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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.