unit one animal behavior experimental design

8/17/2019 Unit One Animal Behavior Experimental Design

1/42

Unit One: Animal Behavior & Experimental Design

Chapter 1 - A View of Life

● Controlled experiment

○ Hypothesis: a possible explanation for a natural event

○ Control (group): goes through the same steps of the experiment but lacks the factor being

tested

○ Experimental Variable: variable being tested know

○ Dependent Variable: result/change that occurs due to experimental variable (measurable)

know

○ Controlled Variables: all other variables kept constant so they don’t affect the outcome of

the experiment

○ Data: results of the experiment. Must be statistically significant, measurable, and

observable

● Inductive vs. Deductive Reasoning

○ Inductive Reasoning: (specific to general), “bottom up” approach - conclusion has to be

figured out■ Dead person to who dunnit?

○ Deductive Reasoning: a “top down” approach - start w/ conclusion to see if evidence for

that conclusion are valid (general to specific)

■ Tim is a bachelor -- all bachelors are single -- thus, Tim is single

Chapter 45 - Animal Behavior

● Proximate vs. Ultimate

○ Proximate Cause: physiological mechanism for behavior. What enables organism to

exhibit that behavior

○ Ultimate Cause: evolutionary purpose for a behavior (how it influences reproductive

success). Why organism performs that behavior● Taxis vs. Kinesis - Animal Movement

○ Taxis: movement towards or away from a stimulus

■ Mosquitos go towards the light (stimulus)

○ Kinesis: random movement, changes in activity level (ultimate goal is to find optimal

habitat) know

■ Pillbugs look for dark/moist areas, so it looks random at first, but they’re moving

towards the dark areas\

● Sexual Selection, male competition, altruism

■ Sexual Selection - Females choose males on the basis of appearance and/or

fitness

● Female birds look for the most attractive chest of male birds

■ Male competition - for territory or mates

● Moose fight with antlers

■ Altruism - “unselfish” behavior for the good of the group

● Meerkats and alarm calling, even though they’ll die, they’re warning

others

○ Kin selection - when altruism occurs within families


2/42

● Animal communication: tactile, chemical, auditory, visual

■ Tactile - touch

■ Chemical - pheromones

■ Auditory - hearing/listening

■ Visual - seeing

○ Konrad Lorenz - Imprinting

■ Imprinted to 1st moving object

○ Karl Von Frisch - Honeybee Communication

■ Dances that point to location of food source

○ Ivan Pavlov - Pavlov’s salivating dogs

■ Classical conditioning, salivate at bell

○ Niko Tinbergen - Behavioral Ecologist, studied mating behavior and fixed action patterns

■ Fixed action patterns - animals always do one thing, they’re inclined to do that

one thing and will keep doing it

○ B.F. Skinner - Operant Conditioning (positive reinforcement)

■ Rats push down a lever for food or to not get shockedUnit Two: Evolution

Chapter 17 - Darwin and Evolution

● Catastrophism (Cuvier)we

○ new species w/ anatomical changes arose AFTER catastrophe

● Theory of Acquired Characteristics (Lamark)

○ changes acquired through use/disuse

○ happens in one lifetime (fluids will pass on characteristic)

● Theory of Evolution (Darwin)

○ variation in phenotype allows fitness, live long enough to reproduce and pass on genes to

next generations● People & Evidence (Influencing Theory of Evolution)

○ Charles Lyell

■ evidence that Earth is older than thought (4.6 billion, not 40000)

○ Thomas Malthus

■ resources grows arithmetically, population grows geometrically

● Shortage of resources - struggle for survival

○ Biogeography

■ related species (found in different but neighboring geographic locations)

● Ex. Galapagos Islands finches

○ Artificial Selection

■ Desirable characteristics can be selected

● Examples: Horses, dogs

○ Alfred Russel Wallace - proposed similar ideas to Darwin’s idea that natural selection is a

mechanism for evolutionary change)

■ Pushed Darwin to publish “On the Origin of Species” in 1859

■ Made Darwin confident and published book so he could take credit

● Evidence for Macroevolution


3/42

● Fossil Record

■ progressive change (arrange fossils oldest to most recent)

■ Radioactive Dating - makes fossil records more accurate

○ Molecular Record

■ study DNA sequence or protein structure

● common ancestry

○ Homology

■ structures derived from a common ancestor

■

■ same bone structure

○ Development/Embryology

■ similarities in embryo development

○ Vestigial Structures

■ structures w/ no present function

○ Parallel Adaptation

■ if in similar environments, plants & animals evolve similar characteristics○ Biogeography

■ animals on neighboring islands are similar to one another, but have slight

differences (adaptations to their environment)

● Ex. Galapagos Island Finches

● Criteria for Natural Selection know

○ variation exists in natural populations

○ more individuals are produced than the environment can support

○ some individuals have adaptive characteristics that enable them to survive and reproduce

better than others

● Macroevolution Biochemical Evidence○ Structure of ATP, DNA same in all organisms

○ Universal genetic code

○ Many developmental genes shared by very different organisms (evolutionary

development)

● Two Schools of Thought

○ Punctuate Equilibrium

■ “rapid” change followed by long periods of stability

○ Phyletic Gradualism

■ constant, gradual change (transitional links more likely to be found)

Chapter 18 - Process of Evolution

● Microevolution - changes in allele frequencies over time w/in a population, can be observed

● Macroevolution- new species → formed speciation, old species became extinct, not necessarily

easy to see

○ Microevolution → Macroevolution (small, local → big, worldwide)

● Hardy-Weinberg Equilibrium

○ If allele frequencies do not remain constant, we know that evolution has occurred and we

can look at which conditions are violated to determine the cause of evolutionary change


4/42

● Hardy Weinberg Equation know

○ p + q = 1 (allele frequencies)

○ p 2 + 2pq + q 2 = 1 (genotype frequencies)

○ p = dominant allele frequency

○ q = recessive allele frequency

○ p

2 = frequency of homozygous dominant genotype○ 2pq = frequency of heterozygous genotype

○ q 2 = frequency of homozygous recessive genotype

● Genetic drift - chance events in small populations know

● Founder effect - mutation w/in population, new population started by a few members of

the original population. This small population size means that the colony may have rare

alleles

● Heterozygote advantage - (Maintenance of Genetic Variation)

○ Homozygous recessive individuals often die of disease (sickle cell)

○ Heterozygotes have resistance to malaria (so deleterious gene is not selected out

of the gene pool)

● Directional stability - favors one extreme phenotype (graph is either way left or wayright) know all 3

● Stabilizing selection - favors intermediate (graph is very high in middle)

● Disruptive Selection - two or more phenotypes are favored (high on both sides, low in

middle)

● Species- organisms that can interbreed and produce fertile offspring

● Niche- role of the organism in environment know

● Intergrade- result from 2 subspecies (variety)

○ Ex. Labradoodle

● Hybrid- result from two different species -- breeding

○ Ex. Liger, Zonkey

● Race, subspecies, variety- intermediate stages of evolution

● Speciation- new species

○ Sympatric → two groups w/ similar ranges (overlap)

○ Allopatric → separated by barrier (geographic) know

● Prezygotic isolating mechanism -

○ Habitat Isolation (geographic and ecological) - different habitats

○ Temporal Isolation - time zones

○ Behavioral Isolation - different mating times know

○ Mechanical Isolation - incompatible

○ Gamete Isolation - prevention of gamete fusion, gametes not compatible

● Postzygotic isolating mechanism -○ Zygote Mortality - fertilization occurs, but zygote doesn’t survive

○ Hybrid sterility - hybrid survives, but is sterile and cannot reproduce

○ F2 Fitness - Hybrid is fertile but F2 hybrid has reduced fitness

● Convergent evolution - tendency of unrelated organisms (no recent common ancestor ) to

develop analogous adaptive structures or behavior that serve the same purpose


5/42

● Divergent evolution - development of different forms of organisms from a single

ancestral stock which results in a variety of forms adapted to various types of

environments

○ aka adaptive radiation know

● Parallel evolution - occurs when a trait has evolved similarly, under similar selection

pressures, in two or more groups having a common ancestor that lacked that trait

Unit Three: Origin and Diversity of Life

Chapter 19 - Origin and History of Life

● Timeline

● inorganic molecules→RNA and DNA form→prokaryotes→photosynthetic bacteria→single cell

eukaryotes→diverse prokaryotes→mutlicellular protist/algae appear→sexual

reproduction→shell-bearing invertebrates, vertebrates first appear, jawless fish

appear→extinction 1→seedless vascular plants, lobe-finned fish→non-vascular land plants

appear→jawed fish appear→gymnosperms appear→amphibians and insects appear→extinction

2→reptiles appear→archaeopteryx (reptile/bird) appears→extinction 3 →mammalsappear→extinction 4→first birds appear→angiosperms appear→extinction 5 → early primates

appear→homo sapiens appears-

Chapter 20 - Classification of Living Organisms

● Taxonomy - identifying, naming and classifying organisms

● Binomial Nomenclature - each species receives 2-part name

○ Genus Species

● Species is the most specific category of classification

● Levels of Classification

○ Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species

○ Dear King Phillip Came Over For Good Soup know● Phylogenetic tree

○ Diagram indicating common ancestors & line of descent

○ Each branching point is divergence from a common ancestor

● Derived characteristics - trait not related to common ancestor

● Ancestral characteristics - trait related to common ancestor

● Phylogeny Evidence

○ Fossil Record

○ Homology

○ Molecular Data

■ similar DNA base pair sequences○ DNA-DNA Hybridization

■ DNA double helix of each species is separated into two strands

■ Strands of both species combine, the better they stick together, the more closely

related the 2 species are

○ Molecular Clock

■ Nucleic acid changes may accumulate at a constant rate. These changes can be

used as a “molecular clock” to indicate evolutionary time


6/42

● Systematics

○ Traditional

■ use anatomical data to classify organism

■ Problem: a group that has adapted to new environment and evolved may NOT be

classified w/ common ancestor

○ Phenetic

■ species are classified according to # of similarities

■ Problem: doesn’t account for convergent or parallel evolution

○ Cladistic

■ uses shared derived characteristics to classify organisms

● arrange taxa into cladogram

● *Know how to make a Cladogram

● 3 Domain System

○ Domain Bacteria

■ Prokaryotic

■ Most bacteria (but not all)■ Most are heterotroph

● Cyanobacteria - photosynthetic

■ Asexual reproduction

○ Domain Archaea

■ Prokaryotic

■ Thrive in Extreme Environments

● High temps

● Acidic areas (Thermoacidophiles)

● Salty areas (Halophiles)

● Anaerobic areas - w/out oxygen○ Domain Eukarya

■ Kingdoms Protista, Fungi, Plantae, Animalia

■ Eukaryotic

■ Sexual reproduction is common

Chapter 22 - The Protists

● Protist Characteristics

○ Eukaryotes

○ Mostly unicellular

○ Vary in size

○ Complex

○ Multicellular organisms originated from Protists

■ ex. plants - green algae

● Protists are grouped by nutrition and movement

● Complexity and Diversity make classification difficult

Chapter 23 - The Fungi

● Fungi Characteristics

○ Eukaryotes


7/42

○ Mostly multicellular

○ Heterotroph

○ Nonmotile

○ Reproduction can be sexual or asexual (spores)

● Fungi Phyla

○ Zygospore Fungi

■ Bread Mold

○ Sac Fungi

■ Yeast, Morels, Truffles

○ Club Fungi

■ Mushroom, Puffballs, Shelf Fungi

● Symbiotic Relationships of Fungi

○ Lichen = Algae + Fungus

○ Mycorrhizae = Fungus + Plant (roots)

■ High surface absorbing area of roots; improve plants ability to gain soil resources

Chapter 29.1 - Evolution of Animals (Animal Phyla/Classification)● Tissue Layers (germ layers) in Embryo

○ Parazoa

■ Simplest - no tissues formed, ex. sponges

○ Eumetazoa

■ Diploblastic - two layers (endoderm, ectoderm) ex. jellyfish

■ Triploblastic - three layers (endoderm, mesoderm and ectoderm) ex.octupus

● Types of Symmetry

○ Asymmetrical - no apparent body symmetry

○ Bilateral - mirror images, fold in half

○ Radial - radiates out from the center (spokes of a wheel)● Coelom (body cavity) formation (specific to triploblastic animals)

○ Coelomate - coelum lined by mesodermal tissue ex. chordates, ventral and dorsal cavities

know

○ Acoelomate - w/out coelom, ex. flatworm

○ Pseudocoelomate - coelom not fully lined by mesodermal tissue - mesoderm inside body

wall but not surrounding the gut ex. roundworm

● Types of Coelomates

○ Protostome - spiral, determinate cell cleavage - unequal division, coelom forms by

splitting of mesoderm, blastopore becomes mouth

○ Deuterostome - radial, indeterminate cell cleavage - equal division, coelom forms by

outpocketing of primitive gut (echinoderms, chordates), blastopore becomes anus

● Cephalization - Location of brain (concentration of nerve cells) and sense organs at the anterior

end of an animal, more highly evolved animals show greater degree of cephalization

Chapter 24 - Origins and Diversity of Plants

● Four types

○ Nonvascular Byrophytes

○ Nonvascular Mosses


8/42

○ Seed Vascular Plants

○ Seedless Vascular Plants

● Increasing degrees of evolutionary adaptation (sporophyte 2n on top, gametophyte n on bottom)

Unit Four: Ecology

Chapter 46 - Ecology of Populations

Ecology- the study of the interactions of organisms with each other and with the physical environment

Levels of ecology:

● Organism- one living individual of a species

● Population- all organisms in an area belonging to the same species (a herd of zebras)

● Community- all the various populations interacting in a locale (all the different types of species

living in a savannah)

● Ecosystem- contains a community of populations and the abiotic environment

● Biosphere (largest)- the zones of the earth’s soil, water, and air where living organisms are found

know

Population Density vs Population Distribution- population density is the number of individuals per unit

area (measured by per square unit) while population distribution is the pattern of dispersal of individuals

across an area of interest.Three basic patterns of distribution:

● Clumped (most common-animals like to be in groups/herds)

● Random

● Uniform

We measure population growth using biotic potential, the highest possible rate of natural increase when

resources are limited Whether biotic potential is high or low depends on:

● Usual number of offspring per reproductive event

● Chances of survival until age or reproduction

● How often each individual reproduces

● Age at which reproduction beginsSurvivorship Curve- The curve created when we plot the number surviving at a particular age

( 3 different types of curves displayed on pg 841 of textbook) know


9/42

Structure diagram- either increasing, decreasing, or stable populations, creating three different shapes (

On pg 843 of textbook). There are three major age groups, prereproductive, reproductive, and post

reproductive. The left half of each shape represents the males, and the right half represents the females.

● A structure diagram would look different in a more developed country vs a less developed

country. In a more developed country, the population would be more stable. In a less developed

country, the population may be increasing, having a larger reproductive ages group.Exponential growth accelerates over time, starting slower (lag) then increasing.

Exponential growth differs from logistic growth because exponential

will keep increasing (with unlimited resources) but logistic growth

will eventually slow down and level off into equilibrium

Carrying capacity- the maximum number of individuals of a given

species the environment can support

Factors that limit population growth:

● Density- dependent factors- biotic factors such as competition, predation, and parasitism

● Density- independent factors- abiotic factors such as forest fires and flash flood (can not regulate

population themselves because the effect is not influenced by the population)

R-selection favors r-strategists- for those species that produce many cheap offspring and live in unstable

environments

● opportunistic species

● bacteria and roaches

K- selection favors k-strategies- for those species that produce few expensive offspring and live in stable

environments

● Have fewer offspring, but invest heavily in their offspring

● equilibrium species

● humans, elephants, and kangaroos know

Chapter 47 - Community Ecology


10/42

● Community- population of organisms interacting with one another within the same environment

● Habitat- place where an organism lives and reproduces

● Niche- the role an organism plays in its community (their job)

● Generalist species vs a specialist species: generalist species have a broad range of niches

(racoons, roaches, humans) while specialist species have a narrow range of niches (pandas, owls)

● Competition- two species fighting for resources

● Predation- predator hunts after prey, only predator benefits

● Parasitism- predation but with a host

● Commensalism- one organism is benefited and one is neither benefited nor harmed

● Mutualism- both members benefit

● Interspecific competition vs intraspecific competition- interspecific occurs when members of

different species try to use a resource that is limited (light, space, nutrients) and intraspecific is

the same competing of resources, but between the same species

● Competitive exclusion- states that no two species can indefinitely occupy the same niche at the

same time

● Predator- prey relationship- (cyclic) As prey population increases, the predator population alsoincreases because more food becomes available. The reproductive rate of the predator is so great

that its increased numbers over-consume the prey, then the prey population declines, and so does

the predator population and so on.

● Prey defense mechanisms:

○ Chemical defense- odor, poisonous chemicals ect

○ Physical defense- bright coloration, tough epidermis,ect

○ Camouflage- the ability of a species to blend into the background

○ Mimicry- one species resembles another that possesses an overt anti- predator defense

● Batesian mimicry vs Mullerian mimicry- Batesian mimicry is when the mimic lacks defense of

the organism it resembles ( mimic of monarch butterfly) and Mullerian mimicry is when themimic shares same protective defense know

● Ecological succession- a change involving a series of species replacements in a community

following a disturbance (primary to secondary)

○ Primary vs secondary succession- primary succession occurs in areas where there is no

soil formation, such as following a volcanic eruption.

○ Secondary succession begins in areas where soil is present and returns to a natural state.

● Climax community- the community that results when succession comes to an end, determined

somewhat by climate and soil

● Keystone species- organisms that play a greater role in maintaining the function and diversity of

an ecosystem know

● Exotic species cause problems for an ecosystem by influencing predation and competition,

ruining the balance. ( endemic bird populations were devastated due to the accidental introduction

of the brown tree snake, which preys on birds)

Chapter 48 - Ecosystems and Human Interferences

● Ecosystem- a place where organisms interact among themselves and with a physical and chemical

environment


11/42

● Trophic levels (feeding levels of one or more population in an ecosystem):

● First trophic level- producers

● Second trophic level- primary consumers

● Third trophic level- secondary consumers know

● Herbivores- eat only plants or algae

● Carnivores- feed on other animals

● Omnivores- consume both plants and animals

● Detritus feeders- feed on decomposing particles of organic matter (earthworms)

● Decomposers- acquire nutrients by breaking down dead organic matter into simple inorganic

substances (bacteria/ fungi)

● The flow of energy decreases as you climb the food chain. Only 10% of energy from one level is

available for the next level (10% rule)

● Pyramid models of ecosystems:

● The biomass decreases as you go higher up the pyramid

● The number of organisms decreases as you go higher up the pyramid

● Energy decreases as you go higher up the pyramid● Basic steps of biochemical cycles:

● Water cycle- Evaporation- Condensation- Precipitation- - Aquifers(rock layers containing

water) are recharged

● Carbon cycle- Burning of fossil fuels releases carbon dioxide into the atmosphere which

is then released into sediment and into trees through photosynthesis. Global warming also

occurs because the greenhouses gasses in the atmosphere (carbon dioxide) prevent the

escape of heat, redirecting it back to Earth.

○ Nitrogen cycle-nitrogen converted between various forms

○ denitrification: microbes convert nitrate into nitrogen gas

■ under aerobic conditions, nitrous oxide is produced, contributing toglobal warming

○ nitrogen fixing bacteria take in nitrogen gas in legume roots (roots eaten

by animals, thus entering the cycle)

● Phosphorous cycle

○ mineral phosphorus dissolved in water, absorbed by plants, eaten by

animals, given off in waste back into the soil

○ involved in eutrophication

○ can cause overgrowth of algae in highly fertilized areas

● Understand the concept of biological magnification and know examples.○ process by which substances become more concentrated in organisms in

higher trophic levels

○ water plants absorb pollution, which is eaten by fish, which are eaten by

bears, etc.

Chapter 49—The Biosphere

● Know how the distribution of solar radiation affects climate.


12/42

○ more intense radiation = hotter, dryer climate

● What is the rain shadow effect?

○ the side sheltered from the wind of a mountainous barrier receives much

less precipitation than the windward side

● What is eutrophication and what causes it?

○ runoff of phosphate and nitrogen due to fertilizer use, animal waste, and

discharge from sewage treatment plants into waterways

Chapter 50—Conservation Biology

● The goal of conservation biology is to preserve biodiversity. What is

biodiversity and why is it important?

○ degree of variation of life

○ importance: diverse gene pool allows natural selection and niche

specialization to occur

● What is the difference between a threatened and an endangered species?

○ threatened- any species that is likely to become an endangered species

within the foreseeable future

○ endangered- any species that is in imminent danger of extinction

● What are some of the reasons that biodiversity is valuable—direct (medicinal,

agricultural, and consumptive use value), indirect (biogeochemical cycles, waste

disposal, provision of fresh water, prevention of soil erosion, climate regulation,

and ecotourism).

○ direct values- goods; pertains to the specific uses of an ecosystem.

○ indirect values- services; pertains to values that are derived from the

ecosystem that protect and support direct values and activities● Describe the major causes of loss of biodiversity: habitat loss, exotic species,

pollution, overexploitation.

○ habitat loss- human/natural involvement results in the destruction of

populations’ habitats

○ exotic species- a species living outside of its native distributional range

which has arrived there by human activity (whether deliberate or

accidental)

○ pollution- contamination of natural environment by harmful substances

produced by human activity○ overexploitation- overhunting & overharvesting

■ even though mass hunting is illegal, poaching occurs

■ rate of depletion > rate of replacement

● Define the following: keystone species, flagship species, source population, sink

population.


13/42

○ keystone species- a species that plays a bigger role in maintaining the

function and diversity of an ecosystem than would be predicted by their

abundance

○ flagship species- species that evoke an emotional response in humans

(cute, beautiful, charismatic, regal)

○ source population- A breeding group that produces enough offspring to be

self-sustaining and that often produces excess young that must disperse to

other areas.

○ sink population- A breeding group that does not produce enough offspring

to maintain itself in coming years without immigrants from other

populations.

Unit 5: Chemistry Review

Chapter 2 - Basic Chemistry

● Bond Types○ Ionic

■ Electrons are transferred from one atom to another, both atoms will have a full

outer shell

■ Occur between a metal and a nonmetal (an anion and a cation)

○ Covalent

■ Two atoms share electrons in such a way that each atom has an octet of electrons

in its outer shell

■ Occur between 2 nonmetals

■ Strongest type of bonding

■ Polar and nonpolar bonds■ Intermolecular forces

● Hydrogen bond

○ Between hydrogen and fluorine/nitrogen/oxygen

○ Strongest intermolecular force

● Dipole-dipole

○ One atom pulls the electrons slightly more towards it

● London dispersion forces//Vanderwaals

○ Weaker or temporary dipole-dipole forces

○ Metallic

■ Occur between 2 metals● Radioactive isotopes and dating

○ Isotopes: atoms of the same element that differ in the number of neutrons

○ Radiation is used to date objects, create images, and trace movement of substances

○ Radioactive isotopes (i.e. carbon-14) decay over time to become more stable substance

(i.e. carbon-12 or carbon-13)

■ When small amount of radioactive isotope is placed in a sample, it is called a

tracer


14/42

● Electron energy vs. orbitals

○ Orbital: particular volume of space where an electron is most apt to be found most of the

time

○ More distant the orbital from the nucleus, the more energy the electrons have

○ When electrons absorb energy, they are boosted to a higher level

○ When electrons return to their original energy level, they give up energy in the form of

chemical energy

○ Octet rule: outer shell is most stable when it has 8 electrons (except when there is only

one shell)

○ Atoms react with other atoms by giving up, accepting, or sharing electrons to fulfill octet

rule

● Polar vs. nonpolar

○ Polar: covalent bond; unequal sharing of electrons (one atom exerts greater attraction for

the shared electrons and a slight charge separation results)

○ Nonpolar: covalent bond; sharing of electrons is equal

● Dissociation of water○ Acidic solutions dissociate in water, releasing hydrogen ions (H+)

○ Basic solutions dissociate in water, releasing hydroxide ions (OH-) and taking up

hydrogen ions (H+)

○ When water ionizes, it releases an equal number of hydrogen ions (H+) and hydroxide

ions (OH-)

● Solvents vs. solutes

○ Solvents: substance that does the dissolving; contains solutes

○ Solutes: dissolved substance; dissolves in solvent

● pH

○ pH scale is used to indicate the acidity or basicity of a solution○ Acids = 0-7

○ Bases = 7-14

○ pH = -log(H+)

■ pH is negative log of the hydrogen ion concentration

○ Buffer = chemical or combination of chemicals that keeps pH within normal limits

● Redox reactions

○ Reduced: atom which gains an electron; overall charge goes down

○ Oxidized: atom which loses an electron; overall charge goes up

○ OIL RIG (oxidation is loss, reduction is gain)

● Significance of hydrogen bonding to the unique properties of water and to life on Earth

○ Water has a high heat capacity

■ The many hydrogen bonds that link water molecules help water absorb heat

without a great change in temperature

■ Because the temperature of water rises and falls slowly, organisms are protected

from rapid temperature change

○ Water has a high heat of vaporization


15/42

■ This is because hydrogen bonds must be broken before water boils and water

molecules vaporize

■ Temperatures along coasts are moderate

○ Water is a solvent

■ Certain substances cannot dissolve in water and some break in water

○ Water molecules are cohesive and adhesive

■ The molecules cling together because of hydrogen bonding

■ Cohesion: water molecules cling together

■ Adhesion: water molecules cling to polar surfaces

■ This allows plants to move water from the soil up to its leaves

○ Water has a high surface tension

■ This allows some insects to walk on the surface of water

○ Frozen water (ice) is less dense than liquid water

■ As temperatures fall, hydrogen bonding becomes more rigid but also more open,

so water expands when it freezes

■ This allows life under the layer of ice in the winterChapter 3 - The Chemistry of Organic Molecules

● Organic molecule

○ Organic molecules must contain both carbon and hydrogen atoms

● Macromolecule, polymer, monomer

○ Macromolecule = a large molecule made by joining many smaller subunits

■ 4 main types = carbohydrates, lipids, proteins, nucleic acids

○ Polymer = large chain of smaller molecules

■ Constructed by covalently linking together a large number of monomers

○ Monomer = small molecules that is a subunits of a polymer

● Dehydration synthesis and hydrolysis reaction○ Dehydration synthesis = a water molecule is removed to form a bond

○ Hydrolysis reaction = a water molecule is added to break a bond

● What makes up carbohydrates, triglycerides, phospholipids, proteins, and nucleic acids

○ Carbohydrates = contain carbon, hydrogen, oxygen (1:2:1 ratio)

■ Monosaccharide = a simple sugar

■ Disaccharide = 2 connected simple sugars

■ Polysaccharide = larger chains of sugars

● Not soluble in water (unlike simple sugars), so they’re useful for energy

storage

○ Triglycerides = contain 3 fatty acid tails attached to a glycerol head/molecule

■ Glycerol head is polar

■ Fatty acid tails are nonpolar

■ Have many C-H bonds, so they do not mix with water

○ Phospholipids = contain 2 fatty acid tails, head made of a phosphate group, and glycerol

backbone

■ Head is polar and hydrophilic

■ Tails are nonpolar and hydrophobic


16/42

○ Proteins = contain chains of amino acids joined by covalent/peptide bonds

■ Amino acid has a central carbon atom surrounded by 3 constant groups (H,

COOH, and amino group NH2) and a functional group (different in each type of

amino acid)

■ There are 20 types of amino acids

○ Nucleic acids = contain chains of smaller units called nucleotides

■ Nucleotide has a phosphate (phosphoric acid), a pentose sugar, and a

nitrogen-containing base (A, T, G, C, U)

■ Sugars connected to phosphate groups by phosphodiester bonds

● Saturated vs, unsaturated fats

○ Saturated fat = fat containing no double bonds between carbon atoms; fat is completely

“saturated” with hydrogens

■ Solid at room temperature

■ Bad for you

○ Unsaturated fat = fat containing at least 1 double bond between carbon atoms

■ Liquid at room temperature■ i.e. most plant fats

● Primary, secondary, tertiary, and quaternary structures of proteins

○ Primary: sequence/order of amino acids

○ Secondary: folded shape of the polypeptide chain (i.e. helix, pleated sheet)

○ Tertiary: how folded portions interact with one another, creating the distinctive 3D shape

of the protein

■ 3D shape is due to hydrogen, ionic, and covalent bonding between non-adjacent

amino acids, as well as hydrophobic/hydrophilic interactions between different

parts of the amino acid chain

○ Quaternary: shape after the polypeptide chains bind to one another● Detailed structure of DNA

○ Pyrimidines

■ Thymine and cytosine

■ Smaller than purines

■ 1 carbon ring

○ Purines

■ Adenine and guanine

■ Larger than pyrimidines

■ 2 carbon rings

○ 2 hydrogen bonds connect adenine and thymine

○ 3 hydrogen bonds connect cytosine and guanine

○ Phosphodiester bond = connects sugar and phosphate groups

● Basic structure of ATP


17/42

○ ATP is a nucleotide made of adenosine (adenine + ribose) and 3 phosphate groups

Unit Six: Cell Structure & Function, Cell Transport, and Cell Communication

Chapter 4 - Cell Structure and Function

● Cell parts and cell theory sheets

○ (M) = membrane bound organelle

Organelle Location Function

Nucleus (M) Floating in the cytoplasm Enclose DNA (which is

typically organized into

chromosomes, which aresections of chromatin)

-Genetic Material

(chromatin)

In the space between

nucleolus and nuclear

envelope

diffuse threads containing

DNA and protein

-Envelope Surrounding nucleus Separates nucleus from

cytoplasm, has a double

membrane

-Nucleolus Inside the nucleus Make rRNA and join with

proteins to form thesubunits of the ribosome

-Nuclear Pores Holes in nuclear envelope Permits passage of proteins

into nucleus and ribosomal

subunits out of nucleus

Mitochondria (M) Floating in the cytoplasm Powerhouse of the cell,

site of cellular respiration,

produces ATP

Endoplasmic Reticulum

(M)

Very close to the nucleus Membrane of folded sacs,

comes in rough andsmooth versions

-Rough (granular) Right next to the nucleus,

between nucleus and

smooth ER

Hold ribosomes, help with

folding process of proteins

-Smooth After the rough ER, Produce testosterone,


18/42

slightly farther away from

nucleus

detoxify drugs, form

vesicles

Ribosome Some are found floating in

cytoplasm, some are

attached to rough ER

Place where amino acids

are joined via dehydration

synthesis to make proteins

Golgi Apparatus (M) In the cytoplasm, with one

side facing the ER and one

side facing the plasma

membrane

Processes, packages, and

secretes modified cell

products

Lysosome (M) Floating in the cytoplasm,

not in plant cells

Recycling center of cell,

recycle cellular material,

destroy organelles and

cells (via apoptosis) that

cease to function, digests

macromolecules and evencell parts

Centrosome (2 centrioles) Floating in the cytoplasm,

usually close to the

nucleus

Play a role in cell division,

organize the mitotic

spindle

Plastids Floating in the cytoplasm

of plant cells

Generally involved in

either the manufacture or

storage of food

-Chloroplasts (M) Floating in the cytoplasm

of plant cells

Converting light energy

into chemical energy

-Leucoplasts

(amyloplasts)

Floating in the cytoplasm

of plant cells

Starch collects around

these

-Chromoplasts Floating in the cytoplasm

of plant cells

Responsible for the

distinctive colors found in

fruits, flowers, roots, and

stressed and aging leaves

-Carotenoids

-Anythocyanins

Found in chromoplasts Pigments found in

chromoplasts

Vacuoles (M) Floating in the cytoplasm Store substances like food

or waste

-Foods Found in protists Handle process of

digestion and excretion

-Contractile Floating in the cytoplasm Regulatory organelle,


19/42

collect excess H2O and

empty it into the

surrounding medium

-Central Not in animal cells Large, fluid-filled sac that

stores metabolites andhelps maintain turgor

pressure

Vesicle (M) Floating in the cytoplasm Sac that transports

substances

-Peroxisome (M) Floating in the cytoplasm Breaks down fatty acids

and converts resulting

hydrogen peroxide to

water

Plasma Membrane Surrounds cytoplasm regulates entrance and exitof molecules

Cell Wall Not in animal cells Shapes, supports, and

protects cell

Nucleoid region Region inside bacterial cell DNA is found here

Cytoplasm Fills interior of cell,

outside nucleus

semifluid matrix that

contains organelles

Cytoskeleton Extend from nucleus to

plasma membrane ineukaryotic cells

Skeleton of the cell,

provide supports and giveshape to cell, move the cell

and its parts when

necessary

-Actin filaments Floating in the cytoplasm Protein fibers that allow

cell to move

-Microtubules Floating in the cytoplasm Cylinders of protein

molecules, help maintain

shape of cell, act as tracks

along which organelles can

move

-Intermediate fibers/

filaments

Floating in the cytoplasm Protein fibers that provide

support and strength

Cilia and Flagella Have a base in cytoplasm,

extend outwards

Helps cell move around

● Basic structures present in all cells


20/42

○ Plasma membrane

○ Nuclear region

○ Cytoplasm, which contains sugars, amino acids, proteins, and organelles (in eukaryotes)

○ Ribosomes (in prokaryotes, they are not on endoplasmic reticulum)

● Difference between eukaryotes and prokaryotes

○ Eukaryotes = more complex; have defined nucleus and organelles

○ Prokaryotes = bacterial cell, with no defined nucleus or other membrane-bound

organelles

○ Both have vesicles, vacuole, golgi apparatus

○

Eukaryotes Prokaryotes

Nucleus, which is membrane-bound No nucleus

Multiple chromosomes One plasmid

Membrane-bound organelles No membrane-bound organelles

Mitochondria No mitochondria

Larger ribosomes Smaller ribosomes

Chlorophyll in chloroplasts (in plants) Chlorophyll scattered throughout

cytoplasm

Size is usually 10 um-5 cm Size is usually 1 um-10 um

i.e. animals, plants i.e. archaea, bacteria

● How large cells are why is surface-area-to-volume ratio important

○ Eukaryotic cells are usually 10um - 5cm

○ Prokaryotic cells are usually 1 um-10 um

○ Having a large surface-area-to-volume ratio allows adequate nutrients to enter and to rid

itself of wastes

○ Small cells, not large cells, are likely to have an adequate surface area for exchanging

wastes for nutrients

● What are the Domains of prokaryotes

○ Prokaryotes can be divided into 2 domains: Archaea and Bacteria

○ Archaea

■ More diverse in shape

■ Cell wall made of polysaccharides and proteins

■ Plasma membrane lipids = glycerol and hydrocarbons

■ DNA and RNA base sequences more similar to Eukaryotes than to Bacteria

■ Live in extreme environments

○ Bacteria

■ Significance to humans


21/42

● Cause disease

● Decomposers

● Manufacturing (drugs, food, chemicals)

■ Shapes

● Bacillus (rod-shaped)

● Coccus (spherical)

● Spirilla (spiral)

■ Plasma membrane = phospholipid bilayer (phosphate and fatty acids)

■ Cell wall made of peptidoglycan

● What is included in the eukaryotic domain

○ 4 kingdoms = Protista, Fungi, Plantae, Animalia

○

Kingdom Nutrition Cell Wall Reproduction Other

Protista Photosynthetic or

heterotrophic byvarious means

None Sexual:

conjugation;Asexual:

binary fission

Paramecium,

amoeba, algae,euglena

Fungi Heterotrophs by

absorption

Present Sexual: spores Club fungi, sac

fungi, yeasts,

molds,

mushrooms

Plantae Autotrophs by

photosynthesis

Present Sexual: egg

and sperm,

spores

Grass, oak

trees, moss,

ferns, flowers

Animalia Heterotrophic by

ingestion

None Sexual: egg

and sperm

Humans, ants,

koalas, seals,

snails, sharks,

tuna, wolves

● Theory of endosymbiosis

○ Origins of eukaryotic organelles

○ Organelles were once free-living bacteria that were incorporated into a larger eukaryotic

cell

○ Evidence:

■ Virtually all organelles resemble bacterial cell in size and appearance■ Double membrane on cell organelles

■ DNA found in mitochondria and chloroplasts

Chapter 5 - Membrane Structure and Function

● Role of plasma membrane

○ Separates inside of cell from external environment

○ Regulates movement of materials into and out of cell (because plasma membrane is

semipermeable)


22/42

● Phospholipids and how they make up the bilayer membrane

○ Phospholipids = contain 2 fatty acid tails, head made of a phosphate group, and glycerol

backbone

■ Head is polar and hydrophilic

■ Tails are nonpolar and hydrophobic

○ In membrane, heads face outside and tails face inside, forming a sandwich of sorts

■ Phospholipids move laterally, but rarely flip flop

● Different roles of integral proteins

○ Channel proteins = passageway for molecules

○ Carrier proteins = combine with substance to help it pass through

○ Cell recognition proteins = glycoproteins recognize “self” cells; identify cell to

surrounding cells (MHC - major histocompatibility complex - unique to each person)

○ Receptor proteins = bind to a specific molecule causing a change in cell activity

○ Enzyme proteins = catalyze cellular reactions

● “Fluid-Mosaic Model” and how membrane is both a fluid and has a mosaic aspect

○ Fluid-mosaic model = individual components are loosely held together and movelaterally; made of phospholipids.proteins, and carbohydrate chains

○ Fluid aspect = the membrane can move and shift

○ Mosaic aspect = distribution of proteins

■ Supported especially by electron micrographs of freeze-fractured membranes

● Glycolipids/glycoproteins and their roles

○ Glycolipids = phospholipid with attached carbohydrate (sugar) chain

○ Glycoproteins = proteins with attached carbohydrate (sugar) chain

○ Function = adhesion, reception, cell recognition

● What can freely flow through the membrane and what cannot

○ Water and small, non-charged molecules (i.e. CO2, O2) freely pass through○ Ions, polar molecules (i.e. glucose, amino acids) require carrier proteins

○ Large molecules (i.e. macromolecules) are transported by vesicle formation

● Passive transport (diffusion, facilitated diffusion, osmosis)

○ Do not require energy

○ Diffusion = movement of molecules (CO2, O2, AA) down a concentration gradient (from

high to low concentration)

■ Continues until solute and solvent are evenly distributed

○ Facilitated diffusion = uses carrier proteins specific to certain molecules

■ Movement down a concentration gradient

■ Number of carriers available limits rate of diffusion

○ Osmosis = diffusion of water down a concentration gradient across a selectively

permeable membrane

● Osmotic pressure

○ Pulling pressure; the higher the osmolarity (solute concentration), the greater the pulling

power

○ Hypertonic solutions have high osmotic pressure

○ Hypotonic solutions have low osmotic pressure


23/42

● Water potential, its equation, and how to solve problems with it

○ Water always moves from an area of higher water potential to an area of lower water

potential

○ Water potential is affected by 2 factors: pressure and amount of solute

○ Water potential ( ) = Pressure potential ( ) + solute potential )

■ Pressure potential in an open container = 0

● Pressure raises water potential

■ Solute concentration of pure water = 0

● More solute decreases water potential

● Solute concentration is inversely related to solute potential

■ Solute potential = -iCRT

● i = number of particles that the molecule will make in water (for NaCL it

is 2, for sucrose or glucose it is 1)

○ Ionic compounds ionize in water, covalently bonded substances

don’t ionize in water)

● C = molar concentration● R = pressure constant = 0.0831 liter bar/mol K

● Temperature = temperature in degrees Kelvin = 273 + Co of solution

○ Low osmotic pressure = high free energy = low entropy = hypotonic = high WP

○ High osmotic pressure = low free energy = high entropy = hypertonic = low WP

● Isotonic, hypertonic, hypotonic (and apply these concepts)

○ Isotonic = solute concentration equal on both inside and outside membrane

○ Hypertonic = higher concentration of solute

■ Plasmolysis = shrinking of plant cell cytoplasm in hypertonic solution

■ Crenation = shrinking of animal cell

○ Hypotonic = lower concentration of solute■ Turgor pressure = swelling of a plant cell in a hypotonic solution

■ Lysis = cell bursts due to swelling of animal cell

○ Water always moves from a hypotonic solution to a hypertonic solution

● Active transport and some examples

○ Movement of molecules against concentration gradient

○ Purpose = to concentrate molecules or to create/maintain a gradient

○ Results in proton gradient

○ Require energy (ATP) and carrier proteins

○ i.e. Na-K pump, proton pump, membranes of mitochondria, chloroplasts

○ Na-K pump■ Occurs in neurons membranes

■ Results in concentration and electrical gradient

■ 3 Na+ from inside cell bind to transport protein

■ P group causes shape change and 2 K + ions enter

○ Proton pump and chemiosmosis: Formation of ATP

■ During redox reaction, H+ moves out through pump

■ Concentration gradient develops


24/42

■ H+ must pass back through channel via ATP synthase

■ Movement of ions (like waterfall) generates energy to make ATP from ADP and

PO43-

● Endocytosis, exocytosis, phagocytosis, pinocytosis (and all of their energy requirements)

○ They are all forms of vesicle formation

○ They all require ATP

○ Endocytosis = takes in substances

■ Phagocytosis = “to eat”; takes in food particles and other cells

■ Pinocytosis = “to drink”; takes in liquids and other very small particles

○ Exocytosis = eliminates waste and other substances

● Types of junctions between cells and their uses

○ Anchoring junctions = attach cells to one another (found in tissues that stretch - smooth

and cardiac muscle); 2 types are adherens junctions and desmosomes

■ Adherens junctions = anchoring junction that connects actin filaments of one cell

with actin filaments of adjacent cell

■ Desmosomes = anchoring junction that binds 2 cells together by connectingcytoskeleton with special proteins

● Contain keratin that increase rigidity in tissues

● Found in epithelium and smooth muscle

○ Tight junctions = fusion of plasma membranes between cells

■ Prevent leakage

■ In tissues, they act as barriers (i,e, intestines, kidneys)

○ Gap junctions = channels between cells

■ Allow for exchange of small molecules

■ Only in animal cells

○ Plasmodesmata = channels between plant cells■ The “gap junction” for plant cells

Chapter 33.3 - Maintenance of Homeostasis

● Define and give examples of homeostasis

○ Homeostasis = maintenance of constant internal body conditions; ability to return to

appropriate “set point” and maintain stable internal environment

■ Interplay between events that change internal environment and events that keep it

the same

■ Involves:

● Sensory receptors (sensory neurons) = carry impulses to central nervous

system (CNS) for processing

● Interneurons = direct impulses to CNS for processing; located in central

nervous system

● Efferent neurons = carry impulses away from CNS to effectors; efferent

is “exit” from CNS

○ Examples = regulation of body temperature, pH, blood pressure, and glucose

concentration


25/42

● Negative and positive feedback loops and how the body regulates temperature using a feedback

loop

○ Negative feedback loop = response acts against the stimulus (disturbance) and effects

changes in body to restore proper “set point”

○ Positive feedback loop = response acts to amplify stimulus

■ i.e. blood clotting results in more clotting and stops loss of blood, contractions

during labor and delivery continue and intensify until goal (birth) is

accomplished

Chapter 38 - Body Fluid Regulation and Excretory System

● Purpose of excretory system

○ Osmoregulation = maintain water and ion balance in the body

○ Excrete waste

○ Maintenance of homeostasis

● What challenges do freshwater, saltwater, and terrestrial organisms face with respect to water and

ion balance

○ Freshwater = hypertonic to environment■ Challenge = losing water

■ Solution = actively transport salt into cells in gills, produce dilute urine

■ Have scales and impermeable skin to reduce osmosis

○ Saltwater = hypotonic to environment

■ Challenge = gaining water

■ Solution = drink sea water, excrete salt through cells in gills

■ Have scales and impermeable skin to reduce osmosis

○ Terrestrial

■ Challenge = to get rid of excess solutes and toxins without losing too much water

■ All animals make nitrogenous water due to protein and nucleic digestion■ NH3 is toxic if not diluted & quickly excreted

● In simple organisms, excretion via cells

More complex organisms have excretory organs

● Water vs. energy input for making and excreting: ammonia, urea, and uric acid

○ Ammonia = most water needed to excrete, least energy needed to produce

○ Uric acid = least water needed to excrete, most energy needed to produce


26/42

○

● Structure of the human excretory system

○ Nephron = functional unit of kidney

■ Produces urine and maintains homeostasis

○ Blood goes to kidneys from inferior vena cava

○ Urine goes from kidney to ureter to urinary bladder to urethra

○

● Filtration, reabsorption & secretion, and excretion

○ All excretory systems utilize these 4 processes

○ Filtration = blood pressure pushes small molecules out of capillaries through

semi-permeable membrane into nephron, producing a filtrate

■ Not very selective

○ Reabsorption = returns “good things” from filtrate to blood

○ Secretion = removes potentially harmful substances from blood to filtrate

○ Excretion = final, “readjusted” filtrate (urine) is excreted

■ Urine is highly concentrated and contains just substances/molecules the bodywants to eliminate

■ Needed substances/molecules (water, nutrients) have been reabsorbed back into

bloodstream

● Know how water and salt balance is maintained in the kidneys

○ ADH (anti-diuretic hormone) from posterior pituitary increases reabsorption of water and

decreases urine output


27/42

○ Aldosterone from adrenal cortex stimulates reabsorption of sodium ions

● Example of ADH in kidney (example of maintenance of homeostasis, a negative feedback loop,

and cell communication)

○ Negative feedback loop

■ Release of ADH posterior pituitary into blood triggered when osmoreceptors in

hypothalamus detect an increase in the osmolarity of the blood above a set point

(plasma is too concentrated)

■ ADH acts on collecting ducts and distal tubule

■ H2O reabsorbed; H

2O moves back into peritubular capillaries

■ Thirst is promoted⇒ drinking reduces the osmolarity of the blood, which

inhibits the secretion of ADH, thereby completing the feedback circuit

○ ADH’s effects are an example of cell signaling

■ ADH binds to specific membrane receptor on a nephron cell

■ cAMP second messenger system is activated

■ Vesicles containing aquaporin water channels fuse with cell membrane lining the

lumen of the collecting tubule■ Additional aquaporin channels increase the rate of water reabsorption by the

collecting tubules

Cell Communication (supplemental reading)

● Purpose of cell communication

○ Necessary for all multicellular organisms to carry out crucial functions such as

development and survival

○ Universal mechanisms of cell communication is evidence of common ancestry

● Difference between local and long-distance signaling and how do cells perform each one

○ Local signaling = between adjacent cells

■ Direct contact● Signaling molecules pass between cells through cell junctions (gap

junctions in animal cells; plasmodesmata in plant cells)

● Molecules on cell membrane of 1 cell contact the receptors on an

adjacent cell

■ Messenger molecules

● Local regulators (i.e. growth factors, neurotransmitters) travel short

distances

○ Long-distance signaling = throughout body

■ Chemical (hormones)⇒ target cells

■ Electro-chemical via AP in NS

● Three steps in cell communication

○ Reception = signaling molecule is received at cell

○ Transduction = message is carried from the outside to the inside

○ Response = cell responds to signal

○ For more on these 3 steps, look at the next 3 questions

● Membrane receptor vs, intracellular receptor, and when would a cell use each one

○ Both are types of reception (step 1)


28/42

○ Membrane receptor = is embedded in cell’s plasma membrane

■ Examples

● Integral protein receptors bind to signaling molecules outside cell

● Signal transduction takes place without entering the cell

● 3 different classes

● Class names = means by which receptors transform external signals into

internal signals - via protein action, ion channel opening or enzyme

activation

○ Intracellular receptor = in cytoplasm or nucleus of target cell

■ Used if chemical signal = steroid hormone (hydrophobic) - can cross cell

membrane and nuclear membrane

■ Hormone/receptor complex turns on/off transcription

■ Examples

● Steroid hormones diffuse through cell membrane and bind with receptor

inside cell

● Hormone-receptor complex interacts with DNA turning on/off genes● Can change proteins being made

● Possible methods of signal transduction

○ Transduction (step 2) = binding of chemical signal causes a conformational (shape)

change in membrane protein

■ Changed shape triggers activities in the cell

■ Can be 1 step or a series of steps (= signal transduction pathway) involving relay

molecules (proteins) and/or second messengers

○ Phosphorylation cascade = in this signal transduction pathway, proteins activated by

addition of a phosphate group

○ Secondary messenger (cAMP) = in this signal transduction pathway, cAMP is used as a“Second messenger” (epinephrine, a hormone, is the first messenger)

● Possible responses to cell communication

○ Responses (Step 3)

○ Changes inside the cell leads to a specific cellular response

○ Responses can be:

■ In cytoplasm

● i.e. open/close ion channel, change cell metabolism

■ In nucleus

● i.e. turn on/off transcription of a gene (changes protein production)

○ Responses to same chemical signal can be different in different in different cells

■ i.e. epinephrine affects DS cells and CS cells differently

○ Examples

■ During fight or flight

● Cytoplasmic response = binding of epinephrine liver cells causes

glycogen to be converted to glucose

■ Treating anemia with erythropoietin


29/42

● Nuclear response = binding of growth factor causes transcription of a

specific gene (which will lead to production of a specific protein)

● More red blood cells produced

Unit Seven: Metabolism & Energy and Immunity

Chapter 6 - Metabolism and Energy

● What are the forms and types of energy?

○ The two main types of energy are Potential (stored energy or energy at rest) which is

stored in the chemical bonds of food, or Kinetic energy (energy of motion) which can be

solar, thermal, electrical, mechanical, nuclear, or sound energy.

● What are the two laws of thermodynamics?

○ First Law (aka- Law of Conservation of Energy): Energy is not created or destroyed, only

changed between forms.

○ Second Law: Energy cannot be changed from one form to another without a loss of

usable energy (no energy conversion is 100% efficient)

● What is heat--how is it a form of energy?

○ Heat is the most common form of energy to be lost in energy conversions, as in photosynthesis and cellular respiration. Heat is a measure of average kinetic energy.

● What is entropy?

○ Entropy is the degree of disorder in the universe. More entropy is a more stable

environment, with less potential energy: In a messy room there is less potential for it to

get more messy. An organized room has more potential energy because it could easily get

messy, so it has less entropy. Entropy= the measure of the amount of energy not available

to do work and the measure of disorder of a system.

● What is metabolism? Relate it to anabolism and catabolism

○ Metabolism is all the chemical reactions in a cell. Catabolism is made up of break-down

reactions that are exergonic. Anabolism is building reactions, which are endergonic.● Know vocab: Free energy (G), exergonic, endergonic, coupled reactions

○ Free energy (G) is the amount of energy available to do work. Exergonic reactions

release energy, they occur spontaneously.

○ Endergonic reactions require an input of energy.

○ Coupled reactions are when exergonic reactions fuel endergonic reactions, ATP works in

the cell to couple these reactions.

○ Vmax= initial reaction rate when excess substrate is available.

● What is activation energy? What do catalysts do to an activation energy?

○ Activation energy is the energy that must be added to make molecules react. catalysts put

stress on chemical bonds to lower the activation energy needed.

● What is the structure of an enzyme? How does it actually speed up a reaction?

○ Enzymes are specific to their substrate and have names similar to the substrate they react

on but end in -ase. Enzymes are proteins with active sites where they bind with the

substrate and the enzyme’s amino acids put stress on the substrate’s bonds to lower

activation energy. Enzymes are not changed or consumed in a reaction.

● What is the induced fit model?


30/42

○ The induced fit model occurs when the substrate makes the active site change shape to fit

better.

● What factors affect enzyme activity?

○ Temperature- Cold makes the enzymes too rigid to induce fit. Too hot denatures the

enzyme, the peptide bonds fail. Human enzymes temp should be 35-40 degrees C

○ pH- influx of ions disrupts ionic bonds that change the enzyme shape. Human enzymes

should be around 6-8.

○ Substrate concentration- reaction rate levels off as less substrate is available.

○ Enzyme concentration- reaction rate increases until all enzymes are in use

● What is competitive and noncompetitive inhibition?

○ Competitive: an inhibitor binds at an enzyme’s active site so it is “turned off” (blood

clotting)

○ Noncompetitive: Inhibitor binds to the allosteric site which causes an allosteric change in

shape so the substrate can’t bind to the enzyme.

○ Feedback inhibition is a type of noncompetitive inhibition where the end product of a

pathway can inhibit an earlier reaction in that sequence.● What are activators/ activation?

○ The activators cofactors or coenzymes are needed for enzymes to be active.

● What are coenzymes/cofactors? Give examples?

○ Cofactors are often metals that draw electrons from the substrate. (Copper, iron, zinc,

magnesium)

○ Coenzymes are organic molecules that aren’t proteins (vitamins- NAD, NADP). they act

like an electron shuttle between enzyme active sites.

■ OIL-RIG: oxidation is loss, r eduction is gain (of electrons)

● For what is ATP used? How is it created using ADP? What is the structure? How does that allow

for it to carry and release so much energy?○ Structure: adenine and ribose combine to form adenosine and 3 phosphate groups. ADP

has one less phosphate group.

○ The creation of the new bonds when ADP is hydrolyzed into ATP gives off 7.3 kcal per

mole. These bonds held high energy electrons extracted from glucose.

○ ATP is the usable energy in a cell.

● What is substrate level phosphorylation?

○ Substrate level phosphorylation is the creation of ATP by combining ADP and another

molecule that has a phosphate group by way of an enzyme.

● What is chemiosmosis?

○ The production of energy through protons diffusing down the concentration gradient of

the cell membrane to synthesize ATP is called chemiosmosis.

● What are the uses of ATP in a cell?

○ Chemical work- synthesize macromolecules

○ Transport work- pump substances across membrane

○ mechanical work- contract muscles, moves cilia+flagella or chromosomes

Chapter 36 - Digestive System and Nutrition

● What four things does digestion accomplish?


31/42

○ Ingestion (of food)

○ Digestion (of food into smaller molecules)

○ Absorption (of these molecules)

○ Elimination (of waste)

● Understand the difference between complete and incomplete digestive systems

○ No digestive system- cells use phagocytosis, vacuole merges with lysosome,

waste removed via exocytosisis

○ Incomplete- one opening, digestive sac. In acoelomates. Includes extracellular

digestion by enzymes and intracellular digestion in the cells lining the digestive

cavity

● What occurs during chemical vs. mechanical digestion?

○ Mechanical digestion involves only the chewing of food and the stomach

churning it. .

○ Chemical digestion is the breaking down by enzymes and HCl

■ Pepsin in stomach and trypsin in small intestine digest protein

■ Amylases digest starch

■ Lipases digest lipids

■ nucleases digest nucleic acids

● What is the pathway of food entering a human body?

○ Mouth → (salivary glands) → tongue → (epiglottis) → esophagus→ stomach →

pyloric sphincter → duedenum → (pancreas releases bicarconate)→ (gallbladder

releases bile) →jejunum→ ileum→ → (absorbed nutrients go to the liver) →

ileocecal valve→ ascending colon → transverse colon→ descending

colon→sigmoid colon→rectum→ anal sphincter● What role does each organ of the digestive system have?

○ Mouth is a site of mechanical digestion and chemical by saliva

○ the tongue forms balls of food called bolus, and pushes it down the throat

○ The esophagus uses muscle contractions called peristalsis, and moves the bolus

down

○ The cardiac sphincter controls passage of bolus into the stomach

○ The stomach digests food, both mechanically by churning, and chemically by

using HCl to lower pH, activating pepsin to denature proteins, and killing

bacteria. Here, bolus is turned into liquefied chyme.○ pyloric sphincter controls passage of chyme into the duodenum.

○ Most digestion takes place in the duodenum - the pH of chyme increases and bile

from gallbladder and amylase, protease, lipase, and nucleases from the pancreas

break down the chyme further.

○ The jejunum and ileum absorb these nutrients into the bloodstream


32/42

○ the large intestine/colon reabsorbs water from the digested material, being very

firm at the sigmoid colon

○ Rectum stores waste until elimination

○ anal sphincter prevents elimination until one is ready.

● What are the accessory organs and what are their roles?

○ Accessory organs are organs that food does not pass through, but they aid the

digestive process.

○ Salivary glands make mucous and amylase released in the mouth

○ epiglottis covers trachea to prevent choking

○ the liver produces bile (used to break down fats), which is then stored in the

gallbladder. The liver also processes nutrients and detoxifies chemicals

○ The pancreas releases bicarbonate to increase the pH of chyme and tells

gallbladder to release bile.

■ Exocrine pancreatic functions- produce and release bicarbonate + enzymes

■ Endocrine pancreatic functions- make and release insulin and glucagon to

regulate blood sugar

● Relate the concept of maximum surface area to the structure of the small intestine

○ Maximum surface area allows for more efficient absorption, which is why the

jejunum and ileum in the small intestine are lined with villi and microvilli to

absorb nutrients.

Chapter 21 - Viruses, Bacteria, and Archaea

● Describe the structure of a virus

○ viruses are “non-cellular infectious agents”

○ outer capsid of protein subunits○ inner core of DNA or RNA

○ possible outer membrane envelope

○ possible enzymes for DNA/RNA production

● Understand the relationship between a virus and its host

○ Viruses are obligate intracellular parasites- meaning they need to enter cells to use their

organs to reproduce. They are host-specific, only certain viruses attack certain cells.

● Understand the life cycle of a virus (lytic and lysogenic)


33/42

○

● What is a bacteriophage?

○ Bacteriophages are viruses that target bacteria as their hosts. They kill bacteria via the

lytic cycle.

● What are viroids and prions?

○ Viroids are naked strands of RNA (no capsid) that are found in plants and cause plant

diseases.

○ Prions are proteins in the brain that were folded wrong and, when interacting with other

brain cells, cause them to fold in different ways, making them function wrong.

● Describe the structure of a prokaryotic cell

○ Prokaryotic cells have no nucleus or membrane-bound organelles. They have a nucleoid

region where a single chromosome DNA ring resides, with accessory plasmids (smaller

rings of DNA). They either have a capsule (well-organized exterior of glycocalyx), or a

slime layer (less-organized exterior of glycocalyx)

● How is a bacterial cell wall different from a eukaryotic cell wall?

○ Bacterial cell walls have peptidoglycan, while eukaryotic cells contain cellulose.

● How do prokaryotic cells reproduce?

○ Binary Fission. The chromosome replicates, the DNA drifts apart, the cell enlarges, and

then pinches in the middle to divide into two cells. Neither metaphase or anaphase take

place.

● What are some ways that genetic recombination can occur in prokaryotes?

○ Conjugation- bacterium pass DNA to each other through sex pili (pili tube that joins the

cells)

○ Transformation- Bacterium pick up free pieces of DNA

○ Transduction- Bacteriophages carry segments of bacterial DNA between cells they infect

● What are the various modes of nutrition in prokaryotic cells?

○ Photoautotrophs- use CO2 and sunlight to make energy, primitive cells don’t give off O2,

but advanced ones do.


34/42

○ Chemoautotrophs- carry out chemosynthesis by oxidizing H2, H2S, or NH3 to get energy

to reduce oxygen into an organic compound

○ Chemoheterotrophs- decompose large organic molecules into smaller ones and then

absorb them. These cells may form symbiotic relationships with roots to fix nitrogen.

● What is the difference between gram-positive and gram-negative bacteria?

○ Gram-positive- Thick layer of peptidoglycan, retain iodine stain and turn purple

○ Gram-negative- Thin layer of peptidoglycan, do not retain stain and look pink.

● Compare and contrast the domain Archaea to the domain Bacteria

○ Bacteria and Archaea diverged shortly after life began. Archaea are said to be closer to

Eukarya evolutionarily because they have similar ribosomal proteins. Archaea and

Bacteria are both prokaryotic, but only bacteria are found in humans. Archaea exist only

in extreme environments. Bacteria and Archaea rRNA are sequenced differently.

● What are some types of Archaea?

○ Methanogens- found in anaerobic environments or animal intestines. produce methane

which contributes to the greenhouse effect.

○ Halophiles- live in high salt concentration○ Thermophiles- live in high temperatures

○ alkaliphiles- live in high pH

○ acidophiles- thrive at low pH

Chapter 35 - Lymph Transport and Immunity

● Understand the differences between specific and nonspecific defense mechanisms.

○ non-specific: first response, reacts to any infectious agent the same way, no

memory

○ specific: responds to only certain antigens, forms memory

● Understand the various types of non-specific defense (physical barriers, chemical

defense, inflammatory response, phagocytosis, the complement system, the

temperature response).

○ First line: Skin, mucous membranes, chemicals (oils, lysozyme in tears, HCl in

stomach)

○ Second line: internal defense

■ Phagocytic cells eat antigens, neutrophils are small, macrophages are big

eaters.

■ The complement system uses the Membrane Attack Complex to kill

non-self microbes by poking holes in their membrane, making water rush

in.■ Inflammatory response- Mast cells release histamines to trigger

vasodilation (widening of blood vessels) to attract more WBC’s

■ An increase in temperature (fever) causes an increase in phagocytosis and

stops microbe growth

● Identify the types of white blood cells that are involved in non-specific defense

(macrophages, neutrophils, natural killer cells).


35/42

○ Neutrophils= first responders, small eaters

○ Macrophages=BIG eaters, the clean-up crew

○ Natural killer cells poke holes in non-self cells

● Explain what the MHC (Major Histocompatibility Complex) is and how it helps the body

determine self vs. non-self.

○ The MHC involves the glycoprotein markers that all self-cells have, but

non-self-cells do not have. Immune cells attack those without the self-cell markers

● Identify the types of white blood cells involved in the body’s specific immune defense.

○ T-Cells: Mature in thymus, cell mediated immunity

■ Helper-T cells

■ Killer T-cells

○ B-Cells: Mature in bone marrow, humoral immunity. Produce antibodies

● Explain, in detail, the two parts of the body’s specific immune defense (cell-mediated

response, humoral response).

○ Cell-Mediated

■ Activation phase- Macrophage eats antigen, presents pieces of antigen,

which activates helper and killer-t cells

■ Effector Phase- Helper and killer-t form memory and replicate, Helper-t

releases cytokines (alarms) to alert other cells, killer-t kill infected cells.

○ Humoral Immunity

■ Activation Phase- macrophage eats and presents antigen, helper-t binds to

macrophage, macrophage releases Interleukin-1 which activates helper

t-cells to release cytokines to clone self. Helper t-cells bind to immature

b-cells and release cytokines, making b-cells clone. Most become plasmacells which make and release antibodies, others become memory cells.

● Explain what an antibody is and what it does.

○ Antibodies bind to antigens to prevent attachment to other cells and make it easier

for macrophages to eat them. They are Y shaped.

● Explain the concept of clonal expansion and its role in the body’s specific immune

response.

○ Clonal expansion makes more Helper t-cells with the memory of that antigen

○ clonal expansion of B-cells means that antibodies are produced faster for that

specific antigen● Explain the difference between primary and secondary responses to infection.

○ primary- the first time a body is exposed. 10-17 days for peak response

○ secondary- cells already have memory formed, 2-7 days for peak response

● Explain the difference between active and passive immunity and examples of each.

○ Active is when your own body makes the antibodies, passive is when they are

obtained from elsewhere.


36/42

○ Naturally acquired active immunity- exposure to live pathogen

○ Artificially acquired active immunity- exposure to vaccine

○ Artificially Acquired Passive Immunity- obtained antibodies from blood/fluid of

another animal, short-term (like with rabies)

○ Naturally Acquired Passive immunity- newborn gets antibodies from mother via

placenta or breastmilk

● Explain how a vaccine works and how they were discovered.

○ Edward Jenner first used cowpox as a vaccine for smallpox. Louis Pasteur

injected weakened cholera into chickens, who were later immune. Vaccines

trigger the production of antibodies, forming resistance.

● Discuss various disorders of the immune system and their causes.

○ AIDS/HIV: attacks helper T-cells

○ Allergies: immune response to a harmless antigen

○ Auto-immune diseases like rheumatoid arthritis and multiple sclerosis- immune

system fights itself.

Unit Eight: Respiration & Circulation

Chapter 8 - Cellular Respiration

● What is the over-all goal/purpose of cellular respiration

○ conversion of chemical energy to ATP; breakdown carbohydrates and other metabolites

○ Requires oxygen and gives off ATP

● What are the end products of cellular respiration

○ 36-38 ATP

○ 4 CO2

○ 6 H2O

● What are the inputs and outputs of: glycolysis, oxidation of pyruvate(prep state), Krebs cycle, and

oxidative phosphorylation? Know where the steps occur.

○ Glycolysis Inputs: Glucose, 2 ATP(came from the electron transport chain) NO

OXYGEN!!!; Outputs: 2 Pyruvate, 2 NADH, 4 ATP (2 ATP used to start glycolysis);

Where: cytoplasm

○ Prep Reaction Inputs: 2 Pyruvate; Outputs: CoA (Acetyl CoA), CO2 given off, 2

NADH ( electrons taken from pyruvate and added to NAD+); Where: Mitochondrial

Matrix

○ Krebs Cycle Inputs: 2-C Acetyl CoA, 4-C molecule(OAA), 6 NAD+, 2 FAD; Outputs:

4 CO2, 6-C citrate molecule, 6 NADH, 2 FADH2, 2 ATP; Where: mitochondrial matrix

○ Oxidative Phosphorylation Inputs: Electrons carried from the 10 NADH and 2

FADH2, 6 O2; Outputs: 6 H2O, 34 ATP; Where: Cristae of mitochondria

● What is the fate of a glucose molecule if no oxygen is present?

○ Fermentation - Lactic acid or alcoholic

○ Alcoholic fermentation - yeasts produce ethyl alcohol, CO2, 2 ATP; Uses- baking (CO2

helps bread rise)


37/42

○ Lactic acid fermentation - humans, certain bacteria, fungi produces - lactate (from the

pyruvate), 2CO2, and 2 ATP; Uses - build up in the muscles when there is lack of oxygen

in the muscles

● What is the role of oxygen in cellular respiration? How does it work?

○ Oxygen combines with the H+ transported to the electron transport chain to create H2O.

Since oxygen is the final receptor, if oxygen isn’t present the chain will not work and

ATP will not be produced.

○ How it works - the oxygen at the end of the transport chain pulls the electrons through the

chain to generate enough energy to create ATP.

● What is the purpose of of fermentation? Know the differences between plant and animal

fermentation.

○ Purpose - since there is no oxygen, it doesn’t use oxygen as the final receptor.

Fermentation prevents NADH from building up and helps to create NAD+ and keep the

chain going

○ Differences - (look at the question: what is the fate of a glucose molecule…)

● Understand the role of NAD and FAD and how many ATP can be generated from NADH andFADH2

○ Role of NAD and FAD - to transport the H+ ions from each step of cellular respiration to

the electron transport chain.

○ NADH produces 3 ATP while FADH2 produces 2 ATP

● What is the net ATP gain per glucose molecule when no oxygen is present and when it is present

(know their efficiencies as well)?

○ Net ATP no oxygen - 4 ATP; 2% efficiency

○ Net ATP oxygen - 36-38 ATP; 38 % efficiency

● Understand how the electron transport chain operates chemiosmosis

○ NADH passes its electrons through the electron transport chain○ The H+ ions are pushed through protein pumps outside to create a concentration gradient

○ The H+ ions then go through ATP synthase to generate enough energy to combine the

ADP and phosphate group to create ATP (not really sure if thats how it works)

■ ATP Synthase is going up the concentration gradient (H+ ions are going to a

more concentrated area) so the energy needed for that to happen basically

combines ADP and the P1 group to create ATP (which is used I think)

● Be able to trace the carbons, hydrogens, and oxygens of the original glucose molecule to their

final fate at the end of cellular respiration

○ Glucose (C6H12O6) + 6O2

○ Carbon - 2 CO2 removed from pyruvate in prep reaction; 4CO2 made in the Krebs cycle

○ Hydrogen - 2 NADH from glycolysis, 2 NADH from prep reaction, 6 NADH and 2

FADH2 from Krebs cycle; final fate: 6H2O made in oxidative phosphorylation

○ Oxygen - 6O2 becomes 6CO2; O6 (from glucose) combines with the H+ to become H2O

Chapter 34 - Circulation and Cardiovascular Systems

● Understand the difference between open and closed circulatory systems and what type of animals

have each type


38/42

○ Open: Heart pumps hemolymph vis vessels into tissues spaces (hemocoel); animals-

grasshopper (arthropod), molluscs DOES NOT CARRY OXYGEN!

○ Closed: Blood pumped by the heart into a system of blood vessels (valves prevent

backflow); animals- annelids (earthworms), some molluscs, all vertebrates

● Describe the flow of blood through the pulmonary and systemic circuit

○ Pulmonary - heart pumps blood the deoxygenated blood to the lungs and then back to the

heart (O2 - CO2 exchange)

○ Systemic - heart pumps blood to the tissues in the body back to the heart

○ Double pumping action is an adaptation to breathing air on land

● Understand the difference between arteries and veins. How are they different in structure and

function?

○ Arteries - Structure:have thick walls, muscular, able to expand with sudden increase of

blood (resilient); Function: carry blood away from the heart (oxygenated)

○ Veins - Structure: larger than arteries, walls much thinner than artery, valves open

towards heart (prevents backflow); Function: returns blood to the heart, collect blood

from capillary beds● What are the components of blood? What are roles of each component?

○ Plasma: maintains blood osmotic pressure and pH, blood volume, fight infection,

clotting; components - H2O, proteins (albumin, globulins, fibrinogen), and solutes

○ Red Blood Cells: carry oxygen through the body; components - hemoglobin, oxygen

○ White Blood Cells: fight infection; component - lacks hemoglobin

○ Platelets: help form blood clots; components - no nuclei, serum

○ Serum: fluid above the clotted material; components - part of platelets, contains all the

same parts as plasma except fibrinogen

● How do the materials carried in the blood get into body tissues?

○ The capillary beds are very thin the red blood cells pass through and exchange with tissuefluid (i think)

● How does blood clot?

○ Platelets clump at the site of the wound to seal it.

■ platelets release a clotting factor that converts prothrombin to thrombin (forms

long threads of fibrin)

■ fibrin winds around the clot to provide framework

● How is blood pressure determined? What is systolic and diastolic pressure?

○ determined by the amount of pressure required to stop the flow of blood through an artery

○ Systolic Pressure: pressure of blood pushing out on the wall of arteries during ventricular

contraction/ results from blo

unit one animal behavior experimental design

Documents