Bio notes

Chapter 4: ecosystems/communities/biomes

Weather: the day to day conditions of Earth’s atmosphere at a particular time/place

Climate: refers to average, year to year conditions of temperature/precipitation in a particular
region
Energy from the sun drives earth’s weather and helps determine climate, the atmosphere is a
natural insulating blanket. CO2, methane, H2O vapor and other atmospheric gasses trap heat
energy and maintain Earth’s temperature range (greenhouse effect)
As a result of differences in latitude + angle of heating, earth has 3 main climate zones, polar,
temperate, and tropical. Unequal heating of the earth’s surface drives winds and ocean current
that transports heat throughout the biosphere.
Ocean currents: cold water sinks, warm rises, they create a cycle and cause el nino (warm) and
la nina (cold)

Biotic factors: biological factors that influence organisms in an ecosystem, ecosystems are
influenced by a combination of biological/physical factors
Abiotic factors: physical (nonliving) factors that shape ecosystems (temperature, precipitation,
wind, soil type)
Biotic and abiotic factors determine the survival/growth of an organism and the productivity of
the ecosystem that the organism lives in.

Niche: a subset of a habitat where only a particular species lives (a certain type of bird that lives
in a part of a tree)
Competitive exclusion principle: no 2 species can occupy the same niche in the same habitat at
the same time.
Predation: an interaction between in which type of organism captures and feeds on another
organism

Symbiosis a relationship where 2 species live closely together, 3 types

#1: commensalism: one organism benefits and the other organism isn’t helped/harmed
(barnacles/whales)
#2: mutualism: both organisms benefit from the relationship (flowers/insects)
#3: parasitism: one organism lives another and harms it, parasites obtain all or part their
nutritional needs from other organisms (host) (tapeworms, fleas, ticks)

Ecological succession: ecosystems are constantly changing in response to natural/human

disturbances. As an ecosystem changes, older inhabitants gradually die out and new organisms
move in, causing more changes in the community. (series of predictable changes that occurs in
a community over time)

Primary succession: succession that occurs on surfaces where no exists, begins with ash or
rock,
pioneer species: first species to populate the area, ex: lichens/mosses, helps form soil and
break up rock
Secondary succession: succession following a disturbance that destroys a community without
disturbing the soil (fire, farming, flood) “Climax Community” old growth forest in the Pacific
Northwest, ancient cypress swamps.

Climate is especially important in determining the characteristics of a biome, main factors of

climate temperature and precipitation
Microclimate: climate within a small area that differs significantly from the climate around it

Mountain ranges: abiotic/biotic conditions vary with elevation: from base to summit,
temperatures become colder and precipitation increases. Grasslands, open woodland pines,
forest of spruce and pines and wildflowers, like tundra.
Polar ice caps: border tundra is cold year round, mosses lichens

Aquatic ecosystems: determined primarily by the depth, flow, temperature, and chemistry of the
overlying water (often grouped according to the abiotic factors that affect them, depth distance
from shore)

Freshwater ecosystems: divided into 2 types flowing and standing water

Flowing water: (rivers streams, and creeks) organisms are well adapted to flow rate, some
insects larvae have hooks, some catfish have suckers to anchor, and trout are streamlined

Water originates in mountains/hills or underground

#1: near source
#2: high dissolved oxygen
#3: little plant life
#4: sediments build up
#5: more and more plant life
#6: meander slowly
#7: flat areas = more animal life

Standing water: lakes/ponds

Plankton: general term for tiny, free floating/weakly swimming organism that live in fresh/salt
water

#1: phytoplankton: single celled algae, supported by nutrients in water, base of aquatic food
webs (producers)
#2: zooplankton: feed on phytoplankton (consumers, look like shrimp)

Freshwater wetlands: ecosystem in which water covers the soil or covers the soil for part of the
year, many serve as breeding grounds for insects, fish, other aquatic animals, and migrating
birds.
3 types:
#1: bog: typically forms in depressions kettle holes, sphagnum moss grows, acidic water
#2: marshes- shallow wetlands along rivers, maybe underwater part or all of the year (cattails,
tall grasses)
#3: water moves slowly - trees + shrubs present all year round

Estuaries: wetlands formed where rivers meet the sea, have both salt and freshwater, affected
by tides, organic matter enters food web as detritus, supports a lot of biomass, serves as
spawning and nursery grounds, fewer species
Mangrove swamps: coastal wetlands dominated by mangroves and salt-tolerant woody plants

Aquatic Biomes
Marine ecosystem photic zone: well lit upper layer, 200 meters, producers grow
Aphotic zone: permanently dark, chemosynthetic autotrophs are the only producers

Coral reef: warm, shallow, tropical oceans, diverse and productive, named after coral animals
whose calcium carbonate skeleton make up the primary structure, coral lives in symbiosis with
algae, won’t live below 40 meters

Types of biomes
Tropical Rainforest
Tropical dry forest, like rainforest, but with less precipitation and cluster around rainforest
Savanna: lots of grasses with little trees and rain
Desert: lowest amount of precipitation, plants adapt to hold water
Chaparral: desert like, more moisture than desert, wildfires, droughts
Temperate grassland: open grassland, wildfires
Temperate deciduous forest: moist, rich soil, trees lose leaves, 4 seasons
Coniferous/boreal forest: large amounts of evergreen trees, warm summers cool winters
Tundra: cold frozen land, little moisture, low temps, poor nutrients in soil

Chapters 5 & 6
Chapter 5
How populations grow
Population density: number of individuals per unit area, # can vary depending on species and its
ecosystem, factors include: # of deaths, individuals that enter/leave, and births
Immigration: individuals coming to an area
Emigration individuals coming out of an area

Exponential Growth = logarithmic growth

Occurs when individuals in a population reproduce at a rate that is constantly increasing
*at first the number increases slowly, then over time the population becomes larger and under
ideal conditions will continue to grow to an infinitely large size* (under ideal conditions with
unlimited resources, a population will grow exponentially)
Exponential growth curve: the rate of increase in the population under ideal conditions,
produces J shaped curve.

Logistic growth: occurs when a population’s growth slows/stops following a period of

exponential growth, s shaped curve.

Carrying capacity (k): largest number of individuals that a given environment can support

Species distribution: the manner in which a population is spatially arranged, there are 3 types
Clumped: organisms cluster together into groups (most common), Random: organisms have an
unpredictable distribution, Uniform: organisms are evenly spaced in the area they live in.

Density dependent (limiting factor) - factors that limit the growth of a population as the
population grows larger. (doesn’t impact scattered population as greatly)

Predation: regulation of a population size as one organism preys (predator) on another

organism (prey), best known way to control a population

Density independent (limiting factor): factors that limit the size of a population regardless of
size, this determines carrying capacity, the maximum population size that an environment can
support

Human population growth: the size of the population tends to increase with time, the human
population began growing more rapidly 500 years ago.

Demography: scientific study of human populations, examines characteristics of human

populations, attempts to explain how those populations will change over time. Birth/death rates
and the age structure of a population help predict why some countries have high growth rates
while other countries grow more slowly.
Demographic transition: many countries experience a dramatic change in birth and death rates
As societies continue to modernize: they have fewer children, birth rate falls + population's
growth slows, demographic transition is complete when birth rate falls to meet the death rate
and population growth stops

Chapter 7:
(1674) Anton Van Leeuwenhoek used the microscope to study cells, he called his findings
“animalcules”.
(1665) Robert Hooke looked at a cork under a microscope and coined the term “cell” because it
reminded him of the rooms of a monastery (wtf?).
(1831) Scottish botanist Robert Brown discovered the nucleus.
(1838 + 1839) German scientist Matthis Schledian concluded that plants were made of cells
(38), and then Theodor Schwann concluded all animals are made of cells (39)
(1855) Rudolf Virchow concluded cells come from preexisting cells
These discoveries led to the cell theory
#1: all living cells are made of cells
#2: cells are the basic structure and function of living things
#3: cells are produced from existing cells

Only light microscopes are used because electron microscopes will kill the organism
The highest magnification for light microscopes is 1,000x and the highest magnification for
electron microscopes is 100,000x

Resolution
#1: the ability to separate 2 objects that are very close
#2: light microscope: 2 um (micrometers)
#3: An electron microscope can separate objects 1,000 times closer together than a light
microscope

Cell types
Eukaryote: multicellular, found in animals, plants, fungi and protists
Prokaryotic: don’t have a nucleus, unicellular, bacteria

Characteristics of Eukaryotic cells

#1: cell membrane: thin, flexible barrier around the cell (controls what comes in and out, gives
cell shape and structure)
#2: nucleus: controls most cell processes and contains DNA, ID by Robert Brown
#3: cytoplasm: material surrounding the nucleus

Cell membrane
Lipids: the basic unit of construction; lipid bilayer (2)
Proteins: disturbances are taken in/out through them
Carbohydrates: acts as a chemical ID, allows cells to recognize and interact with each other
Cell membranes can be permeable, impermeable, or semi-permeable (carbs decide what to let
in for semi-perm) proteins act as pumps, pumping things in/out

Cell wall
-only found in plants, not in animals
-need tougher tissue because plants can’t move
-lies outside the cell membrane
-porous, things can go in/out
-helps support/protect cell
-composed of cellulose

Outer area
-develops where two plant cells meet
-contains pectin, which helps hold cells together (acts like glue)
Primary cell wall (outer cell wall)
-made of cellulose (fibrous material)
-allows cells to stretch

Secondary cell wall (inner cell wall)

-cellulose and lignin (not all plants have lignin)
-lignin makes cellulose more rigid
*wood consists of mainly secondary cell walls*

Nucleus (only found in animal cells)

-the nucleus is the control center of the cell
(chemically different from the rest of the cell and contains DNA)

-chromatin is indistinct genetic material visible within the nucleus

(consists of DNA coiled around proteins)

-chromosomes are the condensed distinct genetic information

(when cells divide, chromatin becomes chromosomes)

-nucleolus: small, dense region where ribosomes are produced

-nuclear envelope/membrane allows material to move in/out of the nucleus
-nuclear pores allow things in/out

Cytoplasm
-contains organelles = “little organs”
- contains everything but the nucleus

Organelles
-Endoplasmic reticulum: internal membrane system in cells in which components of the cell
membrane are made and proteins are modified, transport system of the cell has Rough ER (has
ribosomes) or smooth ER (no ribosomes)
Ribosomes
-can be free or attached ribosomes
- assemble proteins
-made of RNA and proteins
-produce proteins following coded instructions from the nucleus
- process = protein synthesis

Mitochondria - powerhouse of the cell

-found in plant and animal cells
-where ATP is produced by the process of cellular respiration
-change chemical energy from food to ATP
-organelle has inner/outer membrane

Chloroplast: contains chlorophyll

-only found in plants and algae
- location of photosynthesis
-make sugars (glucose)
*mitochondria and chloroplast can reproduce within the cell*

Golgi apparatus: takes proteins and modifies them by special enzymes

-Attach carbohydrates and lipids
-collect, package, and distribute molecules made at other areas of cells

Lysosome: “clean up crew”

-only found in animals
-contains enzymes and chemicals
-formed by golgi apparatus

Vacuoles: found in animals, plants, and protists

-plants: one large vacuole called central vacuole
-animals: many small vacuoles
-central vacuole is filled with liquid

Plastids
-only found in plants, store food and pigments
-chloroplasts: photosynthesis
-leucoplast: stores starches
-chromoplasts: stores pigments

Chapter 12: Genetic Code

Genetic code: program of the cell, the way in which cells store the program that they seem to
pass from one generation of an organism to another.

Genetics: anything that relates to heredity

1928: Frederick Griffith: worked with pneumonia bacteria in culture, used 2 strains
- S (smooth culture): virulent, disease causing
- R (rough culture): harmless
Experiment results: somehow heat killed (smooth) strain had passed on the disease causing
ability to the living harmless (rough) strain
Conclusion: one strain of bacteria had transformed into another (rough → smooth)
Transforming factor: Griffith: some “factor” was transferred from the dead smooth bacteria to the
living cells (rough strain)

1944: Avery, MacLeod, & McCarty: repeated Griffth’s experiments to discover which
molecules were responsible for transformation
*they treated a “juice” extract from the heat killed bacteria with enzymes that destroy lipids,
proteins, carbs, and RNA (all were put into separate containers that were destroyed and
injected into mice) transformation still occurred* mouse died

Therefore these molecules weren’t responsible but when DNAase was used, transformation
didn’t occur (mouse lived)

Therefore, DNA is the nucleic acid that stores and transmits the genetic information from
one generation to the next, DNA carries the genetic code.
Some didn’t want to believe that DNA was important

1952: Hershey and Chase: studied viruses that infect bacteria (bacteriophages) consist of an
outer protein coat and inner DNA core

Lytic cycle:

Lytic cycle in words:

#1: attachment to the surface of bacteria
#2: enzymatic hole
#3: injected genetic material into bacteria
#4: formation of new protein coats + genetic material from the bacterial cell machinery = new
copies of bacteriophage
#5: lysis = bursts the cell
#6: reinfestation = bacteriophages can infect other cells

*because the material injected into bacterium produces new bacteriophages, it must be the
“transforming factor” = genetic

Hershey and Chase’s problem = was the “transforming factor” the protein coat, DNA or
both?
They used tracers (radioactive substances that can help see things on CT scan, Sulfur-35 and
Phosphorus-32) DNA was injected with Phosphorus-32 and protein was injected with sulfur-35.
If sulfur-35 was found in the bacteria, it meant that the virus's protein into the bacteria and if
phosphorus-32 was found in the bacteria it was the DNA had been injected
Procedure: 1: mixed radioactively labeled viruses with bacteria and waited for viruses to
attach/inject
2: seperated viruses from bacteria using a blender and centrifuge
Results: *nearly all of the sulfur remained with the virus and nearly all of the labeled
phosphorus had entered the bacteria
Conclusion: viruses DNA enters bacteria and protein coat remains outside bacteria
Therefore, DNA contains genetic information

The structure of DNA: How could DNA perform two tasks: store information and duplicate itself
easily?

DNA is a polymer made of individual units called nucleotides

Nucleotides: a 3 part molecule made of a sugar (deoxyribose), phosphate, and nitrogenous

base

4 nitrogenous bases:
Adenine and guanine: purine group (2 rings) adenine always bonds with thymine
Cytosine and thymine: pyrimidine group (1 ring) cytosine always bonds guanine
-sugars and phosphates are backbone (uprights)

Differences between RNA and DNA

#1: DNA is a double helix and RNA is a single strand
#2: DNA has Adenine, guanine, cytosine and thymine and RNA has the first 3 but no thymine
(replaced with uracil)
#3: RNA has ribose and DNA has deoxyribose

X-Ray evidence: early 50’s: Rosalind Franklin and Maurice Wilkins aimed x-rays at tin parallel
strands of DNA in a glass tube, pattern was recorded on film and it was diffracted
Proves that the fibers of DNA were twisted (x pattern) and that there are regular intervals
(spaces) between molecules

James Watson and Francis Crick took the X pattern results

This alone wasn’t enough proof to determine the exact structure of DNA

Building DNA model:

Double helix: Watson and Crick twisted the model (helix), used Franklin’s idea that there were
2 strands (double helix) and placed the nitrogenous bases inside bonded by weak H bonds
Erwin Chargaff’s research concluded A bonds to T and G bonds to C

Base Pairing: very specific, holds double helix together

Hydrogen bonds: not too weak but not too strong, holds base pairs together
Watson and Crick published their version of the structure of DNA in 1953, recognized
immediately and their model explained the mystery of how DNA can copy itself

1962: Nobel prize for medicine/physiology, awarded to Watson, Crick, and Wilkins (Franklin’s
associate) Franklin didn’t get an award because she died of cancer in 1958.

Replication of DNA:
DNA consists of complementary strands
Each half of the double helix serves as a template/pattern against which a new strand is made
Before a cell divides, DNA must be duplicated, process is called replication -uses enzymes
Enzymes: have the ability to copy DNA strand by:
1: unzipping double helix
2: insent approriate bases
3: producing covalent sugar-phosphate links to extend helix
4: proofread the completed base pairing to ensure they are correct

DNA polymerase reads the base and adds the compliment, add nucleotides, (a,g,t,c) (adenine -
thymine)
DNA ligase is like a glue that splices segments of DNA together

Telomere: the end of a chromosome and they are the toughest points to copy

Chapter 10: Cell growth + division

Cells divide because there’s a limit to how large it can become

#1: the larger the cell becomes that more demands it places on DNA
#2: the more trouble the cell has moving enough nutrients and wastes across the cell
membrane

These problems are correlated to the surface area to volume ratio

As the cell grows both the SA and the volume increase, but which increases at a faster rate?

The larger the first # the better and the smaller the the 2nd # the better.
SA : V (ex: 6:1 is better than 2:1)

Cells must exchange materials

- Water, food, oxygen goes out in
- Carbon dioxide, various wastes go out

To answer the question, volume increases more rapidly the surface area
To decrease the likelihood of problems, the cell must increase the SA:V ratio
= *have a large SA to small V*
= have a lot of area to act on a small volume

How does the cell ensure that it always has a high surface area to volume ratio? Division
(mitosis)

Before a cell divides what must it do in order to ensure that the new daughter cells will have the
necessary information for development?
-> A copy of DNA has to be made

Cell division solves the increasing size problem by reducing cell volume, each new daughter cell
has an increased ratio of surface area to volume.

Chromosome structure of Eukaryotes

-these are condensed chromosomes that form during mitosis
- they are composed of chromatin (protein + DNA) which is normally uncoiled (uncondensed)
and is about 10,000x the length of a chromosome

Chromosome structure
-DNA double helix will coil up around proteins (histones)
- chromatin = normal uncondensed form of DNA when the cell isn’t splitting (interphase)
-chromosomes = condensed DNA + protein that becomes distinct during cell division

Once replication has taken place each chromosome consists of 2 sister chromatids (=2 sets of
identical DNA)
 - Chromatid: 1 of 2 identical parts of a duplicated chromosome, each pair chromatids is
attached at an area called a centromere ( people have 46 (if you’re genetically normal),
carrots have 18 and fruit flies only have 8)
- Plants can handle adding/removing chromosomes without problems, but if the same
were done to people it can cause major problems

Cell cycles includes interphase (which includes g1, s, and g2 phases) and mitosis (prophase,
metaphase, anaphase and telophase)

Cell cycle: cell grows, prepares for division, and divides into 2 daughter cells
#1: m-phase = mitosis; the division of the nucleus
#2: interphase = period between cell divisions (3 parts)
A: g1 (growth 1): cells do most growing, makes proteins + organelles
B: s (synthesis): DNA replication, sister chromatids
C: g2 (growth 2): cell prepares for division, many organelles + molecules required for cell
division are produced.

M-phase consists of 4 phases (in order)

#1: prophase:
#2: metaphase
#3: anaphase
#4: telophase

Prophase: longest phase in mitosis

Formed:
- Centrioles begin functioning, separate and move to opposite sides of the cell (composed
of microtubules)
- Centrioles are in pairs and at right angles to each other *plants cells don’t have
centrioles*
- Spindle fibers: fanlike microtubules that help chromosomes move apart and are
organized by a centrosome
- Uncondensed chromatin becomes distinct condensed chromosomes (X’s)

What disappeared:
The nucleus
Nuclear membrane

Metaphase: the shortest phase of mitosis

- Chromosomes line up across center/equator of cell
 - Microtubules connect the centromere of each chromosome to poles of spindle
- Aster: starlike arrangements around each pole (composed of spindles and centrioles)
and means starlike

Anaphase:
- Chromosomes split apart and move to poles
- Begins when centromeres that join sister chromatids, split, and cause separation
becoming individual chromosomes
- End when chromosomes reach the poles

Telophase (cytokinesis also occurs)

- Chromosomes begin to uncoil and become chromatin
- All takes place in 2 regions where nuclei will form
- Nuclear envelope forms around chromatin
- Nucleus becomes visible
- Spindle fibers break down
- Centrioles stop functioning

Cytokinesis
Mitosis (nucleus splitting) may be over but the cytoplasm still needs to split
- Cytokinesis often occurs during telophase
- Occurs in animal and plant cells
Animal cells: a cleavage furrow (indent) forms and the cytoplasm pinches off
Plant cells: structure known as the cell plate forms between divided nuclei and develops
into separating membrane and cell wall

Regulating Cell cycle:

- Not all cells move through the cell cycle at the same rate
- Cells grow and then stop when they come into contact with each other
- Hunt and Krischner concluded that protein (cyclins) regulate the cell cycle
- Cyclins regulate timing of cycle in eukaryotic cells
Internal regulators: proteins that respond to events inside the cell
- Several regulator proteins that make sure that the cell doesn’t enter the cell cycle
- Another prevents the cell from entering anaphase
External regulators: proteins that respond to events outside the cell
- Direct cells to speed up / slow down the cell cycle
- Growth factors stimulate growth and division

The cell cycle: period of one cell division to the next

- It is not the life and death of a cell but it could be
How long does it take?
The cycle can be:
Fast = 6 hours
Average = 12 - 24 hours
Long = 1 year
- M phase portion usually lasts 1-2 hours

Some cells divide regularly = skin cells

Some cells can’t divide at all = nerve cells
Controlled cell growth = normal cell mitosis
Uncontrolled cell growth = tumors, cancer, etc

Chapter 11 Meiosis:

Meiosis is how sperm and eggs are formed

People are mostly composed of somatic cells (normal body cells, 44 chromosomes)
These cells are also known as diploid because they contain two sets of chromosomes.
Diploid is abbreviated as 2n and are haploid (½ of chromosomes) Meiosis cuts the cells
in half

Humans have 23 pairs of chromosomes (if genetically normal) and half from each
parent. 22 of them are autosomes (dictate the traits you have) 23rd are sex
chromosomes.

Chromosomes are found homologous pairs which have the same type genes (eg: hair
color) *however the expression of these genes can come in different (black hair vs red
hair), these different forms are called alleles.*

Gene locus = location on a gene

Sex chromosomes are XY (male) and XX (female) , always a 50% for a boy or a girl.

Karyotype: a picture of the chromosomes within a cell

A blood sample is taken and this is done by stopping the cell cycle during mitosis
(metaphase) when the cells are lined up across the center of the cell. Then a picture of
the chromosomes is taken and a scientist pairs up each of the homologous pairs. This
can be used to determine the gender of an individual/ potential genetic abnormalities.

Meiosis is a reduction (46 -> 23) and division (2 -> 4) process.

Diploid Cells (2n or 46) = have both sets of chromosomes (humans have 46)
Haploid cells (n or 23) = have only 1 set of chromosomes (sperm/egg)
Has 22 autosomes and 1 sex chromosome (either x or y), when sperm (n) + egg (n) = diploid
(2n)

Meiosis 1:
 - Prophase 1: each chromosome seeks out its corresponding homologous chromosome
to form a tetrad (4 chromosomes)
- Metaphase 1: homologous chromosomes pair up forming tetrads, they may exchange
chromosomes (crossing over) and the result is new gene combos
- Anaphase 1: disjunction occurs, homologous chromosomes separate and move towards
the poles
- Telophase 1: each one goes through mitosis and cytokinesis

After Meiosis 1 each cell is haploid and the homologous chromosome pairs are separated. Now
meiosis 2 separates sister chromatids

Meiosis 2:
- - short interphase with no DNA replication
- prophase 2: DNA condenses
- Metaphase 2: chromatids line up on equator
- Anaphase 2: chromatids separate
- Telophase 2: four daughter cells contain haploid # of chromosomes

Spermatogenesis (males)
- Produce 4 haploid gametes (sperm)
- Most sperm are the same size
- All sperm are genetically different
- Gamete is sperm in animals and pollen in plants

Oogenesis (female)
- Produce 4 haploid gametes (1 egg, 4 polar bodies)
- At cytokinesis of meiosis 1 there is an uneven division of cytoplasm, the larger resulting
structure will become the egg
- In meiosis 2 there is another uneven division of cytoplasm and again the larger structure
will become the egg
- Egg and all polar bodies are genetically different
- Gamete is egg in animals and ovule in plants
- 3 polar bodies disintegrate

Chiasmata: a point where paired chromosomes cross over and exchange genetic information
Meiosis produces varied offspring for 4 reasons:
1: independent orientation of the chromosomes = random
2: random fertilization between sperm + egg
3: crossing over
4: rearrangements (4 types of chromosomal mutations: duplication, deletion, inversion,
translocation, and deletion + translocation increase the chance of harm)

What are the odds: humans have 2 to 23rd different combinations of chromosomes,
approximately 8 million variations for #1 alone
Fertilization combinations: 8 million (sperm) x 8 million (egg) combinations
64 trillion combinations for only #1 and #2 above

Inheritance of Acquired characteristics: if a ability is gained that trait can be passed on to their
offspring (old belief, not true)
Another old belief, crossing short + tall plants will give you medium plants (theory of blending)

Gregor Mendel was an Austrian monk who is considered the father of genetics and had a good
background in botany.
He knew how to pollinate and cross fertilize plants
Hybrid: cross between 2 different plants
Purebred: cross breed between the 2 types of plants

Genetics is the branch of biology that studies heredity

Self pollination produces offspring identical to the parent
Cross pollination is when pollen fertilizes eggs from a different plant (offspring isn’t identical)
Dominant or recessive alleles (T = dominant, t = recessive) = principle of dominance
Genotype = genetic makeup Phenotype = physical makeup
Genotype: homozygous = consisting of the same allele (homo recessive or dominant)
Heterozygous: consisting of different alleles (dominant always comes first)

Mendel applied probability to biology

1: rule of probability: larger # of trials = closer to expected ratio (in theory)
2: rule of probability: previous event don’t affect future outcomes
Applied these ideas to genetics: greater # of organisms = closer to expected ratios
Previous ratios don’t affect future outcomes

Mendel came up with 4 principles

#1: individual factors (that do not blend) control each trait = these are called genes
Alleles = different forms of a gene (eg: tall vs short)

#2: principle/law of dominance = dominant trait masks the recessive trait

#3: principle/law of segregation = pairs of genes segregate/separate during gamete formation

Fusion of gametes at fertilization pairs genes once again

#4: principle/law of independent assortment = each pair of alleles segregate independently

during gamete formation = 2 homologous chromosomes line up on either side of the equator
randomly, makes 223 (8 million) combos in humans

Testcross: a cross to determine if an unknown genotype that it shows a dominant trait is either
homozygous dominant or heterozygous
Incomplete dominance: both alleles are equally dominant (eg: 2 flowers RR (red) and WW
(white) are crossed and the offspring are a combo of the two, the flower would be RW (pink)

Multiple alleles: when 3+ alleles that code for the same trait, eg human blood type or rabbit coat
color
Codominance: when both alleles contribute to the phenotype of the offspring (eg: A + B portions
of blood groups, sickle cell anemia, red and white coats in cattle)

Polygenic traits (inheritance): trait produced by interaction of many genes (height, skin color)
Incomplete dominance: when one allele isn’t completely dominant over the other
- Heterozygous phenotype is somewhere in between the 2 homozygous phenotype
Ex: red x white = pink
Not blending because pink x pink = red, white or pink

Ex 2: hypercholesterolemia
HH (good) Hh (½ bad) hh (bad)

Multiple alleles: 3+ alleles that code for the same trait (ex: human blood type, rabbit coat color)
A, B blood types are carbs (and dominant) O doesn’t doesn’t have an antigen and is recessive
O is the universal donor and can only give to itself and A is the universal receiver and can only
give it itself

Sickle Cell Anemia = codominant (AA = bad SCA, NN = normal, AN = some SC)
Malaria = disease spread by anopheles mosquito
If AA = died from SCA, if NN = died from malaria, AN = had some SCA but were resistant to
malaria, surrived

Pleiotropy: 1 gene impacts several characteristics (SCA linked to lower chances of dying from
malaria) All caused by 1 gene: causes red blood cells to bend and get stuck in capillaries, can
block and can be fatal (point mutation)

Chapter 14 Human Heredity:

Karyotype: picture of chromosomes arranged in pairs
44 autosomes 2 sex chromosomes
½ of all sperm carry x and the other half carries y
Can’t develop without x chromosomes

How does Down syndrome (trisomy 21) occur?

Nondisjunction, it can happen in meiosis (all 4 are abnormal) 1 or 2 (2 abnormal cells)
Other examples of nondisjunction: down syndrome, klinefelter syndrome (xxy), Turner
syndrome (only 1 x chromosome)

Other disorders seen in a karyotype:

1: cri du chat: deletion of the long arm of chromosome 5, developmental issues, low birth
weight, etc)
2: patau’s syndrome: trisomy 13, cleft palate, polydactyly, developmental issues, etc
3: Angelman syndrome: deletion of short arm 15: developmental issues, ataxic gait, seizures

Sex linked traits:

1: color blindness: inability to distinguish certain colors
2: muscular dystrophy: progressive wasting away of the skeletal muscles
2: hemophilia: recessive allele on the x chromosome (anti-hemophilic factor is needed)
Males can’t carry sex-linked disorders because they only have 1 x chromosome

Recessive (have to be rr to have it, ex: albinism, cystic fibrosis) and dominant disorders (RR or
Rr has it but RR has it worse, ex: Huntington’s, acondroplasia aka dwarfism) have nothing to do
with gender

Chapter 15: Genetic Engineering

Selective breeding: allowing only those organisms with desired characteristics to produce the
next generation (eg: dog breeding)
Takes advantage of naturally occurring genetic variation in plants, animals, and other
organisms, to pass desired traits onto the next generation of organisms
Nearly all domestic animals and crops have been producing by selective breeding

Hybridization: crossing dissimilar individuals to bring together the best of both organisms
Hybrids are often stronger/hardier than either of the parents (ex: Burbank potato)

Inbreeding: continued breeding of individuals with similar characteristics. Inbreeding makes sure
that the trait is preserved. There are high risks with inbreeding because of the increased risks of
genetic defects

Reading the sequence: determining the order of DNA bases. A single strand of DNA whose
sequence of bases is not known is placed in a test tube and 4 nucleotides are added to the
bases and as the enzyme starts working, it uses the unknown strand as a template to make one
new DNA stand after another. A small amount of bases that have a dye is also added.

Cloning: a clone is a member of a population of genetically identical cells produced from a

single cell.

Dolly the sheep was cloned in 1997 by:

#1: the nucleus of an egg cell is removed
#2: the cell is fused with a cell taken from a other another adult
#3: the fused cell begins to divide and the embryo is then placed in the reproductive system of
a foster mother where is develops normally
Chapter 16 Evolution
Charles Darwin is the “father” of evolution

Evolution: change over time = process by which modern organisms have descended from
ancient organisms

Theory (evolution, etc) vs Law (gravity) law: an official and nearly universally accepted concept
while a theory is a well-supported, testable explanation of phenomena that have occurred in the
natural world but can also have a widely accepted opposable concept

Other theories for the existence of earth exist (creationism = intelligent design)

Darwin voyaged on the Beagle for 5 years starting in 1831

He visited several continents and many islands, observed and collected numerous
animals/plants, and compared them to species from England which led to his theory about how
life changes over time, collected many fossils resembling living organisms

Argentina and Australia: similar grassland ecosystems but inhabited by very different animals

Fossils: preserved remains of ancient organisms = evidence of evolution

Darwin collected many fossils

Galapagos Islands: islands were close together yet species varied greatly from island to island
Hypothesis: these separate species would evolve from a common ancestor

Darwin’s idea shocked many and most people accepted what the church taught them (earth is
only a few thousand years old)

The ideas of geologists Hutton and Lyell helped scientists recognize that the earth is millions of
years old and that what changed Earth now still changes Earth today.

Geologist James Hutton published the idea that rock layers form very slowly (1795)
Mountains and valleys are shaped by natural forces (rain, heat, cold) So, the earth is older than
a few thousand years
Geologist Charles Lyell wrote the book “Principles of Geology” published in 1830 and Darwin
read it before going on the Beagle, influenced Darwin in 2 ways, #1: if the earth can change
over time, life can too #2: it takes many years for life to change
Scientists must explain past events with evidence, explain how geological features can be built
up/torn down

Jean-Baptiste Lamarck published his theory of evolution in 1809 and proposed that living thing
change over time (all species are descendents + adapt to the environment) Also proposed that
certain traits can be lost/acquired over a lifetime and can be passed down to offspring and leds
to change over time

3 mechanisms of change:
#1: a tendency toward perfection
#2: use + disuse
#3: inheritance of acquired traits

Lamarck’s theory wasn’t correct but he is still given credit for it

Thomas Malthus reasoned if the human population continued to grow unchecked, sooner or
later there would be insufficient living space and food for everyone. War, famine, and disease
also work against growth

Charles published “On the Origin of Species through Natural Selection” (1859) where he
described: the origin of species: he proposed a mechanism for evolution called natural selection
that was based on natural variation (differences among individuals of a species, found naturally)

Darwin proposed that much of this variation could be inherited or passed on to the next
generation, he was also worried about publishing his book.

Darwin was concerned about his competition (from Alfred Wallace) which motivated him to
publish quickly

Darwin studied farming and concluded that artificial selection (humans/outside sources dictate
which animals mate, breeding of useful traits from natural variation among species) Might
benefit humans, but not nature

Evolution by Natural selection:

#1: struggle for existence: members of each species compete regularly to obtain food, living
space, and other necessities of life
#2: survival of the fittest: some organisms are better fit for survival (fitness: the ability of an
individual to survive + reproduce = result of adaptation)

Over time, natural selection results in changes in the inherited characteristics of a population,
these changes increase a species fitness in its environment (Darwin referred to these changes
as Descent with Modification)

Darwin concluded that life has evolved for millions of years and the evidence he gave was,
fossil records, geographical distribution of living species, homologous structures of living
organisms, similarities in early development

Current evidence that Darwin didn’t use include molecular biology (genetic similarities)
Fossil records: gives information about past life (including structure, what they ate, ate them,
order they lived, and environment they lived)

Fossils provide the most evidence for evolution but they are rare because of the way they form
Fossils are rarely formed from soft tissues and fossil remains of bone/teeth are protected and
retain structure
Mold fossil: animals covered -> decays -> forms mold
Impression: minerals replace organic tissue (eg petrified wood) paleontologists: study of fossils

Only sedimentary rock has fossils because it hasn’t been melted/changed by the earth
2 types of fossil dating: relative and radioactive dating

Relative dating: placement in layers only gives relative age (older is lower, higher is younger)
Index fossils (easy to recognize, short time frame, and existed over wide range) can be used as
comparison

Radioactive dating: uses half-life of radioactive elements/isotopes

Carbon 14 is commonly used (organic), its half life is 5,730 years but only reliable up to 50,000
(generally 10,000) K-40 is also used but has a half-life of 1.3 billion years

2: geographic distribution of living species (descent with modification, similar pressures of

natural selection)

3: homologous structures: structures that have different mature forms in different organisms but
develop from the same embryonic tissue, some homologous organs have become vestiges
(traces) = vestigial organ (eg: appendix) and serve no useful function.

Homologous structures: similar structures but different function

Analogous structures: different structures but similar function (ex: moles vs mole crickets)

Basilosaurus: an extinct whale whose hind legs link living whales with their land-dwelling
ancestors.

Similarities in early development: same groups of embryonic cells develop in the same order
and in similar patterns to produce the tissues and organs of all vertebrates (Ernst Haeckel:
evolution will less successfully modify early stages of development)

Molecular biology similarities: genetics

Summary of Darwin’s theory

#1: organisms in nature differ from one another, and some variation is inherited
#2: more organisms are produced than survive and compete for resources
#3: more offspring is produced and many don’t reproduce
#4: each has advantages and disadvantages in the struggle for existence
#5: individuals best suited to their environment survive and pass traits onto offspring, weaker
individuals die or have fewer offspring
#6: species change over time (natural selection)
#7: species today descended with modifications from past species
#8: all organisms on Earth are united by a common ancestor

Chapter 17: Evolution of Populations

Gene pool: combined genetic information of all the members of a particular population
A gene pool typically contains 2+ alleles for each inheritable trait

Relative frequency: the number of times an allele occurs in a gene pool compared with the
number of times other alleles occur (often expressed as percents)

Sources of genetic variation: 2 main sources of genetic variation are mutations and genetic
shuffling that results from sexual reproduction
#1: mutations (mostly bad but can be good): any change in a sequence of DNA; some can
affect an organism's fitness, or its ability to survive and reproduce; others may have no effect on
fitness
#2: gene shuffling: most inheritable differences are due to gene shuffling that occurs during the
production of gametes, 3 types ( (a)law of independent assortment: each chromosome moves
independently during meiosis, 23 pairs = 8.4 million different combinations, (b) crossing over:
increases the # of different genotypes (c) sexual reproduction produces many different gene
combinations, doesn’t change the relative frequency of alleles)

Single gene: number of phenotypes produced for a given trait depends on how many genes
control the trait, single gene trait: trait controlled by a single gene
Polygenic trait: trait controlled by 2+ genes

Natural selection doesn’t act directly on genes, it acts of on phenotypes

Natural selection on single-gene traits can lead to changes in allele frequency and thus to
evolution. Natural selection can affect the distributions of phenotypes in any of these 3 ways
#1: stabilizing selection: a form of natural selection by which the center of the curve remains
at the current position (average has better fitness than outliers)
#2: directional selection: a form of natural selection in which the entire curve moves;
individuals at one end of distribution have higher fitness than individuals in the middle or other
ends
#3: disruptive selection: natural selection in which a single curve splits into 2: occurs when
individuals at the upper and lower ends of a distribution curve have a higher fitness level than
individuals in the middle

Hardy-Weinberg equilibrium: evolution will not occur as long as the following conditions are met
1: natural selection does not occur
2: the population is very large
3: the population is isolated / no migration
4: there are no mutations/they don’t change the gene pool
5: mating is random
Does any of the above occur? No, so evolution will take place

Deviations from the Hardy-Weinberg equilibrium cause changes in the gene pool
(microevolution) natural selection and genetic drift (a)Bottleneck effect (B) founder effect are the
2 most common forms
3: gene flow 4: mutations 5: non-random mating because these things occur, evolution
occurs

Genetic drift: change in a gene pool of a small population due to chance

- Is microevolution caused by chance
- Remember population size in terms of probability
- Hardy-weinberg requires an infinitely large population \
Two situations that shrink a population: bottleneck effect (earthquake, flood, fire) elephant seal
population down to 20 individuals, now over 30,000 and little variation in the population
And founder effect (small group moving to a new area, can be 1 pregnant female) e.g. Darwin’s
finches, Tristian de Cunha: recessive allele for retinitis pigmentosa increased (1 person with the
disorder in 1814 and 4 with and 9 carriers in the 60s)

Gene flow: when people/gametes move in or out of populations

- Humans are now a melting pot but used to have more clearly defined genetic distinctions
and it happens
Mutations: random change can alter allele frequencies
- It happens
Nonrandom mating: it happens, so there is evolution

New species form by speciation (formation of new species) species (a group of organisms that
breed and produce fertile offspring) vs population (group of individuals of the same species
living in the same place at the same time and are the smallest unit that can evolve)

Isolating mechanisms: as new species evolve, populations become reproductively isolated

from each other -> this leads to -> reproductive isolation: and separation of species of
populations so that they cannot interbreed and produce fertile offspring
Gene pools are separate and respond to natural selection of genetic drift as separate units and
there are 3 isolating mechanisms
#1: behavioral isolation: occurs when 2 populations are capable of interbreeding but have
differences in courtship rituals or other types of behavior (eg: eastern and western
meadowlarks)
#2: geographic isolation: 2 populations are separated by geographic barriers (oceans, rivers,
etc) (abert squirrels and Kaibab squirrels) *geographic barriers do not guarantee the formation
of new species*
#3: temporal isolation: 2+ species reproduce at different times (some orchids that only release
their pollen on a single day, can’t cross-pollinate at the same time)

Galapagos Finches: When Darwin discovered that they were all finches, he hypothesized that
they descended from a common ancestor, natural selection shaped the beaks of the birds. In
order for the beak size/shape evolve: there must be enough inheritable variation in those traits
to provide raw material for natural selection and they must produce differences in fitness.

Speciation of Darwin’s finches:

#1: founding finches from the mainland arrive
#2: some of the population separates and goes to another island (no shared gene pool)
#3: changes in the gene pool: the directional selection on different islands and natural selection
caused the population to evolve
#4: reproductive isolation could be caused by differences in beak size combined with mating
behavior
#5: ecological competition between species
#6: continued evolution

Peppered Moths are a classic example of natural selection in action

Chapter 18: Species Classification

Biologists have identified and named about 1.5 million species and they must be organized into
groups that have biological meaning

To study the diversity of life, biologists use a classification system to name organisms and group
them in a logical pattern (common names)

Taxonomy: classify organisms and assign each organism a universally accepted names
In a good system of classification, organisms placed into a particular group are more similar to
each other than they are to organisms in other groups (latin and greek are often used for
scientific names because they are the root language for other languages)

Early Efforts: names often described the physical characteristics, names could be 20 words long
Originally names were descriptions of the characteristics of a species (ex: yellow + red moth
with short wings) but these names were too long

Systematics: carried out by taxonomists Naming organisms was always a problem (historically it
was done as a matter of life and death) it organizes life and allows clear communication about
the natural world (system of classification slide (2nd slide on 2nd page) to last slide of page 3)

The need for a universal naming system arose = system of binomial nomenclature (created by
Carolus Linnaeus, Linnaeus named many species)

Binomial Nomenclature: Carolus Linnaeus’ naming system

The scientific name is written in italics/underlined
The first word is capitalized and the second word is lowercase
The first part of the scientific name = is the genus and the second part is the species
Often Latinized description of some trait/indication of where the organism lives

Lineaus’s system of classification uses taxons (a group/level of organization) and uses 7

categories, from smallest to largest) species (smallest) -> genus -> family -> order -> class ->
phylum -> kingdom -> domain (largest) There are super (ex: superfamily) and subtaxons (ex:
subspecies) Domain is the largest level of organization

Traditional classification (no longer used)

Based on structure alone = physical similarities but can be misleading because of convergence
(analogous structures)

Modern evolutionary classification

Method of grouping organisms together according to their evolutionary history
Sometimes due to convergent evolution organisms that are quite different from each other
evolve similar body structures
Biologists now group organisms into categories that represent lines of evolutionary descent, not
just physical similarities
Species placed within the same genus should be more closely related to one another than to
species of other geniuses
Behavior (ex: parental care) is also considered in evolutionary advancement
What characteristics do they have? (paternal care, mammary glands, etc)
Cladistic means evolution

Classification using cladograms: cladograms are diagrams that show the evolutionary
relationships among a group of organisms
Cladistic analysis: identifies and considers only those characteristics of organisms that are
evolutionary innovations, new characteristics that arise as lineages evolved over time, it
represents a type of evolutionary tree (gives info as to when organisms branched off from one
another) DNA and evolution are most reliable forms of determining which organisms are closely
related, physical characteristics can also be used but are the least reliable

The cladistic analysis takes evolution into account

Evolution is good for cleaning up classifications
Similarities in DNA and RNA: the genes of many organisms show important similarities at the
molecular level, these similarities can be used as criteria to help determine classification
Ex: human + yeast both have a gene that codes for myosin (protein in muscles)

Historically, which 2 were classified together? American vultures urinate on their legs (wtf?)
That evaporates and takes body heat with it and storks are the only other bird that does that
DNA analysis revealed that American Vultures are more closely related to storks than African
Vultures DNA evidence helps to prove what evolution and physical characteristics already show
Depending on how recently 2 species branched off, they can mate and create fertile hybrid
offspring

Molecular clocks use DNA comparisons to estimate that 2 species have been evolving
independently and depend on repeating processes to mark time (mutation) Some mutations
have a major positive/negative effect on an organism’s phenotypes. These neutral mutations
accumulate in the DNA of different species at about the same rate. A comparison of such DNA
sequences in 2 species can reveal how dissimilar the genes are. The degree of dissimilarity is in
turn an indication of how long ago the species shared a common ancestor
Molecular clocks look for neutral mutations that build up over time

6 kingdom system: eubacteria, archaebacteria, protista, fungi, plante, and Animalia

Monera used to be used for bacteria and was then replaced with bacteria and archaea

3 domains bacteria/ kingdom: eubacteria

archaea/kingdom: archaebacteria
eukarya/kingdom: (Protista, fungi, plante, and Animalia)

Domain Bacteria: Kingdom = eubacteria, unicellular, prokaryotic Peptidoglycan is the reason species go
into this category cells have thick rigid cell walls that surround a cell membrane (composed of
Peptidoglycan = protein + sugar) ecologically diverse, ranging from free-living soil organisms to deadly
parasites some photosynthesize, some need oxygen, others don’t most bacteria in this domain don’t help
or harm people

Domain Archaea: Kingdom = Archaebacteria, unicellular and prokaryotic

*cell walls lack peptidoglycan* this separates it from domain bacteria
Some live in the most extreme environments (volcanic hot springs, brine pools, black organic mud with no
oxygen) cell membranes contains unusual lipids Monera was discontinued because one group had
peptidoglycan and the other didn’t have peptidoglycan

Domain eukarya: all organisms that have a nucleus

1: protista: eukaryotic (display the greatest variety, most are single celled but some are multicellular,
includes algae, some photosynthetic and others are heterotrophic, some share characteristics with plants,
fungi, or animals

2: Fungi (heterotrophs, most feed on dead/decaying organic matter, will secrete digestive enzymes into
food then absorb, most are multicellular, most have root like structures underground)

3: plante (multicellular, photosynthetic autotrophs, nonmotile (can’t move), cell walls contain cellulose)

4: animalia (multicellular, heterotrophic, NO cell wall, most can move for at least some part of their life,
incredible diversity)
Chapter 19: History of life on Earth:
Geologic time scale: covers 88% of Earth’s history
Eras: one of several subdivisions of the times between the Precambrian and the present
Periods: unit of time into which eras are subdivided
Precambrian: simple anaerobic forms of life appeared, followed by photosynthetic forms ->
added o2, aerobic forms evolved and eukaryotes appeared *life increased in complexity*

Few fossils, soft-bodied animals, and life in the sea

Earth’s early history: 4.6 billion years old

Earth was formed by pieces of cosmic debris that were probably attracted to one another over
100 million years to form the earth, the planet was struck by 1+ large objects, and collision
produced enough heat to melt the entire globe and rearrange the planet (most dense to least
dense, magma in center of the earth, etc)

Abiogenesis: the origin of life, theory of how 1st life began and not the regeneration of life
Harold Urey and Stanley Miller made an experiment where they made organic molecules from
inorganic substances, they filled a flask with hydrogen, methane, and ammonia (H2O
represented earth’s atmosphere), passed electric sparks through the mixture to simulate
lightning, over a few days = several amino acids began to accumulate and produced cytosine
and uracil in 1995

Formation of microspheres: large organic molecules can form tiny bubbles (protocells have
selectively permeable membranes), a simple means of storing and releasing energy

Evolution of RNA and DNA: 1 hypothesis suggests that RNA could have evolved before DNA
Free Oxygen: microfossils = microscopic fossils = 3.5 billion years - prokaryotic organisms, no
O2

Photosynthetic bacteria: became common 2.2 billion years ago (O2 +iron combined = iron
oxide), oxygen gas accumulated in the atmosphere, and the ozone layer formed (O3), the rise
of oxygen in the atmosphere drove some life forms to extinction and others evolved to use
oxygen

Origin of eukaryotic cells: endosymbiotic theory: eukaryotic cells formed form a symbiosis
among several different prokaryotic organisms Lynn Margulis (mitochondria and chloroplasts
have DNA, have ribosomes like bacteria, reproduce by binary fission)
Sexual reproduction: this development enabled evolution to take place at a greater speed

Patterns of Evolution: macroevolution: refers to large-scale evolutionary changes that take place
over long periods of time; six patterns (mass extinction, adaptive radiation, convergent
evolution, coevolution, punctuated equilibrium, and changes in developmental genes)
#1: mass extinction: an event in which many types of living things become extinct at the same
time
#2: adaptive radiation: a process by which a single/small group of species evolved into several
different forms that live in different ways
#3: convergent evolution: a process by which unrelated organisms independently evolve
similarities when adapting to similar environments
#4: coevolution: the process by which 2 species evolve in response to changes in each other
#5: punctuated equilibrium: pattern of evolution in which long stable periods are interrupted by
brief periods of more rapid change
#6: changes in developmental gene: hox genes control growth of embryo and homologous hox
genes establish body plans = humans and insects