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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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