(1) all organisms are composed of one or more cells

(2) cells are the smallest living hting

(3) cells arise from previously living organisms 

All Cells Have...

(1) Plasma membrane

(2) Centrally located DNA

(3) Ribosomes

(4) Cytosol 

Macromolecules and Monomers:

(1) Proteins

(2) Complex Carbs

(3) Lipids and Phospholipids

(4) Cytosol 

(1) amino acids

2) simple sugars

(3) glycerol + FAS (+ PO4)

(4) nucleotides 

Secondary Protein Structure

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Tertiary Protein Structure

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Quaternary Protein Structure

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(1) Catalysts-enzymes

(2) Defense-recognize foreign molecules

(3) Transport- transport small molecules and ions

(4) Support- structural support in cells

(5) Motion- moving materials in cells

(4) Regulations- intercellular messengers 

A and T

G and C 

A and U

G and C 

Core of biological membranes

Made of glycerol, fatty acids, and phosphate

Hydrophobic middle prevents water/polar molecules from entering 

C:H:O ratio

-Simplest sugars

-most common have 6 sugars

-macromolecules made of monosaccharide subunits

-starch and cellulose 

-Protists, Fungi, Plants, Prokaryotes

-Protection and Support

-Made of fibers of cellulose 

(1) Cellular Organization

(2) Sensitivity

(3) Growth

(4) Development

(5) Reproduction

(6) Regulation

(7) Homeostasis 

-Cell wall composed of peptidoglycan

-Flagella used for movement

-Ribosomes

-no membrane bound organelles

-simple circle of DNA 

-DNA complexed with proteins

-Thread-like strands of DNA during division 

-Bonds monomers to make lipids and carbs

-Makes proteins

-Rough ER and Smooth ER 

-Manufatures proteins for export

-Studded with ribosomes

-Synthesize proteins on surface and export from the cell by being sent to vacuole, lysosome, or embedded in membrane

-Makes lipids 

-Little to no ribosomes

-Embedded with enzymes which catalyze the synthesis of lipids 

-Made up of rRNA

-serve as sites of protein synthesis by translating mRNA 

-Double membrane

-Own DNA

-Powerhouse - makes ATP

-Own DNA

-Double Membrane

-Photosynthesize 

Actin Filament

-Thinnets

-Labile

-Very easy to break down and rebuild 

-Most Stable

-Generally isn't broken down

-3 dimensional to keep structures in place 

Microtubule

-Largest

-Hollow

-Important for transport

-V. hard to break down and rebuild 

-Two layers of of phospholipids with hydrophobic end on the inside

-Impedes the passage of water soluble molecules 

(1) Transporters-allow only certain substances to enter/leave

(2)Enzymes-carry out many chemical reactions on the interior surface of the plasma membrane

(3) Cell Surface Receptors- detect chemical messages with receptor proteins on surface

(4) Identity Markers- identify to other cells

(5) Adhesion - Glue themselves to another cell

(6) Anchor membrane to cytoskeleton 

-Through the Phospholipid Bilayer

-Small, nonpolar molecules and ions diffuse freely through hydrated channels in proteins 

-Transports solutes like sugar and amino acids

-Transport in either direction depending on concentration gradient

-If more conc. outside then protein moves solute inside cell

-Physically binds solute to one side of protein and releases on other end 

-Transport of Water

-Hyperosmotic: more concentrated

-Hypoosmotic: Less concentrated 

-Requires energy (ATP)

-Protein is fueled by ATP and the shape changes to allow a proton to pass through 

A protein binds to another protein and makes a channel to the other side

-Direct communication and very efficient 

-Part of Aerobic Respiration

-Takes place in cytoplasm 

-Input: Glucose, 2 ATP, 4 ADP, 2 P, 2 NAD 

-Output: 2 ATP, 2 Pyruvate

-Enzymes are catalysts 

-Occurs in Mitochondria

-Input: 2 Pyruvate, 2 NAD,

-Output: Acetyl CoA, CO2, NADH

-In mitochondria

-Input: Acetyl-CoA, 2 CO2

-Output: 2 CO2, 4 carbons, 3 NADH, 1 FADH2, 2 ATP, and many electrons 

-NADH transfers electrons to a series of electron carriers that extract the energy and use it to pump hydrogens across the membrane. ATP synthase then uses the energy of the falling hydrogens to make ATP

-Input: NADH and electrons

-Output: Lots of ATP 

6 CO2 + 12 H2O + energy -> C6H1206 + 6CO2 + 6 H2O

-Light dependent reaction

-Produce ATP and NADPH

-Goes through calvin cycle  

- Reduces Carbon Dioxide

-Occurs in the chloroplasts 

Internal membrane of plants stacked in columns called "granum" which house photosynthetic pigments which capture light energy and store machinery for making ATP 

An electron is emitted and never comes back but moves to a second system because it needs to fill the hole. The emitted electron reduces NAD.

-Lost electrons are replenished by splitting water

-NADPH is the electron accepter 

-Light independent reactions

-Carbon is fixed

-occurs in stroma

-5 carbon sugar is carboxylated to forma 3-carbon compound via rubisco activity 

-Makes glyceraldehyde 3-phosphate that is converted to fructose and glucose which combine to make sucrose 

-Conversion of fructose to glucose

-enter into glycolysis

-formation of transport disaccharides

-formation of starches

-other biosynthesises 

-acts as an oxidizer and interferes with the calvin cycle

 -If CO2 present it binds to make glucose, if O2 is present it binds 

-O2 is incorporated into RuBP, which undergoes additional reactions that release CO2

-No energy is harnessed!!!!! 

-2 identical daughter cells

-enzyme breaks H bonds between nitrogenous bases and as strands fall apart enzymes come in with new nucleotides and assemble complementary strands 

-2(n)

-twice the number of haploid due to contribution from mom and dad 

An identical strand of DNA which shares a centromere with another chromatid after replication

-can be a single or double chromatid chromosome 

Cell expands and makes structures and molecules

-Single chromatid present 

-2nd growth phase

-Prepares for genome separation

-Organelles are duplicated

-Enzymes are made to help with process

(1) Interphase

(2) Prophase

(3) Metaphase

(4) Anaphase

(5) Telophase 

-DNA condenses

-Assembling of microtubules lead by centrioles

-Nuclear membrane breaks down 

Telophase

-Cell elongates

-Nuclear membrane reforms

-c'somes decondense

-centrioles and microtubules disappear 

Controls at

1) G1/S

(2) G2/M

(3) Spindle 

(1) cell decides whether or not to divide based on growth factors and nutritional state and genome being intact

(2) asses DNA replication if bad it doesn't go

(3) ensures all c'somes are attached before anaphase 

(1)Prophase 1

(2) Metaphase 1

(3) Anaphase 1

(4) Telophase 1

(5) Prophase 2

(6) Metaphase 2

(7) Anaphase 2

(8) Telophase 2 

-DNA condenses

-Homologous c'somes become closely associated

-crossing over occurs and DNA segments are exchanged 

-Nuclear membrane breaks down

-Spindles form 

-Nuclear membrane reforms

-4 different haploid cells

-no two cells are the same because of crossing over 

-composed of a particular DNA sequence

- 2 alleles 

Mating between a phenotypically dominant individual of unknown genotype and a homozygous "tester" done to determine if the individual is homozygous or heterozygous

-If homozygous they will alll show the dominant allele

 -If heterozygous both will show

More than 2 alleles

-Codominate  

Each allele has it's own affect and no single allele is dominant

-the effects of both alleles are seen 

-Allele has more than one affect on phenotype

-Allele can be dominate for one thing and recessive for another

ex: Y allele is dominant for black hair and recessive for abnormal fetal development 

-Phenotype is controlled by two genes

-Mouse coat colors are controlled by a gene for pigment and a gene for banding 

-Heterozygote is different from both homozygotes

-both alleles are different in how they are expressed

-Ex: white spotting in cat coat color, two alleles S and s. 

-SS = white on more than half of body

-Ss =less than half are white

ss= no white at all 

-When hot, pigments aren't deposited and coat is white

-When cold, pigments are deposited and cats are black  

-Multiple genes involved in what the trait looks like

-continuous variation because the gradation in degree of difference between phenotype and genotype

-Trait determined by a gene on the x chromosome 

- Inherited (and carried) together on the same c'some

-Loci near to eachother are less likely to be separated by crossing over

-Info passes from genes to an RNA copy and hte RNA copy directs the sequential assembly of a chain of amino acids

-DNA goes through transcription to form RNA which goes through translation to make a protein 

-ribosomal RNA

-Provides site where polypeptides are assembled 

-Transfer of DNA to RNA

-RNA polymerase binds to a promoter binding site located at the beginning of a gene and moves along the strand adding G, C, A and U to the chain until hitting a stop signal 

-In prokaryotes a ribosome binds to mRNA as soon as its spit out

-In Euks a series of enzymes come in and recognize non-coding areas and then splice together coding areas to make mature RNA 

-Information in transcribed mRNA is used to direct production of amino acids

-nucleotide squence of mRNA transcript is translated into amino acids in the polypeptide

-rRNA binds to "start" sequence on mRNA and it is assembled three peptides at a time 

-set of 3 nucleotides which codes for a specific amino acid

-amino acids can have more than one codon

-Not all genes are expressed at the same time because every cell has identical DNA and they have to be able to turn off some traits so that they can function differently.

-Allows organisms to direct development, respond to changes, maintain homeostasis 

-During crossing over in prophase 1

-Mistakes in pairing due to several copies o f asequence existing in diff location on a c'some

- one c'some has extra and the other has not enough 

-Tetraploid

-Has 4 sets instead of 2

-end with extra sets of c'somes

-tetras and diploids cannot mate 

-occur between homologous c'somes

-A break and before repair the segment flips and as a result crossing over doesn't occur right and there is extra on some and missing parts on others

-ionizing radiation

-Gamma and X-rays induce loss of electrons in molecules that can absorb their waves

-creates free radicals

-breaks DNA and changes bases 

-nucleoside analogs which mimic DNA nucleotides and pair incorrectly with DNA strand

Over many thousands of generations a high degree of inbreeding will tend to ___ the frequency of lethal double recessive combinations in a population 

-small change in a species

 -change within a population

- 4 phenomena critical to evolution of eukaryotes and diversification of eukaryotes 

(1) Endosymbiosys

(2) Colonial Organization

(3) Multicellularity

(4) Sexual Reproduction 

-eukaryotic plan is a combination of organisms coming together

-mitochondria, flagella, chloroplasts

-Archaebacteria which help do respiration where swallowed 

-huge organisms (multicellular) may have come from colonialization

-functional division of labor among somatic cells

-tissue level organization 

-gives the advantage of diversity by rapidly developing new life and variance

-gets rid of lethal double recessives and fixes mutations 

-Species change over generations

-Earth is very old 

-plants preceded animals

-all organic life has the same origin 

-organisms arise spontaneously and change over time

-inheritance of aqcuired characteristics

-wrote first book on evolution 

-sent paper to Darwin

-came up with same idea as Darwin and the two converged 

(1) All species share a common ancestry

(2) each species arose from another that preceded it in time

(3) each species originated in a single geographic location

(4) similar species are closely related (relatively recent divergence)

(5) extinction is permanent 

(1) Populations have the tendency and potential for unlimited growth

(2) The conditions of life are limited

(3)The environment is constantly changing

(4) Only a fraction of individuals reproduce

(5) Traits vary and can be heritable

(6) Life activities determine the success of variants

(7) Successful variants produce more offspring

(8) Natural Selection results in the accumulation of favorable variations and the loss of unfavorable variations 

(1) Variation in trait

(2) heritable

(3) advantagous

(4) mating opportunities 

(1) Natural Selection

(2) Mutation

(3) Migration

(4) Nonrandom Mating

(5) Genetic Drift 

-adaptive change

-phenotypes are selected for 

-Loci with more variation than can be explained by mutation

-Frequency is >5%  

-change in the median value of a trait

-the average gets higher or lower 

-changes the distribution

-stabalizes median value

-minimizes small and big so that most have medium trait 

-moving away from the median trait

-disrupting the median so there is no middle but only the extremes 

-most mutations are harmful in the environment that the organism is experiencing

-exception: albinism

-must be in germ line tissuesto be heritable 

Nonrandom Mating

Assortative vs. Disassortative 

Assortative: like with like

Disassortative: opposites attract 

Sexual Selection

Intersexual vs. Intrasexual 

Intersexual: females choose males based on good genes

Intrasexual: male to male combat where mating is controlled by dominant male or by displacing dominant male 

-random loss of alleles

-can drift to fixation or loss randomly

-more important in small populations becuase the chance of a complete loss of an allele is higher 

-Type of genetic drift

-reduction of population to a small, random sample due to some sort of catastrophe 

-migratory populations

-moving to geographically isolated area so that now there is a sample of the population from the homeland  

-Large, randomly mating, isolated, mutation and natural selection-free population

-all of this results in no change in allele frequency 

-percievable difference

-it looks different and is an arguably different species 

-a group of interbreeding individuals

-reproductive isolation precedes divergence 

Morphological Divergence

-"other"

-Species can form when populations split and become isolated geographically 

-widespread, long periods of time 

-large scale movements of populations

-a start to divergence 

-speciation without geographic isolation

-reproductive barriers arise within populations

-"same place" 

-isolation based on environment and ecological surroundings

-preference of breeding habitat or general habitat rarifies mixed breeding 

-separated by time periods

-can be for mating, spawing, etc 

-event does not produce another generation

-because hybrid is apparent to enemies  or becuase c'some pairing fails as a result of unmatched number of c'somes

- reduction division failure of diploid gamete 

-instand speciation

-cannot breed back in

-important in evolution of flowering plants 

-when two species hybridize

-c'somes do not pair right as a result of one set from two different species 

-all of the c'somes come from one species

-due to an error in meiosis that causes individual to have four sets of c'somes 

-less common 

-speciation event produced by multiple speciation events in a short period of time

-one event lead to a cluster of species

-colonization leads to establishment in another place where the new niches were open for the organism to fit into 

-system is more nutrient rich

-reduction of oxygen in the bottom of the lake 

106:16:1

C:N:P 

1.7% of total water and  68.7% of freshwater comes from

-water moves through plants and evaporates off of plant surfaces

-10%atm water 

-water bearing rock and rock material

Unconfined: flow is unconfined and can be tapped into by a plant root or it goes to streams

Confined: Confined by a layer of impervious Silt which is only tapped by humans for well water 

-water from rain weeks ago is released during another storm causing a change in level

-the water from the past is being pushed out to make room for new water 

-Combination of ecology and hydrology

-biological consequence of aquifer and stream interactions 

-99.9% from sediments and rocks

-chemical weathering (and oxidation processes) releases the carbon 

-rocks continuously created and destroyed 

-enzyme which is possessed by algae and some plants

-convert H2CO3 to CO2 for use in reactions

-CO2 takes place at photosynthesis after dark 

-Photosynthesis without oxygen

-Done by green and purple bacteria

-use H2S as an electron donor 

-greenhouse gas

-another way of getting energy out of carbon reactoins

-methanogeneis: creation of methane 

-N2 is difficult to bring into the ecosystem but is the most common gas

-During nitrogen fixation N2 is converted into a useable form

-Only photosystem 1 is functional

-cyclic phosphorylation provides ATP

-no O2 produced

-Still have part of photosynthetic process but only that which generates energy

-isolated from oxygen 

-done by microbes and many animals

-organic N to NH4

-heterotrophs can ammonify N2 

-NH3->NO2->NO3

-Nitrosomonas, nitrobacter 

-converting NO3 back to N2

-done by many bacteria 

Autotrophs do what with N2?

Heterotrophs do what with N2? 

Auto: Organic N Synthesis (by primary producers)

Hetero: Ammonification

-weathering is main cause of deposition and liberation of Phosphorus

-Greatest concentration in sedimentary rocks of marine origin

-systems are limited by P 

-toxin that accumulates

-most potent

-agent orange derivitive

-non-nutritive 

-randomly spaced

-very rare 

-most common

-clumped because resources are clumped or dispersed non-randomly

-habitat requirements

-social groupings

-mating systems 

-death=birth

-The carrying capacity for a population, or the amount the environment can support

-rate of population growth

-weeds and such 

Density Dependent Controls

(1) Resources (bottom up)

(2) Enemies (top down)

(3) crowding effects

-regulate population size and growth rate 

(1) Generation Time- average interval between the birth or an individual and the birth of it's offspring

(2) birth rate and mortality rate (fucundity and mortality)

(3) age-the relative number of individuals in each cohort fines a populatio's age structure

(4) sex ratio- number of births is usually related to the number of females

-K selected adaptations

-intraspecific competition

-humans are type 1

-high degree of potential investment

-low potential of dying

-reproduction around carrying capacity 

-probability of death is independent of age

-die when something eats it 

-high probability of early mortality

-r adapted life histories

-rapid population growth

-large number of unprotected offspring  

-subpopulations w/ partially independent dynamics

-landscape fragmentation

-somewhat isolated with periodic gene flow in between population and species 

-source and sink subpopulations 

-rate which determined how quickly populations came back was determined by quality, size, degree of isolation, and resources

-hints at competition in the past which caused species to split up a niche to survive

-Specializations have occured to end competition resulting in partition

-lowers fitness 

-The entire niche that a species is capable of using based on its physiological tolerance limites an resource needs

-when the species is alone it is able to occupy this entire niche 

-No 2 species can share the same niche indefinitely

-there must be niche partitioning or kill off 

-when it's a coordinated response to an environmental stiumul

-when it's based on genetics and can evolve 

-a fixed action pattern

-an innate releasing mechanism

- initiated by a sign (key) stimulus 

Migratory Behavior

Taxis and Kinesis 

-Taxis=toward or away from targe

-Kinesis=strength of taxis

-only more mature are capable of true navigation 

-nonreproductive castes

-nearly identical genotypes

-Form of kin selection where males are haploid and females are diploid and all females inherit exactly he same thing from the male parent 

-Female is diploid and male is haploid so if fertilized by one male then all offspring have the same genetic informatio from the dad

-very common in insect societies 

-a species may exhibit a metapopulation structure in areeas in which some habitats are suitable for long-term population maintainence, wheras others are not

-Populations in better areas continually send out dispersers that bolster the populationsin the poorer habitats (the sinks)

-in the absence of replenishment the population would become extinct 

-the growth rate does not correspond to the logistic growth equation because it is always at any instante limited by something unrelated to the size of the population  (ie. environment and disasters)

-Several unrelated but protected specie come to resemble one another.

-All are poisonous/dangerous 

-Species that have particularly strong effects on composition of communities

-Prevent one species from outcompeting others thus maintaining high levels of species richness in a community 

Succession

Primary Vs. Secondary 

-When the climate of an area remains stable year after year, communities have a tendency to change from simple to complex

-Primary: Occurs on bare, lifeless, substrate such as rocks or in open water where oorganisms gradually move into an area and change it's nature

-Secondary: occurs in areas where an existing community has been disturbed but soil still remains to allow the environment to regrow 

(1) Autotroph/Primary Producers: manufacture own food

(2)Heterotroph/Primary Consumers: Herbivores

(3) Secondary Consumers: Carniovres and parasites

(4) Decomposers/Detritivore: Break down the organic matter accumulated in the bodis or other organisms  

-Bottom up:  factor acting at the bottom of food webs may have consequences that ramify to higher trophic levels

-Top Down:  Predators keep the lower trophic levels in check