2.1. molecules to metabolism
TRANSCRIPT
![Page 1: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/1.jpg)
2.1. Molecules to Metabolism
Miltiadis-Spyridon Kitsos Platon IB Diploma
http://www.edupic.net/Images/Mitosis/prometaphase.png
![Page 2: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/2.jpg)
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
![Page 3: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/3.jpg)
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?
![Page 4: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/4.jpg)
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
![Page 5: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/5.jpg)
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
![Page 6: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/6.jpg)
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
![Page 7: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/7.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
![Page 8: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/8.jpg)
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
![Page 9: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/9.jpg)
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
![Page 10: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/10.jpg)
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
![Page 11: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/11.jpg)
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
![Page 12: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/12.jpg)
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
![Page 13: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/13.jpg)
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
![Page 14: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/14.jpg)
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
![Page 15: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/15.jpg)
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
![Page 16: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/16.jpg)
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
![Page 17: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/17.jpg)
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)
![Page 18: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/18.jpg)
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.
![Page 19: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/19.jpg)
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.
https://s-media-cache-ak0.pinimg.com/736x/fb/c9/f6/fbc9f62d6bdad037c9b4de249845d6f6.jpg
http://www.essentialchemicalindustry.org/images/stories/520_Urea/Urea_04.JPG
![Page 20: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/20.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
![Page 21: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/21.jpg)
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
![Page 22: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/22.jpg)
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
![Page 23: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/23.jpg)
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
![Page 24: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/24.jpg)
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.
![Page 25: 2.1. Molecules to Metabolism](https://reader035.vdocuments.us/reader035/viewer/2022062306/5878c4461a28ab26728b5ab1/html5/thumbnails/25.jpg)
http://www.stepsinbiology.com