AP BIO MIDTERM!

Viruses

• Nucleic Acids

• DNA or RNA

• Protein coat called capsid

• Can’t grow

  • Needs to invade a cell to grow / reproduce 

• Can’t reproduce on its own

• Can’t metabolize

Characteristics of life

• Growth

• Metabolize

• Reproduce

• cellular organization

• response to stimuli

• evolution

Red blood cells

• Hold oxygen

• Deliver oxygen

  • Delivers it to organs that need oxygen

• No nucleus or organelles

  • Born with nucleus but as they mature they produce hemoglobin then don’t need the nucleus anymore

• Made in the bone marrow

• Cup shaped

  • Concave on both sides

  • Shape increases surface area

  • Structure dictates function

• Thin membrane that helps oxygen pass through

Antibodies

• A protein molecule

• Produced and released by plasma

Prokaryotes

• Normal typical bacteria

• Domain bacteria and archaea

  • Archaea

    • Dont really resemble prokaryotes, resemble eukaryotes

    • Eubacteria, Archaea, eukarya

      • Eubacteria = prokaryotes 

  • Find archaea in sulfur vents, salty regions, guts of animals

Eukaryotes

• Normal bacteria but all of their RNA DNA and chemical reactions are more like their eukaryotes then regular bacteria

  • Used to have 5 kingdoms (eukaryotic)

    • Fungus, animal, plant, protists

• Domain eukarya

• Protists

• Fungi

• Plants

Endomembrane system

• Regulates protein and lysosome traffic and performs metabolic functions

Endoplasmic reticulum

• Network of membranes and sacs

• Produce proteins

Rough ER

• Ribosomes on surface

• Made in the nucleolous

• Not a fixed organelle

• Ribosomes are constantly attaching and breaking off

  • Package proteins for sections, send transport vehicles to Golgi, make replacement membrane

Smooth ER

• No ribosomes on surface

  • Synthesize lipids, metabolize carbs, detox drugs and poisons, stores Ca

Golgi Apparatus

• Synthesis and packaging materials

  • Small molecules get transported by vesicles

  • Produces lysosomes

• The “post office”

• Series of flatted membrane sacs

• Materials go to Golgi and fuse to the cis face and go to the trans face

Lysosomes

• Intracellular digestions

• Recycles cells materials 

• Programmed cell death

  • Aptosis

    • Lysosome membrane breaks and breaks down the cell

• Contains hydrolytic enzymes

• Phagocytosis

  • surround and destroy substances

• Autophagy

  • cells ability to break down and repurpose cell parts

Vacuoles

• Storage of materials

  • Food

  • Water

  • Minerals

  • Pigments

  • Poisons

• Membrane bound vesicles

• Food vacuoles

  • Stores food

• Contractile vacuole

  • Controls water balance in unicellular fresh water protists

• Central vacuole

  • Controls water balance in a plant cell

  • Stores water and ions

  • Retains water for turgor pressure

Mitochondria

• Site of cellular respiration

• Double membrane

  • Outer and inner membrane

• Cristae

  • Folds of inner membrane

  • Contains enzymes for ATP production

  • Increased surface area to increased ATP made

• Matrix

  • Fluid filled inner compartment

Chloroplasts

• Site of photosynthesis

• Double membrane

• Thylakoid disk in stacks

  • Grana

  • Stroma is the fluid

• Contains chlorophylls (pigments) for capturing sunlight energy

Endosymbiotic theory

• Mitochondria and chloroplasts share similar origin

• Prokaryotic cells engulfed by ancestors of eukaryotic cells

• Evidence

  • Double membrane structure

  • Have own ribosomes and DNA

  • Reproduce independently within cell

Cytoskeleton

• Network of protein fibers

• Support, motility, regulate biochemical activities

• Made of three main types of fibers

  • Microtubules

    • Hollow tubes

    • 25nm with 15 nm lumen

  • Microfilaments

    • Two intertwined strands of actin

    • 7 nm

  • Intermediate filaments

    • Fibrous proteins called into cables

    • 8-12 nm

Plant cells

• Cell wall

  • Protect plant, maintain shape

  • Composed of cellulose

• Plasmodemata

  • Channels between cells to allow passage of molecules from cell to cell 

  • Doesn't have to pass through cell membrane - cell membranes are connected

Extracellular matrix

• GLycolipids and glycoproteins

  • Communication devices for animal cells to recognize each other 

• Function

  • Strengthens tissues and transmits external signals to cell

Intercellular junctions

• Tight junctions

  • Two cells are fused to form watertight seal

  • Skin, gastrointestinal

• Desmosomes

  • “Rivets” that fasten adjacent cells into strong sheets

• Gap junctions

  • Channels through which ions, sugar, small molecules can pass 

Surface area to volume

• Shapes with a higher ratio are more efficient in exchanging oxygen with the environment

• Cubes are efficient

Cell membrane

• Plasma membrane is selectively preamble

  • Allows some substances to cross more easily than other

• Fluid mosaic model

  • Fluid: membrane held together by weak interactions

  • Mosaic: phospholipids, proteins, carbs

• Freeze fracture

  • Freeze chemically what's being looked at

  • Used to look at the cell membrane, peeled it apart to see what's on the inside

Phospholipids

• Biylaer

• Ampipathic 

  • Hydrophilic head, hydrophobic tail

• Membrane fluidity

  • Low temps: phospholipids with unsaturated tails (kinks prevent close packaging)

  • Cholesterol holds fatty acids together so they cannot change state

    • Reduces membrane fluidity at moderate temperatures, but at low temperatures hinders solidification

  • Adaptations

    • Bacteria in hot springs (unusual lipids)

      • Prevents them from evaporating

    • Winter wheats (unsaturated phospholipids)

      • Prevents from packing

Membrane proteins

• Integral proteins

  • Embedded in membrane

  • Transmembrane with hydrophilic heads/tails and hydrophobic middles

• Peripheral proteins

  • Extracellular or cytoplasmic sides of membrane

  • Held in place by cytoskeleton or ECM

Membrane function proteins

• Transport

• Enzymatic activity

• Signal transduction

• Cell-cell recognition

• Intercellular joining

• Attachment to the cytoskeleton and ecm

Carbohydrates (cell function)

• Function: cell to cell recognition, developing organisms

• Glycolipids, glycoproteins

• Blood transfusions are type specific (carbs attached to proteins)

Selective permeability

• Small nonpolar molecules cross easily

  • Hydrocarbons,

  • Hydrophobic molecules

  • Co2, O2, N2

• Polar uncharged molecules 

  • H2O

  • Pass in small amounts 

• Hydrophobic core prevents passage of ions, large polar molecules- movement through embedded channel and transport proteins

Passive transport

• No energy required

• Diffusion down concentration gradient

  • High to low concentration

  • Low entropy (organized, high concentration) to high (disorganized, low concentration)

  • Smells being highly concentrated at the source and diffusing as it travels farther

Osmosis

• Dynamic equilibrium

  • Moving equilibrium

• U-Tube

• Hypotonic solution

  • Cell is hypertonic to environment

• Hypertonic solution

  • Cell is hypotonic to environment

Turgid

Plant cell in a hypotonic environment

Flaccid

equilibrium/normal

Plasmolyzed

• Fatal to plants

• Almost completely dry

Water potential

• Water moves from high φ to low φ

• Water potential equation

  • Φ = φs + φp

  • φ= Free energy water

  • Φs = Solute potential = solute concentration

  • Φp = pressure potential = physical pressure on solution

    • Turgor pressure

    • YOU WILL NEVER HAVE PRESSURE POTENTIAL UNLESS IT IS A PLANT CELL IN A HYPOTONIC SOLUTION

  • Pure water: φp = 0 bars, 0 MPA

  • Open container: φp = 0 bars, 0 MPA

Solute potential

• Φs = -iCRT

  • I = ionization constant (#particles made in water)

    • 1M Sucrose = 0 particles made, i=1

    • 1M NaCl = 2 particles made, i=2

    • On test, it will always be 1 as they only use glucose or glucose

  • C= molar concentration

  • R= pressure constant (.0831 liter bars/mole-K)

  • T= temperature in K (273+C)

• Addition of solute lowers the solute potential (more negative) and therefore decreases the water potential

Where does water move

• Water moves high φ to low φ

• Low solute concentration to high solute concentration 

  • (high water φ to low φ)

• High pressure to low pressure

Facilitated diffusion

• Still moves from high to low concentration

• Particles are too large, or polar 

• Needs help from transport proteins

  • Help hydrophilic substances cross

• Two ways

  • Provide hydrophilic channel

  • Loosely bind/carry molecule across

  • Ex: ions, polar molecules

Aquaporin

Channel protein that allows the passage of H2O

Bulk flow

• Glomerular Filtrate

  • “Cheese cloth”

  • Nefrons

    • Blood vessels go in and out

    • High blood pressure in the nephron

    • Squeezes stuff through the membrane 

    • Salts get squeezed out in the kidneys

Active transport

• Requires ENERGY (ATP)

• Proteins transport substances against concentration gradient (low -> high conc.)

  • Na+ / K+

    • Pump

    • Proton Pump

• Against the concentration gradient

• Pumps, exocytosis, endocytosis

Electrogenic pumps

• Generate voltage across membrane

Sodium Potassium Pump

• Na+ / K+ Pump

• Pump Na+ out and K+ into cell

• Nerve transmission

Proton pump

• Push protons (H+) across membrane

  • Mitochondria (ATP production)

• Use energy to create a gradient 

  • High concentration on the outside and low on the inside

Cotransport

Membrane protein enables “downhill” diffusion of one solute to drive “uphill” transport of other

Passive transport

• Little or no energy

• High -> low concentrations

• Down the concentration gradient

• Diffusion, osmosis, facilitated diffusion

Asmoregulation

• Control solute and water balance

• Contractile vacuole

  • Bilge pump

    • Forces out fresh water as it enters by osmosis

      • Paramecium caudatum - freshwater protist

Endocytosis

• Take in macromolecules and particular matter, form a new vesicles from plasma membrane

  • Phagocytosis

    • “Cellular eating” - solids

    • Endocytosis of larger molecules

  • Pinocytosis

    • “Cellular drinking” - fluids

    • Endocytosis of small solids and liquids

  • Receptor - Mediated Endocytosis

    • When the bubble forms due to the signal from a hormone

    • Ligands bind to specific receptors on the cell surface

Exocytosis

• Vesicles fuse with plasma membrane, secrete contents out of cell

Standard Error of the mean (SEM)

• If error bars overlap, there is no statistical difference 

Behavior

• What an animal does and how it does it

• Essential for survival and reproduction

• Both genetic and environmental factors

• Subject to natural selection over time

Proximate Causation

• How a behavior occurs or is modified

Ultimate causation

• Why a behavior happens in the context of natural selection

Fixed action patterns

• Sequence of acts (not learned) that are unchangeable and usually carries to completion

• Triggered by sign stimulus

• Ensures that activities essential to survival are performed correctly without practice

Kineses

• Simple change in activity or turning rate in response to a stimulus 

• Random motion

  • Increases the chance that a sow bug will encounter and stay in a moist environment

Taxis

• Automatic movement, oriented movement +/ - from stimulus

  • Certain fish know how to orient themselves in currents to stay in the same spot

Migration

• Often innate

• Environmental cues signal migration

Animal communications

• Pheromones

  • Chemicals emitted by members of one species that affect other members of the species

• Visual signals

  • Warning flash of white of a mockingbirds wings

• Tactile

  • Male fruit fly taps female fly

• Auditory signals

  • Screech of blue jay or song of warbler

Learned behaviors

• Taught or through experience

• Habituation

  • Loss of responsiveness to stimuli that convey little or no information

• Imprinting

  • Learning + innate components

  • Limited to sensitive in life, generally irreversible

    • Chicks following their mother

• Associative learning

  • Ability to associate one stimulus with another

    • Monarch butterflies = foul taste

• Classical conditioning

  • Arbitrary stimulus associated with particular outcome

  • Pavlovs dogs

• Operative conditioning

  • Trial and error learning

    • Associate its own behavior with reward or punishment

• Foraging behavior

  • When a reward outweighs a risk 

  • Travelling into other territories for food

Habituation

• Loss of responsiveness to stimuli that convey little or no information

Imprinting

• Learning + innate components

• Limited to sensitive in life, generally irreversible

  • Chicks following their mother

Associative learning

• Ability to associate one stimulus with another

  • Monarch butterflies = foul taste

Classical conditioning

• Arbitrary stimulus associated with particular outcome

• Pavlovs dogs

Operative conditioning

• Trial and error learning

  • Associate its own behavior with reward or punishment

Foraging behavior

• When a reward outweighs a risk 

• Travelling into other territories for food

Dominance hierarchies

• A higher ranking animal has greater access to resources than a lower ranking animal.

•  Decided by confrontation during which one animal gives way to another.

•  Once established, little or no time is wasted in fighting

Altruism

• Putting themselves at risk for the benefit of others

• Reduce individual fitness but increase fitness of others in population

• Inclusive fitness

  • Total effect of producing own offspring + helping close relatives

• Kin Selection

  • Type of natural selection; altruistic behavior enhances reproductive success of relatives 

• Hamilton's rule

Population

Group of single individual of a single species living in same general area

Definition of Species

Organisms are considered in the same species if they mate under natural conditions and produce fertile offspring

Determining population size

• Count every individual

• Random sampling

• Mark and recapture

Patterns of dispersal

• Clumped - Food, reproduction, dependant, like each other, near required resource

• Uniform - territorial, agonistic

• Random - no real rhyme or reason as to why they live

Survivorship curves

• Represent # individuals alive at each age

  • Humans - live a long life then die off

  • Birds - some live and some don’t live long lives

  • Fish don’t survive very long and don’t live long lives (have tons of offspring cause most don’t survive)

Exponential growth

• Population growth in an idealized situation

• Called J growth

• Shows what population would do in it;s environment

• Helps understand species ability and the conditions that may facilitate this growth

• Results in J shaped curve

J Growth

• Under these conditions th rate of increase is at its maximus, denoted as rmax

• Exhibited maximum biotic potential

• There are no density dependent limiting factor

• A factor that affect the growth of a population the more larger or more dense the population is

  • Space

  • Predation

  • Sickness

    • Food

  • Housing

Logistic growth

• Environmental resistance

• When the environment fights back

• S chapped curve

• Exponential Growth cannot be sustained for long in any population

• More realistic model limits growth by incorporating carrying capacity

• The per capita rate of increase declines as carrying capacity is reached

Density dependent factors

• Predation

• Space

• Food

• Disease

• All of these factors become more severe as population density increases

Intrinsic factors

• For some populations, intrinsic (physiological) factors appear to regulate population size

• As population density gets larger, lifespan gets shortened and less offspring

• as the population density increases hormonal changes depress the immune system increasing the death rate and decreasing the birth rate.

K-Selection

• Density dependent selection, selects for life history traits that are sensitive to population density

• Organisms that are sensitive to the caring capacity

  • Long life spans (type I or type II survivorship curve)

  • Parental care

  • Large organisms 

  • Multiple reproductive cycles (iteroparity)

  • Fewer offspring

  • K strategists because they are sensitive to density dependent factors so they are affected most at k

R-Selection

• Density independent selection

  • Selects for life history traits that maximize reproduction

• Many offspring (type III survivorship curve)

• Little parental care 

• Opportunists

• Small organisms

• One reproductive event (semelparity)

• Discrete generations

  • Generations do not live at the same time (no overlapping generations)

• Not affected by density dependant factors because they tend to die before they reach carrying capacity

• R strategists because they exhibit max biotic potential

Human population growth

• No population can grow indefinitely, humans are no exception 

•  ecologists predicted a global population 7.8-10.8 billion in 2050

• Average estimate for carrying capacity for humans is 10-15 billion 

• Ecological footprint

  • Summarizes the aggregate land and water area needed to sustain the people of a nation

  • It is one measure of how close we are to the carrying capacity of Earther(yes!)

  • Countries vary greatly in footprint size and available ecological capacity

Age structure

• The relative number of individuals at each age

• Each age group is called a cohort

• Quick vs. slow growth

• Zero population growth

  • Birth rate and death rate is nearly the same

Community

• Group of populations of different species living close enough to interact

Interspecific interactions

• Can be positive, negative, or neutral

  • Competitions (-/-)

    • Two or more species compete for a resource that is in short supply

  • Exploitation (+/-)

    • One species benefits by feeding upon the other species, which is harmed

    • Predation, herbivory, parasitism

Interspecific competition

• Resources are in short supply

• Competitive exclusion principle

  • Two species cannot coexist in a community of their niches are identical

    • Niche - the role an organism plays in the environment

    • Where it lives, where in the food web it is, predator or prey

  • One would outcompete the other, killing the organism or forcing it to find another niche

  • Resource partitioning

    • Differences in niches 

  • Fundamental niche

    • Potential occupied by the species 

    • Determined by environmental factors

    • Abiotic 

  • Realized niche

    • Portion of the fundamental nice the species actually occupies

    • Controlled by abiotic and biotic factors

  • Character displacement

    • Tendency for characteristics to be more divergent in sympatric (same place)  populations of two species that in allopatric (different) populations of the same two species

    • ex  bird beaks

      • Variation of beak size between populations of two species of galapagos finches

      • Evolved to not compete for the same food

Defensive adaptations

• Cryptic coloration

• Aposematic or warning coloration

• Batesian mimicry

• Mullerian mimicry

• Herbivory

Cryptic coloration

• Camouflaged by coloring

Aposematic or warning coloration

• Bright colors of poisonous animals

• Dart frog

Batesian mimicry

• Harmless species mimic color of harmful species

• Larvae imitating a green parrot snake

Mullerian mimicry

• 2 bad tasting species resemble each other, both are avoided

• Bees and yellow jackets

Herbivory (defensive adaptations)

• Plants avoid herbivory by chemical toxins, spines, and thorns

Mutualism

• +/+

• An interspecific interaction that benefits both species

  • Acacia tree and ants

Commensalism

• +/0

• Water buffalo and birds

• One species benefits and the other is neither harmed nor helped

• Clownfish lives in an anemone

Invasive species

• Organism that become established outside native range

• Go into ecosystem and there's nothing to check them

• Characteristics

  • Tolerates a wide range of conditions

  • Has a long growing season or short generation time

  • Has few natural controls, such as predators, disease, or insects

  • Disperses itself with ease

  • Produces lots of seeds or eggs

  • New location has climate and environmental conditions similar to native habitat

• Dutch Elm Disease , kudzu, potato blight, spotted lantern flies

Community structure

• Species diversity

  • Species richness (# of different species) + relative abundance of each species 

  • More stable ecosystem

  • Simspon diversity index

    • Calculate diversity based on species richness and relative abundance

    • Highly diverse communities more resistant to invasive species

    • picture here 

    • High D value (close to 1) = greater biodiversity

    • Low D value = less biodiversity 

Trophic structures

• Trophic levels = links in the trophic structure (food webs and food change)

• Trophic structure of a community is determined by the feeding relationships between organisms

• Transfer of food energy from plants to herbivores to carnivores to decomposers is called the food chain 

• Length limit of food chain

  • Inefficiency of energy transfer along chain

  • Long food chains less stable than short chains

  • Energetic hypothesis

    • 10% of energy available at 1 level travels to the next level

    • Suggests that length is limited by inefficient energy transfer

    • A producer level consisting of 100kg of plant material can support about 10 kg of herbivore biomass (the total mass of all individuals in a population)

    • Pyramid of biomass

    • Pyramid of numbers

    • Pyramid of energy

Food web

• Two or more food chains linked together

• A given species may weave into the web at more than one trophic level

Dominant species

• The most abundant or have the highest biomass

• Dominant species exert powerful control over the occurrence and distribution of other species

  • Sugar maples

    • Major impact in shading, and soil nutrient availability in eastern North America; this affects the distribution of other plant species

Keystone species

• Exert strong control on a community by their ecological roles or niches

• They are not necessarily abundant in a community

• If they are removed from a community biodiversity significantly drops 

  • Sea otters

    • Increase sea urchins, destruction of kelp forests

  • Grizzly bear

    • Transfer nutrients from sea to land by salmon diet

  • Prairie dogs

    • Burrows, soil aeration, trim vegetation

Ecosystem engineers

• Foundation species

• Cause physical changes in the environment that affect community structure

  • Beaver dams can transform landscapes on a very large scale

Disturbances influence species diversity

• Changes a community by removing organisms or changing resource availability 

• Ecological succession

  • Transitions in species composition in a certain area over ecological time

• Pioneer organisms

  • Can live on anything, colonize an area

Primary succession

• Plants and animals invade where soil has not yet formed

  • Colonization of a volcanic island or glacier

Secondary succession

• Starts with something

• Occurs when existing community is cleared by a disturbance that leaves oil intact

• Energy flow in an Ecosystem

  • Energy cannot be recycled

    • Must be constantly supplied to an ecosystem (mostly by SUN)