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Biol&160 A & BBiol&160 A & B

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Introduction- class rollIntroduction- class roll Syllabus/ExpectationsSyllabus/Expectations Intro to science & scientific methodIntro to science & scientific method Organization of lifeOrganization of life Cell chemistry and moleculesCell chemistry and molecules

SyllabusSyllabus

Questions?

Study HabitsStudy Habits

Find out what works best for YOUFind out what works best for YOU Try different methodsTry different methods

– Combine methodsCombine methods Use shorthandUse shorthand Read the chapter BEFORE lecture Read the chapter BEFORE lecture

and be prepared with any questionsand be prepared with any questions

What is science?What is science?To Know

Seeks natural causes to phenomenon– Therefore limited to things that we can OBSERVE and MEASURE

Ex: Rate of flow of water over a dam Ex: Deity

Explanatory –study of the world around us to explain our observations

Testable – based on observations or measurements Reproducible – others must be able to confirm and

duplicate scientific findings Predictive – we use scientific knowledge to predict answers

to questions Tentative – each new discovery can change the way we

look at other things we know

What is science

Observational science– What is observed in nature

Experimental science– Usually derived from observational

science– Attempts to answer/understand specific

questions about what is observed

What is What is BiologyBiology

Study of lifeStudy of life– Encompasses Encompasses

EthologyEthology Evolutionary BiologyEvolutionary Biology PhysiologyPhysiology GeneticsGenetics Molecular BiologyMolecular Biology MorphologyMorphology SystematicsSystematics EcologyEcologyAnd more…..And more…..

Hypothesis based scienceHypothesis based science

Hypothesis- a tentative statement Hypothesis- a tentative statement that proposes a possible explanation that proposes a possible explanation to some phenomenon or event to some phenomenon or event

TestableTestable– may include a predictionmay include a prediction

Simple and conciseSimple and concise FalsifiableFalsifiable

– Accept or rejectAccept or reject

Scientific TheoryScientific Theory

Explanation of something that has been Explanation of something that has been substantiated by a large amount of data collected substantiated by a large amount of data collected over multiple experimentsover multiple experiments

Best possible explanation at the time based on Best possible explanation at the time based on experiments and available dataexperiments and available data

Theories are altered, revised, adapted or simply Theories are altered, revised, adapted or simply abandoned as new data becomes availableabandoned as new data becomes available

Scientific methodScientific method

ObservationObservation QuestionQuestion

– This turns into a testable…This turns into a testable… HypothesisHypothesis PredictionPrediction ExperimentationExperimentation

– Controlled Controlled – ReplicationReplication

Analysis of resultsAnalysis of results Evaluate hypothesis against resultsEvaluate hypothesis against results Generate Scientific TheoryGenerate Scientific Theory

ReasoningReasoning

Inductive- Extrapolate general Inductive- Extrapolate general principles from specific examplesprinciples from specific examples

Deductive- Extrapolate specific Deductive- Extrapolate specific examples from general principlesexamples from general principles

Humans are made of cellsHumans are made of cells InductiveInductive

– Every biological sample for the past 200 years Every biological sample for the past 200 years has been made of cells (specific)has been made of cells (specific)

THEREFORETHEREFORE– All organisms (including humans) are made of All organisms (including humans) are made of

cells (general)cells (general) DeductiveDeductive

IFIF– all organisms are made of cells & humans are all organisms are made of cells & humans are

organisms (general)organisms (general)THENTHEN– Humans are made of cells (specific)Humans are made of cells (specific)

Spontaneous GenerationSpontaneous Generation

Living things arrive from lifeless Living things arrive from lifeless mattermatter– Air had a “life force”Air had a “life force”

Rotting meat, when left, produced Rotting meat, when left, produced fliesflies

Redi’s blowfly experimentRedi’s blowfly experiment

Spontaneous GenerationSpontaneous Generation Observation- Flies spontaneously appear on

rotting meat Question- Does rotting meat produce flies Hypothesis- Rotting meat produces flies Prediction- A flask of rotting meat will produce

flies in 21 days Experimentation- 3 jars of meat were

subjected to being open, semi-sealed with parchment paper or sealed while other variables remained identical– Control is flask of meat set out with no cover– Experiment is 2 flasks semi-sealed and sealed

Analysis of results- Presence/absence of flies was recorded. No flies were present in closed jars, semi-closed jars had fly eggs on the parchment

Evaluate hypothesis against results- Reject hypothesis as sealed jars did not produce flies and semi-sealed jars had fly eggs on the parchment paper– Flies came from other flies not from the meat

©Barrons 2009

Experiments & TheoriesExperiments & Theories

Experiments & hypotheses only test Experiments & hypotheses only test NEVER prove theoriesNEVER prove theories– The very next experiment may falsify The very next experiment may falsify

theorytheory– Always falsify a hypothesis, not prove itAlways falsify a hypothesis, not prove it

Correct- A sealed jar will not produce Correct- A sealed jar will not produce fliesflies

Not- an unsealed jar will produce fliesNot- an unsealed jar will produce flies

Data InterpretationData InterpretationA team of scientists A team of scientists designed an investigation that designed an investigation that used artificial snakes to test used artificial snakes to test the following hypotheses. the following hypotheses.

– HH11: The coral snake’s : The coral snake’s bright color pattern bright color pattern serves to warn off serves to warn off potential predators.potential predators.

– HH22: The king snake : The king snake suffers less predation suffers less predation because it mimics or because it mimics or looks like the coral snake.looks like the coral snake.

– HH33: The protection that : The protection that king snakes receive by king snakes receive by mimicking coral snake will mimicking coral snake will depend on the presence depend on the presence of coral snakes.of coral snakes.

– Both 1 and 2Both 1 and 2

Data InterpretationData InterpretationBiologists placed artificial Biologists placed artificial snake mimics in two snake mimics in two different localities to test different localities to test the hypothesis that looking the hypothesis that looking like a poisonous snake like a poisonous snake only works where the only works where the poisonous snake is found:poisonous snake is found:

1.1. Outside of the coral Outside of the coral snake range—only king snake range—only king snakes present.snakes present.

2.2. Inside the coral snake Inside the coral snake range—both coral and king range—both coral and king snakes are present.snakes are present.

Data InterpretationData InterpretationThe graphed data The graphed data __________ the hypothesis __________ the hypothesis that the effectiveness of that the effectiveness of mimic coloration depends mimic coloration depends upon the presence of the upon the presence of the poisonous model is:poisonous model is:

– supportssupports– does not support does not support – is irrelevant tois irrelevant to

Data InterpretationData InterpretationBased on this data which of Based on this data which of the following is a logical the following is a logical hypothesis or prediction?hypothesis or prediction?

– King snakes outside of the King snakes outside of the range of coral snakes will range of coral snakes will more closely resemble coral more closely resemble coral snakes than populations of snakes than populations of king snake living within the king snake living within the range of coral .range of coral .

– King snakes outside of the King snakes outside of the range of coral snakes will range of coral snakes will not resemble coral snakes not resemble coral snakes as closely as populations of as closely as populations of king snakes that live within king snakes that live within the range coral snakes. the range coral snakes.

– Neither prediction is valid.Neither prediction is valid.

Why do I care about Hypothesis testing and scientific method?

Used in every day life and decision making– Ex: Medical- use scientific method to

determine cause of patients ailment

Organization of LifeOrganization of Life

Life’s levels of organization define the scope of biology

Hierarchical organization

Levels organized according to complexity– “Higher” and “lower” order life forms do

not exist, simply a matter of complexity Emergent properties

– Properties that were not present at the previous lower level and result from the specific arrangement and interactions between components

“The whole is greater than the sum of its parts”

Environmental interactions

Living organisms and their environments form interconnecting webs

Environmental Interactions

Producers– Organisms that produce organic compounds

from inorganic compounds These organisms are autotrophs Photosynthesis, chemosynthesis, etc

Consumers– Organisms that obtain nutrients from other

organisms Heterotrophs

Decomposers– Decay organic matter, releasing energy back

into the ecosystem Saprobes

Common features of all living Common features of all living formsforms

Order/organizationOrder/organization RegulationRegulation Growth & DevelopmentGrowth & Development Energy utilization/processingEnergy utilization/processing Response to the environmentResponse to the environment ReproductionReproduction EvolutionEvolution

In-class Exercise

Get into groups Each group identify a scientific question,

hypothesis and experimental outcome for each scenario– Don’t worry about figuring out an experiment,

just make up the results of one Decide if your outcome supports or refutes

your hypothesis

Example While walking to class today, I notices a

fire hydrant in the middle of the pathway Question- Why was the hydrant placed in

the middle of the path Hypothesis- The middle of the path was

the most accessible location for the hydrant

Experimental outcome- The middle of the path was not found to be the most accessible location for a hydrant

My findings do not support my hypothesis and thus, my hypothesis is rejected.

Exercise Scenario 1-While hiking in the forest one

day, you notice that while on the left side of the trail, the frogs are bright green, but on the right, they are a mottled green-brown color.

Scenario 2- As a nurse, one of your patients presents with an unusually low temperature, but no other symptoms

Scenario 3-You are fishing out in Puget Sound and find that all the other fishermen are pulling up salmon, but you are catching fish.

Cellular ChemistryCellular ChemistryCh 2Ch 2

Life primarily Life primarily consists of consists of carbon, carbon, hydrogen, hydrogen, oxygen, and oxygen, and nitrogen nitrogen

Rest are present Rest are present in trace in trace amountsamounts

Table 2.1

Trace elements Trace elements Are essential to life, but occur in Are essential to life, but occur in

minute amountsminute amounts Trace elements are common Trace elements are common

additives to food and wateradditives to food and water Dietary deficiencies in trace Dietary deficiencies in trace

elements can cause various elements can cause various physiological conditionsphysiological conditions

Interpreting DataInterpreting DataThese are the These are the results of a laboratory results of a laboratory experiment to test experiment to test the effect of trace the effect of trace nutrients on the nutrients on the productivity of Pacific productivity of Pacific Ocean water. After 6 Ocean water. After 6 days which nutrient days which nutrient had the greatest had the greatest effect on effect on productivity? productivity?

– IronIron– ManganeseManganese– CopperCopper– ZincZinc

Adapted from Coale, Kenneth H. 1991. Effects of Iron, Manganese, Copper and Zinc Enrichments on Productivity and Biomass in the Subarctic Pacific. Limnology and Oceanography. 36: 1851-1864

Subatomic ParticlesProtons- positive Protons- positive chargechargeNeutrons- neutral Neutrons- neutral chargecharge

Protons and Protons and neutrons neutrons occupy the occupy the nucleusnucleus

Electrons- negative Electrons- negative chargecharge

Arranged in Arranged in electron electron shells shells around the around the nucleusnucleus

Figure 2.4A

+

+

– –

+

–

2

2

2

Protons

Neutrons

Electrons

Massnumber = 4

+

+

2e–

Electroncloud

Nucleus

Differences in ElementsDifferences in ElementsAtoms of each element Atoms of each element

always have the same always have the same number of protonsnumber of protons

Atomic Number=# Atomic Number=# protonsprotons

Mass Number (atomic Mass Number (atomic weight) = Protons + weight) = Protons + neutronsneutrons

Atoms have no overall Atoms have no overall charge, thus…charge, thus… Figure 2.4B

+

–

6

6

6

Protons

Neutrons

Electrons

Mass # = 12

+ +

6e–

Nucleus

Electroncloud

Thus….Thus…. Number of protons (+ charge) must be Number of protons (+ charge) must be

equal to the number of electrons (-)equal to the number of electrons (-)

For any element:For any element:

Number of Protons = Atomic NumberNumber of Protons = Atomic Number

Number of Electrons = Number of Number of Electrons = Number of Protons = Atomic NumberProtons = Atomic Number

Number of Neutrons = Mass Number - Number of Neutrons = Mass Number - Atomic NumberAtomic Number

ExampleExample

KrKr

KryptonKrypton

Atomic # = 36Atomic # = 36

Atomic weight = 84Atomic weight = 84

# Protons=?# Protons=?

# Neutrons=?# Neutrons=?

# Electrons=?# Electrons=?

CompoundsCompounds

Chemical elements combine in fixed ratios to form Chemical elements combine in fixed ratios to form compoundscompounds

Different combinations of atoms determine the Different combinations of atoms determine the unique properties of each compoundunique properties of each compound

Sodium Chlorine Sodium ChlorideFigure 2.3

IsotopesIsotopesThe number of neutrons in an atom may vary The number of neutrons in an atom may vary

Variant forms of an element are called isotopes Variant forms of an element are called isotopes Some isotopes are radioactiveSome isotopes are radioactive

Table 2.4

Isotopes

aXzA = mass number (the total number of protons + neutrons)Z = atomic number (the total number of protons)X = element symbol

Ex: Ordinary hydrogen is written 1H1,

deuterium is 2H1 (heavy water, label in chemistry experiments)

tritium is 3H1 (radioactive)

Radioactive isotopes

Particles that are emitted from the nuclei as a result of nuclear instability

Usefulness of radioactive isotopesUsefulness of radioactive isotopes

IrradiationIrradiation– Material is subjected to radiation for the Material is subjected to radiation for the

purposes of disinfestations, purposes of disinfestations, pasteurization or sterilizationpasteurization or sterilization

ResearchResearch– Radioactive tracers enable researchers Radioactive tracers enable researchers

to follow particular molecules as they to follow particular molecules as they undergo change such as through undergo change such as through photosynthesisphotosynthesis

Usefulness of isotopesUsefulness of isotopes

Medical DiagnosisMedical Diagnosis– Kidney disordersKidney disorders– Medical ImagingMedical Imaging

PET scansPET scans

PET scan image of Parkinson's diseased brainBrown.edu 2008

Electrons, Electrons, Electrons!Electrons, Electrons, Electrons!

The active part of the atomThe active part of the atom– They are the only part directly involved They are the only part directly involved

in chemical activityin chemical activity

Interactions between electrons Interactions between electrons form chemical bondsform chemical bonds

Electron shellsElectron shells– Arranged in shells, which may contain Arranged in shells, which may contain

different numbers of electronsdifferent numbers of electrons

Electron arrangement determines the chemical properties of an atom

– Electrons in an atom are arranged in shells, which may contain different numbers of electrons

Hydrogen (H)Atomic number = 1

Electron

Carbon (C)Atomic number = 6

Nitrogen (N)Atomic number = 7

Oxygen (O)Atomic number = 8

Outermost electron shell (can hold 8 electrons)

First electron shell (can hold 2 electrons)

Figure 2.6

Electron ShellsElectron Shells

Electron shells Valence electron shell

– Outermost shell of electrons– These electrons interact with other

atoms

Hydrogen (H)Atomic number = 1

Electron

Carbon (C)Atomic number = 6

Nitrogen (N)Atomic number = 7

Oxygen (O)Atomic number = 8

Outermost electron shell (can hold 8 electrons)

First electron shell (can hold 2 electrons)

Figure 2.6

IonsIons

Created when an atom gains or looses and Created when an atom gains or looses and electronelectron

Results in an net positive or negative charge Results in an net positive or negative charge depending on if the atom gained or lost the e-depending on if the atom gained or lost the e-

Ionic BondsIonic Bonds•Attractions between ions of opposite chargeAttractions between ions of opposite charge

– An electrical attraction between ions with opposite An electrical attraction between ions with opposite charges results in an ionic bondcharges results in an ionic bond

Transfer of electron

NaSodium atom

ClChlorine atom Na+

Sodium ion

Cl–

Chloride ion

Sodium chloride (NaCl)

Na Cl ClNa

+ ––

–

Figure 2.7A

NaClNaCl

Na has 1 e- in the outer shellNa has 1 e- in the outer shell Cl has 7 e- in the outer shellCl has 7 e- in the outer shell Na “donates” its e- to Cl, leaving Na Na “donates” its e- to Cl, leaving Na

with only 2 shells and Cl with a full with only 2 shells and Cl with a full outer shellouter shell– This moves 1 “unit” of negative charge This moves 1 “unit” of negative charge

from Na to Cl, resulting in a net from Na to Cl, resulting in a net electrical charge of +1 for Na and -1 for electrical charge of +1 for Na and -1 for ClCl

NaClNaCl

The atom is now an ionThe atom is now an ion– Recall that an ion is an atom or Recall that an ion is an atom or

molecule with an electrical charge form molecule with an electrical charge form either gaining or loosing electronseither gaining or loosing electrons

Covalent BondsCovalent Bonds

Two atoms share one Two atoms share one or more pair of outer or more pair of outer e-e-

–# of bonds is equal to # of bonds is equal to additional e- necessary additional e- necessary to fill the outer shellto fill the outer shell

–Valence or bonding Valence or bonding capacity of the atomcapacity of the atom

Join atoms into Join atoms into molecules through the molecules through the electron sharing electron sharing

Covalent bond Diamond with 4 covalent bondsinfo.lu.farmingdale.edu/.../atomicbonds.html

Polar moleculesPolar molecules

Unequal e- sharing Unequal e- sharing produces polar produces polar bondsbonds

Electronegativity Electronegativity – Atom’s attraction Atom’s attraction

for shared electronsfor shared electrons– Greater the Greater the

electronegativity, electronegativity, stronger the pull on stronger the pull on e-e-

(–) (–)

(+) (+)

O

HH

Figure 2.9 Water Molecule

Polar moleculesPolar molecules

If the atoms exert a equal pull on the If the atoms exert a equal pull on the e-, bond is non-polar covalente-, bond is non-polar covalent– Overall charge of 0Overall charge of 0

If the atoms exert an unequal pull on If the atoms exert an unequal pull on the e-, bond is polar covalentthe e-, bond is polar covalent– Overall charge on the more Overall charge on the more

electronegative atom is partially electronegative atom is partially negative and the less electronegative negative and the less electronegative atom is partially positiveatom is partially positive

Polar moleculesPolar molecules

Polar Polar molecules molecules have an have an unequal unequal distribution of distribution of chargescharges

(–) (–)

(+) (+)

O

HH

Figure 2.9 Water Molecule

Visual representation of a moleculeVisual representation of a molecule

– Molecules can be Molecules can be represented in represented in many ways many ways

Table 2.8

Hydrogen BondsHydrogen Bonds

Partial + charge allows shared attractions with – charged molecules

+ charged region always H

Hydrogen bond(+)

(+)

H

H(+)

(+)

(–)

(–)

(–)(–)

O

Figure 2.10

The importance of hydrogen bondingThe importance of hydrogen bonding Cohesion between HCohesion between H220 molecules0 molecules

– Droplet formationDroplet formation– TransportationTransportation

Adhesion to substrateAdhesion to substrate Surface tensionSurface tension Temperature moderation (body and climatic)Temperature moderation (body and climatic)

– H bonds absorb a great deal of energy before H bonds absorb a great deal of energy before breaking, thus, a lot of energy is required before an breaking, thus, a lot of energy is required before an increase in temp occursincrease in temp occurs

DensityDensity– Ice vs. liquid waterIce vs. liquid water

Solvent

Water is the solvent of life dissolving any Water is the solvent of life dissolving any charged or polar substancescharged or polar substances

SolutionSolution Aqueous solutionAqueous solution SolventSolvent

– Dissolving agentDissolving agent SoluteSolute

– Dissolved substanceDissolved substance EX: Salt waterEX: Salt water

– Water is the solvent and salt the soluteWater is the solvent and salt the solute

Ph Scale

Some H20 molecules disassociate into H+ and OH-

A compound that releases (donates) H+ ions in solution is an acid– Increases the net H+ ions in solution

A compound that accepts (removes) H+ ions in solution is a base– Increases the net OH- ions in solution

Ph Scale 0-14 7 is neutral 0-6.9 acidic 7.1-14

basic/alkaline

Each unit is 10 fold change in concentration of H+ ions

Buffers act to minimize Ph changes

Basic solution

Oven cleaner

Acidic solution

Neutral solution

pH scale0

1

2

3

4

5

6

7

8

9

10

11

12

Lemon juice, gastric juice

Grapefruit juice, soft drink

Tomato juice

Human urine

Pure waterHuman blood

Seawater

Milk of magnesia

Household ammonia

Household bleach

Incr

easi

ngly

AC

IDIC

(Hig

her

conc

entr

atio

n of

H+)

NEUTRAL[H+]=[OH–]

H+ H+

H+ OH– H+

H+ H+

OH– H+ H+

OH–

OH–

H+ H+OH–

OH– OH–

H+ H+H+

OH–

OH–

OH– OH–

OH–OH– H+

Incr

easi

ngly

BA

SIC

(Low

er c

once

ntra

tion

of H

+)

OH–

H+

14

13

CHEMICAL REACTIONSChemical reactions change the composition of matter

reactants products

2 H2O2 2 H2OFigure 2.17A

Interpreting Data

This is the general equation for photosynthesis—the process of capturing sunlight energy and converting it to chemical energy. Which of the following are the reactants of this reaction?

– C6H12O6 and O2.

– CO2 and H2O.

Interpreting Data

Earth’s oceans are immense. Small floating plants called phytoplankton contribute to ocean productivity. As ocean productivity (the rate of photosynthesis) goes up what would you predict would happen to global carbon dioxide levels?

– CO2 levels should also go up.– CO2 levels should go down

– CO2 levels should remain constant.