Chapter 2: The Chemistry of Life itl/2045_s00/matter/FG01_011.GIF.

Chapter 2: The Chemistry of Life

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

Chapter 2 Vocab

1. Reactant

2. Product

3. Activation energy

4. Substrate

5. Enzyme

6. Carbohydrate

7. Nucleic acid

8. Nucleotide

9. Protein

10. Amino acid

11. Lipid

12. pH scale

13. Acid

14. Base

15. Ionic bond

16. Covalent bond

2-1 Objectives

• 1. Use a periodic table to give atomic number and mass.

• 2. Name simple ionic and covalently bonded compounds.

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

If you are not able, use the table!

http://www.corrosionsource.com/handbook/periodic/periodic_table.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 (which = p+n) 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 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!

Why does everyone want to be a noble gas?

Hindenburg Video 2

Hindenburg Video

http://www.youtube.com/watch?v=F54rqDh2mWA

http://dsc.discovery.com/videos/mythbusters-burn-blimp-burn.html

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.

Caring is sharing!

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

http://www.roboimages.com/image/ri33813/Care_Bears_Easter.jpg

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

Common Prefixes

• 1 — mono

• 2 — di

• 3 — tri

• 4 — tetra • 5 — penta

• 6 — hexa

• 7 — hepta

• 8 — octa

• 9 — nona • 10 — deca

Naming Covalent Compounds

Prefix + First element

+

Prefix + Second Element + -ide

Example:

CO2 becomes -

Carbon dioxide

Unless! the element is bonded to itself (Ex: Cl2 = chlorine)

What is Dihydrogen Monoxide?

• Name the following covalent compounds:a) SiF4

b) N2S3

c) HBr

d) Br2

a) silicon tetrafluoride

b) dinitrogen trisulfide

c) hydrogen bromide (or hydrobromic acid)

d) bromine

Ionic Bonds

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

• 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 -1

http://www.sci.sdsu.edu/classes/biology/bio100/truesdale/Lectures%2005/lec2/Image6.gif

4. Ionic Bonding: all metals

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

Name the following Ionic Compounds

• NaOH

• KCl

• H2S

• Sodium hydroxide

• Potassium chloride

• Hydrogen sulfide

Naming Ionic Compounds• Step 1: What chemical

symbols do you need?

• Step 2: How many atoms of each element are needed to make the bond?a. Find the charges for each ion

using the periodic table

b. “Cross the charges”

Example:

Magnesium iodide• Step 1: Mg and I

• Step 2:

a. Mg = +2

I = -1

b. Mg(1)I(2) => MgI2

2-2 Objectives

• 1. Analyze the properties of water.

• 2. Distinguish between acids and bases.

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

Water bonds to itself and other surfaces

• Adhesion- between different substances

*includes capillary action

http://images.google.com/imgres?imgurl=http://resources.ed.gov.hk/~s1sci/R_S1Science/sp/en/syllabus/unit5/images/roots%26soil1.jpg&imgrefurl=http://resources.ed.gov.hk/~s1sci/R_S1Science/sp/en/syllabus/unit5/article-ce.htm&h=150&w=150&sz=6&tbnid=_euQe4K3sE8J:&tbnh=90&tbnw=90&hl=en&start=9&prev=/images%3Fq%3Dcapillary%2Baction%26svnum%3D10%26hl%3Den%26lr%3D%26sa%3DN

Cohesion-between similar substances

Water Dissolves Many Substances

• Solution- mixture in which one or more substances is evenly distributed.

• Many important substances are dissolved in blood.

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 – oil

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

http://www.youtube.com/watch?v=VhWQ-r1LYXY&feature=player_embedded

Polarity Video!

Hydrogen Bondswater molecule

hydrogen bond

-

-

-

-

+

+

+

+

+

+

-

+

+

+

+

-

+

Water molecules adhere to other polar molecules.

HCl

Acids and Bases

• Water can be broken down into acids and bases

• Acids-

1) high concentration of hydrogen ions.

2) pH less than 7

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

Acids and Bases

Bases –

1) Low concentration of hydrogen ions

2) pH is greater than 7

7 is neutral-pure water

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

pH (2)More H+

More OH-

Review Question• 1. What type of molecules will dissolve in

water?

• 2. What is a pH scale?

• 3. What is an acid and a base?

• 4. What is neutral on the pH scale.

• 5.Will oil dissolve in water?

• 6. Which has more hydrogen ions, an acid or a base?

2-3 Objectives

• 1. Summarize the characteristics of organic compounds.

• 2. Distinguish between carbohydrates, lipids and proteins.

• 3. Describe the structure and function of nucleic acids and ATP.

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

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

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

Let’s Draw a Glucose molecule!• 1. Draw the carbon ring

– It has 6 sides

• 2. Number the carbons 1-6

• 3. Label # 6 carbon

• 4. carbons 1, 2, 4 are the same, have OH on the bottom.

• 5. # 4 carbon is a HO!

• 6. # 3 carbon is odd, OH on top

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

Dehydrations synthesis: making carbohydrates

http://kentsimmons.uwinnipeg.ca/cm1504/Image71.gif

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

Lipids- are nonpolar• Fats, phospholipids,

steroids(cholesterol) and waxes.

• Found in plant pigments such as chlorophyll.

• Fats are lipids that store energy– Saturated fat- animal

fat, solid at room temp.

– Unsaturated fat-plant oils, liquid at room temp.

http://www.bodybuilding.com/fun/crisco1k.jpg

http://www.healingtouchwebhelp.net/image/heart31.jpghttp://cwx.prenhall.com/bookbind/pubbooks/hillchem3/medialib/media_portfolio/text_images/CH09/FG09_16-05Box.JPG

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

Dehydration Synthesis: lipids

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

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

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

Amino Acids form bonds

• 1. forms peptide bond.

• 2. Oxygen is taken from the carboxyl group

• 3. Hydrogen is taken from the Amino group

• 4. Called Dehydration Synthesis

Peptide Bonds: dehydration synthesis

http://bill.srnr.arizona.edu/classes/182/PeptideBond-HiRes.JPEG

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.

Objective 2-4

• 1. Describe the role of enzymes in chemical reactions.

• 2. Explain how enzymes work.

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

https://www.google.com/search?q=lactose+and+lactase+reaction&source=lnms&tbm=isch&sa=X&ei=Mkc3UufDMtPH4AP6goEY&ved=0CAcQ_AUoAQ&biw=1440&bih=805&dpr=1#facrc=_&imgdii=_&imgrc=_W7J_yOT05rFmM%3A%3BO8f3SM6l45zgtM%3Bhttp%253A%252F%252Fwww.chemicalconnection.org.uk%252Fchemistry%252Ftopics%252Fimages%252Fpp8.jpg%3Bhttp%253A%252F%252Fwww.chemicalconnection.org.uk%252Fchemistry%252Ftopics%252Fview.php%253Ftopic%253D5%2526headingno%253D8%3B400%3B240

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

https://www.google.com/search?q=lactose+and+lactase+reaction&source=lnms&tbm=isch&sa=X&ei=Mkc3UufDMtPH4AP6goEY&ved=0CAcQ_AUoAQ&biw=1440&bih=805&dpr=1#facrc=_&imgdii=_&imgrc=19PXmfPEXBeumM%3A%3BnTw62t7ir-_X6M%3Bhttp%253A%252F%252Fweb.mit.edu%252Fkevles%252Fwww%252Flactose.gif%3Bhttp%253A%252F%252Fweb.mit.edu%252Fkevles%252Fwww%252Fnomilk.html%3B677%3B233

Review Questions

• 14. What is activation energy?• 15. What is a catalyst?• 16. Why are enzymes important?• 17. Where does the substrate bind to on the

enzyme?• 18. What do all enzymes end in?• 19. What three thing can effect how an

enzyme works?