Name the subatomic particles, charges, location, and mass.

Bellwork 8

The Chemistry of Life

biology

Why are we studying chemistry?Chemistry is the foundation of Biology

Levels of Biological Organization

AtomsThe simplest particle of an element that retains all the properties of that element

Proton Neutron Electron

Hydrogen1 proton1 electron

Oxygen8 protons8 neutrons8 electrons

+ 0 –

Everything is made of matter Matter is made of atoms

Elements

• Substances that cannot be broken down into other substances with different properties by ordinary chemical means

The World of Elements

Bellwork 9

• Draw a model of an electrically neutral atom that has an atomic number of 3 and a mass number of 6.

• About 25 elements are essential for life– Four elements make up 96% of living matter:

• carbon (C) • hydrogen (H)

• oxygen (O) • nitrogen (N)

– Four elements make up most of remaining 4%: • phosphorus (P) • calcium (Ca)

• sulfur (S) • potassium (K)

Atomic number

• The number of protons found in the nucleus of an atom

Mass number

• The total number of protons and neutrons in the nucleus of an atom

Ions• An atom that has lost or gained one or more

electrons

• A cation is a positively charged ion• An anion is a negatively charged ion• An ionic bond is an attraction between an anion

and a cation

Animation: Ionic Bonds

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Importance of ions in biology

• Transmit signals across the cell membrane or along the surface of the cell.

• 1/3 of enzymes dependent on ions for activity

• Isotopes--variants of a particular element that differ in the number of neutrons

Importance of isotopes

• Dating• Radiation treatment for cancer• Imaging (PET)

Molecules and Compounds

• Molecule – when two or more atoms bond. CO2

, O2 , H2 and H2O are all molecules.• Compound – when different elements combine.

Bellwork 10

• How does an ion differ from an isotope?• Why are ions and isotopes important in

biology?

Bonding properties• Importance of electrons

– electrons determine chemical behavior of atom

– depends on numberof electrons in atom’s outermost shell

• valence shell

How does this atom behave?How does this atom behave?

Bonding properties

How does this atom behave?How does this atom behave? How does this atom behave?How does this atom behave?

Elements & their valence shells

Elements in the same row have the same number of shellsElements in the same row have the same number of shells

Moving from left to right, each element has a sequential addition of electrons (& protons)Moving from left to right, each element has a sequential addition of electrons (& protons)

Elements & their valence shells

Elements in the same column have the same valence & similar chemical properties

Elements in the same column have the same valence & similar chemical properties

Electron configurationThe distribution of electrons of an atom in atomic orbitals

orbitals

–

–

–

Chemical reactivity• Atoms tend to

– complete a partially filled valence shell or– empty a partially filled valence shell

This tendency drives chemical reactions…This tendency drives chemical reactions…

and creates bondsand creates bonds

–

–

H2 (hydrogen gas)

Covalent bond

Bonds in Biology• Weak bonds

– hydrogen bonds• attraction between + and –

– hydrophobic & hydrophilic interactions

• interaction with H2O

– van derWaals forces– Ionic

• Strong bonds– covalent bonds

Hydrogen bond

H2O

H2O

Chemical reactions make and break chemical bonds

• Chemical reactions are the making and breaking of chemical bonds

• The starting molecules of a chemical reaction are called reactants

• The final molecules of a chemical reaction are called products

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 2-UN2

Reactants Reaction Products

2 H2 O2 2 H2O

• Photosynthesis is an important chemical reaction

• Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen

6 CO2 + 6 H20 → C6H12O6 + 6 O2

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Covalent bonds• Why are covalent bonds strong bonds?

– two atoms share a pair of electrons– both atoms holding onto the electrons– very stable

–

–

H2 (hydrogen gas)H2 (hydrogen gas)

H — H

H2O (water)H2O (water)

H

H

OxygenH

HO

Multiple covalent bonds• 2 atoms can share >1 pair of electrons

– double bonds • 2 pairs of electrons

– triple bonds• 3 pairs of electrons

• Very strong bonds

H

H–C–H

H

––

Nonpolar covalent bond• Pair of electrons shared equally by 2 atoms

– example: hydrocarbons = CxHx

• methane (CH4 )

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

balanced, stable,good building block

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

H

H

Oxygen

Polar covalent bonds• Pair of electrons shared

unequally by 2 atoms– example: water = H2O

• oxygen has stronger “attraction” for the electrons than hydrogen

• oxygen has higher electronegativity

• water is a polar molecule– + vs – poles– leads to many interesting

properties of water…

+

+

––

––

Ionic Bonds

• Because oppositely charged ions attract, sodium and chlorine atoms that have formed ions may react to form an ionic bond

• Sodium ions (Na+) and chloride ions (Cl-) form the compound sodium chloride or table salt

• Compounds formed by ionic bonds are called ionic compounds, or salts

• Salts, such as sodium chloride (table salt), are often found in nature as crystals

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Hydrogen bonding• Polar water creates molecular attractions

– attraction between positive H in one H2O molecule to negative O in another H2O

– also can occur wherever an -OH exists in a larger molecule

• Weak bond

HO

H

Properties of Water

biology

WaterWhy are we studying water?Why are we studying water?

All life occurs in water inside & outside the cell

All life occurs in water inside & outside the cell

Chemistry of water• H2O molecules form H-bonds

with each other– +H attracted to –O– creates a

sticky molecule

Elixir of Life• Special properties of water

1.cohesion & adhesion• surface tension, capillary action

2.good solvent• many molecules dissolve in H2O• hydrophilic vs. hydrophobic

3.lower density as a solid• ice floats!

4.high specific heat• water stores heat

5.high heat of vaporization• heats & cools slowly

1. Cohesion & Adhesion• Cohesion

– H bonding between H2O molecules– water is “sticky”

• surface tension• drinking straw

• Adhesion– H bonding between H2O & other substances

• capillary action• meniscus• water climbs up

paper towel or cloth

How does H2O get to top of trees?Transpiration is built on cohesion & adhesion

2. Water is the solvent of life• Polarity makes H2O a good solvent

– polar H2O molecules surround + & – ions– solvents dissolve solutes creating solutions

What dissolves in water?• Hydrophilic

– substances have attraction to H2O– polar or non-polar?

What doesn’t dissolve in water?• Hydrophobic

– substances that don’t have an attraction to H2O

– polar or non-polar?

fat (triglycerol)

3. The special case of ice• Most (all?) substances are more dense when

they are solid, butnot water…

• Ice floats!– H bonds form a crystal

Ice floats

Why is “ice floats” important?• Oceans & lakes don’t freeze solid

– surface ice insulates water below• allowing life to survive the winter

– if ice sank…• ponds, lakes & even oceans would freeze solid• in summer, only upper few inches would thaw

– seasonal turnover of lakes• sinking cold H2O cycles nutrients in autumn

4. Specific heat• H2O resists changes in temperature

– high specific heat – takes a lot to heat it up– takes a lot to cool it down

• H2O moderates temperatures on Earth

Specific heat& climate

5. Heat of vaporizationEvaporative cooling

Organisms rely on heat of vaporization to remove body heat

Organic v. Inorganic Compounds• Organic Compounds – contain

both Carbon and Hydrogen• Ex. Glucose (C6H12O6)

• Other characteristics – Can be complex molecules found in

chains (linear), rings (cyclic), or chains with branches

– Contains Functional groups like alcohols (OH), amino group (contains N), carboxyl group (C, O and H)

– Has covalent bonds between the atoms

• Inorganic Compounds – any molecule that does not contain both Carbon and Hydrogen

• Ex. NaCl, H2O, CO2, O2

Carbon is essential to life!!

• All living things are composed mostly of carbon.• All life on Earth is carbon based.• There are four basic types of organic (carbon

based) molecules.– Carbohydrates– Lipids– Nucleic Acids– Proteins

Macromolecules• Smaller organic molecules join together to

form larger molecules– macromolecules

• 4 major classes of macromolecules:– carbohydrates– lipids– proteins– nucleic acids

Carbohydrates

• Provide energy for cells • Carbohydrates include sugars

and starches.• Sugars - Monosaccharides,

disaccharides, polysaccharides

Lipids

• Lipids are insoluble (do not dissolve) in water.• Lipids are fats • Lipids store energy. • Building Blocks - Fatty acids, glycerol

• Saturated Fat – solid at room temperature• Unsaturated Fat – Liquid at room temperature

This is what fatty acids look like

Organic Substances…Lipids• Phospholipids – similar to fat

molecules, however contains only two fatty acid chains. In the position of the third is a portion containing a phosphate group

• “head” – phosphate portion (water soluble, hydrophilic)

• “tail” – fatty acid portion (hydrophobic)

• Important in cellular structures

Organic Substances … Lipids

• Steroids – complex molecules that include four connected carbon rings

• Examples: Cholesterol, estrogen, progesterone, testosterone…

Nucleic Acids

• Nucleic Acids – store information

• Theycontain the genetic instructions for all living things.

• Two types of nucleic acids

– RNA– DNA

Proteins

• Proteins serve as: • Structural materials • Allow chemical reactions to

happen in cells (Enzymes)• Energy sources• Hormones• Receptors on cell surfaces• Antibodies

Organic Substances…Proteins

• Proteins always contain nitrogen atoms and sometimes sulfur atoms

• The building blocks of proteins are molecules called amino acids– There are 20 different amino acids

• The shape or conformation of a protein determines its function

Functional Groups

• functional groups are groups of atoms or bonds within molecules that are responsible for the characteristic chemical reactions of those molecules.

• Examples:Hydroxyl –OH Carboxyl –COOHCarbonyl =CO Amino –NH2Phosphate –OPO3 Sulfhydryl -SH

H2O

HO

HO H

H HHO

Polymers• Long molecules built by linking repeating

building blocks in a chain – monomers

• building blocks• repeated small units

– covalent bonds

Dehydration synthesisDehydration synthesis

H2O

HO

HO H

H HHO

How to build a polymer• Synthesis

– joins monomers by “taking” H2O out• one monomer donates OH–

• other monomer donates H+ • together these form H2O

– requires energy & enzymes

enzymeDehydration synthesisDehydration synthesis

Condensation reactionCondensation reaction

H2O

HO H

HO H HO H

How to break down a polymer• Digestion

– use H2O to breakdown polymers • reverse of dehydration synthesis• cleave off one monomer at a time

• H2O is split into H+ and OH–

– H+ & OH– attach to ends

– requires enzymes– releases energy

HydrolysisHydrolysis

DigestionDigestion

enzyme

– Cellular respiration, the breakdown of glucose in the presence of oxygen, is an example of a pathway of catabolism

– This is how your body gets energy from food.

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

H2O

HO H

HO H HO H

Catabolic Reactions release energy by breaking down complex molecules into simpler compounds

Catabolic Reactions

– The synthesis of protein from amino acids is an example of anabolism

– This is how plants store energy during photosynthesis

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

H2O

HO

HO H

H HHO

Anabolic Reactions

Anabolic Reactions consume energy to build complex molecules from simpler ones

ATP

• ATP = Adenosine triphosphate• Adenosine molecule with 3 phosphate groups

attached

Adenosine P P P

Fig. 8-8

Phosphate groupsRibose

Adenine

ATP

• The charged phosphate groups act like the positive poles of two magnets, they repel each other

• Energy is contained in the bond that holds the phosphate molecules to the adenosine

• When a bond breaks, energy is released resulting in ADP (adenosine diphosphate)

• Refer to pg 229 fig 9.2

Ionization of water & pH• Water ionizes

– H+ splits off from H2O, leaving OH–

• if [H+] = [-OH], water is neutral• if [H+] > [-OH], water is acidic• if [H+] < [-OH], water is basic

• pH scale– how acid or basic solution is– 1 7 14

H2O H+ + OH–H2O H+ + OH–

pH Scale10–1

H+ IonConcentration

Examples of Solutions

Stomach acid, Lemon juice1

pH100 Hydrochloric acid0

10–2 2

10–3 Vinegar, cola, beer3

10–4 Tomatoes4

10–5 Black coffee, Rainwater5

10–6 Urine, Saliva6

10–7 Pure water, Blood7

10–8 Seawater8

10–9 Baking soda9

10–10 Great Salt Lake10

10–11 Household ammonia11

10–12 Household bleach12

10–13 Oven cleaner13

10–14 Sodium hydroxide14

tenfold changein H+ ions

pH1 pH210-1 10-2

10 times less H+

pH8 pH710-8 10-7

10 times more H+

pH10 pH810-10 10-8

100 times more H+

1001

2

3

45

6

7

89

3Amount of base added

Bufferingrange

4 52

pH

Buffers & cellular regulation• pH of cells must be kept ~7

– pH affects shape of molecules– shape of molecules affect function– pH affects cellular function

• Control pH by buffers– reservoir of H+

• donate H+ when [H+] falls

• absorb H+ when [H+] rises

Enzymes

• Enzymes are important proteins because they speed up chemical reactions.

• Without enzymes, the chemical processes carried out by your cells would happen too slowly to keep you alive!

Enzymes

• Your body requires enzymes to digest food and to convert fats and carbohydrates to energy.

• Some examples of enzymes are pepsin, lipase, and lactase.

Enzymes

Lactose intolerance is an example of the trouble that can be caused by an enzyme deficiency. People who are lactose intolerant lack the enzyme lactase. Lactase breaks down the sugar lactose. If a lactose intolerant person consumes dairy products, they can feel really sick. Fortunately, lactase supplements are available to allow lactose-intolerant people to safely consume dairy products.

More about enzymes!

• Each enzyme has a specific chemical reaction it speeds up.

• Pepsin breaks down proteins and is found in your digestive tract.

• Lactase breaks down lactose (a sugar found in milk).

• Lipase breaks down lipids (fats).

The Enzyme-Substrate Complex

• Substrates are the reactant(s) upon which the enzyme acts

• Enzymes form a complex with their substrates called the enzyme-substrate complex (ES complex) at the active site

• When the ES complex breaks up it releases product

This link shows how enzymes work

• http://www.lpscience.fatcow.com/jwanamaker/animations/Enzyme%20activity.html

This link shows how enzymes work under various conditions!

http://www.kscience.co.uk/animations/anim_2.htm

Enzymes Are Picky About Their Working Conditions!

• As we saw in the animation, enzymes need the correct temperature or pH in order to work.

• If the temperature is too cold, or too hot, the enzymes may not work.

• Generally, chemical reactions happen more quickly in warmer temperatures. But too much heat can destroy an enzyme.

Enzymes are Very Sensitive

• Each enzyme has an optimal temperature, pH, and ionic strength

• Human enzymes are optimized to work at body temperature (37OC)

• Certain body enzymes are most active at the pH of a given body compartment: – Pepsin’s optimum pH matches that

of the stomach (acidic)– Trypsin’s optimum pH is basic, like

the upper intestine

What does heat do to an enzyme?

• View animation of how heat affects the structure of a protein.

• Remember, enzymes are proteins!!!

• Frying eggs

Picky enzymes!

• Some enzymes need acidic conditions in which to work, like the enzymes in your digestive tract.

• If an enzyme doesn’t have the right conditions, it cannot do its job!

What factors affect enzyme function?

• We will be conducting a laboratory investigation in order to answer the question above.

• For help in getting started, go to the link below

• Liver lab

Answer the following questions on your own paper.

1. What is the difference between a molecule and a compound?

2. What are four types of organic compounds? Describe how each is important to living things.

3. What does an enzyme do? What type of organic compound is an enzyme?

4. List two conditions that can affect the ability of an enzyme to function.