biology unit 1: introduction, chemistry, molecules and cells
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TRANSCRIPT
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
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.
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.
Interpreting Data
•Predators in areas with a brightly colored and poisonous snake are less likely to attack the bright colored snake.•Therefore…
• 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
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
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.
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.
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”
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
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