2.1. Molecules to Metabolism

Miltiadis-Spyridon Kitsos Platon IB Diploma

http://www.edupic.net/Images/Mitosis/prometaphase.png

The official IB Diploma Biology guideEssential idea: Living organisms control their composition by a complex web of chemical reactions.

https://ibpublishing.ibo.org/server2/rest/app/tsm.xql?doc=d_4_biolo_gui_1402_1_e&part=8&chapter=1

Introduction to Molecular BiologyMolecular biology explains living processes in terms of the chemical substances involved.

http://dataphys.org/list/wp-content/uploads/2014/12/Watson-Crick-DNA-model.jpg

In 1953 Watson and Crick suggested a model on the structure of DNA and this completely revolutionized our understanding of biological processes which can be looked through the “molecular” glass

Later one Watson proposed the Central Dogma of Molecular Biology which safely connected the production of proteins, a diverse group of molecules with DNA, the genetic material of most organisms.

https://upload.wikimedia.org/wikipedia/commons/thumb/6/68/Central_Dogma_of_Molecular_Biochemistry_with_Enzymes.jpg/256px-Central_Dogma_of_Molecular_Biochemistry_with_Enzymes.jpg

Other molecules are also important for living organism. Can you name some of them?

Molecular biologists have a reductionist approachMolecular biology explains living processes in terms of the chemical substances involved.

System’s biology approachLooking at the interactions and dynamics between the components.

BenefitsLooks at the emerging properties arising from the interactions among the components.

Reductionist approachLooking at the components

BenefitsEffective process, may yield useful information by breaking down complex processes into simpler parts.

Biological system/Organism

In 1966 Francis Crick said that “The ultimate aim of the modern movement in biology is to explain all biology in terms of physics and chemistry”. This statement is the epitome of the reductionist approach in biology. Can you think of examples where this approach may not be appropriate?

Read more https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1299179/Reductionism and complexity in molecular biology

Carbon compoundsCarbon atoms can form four covalent bonds allowing a diversity of stable compounds to exist.

C6 2

4

Carbon12.0107

Carbon is the 15th most abundant element on earth but can be used to create a diverse group of compounds which contribute to a diverse palette of structures and functions.

Chemical properties of carbon• May create four covalent bonds (strongest bonds) with other

atoms. Remember that covalent bonds result from the sharing of pairs of electrons by two adjacent atoms. Look at the CH4 molecule

https://upload.wikimedia.org/wikipedia/commons/thumb/2/29/Electron_shell_006_Carbon.svg/558px-Electron_shell_006_Carbon.svg.png

Carbon electron configuration

Carbon in the period table

https://upload.wikimedia.org/wikipedia/commons/thumb/1/17/Covalent.svg/334px-Covalent.svg.png

covalent bond Biological significance• The large number of covalent

bonds leads to the development of complex structures either with other carbon atoms (carbon chains)

https://upload.wikimedia.org/wikipedia/commons/thumb/3/31/Linoleic_acid_shorthand_formula.PNG/800px-Linoleic_acid_shorthand_formula.PNG

• or with other chemical elements

https://upload.wikimedia.org/wikipedia/commons/thumb/8/88/D-Phenylalanine.svg/228px-D-Phenylalanine.svg.png

Bonds between carbon atoms and other chemical elements may be single or double or even triple https://qph.ec.quoracdn.net/main-qimg-d3f0d78f8981ac6da4fea

003c673aa07?convert_to_webp=true

Groups of carbon compoundsLife is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.

Carbohydrates• Composed of C, H and O • General chemical formula (CH2O)x• Used as fast-access energy storage

molecules• Glucose, fructose and galactose are

monosaccharides, that is, monomers used to build more complex carbohydrates like starch or glycogen (polysaccharides)

Macromolecules

• Molecules of large molecular weight composed of simpler organic compounds, known as monomers, chemically bonded among each other.

http://stopdiabetesmellitus.com/wp-content/uploads/2015/01/Glucose.png

Glucose and other monosaccharides are usually found in ring structure

Fructosehttp://www.wpclipart.com/science/atoms_molecules/molecules/fructose.png

http://chemistry.gravitywaves.com/CHE452/images/Glycogen.gifGlycogenhttp://img.medscapestatic.com/pi/meds/ckb/75/43975tn.jpg

Groups of carbon compoundsLife is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.Lipids

• Composed of C, H and O • Include steroids, waxes fatty acids and

triglycerides• Distinguished in fats (solids) and oils

(liquid)• Diverse group of molecules

https://upload.wikimedia.org/wikipedia/commons/b/be/Fat_triglyceride_shorthand_formula.PNG

Triglycerides

https://courses.washington.edu/conj/membrane/fattyacid.png

fatty acidsSaturated

Unsaturated

Polyunsaturated Saturated fatty acids contain no double bonds in the carbon chain

Monounsaturated fatty acids contain one double bond in the carbon chain

Polyunsaturated fatty acids contain many double bonds in the carbon chain

Phospholipidshttp://figures.boundless-cdn.com/18565/full/figure-05-01-03a.jpeg

Steroidshttp://www.chem.latech.edu/~deddy/chem121/Image195.gif

Groups of carbon compoundsLife is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.Proteins• Composed of C, H, O, N (some may include

sulphur)• Proteins is a diverse group of macromolecules

with numerous functions within the cell.• Proteins are macromolecules composed of

simpler monomers called amino acids.

Remember the numerous roles of the membrane proteinshttp://www.nature.com/scitable/content/ne0000/ne0000/ne0000/ne0000/14706234/U3CP1-4_MemProteinFunction_ksm.jpg

They also act as biocatalysts, catalysing numerous biochemical reactions.

http://4.bp.blogspot.com/-T0SV3qOTFLI/UjToYXUpapI/AAAAAAAAACg/4EEjhi_pP-g/s1600/catalase.gif

http://www.medicalnewstoday.com/content/images/articles/262/262881/collagen.jpg

Proteins may also have a structural role

Collagen

Antibodies are proteins participating in specific immunity

https://www.amgenscience.com/static/files/amgenscience/img/episodes/the-shape-of-drugs-to-come/monoclonal-antibodies/1.png

Groups of carbon compoundsLife is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.

Nucleic acids• Composed of C, H, O, N • Nucleic acids are macromolecules

composed of monomers called nucleotides.

• Each nucleotide has three components: a pentose sugar, a phosphate group and a nitrogenous base.

• There are two main types of nucleic acids DNA and RNA which differ on the type of sugar and composition of nitrogenous bases.

http://ib.bioninja.com.au/_Media/nucleotide_med.jpeg

A nucleotide

Nucleotides joined together via covalent bonds form polynucleotide chains. Two polynucleotide chains form the molecule of DNA which is a double helix.

http://www.mhhe.com/biosci/ap/ap_prep/cem1s9_3.jpg

On the other hand, the RNA molecule is single-stranded

http://www.wiley.com/legacy/college/boyer/0470003790/structure/tRNA/trna_diagram.gif

RiboseSkill: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalised amino acid.

C

CC

C

C

O

Ribose is a pentose (has 5 carbons) forming a ring of four carbons with a side chain (5th)

• Draw the ring of the molecule.• Add the side chain.• Number the atoms starting with number

one on the right. • Add the –OH (hydroxyl) and H groups. Take

care of the order.

C

CC

C

CO OH

HH

OH

H

OH

H

H2OH

http://www.biotopics.co.uk/jsmol/ribose.html

GlucoseSkill: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalised amino acid.

Glucose is a hexose (has 6 carbons) forming a ring of five carbons with a side chain (6th)

• Draw the ring of the molecule• Add the side chain • Number the atoms starting with number

one on the right. • Add the –OH (hydroxyl) and H groups. Take

care of the order

C

CC

C

C O

C

1

23

4

5

6

H

OHH

OH

OH

H

H

H2OH

C

CC

C

C O

C

1

23

4

5

6

OH

http://www.biotopics.co.uk/jsmol/alphabetaglucose.htmlhttp://www.biotopics.co.uk/jsmol/alphabetaglucose.html alpha-D-glucose

Fatty acidsSkill: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalised amino acid.

Any fatty acid has a long unbranched carbon chain with single bonds.

• Draw the carbon chain• Add the carboxyl group (R-COOH).

Remember this is an extra carbon atom • Add the H atoms

Butyric acid

C C C C

O

OH

Carboxyl group

C C C C

O

OH

Methyl group

H H H

H H H

H

http://www.raw-milk-facts.com/images/FatTrio.gif

http://www.biotopics.co.uk/jsmol/fattyacids.html#

Stearic acid

Amino acidsSkill: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalised amino acid.

amino group carboxyl group The R is the functional group of each amino acid and may correspond to different chemical groups http://web.chem.ucla.edu/~harding

/IGOC/A/amino_acid01.png

carboxyl group amino group

http://study.com/cimages/multimages/16/valine.png

Valinehttps://upload.wikimedia.org/wikipedia/commons/6/62/Alanine.png

Alanine

Amino acidsSkill: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalised amino acid.

There are twenty one different amino acids participating in the structure of proteins with each one having a different functional group. Amino acids are grouped according to the properties of the functional groups.

http://upload.wikimedia.org/wikipedia/commons/thumb/a/a9/Amino_Acids.svg/2000px-Amino_Acids.svg.png

Amino acidsSkill: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalised amino acid.

There are twenty one different amino acids participating in the structure of proteins with each one having a different functional group. Amino acids are grouped according to the properties of the functional groups.

http://upload.wikimedia.org/wikipedia/commons/thumb/a/a9/Amino_Acids.svg/2000px-Amino_Acids.svg.png

You don’t need to know them you should be

able to recognize the structure of th

e amino

acids and comment on its properties

Identifying moleculesIdentification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

Identify the following molecules

Molecule 1 Molecule 2Molecules 3

Molecule 4 Molecule 5 Molecule 6

Identifying moleculesIdentification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

Identify the following molecules

Molecule 1

Molecule 2Molecules 3

Molecule 4Molecule 5 Molecule 6

Amino acid Amino group Carboxyl group

Polyunsaturated fatty acid Long carbon chain with double bonds Carboxyl group

Monosaccharide C, H and O Five carbons in a

ring and a side chain

Monosaccharide C, H and O Five carbons in a

ring and a side chain

Monounsaturated fatty acid Long carbon chain with one double bond Carboxyl group

Glycerol (triglycerides)

The discovery of urea and the falsification of vitalismFalsification of theories—the artificial synthesis of urea helped to falsify vitalismIn 1828 the German chemist Friedrich Wöhler synthesized urea artificially  using silver isocyanate and ammonium chloride

https://upload.wikimedia.org/wikipedia/commons/thumb/3/32/Friedrich_Wöhler_Litho.jpg/800px-Friedrich_Wöhler_Litho.jpg

http://www.evolution-textbook.org/content/free/figures/04_EVOW_Art/05_EVOW_CH04.jpg

Till then, urea was known as a product of the kidneys and a component of urine. Moreover, it was believed that living organisms had a vital principle which among others, was giving them the ability to produce organic compounds. This perception was known as vitalism

Wöhler’s accidental discovery refuted the theory of vitalism and proved that the synthesis or urea and other organic compounds in living organisms is governed by the same basic principles of chemistry and physics as in non-living matter.

Read morehttps://www.sciencebasedmedicine.org/the-death-and-rebirth-of-vitalism/

Please remember that there are still processes in living organisms that have not been replicated in vitro. One of them is the synthesis of the polypeptide chains in the ribosomes.

The natural and artificial synthesis of ureaApplication: Urea as an example of a compound that is produced by living organisms but can also be artificially synthesized.

Production in humans

• A series of enzymatically catalysed reactions.

• Produced in the liver when there is an excess of proteins / amino acids.

• Component of urine.• Transported to the kidneys to be

filtered out and exit the body by urine.

Artificial production

• Chemical reactions are not catalyzed by enzymes.

• Over 100 million tones produced annually.

• Used as a fertilizer.• End product identical to naturally

produced.

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http://www.essentialchemicalindustry.org/images/stories/520_Urea/Urea_04.JPG

MetabolismMetabolism is the web of all the enzyme-catalysed reactions in a cell or organismBiochemical reactions happening within cells are catalyzed by globular proteins called enzymes (revisited later in 2.5).

Most biochemical reactions are linked together in pathways where the products of one reaction are the reactants of the next one. In this manner a molecule is gradually converted to another in a series of small steps.

A + B ------> C + D ------> EEnzyme 1 Enzyme 2

There is an immense number of biochemical reactions which are interconnected and form a dense network (may look like a metro map) which is commonly known under the term metabolism

Anabolism vs CatabolismAnabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation reactions.Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.

Anabolism

Purpose: The synthesis of macromolecules from smaller ones.

Main type of reactions: Condensation reactions

Energetics: Energy consumption

Examples: Photosynthesis, protein and DNA synthesis

Catabolism

Purpose: Break down of macromolecules into simpler ones.

Main type of reactions: Hydrolysis reactions

Energetics: Energy yield

Examples: Cellular respiration, digestion of molecules in the intestine

Coupling of energy an matter

Condensation vs HydrolysisAnabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation reactions.Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.

The purpose of condensation reactions is to join monomers and bind them via covalent bonds. A by-product of the process is water.

http://www.cengage.com/biology/discipline_content/animations/reaction_types.html

Covalent bond

This is a condensation reaction between two amino acids

https://upload.wikimedia.org/wikipedia/commons/thumb/6/6b/AminoacidCondensation.svg/576px-AminoacidCondensation.svg.png

And this is a condensation reaction between two monosaccharides

http://www.old-ib.bioninja.com.au/_Media/glycosidic-linkage_med.jpeg

Condensation vs HydrolysisAnabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation reactions.Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.

The purpose of the hydrolysis reactions is to break down polymers into simpler monomers

This is the hydrolysis reaction of a dipeptide into two amino acids

And this is a hydrolysis reaction of a disaccharide into two monosaccharides

H2O

enzyme

https://figures.boundless-cdn.com/30381/large/hydrolysis%20reaction%20amino%20acids.png

http://figures.boundless-cdn.com/18550/full/figure-03-01-02.jpeg

http://www.cengage.com/biology/discipline_content/animations/reaction_types.html

Condensation vs HydrolysisAnabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation reactions. Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.

http://www.stepsinbiology.com