Biology 211 - Chapter 1: The Nature of Science

Science

Fact driven exercise in understanding the universe. DEMONSTRATED not asserted. Very dynamic, changig as new evidence becomes available

Scientific Theories

Are NOT simply “ideas.” Supported by LOTS OF EVIDENCE.

Examples: Heliocentric, plate tectonics, evolution, relativity

Hypotheses

• Testable

• Falsifiable

• Measurable

• Reproducible

• Objective

Controlled experiment

• Control

• Replicates

• Conclusion that is rejected of failed to reject

Observational experiment

An experiment you just observe and not mess with

The Earth is how many years old?

4.6 billion years old, and life began 3.8 to 3.5 billion years ago

What are the 5 big steps in early evolution of life:

• Cells

• Oxygen revolution

• Nucleated cells

• Multicellularity

• Cambrian Explosion

How many major extinctions have there been?

5, currently in 6th which is Anthropogenic, or caused by humans

What is the oldest fossil, and how old is it?

Prokaryotic blue-green algae; 3.5 billion years old

What are the limitations of fossil record:

• Habitat

• Taxonomic

• Tissue

• Temporal

• Abundance

How long is the extant biodiversity estimates?

• 10-100 million species

• 30 million extant species

What does phylogeny represent?

Hypothesized evolutionary relationships

Node on phylogenic tree

Most RECENT common ancestor, right after root. Where branches spkit indicate a common ancestor

Branch on phylogenic tree

Connects node to species. Evolutionary lineages.

Tip (leaves) on phylogenic tree

Current or end-point species or groups. These tips are the taxa or organisms being compared

Clade on phylogenic tree

A common ancestor and all of its descendants. It can be identified by cutting a single branch off the tree; everything that falls off is a clade.

The position of the nodes

Shows evolutionary relationships, not the order of the tips. The arrangement of the tips can vary without changing the tree’s meaning.

Monophyletic

Contains a common ancestor and all its descendants. The most meaningful grouping in evolutionary biology.

Polytomies

Nodes where more than two branches emerge, representing uncertainty in the relationships among those taxa

Homoplasy / Convergent Evolution

• Traits are SIMILAR

• NOT by COMMON ANCESTORS

Homology

• Traits are SIMILAR

• BY COMMON ANCESTORS

Monophyletic group

An evolutionary unit that includes an ancestral population and all of its descendants but no others

Synapomorphy

A shared, derived trait

Domains on taxonomy

Broadest level of classification

• groups organisms based on fundamental cellular and genetic differences

Example of a DOMAIN

Bacteria: Single celled prokaryotes without a nucleus

Archaea: Single celled prokaryotes with distinct biochemical and genetic characteristics

KINGDOMS in taxonomies

Next level after domain. Major groups of organisms

Traditional Kingdoms: Animals, Fungi, Plants, and Protists

PHYLUMS in taxonomies

Based on major structural and functional characters

EXAMPLE: Chordata (vertebraes) animal kingdom, Angiosperms (plants)

CLASS in taxonomies

Divides phylums into groups with more specific groups

EXAMPLE: mammalia, insects

ORDER in taxonomies

Smaller groups, more specific characteristics

EXAMPLE: carnivora, coleoptera

FAMILIES in taxonomies

Within an order that are closely related or shared characteristics

EXAMPLE: Felidae; cats, within the carnivora order

GENUS in taxonomies

Group within a family, share a common ancestor

EXAMPLE: Panthera (Lions, tigers, panthers)

SPECIES in taxonomies

MOST SPECIFIC level, Group of individual that can inetrbreed and produce fertile off spring

What are the differences between phylogenetic trees and taxonomies?

Phylogenetic trees focus on evolutionary relationships

Taxonomies focus on category and naming

Phylogenetic trees: DYNAMIC

Taxonomies: STATIC

Scientific names

Standardized and Universal

Common Names

Limited utility

Adaptive Radiation

Rapid evolution of a clade, happens a lot on islands

What do all species share?

A common ancestor

Prokaryotes are:

Ubiquitous, numerous, and diverse

Basic characteristics of PROKARYOTES

• unicellular

• ring of DNA

• plasmids

• reproduce by BINARY FISSION

Prokaryotes vs Eukaryotes

Prokaryotes: Ring chromosome shape, no membrane bound oragnelles, -karyote nucleus, before. BACTERIA AND ARCHAEA. not MULTICELLULAR.

Eukaryotes: Linear chromosome line, the third domain. ANIMALS, PLANTS, FUNGI, PROTISTS. DNA in a nuclear envelope. Organelles in membranes. Oftenly is MULTICELLULAR

Bacteria vs Archaea

Bacteria: Circular chromosome, Peptidoglycan. Primary phospholipids with fatty acids attached to a glycerol backbone. STRAIGHT chain structure, more fluid or rigid depending on saturation level. Ester bonds are LESS stable in extreme environments.

Archaea: Circular chromosome, Histone proteins. Ether-linked lipids, where isoprenoid characters are attached to a glycerol backbone. These lipids form monolayers or bilayers. BRANCHED chains, contribute to stability of the membrane in extreme environments. More rigid or less permeable. INCREASED stability and more resistant.

Metabolism abbreviations

• ENERGY: SUN (PHOTO)

• CARBON: CO2 (AUTO)

• ENERGY: ORGANIC MOLECULES (CHEMOORGANO)

• CARBON: ORGANIC MOLECULES (HETERO)

What are the 6 types of metabolism?

Photoautotrophs, Photoheterotrophs, Chemoautotrophs, Chemeheterotrophs, Mixotrophs, Anaerobic metabolism, Aerobic metabolism, Fermentation

Photoautotrophs

Use light as their energy source and carbon dioxide as their carbon source. They perform photosynthesis to convert light energy into chemical energy

Photohetereotrophs

Use light for energy but require organic compounds as their carbon source

Chemoautotrophs

Energy: Chemical reactions

Carbon source: Carbon dioxide

Chemoheterotrophs

Energy: Organic compounds

Carbon: Organic compounds

• metabolize a wide range of organic substances

Mixotrophs

Energy: Chemical sources

• Can switch between photoautotrophy and chemoheterotrophy depending on environmental conditions

Anaerobic metabolism

Metabolic processes that occur in the absence of OXYGEN.

Example: Fermentation is an anaerobic process where organic compounds are broken down to produce energy, and gases like carbon dioxide or ethanol are produced.

Aerobic metabolism

This involves metabolic processes that require oxygen.

• Cellular respiration in most Eukaryotes and Prokaryotes is AEROBIC, using oxygen to fully oxidize substrates like glucose to produce energy, carbon dioxide, and water

Fermentation

Form of anaerobic metabolism that allows cells to produce energy WITHOUT OXYGEN. Involving breakdown of sugars to produce energy along with byproducts like lactic acid or ethanol.

Eukaryotes can only perform what two types of metabolism?

• PHOTOAUTOTROPHS

• HETEROTROPHS

What were the earth’s first inhabitants?

Prokaryotes, 3.5 billion years

Obligate aerobes

Require oxygen to survive and grow

Obligate anaerobes

CANNOT tolerate OXYGEN and must live in environments that devoid of it.

What limits prokaryote reproduction?

• Waste

• Accumulation

• Competition

• Exhaustion of food resources

What do prokaryotes use for genetic diversity?

• Transformation

• Transduction

• Conjugation

Transformation

Ambient Uptake

• Dead cells release DNA into environment

• New DNA incorporated into living cell by recombination

Transduction

Viral transfer

• Bacteriophage infect host donor, which produces phages with both viral and bacterial DNA

• Bacteriophage injects donorDNA into recipient bacterial cell

Conjugation

Genetic material is transferred between two cells that are temporarily joined

What are the different prokaryote shapes?

Cocci

Bacilli

Spirilla

Cocci

Spherical or round shaped bacteria. Can be found as single cells, in pairs, chains, or clusters.

Examples: Streptococcus and Staphylococcus

Bacilli

Rod-shaped bacteria. They can occur as single rods or in chains.

Examples: Include Bacillus and Escherichia coli

Spirilla

Spiral or helical shaped bacteria. They can be rigid or flexible.

Examples: Helicobacter pylori and Treponema pallidum

What are the two cell wall types?

• Gram positive

• Gram negative

Gram positive

Thick peptidoglycan layer in their cell walls, which retains the crystal violet stain used in Gram staining, appearing PURPLE under the microscope.

Examples: Streptococcus and Staphylococcus

Gram negative

An additional protective layer called capsule, which is a gelatinous layer outside the cell wall. It can help with adherence to surfaces and protection against the host’s immune system

What are the different kinds of Flagella

• Monotrichous

• Lophotrichous

• Peritrichous

• Amphitrichous

Flagella

Many prokaryotes have flagella, which are long, whip like structures used for motility.

Monotrichous Flagella

A single flagellum at one end

Lophotrichous flagella

A cluster of flagella at one of both ends

Peritrichous flagella

Flagella distributed over the entire surface

Amphitrichous flagella

Flagella at both ends of the cell

Pili

Hair like appendages that can be involved in attachment to surfaces, conjugated, and sometimes motility

Fimbriae

Shorter and more numerous than pili and its function in adhesion to surfaces

Endospores

Some GRAM POSITIVE bacteria can form endospores, which are highly resistant structures that help the bacteria survive extreme conditions like heat, desiccation, and radiation

Nucleoid region

Prokaryotes lack a defined nucleus. INsteadm their genetic material is located in a region called nucleoid

Cytoplasmic membrane

A phospholipid bilayer with embedded proteins that controls the movement of substances into and out of the cell

Cell wall composition in bacteria can:

Lead to resistance to penicillin

Gram + cells

Thick peptidoglycan layers and are susceptible to penicillin

Gram - cells

Have thin peptidoglycan layers and are resistant to penicillin

What is a Microbiome?

The collection to ALL the microorganisms that live in a specific environment, along with their genetic material. Most often used to describe the community of microbes living in or out of a multicellular organism, such as animals, plants, or even in specific environment like soil or water.