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Biology

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* Chapter 25 * Evolution has to work with existing forms * Heterochrony
Evolutionary change in rate or timing of developmental events * Padomorphosis
Mature state of an organism retains juvenile characteristics
Spatial Patterns
Rearranges structural features through changes in gene expression or gene duplications.
Homeotic genes control 3-D patterns of multicellular organisms
Hox gene family: HoxC6 expressed (no limbs), HoxC6 not expressed (limbs can form)
Jellyfish to humans
Exaptation
Traits evolved in one context are used for an entirely different function
Feathers first thought to be used as insulation. Feathers are an exaptation- evolved in context of insulation, now used for different function (flight)

Adaptive Radiation: a single lineage (common ancestor) undergoes rapid speciation and ecological diversification to form multiple new species. Can occur when:
Key Adaptation
Adaptations that allow a lineage to exploit new habitats( or resources) and diversify rapidly
If key adaptations evolve convergently in different groups: compare diversity of group with key adaptation to diversity of sister group lacking key adaptation (paired t-test)
After mass extinction event (leaves many vacant niches for organism to diversify and fill
Colonization of a new habitat/location
Rapid diversification of “picture-winged” Drosophila on Hawaiian Islands

Hypothesis of Chemical Evolution
Abiotic synthesis of small organic molecules
Observed early synthesis of amino acids
Energized by lightning/intense UV radiation
Organic molecules formed from simpler moelcules in “primordial soup”
Early atmosphere “reducing”-electron-adding
Experiments by Miller &Urey 1953
Formation of polymers (joining of organic molecules)- proteins/ nucleic acids
Small organic molecules form polymers when concentrated on hot sand, rock or clay
Packaging into membranes- protocells
Liposomes
Aggregates of abiotically produced molecules surrounded by membranes * Self-replicating molecules
RNA molecules can have variety of nucleotide sequences and molecular shapes
Replication results in similar molecules
Environment varied in temperature, salinity, etc.
Mutations in RNA could cause differences in replication, change ability to survive in different environments * * The Fossil Record
Sources of Bias:
Where do fossils form
Depositional environments such as river deltas, beaches, flood plains, marshes, lakeshores, sea floors
What fossilizes: Hard structures
Who fossilizes: ecologically abundant organisms, often with a wide geographic range

Key Events in evolutionary history
Formation of earth (4.6 BYA)
Volcanoes, oceans
Meteor bombardment
Atmosphere
No free oxygen
Carbon dioxide, hydrogen, methane, hydrogen sulfide * First cells/life (prokaryotes) (3.9-3.5 BYA)
Unicellular prokaryotes used other gasses as a fuel source
Photosynthesis and oxygen revolution (2.7 BYA)
Oxygen began to accumulate, allowing more complex eukaryotic organisms to evolve
Early prokaryotes (cyanobacteria) split water molecules & released oxygen
React with dissolved iron to form iron oxide
Oxygen released into atmosphere after oceans were saturated
The first multicellular eukaryotes (1.2-1.5 BYA)
Make use of oxygen, were green algae
Cambrian explosion (542-525 MYA)
Can see origins of nearly all modern phylas- fossil evidence

Chapter 27
Prokaryotes (Archaea and Bacteria) Basic Cell Structure
Unicellular
No membrane-bound nucleus
No membrane- bound organelles
Very small
Circular DNA
Cell Wall

Prokaryote Cell Walls
Archaea: no peptidoglycan
Bacteria
Gram negative: complex walls with little peptidoglycan
More harmful, more resistant to antibiotics
Gram positive: simple walls with lots of peptidoglycan
Amoxicillin and Penicillin antibiotics
Prevents peptidoglycan cross-linking
Treats pneumonia, UTI, lyme disease, etc.
Gram stain- quickly assess whether gram-positive or gram-negative bacteria * * Prokaryote DNA/ Reproduction
Circular
Many fewer genes/proteins than eukaryotes
Not enclosed in membrane
Asexual reproduction, but high genetic variation
Via binary fission
Rapid generation times and high population sizes
Genetic recombination/ horizontal gene transfer
Transfer of genetic material between individuals
High genetic diversity and rapid adaptation * * Prokaryote Metabolism and Nutrition
Need ATP
Energy sources is light or molecules
Electron acceptor is oxygen
Organic compounds
Synthesize them from carbon dioxide or acquire from organisms
Autotroph : Plants
Heterotroph: Animals
Photoautotroph: cyanobacteria
Chemoautotroph : symbiotic bacteria
Photoheterotroph
Chemoheterotroph

Prokaryote Habitats
Extremophiles
Live in habitats not suitable for most life
Extreme Halophiles
Salt-loving- Great Salt Lake
Extreme Thermophiles
Heat-loving- Geysers
Methanogens
Use Carbon dioxide to oxidize Hydrogen poisoned by oxygen
Cow stomachs
Marsh sediments

Chapter 27
Prokaryote Diversity
Proteobacteria
Gram-negative
Many nitrogen-fixing
Not photosynthetic
E.coli
Cyanobacteria
Photosynthetic
Unicellular or colonial
Anabaena
Before cyanobacteria, all prokaryotes were anaerobes (no oxygen in atmosphere)
Cyanobacteria started the oxygen revolution
Chlamydias
Gram-negative
Endosymbionts
Causes STDs, blindness * Spirochetes
Gram-negative
Spiral shape
Syphilis, Lyme Disease
Gram-positive
Make antibiotics
Abundant in soil
Commensals: Yogurt
Pathogens: M. Tuberculosis

Chapter 28

Modern eukaryotic cell originated via endosymbiosis
Mitochondria and chloroplasts have their own membranes
Mitochondria and chloroplasts have a set of their own circular DNA passed on to offspring independently
Mitochondria reproduce by splitting in half
Semi-autonomous: proteins needed by mitochondria now produced by nuclear genome
Endosymbiosis involves some kind of gene transfer
Genes responsible for making enzyme had been transferred to bacterial genome
Elysia eats algae and discards all but the chloroplasts
Naked chloroplast incorporated into body so photosynthetic products can be used by sea slug
Sea slug has genes in its nuclear genome that care for and support stolen chloroplasts
Mitochondria (originally a proteobacteria) and chloroplasts (originally a cyanobacteria) both originated via endosymbiosis
Primary endosymbiosis: red and green algae
Secondary endosymbiosis: dinoflagellates, brown algae, and euglenids

Protist Locomotion
Amoeboid motion
Swimming via flagella
Swimming via cilia

Slim molds
“fungus-like”
unicellular or multicellular become multicellular when food is scarce, form fruiting bodies

Euglenids
Use flagella to move
Can be hetertrophic or photoautotrophic

Fungi
Euakryotes
Chemeoheterotrophs and absorptive feeders
Range of habitats, nutritional modes
Important decomposers
Some parasites, pathogens,
Cell wall composed of chitin and β-glucan
Two growth forms
Unicellular- yeasts
Multicellular- mushrooms: fruiting body that emerges after hyphae mate; disperse reproductive spores
Hyphae- threadlike, individual filaments that together make up mycelium (body) of the fungus *
Ecological Interactions
Symbiosis
The living together of unlike organisms
Microbes (bacteria, protists, fungi) are symbionts in many larger hosts
Mutualism: +/+ both benefits
Bacteria-host
Rhizobium converts atmospheric nitrogen to a form of nitrogen useable for plants
Commensalism: +/0 one benefits, no effect on other
Bacteria-host
Human gut microbiome: many bacteria live commensally in human intestinal systems. – little effect on us
Parasitism: +/- one benefits, other is harmed but not killed
Parasites that cause diseases are called pathogens

Bacteria (prokaryote)
Unicellular
Phospholipid cell membrane
Circular DNA, in nucleoid region
No organelles
Ribosomes
Smaller
Asexual reproduction
Cell wall
Peptidoglycan
Complex, but no peptidoglycan
Many bacteria are also important link in nitrogen cycle
Nitrogen necessary for amino acids, nucleic acids

Eukaryotic microbes Protists, Fungi
Phospholipid membrane only
Linear DNA in nucleus
Ribosomes
Organelles
Mitochondria
Chloroplasts
Larger

Fungi
Chemoheterotrophic
Unicellular or multicellular
Cell covering composed of chitin and -glucan
Range of habitats, range of nutritional modes

Fungal Pathogens: Human
Athlete’s foot
Walking barefoot in moist areas or sharing shoes

Yeast
Fermentation: metabolism in absence of oxygen
Lactic acid fermentation
Alcoholic fermentation
Alcoholic fermentation occurs in yeast cells to produce wine

Proper experimental design should
Reduce/eliminate bias
Reduce sampling error

Eliminating or Reducing Bias
Control group
Group of subjects that do not receive the treatments of interest, but receive the placebo
Reduce experimental artifacts
Control and treatment groups should be chosen randomly
Blinding
Concealing information from participants about which subjects get which treatment
Prevents subject/researchers from changing their behavior or assessment
Single-blind
Subjects are unaware of treatments
Double-blind
Researchers and subjects are unaware of which treatments they are administering/receiving

Reducing Sampling Error
Using experimental design
Replication
Using multiple samples in each treatment
Without replication, we would not know whether response was due to treatments or random variation between individuals
Standardize experimental conditions
Everything should be the same for all treatments

Two main kinds of variables
Categorical -Discrete or qualitative
Describe membership in group
Chi-Sq test
# males vs. females in two different classes
Continuous – numeric, quantitative
Quantitative and have magnitude numbers
T-test
Ex: mean height males vs females

P-value
Ex: p=0.67 there were no significant differences in height between males and females
Ex: p=0.02 mortality was significantly higher in the UV group than the control group

Increasing sample size typically increases statistical power
Chapter 29

Evolution of Land Plants
Closest living ancestor of land plants hypothesized to be green alage called charophytes
First land plants- 475 MYA

How plants colonized land? water loss gravity (need more support/transport systems) resources in two different places (water/minerals in ground, light/CO2

What types of problems might plants have encountered on their move on to land?
Problems: Dry conditions/water loss
Solutions:
cuticle and Stomata
Reproductive encasements
Sporopollenin
Prevents charophyte cells from drying out
Encase spores of some plants
Spores produced by sporangia
Gametangia
Produce gametes
Zygote remains in parent plant
Problems: Gravity (need support structures)
Solutions:
Vascular tissue
Cells joined into tubes
Transport water &nutrients against gravity
Lignin
Strong polymer in cell walls
Problems: resources in different places
Solutions
Tissue specialization
Leaves, steams, roots
Apical meristems
Cell division at tips of roots/shoots-continue to grow and expand

Alternation of Generation
1. Gametophyte (n) produces haploid Gametes by mitosis
2. Two gametes unite to form diploid (2n) zygote
3. Diploid (2n) zygote develops into multicellular diploid sporophyte
4. Sporophyte produces haploid spores by meiosis
4. Spores develop into multicellular haploid gametophytes

Major Plant Groups
Non-vascular plants
Liverworts
Hornworts
Mosses
Vascular plants
Seedless
Lycophtes (club mosses)
Pterophytes (Ferns)
Seeds
Gymnosperms (conifers)
Angiosperms ( flowering plants)

Bryophytes
Gametophyte dominant form
Seedless
Sporophytes produces spores
Flagellated sperm
Flowerless
Gametes are produced by gametangia on gametophyte
Non-vascular
Thin structure allows transport without vessels
Mosses
Grow more vertically than the ‘worts
No vascular tissue
Leaves are 1-2 cells thick
Erosion control
Nitrogen-fixers

Ecological and Economic Importance of Mosses
Fix nitrogen with help of nitrogen-fixing cyanobacteria
Can colonize cold or dry habitats (lose most of body water, then rehydrate)
Peat moss- decays slowly, accumulates in boggy peatlands

Vascular Plants I- Ferns and Gymnosperms
Pterophytes, lycophtes, and gymnosperms
The factors that led to their adaptive radiation
Familiar with general life cycle for seedless and seeded vascular
Advantages of seeds and reduced gametophytes for life on land

Key Adaptations of Vascular Plants
Vascular tissue (Xylem & phloem)
Strengthened by lignin
Roots
Evolution of leaves
Sporophylls-modified leaves that bear sporangia
Homosporous (1)
Heterosoporous (2)

Evolution of Leaves
Leaves
Increased area for photosynthesis
Vasculature
Microphylls (only in Lycophytes)
Small, spine-shaped with single vein
Megaphylls
Larger, broader with branched veins

Soprophylls
Leaves that have sporangia

425 MYA- first vascular plants
Seedless vascular plants diversified and formed huge forests during Carboniferous (359-299 MYA)
Carboniferous- age forest dramatically reduced CO2 levels ( global cooling/ glacial formation)
Burning of coal created from Carboniferous forests puts CO2 back in atmosphere (global warming)

Seed Plants- 360 MYA
Reduced gametophytes & heterospory
Pollen-houses microscopic male gametophytes
Seeds
Embryo + food supply surrounded by thick caot
With or without flowers
Gymnosperms- no flowers (305 MYA)
Angiosperms- flower (~150 MYA)
Dependent on sporophyte
Protection
Nutrients
Heterosporous: 2 types of spores
Microsporangia-Microspores-Male gametophyte- sperm
Megasporangia- Megaspores- Female gametophyte- eggs

What are advantages of reduced, dependent gametophytes?
Protection of gametophyte from stress (UV/ desiccation)
Gametophyte can obtain nutrition from surrounding sporophyte tissue

Chapter 30
Seed plants: Male and Female Gametophytes
Female ovules consists of sporophyte tissue (2n) and integument (protective tissue) housing female gametophyte, which produces egg (Gamete,n)
Male pollen consists of tough pollen wall (2n sporophyte tissue) housing male gametophyte (n), producing sperm (n)
Transfer of pollen to ovule=pollination

Advantages of pollen?
In non-vascular plants (mosses) and seedless vascular plants (ferns), male gametophytes release flagellated sperm
Does not travel far
In seed plants, gametophyte is protected within tough pollen coating, can be carried long distances by wind or animals

Fertilization of ovule by pollen creates, finally, the seed
Seed
Embryo +food supply + protective coat
Evolutionary advantages
Resist harsh conditions
Disperse widely

What are the advantages of seeds over spores?
Before seeds, spores were the only protective stage where organisms can survive harsh conditions or be dispersed
Have supply of food to nourish them when they do germinate
Can usually remain dormant for much longer than spores
Seed bank in soil

Gymnosperms
Naked seeds on cones
No flowers
Angiosperms
Seeds encased in ovaries
Fruits can be fleshy or dry
Flowers

Ecological Dominance and Adaptive Radiation of first seed plants(gymnosperms), about 250 MYA
Ecological opportunity –end Permian extinction event
96% of marine species went extinct
70% of terrestrial species went extinct
Changes in climate: drier climactic conditions favored gymnosperms
Needle-shaped leaves with thick cuticle conserved water
Key Adaptations
Seeds, pollen (disperse in dry climates)

Cycads
Thrived during Mesozic (250-65 MYA)
Palm-like- large cones

Ginko
Ginko biloba only existing species (common ornamental)
Dioecious-male or female

Welwitschia
Ovulate cones
Largest leaves

Conifers
Redwoods, pines, larches, firs
Evergreen
Retain leaves (needles) year-round
Adaptation for harsh, dry winters
Larches are NOT evergreen
Turn gold and lose needles in fall
Commercially important
Douglas fir produces more timber than any other North American tree species
Tallest and largest trees
Sequoia
Coast redwoods
Plain cool
Pacific yew
Anti-cancer compound isolated from bark
Bristlecone pine
Oldest living organism
4600 years old

Key Adaptations of Angiosperms
Flowers
Structures specialized for sexual reproduction ( get pollen to ovule)
Gymnosperms- no flowers, wind pollinated
Angiosperms- flower, animal pollinated or wind pollinated
Fruits typically enlarged ovary
Protect and aid in seed dispersal
Contains one or more seeds

Flowers: Specialized for Sexual Reproduction
Sepals
Encase flower before blooming
Petals
Brightly-colored, attracted pollinators
Stamens
Ultimately produce pollen (housing male gametophytes)
Anther + filament * Carpels
Contain ovules (Female)
Stigma- receives pollen
Style
Ovary

Angiosperm Fertilization
2 sperm in 1 pollen grain need to be transported to sticky stigma travels via pollen tube to ovule self-pollinate cross-pollinate
Double fertilization
1 sperm fuses with egg=zygote
1 sperm fuses with central cell in ovule to form endosperm triploid tissue as food source

Fruits mature ovary protect and aid in seed dispersal contains one or more seeds

Dry Fruits
Bean nuts and grains
Split open to release seeds wind dispersed (maize, rice, wheat)- actually dry fruits, not seeds!

Fleshy Fruits
Edible, colorful, sweet soft
Primarily by birds and mammals
Dispersal by fish

Angiosperm Evolution
Originated (~140 MYA)
First fossils (~125 MYA)
Early angiosperms: seed inside carpels, but lack petal s

Most living angiosperms can be classified into monocots or dicots
Cotyledon
Embryonic leaf
First leaves that sprout after germination
Monocots
One cotyledon
Parallel leaf veins
Scattered vascular structure
Fibrous root system
Floral organs in 3x
Dicots
Two cotyledons
Branching leaf veins
Vascular tissue in ring
Taproot (main root) present
Floral organs 4x or 5x

Angiosperms and animals
Herbivory : one benefits (consumer), one is consumed (the plant)
Angiosperm-pollinator relationships are typically mutualistic

Pollination Syndromes
Sets of flower traits evolved via natural selection to optimize pollination via different “vectors”
Bee pollination
Nectar or pollen as food reward
Bee pollinated flowers: yellow, blue & UV, but not red
Wind pollination
Flowers not showy
Lots of tiny pollen produced (allergens)
Butterfly pollination
Large and showy flowers, pink or lavender
Scented with nectar reward
Often with landing area
Moth pollination
Flowers white, open at night
Strong, sweet scent produced night/ evening
Nectar rewards
Hummingbird pollination
Odorless, nectar reward secreted during day
Red or orange tubular flowers
Bat pollination
Flowers white, open at night
Large pollen
Substantial nectar rewards
Carrionfly/beetle/sweatbee pollination
Normally visit dead animals or dung
Flowers with disgusting odor
No reward, but traps that slows flies down
Review
Land plants (475 MYA) share many derived traits that are adaptations to life on land
Shared, derived traits of seed plants

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...Lecture 01 Nature & Scope of Biological Science What is Biology? A brief history. Biology today. Group of organisms being studied. Approach taken to the study of organisms. New definition of Biology. Why study Biology? Aspects of Science Science has two aspects. It is both (1) a body of knowledge and (2) a method used for discovering new knowledge. What is biology? The word biology comes from the Greek words bios, which means life, and logos, which means thought. Thus, biology is the science that deals with the study of life. Origin of Life |According to this theory, about 15 billion years ago (15,000,000,000) the Universe was nothing more than a very small speck of mass. This speck| |was probably no bigger than the head of a pin. Everything in the Universe, all the galaxies, stars, planets, and even the matter making up your| |body, was squished up tightly in this tiny space. | |Eventually, after a very long time, this speck exploded. All of a sudden, in a giant flash of unimaginable heat and power, the Universe was | |born. Over a period of billions and billions of years, the Universe became what we see today. Slowly stars began to form, and around these | |stars planets formed. | |About 4.6 billion years ago our Earth looked very different...

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Branches of Biology

...Branches of biology * Aerobiology – the study of airborne organic particles * Agriculture – the study of producing crops from the land, with an emphasis on practical applications * Anatomy – the study of form and function, in plants, animals, and other organisms, or specifically in humans * Arachnology – the study of arachnids * Astrobiology – the study of evolution, distribution, and future of life in the universe—also known as exobiology, exopaleontology, and bioastronomy * Biochemistry – the study of the chemical reactions required for life to exist and function, usually a focus on the cellular level * Bioengineering – the study of biology through the means of engineering with an emphasis on applied knowledge and especially related to biotechnology * Biogeography – the study of the distribution of species spatially and temporally * Bioinformatics – the use of information technology for the study, collection, and storage of genomic and other biological data * Biomathematics (or Mathematical biology) – the quantitative or mathematical study of biological processes, with an emphasis on modeling * Biomechanics – often considered a branch of medicine, the study of the mechanics of living beings, with an emphasis on applied use through prosthetics or orthotics * Biomedical research – the study of the human body in health and disease * Biophysics – the study of biological processes through physics, by applying the theories and methods...

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Biology Article

...Assignment 1: Biology Article Cinthya Jacobo Professor: Dr. Francie Coblentz Introduction to Biology: SCI115 11/08/2015 The article “Therapeutic Cloning, and stem cell Research” by Gena Smith is about how we can extract stem cells from replicated human embryos and use them for medical and therapeutic purposes. The stems cells are perfect because they are what the article calls “master cells” which with the help of science, can be manipulated to become anything from brain cells to kidney cells. The article also revolves around the amount of controversy over the issue of cloning. The article mostly reviews the medical side of cloning rather than the reproduction side which can one day lead to the cloning of individual people. The article has high hopes for the potential use of cloning stating that “Down the road, scientists believe it will be possible to create complicated structures such as blood vessels, liver tissue, and whole kidneys. In fact, ACT scientists have already succeeded in building tiny cow kidneys that could be used for kidney transplants. It isn't hard to envision, Lanza says, a future where pretty much any kind of organ or tissue could be engineered to replace those damaged by age, injury, or disease.” Overall, this new study of cloning could help clone new body tissues which can help regulate, maintain and potentially replace importance body organs that could then lead to the salvation of millions of lives. According to an article by Norwegian University...

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Branches of Biology

...Branches of Biology Biology, the study of life, has many aspects to it and many specializations within this broad field. Below is an alphabetical list of many of the branches of biology. Agriculture - study of producing crops from the land, with an emphasis on practical applications Anatomy - the study of the animal form, with an emphasis on human bodies Biochemistry - the study of the chemical reactions required for life to exist and function, usually a focus on the cellular level Bioengineering - the study of biology through the means of engineering with an emphasis on applied knowledge and especially related to biotechnology. Bioinformatics - also classified as a branch of information technology (IT) it is the study, collection, and storage of genomic data Biomathematics or Mathematical Biology - the study of biological processes through mathematics, with an emphasis on modeling. Biomechanics - often considered a branch of medicine, the study of the mechanics of living beings, with an emphasis on applied use through artificial limbs, etc. Biophysics - the study of biological processes through physics, by applying the theories and methods traditionally used in the physical sciences Biotechnology - a new and sometimes controversial branch of biology that studies the manipulation of living matter, including genetic modification Botany - the study of plants Cell Biology - the study of the cell as a complete unit, and the molecular and chemical interactions...

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Biology Article

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Biology Introduction

...including their structure, function, growth, evolution, distribution, and taxonomy.[1] Modern biology is a vast and eclectic field, composed of manybranches and subdisciplines. However, despite the broad scope of biology, there are certain general and unifying concepts within it that govern all study and research, consolidating it into single, coherent fields. In general, biology recognizes the cell as the basic unit of life, genes as the basic unit of heredity, and evolution as the engine that propels the synthesis and creation of new species. It is also understood today that all organisms survive by consuming and transforming energy and by regulating their internal environment to maintain a stable and vital condition. Subdisciplines of biology are defined by the scale at which organisms are studied, the kinds of organisms studied, and the methods used to study them: biochemistry examines the rudimentary chemistry of life; molecular biologystudies the complex interactions among biological molecules; botany studies the biology of plants; cellular biologyexamines the basic building-block of all life, the cell; physiology examines the physical and chemical functions oftissues, organs, and organ systems of an organism; evolutionary biology examines the processes that produced the diversity of life; and ecology examines how organisms interact in their environment.[2] HistoryThe term biology is derived from the Greek word βίος, bios, "life" and the suffix -λογία, -logia, "study of."[3][4] The...

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