Evolution Biology

What is our Microbiome?

Symbiotic relationship you have with bacteria

-the bacteria is on or in you (digestive system)

-most bacteria are beneficial or non harmful

How does the microbiome help us?

-breakdown food we are unable to digest

-produce important nutrients

-regulate immune system

Global microbiome

-foliage brown

-reduced O2

-crops die

-no more decay

5 elements that change the composition of a population

1.) pinky finger: small populations means higher possibility of chance/randomness taking over

2.) ring finger: mating only with specific traits, choosing a mate (non random mating)

3.)middle finger: mutation, new allele

4.) pointer finger: movement, immigrate/immigrate (gene flow)

5.) Thumb: natural selection-leads to adaption

population

a group of localized interbreeding individuals

Gene pool

a collection of all the alleles in the population

Allele frequency

is how common the allele Is in the population (percentage)

-how many A vs a in the whole population

what would you find in a non-evolving population (null hypothesis)?

remove all agents of evolutionary change

1.) very large population size (no genetic drift)(randomness has little effect)

2.) no migration (no gene flow in or out)

3.)no mutation (no genetic change)

4.) random mating (no sexual selection)

5.) no natural selection (everyone is equally fit)

What does p and q stand for?

Frequency of dominant allele: P

Frequency of recessive allele: Q

Electrophoresis definition and purpose

Definition: process to seperate DNA fragments based on size

Purpose: detect diseases or differences between species

Restriction enzymes

cut the DNA specifically in its own cutting place

How DNA moves during gel electrophoresis (3)

-DNA is negatively charged

-DNA gets pulled through the positive side

-the shorter pieces of DNA move farther than the larger ones

RFLPS (Restriction fragments length polymorphisms)

says all DNA gets cut and will yield different size pieces “Bands”

What is PCR (DNAPolymerase chain reaction)?

amplifies (replicates) DNA in vitro (test tubes) making billions of DNA

What does PCR need? (4)

-DNA polymerase (heat tolerant)

-primer

-original DNA piece

-nucleotides

What is the process of PCR?

heat, cool, anneal

thermocycer is the machine

RNAi (RNA silencing) process definition? What can we use it for?

process: where enzymes destroy mRNA before it turns into a protein

Use it for: to make drugs that stop protein production or for gene knockout to figure out what specific genes do

RNAi process steps (4)

1.) insert dsRNA(double stranded) which looks like the gene you want to turn off

2.) Dicer enzyme chops dsRNA and then turns into siRNA (small interfering rNA)

3.) Risc enzymes uses siRNA as a “wanted poster”

4.) Risc will destroy any mRNA that looks like this “wanted poster”

How does skin color relate to geographical position

Higher UV environments=more melanin=darker skin

Lower UV environments=less melanin=lighter skin

How does skin color relate to Vitamin D formation and folic acid

Folate is needed for reproductive success, however, UV destroys Folate. Therefore, people in higher UV areas need darker skin. Vitamin D is also needed to absorb calcium, so without a lot of UV exposure, people need lighter skin to absorb it. Darker skin can not absorb enough sun to make vitamin D is low UV environments.

Operon

section of DNA that can be turned on and off

RNA Polymerase

makes mRNA from the DNA gene

Repressor

blocks the DNA Polymerase when it is attached to the operator

Promoter

tata box that “calls” RNA Polymerase to the site (beginning of the gene)

Opperator

spot where the repressor binds to

Inducer

molecule that pulls the repressor off (sometimes on)

operon- gene control (cell signaling) components (5)

1. RNA Polymerase

2. repressor

3. promoter

4. operator

5. inducer

cAMP

works to bring RNA Polymerase to the promoter

Lacoperon

inducer (lactose)

cAMP and Lacoperon

-double environment control

-glucose is low cAMP is high

-CAMP helps CAP bind to promoter region=RNA Polymerase can “find” the promoter region

When glucose is high and lactose is high is the Lacoperon on/off and why?

off

DNA poly can not find the promoter

when Glucose is low and lactose is high is the Lacoperon on/off and why?

On

found the promoter and repressor is off

when Glucose is high and lactose is low

off

can not find the promoter and repressor is on

when glucose is low and lactose is low is the Lacoperon on/off and why?

off

you can find the promoter but the repressor is still on

Ligans

the chemicals that are used in the chemicals language which is how cells communicate

-ligans are specific to the integral protein they attach to

Steps of quorom sensing

1.) reception

2.) transduction

3.) response

Quorom sensing: What is it? What is the result of it?

What is it:

A way for bacteria to sense how many other bacteria are around, both of their own species and other species

Result:

Use this to create phenotypic effects as a group

ex: lighting up, protective clusters, virulence factors

Restriction enzyme

cut DNA at very specific sequences and produce sticky ends at the cut site (molecular scissor)

-if you want to join two different pieces of DNA together use the same restriction enzyme (matching sticky ends)

Reverse transcriptase

enzyme that helps make cDNA

cDNA

DNA without introns (complimentary)

When does reverse transcriptase do itjs role

after DNA has been turned into mRNA and gone through RNA splicing

Microarrays

(involves cDNA)

-take a bunch of mRNA transcripts that are being made by the person (specifically a certain tissue). Turn them into cDNA. Run it across a chip and see what spots activate

epigenetics

What you eat, do, expose yourself to can change what genes get expressed (turned into phenotype) or silenced

DNa methylation

epigenetics

silencing (off switch)

Histone acetylation

epigenetics

opening up the DNA for transcription (on switch)

What is not true about evolution (3)?

1.) evolution is organisms adapting to their environment

-individual organisms can not change themselves as a reaction

2.)survival of the fittest

-unfit still survive

3.)evolutionary purpose

-no goal of a species

What are the 4 components of natural selection?

1.) individuals in a population must vary (variation) (DNA causes variation)

2.) more offspring are born than will survive

3.) there is a struggle for survival (some will die)

4.) organisms that are are more suited to the enviroment will survive and reproduce more often than ones less suited

Conclusion about natural selection

Conclusion: overtime, traits that help individuals survive and reproduce will become more prominent over time

What is adaption?

Definition: It is a phenotype. A physical characteristic (speed, behavior) that natural selection works with

ex:

Chameleon: they have a ling tounge which helps them grab insects

Theory of aquiered traits wrong and right

wrong: Individuals that acquire a trait throughout their lifetime in order to adapt to their environment can pass on that trait to their offspring

ex: body builder children not strong

Right: environment influences populations (epigenetics)

what is Artificial selection?

Humans are selecting the traits

-they choose who gets to mate

-they choose what traits get passed down

-overtime traits that are selecting by humans will show up more in future generations

ex: dog breeding (pugs)

What are fossils? What do they show us?

What are they: the remains or impressions of a prehistoric organism

What do they show us: the fossils help to show change in populations over time, from shape to behavior

Transitions

how environmental changes cause niches to change as a result which causes transitions

Transition ex:

-fish to tetrapods

-dinosaurs to birds

-horse evolution

-mammmals from land to mammals in water

Strata

layers

relative dating

comparison between fossils based on location

strata of transitions

top (youngest)

fish amphibians reptiles mammals birds

fish amphibians reptiles mammals

fish amphibians reptiles

fish amphibians

fish

bottom (oldest)

Anagenesis

one organism now and the linear path back in time

cladogenesis

one organism to ancestor and all other connected species

what does cladogenesis and anagenesis both tell us

describes the changing populations

radiometric dating

Decay of radioactive isotopes into stable elements

Ex: radioactive isotope X turns into stable element Z at a half-life of 500 years. You find a note that contains 6.25g of X and 93.75g of Z. How old is the rock?

100——-50——25——12.5———6.25

4 half-lives times 500

answer: 2000 years old

½ life

amount of time it takes for1/2 of a radioactive isotope

Homology

similar structure make up (common genes) but different use (adaption)

ex: fore limbs on different animals

humans: grasping

whales: swimming

Vestigial structure

homologous structure

organism has a feature that many other groups have, but not much of an adaptation anymore

Hox genes

homologous structure

common controller genes

ex: gene for eyes in a mouse put into a fly will still make the fly's eyes even though the gene came from a mouse

Analogous

similar function (adaption), but different structure (different genes)

-this means they may have similar environmental pressure (probably a similar niche)

ex: bat wings and bees wings are different but both help with flying

Biogeography

studying: organism distribution is based on proximity

ex: fossils on distant sides of the ocean contain fossils of tetrapods of the same species

How does biogeography connect to plate tectonics?

plate tectonic theory: plates that land sits up on are constantly shifting and moving

CRISPR: What does it allow us to do? What is it? What enzyme does it include?

What does it allow us to do: allows us to edit DNA in a cell

What is it: clustered regularly interspaced short palindromic repeats-cas 9

Enzyme: Cas9

Steps to Crispr (2)?

1.) add Cas9, a guide RNA that matches the gene you want to edit, and a “fixed” gene

2.) cas9 uses the guide to cut any DNA that matches and the correct gene fills the gap

Macroevolution

populations evolve, individuals do not

-genetic makeup of the population changes over time

-favorable traits (fitness) become more common

Relative fitness

what is high (favorable) right now, may not be in the future

The two main sources of variation?

1.) mutations

2.)sexual reproduction (meiosis)

Gene flow

movement of individuals and alleles in and out of a population

-seed and pollen distribution by wind and pollinators

variation

raw material for evolution

some individuals are more fit than others

Non random mating

sexual selection (female choice)

-females have the choice because they invest the most

sexual dimorphism

females look different from the males

Genetic drift

the effect of chance (randomness) events having a bigger impact (small populations)

two types of genetic drift

Bottleneck effect:

some factor (diasater) reduces population to small number (populations recovers and expands again)

-alleles lost from gene pool (not due to fitness) which narrows the gene pool

Founder effect: small group splinters off and finds a new colony (skews gene pool of population)

Selection patterns

quantitative traits (polygenic)

1.) Stabalizing selection: middle of curve has the highest fitness

2.) directional selection: one side of the curve is better then the other (has higher fitness)

3.) disruptive/diversify selection: both ends of curve have higher fitness

What defines a species?

population of individuals who can interbreed and produce fertile offspring (does not work for asexual reproducing species or extinct species)

Speciation types

(requires separation)

1.) Allopatric

2.) Sympatric

Allopatric speciation

geogrpahically

-physically living in two separate spots

Sympatric seperation

live in SAME area

-reproductivly different (genes and miosis errors)

-differernces in behavior, new resources, differences across the area

steps of speciation

1.) species become isolated

2.) isolated populations evolve independently of one another

3.) eventually they will not produce fertile offspring with eachother

Pre reproductive (zygotic) Barriers to define a species

barries or obstacles that prevent mating or prevent fertilization from occuring if mating does not take place

Geographic isolation

PreZygotic barrier

organisms live in different places

ecological isolation

PreZygotic barrier

different niches

temporal isolation

PreZygotic barrier

different time (time zones, seasons, years)

behavioral isolation

PreZygotic barrier

different dances or calls

mechanical isolation

PreZygotic barrier

male anatomy must fit female anatomy

gametic isolation

PreZygotic barrier

sperm can fertilize egg

post reproductive (zygotic) barriers to define a species

prevents hybrid offspring from developing into a viable, fertile offspring

reduced hybrid viability

post zygotic barrier

hybrid has low phenotypic fitness

reduced hybrid fertility

post zygotic barrier

hybrid can not produce gametes

hybrid breakdown

post zygotic barrier

hybrid (offspring) and not mate with another hybrid (offspring)

Gradualism

gradual divergence over long spans of time (assumes big changes occur as the accumulation of many small changes)

Punctuated equilbrium

rate of speciation is not constant

-rapid burt of activity (tied to mass extinctions)

-long periods of time with no change

Phylogenetic trees

depictions of evolutionary history using the most recent information (genetics and morphology)

Descent with modification

the passing of genetic traits from parents to offspring over generations, with slight changes accumulating over time

assortive mating

a non-random mating pattern where individuals with similar phenotypes (appearance/traits) or genotypes (genetic makeup) mate with each other more frequently than expected by chanc