Biology

Unit 1: Introduction, Chemistry, Molecules and Cells

Me!

• Henry Valz• Western Washington University• Studied: Fisheries, Marine Biology• SCUBA, hockey, soccer, M’s fan • Best way to contact: Email (gmail) or cell phone

You!

• Biol&160 student (hopefully)– MF: 12:30 to 2:40

• In Section E (Tuesday Lab) or F (Thursday Lab)– T/Th: 12:30 to 2:20

• Read labs before coming• Read book chapter before class• Have fun (or else!)

– Or else what?• Exactly

Your S.I.

• Allison Hood

• Ready to help explain, interpret, re-explain, and console.

My advice to you

• Form study groups– Groups of 3-5– Get emails/phone numbers– Schedule a study time

• Utilize the SI’s time and help• Utilize my office hours• Go to www.mybiology.com and join

VALZ160– Take the reading quizzes I’ve set up.

Syllabus

SCIENCE:Knowledge gained through careful observation

experimentation and reasoning.

• Explanatory

• Testable

• Reproducible

• Predictive

• Skeptical

Questions of Science

• Scientific discoveries create complex questions:– Discovery of the atom led to potential for source of

power combined with radioactive waste.

• Should scientists be free to pursue any research?

• Should government control scientific progress?• What is the progression of science?

– Research normally follows a logical progression.– Interest focuses on problems that impact humanity.

The Importance of Publication

• Results of research are submitted for publication.

• Publication involves peer review by other scientists.

• Publication and peer review establish the legitimacy of scientific progress.

What is a hypothesis?

• An educated guess (statement) that proposes a possible explanation to some phenomenon or event. – Not “I think the Earth revolves around the sun.”– Instead “The Earth revolves around the sun.”

• A useful hypothesis is a testable statement which may include a prediction.– Stated simply and concisely

• At the end of your experiment you will reject it, or not reject it. (Cannot be proven.)

• Observe

• (Do research)

• Hypothesize

• Experiment

• Analyze– Revise Hypothesis– Retest

• Report

ScientificMethod

•A Case Study from Ever yday Life– Deductive reasoning is used in testing hypotheses

as follows• If a hypothesis is correct, and we test it, then we

can expect a par ticular outcome

Observations

Question

Hypothesis # 1:Dead batteries

Hypothesis # 2:Burnt-out bulb

Prediction:Replacing batterieswill fix problem

Prediction:Replacing bulbwill fix problem

Test prediction Test prediction

Test falsifies hypothesis Test does not falsify hypothesis

Figure 1.8A

Which Side is Your Bread Buttered?

• Scientific hypothesis must be subject to experimental test.Hypothesis: The buttered side of bread always lands face down on the floor.

• Test by dropping bread on the floor many times.

Results and Theories

• Buttered side lands face down 90 % of the time.

• Formulate a theory: the height of the table determines what side the bread lands.

• Experiments test a theory but never prove it.

• The next experiments may falsify it.

Hypotheses•A scientist wants to know if snake coloration affects predation.

– Use a plastic snake with bright colors and drab colors to test hypothesis.

– H1: Bright colored snakes will have less predation than drabber colored snakes.

– H2: Bright colored snakes will have more predation…– H0: There will be no difference.

Conclusion?

• The data supports hypothesis #1.

• Artificial snakes have lower predation.

• Why?

Why would brightly colored snakes be less preyed upon?

Interpreting Data

•Predators in areas with a brightly colored and poisonous snake are less likely to attack the bright colored snake.•Therefore…

Biology

• The study and science of life.

Life’s levels of organization define the scope of biology

Life’s levels of organization define the scope of biology

• Biosphere

• Ecosystem

• Population

• Organism

• Organ System

• Organs

• Tissue

• Cell

• Organelle

• Molecule

• Atom I don’t expect you to memorize it.Just understand it.

Living organisms and their environments form interconnecting webs, cycles, and flows

• Nutrients cycle

• Energy flows

3 common features shared by all life forms (on Earth)

• Enclosed by a membrane that controls the internal environment

• DNA is the heritable material

• Perform metabolic processes

– Carbon, hydrogen, oxygen, and nitrogen • Make up the bulk of living matter

Table 2.1

Trace elements– “Micronutrients”

• Are essential to life, but occur in minute amounts

• Trace elements are common additives to food and water

• Dietary deficiencies in trace elements can cause various physiological conditions

Elements can combine to form compounds– Chemical elements

• Combine in fixed ratios to form compounds– Ex. 2 Hydrogen + 1 Oxygen = Water (H20)

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

Sodium Chlorine Sodium ChlorideFigure 2.3

•Subatomic Particles– An atom is made up of protons and neutrons

• Located in a central nucleus

– The nucleus is surrounded by electrons• Arranged in electron shells

Figure 2.4A

+

+

– –

+

–

2

2

2

Protons

Neutrons

Electrons

Massnumber = 4

+

+

2e–

Electroncloud

Nucleus

•Differences in Elements– Atoms of each element always have the same

number of protons and this is the elements’ atomic number

Figure 2.4B

+

–

6

6

6

Protons

Neutrons

Electrons

Massnumber = 12

+ +

6e–

Nucleus

Electroncloud

Periodic Table of the Elements

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

– Iron.– Manganese.– Copper.– Zinc.

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

•Isotopes– The number of neutrons in an atom may vary

• Variant forms of an element are called isotopes

• Some isotopes are radioactive– Give off lots of energy

Table 2.4

Science and Society:Irradiation

• A process of disinfestation, pasteurization or sterilization of food products.

• Bacterial spores and viruses not inactivated by irradiation

• Could still be contaminated by food-service workers after irradiation

Arguments and Opportunities

• Estimated 76 million US cases of foodborne disease

• More than 325,000 hospitalizations, 5000 deaths annually

• Concerns:– Production of 2-alkylcyclobutanones (not proven toxic

or carcinogenic), benzene and malandialdehyde– Irradiation destroys nutritional qualities (no evidence

in FDA review)– Irradiation is a “quick fix”

• Osterholm, M. and Norgan A, The Role of Irradiation in Food Safety, NEJM, 2004;350(18):1898-1901

Electron arrangement determines the chemical properties of an atom

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

– Atoms whose shells are not full (usually with 8 electrons) tend to interact with other atoms and gain, lose, or share electrons

– These interactions form chemical bonds

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

Ionic bonds are attractions between ions of opposite charge

– When atoms gain or lose electrons charged atoms called ions are created

– An electrical attraction between ions with opposite charges results in an ionic bond• Ex) Na+ and Cl- forms Na+Cl-

– Table Salt!Transfer of electron

NaSodium atom

ClChlorine atom Na+

Sodium ion

Cl–

Chloride ion

Sodium chloride (NaCl)

Na Cl ClNa

+ ––

–

Figure 2.7A

Concept Check

• The reactive properties or chemical behavior of an atom mostly depend on the number of ________________.

1. the electrons in each electron shell of the atom.

2. the neutrons found in the nucleus.

3. the filled electron shells.

4. the electrons in the outer electron shell of the atom.

Ionic bond illustration

Covalent bonds join atoms into molecules through electron sharing (illustration)

Covalent Bonds

• Covalent bonds occur through the sharing of the outside electrons.– Allows both shells to be full of electrons (8).

• A very strong bond compared to ionic bonding.

– Molecules can be represented in many ways

Table 2.8

Video!

• http://www.youtube.com/watch?v=QqjcCvzWwww&feature=related

In a polar covalent bond electrons are shared unequally between atoms, creating a polar molecule

(–) (–)

(+) (+)

O

HH

Figure 2.9

Polar bonding through Hydrogen

This attraction forms weak bonds called hydrogen bonds

Hydrogen bond(+)

(+)

H

H(+)

(+)

(–)

(–)

(–)(–)

O

Figure 2.10

Hydrogen bonding!

What is so important about hydrogen bonding?

• It allows water molecules to stick together (cohesion) – Form drops– Transported through tissues

• Moderates body temperature and climate– Takes lots of energy to break

hydrogen bonds so water absorbs a lot of energy before the temp increases

Why Water is Cool, part 2

• Water takes energy with it when it evaporates– Sweating!

• Ice is less dense than water so it floats allowing lakes not to freeze solid.– Good for fish!

• Water is the solvent of life dissolving any charged (ionic) or polar substances– “Universal Solvent”

• http://www.youtube.com/watch?v=cgiNk94XyaI

• http://www.youtube.com/watch?v=oNBzyM6TcK8&NR=1

The chemistry of life is sensitive to acidic and basic conditions

– A compound that releases H+ ions in solution is an acid

• And one that accepts H+ ions in solution is a base

– Acidity is measured on the pH scale

• From 0 (very acidic)• To 14 (most basic)• pH 7.0 is neutral

– The pH scale– Buffers resist

changes in pH

Basic solution

Oven cleaner

Acidic solution

Neutral solution

pH scale

0

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

13Figure 2.15

CHEMICAL REACTIONSChemical reactions change the composition of matter

In a chemical reaction reactants interact to form 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.

H H

HH

H H

Ethane Propane

HH

H H

H

H

H

H

H

H

Carbon skeletons vary in length.

H

H

H

H

H H

H H

H H

H H

H H

H H

H

H

H

H

H

H H H H

H

H

C

HH H

H H

H H

H

H

H

H H

H

H

H

H

H

H

H H

H

H

Butane Isobutane

Skeletons may be unbranched or branched.

1-Butene 2-Butene

Skeletons may have double bonds, which can vary in location.

C

C C

C

C

CH

CC

C

C

CC

Cyclohexane Benzene

Skeletons may be arranged in rings.

C C C C C

C C C C

C

C CC

CCC C CCCH H

• Organic compounds contain at least one carbon atom

• Compounds with only carbon and hydrogen are called hydrocarbons and are mostly nonpolar

• Isomers are molecules with the same number of each atom but a different structural arrangement

Organic Compounds

– Cells make most of their large molecules by joining smaller organic molecules into chains called polymers

– Cells link monomers to form polymers by a dehydration reaction• Mono = one

• Poly = many

H

OH H

OH

H OH

Unlinked monomer

Dehydration reaction

Longer polymer

Short polymer

OH H

H OH

Unlinked monomer

Dehydration reaction

Short polymer

H2O

Figure 3.3A

– Polymers are broken down to monomers by the reverse process, hydrolysis

H

H2O

OH

H OH

OH H

Hydrolysis

Figure 3.3B

Biomolecules(This slide is really important)

• Four types of bio(macro)molecules:– Nucleic Acids (P)

• DNA, RNA• Made of Nucleotides (M)

– Proteins (P)• Made of Amino Acids (M)

– Carbohydrates (P)• Made of Sugars (M)

– Lipids (not polymers)

Carbohydrates• Carbohydrates form

polymers also called saccharides.

• Monosaccharides contain one monomer (glucose).

• Disaccharides contain two monomers (sucrose).

• Oligosaccharides contain several monomers.

• Polysaccharides contain hundreds.

Cells link two single sugars to form disaccharides

– Monosaccharides can join to form disaccharides• Such as sucrose (table sugar) and maltose

(brewing sugar)

H

H H H

H H

H

H

H

H

H

H

H

H

H HH

H

H

H

OH OH

OHOHOH

HO

O O

O

OH

OH

OH

CH2OH CH2OH

CH2OH CH2OH

H2O

OH

HO

O

OH O

H

Glucose Glucose

Maltose

O

OH

– Starch and glycogen are polysaccharides that store sugar for later use

– Cellulose is a polysaccharide found in plant cell walls

Starch granules in potato tuber cells

Glycogen granules in muscle tissue

Cellulose fibrils in a plant cell wall

Glucose monomer

Cellulose molecules

STARCH

GLYCOGEN

CELLULOSE

O O

OOOOOO

O O O

O

OO

OO

OO

OOOO

OO

OOO

OO

OOOO O

OOOOOO

OOOOOO

O

OH

OH

Figure 3.7

Lipids

• Lipids are a large group of different polymers.

• Mostly “fats” or “fatty acids”

Fatty Acids

• Fatty acids are simple lipids.• Two parts:

– Long hydrocarbon chain.– Carboxylic acid functional group.

• Polar and nonpolar character in one molecule: which wins?

Polar

Not Polar

Hydrocarbon Chain Dominates

• Length of hydrocarbon chain means that nonpolar character dominates.– Arranges itself to be “happy” in water.

Saturated vs. unsaturated fats

• Saturated fatty acids contain no double bonds.

• Unsaturated fatty acids contain double bonds.

Double Bonds and Kinks

• Double bonds kink the structure.

• Kinks reduce packing density.

• Lower packing density decreases melting point.– Most oils are

unsaturated– Crisco is not

Trans Fats

• Naturally occurring unsaturated fats are cis: hydrocarbon chain is kinked.

• Trans fats are straight.

Hydrogenation

• Highly unsaturated fats can be very soft and are hydrogenated (saturated) to make them more butter-like.

• Addition of hydrogen to C=C double bond.• Some of the cis bonds are converted to

trans.

Buyer Beware

• Trans fats are straighter than cis fats and the product is stiffer.

• Trans fats pose a health risk – are not broken down readily.

Proteins

• Proteins are polymers of amino acids.• Amino acids contain:

– -NH2.– -COOH.– R groups (R varies from one amino acid to another).

• Link between amino acids in protein is a peptide bond.

20 Building Blocks in the Box

• There are 20 amino acid building blocks for proteins.• Chain forms by combination of amino acids.• The R groups from side chains.• Protein variety comes from sequence of R.

– Each amino acid has specific properties based on its structure

H

H

N

H

C

CH2

CH

CH3 CH3

C

O

OH

H

H

N C

H

CH2

OH

C

O

OH

H

H

N C

H

C

O

OHCH2

C

OH O

Leucine (Leu) Serine (Ser) Aspartic acid (Asp)

Hydrophobic Hydrophilic

Figure 3.12B

•Primary Structure– A protein’s primary structure

• Is the sequence of amino acids forming its polypeptide chains

Levels of Protein Structure

Primary structure GlyThr

Gly GluSer Lys

Cys

ProLeu Met

Val

Lys

ValLeu Asp Ala Val Arg Gly Ser

Pro

Ala

Ile

Asn ValAla

ValHis Val

Amino acids

PheArg

Figure 3.14A

•Secondary structure – A protein’s secondary

structure • Is the coiling or folding of

the chain, stabilized by hydrogen bonding (and other bonding, too)

•Tertiary Structure– A protein’s tertiary structure

• Is the overall three-dimensional shape of a polypeptide

Tertiary structure

Polypeptide(single subunitof transthyretin)

Figure 3.14C

•Quaternary Structure– A protein’s quaternary structure

• Results from the association of two or more polypeptide chains

Quaternary structure

Transthyretin, withfour identical

polypeptide subunits

Figure 3.14D

GrooveGroove

Figure 3.13BFigure 3.13A

A protein’s specific shape determines its function

– A protein consists of one or more polypeptide chains folded into a unique shape that determines the protein’s function

Protein Denaturation

Figure 2.18a

• Reversible unfolding of proteins due to drops in pH and/or increased temperature

Protein Denuaturation

Figure 2.18b

• Changing the folding causes the proteins not to work correctly– Why you get a fever– Why overheating you body is so bad.

NUCLEIC ACIDSNucleic acids are information-rich polymers of nucleotides

– Nucleic acids such as DNA and RNA serve as the blueprints for proteins and thus control the life of a cell

– The “genetic code” in chemistry

Sugar

OH

O P O

O

CH2

H

O

H H

OH H

H

N

N

HN

N H

HHN

Phosphategroup

Nitrogenousbase (A)

Structure of DNA

Figure 2.21a

•Nucleotide = N-containing base, a pentose (5 carbon) sugar, and a phosphate group•Five nitrogen base types – adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U)

Structure of DNA

Figure 2.21b

•Double-stranded helical molecule found in the nucleus of the cell•Replicates itself before the cell divides, ensuring genetic continuity•Provides instructions for protein synthesis

– DNA consists of two polynucleotides • Twisted around each other in a double helix

• Held together by hydrogen bonding

Figure 3.16C

There are five types of nitrogenous bases•DNA has A,T,G and C•RNA has A,U,G and C

• We’ll talk more about this later

C

TA

GC

C G

T A

C G

A T

A

G C

A T

A T

T A

Basepair

T

Ribonucleic Acid (RNA)

• Single-stranded molecule found in both the nucleus and the cytoplasm of a cell

• Uses the nitrogenous base uracil instead of thymine

• Three varieties of RNA: messenger RNA, transfer RNA, and ribosomal RNA