1. Evolution and Classification

1.1 Origin of Life and Plants

1.2 Animal Evolution

1.3 Human Evolution

1.4 Mechanisms of Evolution

1.5 Hardy-Weinberg Equilibrium

1.6 Mechanisms of Speciation

1.7 Classification of Living Organisms

1.1 Origin of Life and Plants

What is evolution?

Earliest forms of life began 4 billion years ago. The earths atmosphere was very different: composed of water, methane, ammonia, hydrogen sulfide, carbon dioxide, carbon monoxide, and phosphate – reducing conditions!

A. J. Oparin The earths reducing atmosphere combined with the earth’s cooling and lightning storms resulted in hot seas (primordial soup) where organic molecules (like amino acids) could be formed

S. Miller and H. Urey Mimicked the earths early atmosphere in experiments where small inorganic molecules were exposed to electric charges and created organic building blocks of life, including amino acids

S. Fox Experiments where amino acids formed dipeptides with ultra violet radiation, and under dry heat, polypeptides that contained up to 18 amino acids

C. Ponnamperuma Showed the formation of adenine and ribose from treating gases similar to those found in earth’s early atmosphere with an electric current

With no O2 present in earth’s early atmosphere, the earliest cells were anaerobic.

Some evolved the ability to make their own energy (autotrophs) introducing O2 into the atmosphere

By producing oxygen as a byproduct of photosynthesis, cyanobacteria are thought to have converted the early oxygen-poor, reducing atmosphere, into an oxidizing one

O2 is normally poisonous to anaerobic cells, but some evolved to not only survive oxygen, but incorporate it into their metabolic pathways (aerobic).

These cells incorporated autotrophs and together they evolved into photosynthetic eukaryotic cells.

The earliest plants were probably aquatic, but over time, as niches began to fill in both salt and freshwater areas, plants evolved anatomical adaptations, like cell walls, to allow for life on land.

1.2 Animal Evolution

Animals are thought to have evolved from marine protists – single-celled living organisms. Animal cells are most similar to protist cells, though the fossil record does not go back that far.

The first evidence of multicellular organisms with armor-like exoskeletons

Cambrian Explosion ca. 530 Ma

Diversification of species that survived mass extinction, the emergence of plants growing on land, and the first record of vertebrates (early fish)

Ordovician Period ca. 500 Ma

Land colonization by both plants and animals, which came with new adaptations (gas exchange, skeletons, circulatory system) to survive

Silurian Period ca. 435 Ma

The end of the Paleozoic Era was punctuated by a number of mass extinction events (nearly 95% of developed species)

1.3 Human Evolution

Humans are believed to have evolved from primates that evolved or developed larger brains over time

Earliest humanoid fossils found in the 1970s – Australopithecus afarensis, aka “Lucy”

Earliest human fossils are thought to be 1.8 million years old -Homo erectus

Homology: The existence of structures in two different species that share a common ancestry

Analogy:

The existence of structures in two different species that share a common function but not a common ancestry

Analogous structures are an example of convergent evolution, more than 1 species evolves to fill a niche

1.4 Mechanisms of Evolution

Darwinian vs. Modern understanding of evolution

Darwin focused on natural selection that happened to individuals, modern theory focuses on changes that happen among populations w/in communities

Charles Darwin

Natural Selection: some individuals within a population are better suited for survival under given environmental conditions

Differential Reproduction: those individuals better suited for survival are also more likely to successfully reproduce This strengthens the frequency of expression of “desirable” traits across a population over time

A random alteration or change in a DNA sequence

Sickle cell anemia – a mutation that switches 1 amino acid

Sometimes the mutation leads to a desirable trait (ex. Mutation of CCR5 gene gives some individuals HIV resistance) Sometimes a mutation can lead to an undesirable trait (ex. Mutation of BRCA1 gene can lead to cancer)

Genetic drift impacts the genetic makeup of a population by random chance. Sometimes individuals leave behind a few more offspring than others, and therefore, more genes These genes are then expressed in following generations, even though they are not necessarily the “fittest”

1.5 Hardy-Weinberg Equilibrium

Definition: The frequency of genotype ratios remains constant from one generation to the next in populations at equilibrium with the environment where random mating is occurring

Requirements for Hardy-Weinberg Equilibrium: Random mating, no migration, mutation, selection, or genetic drift can be occurring

The sum of all frequencies of all possible alleles for a single trait is = 1 (or 100%) If p = frequency of allele “A” and q = frequency of allele “B” Then p+q = 1

The frequency of genotypes within a population can be represented mathematically as: p2 + 2pq + q2 =1

p2 is the homozygous dominant genotype q2 is the homozygous recessive genotype and 2pq is the heterozygous genotype

An example: phenylthiocarbamide (PTC) Found in cabbage and broccoli, can give a “bitter” taste, but only for some people (considered a dominant trait)

NH

S

NH2

T = allele for tasting PTC t = allele for non-tasting of PTC Possible genotypes are: TT, Tt, and tt (TT and Tt can taste PTC, and tt can not) Using our equations (p + q = 1) and (p2 + 2pq + q2 =1), if we know p or q, we can solve for the other!

Question: If the frequency of PTC non-tasters (tt) in a population is 4% (or 0.04), (1) solve for the frequency of the allele for tasting PTC, as well as (2) the frequency of the three possible genotypes (TT, Tt, tt).

Part 1) given: tt = 0.04 If tt = q2 = 0.04, solving for q q = the square root of 0.04, or 0.2 (or 20%). We know that p + q = 1, so solving for p, we get p + 0.2 = 1, p = 0.8 (or 80%)

(2) Solve for the frequency of the three possible genotypes (TT, Tt, tt). Plugging in our values to (p2 + 2pq + q2 = 1) (0.8)2 + 2(0.8)(0.2) + (0.2)2 =1 we can then solve

TT = 0.64, or 64% Tt = 0.32, or 32% And tt = 0.04 (or 4%) was given at the beginning

1.6 Mechanisms of Speciation

What is a “species”? How are different species produced?

Allopatric speciation Two geographically isolated populations experience genetic drift and mutations over time, eventually to the point where they can no longer interbreed successfully

Allopatric means “other homeland”

Sympatric speciation Two non-geographically isolated populations emerge from one due to the development of genetic differences where they can no longer interbreed successfully

Sympatric means “same homeland”

Adaptive Radiation Organisms diversify rapidly from an ancestral species into new forms, particularly when a change in the environment makes new resources available, creates new challenges, or opens new environmental niches

Punctuated Equilibrium– small population with rapid environmental change

Gradualism – large population in a stable environment

1.7 Classification of Living Organisms

What is taxonomy?

“Arrangement Law”

A way to classify organisms to construct internationally shared classification systems with each organism placed into more and more inclusive groupings.

Carolus Linnaeus and the 7 Level System

Binomial nomenclature – “2 names” • genus and species • Canis lupus • Homo sapiens

Species: Canis lupus

Genus: Canis

Family: Canidae

Order: Carnivora

Class: Mammalia Phylum: Chordata

Kingdom: Animalia

Domain: Eukarya

The Modern Classification System

3 Different Domains • Archaea • Eubacteria • Eukaryotes

Archaea • Prokaryotes • Unique RNA • Extreme ecosystems

Morning Glory pool, Yellowstone National Park

Eubacteria • Prokaryotes • Bacteria

Scanning electron micrograph of E. coli bacteria.

Eukaryotes • Eukaryotic cells • Contains 4

kingdoms: Protista, Fungi, Animalia, and Plantae

2. Cellular and Molecular Biology

2.1 Cell Structure

2.2 Transport Across Cell Membranes

2.3 Cellular Metabolism

2.4 DNA Replication

2.5 Cell Division

2.6 Biosynthesis

2.1 Cell Structure

What is a cell?

The smallest and most basic unit of most organisms. Species can be single celled (like Salmonella bacteria) or multicellular and complex, like humans.

There are two main types of cells.

Prokaryotes (like bacteria) have no nucleus or other membrane-bound organelles DNA is a single circular chromosome Unicellular organisms

Eukaryotes (like plants, fungi, and animal cells) have a nucleus as well as other membrane-bound organelles DNA is arranged into multiple chromosomes Unicellular and multicellular organisms

Plant and Animal cells both contain • a cell membrane • a nucleus • cytoplasm • cytoplasmic

organelles

Animal and Plant cells also contain • microvilli • a cytoskeleton • ribosomes • endoplasmic reticulum • Golgi apparatus • lysosomes • mitochondria

Mitochondria – produce energy (cellular respiration)

Ribosomes – site of protein synthesis

Plant cells additionally contain • a cell wall • chloroplasts • a central

vacuole

The cell membrane separates the cell from its environment, allowing for the interior environment of the cell to be very different from the exterior

The cell membrane is composed of • a lipid bilayer • proteins • carbohydrates

2.2 Transport Across Cell Membranes

Cell membranes protect the interior of the cell from the exterior. Transport of molecules across the membrane is possible, and depends upon the size and polarity of the molecule.

Transport across cell membranes has two basic types • Passive transport • Simple diffusion • Osmosis • Facilitated

diffusion • Active transport

Polar Non-polar

Simple diffusion, with a concentration gradient, small nonpolar molecules

Facilitated diffusion, small polar molecules, like glucose, amino acids

In active transport molecules move across cell membranes with an expenditure of energy • Moving against a

concentration gradient

• Requires energy, usually in the form of ATP

2.3 Cellular Metabolism

Cellular Metabolism encompasses all types of energy transformation in cells • Photosynthesis • Respiration • Growth • Movement

Metabolic Pathways

Adenosine triphosphate, or ATP, is the primary energy currency in biological systems • Energy is released by

hydrolysis of one of the phosphate groups to form ADP

• Energy is stored by attaching a new phosphate group to ADP to form ATP

Photosynthesis takes place in cells with chlorophyll, a green pigment that can absorb light • Typically in plants • Two phases • Light reaction • Dark reaction

Respiration takes place in all cells • Glucose is broken

down to release energy (glycolysis)

• Two types • Anaerobic (no O2) • Aerobic (with O2)

Net outcome of glycolysis (from 1 molecule of glucose) • 2 molecules of pyruvate • 4 ATP • 2 NADH

2.4 DNA Replication

What is DNA?

DeoxyriboNucleic Acid

A biopolymer that encodes all of the information needed to form a specific organism and produce proteins for functioning

A gene is a portion of DNA that encodes a specific protein

2’-DeoxyriboNucleic Acid

Since DNA codes for genes, which contain the blueprint for an organism, its important to be able to make copies of this blueprint for each cell The end result of DNA replication is two pieces of double stranded DNA identical to the parent DNA

In transcription, an RNA (ribonucleic acid) copy of the DNA is made.

What does it mean to transcribe something?

In translation, the information contained in the RNA copy of the DNA is used to guide the creation of proteins.

What does it mean to translate something?

DNA

RNA

Protein

replication

transcription

translation

2.5 Cell Division

Cell division is the process of cellular reproduction, where a copy of the cells “blueprint” needs to be made and passed on

centromerechromatids

homologs

Mitosis

A sequence of events that ends with cell division and the creation of two daughter cells from a single parent cell

4 Phases of Mitosis

• Prophase

• Metaphase

• Anaphase

• Telophase

Meiosis is a type of cell division that takes place in eukaryotes. It reduces the chromosome number by half, resulting in 4 daughter cells (gametes) that are all genetically distinct from the parent cell as part of reproduction.

2.6 Biosynthesis

Biosynthesis is the process of making chemical compounds, like proteins and DNA, by living things. Through anabolic processes, small molecules and building blocks can get built up into larger functional systems.

Enzymes are made primarily of protein and act as catalysts to help reactions take place in biological systems by lowering the activation energy, and therefore increasing the rate of reaction.

3. Structure, Function, and Genetics of Plants and Animals

3.1 Structure of Plants

3.2 Plant Physiology and Reproduction

3.3 Structure and Function of Animal Tissues

3.4 Anatomy of Animal Systems, Part 1

3.5 Anatomy of Animal Systems, Part 2

3.6 Homeostasis, Hormones, and Reproduction

3.7 Principles of Genetics

3.8 Modern Genetics and Inheritance

3.1 Structure of Plants

How are species of the plant kingdom classified?

There are three common methods, based upon their physical characteristics.

Vascular plants (tracheophytes) are able to move water and nutrients throughout their structure with specialized tissues (xylem and phloem). Non-vascular plants (bryophytes) do not have tissue to move water and nutrients throughout their structure.

A second method of classification is by growing season. Annuals only survive a single growing season, while biennials have a life cycle that spans two growing seasons. Perennials continue to grow year after year.

Plants can also be classified by their method of reproduction. Plants that produce flowers are called angiosperms, while those that produce seeds without flowers are called gymnosperms.

Angiosperms and gymnosperms differ in stem structure and reproductive organs.

Gymnosperms are mostly trees that produce seeds or cone-like structures.

Stem

Angiosperm Structure

Pistil Stamen

Fruit is a mature ovary and contains the seeds. Each seed contains a plant embryo, a store of food, and a protective seed coat. Under the right conditions, it will germinate (sprout).

The stem provides the main structural support of the plant, as well as producing leaves and branches. It also acts as the primary conduit for transport of nutrients and water throughout the plant.

Moves water up from the roots

Moves sugars down from the leaves

The leaves act as the primary sites for photosynthesis in the plant.

Leaves are attached to a branch or stem by a petiole, which connects the veins in the leaf to the stem.

3.2 Plant Physiology and Reproduction

Vascular plants (tracheophytes) are able to move water and nutrients throughout their structure with specialized tissues (xylem and phloem). Non-vascular plants (bryophytes) do not have tissue to move water and nutrients throughout their structure.

Since plants can synthesize their own sugars for food, the bulk of plant physiology is aimed toward obtaining CO2, water, and minerals from their environment.

Moves water up from the roots

Moves sugars down from the leaves

Water is especially important, as it needs to be able to travel from the roots to the top of the plant through the xylem.

Plants can synthesize their own sugars for food in their leaves, but these sugars need to be able to move out of the leaves and throughout the rest of the plant. This is accomplished by taking advantage of a concentration gradient between the phloem and the stem.

Plants alternate between haploid (n) and diploid (2n) phases in their life cycle. The diploid generation is the sporophyte, and produces haploid gametophytes. The male gametophyte produces sperm, and the female an egg cell, which together can form a zygote.

The diploid generation is the sporophyte, and produces haploid gametophytes, which may be male or female. The male gametophyte produces sperm, and the female an egg cell, which together can form a zygote that can mature into an embryo.

Reproduction in plants can also take place by vegetative propagation, an asexual process that results in offspring genetically identical to the parent.

3.3 Structure and Function of Animal Tissues

1) Animal cells do not have plastids or cell walls

2) Adult animals are multicellular organisms with specialized tissues and organs

3) Animals are heterotrophic – they do not produce their own food

4) Animal species are capable of sexual reproduction

5) Animals develop from embryonic stages

6) Most have symmetrical anatomy – either radial or bilateral

What type of symmetry does this sea star have?

Epithelial TissuesCell shape Description Locationsquamous flat, irregular round

shapesimple: lung alveoli, capillaries stratified: skin, mouth, vagina

cuboidal cube shaped, central nucleus

glands, renal tubules

columnar tall, narrow, nucleus toward base tall, narrow, nucleus along cell

simple: digestive tract pseudostratified: respiratory tract

transitional round, simple but appear stratified

urinary bladder

Connective TissuesTissue Cells Fibers Locationloose/areolar fibroblasts,

macrophages, some lymphocytes, some neutrophils

few: collagen, elastic, reticular

around blood vessels; anchors epithelia

dense, fibrous connective tissue

fibroblasts, macrophages,

mostly collagen irregular: skin regular: tendons, ligaments

Connective Tissues (continued)Tissue Cells Fibers Locationcartilage chondrocytes,

chondroblastshyaline: few collagen fibrocartilage: large amount of collagen

shark skeleton, fetal bones, human ears, intervertebral discs

bone osteoblasts, osteocytes, osteoclasts

some: collagen, elastic

vertebrate skeletons

adipose adipocytes few adipose (fat)blood Red and white

blood cellsnone blood

Types of Muscle TissueType of Muscle Striations Nuclei Control Locationsmooth no single, in

centerinvoluntary visceral

organsskeletal yes many, at

peripheryvoluntary skeletal

musclescardiac yes single, in

centerinvoluntary heart

Bone tissue is part of the skeleton and helps to provide stability and support for internal organs as muscles move and pull on the bones.

Cartilage is a tissue that provides cushioning at the joints and ends of bone, like in your knees and the tip of your nose. This helps to reduce friction as muscles pull and move bones.

Adipose tissue is used for fat storage, and provides cushioning around organs and insulation from extremes of temperature.

Nerve tissue, in the brain and spinal cord, carries chemical and electrical impulses between the brain and the limbs and organs, and nerve tissue in the brain sustains mental activity.

Blood tissue, composed of white and red blood cells in plasma, carries O2 to cells, delivers nutrients and wastes, regulates body temperature, and plays an important role in wound healing and immunity.

3.4 Anatomy of Animal Systems, Part 1

Those systems that most animals have in common are digestive, respiratory, skeletal, nervous, circulatory, excretory, and immune systems.

The digestive system is the central processing plant for ingested food. Food must be found, consumed, and then undergo catabolic processes in the digestive system to release the energy stored in chemical bonds.

Protein and carbohydrates begin breakdown in saliva, lipids not until small intestine, with help of bile acids from the gall bladder.

Gall Bladder

The respiratory system, or gas exchange system, is responsible for bringing in gases from the surroundings, like O2, while also expelling gases as waste products, like the CO2 you exhale. All living things require the ability to exchange gases with their environment.

(1)

(2)

(3)

(4)

(5)

Primary, Secondary, Tertiary bronchi

Alveoli(6)

The musculoskeletal system, combining muscle systems and endoskeletal systems, is unique to vertebrates, though variations utilizing an exoskeleton, like those found in crabs, also exist.

Endo – “internal” Exo – “external”

Axial Skeleton

Includes joints, ligaments, cartilage, muscles, and 206 bones that provide protection for internal organs, as well as the structure and stability necessary to walk upright. Bones also store calcium and phosphates, and produce red blood cells

Appendicular Skeleton

Skeletal muscles are “voluntary” – they move upon command by the nervous system. This contrasts with smooth muscle that lines internal organs and cardiac muscle in the heart which are “involuntary” – the muscles move and contract automatically, without you having to think about it.

Skeletal muscles are “voluntary” – they move upon command by the nervous system. This contrasts with smooth muscle that lines internal organs and cardiac muscle in the heart, both of which are “involuntary” – the muscles move and contract automatically, without you having to think about it.

3.5 Anatomy of Animal Systems, Part 2

Those systems that most animals have in common are digestive, respiratory, skeletal, nervous, circulatory, excretory, and immune systems.

The nervous system is the command center for an organisms, and provides control over all bodily functions and actions, both voluntary and involuntary. Nerve tissue that transmits all of these commands is composed of cells called neurons.

synapseNeurons line up in a network in space, where signals are transmitted from one to the other across a small gap in space called a synapse.

The nervous system is divided into two systems:

The Central Nervous System (brain and spinal cord)

The Peripheral Nervous System (sensory and motor nerves throughout the body)

The circulatory system is responsible for transport of nutrients, gases, and wastes to their destinations.

The circulatory system also plays an important role in homeostasis and regulation of body temperature and pH.

The immune system is the body’s main defense from foreign substances or invader, such as an allergen, bacteria, or virus.

The lymphatic system, including the lymph, lymph nodes, spleen, thymus, and tonsils, is the principal component of the immune system.

Lymph nodes function to produce lymphocytes, cells that work to protect the body from foreign invaders. Lymphocytes originate in the bone marrow as stem cells and are collected and distributed from the lymph nodes.

There are two types of lymphocytes: B Cells, which emerge from bone marrow mature and produce protective antibodies (antibody-mediated immune response) T Cells, which mature in the thymus and can directly destroy foreign invaders (cell-mediated immune response)

Electron micrograph of a T cell

3.6 Homeostasis, Hormones, and Reproduction

Life is only possible with in a narrow range of conditions (pH, temperature, water balance, glucose levels) specific to each organism.

Feedback control, which can be negative or positive, is the primary method by which homeostasis is maintained.

Negative Feedback Response

Positive Feedback Response

Chemical messengers called hormones play a large role in maintaining homeostasis by generating a response to an internal or external stimulus. This can take place by two different pathways.

Mobile Receptor Mechanism

Hormone-receptor complex

xCell membrane receptor

Membrane Receptor Mechanism

Reproduction in multicellular organisms proceeds through the processes of gametogenesis (formation of gametes) and fertilization.

Gametes are sex cells formed in the reproductive organs – sperm in males, and eggs in females. A zygote results from the fertilization of an egg by a sperm cell.

Spermatogenesis

Primary spermatocyte

Oogenesis

3.7 Principles of Genetics

Inheritance is the process by which characteristics pass from one generation to the next.

The concept of genetic inheritance was advanced through the work of Gregor Mendel, an Augustinian friar.

P generation

F1 generation

F2 generation

1) Parents transmit hereditary factors (genes) to their offspring

2) Each individual has 2 copies of a gene, which may be different from each other

3) The 2 genes act independently, and one may mask the effect of the other

A gene that masks the effect of another is referred to as “dominant” A gene that can have its effect masked by another is referred to as “recessive”

It is now known that chromosomes carry genetic information, and that the same gene may have different forms, or alleles. For examples, in Mendel’s experiments, the gene for flower color had two different alleles – one that coded for purple blooms, and one for white blooms.

Sometimes a trait can arise from more than one gene; in that case, there will be several possibilities for traits.

The combination of alleles that make a specific trait is the genotype. The expressed trait is the phenotype.

A Punnett square is a method used to predict the phenotype of simple genetic crosses. A letter is assigned to each gene – capital letters are dominant traits and lower case is recessive. Knowing the genotype of both parents, we can predict the genotype and phenotype of the offspring.

Monohybrid Cross – two individuals, only 1 trait

When alleles for a gene are the same in an individual (YY, or yy on the previous slide) the individual is homozygous for that trait. When alleles for a gene are different in an individual (Yy on the previous slide) the individual is heterozygous for that trait.

3.8 Modern Genetics and Inheritance

Inheritance is the process by which characteristics pass from one generation to the next.

1) The Law of Segregation

Traits are expressed from a pair of genes on homologous chromosomes. Each parent provides one chromosome from every pair of homologs, which randomly recombine during gamete formation.

2) The Law of Dominance

One gene is usually dominant over the other gene.

3) The Law of Independent Assortment

In Mendel’s dihybrid cross, he looked at both seed coat color and texture, and found that most traits were independent of one another.

Dihybrid cross – two individuals, two traits

Incomplete Dominance

Traits exist that have no genes that are dominant, and the resulting offspring have a phenotype that is a mix of that of both parents. This occurs in the cross of white and red snapdragons.

Linkage and Inheritance

While the Law of Independent Assortment held true for pea plants, the same was not found to be true for fruit flies.

It was found that some traits were inherited together, or linked.

Linked traits can be sex-linked – males (XY) will express the trait more often, as they only have 1 copy of X, while females have 2, and the other X may be dominant to the trait. Sex-influenced traits only require one recessive gene to be expressed, so long as there is no dominant gene to mask it.

Polygenic traits are those that arise from the expression of multiple sets of genes, and, as a result, are difficult to map or predict. Example traits are height and skin color in humans.

4. Ecology and Population Biology

4.1 Ecology and The Energy Cycle

4.2 Ecological Cycles

4.3 Population Growth and Models

4.4 Population Growth and Limiting Factors

4.5 Community Structure and Biogeography

4.1 Ecology and the Energy Cycle

What is ecology? eco – “home” ology – “study of”

The study of how organisms interact and influence (or are influenced by) their environment.

Ecosystem – a group of populations within a given area, plus the environment they live in Population – total number of a given species of organism within an ecosystem Organism – an individual of a specific species

Community – the populations that interact with each other within an ecosystem Biosphere – the portion of the earth that includes all living things *also includes atmosphere (air), lithosphere (ground), and hydrosphere (water)

Habitat – the physical place where a species lives, which includes all biotic factors (living) and abiotic factors (non-living) Niche – the role a species plays within an ecosystem, it’s place in the food chain

Ecological Cycles- organisms interact with their environment in order to obtain the resources and energy necessary to live, creating cycles of energy and resources that allow the community to survive

All life requires energy to live, and energy can neither be made nor destroyed When we talk about the energy cycle, we’re talking about a transfer of energy from one form to another

Animals that feed only on other animals are called carnivores. Animals that consume other animals, as well photosynthetic organisms are omnivores. The levels in the food chain are called trophic levels.

Tertiary(apex)Consumer

SecondaryConsumer

PrimaryConsumer

PrimaryProducer

Primary Producers are also called autotrophs, as they produce their own food.

4.2 Ecological Cycles

Ecological Cycles- organisms interact with their environment in order to obtain the resources an energy necessary to live, creating cycles of energy and resources that allow the community to survive

4.3 Population Growth and Models

While there are a number of factors that support growth of a population, the growth of a population is held in check by limiting factors that exist within the environment. This balance of growth is at equilibrium under normal, unchanging, conditions.

Two major factors affect the rate of population growth: Birth rate, or natality

Death rate, or mortality

When the birth rate is equal to the death rate, the rate of population growth is constant.

There are two models for describing population growth: The exponential curve (J curve) The logistic curve (S curve)

The exponential curve model describes a population where there is no limit on the population growth.

Realistically, this type of growth only exists during initial population growth.

The logistic curve model describes a population where the limits on the population growth are beginning to have an impact, and population growth is reaching an equilibrium state.

4.4 Population Growth and Limiting Factors

The limiting factors that keep population growth in check can be either biotic or abiotic.

Biotic means biological factors, like over-population and food supply. Abiotic means physical factors, like fire and water conditions

As a general rule, the survival and establishment of an organism in an area is dependent upon 1) The availability of

necessary elements for life in the minimum quantity

2) The controlled and constant supply of those elements

Because a number of factors contribute to maintaining homeostasis, population growth and density are usually controlled by multiple factors.

Population density = # of organisms / area

Abiotic limiting factors (density-independent factors): the density of the population has no effect on the limiting factor.

An example of this would be a forest fire. The density of populations in the area prior to the fire have no impact.

The limiting factors that are biotic are also called density-dependent factors; the density of the population can have a large impact on the limiting factor.

An example of this is fecundity, or number of eggs, in round worms.

Species will compete for limited resources and they may move in or out of an area to find new niches, a process called dispersion.

Species may disperse via emigration, immigration, and migration.

In some rare cases, one species will be wiped out by the other, a process called competitive exclusion.

Species sharing a range can have various relationships with each other. A predator is an organism that eats another for food, it’s prey.

Species that interact with each other have a relationship called symbiosis.

Mutualism is a symbiotic relationship where both parties benefit from the interaction.

Amensalism is where one species is neither harmed nor helped, while the other is inhibited.

Parasitism is where one species benefits, and the other is harmed.

The survival of a population is dependent upon maintaining a minimal viable population size. When the population drops below this size, there is the potential for extinction, or elimination of that species.

4.5 Community Structure and Biogeography

The limiting factors that keep population growth in check can be either biotic or abiotic.

Community structure – the characteristics of a specific community A community can be closed or open. An open community has indefinite boundaries, while a closed community has defined boundaries, called ecotones.

Communities grow and change over time, and sometime one community can take over another, a process called succession.

Biomes are large areas of land with similar climate, flora, and fauna.

The earths biomes are divided into terrestrial and aquatic biomes.

Oceans may be thought of as consisting of different zones based on water depth and distance from the shoreline and light penetrance. Coral reefs, estuaries, and the freshwater biomes (include lakes, ponds, rivers, streams, and wetlands) are all unique aquatic biomes.

5. Atomic Chemistry

5.1 Structure of the Atom

5.2 The Periodic Table

5.3 Nuclear Reaction

5.4 Rate of Decay and Half-Life

5.1 Structure of the Atom

What is chemistry?

Chemistry is the study of matter. Matter makes up everything around us – everything we can see, and some we can’t!

All matter is made up of building blocks called atoms.

An element cannot be broken down into any other substance; an atom is the simplest unit of an element that retains the elements characteristics.

H H

O

H2O

A molecule of water is made up of two atoms of hydrogen and one atom of oxygen.

Hydrogen and Oxygen are both elements; water is a molecule.

Atoms consist of a small, densely packed nucleus composed of positively charged protons and neutrally charged neutrons, surrounded at its periphery by clouds of negatively charged electrons.

outermost “valence” shell, max of 8 e-

5.2 The Periodic Table

Knowing how to navigate the Periodic Table can help us know how a particular element forms a molecule and how tightly it will hold onto the electrons in those bonds.

Elements are arranged on the periodic table by atomic number, or the number of protons in the nucleus. Elements that have the same number of protons, but a different number of neutrons are isotopes of each other. (Like Carbon 13)

The mass of an atom is the sum of the masses of all of the particles that compose that atom protons + neutrons + electrons = atomic mass Protons and neutrons each have a mass of 1 AMU, but electrons are so small, their mass is considered to be negligible, or 0.

What is the atomic mass of carbon?

How many protons and neutrons does Carbon 13 have?

8 is the magic number!

1 2 3 4 5 6

6 e-

1 2

2 e-

5.3 Nuclear Reactions

Atoms are not always stable! Sometimes the nuclei of an atom is unstable, and releases one or more sub-atomic particles in order to become more stable. When this happens, an element is said to be radioactive.

There are three common modes of decay from radioactive nuclei:

α (alpha) decay β (beta) decay and γ (gamma) radiation

In alpha decay, an alpha particle (a package of two protons and two neutrons) is released. This usually occurs in elements with a mass number above 60.

Po21084 Pb206

82

He42

α particle

Beta decay can be (+) or (-). A beta particle is a high speed electron or positron (same particle with reversed charge).

Beta decay results in an increase or decrease in atomic number, with the mass number remaining the same. Beta decay converts a neutron into a proton while releasing a beta particle.

I13153 Xe131

54

e0-1β particle

Gamma radiation is high frequency and high energy electromagnetic radiation, usually given off along with alpha or beta decay. Gamma rays are photons, and gamma radiation has no impact on either mass or charge.

5.4 Rate of Decay and Half-Life

Atoms are not always stable!

Sometimes the nuclei of an atom is unstable, and releases one or more sub-atomic particles in order to become more stable. When this happens, an element is said to be radioactive.

Half-Life is the amount of time it takes for 50% of an isotope to decay.

Strontium-85 has a half-life of 65.2 days. If you start with 20 grams of strontium-85, how long will it take before you have only 5 grams left?

Strontium-85 has a half-life of 65.2 days. If you start with 20 grams of strontium-85, how long will it take before you have only 5 grams left? 1 half-life leaves you with 20/2 = 10 grams.

Another half-life leaves you with 10/2 = 5 grams

Strontium-85 has a half-life of 65.2 days.

2 half-lives = (65.2)(2) = 130.4 days

6. Reaction Chemistry

6.1 Chemical Elements

6.2 Chemical Bonding

6.3 Chemical Reactions

6.4 Thermodynamics

6.5 Properties of Water

6.6 Important Biomolecules

6.1 Chemical Elements

It is common for elements to exist as part of a larger structure. Since atoms are the building blocks of matter, we need some way of taking these pieces and building them up into larger functional structures (like people!).

H H

O

H2O

H H

O

H2O

=

H H

O

H2O

16.00

1.008 1.008

What is the molecular weight of water? What is the mass % of H in a water molecule?

H H

O

H2O

16.00

1.008 1.008

1) 1.008 + 1.008 + 16.00 = 18.016 -> 18.02

2) H x 2 = 2.016 (2.016/18.02)100 = 11.19%

6.2 Chemical Bonding

A molecule is two or more atoms held together by shared electrons – like H2.

A compound is two or more different elemental atoms bond together through the sharing of electrons – like water!

Valence shell electrons are electrons in the outermost energy level in an atom. Atoms are most stable when their valence shell is full (8!). Atoms will exchange or share electrons in order to fill the valence shell. This is chemical bonding!

There are two common modes of bonding:

Covalent, where a pair of electrons is shared

and

Ionic, where electrons are exchanged

1 valence e- 6 valence e-

8 is the magic number! (2 for H)

H H

O

H2ORepresents 2 electrons being shared – one from O and one from H

Carbon has 4 unpaired valence shell electrons. Hydrogen has one. How many atoms of hydrogen can carbon form covalent bonds with?

Some elements pull electrons more strongly. These elements are more electronegative, and in a molecule can lead to a polar bond, like that in water.

HH

O

H2OH H

O

H2Ov

v

(-)(+) (+)

In ionic bonding, one atom loses an electron and another takes it. The atom that loses an electron has a (+) charge and is called a cation.

The atom that gains an electron has a (-) charge and is called an anion.

Na+ + Cl-

NaCl

A compound held together by an ionic bond is often called a salt.

1 valence e- 7 valence e-

8 is the magic number!

6.3 Chemical Reactions

Chemical reactions occur when molecules or atoms interact with each other. Reactions are symbolized with an arrow showing reaction progress from reactants to products.

There a many ways to categorize chemical reactions. We will categorize reactions using the following four reaction types: decomposition, combination, replacement, and double displacement.

A decomposition reaction often starts with a single reactant that degrades into multiple products.

AB à A + B

2NaN3 (s) 3N2 (g) 2Na (s)+

A combination reaction often starts with multiple reactants that react to form a single product.

A + B à AB

2NH3 (g)N2 (g) 3H2 (g)+

Fritz Haber

A replacement reaction is when one compounds breaks apart and forms a new compound with a different reactant.

AB + C à AC + B

Cu (s) 2AgNO3 (aq)+ Cu(NO3)2 (aq)+2Ag (s)

A double replacement reaction is when two compounds break apart and exchange components to form new compounds.

AB + CD à AC + BD

Pb(NO3)2 (aq) 2KI (aq)+ PbI2 (s) 2KNO3 (aq)+

A chemical reaction can also be categorized as an oxidation or a reduction. remember LEO GER!

Element Loses Electrons – Oxidation

Element Gains Electrons - Reduction

6.4 Thermodynamics

Chemical reactions occur when molecules or atoms interact with each other.

Reactions are symbolized with an arrow showing reaction progress from reactants to products.

?

Chemical reactions are either exothermic or endothermic. Exothermic reactions release energy. Endothermic reactions require an input of energy to proceed.

However all reactions must follow the laws of thermodynamics. 1) The law of conservation of energy and matter – matter and energy can be neither created or destroyed

2) The law of increasing disorder (entropy) – all reactions spread energy, which will tend to diminish its availability Taken together, this means that in reactions, energy and matter must always be balanced, and that reactions progress to degrade potential energy

Exothermic or endothermic?

Exothermic or endothermic?

6.5 Properties of Water

Water has a number of properties that make it a unique substance: • It is polar • It expands when

frozen (solid phase is less dense than liquid phase)

• High specific heat • High surface tension

Hydrogen bonding interactions…

lead to high surface tension

6.6 Important Biomolecules

What makes a compound “organic”?

Composed of C, H, O, and N.

Important organic biomolecules: carbohydrates, lipids (fats), and proteins

Carbohydrates: “hydrates of carbon” C, H, and O Important fuel for plants and animals

OHC

HC

HC CH

CH

OH

OH

H2COH

OHHO

Glucose

Lipids (fats): C, H, and O (mostly C and H – non-polar!) Important for fuel storage for animals

H2C

HC

H2C

O

O

O

C

C

O

CH2O

CH2

C

O

H2C

CH2

H2C

CH3

H2C

CH2

H2C

CH3

CH2

H2C

CH2

H2C

CH3

20-30

20-30

20-30

Proteins: C, H, O, N, and sometimes S Polymers of Amino Acids Molecules like enzymes

OC

HC

O

H NH2

R

Amino

CarboxylicAcid

Side Chain- highly variable!

Amino Acid Structure

7. Physics

7.1 Heat and Thermodynamics

7.2 States of Matter, Density, and Gravity

7.3 Classical Mechanics and Relativity

7.1 Heat and the Laws of Thermodynamics

Heat is energy that flows from an object and can increase the temperature of an object that is cooler.

Temperature is a measure of the average kinetic energy of that object.

The particles in a substance are always moving – even in a solid. The temperature at which the motion of the particles stops is called absolute zero, or 0 Kelvin, though it has never been reached by any substance.

There are three common methods of heat transfer: 1) Radiation 2) Convection 3) Conduction

Different materials have different capacities for storing energy. It takes water 20 minutes to heat to 75 degrees, 2 minutes for copper to reach the same temperature. Water stays hotter longer – it holds the heat.

The measure of this ability to store energy is called specific heat. (the amt. of energy to raise 1g by 1 degree C)

The specific heat of water is 4.2 J/(g x Co). What mass of water will be heated by 10 degrees when 840J of heat is added? Q = cmΔT Q – heat added c – specific heat m – mass ΔT – change in temperature

The specific heat of water is 4.2 J/(g x oc). What mass of water will be heated by 10 degrees when 840J of heat is added? Q = cmΔT Q / (cΔT ) = m (840J) / (4.2 J/(g x oC) x 10oC = m = 20g

The laws of thermodynamics explain the relationship between heat and energy in the universe. There are four laws we will discuss.

1) The law of conservation of matter and energy – matter and energy can neither be made nor destroyed

2) The law of entropy – whenever energy is exchanged in a process, some energy becomes unavailable for use

3) The law of absolute zero – absolute zero cannot be attained by any system

0) The zeroth law – whenever two bodies are in contact, they will move toward a state of thermodynamic equilibrium where both are at the same temperature

7.2 States of Matter, Density, and Gravity

All matter has physical properties that can be observed, and typically exists in one of four fundamental states, or phases: solid, liquid, gas, or plasma.

Solid – definite volume and shape, strong attractions Liquid – definite volume, no definite shape Gas – no definite volume, no definite shape, weak attractions

Ideal Gas Law

PV = nRT

P – pressure V – volume n – amount of gas R – gas constant T – temperature of the gas

Pressure and volume are proportional to temperature, assuming nR is constant. Pressure and volume are inversely proportional to each other – if one goes up, the other must drop

Important Temperatures Melting point – solid to liquid Freezing point – liquid to solid Boiling point – liquid to gas Heat of fusion – melt 1 kg of solid Heat of vaporization – 1 kg liquid to gas Condensation – gas to liquid Evaporation – liquid to gas

Density is a measure of matter per units of volume.

D = m/v

Pressure is a measure of force per units of area.

Pressure in a gas can impact it’s density, as a gas will always spread, or compress, to fill the container it is in. (liquids and solids are less responsive to pressure)

The force of gravity (F) is a measure of both mass(m) and pressure. The weight of an object is a function of the mass and the pull of gravity upon it. The force of gravity (F) = Mass (m) x acceleration caused by gravity (g) or F = mg

The acceleration caused by gravity is 9.8m/s2

The weight of an object = mg A falling object will continue to accelerate until the force of air resistance equals the acceleration due to gravity – a point called terminal velocity. This is independent of the weight of the object.

7.3 Classical Mechanics and Relativity

Mechanics is the study of objects in motion. Classical mechanics studies objects larger than atoms but slower than light.

Newton’s Laws of Motion: 1) Law of Inertia – an object at rest (or in motion) will stay at rest (or in motion) until acted upon by another object or force

Newton’s Laws of Motion: 2) Law of Force vs. Mass – the rate of change of an object is proportional to its mass and the force acting upon it, or F = ma

Newton’s Laws of Motion: 3) Law of Action and Reaction – interactions between two objects produces two forces that are equal in magnitude and opposite in direction

Work – movement of mass over distance (w=fd) Speed – rate of change of distance traveled (s=d/t) Displacement – change in position, noting the starting point and the end point (not always = distance) Velocity – rate of change of displacement (v = d/t)

Friction – rubbing motion that acts against motion between two touching surfaces Acceleration – rate of change of velocity (a=v2-v1/t2-t1) Momentum – product of mass and velocity Force – push or pull exerted

Si Units – International System Mass – kilograms Length – meters Time – seconds Volume – liters

Einstein’s theory of relativity summed up states 1) The speed of light is

constant 2) The laws of physics

are the same for all inertial frames of reference

E = mc2

8. Energy

8.1 Electricity and Circuits

8.2 Electricity and Magnetism

8.3 Introduction to Waves

8.4 Sound and Light Waves

8.5 Sound Waves and the Doppler Effect

8.1 Electricity and Circuits

An electrical charge is electrons gathered on the surface of an object. When they are not moving, it is called static electricity. When attracted by a positive charge, the transfer of the electrical charge can cause a spark.

Electrons can flow through substances called conductors as an electrical current. Some materials, like most metals, are good conductors. Other materials, like plastic, rubber, glass, and wood are very poor conductors; they are called insulators.

An electrical current follows a path called a circuit; every circuit has 4 parts. 1) Source of charge, or

voltage 2) A set of conductors 3) A load 4) A switch

A circuit may be closed, and have a continuous path for the flow of electrons. An open circuit has an inhibited flow of electrons due to the path being interrupted, either by a switch or disconnection.

Voltage is the electromotive force that pushes the electrons through the circuit. Amperage is the measure of the amount of current. Resistance is hindrance to a current, which can arise from a number of causes.

In a series circuit, there is only 1 path for the current to travel along. Linking them together in a series results in the total voltage of the circuit being equal to the sum of all of the voltages in each cell.

In a parallel circuit, there are multiple paths for the current to travel along. Linking them together in a series results in an increase in the total amperage of the circuit, with the current being equal to the sum of all of the currents in each cell.

8.2 Electricity and Magnetism

Magnetism is the ability of a substance to produce a magnetic field. Magnets can be temporary or permanent. Electromagnets are magnets that are electrically induced by wrapping metal coils around an iron core.

Magnets come in a large variety of shapes, sizes, and strengths. All magnets attract iron and have two poles. If suspended from a string, one pole points north, and one pole points south – a north magnetic pole and a south magnetic pole.

In our experiment, one end points north, one south. The earth has a core of iron, so it makes sense that is also acts like a huge bar magnet

Unlike poles attract, whereas like poles repel.

North and south poles always occur in pairs. Attempts to separate them result in more pairs of poles. If we continue to split the magnet, we will eventually get down to an iron atom with a north pole and a south pole—these, too, cannot be separated.

Magnets can be permanent - permanent magnets contain a natural magnetic element, like iron, nickel, and cobalt. Temporary magnets can be induced to carry a magnetic field. An electromagnet is created by wrapping wire coils around an iron core.

8.3 Introduction to Waves

Water can travel in waves…

A wave itself has no mass; it is a movement or disturbance within a medium.

There are two types of waves we will discuss.

A transverse wave causes particles to move up and down as the wave moves forward (perpendicular to the wave motion). Light waves and waves on the ocean travel in transverse waves.

A longitudinal wave causes particles to move back and forth as the wave moves forward (perpendicular to the wave motion). Sound waves and some earthquake waves travel in longitudinal waves.

8.4 Sound and Light Waves

Water can travel in waves…

Sound and light can also travel in waves!

Even though waves have no mass, we can still discuss the features and parts of waves, using the terms wavelength, frequency, amplitude, trough, and crest.

Wavelength (λ)

Amplitude

Crest

Trough

Speed (v)

Frequency (f) – the number of wavelengths that pass a point in one second

Speed (v) = Frequency (f) x Wavelength (λ)

Waves can be reflected if they hit a solid surface, or experience interference with another wave.

Sound travels in longitudinal waves. Changes in wave amplitude result in changes in volume; changes in frequency result in changes in pitch.

Light is considered to move in transverse waves, but light also has characteristics of a particle. The arrangement of the components of a light wave are identified in a spectrum. Visible light is in the middle of the electromagnetic spectrum.

High EnergyLow Energy

Light moves in a straight line until it hits an object Diffraction – bending of light around an object Reflection – bouncing of light off of an object Refraction – change of direction of a wave passing from one medium to another

8.5 Sound Waves and the Doppler Effect

Doppler Effect

9. The Universe

9.1 The Universe and Solar System

9.2 Seasons and the Moon

9.1 The Universe and Solar System

What is a galaxy? A system of stars, star systems (like our solar system), dust, and any other objects within range of the star systems gravitational pull. Ex. The Whirlpool Galaxy

What are stars? Huge masses of plasma with large amounts of energy and gravity.

At the core of stars is hydrogen. Under the intense heat and pressure, the protons form helium, gamma rays, positrons, and neutrinos, some of which can slip out of holes in a stars magnetic field.

The Big Bang Describes the birth of our universe as a massive explosion. A very small area of highly compacted matter and energy began an explosive expansion process, that some speculate is still happening today – though at a much slower rate.

The sun is a mid-size star that, like other stars, emits heat and light energy. The sun is about 10 times more massive than Jupiter, and about 109 times larger than earth’s diameter.

Sunspots are due to low temperatures compared with the surrounding surface Scientists estimate the age of the Sun to be about 4.6 billion years old

Our solar system consists of planets, moons, and asteroids that orbit the sun. A planet is a celestial body that orbits the sun, has enough mass for its self-gravity to assume a nearly spherical shape, and has cleared the area around its orbit.

The eight planets, in order from the sun are: Mercury Venus Earth Mars Jupiter Saturn Uranus Neptune

Planet Type Size Distance from sun

Moons

Mercury Terrestrial 3,000 mi 36 million mi 0Venus Terrestrial 8,000 mi 67 million mi 0

Earth Terrestrial 8,000 mi 93 million mi 1

Mars Terrestrial 4,000 mi 142 million mi 2

Jupiter Gas Giant 89,000 mi 483 million mi 67

Saturn Gas Giant 75,000 mi 885 million mi 62

Uranus Gas Giant 32,000 mi 1,787 million mi 27

Neptune Gas Giant 31,000 mi 2,800 million mi 13

Why isn’t Pluto a planet (as of 2006)?

A planet is a celestial body that orbits the sun, has enough mass for its self-gravity to assume a nearly spherical shape, and has cleared the area around its orbit.

Planets farther from the sun are larger, have more mass, and are colder than those that are closer. Terrestrial planets are composed of solid elements. Gas Giants are composed of mostly gases with huge atmospheric layers.

9.2 Seasons and the Moon

The sun is a mid-size star that, like other stars, emits heat and light energy. The sun is about 10 times more massive than Jupiter, and about 109 time large than earth’s diameter.

Earth tilts on its axis at an angle of 23.5 degrees as it rotates around the sun. This tilt, along with rotation, creates what we know as “seasons”.

For half of its yearly orbit, the northern hemisphere is tilted toward the sun and experiences “summer” For the other half, the southern hemisphere experiences “summer” while the northern half experiences “winter”.

North Pole

South Pole

W

S

North Pole

South Pole

W

S

The moon makes a complete orbit around the earth every 29 days, which is the origin of our months. One day is the time it takes earth to rotate on its axis once. In one orbit we can observe several moon phases.

EarthFull New

First Quarter

Third Quarter

Waxing Crescent

Waning Crescent

Waxing Gibbous

Waxing Gibbous

10. The Earth

10.1 Earth’s Atmosphere

10.2 Earth’s Layers

10.1 Earth’s Atmosphere

What is the atmosphere? The earth is surrounded by several layers of gases, which are essential to supporting life by absorbing energy and heat from the sun, trapping water near the surface, and moderating weather. These layers extend 350 miles into space.

The atmosphere of earth is made up of mostly nitrogen and oxygen.

78%

21%

1%

NitrogenOxygen

Other

The atmosphere is divided into five different layers, or strata, that differ from each other in temperature, density, and chemical composition. They are separated from each other by four transition zones.

The troposphere is closest to earth’s surface, extending 9 miles from the surface. It has the greatest density, and contains 99% of the water vapor in the atmosphere. Most weather is caused by the interactions of gases in the troposphere. It is separated from the stratosphere by the tropopause.

The stratosphere extends 9 miles from the tropopause. The protective ozone (O3) layer that absorbs UV radiation is here It is separated from the mesosphere by the stratopause.

The mesosphere is 30-50 miles above earth’s surface, with temperature decreasing outwards to as low as -110 degrees C. It has a very low density of gases, with almost no ozone or water. It is separated from the thermosphere by the mesopause.

The thermosphere is 50-300 miles above earth’s surface, with low gas density. The temperature in the thermosphere can rise as high as 1980 degrees C with the absorption of solar radiation by O2. It is separated from the exosphere by the thermopause.

The exosphere extends from the thermopause by about 620 miles. Due to its extremely low density of mostly hydrogen and helium particles and low gravitational forces, it is difficult to define.

10.2 Earth’s Layers

The earth itself is also divided up into layers, either chemically (crust, mantle, and core) or functionally (lithosphere and asthenosphere) The crust is the entire outer surface of the earth, and is rich in oxygen, silicon, and aluminum.

The mantle is the middle layer of earth and accounts for 82% of the earths volume. It is thought to be rich in iron, magnesium, silicon, and oxygen. The mantle is aplastic – it has the properties of a solid but flows like a liquid under high pressure.

The core is the center layer of earth and is composed of mostly molten iron and nickel. The core itself has two zones – a liquid outer core and a solid iron inner core.

The layers of earth can also be classified as the lithosphere and the asthenosphere. The lithosphere (lithos - stone) is composed of the crust and the rigid mantle layer. The asthenosphere (asthenos – no force) is composed of the molten plastic outer mantle of rock beneath the lithosphere.