Big Idea 4: Biological systems interact, and these systems and their interactions possess complex properties.

All biological systems are composed of parts that interact with each other. These interactions result in characteristics not found in the individual parts alone. In other words, “the whole is greater than the sum of its parts.” All biological systems from the molecular level to the ecosystem level exhibit properties of biocomplexity and diversity. Together, these two properties provide robustness to biological systems, enabling greater resiliency and flexibility to tolerate and respond to changes in the environment. Biological systems with greater complexity and diversity often exhibit an increased capacity to respond to changes in the environment.

At the molecular level, the subcomponents of a biological polymer determine the properties of that polymer. At the cellular level, organelles interact with each other as part of a coordinated system that keeps the cell alive, growing and reproducing. The repertory of subcellular organelles and biochemical pathways reflects cell structure and differentiation. Additionally, interactions between external stimuli and gene expression result in specialization and divergence of cells, organs and tissues. Interactions and coordination between organs and organ systems determine essential biological activities for the organism as a whole. External and internal environmental factors can trigger responses in individual organs that, in turn, affect the entire organism. At the population level, as environmental conditions change, community structure changes both physically and biologically. The [[#|study]] of ecosystems seeks to understand the manner in which species are distributed in nature and how they are influenced by their abiotic and biotic interactions, e.g., species interactions. Interactions between living organisms and their environments result in the movement of matter and energy.

Interactions, including competition and cooperation, play important roles in the activities of biological systems. Interactions between molecules affect their structure and function. Competition between cells may occur under conditions of resource limitation. Cooperation between cells can improve efficiency and convert sharing of resources into a net gain in fitness for the organism. Coordination of organs and organ systems provides an organism with the ability to use matter and energy effectively.

Variations in components within biological systems provide a greater flexibility to respond to changes in its environment. Variation in molecular units provides cells with a wider range of potential functions. A population is often measured in terms of genomic diversity and its ability to respond to change. Species with genetic variation and the resultant phenotypes can respond and adapt to changing environmental conditions.

  • exponential growth- submitted by maddy harmon

ess.know. 4.A.5.- communities are composed of populations of organisms that interact in complex ways.
pages 1181-1183

interactions between different population in ecosystems are important to the regulation of the system's overall balance. when a population is allowed to reproduce without contraints from interactions with predators or limitations from the abiotic environment, it will grow at an exponential rate, as seen in this graph of huan population growth
external image population%20growth.jpg
this model makes it appear like human populations will [[#|continue]] to rise into infinity, however that is unrealistic. interactions with the enviroment such aas limited space, drinkable water, and food provide a block to constant human population growth. the fact that we have been so uninhibited in the modern age because of advancements in science and technology explains why our global situation is becoming out of balance. when interactions in ecosystems do not sufficiantly limit the growht of its population, other populations are greatly effected. (example- the extinction of nearly 10,000 species a year due IN PART to human encroachment into different environments- ie rainforest deforestation)

  • bacterial flora in the human intestine- submitted by maddy harmon
ess.know. 4.b.2- cooperative interactions within organisms promote efficiency in the uses of energy and matter
page 890- Absorbtion in the Large intestine.

a variety of mostly harmless bacteria live in the large intestines of human and other animals. in humans, some of these bacteria interact sybiotically with their human hosts. bacteria live off of the energy gained from digesting the food molecules in our intestines. in exchange, some bacteria release vitamins such as biotin, vitamin K, and several B vitamins including folic acid. the human body is unable to otherwise produce these vitamins, and therefore benifits from the prescence of this bacteria.
external image ImmuneDiagram.gif

  • Interactions Between Organ Systems by Grace Goodfellow
Appendix A: Essential knowledge 4.A.4: Organisms exhibit complex properties due to interactions between their constituent parts (Letter B)

Each organ system interacts with at least one other organ system. Organ systems do not work independently; organ systems interact with each other to keep the organism functioning. The systems of the body are interdependent. The jobs that one system carries out depends on and influences jobs carried out by other systems.
  • The digestive system relies on the circulatory system to deliver the nutrients to the entire body of the
    • The respiratory system provides oxygen to the circulatory system. The circulatory system delivers this oxygen and the nutrients to body cells. Carbon dioxide from cells is delivered from the circulatory system back to the respiratory system so it can exit the body. The circulatory system carries the waste from throughout the organism to the urinary system, which takes care of excreting the waste from the organism.
  • The nervous and the musculoskeletal systems interact to coordinate movement
  • For example, eating does not just involve the digestive system, it also involves the circulatory system and the nervous system. The food eaten is used for growth and repair of all body systems.
  • Interactions with the nervous system:
    • Skeletal System
      • Bones provide calcium that is essential for the proper functioning of the nervous system
      • The skull protects the brain from injury, vertebrae protect the spinal cord
      • Sensory receptors in joints between bones send signals about body position to the brain
      • The brain regulates the location of bones by controlling muscle movement
    • Cardiovascular System
      • Endothelial cells maintain the blood-brain barrier
      • Baroreceptors send information about blood pressure to the brain
      • Cerebral spinal fluid (CSF) drains into the venous blood supply
      • The brain regulates heart rate and blood pressure
    • Muscular System
      • Receptors in muscles provide the brain with information about body position and movement
      • The brain controls the contraction of skeletal movement
      • The nervous system regulates the speed at which food move through the digestive tract (controls smooth muscle)
    • Endocrine System
      • Hormones provide feedback to the brain to affect neural processing
      • Reproductive hormones affect the development of the nervous system
      • The hypothalamus controls the pituitary gland and other endocrine glands
    • Lymphatic System
      • The brain can stimulate defense mechanisms against infection
    • Respiratory System
      • The brain regulates respiratory volume and blood gas levels
      • The brain regulates respiratory rate (medulla oblongata)
    • Digestive System
      • Digestive processes construct the building blocks for some neurotransmitters
      • The autonomic nervous system controls the rate of digestion
      • The brain regulates drinking and eating behavior (hypothalamus)
      • The brain controls muscles for eating and elimination
      • The digestive track sends sensory information to the brain
    • Reproductive System
      • Reproductive hormones affect brain development and sexual behavior
      • The brain controls mating behavior
    • Urinary System
      • The bladder sends sensory information to the brain
      • The brain controls urination (controls sphincter muscles that open and controls the urethra)
    • Integumentary System
      • Receptors in skin send sensory information to the brain
      • The autonomic nervous system regulates peripheral blood flow and sweat (sudoriferous) glands
      • Nerves control muscles (arrector pilli) connected to hair follicles


  • Relationships Amongst Individuals in a Community by Grace Goodfellow
Appendix A: Essential knowledge 4.B.3: Interactions between and within populations influence patterns of species distribution and abundance (Letter A)

  • Competition: an interaction between organisms or species, in which the fitness of one is lowered by the presence of anotherParasitism: a non-mutual relationship between organisms of different species where one organism, the parasite, benefits at the expense of the other, the host
    • Limited supply of at least one resource (such as food, water, and territory) used by both is required
    • According to the competitive exclusion principle, species less suited to compete for resources should either adapt or die out, although competitive exclusion is rarely found in natural ecosystems
  • Parasitism: a relationship between two organisms where one is usually harmed and the other gets benefits from the relationship
    • Parasites are smaller than their host organism and can reproduce quicker, causing more damage to the host
    • Example: Tapeworm inside any type of vertebrate
  • Predation: a predator (an organism that is hunting) feeds on its prey (the organism that is attacked)
    • Decrease, or maintain the population size of the specific prey they are feeding on
    • If too many predators prey on the same type of species in the same community or ecosystem, that population of prey will decrease and could possibly be eliminated
  • Mutualism: the way two organisms of different species exist in a relationship in which each individual benefits
    • Example: Pollination... Both the flower and bee benefit
    • Beneficial for organisms in a community and increases their ability to survive
  • Commensalism: a relationship between two organisms where one organism benefits without affecting the other
    • Example: Orchids and mosses can exhibit commensalism with trees
      • These plants grow on the trunks or branches of trees, getting the light they need as well as nutrients that run down along the tree
      • As long as these plants do not grow too heavy, the tree is not affected

  • Animal Form and Function are correlated at all levels of organization. (Test Book: page 231) By Bunyad Bhatti

Appendix A: Big Idea 4 (C) : Explaining how interactions between constituent parts of a biological system provide essential biological activities.

Tissues are groups of cells that have a common structure and function, and they are further organized into functional units called organs. groups of organs that work together make up and organ system.

the four types of tissues are:

1. Epithelial Tissue: occurs in sheets of tightly packed cells, covers the body, lines the organs, and acts as a protective barrier. One side is always bound to a basement membrane. The other side is facing the air or the environment.

2. Connective Tissue: mainly support and bind other tissues.

3. Muscle Tissue: is responsible for mainly all types of body movements. The types of muscle are: skeletal muscle, cardiac muscle, and smooth muscle.

4. Nervous Tissue: is in the nueron or nerve cells. It senses the stimuli and transmits signals from one part of the body to another part of it.

In order for animals to survive, tissues, organs, and organ systems, must act in a coordinated manner. Two major organ systems that specialize in control and coordination are:

1. The endocrine system: the hormones are released into the bloodstream, and are broadcast throughout the body.
2. The nervous system: nuerons transmit information between specific locations.

  • The effects of a disruption of a component of a community (Page 1206-1207) By Jake Barry

Appendix A, Big Idea #4, Letter E

All Animals in a food chain depend on one other to survive. Energy moves through trophic levels in an ecosystem. This mean that producers create the energy, and primary producers eat them to get energy. The primary producers are eaten by the secondary producers and so on.

If an organism in a low trophic level, like a primary producer plant is wiped out, then the animals that depend on that organism are also hurt.

external image foodweb.gif

In this food web, if a virus were to attack the phytoplankton, then the whole rest of the food web would be disrupted. They are the only producer so nothing in this chart could survive long term without them.

If an animal in the later trophic layers are hurt, a last prey organism, then this will effect the community differently. In this web if the bald eagle were to go extinct, then the trout would overpopulate due to lack of predation, and they would eat too much phytoplankton, and there would be less for the dragon flies and mayflies and this would effect the organisms that prey on these.

This is why the larger the food web, the more stable it is. In a large web there are always more organisms to feed on if something goes wrong with a lower trophic level. Also, there are generally more organisms or prey too, to maintain the populations in the community in the food web.

  • Appendix A, Big Idea 4, F
by Maeve Dalpe

In enzymatic reactions, the substrate is usually held in the active site by weak interactions such as hydrogen bonds and ionic bonds. Here, the substrate is converted to a product by the R groups of amino acids in the active site. The enzyme releases the product and is ready to take in another substrate molecule. This metabolic reaction is reversible and focuses on maintaining equilibrium. Changes in the enzymes structure allows substrates to orient into a position with potential for a reaction.The enzyme will stretch the substrate molecules to products by stressing and breaking chemical bonds that have to be broken for the reaction (pg 154).

The rate at which an enzyme converts substrate to product is partly a function of the initial concentration of the substrate - the more substrate molecules that are available, the more frequently they have access to the active sites of enzymes. However, the concentration of substrate will, at some point, be high enough to occupy every enzyme's active site. At this concentrated, an enzyme is said to be saturated (pg 155).

Temperature and pH are important to enzymatic activity. The rate of an enzymatic reaction increases with increasing temperature, partly because substrates collide with active sites more when the molecules move rapidly. However, above that temperature, the speed of enzymatic reaction slows down dramatically. The thermal sensitivity of enzymes can disrupt hydrogen bonds, ionic bonds and other weak interactions that stabilize enzyme shape. This ultimately denatures the protein molecule which can be life threatening. Just as an enzyme has an optimal temperature, it also has an optimal pH level. Similarly, a pH level that is too high can denature most enzymes in the body (pg 155).

  • Species Diversity (Page 1204) By Jake Barry

Appendix A, Big Idea #4, Letter K, analyzing systems

Species Diversity is the variety or organisms that makes up the community. Species richness is the number of different species in a community. Relative abundance is the proportion of a community that each species represents. The widely used way to calculate relative abundance and species richness is the Shannon diversity. This takes into consideration both, and can be used to compare diversity in a community.

The reason for short food chains is the energetic hypothesis, which states that the length is limited by the inefficiency of energy along the chain. Not all the energy from one trophic level moves on to the next, so with each level there is a smaller amount of energy available.

The dynamic stability hypothesis states that long food chains are less stable than short ones. Population fluctuations are magnified at the higher levels, which makes ti hard for the top predators. The longer the food chain, the harder it is and the longer it takes for a top predator to recover from these fluctuations.

Environmental Impact on Gene Expression By: Kohl Romeiser

Appendix A; Big Idea #4; Letter J.) Use evidence to justify the claim that phenotype is a product of both genetics and environment.

Mostly all of your phenotypic traits are determined by your genetics. Your environment however, has a lot to do with the way your phenotype is portrayed. Nutrition for example, has a large influence on your height regardless of your genetics. Environmental factors such as diet, temperature, humidity, oxygen levels, and the presence of mutagens can all affect and impact which of an organisms genes are expressed.

An excellent example of the environment impacting genetics is in the establishment of a sex. For some organisms, such as the crocodile, the period of early development called the thermo sensitive period determines the sex of the organism. At certain temperatures, gonadal tissue will develop into either testes or ovaries. Thus, temperature has a great effect on gene expression early in development.

In the 1500s, it was rare to come across a person that was above 6’ tall. Population nutrition greatly impacted the heights of most people of the period. People who were malnourished would not be able to use enough energy towards growth, even if they carried genes that would positively impact their height. Similarly, flower color can be drastically affected by soil pH.

Mr. Anderson, Video on Gene Regulation:

How Organs Interact by Brian Millham (pg. 739-742)

Appendix A: Essential knowledge 4.A.4: Organisms exhibit complex properties due to interactions between their constituent parts (Part A)

For a plant to survive, the roots, the stem and the leaves need to interact. A root is a multicellular organ that anchors a vascular plant in the soil, absorbs minerals and water, and stores carbohydrates. The root tips is where the absorption of water and minerals takes place. Root hairs increase the surface are of the root to allow more water and mineral uptake. The stem of the plant is an organ consisting of an alternating system of nodes, and internodes. Nodes are where leaves are attached and internodes are stem segments between nodes. Stems allow for food storage and asexual reproduction along with transportation of nutrients and water along the plant. Leaves are the main photosynthetic organ, although green stems can also photosynthesize. they consist of a flattened blade and stalk,the petiole, which joins the leaf to the stem at a node. Leaves have veins which are the vascular tissue of the leaves. Leaves can provide support, protection, storage or reproduction, along with the ability to make food.

Disturbance and Influences Species Diversity and composition by Brian Millham (pg 1211-1212)
Appendix A concept J

Disturbances keep communities from reaching a state of equilibrium in species diversity or composition. A disturbance is an event like a storm, fire, flood, drought, overgrazing, or human activity, that changes a community by removing organisms from it or altering rescource availability. A community can become a nonequilibrium community very quickly because of these disturbances. Fires are important in maintaining the equilibrium in grassland biomes because it helps control the species composition. The intermediate disturbance hypothesis states that moderate levels of disturbance can create conditions that foster greater species diversity than low or high levels of disturbance. High levels of disturbance create environmental stresses which exceed the tolerances of the species. Low levels of disturbances can reduce species by allowing competitively dominant species to exclude less competitive species. Intermediate disturbance levels can help species diversity by opening habitats for less competitive species.

Concept k: Variation within populations and species diversity increase fitness and system stability
By Kenna Garrison (p. 1246-7)

Genetic diversity in a population decreases the likelihood of the population going extinct. For example, in a population with high genetic diversity that some individuals get infected with a deadly virus, some individuals will have mutations so that they can resist the virus. Genetic diversity can increase the resistance to extinction of a population.
Species diversity is important to keeping an ecosystem stable because it ensures that a problem with one species won’t have as large an effect on the other species in an ecosystem. If there are only 5 species in an area that rely on each other for food and a one species catches a virus and the population greatly decreases, then the other species will suffer too because they are so reliant on each other. However, in an ecosystem with plentiful species in every trophic level that have multiple food sources and or predators, one species that goes through a decrease in population will still affect the other species it interacts with, but the ecosystem overall will stay much more stable than if there were only 5 species.

Concept a: Structure imparts function (cell membrane)
By Kenna Garrison (p.125-131)

The cell membrane functions as a selective barrier that allows sufficient passage of oxygen, nutrients, and wastes to service the cell. It is selectively permeable- it allows some substances to cross it more easily than others. It is the structure of the cell membrane that gives it this selective permeability and allows it to carry out its function.
The membrane is made up of a phospholipid bilayer with the hydrophilic heads on the outsides and the hydrophobic tails in the middle. This makes it easy for nonpolar molecules to cross the membrane, but difficult for polar molecules to. However, there are transport proteins embedded into the membrane which let in certain polar molecules. Cholesterol embedded in the membrane helps resist changes in fluidity of the cell membrane that could be caused by changes in temperature. Glycolipids and glycoproteins attached to the cell membrane are also important in cell to cell recognition. All of these parts of the cell membrane that make up its structure are important in the functioning of the cell membrane as well as the entire cell.

Appendix A: concept g- Cooperative interactions at the cellular, organismal, and system level increases efficiency and fitness of the organism
By: Maggie Garrahan

4.A.3: Interactions between external stimuli and regulated gene expression result in specialization of cells, tissues and organs.
by Maeve Dalpe

Differentiation in development is due to external and internal cues that trigger gene regulation by proteins that bind to DNA.Structural and functional divergence of cells in development is due to expression of genes specific to a particular tissue or organ type. In this study, scientists isolate mRNAs made in particular cells, use these molecules as templates for making the corresponding cDNAs by reverse transcriptase, and then employ nucleic acid hybridization to compare this set of cDNAs with a collection of DNA fragments representing all or part of the genome. The results identify the subset of genes in the genome that are being expressed at a certain time or under certain conditions. Genome-wide expression studies are done by DNA microarray assays which consists of tiny amounts of many single-stranded DNA fragments representing different genes on a glass slide. (pg 410).

Properties of Hormonal Cell Signaling that increase the Efficiency (page 976) By Jake Barry

Appendix A, Big Idea #4, Letter G.

Hormones and other molecules trigger responses to a specific receptor protein in target cells, or can diffuse right through their cells depending on their solubility. (See Chemical Classes of Hormones By Jake Barry under Big Idea #2). The hormones that are lipid soluble may enter all the body cells, and then bind to the intracellular receptors (Page 210), The testosterone is present in all cells in the body, but only the cells that have the receptors will react to the testosterone. This is efficient because with the binding going on inside the cell, the active form of the receptor protein can just enter the nucleus and turn on the specific gene that controls the male sex characteristics. There is no amplification because it is not needed for this response.

The Water Soluble hormones are less efficient than the lipid soluble ones, but they tend to trigger a larger response. This is because the signal amplifies during transduction, as it gets passed by the proteins (page 1089). These pathways often include enzyme-catalyzed reactions, they produce many product molecules by a single enzyme molecule.

Density-Dependent Population Regulation – Gabriela Christian (pages 1187-1188)
Essential Knowledge 4.A.6: Interactions among living systems and with their environment result in the movement of matter and energy.

Populations need some sort of negative feedback system between population density and the birth and death rates, or it would never stop growing. The mechanisms that help reduce birth rates and increase death rates are competition for resources, territoriality, disease, predation, and toxic wastes.

Competition for Resources: when a population is becoming crowded, the increasing population density creates more competition for the decreasing nutrients and other resources. This lowers the birth rate. Crowding can also reduce plant reproduction, which then further reduces a food source, increasing the death rate.

Territoriality: Territory space is the resource for which individuals compete. Maintaining a territory increases the probability that an organism will find enough food to be able to survive and reproduce successfully. If an individual cannot find a territory, it will not reproduce, thus lowering the birth rate.

Disease: If the transmission of a certain disease depends on the level of crowding in a population, the disease’s impact may be density dependent. An infection in plants, for example, could devastate a population if it was too crowded and all the plants became infected. The same goes for humans, with airborne diseases. They are more easily spread in densely populated cities than in rural areas.

Predation: If a certain population of prey is very crowded, the chance of a predator capturing food is more likely. As the population density of the prey is increases, predators may develop a preference for that species, consuming more individuals and increasing the death rate.

Toxic Waste: Metabolic by-products can accumulate as populations increase in size, which poisons the organisms within the environment.

Qualitative and Quantitative Models For Populations (page 18, 1174-1176) By: Christina Dykas
Appendix A Big Idea 4 letter h

Qualitative data is in the form of recorded descriptions instead of numerical measurements.

Quantitative data is usually recorded as specific measurements.

Examples of these would be when in a population, qualitative data would be the color of the organism while quantitative data would be how many offspring the organisms produced. When recording abundance of organisms in a specific area, this is quantitative data because you are recording the exact number of organisms observed.The density of a population in an ecosystem is also quantitative because it is a specific, calculated number of organisms. Distribution would be quantitative because you would record the number of organisms in one area and then record the number of organisms in another area and see the distribution of where they are found. Observing interactions between organisms would be qualitative because you would describe the relationships that are occurring based on observation and there are no concrete numerical measurements for this.

Some effects of human activity on biological systems could include global warming, habitat destruction, competition for resources, extinction of organisms, less area to live in, and new interactions between organisms.
external image images?q=tbn:ANd9GcSNJLI_Q7m6LCBPEYIVfkw9DT-_FkVDIUQ2eEJt8M5IiUEFTI26XQ

Mitochondria and Chloroplasts (Energy providing organelles) By: Kayla Kaufmann
Text Pages (109-11)
Essential knowledge 4.A.2: The structure and function of subcellular components, and their interactions, provide essential cellular processes.

The Mitochondria

The mitochondria is a cell organelle where cellular respiration occurs and most ATP is generated. This important organelle specializes in energy capture and transformation.
You must understand the following about the structure of the mitochondria that helps it carry out its function
  • Mitochondria have a double membrane that allows for compartmentalization (parts within parts that helps increase specialization and surface area) helping the mitochondria function efficiently
  • The outer membrane is smooth while the inner membrane is very complex and forms folds called cristae. The cristae contain enzymes that are very important in ATP production and cristae increase the surface area for ATP production (function of mitochondria related to structure).

Chloroplasts are photosynthetic organelles that convert energy in the form of sunlight to chemical energy stored in sugar molecules
You must understand these components of the chloroplast structure that allow it to function because the structure and function relationship in the chloroplast allows cells to capture the energy available in sunlight and convert it to chemical bond energy using photosynthesis

  • Chloroplasts have chlorophylls that are the reason a plant is green and they are also the key light capturing molecules for photosynthesis. The predominant form in plants is chlorophyll a.
  • The molecular structure of chlorophyll is not something you will need to know.
  • The double outer membrane of a chloroplast creates a compartmentalized structure helping it carry out its function more easily like in the mitochondria as stated above.
  • Membrane bound structures called thylakoids are present within the chloroplasts. In the thylakoids you can find grana. These grana are where the energy capturing reactions are located in stacks in the thylakoids to produce ATP and NADPH2, which fuel carbon-fixing reactions in the Calvin cycle. Carbon fixation occurs in the stroma, where molecules of CO2 are converted to carbohydrates.

Check out this bozeman videos on the cellular organelles... start watching at 6:48 where he begins to talk about the energy producing oragnelles (mitochondria and chloroplasts)

Mitochondria and Chloroplast

Below are diagrams of these two organelles showing their structures


external image mitochondrion.png


external image chloroplastsfigure1.jpg

Structure and Function of Polymers are Derived from the way their Monomers are Assembled - Focusing on ProteinsBy: Kayla Kaufmann
Text Pages (77-86)
Essential knowledge 4.A.1: The subcomponents of biological molecules and their sequence determine the properties of that molecule.

Structure and properties or the function of biological molecules, proteins for example, are a result of their buidling blocks.
Form and function go hand in hand.
  • Proteins are polymers made up of amino acid monomers
  • Amino acids contain a central carbon bonded to a carboxyl group, an amino group, a hydrogen atom, and an R group which is a variable or side group
  • Peptide bonds link amino acids and are formed by dehydration synthesis (the removal of water). The function of a protein depends on the order and number of amino acids.
  • There are four levels of protein structure: Primary, Secondary, Tertiary, and Quaternary
  • Primary structure = the unique sequence in which amino acids are joined
  • Secondary structure = is one of two three-dimensional shapes that results from hydrogen bonding. The shapes include alpha helix (coiled shape) and Beta pleated sheet (accordian shape)
  • Tertiary structure = results in a complex globular shape as a result of interactions between R groups like hydrohpbic reactions, van der Waals interactions, hydrogen bonds, and disulfide bridges
  • Quaternary Structure = the association of two or more polypeptide chains into one large protein. (Hemoglobin is an example)
  • In a protein primary structure interacts with the environment to determine the overall shape of the protein which also involves the other three structure forms (see above) leading to function. The R group of an amino acid can be categorized by chemical structure (hydrophobic, hydrophilic, and ionic), and the interactions of these R groups decides structure and function of that region of the protein *

Check out the Bozeman video on proteins

Protein Video
Check out these helpful images on protein structure.

external image protein-structure2.png
external image i3_peptide_bond.png

external image amino_acid_structure_2.jpg

Dynamic biological processes influence population density, dispersion, and demographics. (Test book: page 294-296) By:Bunyad Bhatti

Appendix A (J) : Justifying the claim that variation within populations and increased species diversity account for increased population fitness and system stability.

Population ecology explores how biotic and abiotic factors influence the density, distribution, size, and age structures, of the populations.

the characteristics that an organism in a population follow are:

1.Density: the number of individuals per unit area or volume. It increases by births or immigration, and decreases by deaths or emigration.

2. Dispersion: the pattern of spacing among individuals, within the boundaries of the population.

-Clumped: the most common; has individuals in clumps around a required resource.

-Uniform: results from the antagonist interactions; animals that defend territories.

-Random: the unpredictable spacing; usually has a reason to it.

Density-Dependent factors: they reduce birth rates and increase death rates. Some examples are:

-Competition for resources.




Density Independent factors: when a death rate does not change with increase in population density. : Mr. Anderson talks about the poulation variation in it.

Food Webs and Keystone Species – Gabriela Christian (pgs 1205-1208)

Essential Knowledge 4.C.4: The diversity of species within an ecosystem may influence the stability of the ecosystem.

Charles Elton realized in the 1920’s that communities don’t often work in food chains, but in linked units as in a food web. In a food web, arrows link species according to who eats whom, showing the direction of energy. A given species may occupy more than one trophic level, because each species has a variety of sources of food as well as many predators.

Dominant species are the species in a community that are the most abundant or have the most biomass within that community. Therefore, these species have great control over the distribution of other species. There are many hypotheses to explain how dominant species come about. One is that dominant species are competitively superior in gathering resources. Another suggests that dominant species are more successful at avoiding predators. This second idea supports the observation that invasive species tend to obtain a high biomass, for they do not face their normal predators or diseases from their original habitat.

A keystone species is not necessarily the dominant species, or even abundant in population within a community. They exert a strong control on community structure within a food web by their important niches. A way to identify a keystone species is by conducting an experiment in which the species is removed, and then observing the results. This highlights the importance of a keystone species in maintaining the diversity of a community. Sea otters are an example of a keystone species.

external image Keystone-species-image.jpg
Cell Organelles Interact in Key Biological Processes (page 105-106) By: Christina Dykas
Appendix A Big Idea 4 letter a
I could not remember how the golgi apparatus was associated with proteins, so here’s what I found out.
One important biological process is movement of proteins within the cell. Proteins are made by ribosomes (made of ribosomal RNA and protein) usually on the rough endoplasmic reticulum and are sent to the golgi apparatus where they are modified, stored, and sent to other locations in the cell. The golgi apparatus has a structural polarity that allows for this function. One side of the Golgi is the cis face which is the receiving end and is located close to the endoplasmic reticulum to receive the proteins. This location is important to maximize the potential biological processes. The other end is the trans face and this ships the modified proteins away from the golgi apparatus. The golgi is also made of flattened membranous sacs called cisternae that are packed together. Since they are flattened and close, this increases the surface area of the golgi to modify more proteins and allow for biological functions associated with proteins such as extracellular secretion. Based on the structure of the golgi and the interactions with the endoplasmic reticulum and ribosomes, proteins can be moved through the cell.
external image slide0076_image033.jpg
This diagram shows the location of the ER compared to the golgi apparatus and how the structure of the golgi allows for protein modification.

4.B.1 Interactions between molecules affect their structure and fuction

Emily Bernardi

Covalent bonds hold atoms and small molecules together. Covalent bonds do not break when water is boiled, proteins fold, RNA folds, DNA melts, or when membranes assemble. All of these processes are controlled by non-covalent interactions, also known as molecular interactions. Most molecular interactions are relatively weak, but cumulatively energies can be very large. The number of intramolecular pair-wise interactions between the atoms within a globular protein can be counted, or between protein and water atoms in an unfolded protein. Huge numbers of small non-covalent forces drive the spontaneous folding or unfolding of proteins and nucleic acids. The folded/unfolded equilibrium constant of a protein is generally small. The protein is held in a delicate balance between powerful countervailing forces. Large forces provide driving force pushing a protein to fold. Large forces provide driving force pushing to unfold. It is the small difference between these large numbers that determines direction of the folding 'reaction'. A small change in pH or temperature can change the balance.

Maggie Garrahan

a. Ribosomes are small, universal structures comprised of two interacting parts:

ribosomal RNA and protein. In a sequential manner, these cellular components

interact to become the site of protein synthesis where the translation of the genetic

instructions yields specific polypeptides.

b. Endoplasmic reticulum (ER) occurs in two forms: smooth and rough

1. Rough endoplasmic reticulum functions to compartmentalize the cell,

serves as mechanical support, provides site-specific protein synthesis with

membrane-bound ribosomes and plays a role in intracellular transport.

2. In most cases, smooth ER synthesizes lipids

c. Mitochondria specialize in energy capture and transformation.

1. Mitochondria have a double membrane that allows compartmentalization

within the mitochondria and is important to its function.

2. The outer membrane is smooth, but the inner membrane is highly convoluted,

forming folds called cristae.

3. Cristae contain enzymes important to ATP production; cristae also increase

the surface area for ATP production.

d. Chloroplasts are specialized organelles found in algae and higher plants that

capture energy through photosynthesis.

1. The structure and function relationship in the chloroplast allows cells to

capture the energy available in sunlight and convert it to chemical bond energy

via photosynthesis.

2. Chloroplasts contain chlorophylls, which are responsible for the green color of

a plant and are the key light-trapping molecules in photosynthesis. There are

several types of chlorophyll, but the predominant form in plants is chlorophyll a.


Essential knowledge 4.C.2: Environmental factors influence the expression of the genotype in an organism.
By Maggie Garrahan

Environmental factors affect traits directly and indirectly.

Examples: Height & Weight, Seasonal Fur Color, Flower Color based on soil pH.

An organism’s adaptation to the local environment reflects a flexible response of

its genome.

Example: Alterations in timing of flowering due to climate changes

Example: Phenylketonuria is a human genetic condition caused by mutations to a gene coding for a particular liver enzyme. In the absence of this enzyme, an amino acid known as phenylalanine does not get converted into the next amino acid in a biochemical pathway, and therefore too much phenylalanine passes into the blood and other tissues. This disturbs brain development leading to mental retardation and other problems. PKU affects approximately 1 out of every 15,000 infants in the U.S. However, most affected infants do not grow up impaired because of a standard screening program used in the U.S. and other industrialized societies. Newborns found to have high levels of phenylalanine in their blood can be put on a special, phenylalanine-free diet. If they are put on this diet right away and stay on it, these children avoid the severe effects of PKU.

Genes can have great affects on humans, and if mutations occur they can have terrible outcomes.


  • The Endoplasmic Reticulum by Amanda Seale (p. 104-105)

Essential knowledge 4.A.2: The structure and function of subcellular components, and their interactions, provide essential cellular processes

The endoplasmic reticulum is an extensive network of membranes that It accounts for more than half the membrane in many eukaryotes. It consists of a network of membranous tubules and sacs (cisternae). The ER separates the internal compartment of the ER called the lumen from the cytosol. There are two distinct but connected parts of the ER: smooth ER and rough ER.
Smooth endoplasmic reticulum gets it’s namesake from the fact there are no ribosomes on the outer surface. Smooth ER functions in diverse metabolic processes, varying with cell type. These processes include synthesis of lipids, metabolism of carbohydrates, and detox of drugs and poisons. The smooth ER also stores calcium ions. It can trigger different responses.
Rough ER has ribosomes on the outer surface of the membrane and appears rough when looking through the electron microscope. Many types of cells secrete proteins produced by ribosomes attached to rough ER. Most secretory proteins are glycoproteins (proteins that have carbs covalently bonded to them). After they are formed, the ER membrane keeps them separate from proteins produced by free ribosomes and will remain in the cytosol. It grows in place by adding membrane proteins and phospholipids to its own membrane.

Whatup Mr Anderson .. once again.. - an explanation of the endoplasmic reticulum and other organelles found in a cell:

  • The Concept of Primary Productivity by Amanda Seale (p. 1224- 1226)

Essential knowledge 4.A.6: Interactions among living systems and with their environment result in the movement of matter and energy.

Primary production is defined as the amount of light energy converted to chemical energy (organic compounds) by autotrophs during a given time period within an ecosystem. This is the starting point for the studies of metabolism and energy flow within the ecosystem. Gross primary production (GPP) refers to the amount of light energy that is converted to chemical energy by photosynthesis per unit time. Because primary producers use some of the molecules as fuel in their own cellular respiration, not all of this production is stored as organic material. Net primary production (NPP) us equal to the gross primary production minus energy used by primary producers for respiration. [R]


In a lot of ecosystems net primary production is one half of gross primary production. Because NPP is key to representing the storage of chemical energy available to consumers in the ecosystem, NPP is mostly used by ecologists. NPP can be expressed as energy per unit area per unit time. (J/m2*yr) or as biomass, which is the mass of vegetation, added to the ecosystem per unit area per unit time (g/m2*yr).


A more in-depth look at primary productivity:

Structure and function of the vacuole by Lea Adams (page 108)
Big idea 4 letter A
Central vacuoles are membrane-bounded organelles in plants that store and break down waste products and take-up up to 80% of the cell. It develops by the joining of smaller vacuoles and is part of the plants endomembrane system. The vacuolar membrane is selective in transporting solutes so the solution inside is different than the cytosol. Plants use this organelle for holding reserves of organic compounds, holding inorganic ions, disposal sites for metabolic byproducts, and sometimes contain pigment that will give the cell color to attract others. The vacuole plays a role in the growth of plant cells because they enlarge as the vacuole absorbs water.

external image plantvacuolesfigure1.jpg

  • Biological Polymers - Kylie Dolan
    Describing the basic structure and functions of key biological polymers (DNA, RNA, lipids, carbohydrates, proteins) - Appendix A

    • Carbon is the building block of the four major macromolecules which are carbohydrates, lipids, proteins, and nucleic acids (DNA and RNA)
    • o What makes it such a good building block?
      • § Tetra-valence (the ability to form for covalent bonds) causes carbon tobe an optimal element for building molecules
        • Important molecule types:
        • o Macromolecules: large molecules that fall into four categories: carbohydrates, lipids, proteins, and nucleic acids
        • o Polymer: a long molecule made up of similar molecules held together by covalent bonds
        • o Monomers: one of the type of molecules that makes up a polymer
        • o Polymers are composed by a process called dehydration synthesis
          • The macromolecules:
          • o Carbohydrates: Sugar and the polymers of sugar
            • § Monosaccharide form: single sugars with a formula of CH2O
            • § Most common and important monosaccharide is glucose which is C6H12O6
            • § Disaccharides: two monosaccharides linked by dehydration synthesis
              • Function of carbohydrates:
              • Serve as "fuel" by storing energy in bonds
              • The structural elements in the cell walls of bacteria (peptidoglycanor murein), plants (cellulose) and animals (chitin).
              • Many more functions
              • o Lipids:
                • § Lipids are hydrophobic meaning, they fear water
                • § Fats/triglycerides - glycerol and three fatty acids
                • § Fatty acids are long chains of carbon attached to a carbonyl group
                • § Saturated fatty acids have no double bonds between carbon atoms.
                  • For example, animal fats which are solids at room temperature
      • § Unsaturated fatty acids have some double bonds between carbon atoms. For example, plant and fish fats which are liquid at room temperature
      • § Phospholipids are lipids but, unlike triglycerides, only have two fatty acids and contains a phosphate group
      • § The head region contains the glycerol in phosphate. This area is hydrophilic.
      • § The tail contains the fatty acids (one saturated and one unsaturated). This area is hydrophobic.
      • § Phospholipids what primarily compose biological membranes
      • § Steroids are lipids that consist of four fused rings
      • § Several steroid hormones in animals are produced from cholesterol
      • o Proteins, which are made up of monomer units called amino acids, perform structural, catalytic, signaling, defense, and transport duties in the cell.
        • § Amino acids consist of an amino group, a carboxyl group, and a side chain group
        • § Each one of these chain groups gives the amino acid unique physical and chemical properties change in both their structure and function
        • § A dipeptide is formed when two amino acids are linked via dehydration synthesis A peptide bond is the covalent bonds formed between amino acids
        • § When several amino acids come together by dehydration synthesis, apolypeptide is formed.
        • § The polymers of amino acids are called polypeptides, and when one or more polypeptides fold into a specific conformation, a protein formed DNA and RNA

    • DNA (deoxyribonucleic acid) is a polymer of four different nucleotides.Each nucleotide is composed of three parts:
    • a nitrogen base
    • a five-carbon sugar (deoxyribose)
    • a phosphate group (Phosphoric Acid)

    • These nucleotides differ because they have different bases:
    • o (A) Adenine, a double-ring base (purine)
    • o (T) Thymine, a single-ring base (pyrimidine)
    • o (C) Cytosine, a single-ring base (pyrimidine)
    • o (G) Guanine, a double-ring base (purine)
      • DNA's composition supports its antiparallel • double helix shape, and thus function
      • RNA is similar, except it uses ribose as its sugar, and uses the base uracil instead of thymine.

  • Essential knowledge 4.C.2: Environmental factors influence the expression of the genotype in an organism. - Kylie Dolan
    Though Mendel was both brilliant and incredibly correct on many things for his time, Mendelian genetics are not perfect. Though there are very few occurrences that could affect one's genotype or DNA, the way that genotype is expressed (aka the phenotype) can be affected by the environment. This could include sun lightening hair, factors stunting growth, or temperature changing fur color (in cats and other animals). One classic example is the pH of soil and it's effect on the color of Hydrangeas. Depending on the acidity of soil, the hydrangeas may range from pink to blue or any combination.
    external image ql_hc_img1.gif

Mariah Pennington
Appendix A, big idea 4, letter b: Describing how cells specialize and become tissue and organs.

During embryonic development, two basic principles guide the current understanding of cell differentiation.

1. “During early cleavage divisions, embryonic cells must somehow become different from one another.”
In most animal species, the differences between cells are caused by unequal distribution of cytoplasmic determinants in the egg cell. DNA-binding proteins called transcription factors are what activate one set of genes rather than another.

external image 18_15aEarlyEmbryoDevinfo-L.jpg
2. Once initial cell asymmetries are set up, subsequent interactions among the embryonic cells influence their fate, usually by causing changes in gene expression.”
Induction is what eventually causes the differentiation of the many specialized types of cells that the animal consists of. To mediate induction, diffusible signaling molecules or cell-surface contact is used.
The concept of fate mapping has been studied most in the C. elegans worm. It is a relatively simple animal that allows easy experimental observation. (textbook 1038 and 367)

Mariah Pennington
Appendix A, big idea 4, letter d: Organism interaction and matter and energy flow in a biological system and predicting the effects of a change in one of the components.

Every population in a community depends on each other either directly or indirectly. The source for all of the circulating energy can be traced back through a food chain to the sun. The sun’s light energy is captured and used first by the photosynthetic primary producers, which is the most abundant trophic level. Then the glucose produced is taken in by the primary consumers (herbivores). The energy then goes to the secondary and tertiary consumer trophic levels (carnivores). The decomposers cycle the energy back into the system.
If one piece of the food web puzzle is removed, then the entire community’s balance is thrown off. That is why a more diverse community is considered more stable because if there are more possible routes/backup plans, then the less detrimental it would be to lose one food source. Conversely, if the populations in a community are not as diverse, then losing one part would cause a much more drastic result. (textbook 1204-1205)

external image food_web.jpg
external image 382331_611350325557339_1219958290_n.jpg

Cell specialization in early Embryonic Development by Owen Gaffney p 1022/notes

In general I was confused on how cells begin to specialize and become tissues in the body. Here's a quick summary. Important processes regulating development occur during fertilization and the three stages that begin to build the body of most animals. During the first stage called cleavage cell division creates a hollow ball of cells, the blastula, from the zygote. The second stage gastrulation rearranges the blastula into three layered embryo to gastrula. The three layered embryo consists of the ectoderm endoderm and mesoderm. The ectoderm forms the outside of the membrane and will develop into the brain and nervous system, the mesoderm forms into a basic body cavity and is the middle and the endoderm forms the basic lining of the digestive track and respiratory system. During the third stage organogenesis interactions and movements of the three layer's generate rudimentary organs from which adult structures grow.

Here's a couple good videos:

Fertilization: an interaction between biological systems in organisms by Owen Gaffney p 1023

I was not entirely sure if fertilization in sexual organisms would fit under this category but I decided to include it because it is an example of how many complex reactions must occur in order for a system to carry out its intended function. Fertilization begins when the sperm contact the eggs jelly coat triggering exocytosis of the sperms' acrosome. Next comes the acrosomal reaction. Hydrolytic enzymes released from the acrosome make a hole in the jelly coat. Growing actin filaments form the acrosomal process which protrudes from the sperm head and penetrates the jelly coat. Proteins on the surface of the acrosomal process bind to receptors in the egg plasma membrane. Next is contact and fusion of sperm and egg membranes. Fusion triggers depolarization of the membrane which acts as a fast walk to polyspermy, which can cause twins. The cortical reaction involves cortical granules in the egg fusing with the plasma membrane. The secreted contents clip off binding receptors and cause the fertilization envelope to form. Finally the sperm enters the nucleus of the egg in DNA combination begins.