 36 is acquired when ATP yield in ETC are rounded up)

However, remember that pyruvate is transported into the mitochondrion via active transport (ATP is used up) etc.
http://upload.wikimedia.org/wikipedia/commons/thumb/8/89/Mitochondrial_electron_transport_chain%E2%80%94Etc4.svg/600px-Mitochondrial_electron_transport_chain%E2%80%94Etc4.svg.pnghttp://upload.wikimedia.org/wikipedia/commons/thumb/8/89/Mitochondrial_electron_transport_chain%E2%80%94Etc4.svg/600px-Mitochondrial_electron_transport_chain%E2%80%94Etc4.svg.pnghttps://www.youtube.com/watch?v=OXgOsy8yQukhttps://www.youtube.com/watch?v=OXgOsy8yQukhttps://www.youtube.com/watch?v=OXgOsy8yQukhttps://www.youtube.com/watch?v=OXgOsy8yQukhttp://upload.wikimedia.org/wikipedia/commons/thumb/8/89/Mitochondrial_electron_transport_chain%E2%80%94Etc4.svg/600px-Mitochondrial_electron_transport_chain%E2%80%94Etc4.svg.png


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3. 8. 6. State that ATP and hydrogen (derived from the photolysis of water) are used to fix

carbon dioxide to make organic molecules.

Photosynthesis can be divided into the light-dependent and light-independent reactions.

LIGHT-DEPENDENT REACTIONS:

products framed in pink

The light dependent reactions are also an electron transport chain.

LIGHT-INDEPENDENT REACTIONS (Calvin cycle):

from primary phase framed in pink

Photosystem II

(P680)

Photosystem I

(P700)

excitation

of 2e-

excitation

of 2e-

electron

acce tor

electron

acce tor

Plastoquinone cytochrome

complex

electron carriers

pumps H

+ ATP synthase

AT

FerredoxinNAD

Preductase

NADP NADPH+H+

PHOTOLYSIS OF WATER:

,()

cyclic

acyclic


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3. 8. 7. Explain that the rate of photosynthesis can be measured directly by the production

of oxygen or the uptake of carbon dioxide, or indirectly by an increase in biomass.

The simplified equation for photosynthesis is:

Since CO2is a reactant, its amount will decrease as the reaction proceeds.

Since O2and C6H12O6are products of the reaction, their amount will increase as the reaction proceeds.

3. 8. 8. Outline the effects of temperature, light intensity and carbon dioxide concentration

on the rate of photosynthesis.

(See enzymes)

Carbon dioxide is a substrate.

Light intensity:

6 CO2 (1C)

6 (6C) unstable

intermediate

12 glycerate-3-

phosphate (3C)

6 ribulose

bisphosphate

(RuBP) (5C)

12 triose

phosphate (3C)

10 triose

phosphate (3C)

6ADP

6ATP

4Pi

12ATP

12ADP

12NADPH+H+

12NADP+

2 triose

phosphate (3C)

sugar phosphates

(6C)Pi complex carbohydrates


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. (http://www2.geog.ucl.ac.uk/~plewis/geogg124/_images/chapin1.png)

ch3 chemistry of life

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