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Definition of Science
From the national academy of sciences and institute of medicine
The use of evidence to construct testable explanations and predictions of
natural phenomena, as well as the knowledge generated through this process
Science originates in questions about the natural world-Observations and evidence
y Construct explanations and testable hypothesisy Explanations made public through presentations and publicationsy Scientists present their explanations and critique the explanations proposed
by other scientists
OUR TYPICALEXPERIENCE:
y Body tempeture of 37 Cy The tempeture for life is 132 C
Range of conditions for life:y Cell/body tempetures from -2 C to 132 Cy The most common habitat for life on the planet:
o The deep oceany Range of pressures: 1 atm to 100 atmy Conditions at the average depth of the ocean: 2C to 4C and 380 atm of
pressure
y No sunlightOrganisms confront a variety of problems due to their environment
Antarctic Fish
y Live (and have body tempetures) at -2 C (below the freezing tempeture ofmost vertebrates body fluids) [ectotherm]
y Pagotheniay The fish in ice have antifreeze molecules in their system and thats why they
can survive in the below freezing water
Penguins
y Keep warm at similar tempetures [endotherm]Diving Seals
y Can hold their breath up to 90 minutes and go to depths to up to a mileDeep Sea Fish
y Found up to depths of 7000 metersy Experience high pressure, cold tempeture, low food availability
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Piezophiles
y Bacteria- piezophiles (=barophiles) are pressure lovingy Pressures thatkill bacteria
Thermophiles
y Bacteria- thermophiles exist at temperatures up to 132 c (grow at 122c)y Hydrothermal vents- where water up to 360 C comes out from the sea floor,
minerals that were dissolved in the hot water
Sharks
y Live with molar urea in their tissuesy Urea is a potent denaturant of proteins
Halophiles
y Live in osmotic equilibrium with 3 molar saltTuna
y Raise the tempeture of their muscles above ambient (as much as 15 C)y Are endotherms in contrast to ectothermic fishy Other endotherms:
Great white shark
Swordfish
Gutless Tubeworms
y Thrive at deepsea hydrothermal ventsMidwater Fish and Invertebrates
y Organisms living in the water column achieve neutral buoyancy despite thehigh density of biological materials
The body tempeture of an endotherm is set by the environmental tempeture: False
All fish are ectotherms: False
Chemistry background:
Elements- Pure substances that cannot be broken down into 2 or more
similar substances92 naturally occurring elements112th element: copernicium
Atom- basic unit of the element
Components of an atom:
NucleusProton (+1 charge with mass of 1 Dalton
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Neutron (o charge with 1 Dalton mass)
Electron (-1 charge, has no mass)
Atomic number- of element is the number ofprotons in the nucleus
Atomic mass- is the sum ofprotons and neutrons in the nucleus
Electrical charge- is the number ofelectrons has to equal the number of
protons
Ion- is the number of electrons is not equal to the number of protons
Compound- is a substance made up of two or more elements
Example:H20 NaCl
Composition- is definite, and energy is involved in the synthesis or
breakdown (like burning gasoline)
Elements lose their characteristic properties
Gold has the atomic number of 79 and an atomic mass of 197.How many protons are
in the nucleus? 79
Ectotherms?
1. Crayfish2. Crabs3. Gold fish4. Cats5. Dogs6. 1237. 348. All
Ectotherms body tempetures are determined by the environmental tempeture: true
Endotherms:1. Penguins2. Humans3. Crabs4. Tuna5. Great white6. 127. 1248. 12459. 1-5
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Halophites love:
1. High pressure2. High temp3. High salt4. Low pressure5. Low temp6. Low salt
*Look at tables in text book 2.1, 2.5, 2.8,2.10,2.9
Gold has an atomic number of 79 and atomic mass of 197, how many neutrons are in
the nucleus? 118
How many electrons? 79
Chemical bonds- forces that hold atoms together in molecules
-Characterized as strong or weak depending on the energy required tomake/break the bond
-Covalent bond- water
What determines the number and type of chemical bonds?
Number=valence
Type= electronegativity
Electronegativity- is a measure of the tendency of an atom to attract a bonding pair
of electrons
Measures of the attraction an atom has for electrons
*Look on Moodle in the folder biological molecules
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Chemical Bonds
Strong
Covalent bonds involve sharing of electronsWeak
Non-covalent bonds (dont involve sharing of electrons)
Ionic interactions- attraction of opposite charges. One atomdonates an electron to another
Hydrogen bond between partially charged atoms
*figure 2.12 shows covalent bonding in four molecules
Valence vs. Valence Electrons
Valence
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number of electrons needed to fill the outer most shell of an atom
Valence ElectronsNumber ofelectrons contained in the outermost electron shell of an
atom
*figure 4.4 shows valence for the major elements of organic molecules
Moles and Molar Concentrations
1 Mole= the mass of a substance equal to its gram molecular weight
1 molar solution= a solution containing 1 mole of a substance per 1 liter of
solution
*****get clicker questions
Ionic bondsWeak bond
Transfer of electron from one atom to another
*figure 2.14
Covalent bonds
Strong bond
Sharing of electrons to complete the valence shell
*figure 2.13 polar covalent bonds in a water molecule
Polar bonds
Unequal sharing of electrons
Partial + (s+) and partial (s-) chargesNo net charge
Hydrogen bonds
Weak (non-covalent) bonds
Between partials positive (s+) and partial negative charges (s-)
*figure 2.16 a hydrogen bond
*figure 3.2 hydrogen bonds between water molecules
Oxygen has atomic number of 8. How many valence electrons does it have?
6
What is the valence of oxygen?
2
The major categories of chemical bonds:
Weak and Strong
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The major categories of bonds are based on the number of electrons involved.
False
Polar bonds result from the transfer of electrons between atoms
False
*figure 3.1 earth
Water
70-90% of weight of most life formssets the lower temperature limit for life
sets the upper temperature limit? (probably not)
important role in structures and properties of biological molecules
water is a biological molecule
The unusual properties of water
Result from hydrogen bondingWater behaves as a much larger molecule
BondsCovalent:H-O 110 kcal per mole
Angle 104.5 not linear
Weak (hydrogen bond): 4.5 kcal/mol to make or break the bond
-H bonding effectively makes water a larger molecule
-an ice a water molecule interacts with exactly 4 other water
molecules
-in liquid water, on average 3.6 or fewer other molecules ( can be
made and broken very quickly)
small molecules- a comparison of properties
water-H20 boiling: 100 C melting/freezing point: o C
amomonia- NH3 35 C -37 Cethanol- 78.5 C -117.3 C
UNUSUAL PROPERTIES OF WATER:High heat capacity
Amount of heat to raise temperature of 1 g of water by 1 C
1 cal per g waterHigh heat of vaporization
Amount of heat to vaporize 1 g of water
540 cal per g at 100 C to get it to become steam
High heat of fusion
Amount of heat removed to freeze 1 g of water
80 cal per g to get it to form solid state of water
Most dense at 4 C
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Because of the hydrogen bonding structure, ice is lighter than water
Lakes dont freeze from the bottom up
* figure 3.6
High dielectric
Good solvent
*figure 3.7 a crystal of table salt dissolving water*figure 3.8 a water-soluble protein
Unequal sharing of electron pairs in a covalent bond?
polar covalent bond
Capillary action and surface tension
*figure 3.4 walking on water
*figure 3.3 water transport in plants
due to hydrogen bonding
Ionization
Dissociation into acid (hydronium ion)And base (hydroxyl ion)
*unnumbered figure on page 52
Most aquatic animals are ecotherms because of waters?
high heat capacity
pH- a review
some basic principles
oops, some ACIDIC principles
Acids, bases, and saltsAcids produce H+ ions
HCl---H+ and Cl-
Bases produce hydroxide ionsNaOH-Na+ and OH-
Salts produce neitherNaCl-Na+ and Cl-
pH= log[1/H+] = -log [H+]
actually activity ofH+
pH scalelog base 10
the difference between pH3 and pH4 is a 10-fold difference in the
concentration ofH+
the difference between pH 3 and pH 5 is a 100-fold difference in the
concentration ofH+
pH scale
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pH of 7 is neutral
pH below 7 is acidic
pH above 7 is basic
*figure 3.9 the pH of some aqueous solutions
pOH
pOH= log [1/OH-0=-log [OH-]
pH+pOH=14
neutrality
[H+]=[OH-]
-LOG [H+]=-log [Oh-]
ph=pOH
ph=7
PH=7, POH= ?
7
beggining with a solution of pH 8 you increase the [H+] by a factor of 1000 what is
the new pH of the solution?
5 you subtract 3 from 8 and get 5
The pH of a solution decreases by 1 unit. The H+ concentration
increases by 10 fold
pOH=5; pH=
9 bc they have to equal 14
begginning with a solution of pOH 5 you increase the OH- solution by a factor of
1000 what is the new pH of the solution?
12
beginning with a solution of pH 7 you decrease the H+ by a factor of 100 what is thenew pH of the solution?
You add 2 to 7 so the answer is 9
Buffers
Substances that maintain a constant pH
Soluability
Solute
Solvent- the liquid solutes are dissolves in
What determines the solubility of a molecule?
Similariy of the solute and solvent
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What determines soluability?
Like dissolves likeLike in terms of polarity
Polar solutes dissolve in polar solventsNon-polar solutes dissolve in non-polar solvents
Hydrophilic substances interact with water molecules
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Which atom is more electronegative?Clorine or Sodium
Chlorine.
Heat of fusion is the amount of heat removed to freeze 1 gram of water.
Biological Molecules
WaterCarbohydratesLipids
ProteinsNucleic acids
*see table 4.10a Functional groups of Organic Compounds
Functional GroupsHydroxyl- alcohols
Carbonyl- aldehydes 9terminal carbon) and Ketones
Carboxyl- acid groupAmino- amines
Sulfhydryl- thiols
Phosphate- organic phosphates
Carbon SkeletonBackbone
Convalently linked carbon molecules
*figure 4.5 variations of carbon skeletons
Hydroxl group is an alcohol.
Biological molecules
Large molecules constructed from smaller molecules
Polymers constructed from monomers
Mers=units
Mono=single
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Poly-many
Synthesisofpolymers- covalent bond formation between monomer units
Condensation (dehydration) synthesis
Proceeds with the removal of a water molecule
*figure 5.2- the synthesis and breakdown of polymers
breakdown of polymers- breaking down the covalent linkage between monomer
unitshydrolysis
-breaking the covalent bond linking the units of the polymer by the
addition of a water molecule
Why make large biological molecules from simple monomers?Flexible system
Array of complex molecules from a few simpler moleculesFewer enzymes to make biological molecules than if starting from scratch
Carbohydrates
General formula (CH20)n
Ex) n=6
C6H1206
*FIGURE 5.3 the structure and classification of some monosaccharides
What is the formula for the disaccharide maltose, made of two glucose (c6h1206)
monomers?C12h24o12
*figure 5.5 examples of disaccharide synthesis*figure 5.6 storage polysaccharides
*figure 5.7 starch and cellulose
Carbohydrates
Energy roles
1. metabolic fuel2. storage form
Energy roles-fuel
Glucose
Sucrose
Energy roles- storage
Starch (plants)
Glycogen (animals)
Energy roles- structural roles
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Cellulose (in plants)
Chitin (animals)
*figure 5.7 the arrangement of cellulose in plant cell walls
*figure 5.9 cellulose digestion: cow
cellulosedigestion:termine and trichonymphia
*figure 5.10 chitin, s structureal polysaccharide; exoskeleton and surgical
Lipids
y Water- insoluable organic biomoleculesy Lipids are nonpolar- they dont have any partial charges and they dont
dissolve in water, they are hydrophobic
y Structural components of cell membranesy Storage and transport forms of fuely Protective surface coatingy Cell component in cell recognitiony Hormone
*figure 4.6 the role of hydrocarbons in fats*figure 5.11 the synthesis and structure of a fat, or triacylglycerol
Fat typesSaturated- saturates with H, no double bonds between adjacent carbons
Bad because they raise LDL cholesterol (low density)
Unsaturated- double bonds, lower melting point
The good fat
Better than saturated fats
*figure 5.12 examples of saturated and unsaturated fats and fatty acids
Melting Points Differ
y saturated fats are solids at higher temperatures than unsaturated fatsy acyl chains of unsaturated fats are kinky and therefore require a
lower temperature to become a solidPolymers
TriglyceridesMade up of glycerol and fatty acids
Phospholipids
*figure 5.13 the structure of a phospholipids
*figure 5.14 self-assembly of phospholipids in aqueous enviroments
*figure 5.15
energy available per gram
molecule energy
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fat 9.3 kcal/g
carbohydrate
protein
comparison of lipids and carbohydrates
twice as much energy from fatstroed without water
1g of glycogen is stored with 2-5 grams of water
disadvantageof lipids- not as rapidly mobilized as carbohydrates
lipids metabolized in the mitochondria in the presence of O2
what a lipid structure looks like
cholesterol is a lipid.
The hump of a camel is filler with lipid not water.
CamelUp to 20% of body mass is fat when food is plentiful
Subcutaneous fat would cause thermoregulatory problems
Bear
Hibernations 100 days without eating
Human
Normal weight- 40 day reserve of energy
Moderately obese- up to a year
Nitrogenous heterocyclic basesPentose sugar
phosphoric acid
examples:coenzymes (NAD, NADP, FAD)
genetic material (DNA, RNA)ATP
*figure 5.27 the componets of nucleic acids
Proteins
Excellent example of a polymer
Made of amino acids-20 naturally occurings amino acids and are L-isomers
-proteins vary in the number and sequence of the different kinds of
amino acids
Enzymes
Protein catalyst
Every chemical reaction in a living cell is catalyzed by a specific enzyme
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Storage Proteins
SeedsEggs
Transport proteins
Contractile proteins
In muscle
Actin
Myosin
Defensive blood proteins
Antibodies
ToxinsFor example from bacteria
Pertussis toxinBotulinum toxin (BOTOX)
Hormones and receptorsHormones- chemical messengers
Ex) insulin
Receptors- specific recognition sits for chemical messengers
Structural proteins
Silk
Keratin- hair, nail, hooves
*table 5.1
amino acidsmonomers of protein
20 kinds
amino acid structure
consists of a central carbonamino group (NH2)
carboxyl group
hydrogenR group (20 different R groups)
Note there are different types of R groups
Polar- hydraphelicbc they interact with water
Non-polar- dont have charges
Charged (+ or -)
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*figure 5.17 the 20 amino acids of proteins: nonpolar
nonpolar
no partial charges on the R group
hydrophobic
*figure 5.17b the amino acid of proteins: polar and electrically charges
polar or electrically charges r groups
interact with the partial + and charges of waterhydrophilic
The characteristics of the individual amino acids determine the structure of the
protein
The synthesis of a protein from amino acids involve removal of water.
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