Chemistry of life and Metabolism

CALENDAR OF ACTIVITIES

Marilen M. Parungao-Balolong





Lecture 2 MBB1The Fundamentals!

!1. Chemistry of Life!2. The cellular and the acellular world!3. Functional Anatomy of Cells: Prokaryotes and Eukaryotes!4. Metabolism!

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THE CHEMISTRY OF LIFE• CHEMISTRY!

• the science that deals with the interaction between atoms and molecules


LEVELS OF BIOLOGICAL ORGANIZATION


knowledgeclass.blogspot.com

http://knowledgeclass.blogspot.com/2013/08/levels-of-biological-organization.html

THE CHEMISTRY OF LIFE• THE ATOMS!

• the smallest unit of chemical elements that are involved in chemical reactions

• consist of nucleus (protons and neutrons) and electrons moving around the nucleus

• Atomic Number = number of protons

• Atomic Weight = number of protons and neutrons


chemistry.tutorvista.com

http://chemistry.tutorvista.com/nuclear-chemistry/protons-and-neutrons.html

THE CHEMISTRY OF LIFE• THE ELEMENTS OF LIFE


THE CHEMISTRY OF LIFE• THE ATOMS: Electronic Configurations!

• in an atom, electrons are arranged around the nucleus in electron shells

• each shell can hold a characteristic maximum number of electrons

• THUS: chemical properties of an atom is due largely to the number of electrons in its outermost shell


THE CHEMISTRY OF LIFE


≤ 2 e

≤ 8 e

THE CHEMISTRY OF LIFE• THE ATOMS: Electronic Configurations


chemistry.tutorvista.com

The combining capacity of an atom (VALENCE) is the number of EXTRA or MISSING electrons in the outermost shell.

Example: C = 4 (4); N = 5 (3); O = 6 (2); H = 1(1)

http://chemistry.tutorvista.com/nuclear-chemistry/protons-and-neutrons.html

THE CHEMISTRY OF LIFE• ATOMS TO MOLECULES: CHEMICAL BONDS!

• Compounds are molecules made up of two or more atoms

• NOTE: compounds are formed to fill the outermost shell (unfilled spaces)

• Chemical Bonds are attractive forces that bind atomic nuclei of two atoms together

• e.g. Ionic, Covalent, H-bonds


THE CHEMISTRY OF LIFE• IONIC BONDS!

• chemical attraction between ions of opposite charge

• electron donor and electron acceptor


THE CHEMISTRY OF LIFE• COVALENT BONDS!

• atoms share pair of electrons

• stronger than ionic bonds and more common in organisms

• determine POLARITY

• polar -unequal sharing

• non-polar - equal sharing

Marilen M. Parungao-Balolong hyperphysics.phy-astr.gsu.edu

http://hyperphysics.phy-astr.gsu.edu/hbase/chemical/bond.html

THE CHEMISTRY OF LIFE• HYDROGEN BONDS!

• exists when a hydrogen atom COVALENTLY bonded with oxygen or nitrogen atoms are ATTRACTED to another oxygen or nitrogen atom

• form WEAK links between molecules





The H-bonds of LIFE


THE CHEMISTRY OF LIFE• MOLECULAR WEIGHT and the MOLES!

• sum of atomic weights of all atoms in a molecule

• Application in the lab: MW = g/L or g/mole


Example: Tris base used to make Tris-HCL buffer !

If MW = 121.14 g/mole… you need 121.14 g per Liter of buffer to be prepared (1M)

THE CHEMISTRY OF LIFE• CHEMICAL REACTIONS!

• Synthesis - combines to form a larger molecule

• A + B AB!

• Decomposition - large molecule broken down into smaller components

• AB A + B

• Exchange - two molecules are decomposed and their subunits are used to synthesize two new molecules

• AB + CD AC + BD


THE CHEMISTRY OF LIFE• REVERSIBLE CHEMICAL REACTION

Marilen M. Parungao-Balolong www.umich.edu

http://www.umich.edu/~elements/byconcept/faq6.htm


• IMPORTANT BIOLOGICAL MOLECULES: INORGANIC COMPOUNDS!

• Inorganic compounds are small ionically-bonded molecules

• Water

• Acids, Bases and Salts



• WATER!

• most abundant substance in cells

• polar THUS an excellent solvent and a temperature buffer

Marilen M. Parungao-Balolong bio1151.nicerweb.com

http://www.google.com/url?sa=i&source=images&cd=&docid=OfnOJZKVzkiqAM&tbnid=EA-MkhwfFLmVOM:&ved=0CAcQjB0&url=http%3A%2F%2Fbio1151.nicerweb.com%2FLocked%2Fmedia%2Fch03%2Fsolvent.html&ei=F9b9U6veLpaIuATIgoJw&psig=AFQjCNHu5iGzeXL8wABCVRlYsgssMjwY8Q&ust=1409230743925869

THE CHEMISTRY OF LIFE• ACID, BASES & SALTS!

• ACID dissociates into H+ and anions

• HCl = H+ and Cl -

• BASE dissociates into OH - and cations

• NaOH = Na+ and OH -

• SALT dissociates into negative and positive ions

• NaCl = Na+ and Cl -




• pH is the concentration of H+ in a solution

academic.cuesta.edu

http://academic.cuesta.edu/gbaxley/chem1A/notes/ph_scale.htm

THE CHEMISTRY OF LIFE• IMPORTANT BIOLOGICAL MOLECULES: ORGANIC

COMPOUNDS!

• organic compounds always contain C and H

• mostly covalently bonded

Marilen M. Parungao-Balolong www.proprofs.com

http://www.proprofs.com/quiz-school/story.php?title=general-properties-organic-compounds

THE CHEMISTRY OF LIFE• IMPORTANT BIOLOGICAL MOLECULES: ORGANIC

COMPOUNDS



• CARBOHYDRATES (CHOs)!

• contains C, H, O

• examples: sugars and starches

Marilen M. Parungao-Balolong bodybuilding-wizard.com

http://bodybuilding-wizard.com/carbohydrates/

THE CHEMISTRY OF LIFE• Monosaccharide, Disaccharide and Polysaccharide

Marilen M. Parungao-Balolong bioserv.fiu.edu

http://bioserv.fiu.edu/~walterm/Fund_Sp2004/lec2_biomolecule_cell/biomolecules.htm

THE CHEMISTRY OF LIFE• LIPIDS!

• insoluble in water

• simple lipid (fat) = glycerol + 3 FA

• unsaturated FA - one or more double bonds

• saturated FA - no double bonds between carbon atoms (have higher melting points)


THE CHEMISTRY OF LIFE• saturated versus unsaturated FA


www.dradvice.co.uk

www.tackleacne.com

THE CHEMISTRY OF LIFE• PROTEINS!

• amino acids are the building blocks of proteins (C, H, O, N, sometimes S)

• peptide bonds link amino acids to form proteins

• primary (sequence), secondary (helices or pleats), tertiary (overall 3D structure) and quaternary (2 or more polypeptide chains) structures


Marilen M. Parungao-Balolong www.womens-protein.com

http://www.womens-protein.com/best-high-protein-foods.html

THE CHEMISTRY OF LIFE• NUCLEIC ACIDS!

• DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)

• NUCLEOTIDE = pentose + phosphate group + nitrogen-containing base

• NUCLEOSIDE = pentose + nitrogen-containing base


THE CHEMISTRY OF LIFE• DNA versus RNA


THE CHEMISTRY OF LIFE• NUCLEOTIDE versus NUCLEOSIDE

Marilen M. Parungao-Balolong www.siumed.edu

http://www.siumed.edu/~bbartholomew/course_material/nucleic_acids.html

THE CHEMISTRY OF LIFE• ATP!

• stores chemical energy for various cellular activities

• hydrolysis of ATP will release energy

• energy from oxidation reaction will form ATP from ADP and Pi


Marilen M. Parungao-Balolong www.abc.net.au

http://www.abc.net.au/science/articles/2011/05/25/3226741.htm

THE DOMAINS OF LIFE


faculty.southwest.tn.edu

http://faculty.southwest.tn.edu/rburkett/classification_of_organisms.htm

THE VIRUSES: ACELLULAR

Marilen M. Parungao-Balolong www.emporia.edu

http://www.emporia.edu/ksn/v53n1-april2006/

PROKARYOTES & EUKARYOTES


www.phschool.com

http://www.phschool.com/science/biology_place/biocoach/cells/common.html

PROKARYOTES & EUKARYOTES

Marilen M. Parungao-Balolong www.vce.bioninja.com.au

http://www.vce.bioninja.com.au/aos-1-molecules-of-life/cells/eukaryotes.html

ANIMAL CELLS


hubpages.com

http://hubpages.com/hub/Plant-Cells-vs-Animal-Cells-With-Diagrams

PLANT CELLS


hubpages.com

http://hubpages.com/hub/Plant-Cells-vs-Animal-Cells-With-Diagrams

BACTERIAL CELLS


micro.magnet.fsu.edu

indianapublicmedia.org

http://micro.magnet.fsu.edu/cells/bacteriacell.html

http://www.google.com/url?sa=i&source=images&cd=&docid=V7aPjFb_6L1neM&tbnid=QAHAfpmJLGA0lM:&ved=0CAcQjB04BQ&url=http%3A%2F%2Findianapublicmedia.org%2Feartheats%2Fground-beef-recalled-testing-dangerous-ecoli%2F&ei=Wv_9U7DmGpLh8AW3qYKQBQ&psig=AFQjCNERb-BrMW8L1P0O0V5YqDURw1YDuQ&ust=1409241306539234

YEAST CELLS

Marilen M. Parungao-Balolong cnx.org

sharon-taxonomy2009-p3.wikispaces.com

http://cnx.org/contents/[email protected]:49

http://sharon-taxonomy2009-p3.wikispaces.com/Fungi

METABOLISM


www.elmhurst.edu

CATABOLISM & ANABOLISM


library.med.utah.edu

RESPIRATION & FERMENTATION


classes.midlandstech.edu

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Chemistry of life and Metabolism