The Chemistry of Life

http://www.chem.ufl.edu/~itl/2045_s00/matter/FG01_011.GIF

Atom: the smallest unit of matter• Subatomic particles

– 1. neutron• a. In nucleus

• b. No charge

• c. Weight 1dalton

– 2. proton• a. In nucleus

• b. + charge

• c.Weight 1 dalton

– 3. electron• a. Outside nucleus

• b. Move at speed of light

• c. Have a negative charge

• d. Weight1/2000 of a dalton http://www.wjcc.k12.va.us/ROBB/Atom%20Animation%20Resources_files/image003.gif

Atomic Number and Weight• 1. atomic number- number of protons in

nucleus

• 2. atomic weight- number of protons plus neutrons in the nucleus of the atom (a.k.a. -mass number)

http://www.wisegorilla.com/images/chemstry/PeriodicTable.gif

How many neutrons are in an atom?

Subtract the number of protons from the mass number to get the number of neutrons

Mass number – atomic number = # of neutrons

Find the atomic number, atomic mass, and # of protons, electrons and neutrons of the following elements.

Atomic #

Mass # # protons

# electrons

# neutrons

Carbon

Hydrogen

Oxygen

Isotopes: it’s all in the neutrons!

• 1. have same number of protons (atomic number).

• 2. Different number of neutrons.

• 3. carbon – has carbon 12, carbon 13 and carbon 14.

• 4. Radioactive isotopes- the nucleus decays spontaneously, giving off particles and energy

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https://blogs.creighton.edu/blogging/wp-content/uploads/gkd58409_/2007/04/hank1.jpg

Isotopes of Carbon

Isotopes of Carbon

Electron Shells• 1. Energy Shells

– a. first level can only have 2 electrons.

– b. second level can have 8 electrons.

– c. all other levels have 8.

• 2. The chemical behavior of the atom is determined by the atom’s electron shell.

• 3. Valance Electrons- outermost shell

http://static.howstuffworks.com/gif/atom-h-he-li-na.gif

Problem? All atoms want to have their valance electron shells full!

http://www.csupomona.edu/~egoldstein/121/IMAGES/Periodic_noble.gif

I wish I could be a noble gas!

Chemical Bonds

• 1. Making of chemcial bonds Stores Energy.

• 2. The breaking of chemical bonds Releases Energy

http://faculty.clintoncc.suny.edu/faculty/michael.gregory/files/Bio%20101/Bio%20101%20Lectures/energy/energy12.gif

Blah blah balh

Sdf

Chemical Bonds

• 1. Covalent bond -The sharing of a pair of valance electrons by two atoms.

• 2. Bewteen two nonmetals

• 3. Can form single, double and triple bonds

http://www.school-for-champions.com/chemistry/images/bonding_types-water.gif

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Methane: covalent bonds

http://sixthsense.osfc.ac.uk/chemistry/bonding/GRAPHICS/gif15.CH4bp.gif

2. All non-metals form covalent bonds

• 1. glucose

• 2. water

• 3. carbon dioxide

• 4. sucrose

http://www.peoriaendocrine.com/images/diabetes_lecture/glucose.GIF

http://www.brooklyn.cuny.edu/bc/ahp/SDgraphics/PSgraphics/WaterMolecule.GIF

Ionic Bonds

• 1.One atom “steals” electrons from another to complete its outer shell.

• Between a metal and nonmetal

• Example: NaCl– Because one atom has lost

an electron (Na) it has now has an overall charge of +1

– Because the atom that took the electron (Cl) now has an extra electron, its overall charge is -1http://www.sci.sdsu.edu/classes/biology/bio100/truesdale/Lectures%2005/lec2/Image6.gif

4. Ionic Bonding:

http://gcserevision101.files.wordpress.com/2009/02/halogen-ionic-bond.jpg

In a polar covalent bondElectrons are shared unequally

between atoms, creating a polar molecule

(–) (–)

(+)

(+)

O

HH

(–)

(+)

Water is a Major Components of Cells

1. 2/3 of all molecules in the body (all your cells are surrounded by water)

2. Water stores heat efficiently.a. sweating- helps release heatb. helps maintain homeostasis by regulating temperature

http://www.bigbrandwaterfilter.com/water_filter_images/waterdrop_embossed.gif

Properties of Water

1. Water is the solvent of life (universal solvent)

- Polar solutes dissolve when water molecules surround them, forming aqueous solutions

2. Water is less dense as a solid than a liquid. Ice floats on water.

. Hydrogen bonds make water cohesive (holds like to like)

ex: Insects can walk on water due to surface tension

Water is adhesive (holds different substances)

ex: molecules can move from a plant’s roots to its leaves (Capillary Action)

Water Dissolves Many Substances

• Water is the solvent. What it is dissolving is called the solute.

• Solution- mixture in which one or more substances is evenly distributed. Solute and Solvent together make a Solution.

http://www.elmhurst.edu/~chm/demos/images/bluebottle.GIF

Polarity-molecules with an electrical charge

• Water is a polar molecule

• Only polar molecules will dissolve in water

• Nonpolar molecules will not dissolve in water – Ex: oil

http://colossus.chem.umass.edu/genchem/whelan/class_images/Structure_of_Water.jpg

Hydrogen Bondswater molecule

hydrogen bond

-

-

-

-

+

+

+

+

+

+

-

+

+

+

+

-

+

Water molecules adhere to other polar molecules.

HCl

Hydrogen Bond1. Occurs when an atom of hydrogen has a strong attraction to two atoms instead of one

2. The atoms must be highly electronegative (electron loving) like Oxygen, Flourine, Nitrogen, Chlorine and Bromine

Water has high specific heat. Specific Heat is the amount of energy required to change the temperature of a substance. It allows for moderation of climate and helps organisms regulate body temperature.

Water has a high heat of vaporization (the amount of heat required to convert liquid water into gaseous water, aka steam). This makes it an effective coolant for the body. That is why sweating actually cools usdown. (Evaporative Coolant)

Water has a high heat of fusion, or the heat you need to take out of water to get it to solidify (freeze). Water can hold a lot of heat energy before it changes temperatures and states. A high heat of fusion means that, even if the temperature of the air changes a lot, water will shelter you or fish from those changes and provide a stable environment.

Water has a high boiling point (100 degrees Celsius) and low freezing point (0 degrees Celsius)

Water has a neutral pH. Which makes is a good buffer.A buffer is a substance that helps to moderate any changes in pH that result from the addition of acids or bases.

pH Scale: Based on the concentration of H+ (1-14)pH of acid <7pH of base >7pH of neutral = 7If blood pH is either below 6.9 or above 7.8 a person cannot survive

pH Scale

Acids and Bases

• Water can be broken down into acids and bases

• Acids-

1) high concentration of hydrogen ions. H+

2) pH less than 7

EX: HCl

http://www.epa.gov/acidrain/site_students/images/phscale.gif

Acids and Bases

Bases –

1) Low concentration of hydrogen ions. OH-

2) pH is greater than 7

3) Also called alkaline

EX: NaOH

http://www.btinternet.com/~chemistry.diagrams/ph_scale.gif

pH (2)More H+

More OH-

Organic Compounds• Contain carbon -

usually bonded to oxygen, hydrogen, and other carbon atoms.

• Most of the matter in your body is organic!

• These are compounds that usually come from organisms

http://www.chemistryland.com/ElementarySchool/BuildingBlocks/Jungle500.jpg

MacromoleculesCells and their organelles are made up of smaller building blocks called macromolecules.There are 4 basic types of macromolecules. They are:

LipidsProteinsCarbohydratesNucleic Acids

Macromolecules are actually made up of even smaller subunits. Each subunit of a macromolecule is called a monomer.The macromolecules themselves are called polymers, because they are made up of many of these subunits.

Monomers & Polymers

Monomer: one basic unit or subunit

Polymer: a chain of many basic units

Carbohydrates• 1.Made of carbon,

hydrogen, and oxygen in a 1:2:1 ratio.

• 2. Key source of energy-Found in fruits and vegetables.

• 3. Monosaccharides-single sugars,– A. the building blocks

of carbs

– B. Ends in-ose • Examples: glucose,

fructose, maltosehttp://vienna-doctor.com/images/Pictures/carbohydrates.jpg

http://www.exploratorium.edu/cookng/candy/images/sugar-molecule-1.gif

Monomer (basic unit) : Simple sugars or monosaccharidesEX: glucose

Polymer (chain of units): Complex carbohydrates or polysaccharidesEX: starch, cellulose, chitin, glycogen

Disaccharides and Polysaccharides

• 4. Disaccharides- two sugars

glucose + fructose = sucrose

5. Polysaccharides

-a. macromolecule made of many sugars.

-b. storehouse for energy

Excess Energy is stored as:

-c. starch-in plants

d. glycogen- in animals

e. cellulose-found in plant cell walls

http://www.pecanbread.com/new/saccharides.jpg

Carbohydrates: Indicator Tests

Simple Sugars:Benedict’s solutionBlue solution turns orange/green/brown

Complex Carbs:Lugol’s solution/IodineTurns from orange-red-brown to black-purple

Let’s Draw a Glucose molecule!

http://www.thefreshloaf.com/files/u12441/alpha-D-glucose%20ring.gif

Dehydrations synthesis: making carbohydrates

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Taking water away to join molecules

• 1. Dehydrate means to take water away.

• 2. #1 and #4 carbon will form a bond by removing water.

• 3. What is left?

http://www.uq.edu.au/_School_Science_Lessons/16.3.1.4ach.GIF

Hydrolsis- adding water to break the bonds

Lipids- are nonpolar• Fats, phospholipids,

steroids(cholesterol) and waxes.

• Fats are lipids that store energy for long term, make up the cell membrane (phospholipds), provide cell structure, provide insulation

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http://www.chemistryland.com/ElementarySchool/BuildingBlocks/Lipids.jpg

Lipids are made by combining two types of molecules

• 1. glycerol– A three carbon

alcohol• 2. 3 fatty acids

– Long hydrocarbon chains.

– Non polar

http://faculty.clintoncc.suny.edu/faculty/michael.gregory/files/Bio%20101/Bio%20101%20Lectures/Biochemistry/glycerol,%20fatty%20acids,%20triglyceride.gif

Lipids: Structure• Lipids are made up of…

– Monomer (basic unit): fatty acids

– Polymer (chain of units): lipids• Specific examples: triglycerides, phospholipids

Lipids: FatsSaturated vs. Unsaturated

(a)Saturated fat

Structuralformula of asaturated fatmolecule

Stearic acid, asaturated fattyacid

(b)Unsaturated fat

Structural formulaof an unsaturatedfat molecule

Oleic acid, anunsaturatedfatty acid

cis doublebond causesbending

Lipids: Indicator Test• Paper Bag Test:

– Smear substance onto paper bag– If see-thru, it contains lipids

Proteins: Function

• Build and repair muscle and tissues– “No pain, no gain!”

• Enzymes- proteins that speed up chemical reactions

Proteins• Made of chains of

amino acids• There are 20 known

amino acids• These 20 amino acids

are found in all biological species.

• Collagen-protein found in skin

• Hemoglobin, blood clots, and muscles.

http://www.cybered.net/library/Teaching_Resources/Biology/Genetic_Engineering/Image_Gallery/GeneticEng-Proteins.jpg

http://images.apple.com/science/profiles/proteinfolding/images/proteins.jpg

Proteins: Structure• Proteins are made up of…

– Monomer (basic unit): amino acids

• 20 different kinds!*

– Polymer (chain of units): protein• More specifically- polypeptides

dipeptideAmino acids linked by peptide bonds

All Amino Acids have the same basic structure

• 1. alpha carbon- makes center of amino acid

• 2. amino group

• 3. Carboxyl group- this is an acid

• 4. a single hydrogen

• 5 . Variable group-R

– There are 20 R groups

– Therefore there are 20 different amino acids in all living things

http://www.contexo.info/DNA_Basics/images/aminoacidsweb.gif

Let’s draw an amino acid

• 1. draw the alpha carbon

• 2. put in amino group.• 3. put in carboxyl

group• 4. Hydrogen• 5. R group (variable)

http://www.aloeveraibs.com/wp-content/uploads/2008/08/aminoacidstruc.jpg

Proteins: Structure• Proteins have complex

structures. The shape of a protein determines its function!

• The levels of protein structure are:– Primary structure:

polypeptide chain– Secondary structure:

polypeptides in coils or sheets– Tertiary structure: coils or

sheets form a tangle– Quaternary structure: more

than one tangle combine to make a very complex protein!

Proteins: Indicator Test

• Biuret’s Solution:– Turns from blue to purple if protein is present

Nucleic Acids: Function

• Stores and carries genetic information

Nucleic Acids: Structure• Nucleic Acids are made up of…

– Monomers (basic unit): nucleotides

– Polymers (chain of units): DNA or RNA

Nucleic Acids• Made of nucleotides.• Nucleotides contain a

sugar, phosphate and a nitrogen base.

• DNA-double stranded and makes up chromosomes

• RNA-single stranded, used in making proteins.

http://www.duke.edu/web/MAT/jennifer_sohn/unit/images/what_is_rna1.gif

DNA and RNA

http://images2.clinicaltools.com/images/gene/dna_versus_rna_reversed.jpg

ATP-Adenosine Triphosphate

• Energy currency for the cells.

• Cells need a constant supply of ATP to function.

http://www.colorado.edu/epob/academics/web_resources/cartoons/atp.gif

Review Questions• 7. In what ratio is carbon, hydrogen and oxygen

found in carbohydrates?• 8. All sugars end in what?• 9. What is the difference between a

polysaccharides, disaccharide, and a monosaccharide?

• 10. Give and example of 2 polysaccharides.• 11. What are the two types of fats?• 12. What are proteins made up of ?• 13. Name two types of nucleic acids.

Organisms Need Energy for Life Processes

• Energy- the ability to move or change matter.

• A. Energy is stored and released by chemical reactions.

• B.Reactants and products• Chemical reaction absorb

and release energy– 1.Freezing water

releases energy– 2.Melting ice absorbs

energyhttp://www.windows.ucar.edu/teacher_resources/activities_3x3.jpeg

Energy is needed to start a chemical reaction.

• 1. Activation energy- the energy needed to start a chemical reaction.

• 2. Chemical push!

http://www.colorado.edu/intphys/Class/IPHY3430-200/image/04-3.jpg

Enzymes help biochemical reactions occur.

• A. allows reactions to occur quickly and at low temperatures.

• B. increases the speed of chemical reactions.

• C. most are proteins.

• D. act as catalysts-reduce the amount of activation energy required.

• E. helps maintain homeostasis.

http://w3.dwm.ks.edu.tw/bio/activelearner/06/images/ch06c1.jpg

Enzymes End in ase

Enzymes affect specific substances.

http://www.blc.arizona.edu/courses/181summer/graphics/graphics%20lect7/Life7e-Fig-06-10-0%203D%20fit%20of%20enzyme%20and%20substrate.jpg

http://library.thinkquest.org/3659/orgchem/lock-key-enzyme.gif

• 1.Substrate-substance on which an enzyme acts.– A. amylase- breaks starch down into glucose

• 2.Active Site– A deep folds in the surface of the enzyme.– B. substratesubstrate fits into the active site

Enzymes are Biological Catalysts

http://www.staff.uni-mainz.de/lieb/tierphys/enzyme.gif

Three things that effect enzyme action.

• 1. amount of enzyme concentration

• 2. Temperature

• 3. pH