Honors Bio Notes

Scientific Method

Scientific Method

A systematic approach used by scientists to investigate and understand the natural world. It involves collecting observations, forming hypotheses, making predictions, performing controlled experiments, and forming theories based on the results.

Scientific Method step 1

Collection observations:

The process of gathering information and data about a particular phenomenon or event. It involves asking questions like "what is it?" and "what is happening?" to understand the observations made.

Scientific Method step 2

Forming a hypothesis:

A testable explanation or prediction for a phenomenon or event based on prior knowledge or observations. A good one includes the "if, then, and because" format.

Scientific Method step 3

Making predictions:

The act of forecasting or estimating the outcome or result of a particular experiment or event. It involves using the hypothesis to determine the expected outcomes.

Scientific Method step 4

Verifying predictions:

The process of confirming or validating the predictions made based on the hypothesis. It can involve conducting a literature review, researching books and periodicals, and talking to others in the field.

Scientific Method step 5

Performing Controlled Experiments:

An experiment designed to test the effects of one variable (independent variable) on another variable (dependent variable) while keeping all other factors constant. It involves using control and experimental groups, collecting data, and analyzing the results.

Scientific Method step 6

Forming a Theory:

A well-substantiated explanation or set of principles that explain a wide range of phenomena or events. It is based on extensive analysis of data and observations.

Simple Microscope

A microscope that consists of a single lens, such as a magnifying glass, used to magnify the size of an object.

Magnification

The apparent increase in the size of an object when viewed through a microscope or magnifying lens.

Resolution

The ability of a microscope to distinguish between two closely spaced objects or to reveal fine details of an object.

Compound Microscope

A microscope that uses two lenses, an ocular lens (nearest the eye) and an objective lens (nearest the specimen), to magnify the size of an object.

Ocular Lens

The lens nearest to the eye of the viewer in a compound microscope.

Objective Lens

The lens nearest to the specimen in a compound microscope.

Total Magnification

The overall magnification is achieved by multiplying the magnification of the ocular lens by the magnification of the objective lens. (ocular lens mag. x objective mag)

Binomial Nomenclature

A two-part naming system (Genus, species) used to scientifically name and classify organisms.

Systematics

The study of the evolution of biological diversity, which involves analyzing data from fossil records, comparative homologies, cladistics, comparative sequencing of DNA/RNA, and molecular clocks.

Kingdoms

Bacteria, Archaea, Protista, Plantae, Fungi, and Animalia

Cladogram

• A branching diagram that represents the proposed classification (phylogeny) or evolutionary history of organisms based on shared derived characteristics.

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

Dichotomous Keys

Tools used to identify organisms by presenting pairs of contrasting descriptions and directing the user to another pair or identifying the organism based on the responses.

Characteristics of life 1

Made of one or more cells:

Living things are composed of cells, which are organized into tissues, organs, and systems. Some organisms or unicellular, and some are multicellular

Characteristic of life 8

Adaptations evolve over time:

• adaptations are inherited through reproduction

• adaptations changing over time is called evolution

• natural selection determines which adaptations help organisms survive

Characteristic of life 6

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

Characteristic of life 7

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

Characteristic of life 5

Responds to Stimuli:

Organisms can detect and respond to changes in their environment, ensuring their survival.

• 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?

Characteristic of life 3

Grows and Develops:

Living things undergo growth, increasing in size and complexity, and develop into mature forms.

• growth = increase in mass or size

• develops = different abilities

Characteristic of life 4

Reproduces:

Living organisms have the ability to produce offspring, ensuring the continuation of their species.

• produces offspring with similar traits (heredity)

compound microscopes

• Used for magnifying small, transparent specimens

• Consists of two or more lenses to enhance image quality

• Provides high-resolution, three-dimensional images

• Used in various scientific fields, such as biology and medicine

• Allows for observation of cellular structures and organisms

stereomicroscopes

A type of microscope that provides a three-dimensional view of small objects. It uses two separate optical paths to capture and combine images, resulting in a magnified and detailed view. Uses two ocular lenses.

phase contrast microscopes

• Optical instruments used to enhance contrast in transparent specimens

• Utilize a phase plate to convert phase differences into variations in brightness

• bends light in a unique way for studying live cells and observing cellular structures

• Enables visualization of transparent samples without staining or killing cells

  • Widely used in biology, medicine, and research for non-invasive imaging

Transmission Electron Microscopes (TEM)

This microscope revolutionized our understanding of the microscopic world by using a beam of electrons instead of light to magnify and visualize small samples. It operates on the principles of quantum mechanics and provides high-resolution images with magnifications up to 1 million times. Electron microscopy has been instrumental in various scientific disciplines, uncovering hidden details and intricate structures. The process involves emitting a beam of electrons from a cathode, accelerating them towards the sample, and detecting the signals they create to generate images. Different techniques, such as scanning electron microscopy (SEM) and transmission electron microscopy (TEM), enhance the imaging capabilities. Electron microscopy is not only used in scientific research but also in industries like quality control and forensic investigations. Advancements in technology continue to improve electron microscopy. However, all samples must be dead and the views are flat and one dimensional

Scanning Electron Microscopes (SEM)

Microscope that uses a beam of electrons to create high-resolution images of a sample's surface. Provides detailed information about the sample's topography, composition, and morphology (3D view). Offers higher magnification and resolution compared to optical microscopes. Useful in various fields like materials science, biology, and nanotechnology. However, samples must be dead, but it can magnify items +/- 100,000x.

Characteristic of life 2

• Levels of organization

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

Domain Bacteria

• One of the three domains of life

• Prokaryotic organisms without a nucleus

• Found in diverse habitats, including soil, water, and human body

• Play vital roles in nutrient cycling and decomposition

• Some may cause diseases, while others are beneficial for human health and industry

• prokaryotes

• cell walls with peptidoglycan

• unicellular

• auto or heterotrophic

Domain Archaea

• EX: Methanopyrus

• Prokaryotes

• Cell walls without peptidoglycan

• unicellular

• auto or heterotrophic

• One of the 3 domains of life

Kingdom Bacteria

• One of the 6 kingdoms of life

• Prokaryotic organisms without a nucleus

• Found in diverse habitats, including soil, water, and human body

• Play vital roles in nutrient cycling and decomposition

• Some may cause diseases, while others are beneficial for human health and industry

• prokaryotes

• cell walls with peptidoglycan

• unicellular

• auto or heterotrophic

Kingdom Archaea

• One of the 6 kingdoms of life

• EX: Methan opyrum

• Prokaryote

• Cell walls without peptidoglycan

• unicellular

• auto or heterotrophic

Domain Eukarya

• One of the 3 domains of life

• Contains 4 kingdoms of life

• Eukaryotes

• Contains multicellular and unicellular organisms

• Autotrophic and heterotrophic

Kingdom Protista

• One of the 6 kingdoms of life

• EX: Paramecium

• Eukaryotes

• Cell walls have some cellulose

• Uni and multicellular organisms

• auto or heterotrophic

Kingdom Fungi

• one of the 6 kingdoms of life

• EX: Mushroom

• Eukaryote

• Cell walls with chitin

• most multicellular

• Heterotrophs

Kingdom Plantae

• One of the six kingdoms of life

• EX: Moss

• Eukaryote

• cell walls with cellulose

• Multicellular

• Autotrophs

Kingdom Animalia

• one of the six kingdoms of life

• EX: Earthworm

• Eukaryote

• no cell walls

• Multicellular

• Heterotrophs

Heterotrophs

• an organism deriving its nutritional requirements from complex organic substances.

• an organism that eats other plants or animals for energy and nutrients. The term stems from the Greek words hetero for “other” and trophe for “nourishment.”

Autotrophs

• an organism that is able to form nutritional organic substances from simple inorganic substances such as carbon dioxide.

• an organism that can produce its own food using light, water, carbon dioxide, or other chemicals. Because autotrophs produce their own food, they are sometimes called producers.

Prokaryote

• a microscopic single-celled organism that has neither a distinct nucleus with a membrane nor other specialized organelles. This category includes the bacteria and cyanobacteria.

• organisms whose cells lack a nucleus and other organelles. These organisms are divided into two distinct groups: the bacteria and the archaea, which scientists believe have unique evolutionary lineages.

• cells without a nucleus

Eukaryote

• Cells with a nucleus

• an organism consisting of a cell or cells in which the genetic material is DNA in the form of chromosomes contained within a distinct nucleus. This category includes all living organisms other than the eubacteria and archaebacteria.

• an organism whose cells contain a nucleus within a membrane. The genetic material and information of a eukaryote is contained within this nucleus. These organisms vary from single-celled organisms to complex multicellular animals and plants.

Hierarchical Classification

1. Domain

2. Kingdom

3. Phylum

4. Class

5. Order

6. Family

7. Genus

8. Species

Does King Philip Come Over For Green Soup

1. Domain

2. Kingdom

3. Phylum

4. Class

5. Order

6. Family

7. Genus

8. Species

Clade

• groups on a cladogram

• 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 ancestors

Phylogenetic trees (Phylogenies)

Represents hypothesized evolutionary relationships among organisms and may include extinct as well as modern species

Jean Baptiste LaMarck 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 Theory

• Theory:

  • Natural Selection (derived around 1857)

    • Strongest survive

Principles of Natural Selection

Variation, overproduction, heritability, and reproductive advantage

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

Fossils

record of species that lived long ago

Derived traits

• Newly evolved

  • Ex: Feathers

Ancestral traits

• Newly evolved

  • Ex: Feathers

Comparative Anatomy

comparing the anatomy of different organisms

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

a 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

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

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

Stabilizing Natural selection

selection against both extremes

Directional Natural Selection

selection against one extreme

Disruptive Natural Selection

selection against the mean

Sexual Natural Selection

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

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

Rate of Speciation: Punctuated equilibrium

• Abrupt, rapid spurts of change

  • Ex. snails