Molecules of life

“Introduction Biology PART : Molecules of life Kittisak Buddhachat, Ph.D

Outline in molecules of life1. Atoms and interaction2. The chemistry of water3. Biological macromolecules 3.1 Carbohydrate 3.2 Lipid 3.3 Proteins 3.4 Nucleic acid

1.1 Start With AtomsSubatomic particles Atomic massof helium (He) atom It is roughly equal to “Mass number” which is the sum of proton and neutron. 42He proton Atomic Number neutron This is number of proton which is unique toCloud of negative Simplified model that element charge For example 2113Na Mass Number Atomic Number How many neutron does it has?

1.1 Start With Atoms Electron distribution diagram for the first 18 elements in the periodic table Chemical behavior of atom depends on number of valence electron where is the outermost electrons of valence shell For example Fluorine (F)  7 valence electrons Sodium (Na) -> 1 valence electron He, Ne, Ar have full valence shell as 8, said to be inert atom

1.2 Chemical bonds Bonds among atoms 1. Covalent bonds: sharing of a pair of valence electrons Difference in attraction for valence electron of each atom, electronegativity (EN), resulting two types of covalent bond: nonpolar covalent bond polar covalent bond polar covalent bond

1.2 Chemical bonds Bonds among atoms 2. Ionic bonds: Two atoms are so unequal in their attraction for valence electrons depending EN of each atom. Compounds formed by ionic are called ionic compands or salts.

1.2 Chemical bonds Interaction between compounds 1. Hydrogen bonds: This bonds is importance to the chemistry of life. Hydrogen atom has a partial positive charge which attracts to a different EN atom nearby

1.2 Chemical bonds Interaction between compounds 2. van der Waals interaction: uneven distribution of electron in each molecules  different charges on surface of molecule . This interaction occur only when atoms and molecules are very close together. Protein interactions: Protein-protein or Protein-compounds Protein-DNA

1.2 Chemical bondsChemical bondsBonds between atoms Interactions between (strong) compounds (weak) 1. Covalent bonds: sharing of 1. Hydrogen bonds: two valence electron ex. H2, CO2 compounds that are different polar including H--N, H--O and H--F 2. Ionic bonds: donor and ex. Interaction between H2O and H2O acceptor for valence electron ex NaCl 2. van der Waals interactions: uneven distribution of electron in each molecules

2 Chemistry of waterHydrogen bonding of water What does the properties of water contribute to earth’s suitability for life? 1. Cohesion of water molecules: water transportation in plant 2. Moderation of temperature by water: regulation of temperature in atmosphere 3. Floating of ice on liquid water: organism can live under lake with ice 4. The solvent of life: versatile solvent by hydrogen bond with hydrophilic substances but not for hydrophobic.

2 Chemistry of waterAcidic and basic conditions affect living organism1 molecule in 554 million is dissociated.Hydronium ion is represented by Ocean Acidificationhydrogen ion, H+ By the burning of fossil fuelsA buffer consists ofan acid-base pairthat combinesreversibly withhydrogen ions,allowing it to resist pHchanges.Response to a rise in pHH+ donor H+ acceptor Response to a drop in pH

3 Biological MacromoleculesMolecular of lifeWithin living organisms, organiccompounds were synthesized and inthe laboratory.Organic compounds is made mostlycarbon (C), oxygen (O), hydrogen (H)and nitrogen (N) Miller Urey ExperimentHow to form diverse molecules of carbon atoms1. Carbon can bond to various other atoms, including O, H and N2. Carbon can bond to carbon atom, forming the carbon skeletons of organic compounds which vary in length and shape (branching, ring, double bond position) and have bonding sites for atoms of other elements

3 Biological Macromolecules How to form diverse molecules of carbon atoms

3 Biological Macromolecules Chemical groups most important in the process of life Seven group that importance for organic compounds -hydroxyl (-OH) -carbonyl (C=O) -carboxyl (COOH) -amino (-NH2) -sulfhydryl (-SH) -phosphate (-OPO32-) -methyl (-CH3) These group determine the properties of molecules

3 Biological Macromolecules Chemical groups most important in the process of life

3 Biological Macromolecules Chemical groups most important in the process of life

3 Biological MacromoleculesWhat cell do to organic compoundsMacromolecules are polymers, built from monomersPolymer is a long molecules Synthesis and Breakdownconsisting similar building blocks of polymerThese small building blockmolecule are called monomerFour class of life’sorganic compounds1. Carbohydrates2. Proteins polymer3. Nucleic acid4. lipids

3.1 Carbohydrates Where to find carbohydrates Crab shell: chitinCell wall of Cell wall:Plant: Cellulose chitin

3.1 Carbohydrates Carbohydrates include sugars and polymer of sugars which serve as fuel and building material CarbohydratesMonosaccharides Disaccharides Polysaccharidesmultiple of the unit CH2O Consist of two Polymers with a feware molecular formula monosaccharides hundred to thousand monosaccharidesGlucose (C6H12O6) is themost commonmonosaccharideMonosaccharides areclassified by1. Location of carbonyl (ketose or aldose)2. number of carbon skeletons

3.1 Carbohydrates Monosaccharides

3.1 Carbohydrates Monosaccharides In aqueous solutions, glucose molecules, as well as most other five- and six-carbon sugars, form ring

3.1 Carbohydrates Disaccharides Maltose  ingredient used in brewing beer Sucrose  the products from nonphotosynthetic Lactose  glucose+galactose, present in milk

3.1 Carbohydrates Polysaccharides Polymers with a few hundred to thousand monosaccharides Polysaccharides serves as building material for structure and source of fuel. Plant store starch in plastid Animal store glycogen in liver and muscle alpha 1-4 glycosidic linkage 1-6 glycosidic linkage beta 1-4 glycosidic linkage

3.1 Carbohydrates Structure polysaccharides Insoluble fiber

3.1 Carbohydrates Another important structure polysaccharide Chitin It embedded in protein, form the exoskeleton of arthropods (insect, shrimp, crab) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals.

3.2 Lipids Lipids are a diverse group of nonpolar biological molecules resulting in ability to dissolve in organic solvents such as chloroform or benzene but not to dissolve in water Lipids include the following: fats : two kinds of molecules: glycerol and fatty acid steroids: four carbon rings phospholipid: similar to fat but contain phosphate gr. waxes: complex and varying mixture of lipids

3.2 Lipids FatTypes of fatty acid triacylglycerol or triglyceride

3.2 Lipids Major function of fats Energy storage  fat plants are stored in seed and fat in animals and human stored in adipose tissuePalm oil adipose tissueAdipose tissue also cushions such vital organs such as thekidneysA layer of fat beneath the skin insulates the body.

3.2 Lipids Disease from excess of fat Obesity: resulting from excess of body fat with body mass index (BMI) over than 30 kg/m2 …. heart disease, type 2 diabetes, certain types of cancer, and osteoarthritis https://en.wikipedia.org/wiki/Obesity Atherosclerosis: an artery-wall thickens from accumulations which contain both living, active WBCs (producing inflammation) and remnants of dead cells, including cholesterol and triglycerides. https://www.jax.org/news‐and‐insights/jax‐ blog/2013/november/which‐jax‐mouse‐model‐is‐best‐ for‐atherosclerosis‐studies‐apoe‐or‐ldlr‐knoc

3.2 Lipids Cell membrane Phospholipids Double-layered structure is called “phospholipid bilayer”. Structure Polar head: negative charge Nonpolar tail Amphipathic: showing both hydrophilic and hydrophobic properties

3.2 Lipids Steroids Carbon skeleton consisting of four fused rings such as cholesterol in animal and beta-sitosterol as plant sterols.Cholesterol Beta-sitosterolCholesterol  component of animal cell membranes and precursorfor vertebrate sex hormones

3.2 Lipids Steroids

3.2 Lipids Waxes Ester of long chain fatty acid with long chain alcohol. Solid at room temperature

3.3 Protein Protein account for more than 50% of the dry mass of most cells. Overview of protein function I

3.3 Protein Overview of protein function II

3.3 Protein Why proteins have diverse. Proteins as polymer are built from building block molecules of 20 amino acids without branch polymer. So amino acid is monomer which link with peptide bond as polymer, called a polypeptide . Alpha carbon have four different partners as amino group, carboxyl group, hydrogen and variable group (R)

3.3 Protein Types of amino acidsDepending on side chain 1. Nonpolar 2. Polar 3. Acidic 4. Basic The physical and chemical properties of amino acid functional role of polypeptides

3.3 Protein How to synthesis polypeptide Condensation reaction to link two amino acids by dehydration Backbone of polypeptide consists of amide group (peptide bond ).

3.3 Protein Protein structure and Function Polypeptide is not synonymous with the term protein Because a protein may be created by one or more polypeptides After proteins are synthesized, the chain may fold spontaneously for three dimensional structure, assuming their functional structure. Several protein is globular proteins ex. hemoglobin while others are fibrous protein ex. collagen.

3.3 Protein Level of protein structure Hydrogen bond Interaction for forming tertiary structure

3.3 Protein A change in Primary structure

3.3 Protein The importance of protein structure Conditions influence protein structure - pH - Salt concentration - Temperature - others Destroying the weak chemical bond and interaction of protein

3.4 Nucleic acid Polypeptides is synthesized via the code of unit of inheritance known as gene. Gene consist of DNA which is nucleic acid. Nucleic acid are polymer made of monomer called nucleotides The role of Nucleic acids central dogma Deoxyribonucleic acid (DNA) translation Messenger ribonucleic acid (mRNA) transcription Polypeptide

3.4 Nucleic acid Components of nucleic acids Polynucleotide of DNA or RNA

3.4 Nucleic acid Single strand Structure of DNA and RNA Double strand and alpha-helixDirection as antiparallel

3.4 Nucleic acid Other functions of nucleotide Adenosine triphosphate or ATP ATP is the main energy carrier. Energy releases when 3rd phosphate broken off 3rd bond unstable……easily broken ADP left over

Book ReferencesCore books Starr et al., Biology: concepts For more information and applications: withoutCampbell et al., Biology: A physiology, ninth edition Gerald Karp. Cell Biology,global approach, tenth seventh editionedition,Download media athttps://pubhtml5.com/homepage/wfgm/jzmh/