Welcome to General Cell Biology. Study Habits Find out what works best for YOUFind out what works best for YOU Try different methodsTry different methods.

Welcome to General Welcome to General Cell BiologyCell Biology

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 and be Read the chapter BEFORE lecture and be prepared with any questionsprepared with any questions

• Study EVERY dayStudy EVERY day

What is science?What is science?To Know

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

and MEASURE

• Explanatory

• Testable

• Reproducible

• Predictive

• Tentative

What is What is BiologyBiology

• Study of lifeStudy of life– Encompasses Encompasses

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

Approaches

• Discovery- observational– Uses inductive reasoning

• Hypothesis-based- experimental– Uses deductive reasoning

Hypothesis based scienceHypothesis based science

Hypothesis- a tentative statement that proposes a possible explanation to some phenomenon or event – Testable– Tentative relationship is stated– Simple and concise– Falsifiable

• Accept or reject

Prediction vs HypothesisPrediction vs Hypothesis

• Predictions “guess” what will happenPredictions “guess” what will happen

• Hypothesis presents a Hypothesis presents a relationshiprelationship, which , which explains what will happenexplains what will happen– Specific, testable prediction about what will Specific, testable prediction about what will

happenhappen

Language of a hypothesisLanguage of a hypothesis

• Contain the dependent and independent variables

– If leaf color change is affected by (related to) temperature , then exposing plants to low temperatures will result in changes in leaf color.

***If the reader cannot figure out what you are testing, it is not a hypothesis

Scientific TheoryScientific Theory Explanation of something that has Explanation of something that has

been substantiated by a large amount been substantiated by a large amount of data collected over multiple of data collected over multiple experimentsexperiments

Best possible explanation at the time Best possible explanation at the time based on experiments and available based on experiments and available datadata

Can be altered, revised, adapted or Can be altered, revised, adapted or simply abandoned as new data simply abandoned as new data becomes availablebecomes available

Scientific methodScientific method

• ObservationObservation• QuestionQuestion• HypothesisHypothesis• PredictionPrediction• ExperimentationExperimentation

– Controlled Controlled – ReplicationReplication

• Analysis of resultsAnalysis of results• Evaluate hypothesisEvaluate hypothesis• Generate Scientific TheoryGenerate Scientific Theory

ReasoningReasoning

• Inductive- Extrapolate general principles Inductive- Extrapolate general principles from specific examplesfrom specific examples– A conclusion is arrived at based on a set of A conclusion is arrived at based on a set of

observationsobservations

• Deductive- Extrapolate specific Deductive- Extrapolate specific conclusions from general principlesconclusions from general principles– If A then BIf A then B

Reasoning Inductive

All observed crows are black.

Therefore:

All crows are black.

DeductiveAll men are mortal

Socrates is a man

Therefore, Socrates is mortal

Spontaneous GenerationSpontaneous Generation

• Living things arrive from lifeless matterLiving things arrive from lifeless matter– Air had a “life force”Air had a “life force”

• Rotting meat, when left, produced fliesRotting meat, when left, produced flies– Therefore, flies come from rotten meatTherefore, flies come from rotten meat

• Redi’s blowfly experimentRedi’s blowfly experiment

Spontaneous GenerationSpontaneous Generation• Observation- Flies spontaneously appear on rotting

meat

• Question- Does rotting meat produce flies

• Hypothesis- If rotting meat produces flies then any flask with rotten meat will produce 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

• Analysis of results- 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

©Barrons 2009

• What would happen if no control group was included?

Experiments & TheoriesExperiments & Theories

• Experiments & hypotheses only test Experiments & hypotheses only test NEVER prove theoriesNEVER prove theories

– The very next experiment may falsify theoryThe very next experiment may falsify theory– Always falsify a hypothesis, not prove itAlways falsify a hypothesis, not prove it

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

• Understand the world around us

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

• 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 flounder.

Organization of LifeOrganization of Life

Life’s levels of organization define the scope of biology

Hierarchical organization• Organized according to 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• Autotrophs

– Organisms that produce organic compounds from inorganic compounds

• “Producers”• Photosynthesis, chemosynthesis, etc

• Heterotrophs– Organisms that obtain nutrients from other organisms

• “Consumers”

• 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

Cellular Chemistry

Ch 2

Elements of life– Life primarily

consists of C, H, O, N

– Rest are present in small amounts called trace elements

Table 2.1

Trace Elements

• Essential to life

• Occur in minute amounts

• common additives to food and water

• Deficiencies can cause various physiological conditions

Subatomic ParticlesProtons- positive charge

Found in the nucleus

Neutrons- neutral charge

Protons and neutrons occupy the nucleus

Electrons- negative charge

Arranged in electron shells around the nucleus Figure 2.4A

+

+

– –

+

–

2

2

2

Protons

Neutrons

Electrons

Massnumber = 4

+

+

2e–

Electroncloud

Nucleus

Differences in ElementsDifferences in ElementsAtoms of each element

always have the same number of protons

Atomic Number=# protons

Mass Number (atomic weight) = Protons + neutrons

Atoms have no overall charge, thus…

Figure 2.4B

+

–

6

6

6

Protons

Neutrons

Electrons

Mass # = 12

+ +

6e–

Nucleus

Electroncloud

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

to the number of electrons (-)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=?

CompoundsCompoundsChemical elements combine in fixed ratios to

form compounds

Different combinations of atoms determine the unique 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 Variant forms of an element are called isotopes isotopes

• Some isotopes are radioactiveSome isotopes are radioactive

Table 2.4

Isotopes

aXz

A = 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 isotopesParticles that are emitted from the nuclei as

a result of nuclear instability

• Irradiation– Disinfestations, pasteurization or sterilization

• Research– Radioactive tracers enable researchers to

follow particular molecules as they undergo change such as through photosynthesis

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– Only part directly involved in chemical activityOnly part directly involved in chemical activity

• Interactions between electrons form chemical Interactions between electrons form chemical bondsbonds

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

different numbers of electronsdifferent numbers of electrons– Shells are “Full” with either 2 or 8 electronsShells are “Full” with either 2 or 8 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 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

Electronegativity

• Atom’s attraction for shared electronsAtom’s attraction for shared electrons– Greater the electronegativity, stronger the pull Greater the electronegativity, stronger the pull

on e-on e-

Covalent BondsCovalent Bonds•Pairs of e- shared Pairs of e- shared between pairs of between pairs of atomsatoms

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

•Polar and Non-polarPolar and Non-polar

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

PolarityPolarity

• Non-polar covalent- When the atoms exert Non-polar covalent- When the atoms exert a equal pull on the e-a equal pull on the e-– Overall charge of 0Overall charge of 0

• Polar covalent- when the atoms exert an Polar covalent- when the atoms exert an unequal pull on the e-, bond is unequal pull on the e-, bond is – Overall charge on the more electronegative Overall charge on the more electronegative

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

Polar moleculesPolar molecules

• Unequal e- sharing Unequal e- sharing produces polar bondsproduces polar bonds

(–) (–)

(+) (+)

O

HH

Figure 2.9 Water Molecule

Non-covalent bonds

• Depend on attractive forces between e- of opposite charge– Weak bonds, easily broken and reformed

• Ionic

• Hydrogen

IonsIons

• Created when an atom gains or looses and electron

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

• Anion has neg chrge• Cation has positive charge

Ionic BondsIonic BondsAttractions between ions of opposite chargeAttractions between ions of opposite charge

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

Transfer of electron

NaSodium atom

ClChlorine atom Na+

Sodium ionCl–

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 with Na “donates” its e- to Cl, leaving Na with only 2 shells and Cl with a full outer shellonly 2 shells and Cl with a full outer shell

NaClNaCl

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

an electrical charge form either gaining or an electrical charge form either gaining or loosing electronsloosing electrons

Hydrogen BondsHydrogen Bonds

• Partial + charge allows shared attractions with – charged molecules

• + charged region always H

Hydrogen bond(+)

(+)

H

H(+)

(+)

(–)

(–)

(–)(–)

O

Figure 2.10

Water and H bonding

1. H2O is asymmetric

2. Each of the two covalent bonds are highly polarized

3. All three atoms are adept at forming H bonds

The 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)

– When heated, most thermal E is consumed in disrupting When heated, most thermal E is consumed in disrupting the bonds rather than contributing to molecular motionthe bonds rather than contributing to molecular motion

• DensityDensity– Ice vs. liquid waterIce vs. liquid water

Visual representation of a moleculeVisual representation of a molecule

Molecules can be represented in many ways

Table 2.8

Solvent

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

• Solution

• Aqueous solution

• Solvent– Dissolving agent

• Solute– Dissolved substance

Ph Scale

• Some molecules disassociate and release H+ or 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– React with free H+ of

OH ionsBasic 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

http://www.youtube.com/watch?http://www.youtube.com/watch?v=QqjcCvzWwwwv=QqjcCvzWwww