The Scientific Method

1. Collecting Observations

   • what is it?

   • what is happening?

   • why is that happening?

2. Forming a Hypothesis

   • a testable explanation

   • this is causing the problem

   • this will cure the disease

   • a good hypothesis includes: If, then, and because

3. Making predictions

   • this medicine will fix the problem

   • this chemical will make that change

4. Verifying Predictions

   • literature review

   • book research

   • periodicals

   • talk to others

5. Performing Controlled Experiments

   • Control group

   • experimental group

   • independent variable

   • dependent variable

   • constant

   • data gathering

6. Forming a theory

   • analyze the data

     • avg

     • SD

     • SEM

   • report conclusions

Microscopes

Vocab:

• Simple Microscope: one lens (magnifying glass)

• Magnification: apparent increase in objects size

• Resolution: increase in visible detail

• Compound Microscope: two lenses

• Ocular lens: nearest the eye of viewer

• Objective lens: nearest the specimen

• Total magnification: ocular magnification X objective magnification (e.g. 10 X 40 = 400)

Parts:

Types of Microscopes:

• Simple

  • one lens

• Compound

  • two lenses

• Stereomicroscope

  • two ocular lenses

• Phase Contrast

  • bends light in a unique way for the study of living cells

• Transmission Electron (TEM)

  • uses a beam of electrons instead of light

  • can magnify 1,000,000x

  • samples must be dead

  • views are flat, one dimensional

• Scanning Electron (SEM)

  • uses a beam of electrons instead of light

  • can magnify items +/- 100,000x

  • samples must be dead

  • views are 3D

History of Microscopes:

• First used in mid-1400’s

  • simple microscope (magnifying glasses)

• Compound microscopes came in mid-1500’s

  • uses 2 lenses together

  • made by Dutch Father/Son — Hans and Zacharias Janssen

    • Eyeglass makers

    • made first compound microscope in 1590

    • greater magnification, higher distortion

• Anton van Leeuwenhoek, 1670’s - 1680’s

  • Dutch merchant

  • Made over 400 lenses

  • magnification of 50-300x

  • credited with being first to produce drawings of microscoping organisms

• Electron microscopes 1935

  • uses a beam of electrons instead of light

  • can magnify things many times more than light microscope

Use of Microscopes:

1. Handle with care

   1. carry with two hands

   2. don’t force

   3. don’t bend cords

   4. cover when possible

   5. turn off when not in use

   6. loosely wrap cords

2. Use with care

   1. handle slides gently

   2. keep on low power when adding/removing slides

   3. find + focus on low power

   4. increase magnification to next level

   5. refocus

   6. increase magnification to highest level (IF APPROPRIATE)

   7. refocus only with fine focus

   8. return to low power before removing the slide

   9. lower stage to lowest setting

   10. don’t store with slides on stage

Tell The teacher if….

• The microscope doesn’t seem to be working properly

• if anything breaks

• if anything is stuck

Careful in the Classroom

• look out for cords

• watch where you walk: bookbags

• keep a clean/clear work area

Making Lab Drawings

• start with a circle: represents field of view

• title: centered below circle

• total magnification: centered below title

• use pencil

• start with outline and fill in details

Properties of Life

What characteristics do ALL living things share?

1. Made of one or more cells

2. displays organizations

3. grows and develops

4. Reproduces

5. Responds to stimuli

6. Requires energy

7. Maintains homeostasis

8. Adaptations evolve over time

Made of one or more cells:

• cells are the smallest thing considered alive

  • they are the basic units of life

• some organisms are 1 cell (unicellular)

• humans are made of 9-2 trillion cells (multicellular)

Displays organization:

• Levels of organization

  • Atoms - Molecules - Cells - Tissues - Organs - Organ Systems - Organisms

Grows and develops:

• growth = increase in mass or size

• develops = different abilities

Reproduces:

• produces offspring with similar traits (heredity)

Responds to stimuli:

• reacting to internal or external stimuli is called a response

• how does your skin respond to sunlight?

• how do your eyes respond to darkness?

• how does your brain respond to sunlight / darkness?

Requires energy:

• some organisms make their own food (autotrophic) (plants)

• some organisms eat their food (heterotrophic) (humans)

• all the energy and reactions combined are called metabolism

Maintains homeostasis:

• trying to keep the internal conditions stable

  • humans sweat and try to maintain 98.6⁰F or 37⁰C

  • turtles lay in the sun to try and warm up

Adaptations evolve over time:

• adaptations are inherited through reproduction

• adaptations changing over time is called evolution

• natural selection determines which adaptations help organisms survive

Abiogenesis V. Biogenesis

Aristotle: Abiogenesis (fish)

• 300 B.C.

• Greek

• Philosopher

• Hypothesis: Fish came from mud

  • He saw the fish and eggs

  • Didn’t see adult fish when babies hatched

Jean van Helmont: Abiogenesis (mice)

• 1600’s

• Belgian

• Physician

• Hypothesis: mice come from dirty shirt and grain in a dark corner

Francesco Redi: Biogenesis (flies)

• 1668

• Italian

• Physician

• Hypothesis: Flies come from eggs laid by flies

• Experiment: various meats in jars

  • lids on some jars

  • no lids on others

• Results: jars without lids have maggots

• Results: Disagreement. People said he denied “active principle” to the jars with lids

• Experiment 2: Jars with meats

  • some jars with screens, some without

• Results: jars without screens = maggots, jars with = no maggots

John Needham: Abiogenesis (micro)

• Mid 1700’s

• English

• Scientist

• Hypothesis: microscopic living things come from non-living material

• Experiment:

  • boiled meat broth in flasks

  • examined broth immediately

  • no organisms

  • loosely corked flasks

• Results: Days later, micro-organisms in flasks

• Conclusion: Sterile broth produced living things

Lazzaro Spallanzani: Biogenesis (micro)

• late 1700’s

• Italian

• Priest

• Refutes Needhams results based on faulty procedure (corks and flasks weren’t sterile)

• Experiment:

  • boiled seeds for 1 hour

  • sealed flask by melting neck closed

  • boiled flasks for hours

• Results: days later, broke neck and no living things in broth

• Results: people disagreed. He destroyed the “active principle” by overboiling

• Experiment 2:

  • boiled seeds 30 min-2 hrs

• Results: found that longer boiling grew more microorganisms

Louis Pasteur: Biogenesis (micro on dust)

• 1863

• French

• Chemist

• Hired by wine industry to reduce spoilage of grapes

• Hypothesis: microorganisms on dust

• Experiment 1:

  • boiled broth and put in different places where dust might be (orchard, woods, field)

• Results: all contained microorganisms

• Experiment 2:

  • put broth in flasks

  • melted flask necks into S-shape

  • boiled flasks

  • examined flasks: no organisms, even days later

  • poured broth into bend of neck

  • microorganisms grew within a few days

• Results: Microorganisms are on dust

Classification

Vocab:

• Binomial nomenclature:

  • 2 part name (Genus, species)

• 8 taxonomic categories

  • Domain - Species

• Systematics:

  • study of the evolution of biological diversity

Why do we classify organisms?

• biologists groups organisms to represent similarities and proposed relationships

• classifications systems change with expanding knowledge about new and well-known organisms

Systematics: Evolutionary Classification of Organisms

• Systematics is the study of the evolution of biological diversity, and combines data from the following areas:

  • fossil records

  • comparative homologies

  • cladistics

  • comparative sequencing of DNA/RNA among organisms

  • Molecular clocks

Kingdoms and Domains:

Kingdom Characteristics

Hierarchical Classification:

• Domain Does

• Kingdom King

• Phylum Philip

• Class Come

• Order Over

• Family For

• Genus Green

• Species Soup

Binomial Nomenclature:

• 2 name system

  • Genus, species

  • E.g.:

    • Homo sapien

    • Canis domesticus

    • Felis domesticus

• invented by Carolus von Linnaeus

  • Genus

    • Noun, capitalized, underlined if handwritten, italicized if typed

  • species

    • Descriptive, lower case, underlined if handwritten, italicized if typed

Cladogram

• Branching diagram showing proposed classification (phylogeny) or evolutionary history

• Groups on a cladogram are called “clades”

  • a clade is one branch of the cladogram

• “Outgroup” = first, most ancestral characters

• Characters = traits or characteristics

  • Ancestral Characters: found in all descendants

  • Derived Characters: not found in common ancestor

  

Constructing a Cladogram

1. Pick Organisms for your cladogram

2. Pick one ancestral and one derived characteristic to designate the outgroup

3. Pick derived characteristics for the ingroup 1

4. Pick derived characteristics for the ingroup 2

5. Pick derived characteristics for the ingroup 3+

6. Place and draw the outgroup

7. Place and draw the ingroup (Pt 1)

8. Place and draw the ingroup (Pt 2)

9. Place and draw the ingroup (Pt 3)

10. Check your cladogram for errors

Taxonomic Diagrams:

Sometimes, biologists group organisms into categories that represent common ancestries, not just physical similarities. Early naturalists used physical characteristics and later, fossil data, attempting to represent evolutionary relationships among organisms. Today, modern classification systems use fossil data, physical characteristics, and DNA/RNA information to draw increasingly more accurate branching diagrams.

• Phylogenetic trees, or phylogenies represent hypothesized evolutionary relationships among organisms and may include extinct as well as modern species.

• Cladograms are based only on characteristics observable in existing species. The branching patterns in a cladogram are defined by the presence of unique, evolving innovations (derived characteristics) shared by all members of the group.

Dichotomous Keys Identify Organisms

• Dichotomous keys contain pairs of contrasting descriptions

• After each description, the key directs the user to another pair of descriptions or identifies the organism

  • E.g.:

    • 1. a) is the leaf simple? Go to 2

    • 1. b) is the leaf compound? Got to 3

      • 2. a) are the margins of the leaf jagged? Go to 4

      • 2. b) are the margins of the leaf smooth? Go to 5

Evolution

Darwin and the History of Evolution

Competing Ideas About Evolution

• Jean-Baptiste LaMarck

  • French Naturalist, 1744-1829

  • Theory:

    • Parents changes passed to offspring

    • Ex: Giraffes

    • Won’t work because then tattoos, built up muscle, scars, etc., would transfer to babies

• Charles Darwin

  • English Naturalist, 1809-1882

  • 5 year trip (1831-1836) on HMS Beagle

    • collecting samples, investigating biology

  • Theory:

    • Natural Selection (derived around 1857)

      • Strongest survive

  • Wrote book: On the Origin of the Species

Principles of Natural Selection

• Variation: Individuals differ

• Overproduction: populations produce more offspring than can survive

• Heritability: variations are inherited from parents

• Reproductive Advantage: some variations are better than others

Evidence of Evolution

Fossils:

• Record of species that lived long ago

• Derived traits:

  • Newly evolved

  • Ex: Feathers

• Ancestral traits:

  • older, more primitive

  • Ex: Teeth, tails

Comparative Anatomy:

• Homologous Structures:

  • Anatomically similar

  • Inherited from a common ancestor

  • ex: vertebrae, forelimbs

• Vestigial Structures:

  • Reduced form of functional structures

  • ex: snake pelvis, human appendix

• Analogous Structures:

  • Anatomically similar

  • NOT inherited from a common ancestor

  • ex: wings of insects & birds

Comparative Embryology:

Early, pre-birth developmental stages

Comparative Biochemistry:

• Similar chemicals in organisms

• ex: cytochrome C (Needed for respiration)

• ex: DNA/RNA

Geographic Distribution:

• Where plants and animals are found

• closer geographically usually = closer in similarity

Adaptation: Trait shaped by Natural Selection

• Fitness:

  • Measure of relative contribution an individual trait makes to the next generation

• Camouflage:

  • Blend in with the environment

• Mimicry:

  • Resemble another species

  • ex: monarch (poisonous) & viceroy (harmless) butterflies

• Antimicrobial resistance:

  • Bacteria immune to effects of antibiotics

Shaping Evolutionary Theory:

Mechanisms of Evolution:

• Hardy-Weinberg

  • Hardy-Weinberg Principle

    • Populations stay the same unless forced to change

    • Hardy-Weinberg Conditions:

      • 1.  Large Population

      • 2.  No immigration / Emigration

      • 3.  Random mating

      • 4.  No mutations

      • 5.  No natural selection

  • Hardy-Weinberg Equation

    • p² + 2pq + q² = 1

    • Allele + genotype frequencies stay the same unless forced to change

• Genetic Drift

  • Genetic Drift:

    • change in allele frequency due to chance

  • Founder effect:

    • Small, separated populations all have characteristics of “founders”

  • Bottleneck:

    • Population declines to small number + rebounds

    • Gene pool of rebound population is similar to the small population

    • Ex. Cheetahs in Africa

• Gene Flow

  • Genes coming into or leaving a population

• Nonrandom Mating

  • When mates are chosen

  • Based on some characteristic

    • Ex. Galapagos iguana’s: females chose bigger males

• Mutation

  • Change in genetic material

• Natural Selection

  • Selection of individuals that are best adapted for survival

  • Types of Natural Selection:

    • Stabilizing: selection against both extremes (pic 2)

    • Directional: selection against one extreme (pic 1)

    • Disruptive: selection against the mean (pic 3)

    • Sexual: when males + females differ greatly in appearance

• Reproductive Isolation

  • Populations that cannot breed and produce fertile offspring

  • Prezygotic isolation:

    • Before fertilization begins

    • Ex. Meadowlark songs, firefly times

  • Postzygotic isolation:

    • After fertilization begins

    • Ex. Lions + tigers

• Speciation

  • Creation of a new species

  • Allopatric speciation

    • Physical barrier

    • Ex. Mountains, rivers

  • Sympatric speciation

    • No physical barrier

    • Ex. Apple maggot flies: depends on fruit eaten

Patterns of Evolution:

• Adaptive Radiation/Divergent Evolution

  • One species gives rise to many others

  • Ex: Mammals, cichlid fish

• Coevolution

  • Evolution of one species causes evolution of another species because of close relationship

• Convergent Evolution

  • Unrelated species evolve similar traits because of similar ecology / climates in different parts of the world

  • Ex. Mara and rabbit

• Rate of Speciation

  • Gradualism:

    • Evolution happens in small, gradual steps

    • Ex. Stripes of tiger

  • Punctuated equilibrium:

    • Abrupt, rapid spurts of change

    • Ex. snails

Biochemistry

Inorganic: Carbon not present

• Water:  H₂O

  • Polar

    • positive / negative charged ends

    • easily bonds to many things

  • Solvent

    • because of polar ends

    • many things dissolve in it

  • Heat Capacity

    • absorbs + holds great amounts of energy before changing phases

    • Heat of Vaporization: 540 cal/g

    • Heat of Fusion:  80 cal/g

• Acids

  • H+ ions (Hydronium ions)

  • pH of 0-7

• Bases

  • OH- ions (Hydroxide ions)

  • pH of 7-14

• pH Scale

  • 0 ----acids----- 7 -----bases-----14

  • logarithmic scale: each number is 10x greater

    • ex: 4 is 10x weaker than 3

    • ex: 5 is 100x weaker than 3

    • ex: 6 is 1000x weaker than 3

  • 7 is neutral: H+ ions = OH- ions

  • bases dissolve animal matter

    • ex: DRANO

Organics: Compounds with Carbon

• Reactions:

  • Condensation

    • joins molecules together

    • releases water

    • ex: making muscles

  • Hydrolysis

    • breaks molecules apart

    • requires water

    • ex: digestion

• Carbohydrates:

  • Made of C, H, O

  • Used for short term energy storage

    • Simple sugars: monosaccharides

      • ex:

        • glucose — everything dissolves down to glucose

        • fructose

        • galactose

      • C⁶H¹²O⁶

      • Benedict’s test:

        • benedict’s solution (blue)

        • heat

        • reacts with glucose

        • strong positive = orange

        • weak positive = green

    • Disaccharides

      • made from condensation of 2 monosaccharides

        • maltose

        • lactose

        • sucrose

    • Polysaccharides

      • long chain sugars

      • starch

        • storage in plants

        • iodine test (brown)

          • iodine reacts = turns blue/black

      • Glycogen

        • storage in animals

      • Cellulose

        • structures of plants

• Lipids

  • made of C, H, O

  • more C&H than O

  • COmmonly called fats, oils, and waxes

  • insoluble in water

  • used for long term energy storage

  • Used to make cell membranes

  • Made of glycerol and 3 fatty acids

    • joined by a condensation reaction

    • fatty acids contain a carboxyl group

      • carboxyl group = COOH

  • Sudan III Test:

    • attaches to tipids and dyes them pink

Glycerol:

Fatty Acid:

• Proteins:

  • Made of C, H, O, N, and other elements

  • Used to make structures

    • blood plasma

    • enzymes

    • muscle

    • wool

    • fingernails

  • Made of Amino Acids:

  • NH² = amino group

  • COOH = acid (carboxyl group)

  

  • Joined together (condensation reaction) to form:

    • dipeptides = 2 amino acids

    • polypeptides = 3+ amino acids

    • there are + / - amino acids

      • essential amino acids = + / - 10 our bodies can’t make themselves

      • must be acquired via diet

  • fibrous proteins

    • long, stretched out

    • ex: muscles, spider webs, fingernails

  • Globular proteins

    • twisted and folded

    • ex: hemoglobin

  • Conformation:

    • 3D shape of a protein

  • Denature:

    • break down of 3D shape

      • due to high temps and sever pH’s

  • Enzymes:

    • catalysts: speed up chemical reactions

    • protein catalysts

    • coenzymes: help bind to substrate

    • vitamins: act as coenzymes

    • inhibitors: slow enzyme activity (poison)

    • advantages of enzymes:

      • lower activation energy: reactions happen at normal body temperature

      • speed up reactions

      • not used during reactions

  • Biuret test:

    • used to detect proteins

    • NaOH (sodium hydroxide) (clear color)

    • CuSO⁴ (copper sulfate)(light blue)

    • when mixed with protein = blue/purple color

• Nucleic Acids:

  • DNA: Deoxyribonucleic acid

    • records instructions for cell activity

    • passes into the next generation

    • ex: tastebuds

      • proteins shaped by DNA—result: different people have different DNA, so they like different foods

  • RNA: ribonucleic acid

    • reads DNA

    • carries out instructions

SUMMARY:

Genetics

DNA

• DNA:

  • The nucleus of your cells contain chromosomes

  • Chromosomes have genes

  • Genes determine what you look like

  • Chromosomes & genes are made of DNA

  • DNA = deoxyribonucleic acid

• Structure of DNA:

  • Sides

    • Phosphate group

    • Sugar (deoxyribose)

  • Rungs (4 nitrogenous bases)

    • Adenine

    • Guanine

    • Thymine

    • Cytosine

  • Nucleotide = nitrogen base + sugar + phosphate group

  • Double helix

• Nucleotides:

  • Adenine matches with Thymine

  • Guanine matches with cytosine

• Replication: DNA copies itself

  • Our bodies produce 2 trillion cells per/day; 25 million cells per/sec. Each cell needs a copy of the DNA.

    1. Original strand of DNA unzips – bonds between nitrogen bases break

    2. Proper nucleotides match to each base

    3. Two identical DNA strands result

    4. Replication Video Clip
       

• Transcription: mRNA is copied from DNA

  • RNA = Ribonucleic Acid

    • uses sugar, ribose (not deoxyribose)

    • uracil replaces thymine as nitrogen base 

      (and matches with adenine)

    • RNA is single stranded

    • Types of RNA:

      • mRNA = messenger RNA

      • tRNA = transfer RNA

      • rRNA = ribosomal RNA

• Transcription Process:

  1. DNA unzips

  2. mRNA nucleotides match up to DNA nucleotides

     • Uracil-Adenine

     • Guanine-Cytosine

  3. Single strand mRNA forms

  4. DNA rezips

  5. Transcription Video Clip

• Translation: Making Proteins from the mRNA code

  1. Ribosomes  attach to mRNA

  - sequence read 3 nucleotides at a time (codon = 3 nucleotides)

  2. tRNA brings amino acids to ribosome by using anticodon

  (anticodon = complementary 3 nucleotides)

  3. Amino acids are linked in order of codons

  4.  Amino acids joined by peptide bonds

  5. Proteins are formed

  6. Translation Video Clip

Change In Structure = Change in Function

Changes in DNA = Changes in proteins

• Central Dogma of Biology:

  • DNA leads to RNA leads to Protein

• Natural Consequences of change in Structure/Function

  • Variety among individuals

  • Gene types of changes: Meiosis: Crossing over

  • Chromosomal Types of Changes:

    • Nondisjunction:

      • Trisomy 21:

        • Down syndrome

        • Occurs in all racial groups with same frequency

      • Trisomy 23:

        • XXY - Klinefelter’s Syndrome

        • XXX - Triple-X syndrome / super female syndrome

        • No negatives and most female olympians have this

      • Trisomy 18:

        • Edwards Syndrome

        • 92% die within first year

        • 10% live to age 10

      • Trisomy 13:

        • Patau’s Syndrome

        • 80% die within first year

        • 13% live to age 10

      • Most trisomies are lethal

    • Translocation:

      • Part of the chromosome moves to another location

    • Deletion:

      • Part of chromosome is deleted

        • Cri du chat:

          • part of chromosome 5 is deleted

        • Chronic Granulocytic Leukemia:

          • Part of chromosome 21 is deleted

      • Ex: go to the store becomes go to the

Transcription and Translation