homeostasis

regulate their internal state

- requires a barrier separating internal and external spaces

- metabolic processes to provide energy and materials

surviving as a lineage requires

growth and reproduction

capacity to adapt to change (evolution)

hypothesis

a tentative or speculative explanation or prediction that is testable by observation or experiment

theory

an explanation that is well-supported by scientific studies

law

a narrowly focused prediction derived from a wider theory

hypothesis and theories

CANT be proved!! only supported or not supported

evolution

adapting to change - requires growth and reproduction

- change in the genetic composition of a population over time

scientific method

make observation -> generate hypothesis -> make predictions -> test predictions

cells arise spontaneously....

from non-living materials

Louis Pasteur's work

bacterial spread is more efficient when left in an open container rather than closed --broth experiment

DNA structure

a molecule carrying genetic material that is double-stranded made up of nucleotides

nitrogenous bases (purines)

adenine and guanine

nitrogenous bases (pyrimidines)

cytosine and thymine

genes

sequence of nucleotides in DNA encodes genetic instructions needed to build and maintain an organism.

determines order

provides a blueprint for producing specific proteins

DNA replication is a semiconservative process

each new double helix consists of one original strand and a newly synthesized strand

DNA "unzips" then each strand is used to synthesize a new strand through

complementary base pairing

transcription

a process by which the information in a gene DNA sequence is copied into a complementary RNA molecule

translation

when mRNA sequence is used to direct the synthesis of a protein

proteins are made up of

amino acids which are used to determine the nucleotide sequence

genetic code is consisted of codons which match with..

corresponding transfer RNA molecule

mRNA binds to a ribosome

a molecular machine that facilitates the assembly of proteins

- catalyses the formation of peptide bonds between amino acids building the protein chain

Mendelian genetics (principals of heredity)

Gregor Mendel figured out how traits are inherited from one generation to the next

2 laws of inheritance

law of segregation and law of independent assortment

law of segregation

each individual possesses 2 alleles for a gene (one from each parent)

- these alleles separate during formation of gametes (sperm and egg)

law of independent assortment

alleles of different genes assort independently of one another, during the formation of gametes

- inheritance of one trait does not influence the inheritance of another trait

haploid

each gamete carriers one allele for each gene

diploid

organisms that carry 2 copies of each gene

alleles

carry more than one version of genes

locus

individual can have 2 copies of the same allele - homozygous state

individual can have 2 copies of different allele - heterozygous state

dominant

trait seen even with one copy

recessive

need both alleles shown in trait

incomplete dominance

the heterozygous has an intermediate phenotype

polygenic inheritance

multiple genes influence a single trait

codominance

both alleles are fully expressed in heterozygote

DNA

master copy of genetic code

mRNA

message used for gene expression (transcribed from DNA, translated into protein)

genes are organized into codons

1 codon -- 1 amino acid

the central dogma of molecular biology connects

genotype (genes) and phenotype (physical traits)

mutations

can result from DNA damage

point mutation

from single nucleus subunit

frameshift mutation

from nucleus insertions or deletion

gene duplication or deletion

shift in gene

genome of an organism

the entire set of genetic info carried in DNA

- consisted of pieces of DNA called chromosomes

ploidy

the number of sets of chromosomes

gametes

half amount of the chromosomes

mitosis

creates a duplicated cell with an identical genome

binary fission

duplicate in mitosis

meiosis

daughter cells with half genomic content

- genetic info is heritable

diploid organisms

homozygous (2 same alleles)

heterozygous (2 diff alleles)

interaction of alleles leads to

phenotype

assumption of mendelian

1. each gene has 2 copies

2. at a locus individuals can be homozygous or heterozygous

3. gametes are haploid

evolutionary change

- measure the rate of new mutations

- observe the spread of new genetic variants

- see the effects of genetic change on the function of organisms

long- term morphological changes

result of underlying genetic changes

evolutionary theory

understanding and applying the mechanisms of evolutionary change to biological problems

- used to study and treat diseases

- allows biologists to understand how life diversified

- helps us make predictions about the biological world

Charles Darwin

developed the explanatory theory for evolutionary change

- independent discovery (collecting specimens, plants, and animals)

Darwin 3 major propositions

1. species are not immutable; they change over time

2. divergent species share a common ancestor and have diverged from one another over time

3. changes in species over time can be explained by natural selection (increases survival and reproduction of some individuals compared to others based on different traits)

most species are born than survive to reproduce

selection in nature is..

based on traits that increased survival and reproduction of organisms

artificial selection

selective breeding of organisms, commonly practiced by animal and plant breeders, to increase the frequency of a favored trait from one generation to the next

2 naturalists

Charles Darwin and Alfred Russel Wallace

Alfred Russel Wallace

made his way in the world by selling species he found (plants and animals)

Plato's theory of forms

represent new ideas from imperfect ideas

Aristotle's Scala Naturae

rank living things by how relative they are to humans

lowest: plants

highest: humans

natural theology

- all things created by God fit into Naturae

- prefect form of everything

Bishop William Paley

argument from design (watchmaker argument)

- organisms are complex and well-adapted because they were made by God

*all things are like a watch because the insides are designed perfectly, complex, and intellectually*

the challenge of the fossil record:

- multiple layers of fossil species

- many of these species no longer exist

- increasing similarity to modern species

catastrophism

a theory that the Earth's geological features result from sudden, short-lived, and violent events, like earthquakes, floods, and volcanic eruptions.

- some species disappear suddenly and are replaced by new species.

Georges Cuvier

- mass extinctions via major catastrophes

- new groups of species followed

uniformitarianism

forces acting on the Earth were the same in the past as in the present

- change is slow "gradualism"

Charles Lyell

his principles of geology were highly influential: Darwin read his work

Lamarkin Evolution (Jean-Baptiste Lamarck)

spontaneous generation produces simple species that evolve over time due to 2 forces

2 forces from spontaneous generation

1. "drive towards complexity" - innate force tending to move species up the scala naturae

2. "adaptive forces" - individuals change in response to their needs (passed to offspring)

Thomas Malthus

wrote "Essay on Principle of Population"

- observations on problems of human population growth

- population increases over time (causing food and resource shortages)

key observations

- species are highly diversified

- the more similar species are, the more closely they tend to be located to one another

- many species have gone extinct

- modern species tend to differ over time

all species tend to produce more offspring than # of parents

not all individuals survive...

there is a "struggle for existence" between individuals within the population

- individuals within a population differ from one another in # of traits

Some individuals will happen to be better suited to their environment because

they are more likely to survive and reproduce

- differential reproduction is based on trait (natural selection)

- differences in individuals tend to be heritable

selection results in..

changes in the average traits of a population

- a change in genetic composition --- evolution

is reproduction required in evolution?

yes, producing more offspring is important

ex: allele frequency change --> this means evolution occurred

how will changes lead to new allele frequencies from one generation to the next?

relative changes in the relative success of different phenotypes in a population

fitness

a phenotype is determined by the relative rates of survival and reproduction of individuals within that phenotype

qualitative traits

traits distinguished by discrete qualities or genes (black v white)

quantitative traits

traits are more likely to show continuous quantitative variation rather than discrete qualitative variation -- body size - trait influenced by genes

stabilizing selection

preserves the average characteristics of a population by favoring average individuals

direction selection

changes the characteristics of a population by favoring individuals that vary in one direction from the mean of the population

disruptive selection

changes the characteristics of a population by favoring individuals that vary in both directions from the mean of the population

directional selection

is operating when individuals at one extreme of a character distribution contribute more offspring to the next generation than other individuals do

- may result in favoring a particular genetic variant

- increase in the frequencies of alleles that produce the favored phenotype

polymorphism

the presence of 2 or more variants of a character in the same population

frequency-dependent selection

the fitness of a given phenotype dependent on frequency in population

microevolution

changes within species often involve single mutations/ qualitative changes may occur over one generation or thousands

macroevolution

processes are too slow to observe directly

relying on the fossil record, the geographic distribution of species, homologous traits, vestigial traits

-harder to observe directly

mycrobacterium tuberculosis

a disease killing more adults than any other, but an antibiotic was created which reduced the deaths from industrialized countries

Rifampin (antibiotic)

a molecule that binds to RNA polymerase and interferes with transcription

bacteriostatic antibiotic

resistant bacteria have a single point mutation in the gene rPOB that encodes part of RNA polymerase which is a single change in amino acid resistance

mutations are...

beneficial in a particular environment are no more likely to appear

strategies to reduce antibiotic resistance

- restricting use to bacterial infections

- reduced use in agriculture

- rotating antibiotics

transitional forms

evolutionary theory predicts that species and traits evolve and change over time rather than appearing suddenly -- fixed form

fossils show...

intermediate step

ex: from land mammal to whale

evolution of complex eyes

living species show eye structures reflecting a likely evolutionary pathway

intermediary

how a basic structure develops into a complex structure

- each step offers an advantage over the previous form

evolutionary theory states..

new species form from existing species

- closely related species cannot be dispersed

- independent evolution leads to new related species

island biogeography

study of the relationship between the geographic features of island and the evolution of species on those islands

- remote islands support speciation because a single colonizing species may find many open ecological niches

homologous traits

complex structures and functions cannot appear from nothing but must evolve from existing structures

- found at various biological levels

ex: looking at bones, seeing how structural elements have evolved and changes from pre-existing bone structures of similar species

vestigial traits

traits or structures not undergoing selection will tend to persist, even if they are no longer functional

- traits that have lost their function in a particular species or group

ex: pelvic girdles in whales-- remaining elements in some modern whales but it doesn't decrease fitness so they persist

hardy- weinburg equilibrium

allele frequencies do not change across generations and genotype frequencies can be predicted from allele frequencies

- explains why all biological populations evolve

5 principal processes of evolution

1. no mutation

2. no selection among genotypes

3. no gene flow

4. pop size is infinite

5. mating is random

how to measure evolution?

1. each gene has 2 copies in each individual

2. at a locus an individual can be homozygous or heterozygous

3. gametes are haploid and contain one random allele from the diploid parent

4. fusion of 2 gametes produce a new diploid individual

evolution occurs when

frequencies change in a population (mutation, natural selection, genetic drift, non-random mating)

- if any of these don't happen, then evolution is not occurring

gene pool

pool alleles in entire population to give allele frequencies

expected

random and unbiased result

reproduction by itself...

will not change the genotype or allele frequency in a population

how do you tell if a locus is evolving?

- sample, observe frequencies

- calculate frequencies

- develop hypothesis using hardy weinburg

- test hypothesis

- make a conclusion (not evolve? evolving?)

if a population is in Hardy-Weinburg Equilibrium..

the allele frequencies have not changed between recent generations

- this means the population isn't evolving

non-random mating

the likelihood of 2 alleles being paired together is biased in some way

assortative mating

mate chosen based on similarity or dissimilarity

inbreeding

mate chosen based on close familial relationship

sextual selection

particular traits are more generally more attractive to mates -- a different aspect of natural selection

positive assortative mating

mates are selected based on one or more traits being similar

ex: taller men tend to marry taller women

negative assortative mating

mates are selected based on one or more traits being dissimilar

-MHC genes make molecules that enable the immune system to recognize invaders

more variability in alleles appears to increase immunity

inbreeding

means mates are more likely to have the same alleles at locus

- increases the likelihood of homozygosity for each locus

- at least some loci probably have recessive deleterious allele

- increases number of homozygous recessive deleterious alleles (reduces fitness)

inbreeding depression results in

self fertilization which is not as efficient in terms of fitness

self fertilization

the most extreme form of inbreeding -- not efficient

sexual selection

occurs when individuals differ in their ability to obtain mates based on phenotype

a sub-category of natural selection

- differences are heritable traits increasing reproduction and frequency

- matings are non-random but all phenotypes reproduce equally

MALES ARE SHOWIER THAN FEMALES

increased mating success from...

fitness but is not necessarily improved adaptation to enviornment

-- if fitness increases, the frequency would not increase

sexual dimorphism

differences in the phenotype of sexes (due to sexual selection)

- women invest more energy into gametes compared to males with sperm ( this causes women to be more "picky" with their mate)

- dimorphic species -- males are usually larger and showier

intersexual selection

females chose mates on the basis of physical characteristics that signal male genetic quality and resources or parental care are provided

intrasexual selection

males v males

sexual selections can cause...

violations of hardy weinburg equilibrium

evolution without natural selection

- genetic drift

- gene flow

- mutations

genetic drift

change in gene frequency due to change (o ne generation by chance decreases)

- not due to particular traits in the individuals that survive and reproduce

- this can lead to a sampling error

sampling error occurs due to

change of death

chance failures in reproduction

chance distribution of alleles in gametes

fixation

chance losses of a few allele copies can have large effects in small population including complete loss of an allele

bottleneck effect

population that temporarily drops in size are likely to experience drift

only a small number in population survive

founder effect

drift can also occur when a small group finds a new population

- results from a low chance that the new group will have the same allele frequencies as the original populations

natural selection favors a good frequency

gene flow

movement of alleles from one population to another

- brings in new alleles

- involves moving between populations and migrating individuals to have the same allele frequencies

gene flow can also occur between species

- between sexual species by hybridization

- through gene transfer, especially involving bacterial species

- movement of DNA from one organism to another

- new DNA incorporated into genome to recipient

genetic variation

mutation-- starts --- natural selection acts on if a mutation has a greater fitness

mutations

evolutionary change requires new genetic variation (ARE RANDOM)

- the ultimate source of variation

- increase genetic makeup

- most mutations that affect fitness are deleterious

results from damage to DNA or faulty replication

- single-locus mutations

- gene duplications

- gene deletions

if most mutations are deleterious, why does fitness normally improve over the long run

- only beneficial mutations are favored by selection

- many beneficial mutations eventually occur and are selected for

hybridization

2 single strands of DNA or RNA combine to create a double-stranded molecule

heterozygote advantage

occurs when the heterozygote has the highest fitness ( 2 favored alleles)

- this helps maintain allelic diversity even when one homozygote experiences significant fitness cost

sickle cell allele

restricts evolution

- due to a single point mutation a B-globin of hemoglobin mutant B-globin can cause "sticky molecules in law O2 conditions

sickle-cell disease

sticky hemoglobin causes red blood cells to get twisted into sickle shapes. causing deformation

- blocks capillaries, causing pain, tissue damage, death

plasmodium life cycle

complex life cycle

- one stage infects RBCs by multiplying and triggering sickling

- immune cells destroy sickle cells

- HbB/HbB individuals are more strongly affected by malaria

- HbB/HbS individuals, plasmodia trigger sickling

limitations on evolution

evolution does not result in perfectly adapted organisms

- populations can only be fit enough to survive in their environment

- more fit than competing populations to persist over time

genetic constraints

evolution requires genetic changes, but there may be

- limited genetic variation

- genetic correlations among traits-- influence multiple traits and change one trait then you change others

historical constraints

- selection acts on existing characters

- new traits much evolve from old ones

chemical/ physical traits

basic physical laws place limits on

- rate and nature of biochemical processes

- physical characteristics of biological materials

trade-offs

- biological materials, energy, time is limited

- allocating for more, for one thing, means less for another (cant do everything at once)

variable selective conditions

changing environments cause inconsistent patterns of selection

ex: leaf bud growth timing (can be early/late may be advantageous)

adaptations cant perfectly "track" changing conditions