Biology Chapters 12 and 15

Chapter 12.1, 12.3 - 12.5

The Origin and Diversification of Life on Earth and Species

How was the Earth formulated?

Evidence supports that Earth formed about 4.5 billion years ago from clouds of dust and gases. Over the next several hundred million years, Earth gradually cooled, forming a solid crust and oceans

What were the earliest life forms?

The earliest life forms appeared not long after these first rocks formed, with fossilized bacteria-like cells found in rocks that are about 3.5 billion years old

What characteristics distinguish life from non-life?

• The ability to conduct metabolic activity (the use and transformation of energy to perform work)

• The ability to carry information that can be replicated and passed on to offspring

How did life arise?

Many scientists believe that life on Earth originated in several distinct phases (3 phases)

Phase 1

The formation of small molecules containing carbon, hydrogen, and nitrogen

What is the Urey-Miller Experiment

In 1953, Stanley Miller and Harold Urey simulated early Earth’s conditions- they added water (source of oxygen and hydrogen) and gases (H2, CH4, NH3) to a flask and subjected the mixture to electric sparks to simulate lightning. They then cooled the contents to precipitate any compounds formed.

What were the results of the Urey-Miller Experiment?

Many organic compounds were formed, including at least five different amino acids, the building blocks of proteins. This was the first demonstration that complex organic molecules could have arisen in Earth’s early environment.

Phase 2

The formation of self-replicating, information-containing molecules

What do researchers believe was necessary?

A molecule with catalytic properties

What is ribonucleic acid (RNA)?

It can both carry information and catalyze the reactions necessary for replication. It is what researchers speculate could have been the single self-replicating system and precursor to cellular life

Phase 3

The development of a membrane, enabling metabolism, and creating the first cells.

What does an organism need?

It needs a membrane, which acts as a semipermeable barrier separating the inside of a cell from its environment.

What do phospholipids do in water or salt solutions?

They spontaneously form membranes, enabling metabolic processes by maintaining different chemical concentrations inside and outside the cell. These cell-like units can form small spheres that resemble living cells and may even “sprout” new buds.

Combining what two things could make life possible?

Combining a self-replicating molecule with metabolic chemicals within a membrane could make life possible.

What is a species?

They are the basic units of biodiversity that we use to label different kinds of organisms.

Biological species concept:

Species are natural populations of organisms that:

• Interbreed with each other or could possibly interbreed with other organisms of the same species, and

• They cannot interbreed with organisms outside their own group due to reproductive isolation, effectively preventing gene exchange between them

What does the biological species concept focus on?

It focuses on reproductive isolation rather than physical appearance

What are the two barriers to prevent individuals of different species from reproducing?

• Prezygotic barriers (barriers that occur before the formation of the zygote, a fertilized egg)

• Postzygotic barriers (barriers that occur after the formation of the zygote)

What are prezygotic barriers?

• Physical Incompatibility: some species, like pigs and dogs, cannot physically mate.

• Biochemical Incompatibility: The sperm of one species may not fertilize the egg of another

• Habitat Isolation: different species may occupy the same area but different habitats, preventing interaction (ladybugs on different plants)

• Behavioral Differences: diverse mating rituals or breeding times can also prevent mating between species

What are postzygotic barriers?

They affect hybrid offspring (the product of two different species), often do not survive long or are infertile (e.g. mules) survive but are sterile

What is the goal of Systematics?

To categorize organisms based on their evolutionary history

Origin of naming a species

Created by Carolus Linnaeus in the 1700s

What is the naming system?

Species names consist of two parts: a capitalized genus and a lowercase specific epithet, both italicized

example: Homo sapiens for humans

What is the hierarchical structure of naming a species?

Linnaean taxonomy is structured hierarchically from broader to narrower categories: each species falls under a genus, genera under families, families under orders, orders under classes, classes under phyla, and phyla under kingdoms

What are the modern adaptations of naming a species?

Expanded from three to multiple kingdoms, including fungi and protists

All of the kingdoms are now classified under three domains: bacteria, Archaea, and Eukarya

Species are not always easily defined

Due to biological and morphological species concepts

Biological Species Concept:

Useful for most plants and animals

Not suitable for: asexual species (bacteria), extinct organisms, species in transition, ring and hybrid species

Morphological Species Concept:

Based on physical features (body size & shape)

Doesn’t require knowledge of interbreeding

Easier to use through observation, despite being subjective

What is speciation?

It is the process when one species splits into two distinct species

Speciation takes place in two phases:

Reproductive Isolation and

Genetic Divergence

What is Reproductive Isolation?

Two populations are separated from one another- this can occur with:

• Geographic isolation (allopatric speciation)

• Without geographic isolation (sympatric speciation)

What is genetic divergence?

Two populations evolving separately accumulate physical and behavioral differences over time, preventing them from interbreeding

What is Allopatric Speciation?

Initial population: a single species of squirrel:

• Phase 1: Geographic isolation: a river forms, separating the population into two, and creating a barrier that the squirrels cannot cross

• Phase 2: Genetic divergence: each isolated population adapts to its unique environment, including different predators and food sources

• Physical and behavioral differences accumulate over time

Result: the two populations evolve into distinct species that cannot interbreed, even if reunited

What is Sympatric Speciation?

It is common in plants, rare in animals, and happens in two ways:

• Chromosome duplication within a species prevents interbreeding with the original population

• Different but closely related species interbreed, forming a hybrid

This speciation occurs without geographic isolation.

Chapters 12.6 - 12.7, 12.9 - 12.12

Macroevolution and classifying biodiversity

What is macroevolution?

It is evolution above the species level. Evolutionary change is driven by simple but impactful processes, and macroevolution results from numerous minor changes accumulating over a long period.

Over time, significant evolutionary transformations occur, such as dinosaurs evolving into birds, land mammals into whales, and a single species into over 230,000 types of flowering plants. These broad transformations are called macroevolution, defined as extensive evolutionary developments that lead to the formation of new organism groups.

Microevolution and some examples:

Microevolution is the slight change in allele frequencies over one or a few generations. ex. the increase in milk production in cows during the first half of the 20th century or the gradual change in the average beak size of birds with changing patterns of rainfall

Macroevolution and some examples:

Macroevolution is the accumulated effect of microevolution over time, including the diversification of species. ex. the diversification from a single species of flowering plant into more than 230,000 species or the divergence of the eastern and western meadowlark birds into two different species

What does macroevolution include that microevolution does not?

Macroevolution includes speciation and large-scale changes, while microevolution does not lead directly to new species but involves smaller, incremental changes

Describe the pace of evolution

The pace of evolution is not constant. Evolution, whether at the micro or macro level, is one thing only: a change in allele frequencies in a population. Therefore, the pace of evolution varies among species, for some it can be fast, for others slow.

What does punctuated equilibrium mean?

Evolution often includes rapid changes after speciation, followed by long periods of minimal change, showing that the pace of evolution varies and is not uniform across all species

What is adaptive radiation?

It is when a small number of species diversifies into a much larger number of species. Adaptive radiations are times of extreme diversification

What is an example of adaptive radiation?

An explosive expansion and diversification of mammalian species in a brief period following the mass extinction of dinosaurs due to an asteroid crash

What are the three types of events that tend to trigger adaptive radiations?

• Extinction

• Colonization

• Evolutionary innovations

What is an extinction event, and how does it trigger adaptive radiation?

It can be background (occurring at lower rates due to natural selection) or mass (occurring at large rates over a relatively short period due to sudden, extraordinary environmental change)

With their competition suddenly eliminated, the remaining species can rapidly diversify.

What is a colonization event, and how does it trigger adaptive radiation?

Moving to a new location with new resources (and possibly fewer competitors), colonizers can rapidly diversify.

e.g. diversification of Galapagos finches into 14 species from the same mainland finch

What is an evolutionary innovation event, and how does it trigger adaptive radiation?

With the evolution of an innovative feature that increases fitness, a species can rapidly diversify.

e.g. the evolution of insects’ wings and rigid outer skeletons aiding diversification

What is Carolus Linnaeus’s 1700s System?

Hierarchically organized organisms based on physical similarities, subjectively dividing all life into plants or animals. This simplistic two-kingdom model was challenged by the discovery of microbes and organisms like fungi, which did not fit neatly into these categories

What is systematics?

Modern systematics uses common ancestry to classify species, demonstrated through the phylogenetic trees (diagrams that display relationships among species, suggesting their evolutionary histories)

Phylogenetic (evolutionary) trees:

Ancestral species are positioned at the base, with modern species at the tips. Each branch represents a speciation event, marking divergences over time.

What are Monophyletic Groups?

They are a group in which all members are more closely related to each other than to any outside the group, as identified by their common ancestry at tree nodes. Members of a monophyletic group share a common ancestor, and the group contains all of the descendants of that ancestor.

How can comparative anatomy help construct evolutionary trees?

Until recently, evolutionary trees were assembled by comparing numerous physical features of species, such as a comparison that groups lions and hyenas separately from wolves and bears based on their distinct characteristics.

How can comparing DNA sequences be used to create evolutionary trees?

Beginning in the 1980s, biologists began using molecular sequences to generate evolutionary trees. ex. nucleotide sequences are compared between species (species 1-4): species 3 and 4 have five differences in their gene sequences, species 1 and 2 have only two differences, showing they are more closely related. Therefore, in the evolutionary tree, species 1 and 2 have the most recent common ancestor

All living organisms are classified into one of three groups:

In the 1980s, biologist Carl Woese began using nucleotide sequences to construct an evolutionary tree that would reflect the evolutionary history of Earth’s diversity. The main feature of the tree is the presence of three major domains: the bacteria, the archaea (a newly discovered group that is more closely related to eukarya than bacteria), and the eukarya

What are bacteria and archaea?

They are prokaryotes, lacking a nucleus

What are eukarya?

They are eukaryotes, with membrane-bound nuclei and membrane-bound organelles. It includes animals, fungi, plants, and protists

What was Woese’s approach to classification?

Carl Woese and his team used ribosomal RNA (rRNA) sequences to construct phylogenetic trees

Ribosomal RNA, which is essential for translating genes into proteins, is found in all living organisms. This uniform presence across species suggests a common ancestry

By comparing the subtle differences in rRNA sequences among different species, Woese was able to track evolutionary relationships and the historical divergence of life on Earth

According to Woese’s Tree of Life model:

• Bacteria evolved from the earliest self-replicating, metabolizing cells

• A subsequent evolutionary split led to the formation of archaea and eukarya

• Eukarya originated from the merging of a bacterium with an archaea-like prokaryote, later diverging from the archaea

The three-domain system for classifying all life is not perfect and may change due to:

• Horizontal gene transfer among bacteria

• Protists’ varied ancestry

• Viruses are excluded from the standard tree of life

What is horizontal gene transfer among bacteria?

It is where genes are shared directly between individuals, not just from parent to offspring, complicating the tracking of their evolutionary paths

What does protists’ varied ancestry refer to?

It is when they do not share a single common ancestor, making them a non-unified group

Why are viruses are excluded from the standard tree of life?

They are excluded because they lack independent metabolic functions and must hijack a host’s cellular machinery to replicate and survive

Chapters 15.3 - 15.5, 15.7 - 15.8

Bacterial Diversity

What are bacteria?

Bacteria are tiny, single-celled organisms that are part of the larger group known as microbes, which includes various organisms too small to be seen without a microscope

What is the structure of a bacterium?

Bacteria include a cell envelope, cytoplasm, DNA, flagellum, and pili

What is a cell envelope?

It comprises a plasma membrane and often a cell wall to stabilize internal conditions

What is the cytoplasm?

It is the internal fluid where cellular activities occur

What is DNA?

It includes the bacterium’s chromosome and plasmids, which are small DNA pieces that can be exchanged between bacteria

What is flagellum and pili?

Some bacteria possess a flagellum for movement and pili for attachment to surfaces and genetic exchange

What are the classifications by shape?

• Cocci (spherical bacteria)

• Bacilli (rod-shaped bacteria)

• Spirilla (spiral-shaped bacteria)

What does bacteria identification entail?

Colonies of different species of bacteria look different when grown on media plates

Individual bacterial cells, when observed under the microscope are transparent unless stained with a Gram Stain

What is a Gram Stain?

• Gram-Positive Bacteria: stain penetrates the glycoprotein layer that makes up the cell wall and colors it purple (ex. streptococcus pneumoniae causes pneumonia)

• Gram-Negative Bacteria: are not stained by this dye due to the presence of an additional membrane before the glycoprotein layer that prevents staining (ex. escherichia coli can cause food poisoning)

Chromosome:

Usually a single, circular DNA molecule

Contains genes for basic life processes

Related genes are often grouped and controlled from a single promoter, ex. E. Coli contains genes that allow the bacteria to process lactose

Plasmids:

Smaller, circular DNA pieces

Typically carry a few specialized genes, such as those for antibiotic resistance or producing toxins

Binary Fission:

Bacteria usually reproduce via binary fission, an asexual process where a single cell divides into two:

• the cell duplicates its chromosome

• the copies separate

• the cell divides, forming two daughter cells, each with an identical chromosome

What is lateral gene transfer?

Besides transmitting genes to offspring through binary fission, bacteria can also exchange genes with other bacteria in the same generation through various mechanisms

What is conjugation?

A bacterium transfers a copy of some or all of its DNA to another bacterium- genetic information the recipient may not have had

What is transduction?

It is a virus containing pieces of bacterial DNA inadvertently picked up from its previous host infects a new bacterium- passing on genetic information the recipient may not have had

What is transformation?

A bacterium can take up DNA- potentially including alleles it did not carry- from the surroundings (usually from bacteria that have died)

Metabolic diversity among the bacteria is extreme

Bacteria showcase a remarkable ability to adapt and utilize various energy sources

What is chemoorganotrophs?

These bacteria feed on organic molecules, like those found in a typical shower stall, contributing to stains and residue buildup

What is chemolithotrophs?

Utilizing inorganic molecules, such as iron, these bacteria are responsible for features like the rusticles one the Titanic’s wreckage

What is photoautotrophs?

Bacteria like cyanobacteria use sunlight for energy, visible as the gooey green mats in ponds, illustrating their ability to perform photosynthesis

Cyanobacteria:

• resemble first photosynthetic organisms from about 2.6 billion years ago

• able to use solar energy to build organic compounds from CO2 and break down H2O molecules, releasing free oxygen

Oxygen Revolution:

Accumulation of O2 released by cyanobacteria into the Earth’s atmosphere

Aerobic Bacteria:

requires oxygen for growth while anaerobic bacteria do not

Some bacteria (facultative anaerobes) can switch from aerobic to anaerobic if oxygen is absent

Bacteria are incredibly abundant

Of the roughly 68 trillion cells that make up your body, less than half are human cells

A significant portion of the remaining 38 trillion are bacteria, along with viruses and other microorganisms, highlighting the prevalence of these tiny organisms in and on you

Many bacteria are beneficial to humans

Healthy populations of beneficial bacteria in and on our bodies are vital for infection prevention. They occupy spaces and consume nutrients, blocking harmful bacteria from establishing themselves

What is probiotic therapy?

It introduces benign bacteria in large numbers, enhancing our body’s first line of defense against pathogens by outcompeting and diminishing harmful bacteria populations

What lactobacillus acidophilus?

A bacterium used in yogurt production is an example of beneficial bacteria at work:

• It metabolizes lactose to produce lactic acid, which not only helps the bacteria to proliferate rapidly but also creates an environment hostile to pathogens

• This is especially effective in treating conditions like traveler’s diarrhea and urinary tract infections

Only a ___ percentage of microbe species cause diseases, yet they kill millions of people

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Pathogenic Bacteria:

Only a few types of bacteria cause diseases, but these include serious illnesses like cholera, plague, and tuberculosis, which still cause millions of deaths each year. These are always pathogenic

Cholera example:

• Cholera is caused by the bacterium Vibrio Cholerae

• The significant decrease in cholera cases during the 19th-century London epidemic was due to identifying and shutting down a contaminated water source

• Today, cholera continues to be a severe risk in places with inadequate sanitation, leading to fast-spreading outbreaks

Some bacteria become pathogenic only under special circumstances

Bacterium like Streptoroccus pyogenes are part of the “normal flora” of our nose and mouth, and typically are not pathogenic

However, they can become pathogenic under certain conditions, such as when they are not held in check by other bacteria causing strains of this bacteria: strep throat, scarlet fever, flesh-eating “necrotizing fasciitis”

Sexually transmitted diseases reveal battles between microbes and humans

Sexually transmitted diseases (STDs) are caused by many different microbes, and 300 million new cases occur yearly worldwide

Sexually transmitted diseases are difficult to eradicate because:

• symptoms may be mild or absent

• both partners must seek treatment simultaneously

• populations of a microbe can evolve quickly and become resistant to existing drugs

Antibiotic Resistance:

• penicillin, once a groundbreaking antibiotic, now faces widespread resistance that challenges the treatment of common infections in and beyond hospitals

• Microbes display remarkable survival strategies that contribute to antibiotic resistance: rapid growth, nutrient acquisition, and chemical defenses

Rapid Growth:

Microbes grow quickly to outcompete others for resources

Nutrient Acquisition:

They efficiently extract nutrients, often at the expense of other organisms