WIKI REVIEW 2014

  • Below is Mr. Anderson's Final Review. He made it last year in response to student questions. It turns out most of the top ten questions were on Math topics. You are not alone! Watch it!


  • The link below is to Mr. Anderson's complete set of videos. If you are lost on any topic, use them for review. There is also a link to a Pdf file with 45 flash cards with must know terms. It would make a great review. Also, the Math review is a must watch!

http://www.bozemanscience.com/ap-biology


  • Here are my annotated notes on genetics.







  1. Big Idea 1: The process of evolution drives the diversity and unity of life


unit 6 (evolution) fits under big idea 1: the process of evolution explains the diversity and unity of life. To support this, here is a summary of a topic I had difficulty with, cladograms. Cladograms take characteristics shared by organisms and put together a hypothesis of how they are related. The out group has one or none of the characteristics of the rest of the organisms listed on the cladogram, and each branching point is a common ancestor for the organisms that come after it. Organisms at the left are the oldest and organisms furthest down the line to the right are the youngest. Thus distance between two organisms in the down the line direction towards the oldest ancestor determines how closely related organisms are, not just how far apart from each other they are. Organisms are just as likely to lose characteristics over time as they are to gain ones that their descendants have before the descendants have them. Parsimony is a way of simplifying cladogram a/organisms relatedness or place on the cladogram; the simplest explanation is most likely right. Alex f

a) Justify how structure imparts function for key biological molecules (carbohydrates...) Big Idea 4
Submitted by Maddie

Text page 69-74
  • Monosaccharide= monomer, simplest form
  • Disaccharides= double sugars (monosaccharides) joined by a covalent bond called a glycosidic linkage
  • Polysaccharides= many sugar building blocks

Three major structure classifications:
  1. Length of carbon skeleton (ranges form 3-7)
    1. ex- those with six like glucose and fructose are called hexoses
  2. May be aldoses or ketoses (location of the carbonyl group- C=O)
    1. aldoses- the carbonyl group is on the outside
      ketoses- the carbonyl group is on the inside
  3. Spatial arrangement around carbons
    1. Ex- Glucose vs. Galactose (have the same parts just in different places)
glucose.gif
*Glucose molecules along with most other sugars form rings

Functions:
  • monosaccharides are major nutrients for cells (particularly glucose)
  • polysaccharides can serve either for storage or structure
Storage
  1. Starch- polymer of glucose monomers in plants
    1. allows plants to stockpile excess glucose
    2. starch can then be hydrolyzed and release glucose so plant has energy
    3. shape= helical
    4. alpha linkages*
  2. Glycogen- polymer of glucose in animals
    1. stored in liver and muscle cells
    2. can be hydrolyzed to release energy
      1. glycogen stores are depleted in about a day
Structure
  1. Cellulose- polymer of glucose in plants
    1. part of tough plant cell walls
    2. Slightly different ring structure/glycosidic linkages than starch causing differentiation
    3. shape= straight
    4. beta linkages*
  2. Chitin- glucose monomers plus nitrogen-containing appendages
    1. used by arthropods (spiders, crustaceans, insects)
    2. builds hard exoskeleton

*certain enzymes can only digest certain linkages because of their shapes. For example, humans can not digest cellulose (aka insoluble fiber) because we do not have enzymes to digest the beta linkages. Cows however,can digest cellulose in hay and grass, for example, because they have cellulose-digesting prokaryotes in their rumen.

Mr. Anderson's video on carbohydrates



h) Use representations and models to pose scientific questions about the properties of cell membranes and selective permeability based on molecular structure. (Big Idea 2)
Submitted by Maddie
plasma membrane.pngselectively permaible membrane .jpg

  • Selective permeability= a property of biological membranes that allows them to regulate the passage of substances
  • Fluid Mosaic Model= membrane is fluid structure with various proteins embedded in our attached to the double layer
  • Molecular Structure-
    • Phospholipids
      • Amphipathic- has both a hydrophilic and hydrophobic end, form a double membrane accordingly
      • Most abundant lipids in the membrane
      • Ability to form membranes is inherent in their molecular structure
      • Dissolves and easily passes nonpolar hydrophobic molecules (oxygen, hydrocarbons, carbon dioxide)
      • Impedes the passage of hydrophilic or polar molecules (water, glucose, other sugars)
    • Transport Proteins
      • helps hydrophilic substances avoid lipid bilayer
      • Aquaporins- channel that aids in the facilitated diffusion of water molecules
        • can pass 3 billion water molecules per second
      • Ion channels/ Gated channels- open or close in response to a stimuli
      • Electrogenic pump- generates voltage across the membrane
    • Membrane Proteins
      • Function in transport, enzymatic activity, signal transduction, cell-to-cell recognition, intercellular joining, attachment to cytoskeleton
      • Peripheral- not embedded in lipid bilayer, Integral (many are transmembrane)-penetrate the hydrophobic core
    • Carbohydrates
      • cell-to-cell recognition
      • Commonly bind to lipids forming glycolipids, or to proteins forming glycoproteins
      • basis of rejection of foreign cells
      • sorting of cells into tissues and organs in embryos
    • Cholesterol
      • reduces membrane fluidity at moderate/high temperatures (slows movement)
      • keeps it from solidifying at cold temperatures by disrupting the regular packing of phospholipids



h) Evaluate data from a real or simulated population to explain how types of selection might affect the population in the future.
Submitted by Allie Pannoni

Textbook- [476-477]

Bottleneck Effect
  • A sudden change in the environment may drastically reduce the size of a population
  • A severe drop in population size can cause the bottleneck effect
  • Certain alleles may be overrepresented among the survivors, others may be underrepresented, and some may be absent altogether.
  • Ongoing genetic drift is likely to have substantial effects on the gene pool until the population becomes large enough that chance events have less effect
  • Even if a population size that has passed through a bottleneck ultimately recovers in size, it may have low levels of genetic variation for a long period of time
  • Human actions sometimes create sever bottlenecks for other species
  • Example: the Greater Prairie Chicken
    • The Illinois population of greater prairie chickens dropped from millions of birds in the 1800s to fewer than 50 birds in 1993.
    • As a consequence of the drastic reduction in size of the Illinois population, genetic drift resulted in a drop in the number of alleles per locus and a decrease in the percent of eggs that hatched.
external image download



e) Construct and/or use phylogenic representations to pose or answer scientific questions about the relatedness of a group or organisms.
Submitted by Tara

Phylogenetic trees graphically model evolutionary history and can represent both acquired traits and those lost during evolution.

  • All organisms are linked by lines of descent from common ancestry.
  • Phylogenetic trees and cladograms illustrate speciation that has occurred...any two groups on the tree is shown by how recently they had a common ancestor.
  • They can be constructed from morphological similarities of living or fossil species, and from DNA and protein sequence similarites.
    • Morphological example is the heart. Fish have 2 chambers, amphibians have 3, and birds and mammals have 4 chambers.
  • Evolutionary relationships are depicted as a series of dichotomies, or two-way branch points. Each branch point represents the divergence of two evolutionary lineages from a common ancestor.
how to read a phylogenetic tree.jpg

  • In this phylogenetic tree, the Branch point (node) points to the common ancestor of taxa A, B, and C. The branch point to the right of that indicates that taxa B and C diverged after their shared lineage split from that of taxon A.
  • Taxa B and C are sister taxa which are groups of organisms that share an immediate common ancestor. They are each other’s closest relatives.
  • The branch point that shows the common ancestor of taxa A-F shows that this tree is rooted.
  • The lineage leading to taxa D-F includes a polytomy, a branch point from which more than two descendent groups emerge.

  • One type of phylogenetic tree is a cladogram. Biologists place species into groups called clades, each of which includes an ancestral species and ALL of its decendents.
  • Shared ancestral character: a character that originated in an ancestor of the taxon.
    • example: backbones in all mammals
  • Shared derived character: an evolutionary novelty unique to a particular clade.
    • example: hair on all mammals but not their ancestors
cladogram.jpg

*You can review phylogenetic trees in the textbook pages 538-548
*Mr. Anderson sums up phylogenetic trees in this video https://www.youtube.com/watch?v=fQwI90bkJl4


D: Explain and justify conserved core processes and features that support common ancestry within and across domains of life.
Submitted by Orna

Descent with Modification was the phrase that Charles Darwin used to describe the descent of all organisms from an ancestor that lived in the remote past. He thought that as the descendants of that ancestor lived in different habitats over the years, they accumulated modifications that fit their way of life.
  • Closely related species, such as the Asian and African elephants are very similar because they shared the same line of descent until a fairly recent split from their common ancestor.
  • Homology, or characteristics with similarity resulting from common ancestry, is key evidence for evolution and common ancestry.
    • Closely related species share many features
    • Forelimbs of all mammals show the same arrangement of bones
      • Even though a common feature may have different functions in different organisms, the skeletons represent the common theme that was present in their common ancestor.

    • Vestigial structures are the remains of features that served important functions in the organism's ancestors.
      • Ex. Snakes and whales keep remnants of legs of ancestors
    • Embryology is more evidence for common ancestry, as it has been shown that all vertebrates, at some stage in their embryonic development, have a tail and pharyngeal pouches.
Review of evolution, including common ancestry, can be found in the textbook Chapter 22.

D cont.) Describe a limited set of core features and processes shared between the domains of life as evidence of common ancestry
Submitted by Jess

DNA is the genetic material
  • DNA and RNA compose the genetic material in all organisms across all domains, supporting common ancestry

There is one universal genetic code
  • many genes have been conserved through evolution
  • all genes are set up in a triplet codon form
  • All life forms have A,C,T, and G as their bases
  • The fact that genes from one animal can be inserted into another and translated show more evidence for evolution

Common Metabolic processes
  • All organisms gain energy by either photosynthesis or cellular respiration
  • All organisms reproduce either asexually or sexually
  • All living things grow, cells divide
  • All living things are composed of cells
  • Replication of genetic material is also a universal process
Eukaryote core elements
  • Nucleus
  • Membrane bound organelles
  • Linear chromosomes
  • Endomembrane systems


I.) Evaluate and explain several examples of scientific evidence that support the claim that evolution is an ongoing process (e.g antibiotic resistance, pesticide resistance, antiviral resistance). submitted by Kelsey

Antibiotic resistance- form of drug resistance whereby some sub-populations of a microorganisms usually a bacterial species, are able to survive after exposure to one or more antibiotics
During the past few decades, many strains of bacteria have evolved resistance to antibiotics.
Example: Neisseria gonorrhoeae, the bacteria that causes gonorrhea. In the 1960's penicillin and ampicillin were able to control most cases of gonorrhea. Today, more than 24 percent of gonorrheal bacteria in the U.S. are resistant to at least one antibiotic, and 98 percent of gonorrheal bacteria in Southeast Asia are resistant to penicillin.
Infectious bacteria are much harder to control than their predecessors were ten or twenty years ago.
Evolutionary theory suggests some specific tactics to help slow the rate at which bacteria become resistant to our drugs:
  • Don’t use antibiotics to treat viral infections.
  • Avoid mild doses of antibiotics over long time periods.
  • When treating a bacterial infection with antibiotics, take all your pills.
  • Use a combination of drugs to treat a bacterial infection.
  • Reduce or eliminate the “preventive” use of antibiotics on livestock and crops.
Pesticide resistance- the decreased susceptibility of a pest population to apesticide that was previously effective at controlling the pest.
Over 500 species of pests have evolved a resistance to a pesticide
Pest species are usually capable of producing large number of offspring
Increases the probability of random mutations and ensures the rapid build-up in numbers of resistant mutants
Examples: In the US, studies have shown that fruit flies that infest orange groves were becoming resistant to malathoin, a pesticide used to kill them
In England, rats in certain areas have evolved such a strong resistance to rat poison that they can consume up to five times as much of it as normal rats without dying
Antiviral Resistance-virus has changed in such a way that the antiviral drug is less effective in treating or preventing illnesses
Example: flu viruses. Flu viruses change from one season to the next. As a flu virus replicates, the genetic makeup may change in a way that results in the virus becoming resistant the antiviral drugs used to treat influenza. Resistance of influenza A viruses to antiviral drugs can occur spontaneously or emerge during the course of antiviral treatment or antiviral exposure.


external image 1whatIsDrugResistance.gifantibiotic resistance


f) Explain how the different lines of data (morphological, biochemical, genetic) support the concept of a common ancestry within a phylogenetic domain and for all life. Submitted by Kelsey

Three domain system- divides cellular life forms into archaea, bacteria, and eukaryote domains
evidence used such as genetics (DNA), morphology (fossil records) and biochemical support the concept of common ancestry

Morphological- branch of biology dealing with the study of the form and structure of organisms and their specific structural features
Example- Humans share many characteristics with our close relatives, other mammals. Some of these are obvious. We all have four limbs, two eyes, two ears, lungs and a skeleton But we also have features in common with more distantly-related species, including worms, and even single-celled organisms like amoeba.
Middle Ear- humans and all other mammals, the middle ear contains 3 bones: the incus (or anvil), the malleus (or hammer) and the stapes (or stirrup).
Birds, reptiles and amphibians share this characteristic but reptiles have more bones in their jaw

Genetics:One of the strongest evidences for common descent comes from the study of gene sequences.
phylogenetic reconstructions, especially when done using slowly evolving protein sequences, are often quite robust and can be used to reconstruct a great deal of the evolutionary history of modern organisms
These reconstructed phylogenies recapitulate the relationships established through morphological and biochemical studies. The most detailed reconstructions have been performed on the basis of the mitochondrial genomes shared by all eukaryotic organisms
DNA Sequencing- allows organisms to be grouped by sequence similarity, and the resulting phylogenetic trees are typically congruent with traditional taxonomy,
Proteins- supports the universal ancestry of life. Vital proteins, such as the ribosome, DNA polymerase, and RNA polymerase, are found in everything from the most primitive bacteria to the most
The core part of the protein is conserved across all lineages of life, serving similar functions complex mammals.
Example-
Chromosome 2 in humans- presence of a vestigial centromere. Normally a chromosome has just one centromere, but in chromosome 2 there are remnants of a second centromere

Biochemical- All known surviving organisms are based on the same biochemical processes: genetic information encoded as nucleic acid (DNA, or RNA for many viruses), transcribed into RNA, then translated into proteins
Example- familiar vertebrate body plan, whose structure is controlled by the homeobox (Hox) family of genes.

external image 400px-Phylogenetic_tree.svg.png


page 537 in textbook
Video on phylogeny:
https://www.youtube.com/watch?v=fQwI90bkJl4

G) Describe speciation in an isolated population and make a prediction about speciation based on changes in gene frequency, change in environment, natural selection, and/or genetic drift. Submitted by Orna


Speciation is the process by which two species arise from an existing species. This can occur one of two main ways
  • Allopatric- gene flow in a population is interrupted when the population is divided into two geographically isolated populations.
  • Sympatric- speciation occurs in populations that live in the same geographic area.
    • Ongoing contact with each other continues gene flow, however gene flow can be reduced by polyploidy, habitat differentiation, and sexual selection.
Natural selection, genetic drift, and gene flow can alter allele frequencies in a population.
  • Natural selection- Those individuals with traits better suited to their environment tend to product more offspring and therefore are more fit. This selection results in alleles being passed to the next generation in proportions different fro their proportions in the present generation. This results in a better match between organisms and their environment.
  • Genetic Drift- Chance events can cause allele frequencies to change unpredictably from one generation to the next.
    • This happens especially in small populations.
  • Gene flow is the transfer of alleles into or out of a population due to the movement of fertile individuals and their gametes.
    • This is unlikely to happen in an isolated population, as there are no neighboring populations for individuals to move to, so gene flow would not be a likely cause of speciation in an isolated population.

My prediction about speciation in an isolated population is that it would be most likely to occur sympatrically, with genetic drift being the most likely cause. If a chance event happened that caused a major change in the allele frequencies of favorable traits, natural selection may occur and two species could arise from one.

B Evolution.) Describe several models about the origins of life on Earth, explain reasons for revisions of hypotheses based on new scientific evidence from different disciplines, and explain limitations of the various models. (Tory)

Experimental models support the idea that chemical and physical processes on primitive Earth could have produced complex molecules and very simple cells. When under lab conditions, complex polymers and self-replicating molecules can assemble spontaneously. As a result, the first genetic material may not have been DNA, but instead short sequences of self-replicating RNA that were possible polypeptide synthesis templates.

1. Louis Pasteur (1860’s
⁃ Abiogenesis is the concept that life may have spontaneously generated. This explanation suggests that amino acids and proteins arose from primordial soup and arranged themselves into self-replication life forms. It claims that this beginning eventually composed and transcribed the DNA.
⁃ Pasteur developed his germ theory of disease that states that human health is subject to attack by microorganisms and these attacks are what we think of as disease. He showed that microorganisms live everywhere around us
⁃ After revealing the nature of germs, he killed the idea that organic life can generate spontaneously out go inorganic material

2. Panspermia
⁃ This concept claims that life didn’t begin on Earth, but elsewhere in the universe or the solar system. Life was carried here by an astroid or other vehicle and life spread, similar to the germs Pasteur uncovered.

3. Charles Darwin
⁃ Darwin introduced his theory of evolution. His model proposed that species weren’t independently created. Instead they evolved in great numbers from earlier species through the process of evolution by natural selection.
⁃ He proposed that all organisms could have evolved from a single organism; this encouraged the modern investigation into the origin of life.
⁃ Phylogeny: hybrid field where the interrelatedness of organisms is established based on their shared DNA

4. Electric Spark (soup model)
⁃ One model claims electric sparks can generate amino acids from sugars from an atmosphere containing water, ammonia, hydrogen and methane.
⁃ This was tested under lab conditions in the Miller-Urey experiment (1953)
⁃ Suggests that lightening might have helped create the key building blocks of life
⁃ Over millions of years, more complex molecules could form
⁃ Research since has revealed that the early atmosphere was hydrogen-poor

5. Clay
⁃ Alexander Graham Cairns-Smith suggested the first molecules might have met on flat. These surfaces might not only have concentrated these compounds together but also organize them into patterns that resemble our genes
⁃ Suggested that mineral crystals in clay could have organized molecules and then eventually these molecules organized themselves

6. Deep Sea Vents
⁃ Life may have begun at submarine hydrothermal vents, spewing hydrogen rich molecules
⁃ Rocky rigid nooks organized these molecules together and provided mineral catalysts for specific reactions

7. RNA World
⁃ RNA can store info like DNA and serve as an enzyme like proteins and help in creating both. DNA and proteins are more efficient so today they have succeeded RNA.
⁃ Some theorists believe RNA helped create both molecules. RNA may have spontaneously arisen on Earth but others refute such claims.

8. Small molecules
⁃ Instead of complex molecules like RNA, other origin of life models suggest life began with smaller molecules interacting with each other in cycles of reactions
⁃ These models are called “metabolism-first”
⁃ The small molecules potentially contained simple capsules similar to membrane
a153.5 Origin of Life.cmap.jpeg

(A) Apply mathematical methods to data from a real or simulated population and predict what will happen to the population in the future based on the Hardy Weinberg model (Submitted by Katherine)

Evolution : Hardy-Weinberg

The Hardy-Weinberg Principle states that the frequency of alleles in a population will remain constant from generation to generation provided that only Mendelian segregation and recombination of alleles is at work.

Necessary Conditions:

  • No Mutations
  • No Natural Selection
  • No Gene Flow – no immigration or emigration
  • Random Mating
  • Extremely Large Population Size

Equation (Which Will be Provided on Formula Sheet):

p^2 + 2pq + q^2 = 1

Examples of the equation can be found on the math review page or pages 472-475 of the text.

Populations That Have Evolved Over Time

  • Peppered Moths – frequency of dark phenotype more prevalent after air pollution turned trees black, dark coloring = better camouflage from predators
plm.jpg

  • Sickle Cell Anemia – more prevalent in environments with malaria because of heterozygote advantage
  • HIV – mutates rapidly during replication, no true cure


Big idea 2: Biological systems utilize free energy and molecular building blocks to grow, reproduce and to maintain dynamic homeostasis.

Unit 1 (biochemistry) fits under big idea 2: biological systems utilize free energy and molecular building blocks to grow, reproduce, and maintain dynamic homeostasis. To support this, here is a summary of a topic I had trouble with and reviewed from unit 1: functional groups. Functional groups are groups of elements responsible for reactions of compounds; side chains in proteins, proteins being made up of monomers amino acids, are examples of functional groups. Hydrophilic groups have oxygen and are polar, the others are no polar and hydrophobic. alex f.


Unit 3 ( energy) fits under big idea 2: biological systems utilize free energy and molecular building blocks to grow, reproduce, and maintain dynamic homeostasis. To support this, here is a summary of a topic I had trouble with: cellular respiration. Cellular respiration takes place inside the mitochondria, and can be done with oxygen (aerobic) or without oxygen (anaerobic). It generates ATP, a significant source of energy for the cell, created after glucose (C6H12O6) and oxygen (6O2) are taken in and split into carbon dioxide (6CO2) and water (6 H2O). The three processes leading to this are glycolysis, breaking up glucose outside mitochondria, Krebs cycle, releases CO2 by converting acetyl CoA into various acids, then the electron transport chain, which accepts electrons from the Krebs cycle to make water with hydrogen ions and oxygen as the last acceptor in the electron transport chain. Lactic acid fermentation occurs in the absence of oxygen/mitochondria, it converts pyruvate into lactate to accept NADH electrons to recycle NAD+ so it can accept more electrons from
Glycolysis. Alcohol fermentation differs only by giving off carbon dioxide. Alex f


A) Calculate surface area-to-volume ratios for a variety of cell shapes (e.g., spherical, cuboidal) and predict, based on ratios, which cell(s) procure nutrients or eliminates wastes faster.
Submitted by Tara

Surface area-to-volume ratios affect a biological system’s ability to obtain necessary resources or eliminate waste products.

  • The surface area of the plasma membrane must be large enough to adequately exchange materials.
  • For each square micrometer of membrane, only a limited amount of a particular substance can cross per second, so the ratio of surface area to volume is critical.
  • As cells increase in volume, the relative surface area decreases and demand for material resources increases…These limitations restrict cell size.
  • Smaller cells have a more favorable surface area-to-volume ratio for exchange of materials with the environment
Formulas:
  • Volume of a Sphere= 4/3π r²
  • Volume of a Cube= lwh
  • Surface area of a Sphere= 4π r²
  • Surface area of a Cube= 6a
  • Ratio= surface area / volume

Take for example a sphere with a radius of 2, a sphere with a radius of 4, a 2x2x2 cube, and a 4x4x4 cube.

2 unit radius sphere
SA= 4 π 2²
SA= 50.27
V = 4/3 π 2²
V = 16.76
Ratio: 2.99

4 unit radius sphere
SA= 4 π 4²
SA= 201.06
V= 4/3 π 4²
V= 67.02
Ratio: 3

2x2x2 cube
One side of cube = 4 units
SA= 6 x 4
SA= 24
V= 2x2x2
V= 8
Ratio: 3

4x4x4 cube
One side of cube = 16 units
SA= 6 x 16
SA= 96
V= 4x4x4
V= 64
Ratio: 1.5

The bigger the ratio, the better. These examples are very close in their ratios, except the 4x4x4 cube is going to be the least efficient because there is not enough surface area for nutrients to pass through to the entirety of the cell. This is why most cells are microscopic and/or round.

*Page 98-99 in the textbook explains surface area and volume ratios in cells.
*Mr. Anderson explains why cells are small in this video https://www.youtube.com/watch?v=wuXSEOKNxN8

g) Describe the interdependency of photosynthesis and cellular respiration (e.g. that the products of photosynthesis are the reactants for cellular respiration and vice versa)
Submitted by Tara

The products of photosynthesis are the reactants for cellular respiration and vice versa. These substances are able to be exchanged due to the structure of plasma membranes.

  • The plasma membrane which encloses the cell is primarily made up of phospholipids and proteins held together by weak interactions- this makes it fluid.
  • It is selectively permeable. Selectively permeable: allows some substances to cross it more easily than others.
  • Phospholipids provide a hydrophobic barrier that separates the cell from its liquid environment. They consist of a polar phosphate group connected to two fatty acid tails. The hydrophilic head is directed outward and hydrophobic tails directed inward. Phosopholipids form a bilayer. Hydrophilic molecules cannot easily enter the cells, but hydrophobic molecules can.
  • Nonpolar molecules such as hydrocarbons, carbon dioxide, and oxygen are hydrophobic. They can dissolve in the phospholipid bilayer and cross the membrane easily, using passive diffusion.
  • Passive diffusion: substance travels from where it is more concentrated to where it is less concentrated, diffusing down its concentration gradient. (No energy is required.)
*Here is the fluid mosaic model of plasma membrane:
fluid-mosaic-model.fig.3.2.jpg
  • Cellular respiration harvests free energy from sugars to produce free energy carriers, including ATP. The free energy available in sugars drives metabolic pathways in cells.
  • Cellular respiration: the most prevalent and efficient catabolic pathway, in which oxygen is consumed as a reactant along with the organic fuel. Carbohydrates, fats, and proteins can all be broken down to release energy in cellular respiration, but the primary nutrient molecule is glucose.
  • The chemical formula for cellular respiration is:
    • C6H12O6 + 6 O2 à 6 CO2 + 6 H2O + energy
  • Photosynthesis traps free energy from sunlight that, in turn, is used to produce carbohydrates from carbon dioxide.
  • The chemical formula for photosynthesis is:
    • 6 CO2 + 6 H2O + light energy à C6H12O6 + O2
  • The products of photosynthesis are able to diffuse across the plasma membrane to be used in cellular respiration. Likewise, the products of cellular respiration are used in photosynthesis.
*For a quick review on membrane structure and function, look at pages 48-52 in the review book.
*For a quick review of the processes of photosynthesis and respiration, pages 75-89 in review book.


f.) Create a visual representation to describe the structure of cell membranes and how membrane structure leads to the establishment of electrochemical gradients and the formation of ATP. Submitted by Kelsey


Cell Membrane
external image hd8mF13M7BsNvPJN6Ua-RSzQ9jtEXIcY2jxRbaejQjN9wrcVluc_QXIPvCRvAAiFS4357-3lGHLYidBLcvbt1LtkaEhHVWGJOEk3OHlSgR2-Q3zFIdxA5eE_iQ1anqw3Hw
Structure:
surrounds all living cells, and is the cell's most important organelle
Membranes are composed of phospholipids, proteins and carbohydrates arranged in a fluid mosaic structure
Phospholipids- arranged in a bilayer, with their polar, hydrophilic phosphate heads facing outwards, and their non-polar, hydrophobic fatty acid tails facing each other in the middle of the bilayer.
hydrophobic layer acts as a barrier to all but the smallest molecules
The proteins- usually span from one side of the phospholipid bilayer to the other (integral proteins), but can also sit on one of the surfaces (peripheral proteins). Hydrophilic or hydrophobic
The carbohydrates- are found on the outer surface of all eukaryotic cell membranes, and are attached to the membrane proteins or sometimes to the phospholipids.

Electrochemical gradient is a gradient of electrochemical potential, usually for an ion that can move across a membrane.
The energy is stored in the form of chemical potential, which accounts for an ion's concentration gradient across a cell membrane

ATP:
one of the end products of photophosphorylation, cellular respiration, and fermentation and used by enzymes and structural proteins
ATP plays a critical role in the transport of macromolecules across cell membranes, examples:
exocytosis and endocytosis.

Function of Cell Membrane :
controls how substances can move in and out of the cell

Mr, Anderson video on cell membrane
http://www.bozemanscience.com/015-cell-membrane


e.) Pose scientific questions about what mechanisms and structural features allow organisms to capture, store, and use free energy (e.g. autotrophs vs heterotrophs, photosynthesis, chemosynthesis, anaerobic versus aerobic respiration.) Submitted by Kelsey

Autotrophs:
  • capture free energy from physical sources in the environment

Heterotrophs
  • capture free energy present in carbon compounds produced by other organisms
    • metabolize carbohydrates, lipids, and proteins by hydrolysis as free energy

Photosynthesis
  • capture free energy present in sunlight
    • chlorophylls absorb free energy from light
    • chloroplasts
Chemosynthetic
  • capture free energy from small inorganic molecules present in their environment
    • may occur without oxygen
Anaerobic
  • electron acceptors other than oxygen
  • uses an electron transport chain
  • occurs in bacteria, yeasts, some prokaryotes, erythrocytes (red blood cells), and in muscle cells.
  • Produces lactic acid
  • produces Lactic Acid Fermentation
Aerobic
  • uses oxygen
  • occurs in most cells.
  • produces Carbon dioxide, water, ATP

Questions:
What organelle does photosynthesis occur in?
In what organisms do photosynthesis and chemosynthesis occur in?
why doesn't anaerobic reactions need oxygen?
what is the difference between anaerobic and aerobic respiration?
explain the process of the respirations?

__http://www.bozemanscience.com/photosynthesis__



J Cells.) Explain how several internal membrane bound organelles and other structural features work together to provide a specific function for the cell and contribute to efficiency (Tory)
Specialized compartments called organelles exist within eukaryotic cells to perform specific functions. Different organelles play different roles both alone and with the help of other organelles. Organelles increase the efficiency of cellular processes by concentrating the factors necessary to carry out specific biochemical reactions separate from the rest of the cell.

1. Major Organelles & Functions

⁃ Nucleus: The nucleus houses the majority of genetic material of a cell. The nucleus is the “brain” of the cell and controls all activity within the cell. Using DNA as a blueprint, the nucleus directs the production of proteins

⁃ Mitochondria: produce the energy currency of the cell, ATP (i.e., phosphorylation of ADP), through respiration, and to regulate cellular metabolism.

⁃ ER (smooth and rough): extensive network making up approximately half of all membranous tissue of the cell and is the site of membrane and protein synthesis. Rough ER is named for the presence of ribosomes along its membrane and is the source of proteins. Smooth ER lacks ribosomes and is responsible for lipid synthesis and processes a variety of metabolic processes such as drug detoxification.

⁃ Chloroplast: uses sunlight to create energy in plant cells and are the site of photosynthesis

⁃ Lysosomes: digestive sacs that can break down macromolecules in the cell using the process of hydrolysis. The digestion is carried out with lysosomal enzymes found in the lysosome. They help keep excessive macromolecules from building up in the cell.

⁃ Ribosomes: Carry out manual labor in the form of protein synthesis for the nucleus. They bring together RNA (copies of the original DNA blueprints) and amino acids to assemble proteins. The proteins created are essential to cell and organismal function. Ribosomes attached to rough ER aid in the synthesis of proteins before being shipped off to the Golgi apparatus.

⁃ Cytoplasm: semi-fluid substance found inside the cell. The cytoplasm encases, cushions and protects the internal organelles.

⁃ Cell Wall (plants): strong outer wall that protects plant cells from lysing (exploding) in extremely hypotonic (diluted) solutions.

⁃ Cell Membrane: surround the cell and have the ability to regulate entrance and exit of substances, maintaining internal balance and protecting the inner cell from outside forces.

⁃ Golgi Apparatus: integral in modifying, sorting, and packaging macromolecules for cell secretion (exocytosis) or use within the cell. It modifies proteins delivered from the rough endoplasmic reticulum but is also involved in the transport of lipids around the cell, and the creation of lysosomes.

The following is a link to a review video on the cell organelles, their functions, and how they work together:
https://www.youtube.com/watch?v=1Z9pqST72is



cell-organelles.png


k.) Evaluate data that describe the effects of changes in concentrations of key molecules on negative and positive regulatory systems (e.g. operons in gene regulation, temperature regulation on animals, plant responses to water limitations, oxytocin in childbirth.) Submitted by Kelsey

Homeostasis- dynamic equilibrium

Negative feedback:
maintain internal environments by returning the changing conditions back to its target set point
regulate physiological processes
Examples:
temperature regulation in animals and plant responses to drought

external image BQNip2CAXAAdpDAo81yWb0e3uoHTYHiYAKswCq7CgaoC2qNH5B53EMYpmyTgyknn9Vmai9dMxS-mEo0Et-kEbkk-guRkcCW3n6bJkXYq6wbgIf_HMvjRS9E6wDhsZrbnfQ

Positive feedback
amplify responses
Examples:
onset of labor in childbirth and ripening of fruit
  • pressure of baby's head against receptors near the opening of the mother’s uterus stimulates the uterus to contract

external image Xhm4ypJvMV7HjWrhB6x-KUocu7b-QRuADzArQghCHUKtGGko7fCu4bhrBELLNysmrSfQbnvYI49X2dfJixxDeJyH8RgDFwGLr24mUwRFKJ7kVDwTu0iBixOSxVhQpZzaEw

page 861-862 for more information on Homeostasis
http://www.bozemanscience.com/homeostatic-loops




c) Create a visual representation to make predictions about the exchange of molecules between an organism and its environment, the use of these molecules, and consequences to the organism if these molecules cannot be obtained.
Submitted by Allie Pannoni

Example: Carbon
Textbook- pages [58-61] U [1232]

Carbon moves from the environment to organisms where it is used to build carbohydrates, proteins, lipids or nucleic acids. Carbon is used in storage compounds and cell formation in all organisms.

  • Without carbon, life on Earth as we know it would not exist.
  • Carbon forms the framework of the organic molecules essential to all organisms.
  • Carbon is unparalleled in its ability to form molecules that are large, complex, and diverse
  • Carbon has four valence electrons, allowing it to form up to four bonds (usually either double or single covalent bonds)
  • Photosynthetic organisms utilize CO2 during photosynthesis and convert the carbon to organic forms that are used by consumers.
  • The major reservoirs of carbon include fossil fuels, soils, the sediments of aquatic ecosystems, the oceans, plant and animal biomass, the atmosphere, and sedimentary rock.
  • Photosynthesis by plants and phytoplankton remove large amounts of CO2 from the atmosphere. However, this quantity is about equal to the amount of CO2 added to the atmosphere through cellular respiration by producers and consumers.
  • Volcanoes (over geological time) and the burning of fossil fuels add significant amounts of CO2 to the atmosphere as well.


The carbon cycle demonstrates this exchange of carbon:
external image o40BVDiJNIbSry43Pcbriw_m.png


d) Pose scientific questions about how surface area-to-volume ratios influence the movement of nutrients and wastes into and out of cells.
Submitted by Allie Pannoni

As cells increase in volume, the relative surface area decreases and demand for material resources increases; more cellular structures are necessary to adequately exchange materials and energy with the environment. These limitations restrict cell size.

Example: Cells that have microvilli
Textbook- Pages [99] U [888,889]

  • Intestinal cells may have long, thin projections from their surface called microvilli
  • Microvilli increase surface area without an appreciable increase in volume
  • In the small intestine, there are finger-like projections called villi that line the organ
  • Each epithelial cell of a villus has on its apical surface many microvilli
  • The side by side microvilli give the intestinal epithelium a brush like appearance
  • The enormous surface area presented by microvilli is an adaptation that greatly increases the total capacity for nutrient absorption


external image Figure1.5c.gif

Here is Mr. Anderson's video on why cells are small:
https://www.youtube.com/watch?v=wuXSEOKNxN8


m) Justify the selection of the kind of data needed to pose scientific questions about the regulatory mechanisms that organisms use to respond to changes in their external environments.
Submitted by Allie Pannoni

In plants, physiological events involve interactions between environmental stimuli and internal molecular signals.
Example- Photoperiodism and phototropism in plants
Textbook- [825] U [839]

  • Phototropism
    • o Any growth response that results in plant organs curving toward or away from stimuli is called a tropism
    • o The growth of a shoot toward light or away from it is called phototropism
    • o The shoot of a sprouting grass seedling is enclosed in a sheath called a coleoptile, which grows straight upward if the seedling is kept in the dark or if it is illuminated uniformly from all sides
    • o If the growing coleoptile is illuminated from one side, it grows toward the light
    • o This response results from a differential growth of cells on opposite sides of the coleoptile; the cells on the darker side elongate faster than the cells on the brighter side.
  • Phoroperiodism
    • o Seasonal events are of critical importance in the life cycles of most plants.
    • o Seed germination, flowering, and the onset and breaking of bud dormancy are all stages that usually occur at specific times of the year.
    • o The environmental stimulus that plants use most often to detect the time of the year is the photoperiod, the relative lengths of night and day.
    • o A physiological response to photoperiod is called photoperiodism
Mr. Anderson’s video that describes this concept: https://www.youtube.com/watch?v=dju6tTb55Fw



B) Justify the selection of data to explain how cells absorb or eliminate molecules that various organisms acquire as necessary building blocks or eliminate as wastes. Submitted by Orna

Cells absorb and eliminate molecules through their cell membranes. To start, here is Mr Anderson's video on Transport Across Cell Membranes.
http://www.youtube.com/watch?v=RPAZvs4hvGA&list=PLFCE4D99C4124A27A&feature=share&index=19

Transport Proteins: Involved in facilitated diffusion. Cells have transport proteins spanning the membrane, that allow ions and polar molecules to pass into the cell. Certain transport proteins, channel proteins, called aquaporins allow water to enter the cell, resulting in a much more effective rate of water transport in and out of the cell. There are also carrier proteins, such as glucose transporters, translocate the solute-binding site across the the membrane.
In order for cells to maintain its water balance, it must have a way of diffusing water in and out to maintain the perfect balance. This is called osmosis, and is driven by the differences concentration gradients of the water and the solute.
Active transport includes pumps like the sodium-potassium pump, which exchanges the two molecules across the membranes of animal cells, helping to maintain the proper membrane potential (voltage across the membrane) which supplies energy for cellular work.
Endocytosis is the process by which cells take in biological molecules by forming new vesicles from the plasma membrane, for example, cholesterol for the use in synthesis of membranes.
Exocytosis involves the secretion of biological molecules by the fusion of vesicles with the plasma membrane. Examples include
  • Pancreas cells excreting insulin into extracellular fluid.
  • Neuron releasing neurotransmitters that signal other neurons or muscle cells.
  • In plants, the delivery of proteins and carbohydrates from golgi vesicles to the outside of the cell.

b) Identify several chemical elements and molecules that function as key building blocks or are removed as waste
Submitted by Jess

Carbon – C
  • Unparalleled in its ability to form large, complex, and diverse molecules
  • Carbohydrates, proteins, and DNA are all composed of carbon
  • Tetravalence (4 outer valence electrons)
Water- H20
  • Hydrolysis- water formed by the breaking down of molecules by removing 2 Hydrogens and an Oxygen molecule
  • Polar
  • Excellent solvent
  • Cohesive- hydrogen bonds hold water molecules together
  • Needed in respiration
Sugar- C6 H12 O6
  • Made up of monosaccharides
  • Used for nutrients in cellular respiration
  • Plants and animals store sugars in the form of storage polysaccharides
  • Used for structure in plants and insects
Nitrogen- N
  • Used by plants as part of Nitrogen cycle
  • Found in amino acids that make up proteins
  • Found in the bases of DNA
  • Fixed in to usable form by bacteria
  • Can also be found in human waste
Lipids-
  • Hydrophobic
  • Make up plasma membrane
  • Contain fats, steroids, and phospholipids
  • Phospholipids have one hydrophobic and one hydrophilic end causing the semi-permeability of cell membranes.
  • Steroids are used as signaling molecules
  • Fats have high energy storage in their bonds and are made up of a carbon skeleton

*Chapter 5: the chemistry of life

I Biochemistry.) provided with the electrochemical properties of several different molecules, make predictions about the permeability of the membrane to the molecule and describe several methods of transport (Tory)
The permeability of a membrane is the rate of passive diffusion of molecules through the membrane. These molecules are known as permeant molecules.
  • Electric charge and polarity determine the permeability of a molecule
  • Hydrophobic nature of membranes make it easier for small neutrally charged molecules to pass through; large molecules have more difficulties
  • Inability of charged molecules to pass the membrane causes pH partition of substances throughout the fluid compartments
  • Membranes are selectively permeable and there are a series of mechanisms that regulate the passage of solutes such as ions and small molecules through them. The membranes consist of lipid bilayers that contain proteins embedded in them.
  • Only molecules or ions with certain properties will be able to diffuse across a membrane; additional transport mechanisms exist for molecules lacking ideal conditions:
    • Diffusion: small, non charged molecules or lipid soluble molecules pass between the phospholipids to enter or leave the cell. They always move from an area of high concentration to areas of low concentration (ex: oxygen, CO2 and most lipids)
    • Passive (Facilitated) Diffusion: substances move into or out of cells down the concentration gradient by protein channels embedded in the membrane. Unlike simple diffusion, this requires specialized membrane channels. Charged or polar molecules that can’t fit between phospholipids travel through facilitated diffusion.
    • Active Transport: substances move against the gradient from an area of low to high concentration. This is an energetically unfavored reaction because it requires the use of energy by breaking down ATP
    • Osmosis: simple diffusion in which water diffuses through a membrane from areas of high to low water concentration
      • Hypertonic: more solutes and less water
      • Hypotonic: more water and less solutes
      • During osmosis water moves from the hypotonic to the hypertonic solution
  • Endocytosis: this is a mechanism for transporting large molecules across the membrane. A small piece of cell membrane wraps around the particle and is brought into the cell.
    • Phagocytosis: form of endocytosis where the particles are solid
    • Pinocytosis: form of endocytosis where particles are in the form of fluid
  • Exocytosis: used to secrete molecules too large to pass through the membrane using any other apparatus.

Mr Anderson's review video on membrane transport:
https://www.youtube.com/watch?v=RPAZvs4hvGA

The following link provides a membrane simulation activity featuring each type of transport mechanism:
http://www.phschool.com/science/biology_place/biocoach/biomembrane1/structure.html

Active-passive_transport.jpg

H) Use representations and models to pose scientific questions about the properties of cell membranes and selective permeability based on molecular structure. Submitted by Orna
Cell Membrane Structure:
  • Fluid mosaic model
    • Phospholipid bilayer
      • Held together by hydrophobic interactions, and can shift around in the membrane surface.
      • Remains fluid until temperature drops enough for phosopholipids to settle into a closely packed arrangement.
    • Proteins imbedded in the phospholipid layer
      • Some protiens mobile within the membrane, but many are held in place by their attachment to the cytoskeleton.
external image plasma-membrane-structure.png

Selective Permeability:
  • Nonpolar molecules such as hydrocarbons , carbon dioxide and oxygen, are hydrophobic and can dissolve in the lipid bilayer and pass through.
  • The hydrophobic core of the membrane stops ions and polar molecules (hydrophilic) from moving across the membrane.
  • Polar molecules such as glucose and water, pass very slowly across the membrane.
    • Transport proteins help hydrophilic substances move through the lipid bilayer
      • Channel proteins have a hydrophilic channel that molecules use as a tunnel through the membrane.
        • One example is aquaporins, which allow water to pass through the membrane and into or out of the cell.
        • Carrier proteins hold onto the molecules they are bringing across, and change shape to allow them to move across the membrane.
          • Carrier proteins can speed up the diffusion of molecules such as glucose, which is needed by red blood cells.
  • The molecular structure of a substance (polarity, hydrophobic vs hydrophilic, charge, size) all determine how selectively permeable the membrane is.
external image 12_02_diffusion_rate.jpgexternal image Figure_05_02_04.jpg


S Ecology.) Analyze data to support the claim that responses to info and communication of info can affect natural selection (Tory)
  • Responses to the following impact natural selection:
    • Competition: results in differential survival. Individuals with more favorable phenotypes (leading to favorable responses and communication) are more likely to survive and produce more offspring. Essentially this leads to the passing of such traits to future generations
    • Variation and Mutation: a diversified and varied gene pool is important for the survival of a species in a changing environment. The variations are often a result of a mutation. If this change provides the organism with a more favorable way to respond to the environment, it will be more likely to survive and pass on the trait.
    • Environment: environments can fluctuate in stability, affecting natural selection and the evolutionary rate. Those who are most fit and can respond most appropriately in response to the environment will be favored for survival.
  • Organisms also have feedback mechanisms that maintain dynamic homeostasis by allowing them to respond to changes in their internal and external environments
  • Negative feedback loops maintain optimal internal environments while positive feedback loops amplify responses
  • The following responses and modes of communication/behavior also impact natural selection:
    • Changes in light source and phototropism
    • Seasonal behavior (reproduction)
    • Visual and auditory signals
    • Species recognition
    • Mutualistic relationships
The following link to Mr. Anderson's video can be used to study natural selection and it's major influences https://www.youtube.com/watch?v=S7EhExhXOPQ


LO 2.30 The student can create representations or models to describe nonspecific immune defenses in plants and animals.
Submitted by Tara

Plants, invertebrates and vertebrates have multiple, nonspecific immune responses.

  • Innate immune responses are active immediately upon infection and are the same whether or not the pathogen has been encountered previously.
  • Invertebrate immune systems have nonspecific response mechanisms, but they lack pathogen-specific defense responses.
    • insects rely on their exoskeleton as a first line of defense against infection.
      • composed of polysaccharide chitin and acts as barrier defense on the outside of body and also in the intestine
    • Lysozyme, an enzyme that digest microbial cell walls, and low pH further protects digestive system.
    • Hemocytes circulate within the hemolymth (which is the insect equivalent of blood)
      • Some carry out phagocytosis is the ingestion and digestion of bacteria and other foreign substances.
      • Others trigger production of chemicals that kill microbes and help entrap multicellular parasites
    • Hemocytes and certain other cells secrete antimicrobial peptides upon meeting pathogens and they circulate throughout the body to inactivate or kill fungi and bacteria by disrupting their plasma membranes.
  • Plant defenses against pathogens include molecular recognition systems with systematic responses; infection triggers chemical responses that destroy infected and adjacent cells, thus localizing the effects.
  • Vertebrate immune systems have nonspecific and nonheritable defense mechanisms against pathogens.
    • Barrier defenses
      • skin
      • mucous membranes lining the digestive, respiratory, urinary, and reproductive tracts
        • mucus traps microbes and other particles… in the trachea, ciliated epithelial cells sweep the mucus upward to help prevent lung infection
      • saliva, tears, and mucous secretions bathe various exposed epithelia to provide washing action that inhibits colonization by microbes… lysozymes in these also destroy bacteria by creating a hostile environment
      • acid in stomach
      • sweat has pH of about 3-5 to prevent growth of microorganisms
  • Cellular innate defenses
    • Phagocytic white blood cells recognize microbes using Toll-like recptors (TLR). This triggers a series of internal defenses, beginning with phagocytosis in which cell engulfs the invading microbes and traps them in the vacuole which then fuses with a lysosome, leading to the destruction of the microbe in 2 ways.
      • First, nitric oxide and other gases produced in lysosome posin the engulfed microbes
      • Second, lysozyme and other enzymes degrade microbial components
    • Neutrophils
    • Macrophages
    • Eosinophils
    • Dendritic cells
  • Antimicrobial peptides and proteins
    • Pathogen recognition in mammals triggers the production and release of peptides and proteins that attack microbes or impede their reproduction
    • Interferons: proteins that provide innate defense against viral infections by inhibiting viral reproduction which limits cell-to-cell spread of viruses
    • The complement system: about 30 proteins in blood plasma that function together to fight infections
  • Inflammatory responses
    • Inflammatory response: changes brought about by signaling molecules released upon injury or infection
    • Histamine is an important signaling molecule, which is stored in mast cells, connective tissue cells that store chemicals in the granules for secretion
    • Pain, swelling, fever, septic shock
  • Natural killer cells
    • Natural killer cells: help recognize and eliminate certain diseased cells in vertebrates.
    • Attach to infected cells and release chemicals that lead to cell death, inhibiting spread of virus or cancer.

(P) Create representations and models to describe essential aspects of nonspecific and specific immune response systems in plants, invertebrates, and vertebrates. (Submitted by Katherine)

Homeostasis : Immune System

Nonspecific Immunity – active immediately upon infection and are the same whether or not the pathogen has been encountered previously
  • Barrier Defenses – skin, mucous membranes, secretions
  • Internal Defenses – phagocytic cells, antimicrobial proteins, inflammatory response, natural killer cells

Specific Immunity – activated after innate immune defenses take effect and develop more slowly
  • Humoral Response – antibodies in body fluids
  • Cell-Mediated Response – cytotoxic lymphocytes in body cells

PLANTS
Nonspecific – epidermis of the primary plant body and periderm of the secondary plant body
asdf.jpg

Specific – based on binding of molecules from the pathogen to receptors in plant cells
  • Identification triggers signal transduction pathway
  • Hypersensitive response – plant cells produce antimicrobial molecules, seal off infected areas by modifying cell walls, and then destroy themselves
    • o Infected cells release methylsalicylic acid which is distributed to the rest of the plant and activates systematic acquired resistance
qwer.jpg

INVERTEBRATES
Nonspecific – phagocytosis
zxcv.png

Specific – fungal cell walls contain certain polysaccharides which are used as tags so that insect immune cells secrete recognition proteins that bind to the molecule

VERTEBRATES
Nonspecific – inflammatory responses
  • Histamine – dilates nearby blood vessels
  • Enhanced blood flow helps deliver antimicrobial proteins
  • Additional phagocytosis and inactivation of microbes
poiu.jpg

Specific – Helper T Cells enhance humoral and cell mediated response
  • Binds to class II MHC molecule which promotes secretion of cytokines by antigen presenting cell
  • Proliferation of Helper T Cell gives rise to clones of activated Helper T Cells
  • Cytokines help activate B cells and cytotoxic T cells
lkjh.jpg



(D) Describe 2-3 different strategies that organisms employ to obtain free energy for cell processes. (Submitted by Katherine)

Energy : Metabolism

Physical Constraints – as body dimensions increase, thicker skeletons are required to maintain adequate strength
  • As body size increases, the muscles required for locomotion must represent a larger fraction of the total body mass so that mobility becomes limited
  • TRex – so tall, it probably was no faster than a professional soccer player

Endotherms – maintain body temperature higher than the environment so they must counteract constant heat loss
  • Shivering – muscle activity increases heat production
  • Nonshivering thermogenesis – mammals’ hormones can cause mitochondria to increase metabolic activity to produce heat instead of ATP
  • Brown fat – specialized for rapid heat production

Torpor – activity is low so metabolism decreases which enables animals to save energy while avoiding difficult and dangerous conditions
  • Hibernation – body temperatures decline as body thermostat is turned down resulting in huge energy savings



Essential Knowledge 2.a.2 Organisms capture and store free energy for use in biological processes
Submitted by Jess
Citric Acid Cycle (also known as Kreb cycle)
  • If molecular oxygen in present, the two pyruvates from glycolysis enter the mitochondria where enzymes of the citric acid cycle complete the oxidation of glucose.
  • In prokaryotic cells this process occurs in the cytosol
  • The pyruvate is converted into acetyl CoA
  • This then produces citrate
  • After various steps in the cycle 3 molecules of Co2 are removed as waste
  • The cycle generates 1 ATP per turn by substrate- level phosphorylation
  • 3 NADH are produced to be sent to the electron transport chain
  • Glycolysis and the citric acid cycle produce only 4 ATP molecules per glucose molecule
  • Process repeats in cyclic manner
  • The most ATP is made during chemiosmosis.. which is aided by NADH and FADH produced by citric acid cycle
citric acid cycle.jpg


Here’s a video on the citric acid cycle https://www.youtube.com/watch?v=juM2ROSLWfw
*pages 170-172 in text

Big idea 3: Living systems store, retrieve, transmit and respond to information essential to life processes



Unit 4 (genetics) fits under big idea 3: living systems store, retrieve, transmit, and respond to information essential to life processes . To support this, here is a summary of a topic I had trouble with: difference between meiosis and mitosis. In meiosis, chromosomes come together and crossover mixing genetic information, then line up along the cell plate to be separated into two different cells. Another division occurs resulting in four cells with half the number of chromosomes. Mitosis is a single division leading to two identical cells with the same number of chromosomes. Alex f


unit 5 (molecular genetics) fits under big idea 3: living systems store, retrieve, transmit, and respond to information essential to life processes. To support this, here is a summary of a topic I had trouble with DNA replication. DNA replication is tied in with the cell cycle; G1 growth, S phase is copying all DNA, G2 continued growth, and M phase (cell division). The meselson stahl experiment, using e. Coli bred with nitrogen 15 in their DNA then transferred to N14 substance, determined DNA replication as semi conservative. DNA itself runs in two anti parallel strands of phosphate sugar nitrogenous base connected tripod groups, the prime carbon of the sugar tells you the direction of the strand 5-3 or 3-5. (5 carbons a sugar); helicase unwinds DNA, single strand binding proteins stabilize the separated strands keeping them in place, DNA polymerase adds new nucleotides to the separated strand (leading strand) of DNA and the nucleotides can only be added to the 3 prime end. For attaching nucleotides to the 5 prime end, RNA primate adds RNA to the lagging strand allowing DNA polymerase to add nucleotides. DNA ligase connects nucleotides together. Origins of replication/ replication forks are where replication of DNA starts. In prokaryotes it starts in one spot, in eukaryotes it moves in both directions after originating at two different points on the DNA. Alex f


f) Justify how various modes of gene regulation (positive and negative) can explain the differences seen at the cellular, organismal, and population level. Predict how changes in regulation will affect cellular functions.
Submitted by Allie Pannoni

Textbook- [351-377]

Gene regulation results in differential gene expression, leading to cell specialization.

Here is Mr. Anderson’s video on gene regulation:
https://www.youtube.com/watch?v=3S3ZOmleAj0
  • DNA regulatory sequences, regulatory genes, and small regulatory RNAs are involved in gene expression.
  • Regulatory sequences are stretches of DNA that interact with regulatory proteins to control transcription.
  • A regulatory gene is a sequence of DNA encoding a regulatory protein or RNA.
  • Both positive and negative control mechanisms regulate gene expression in bacteria and viruses.
  • The expression of specific gene can be turned on by the presence of an inducer, or inhibited by the presence of a repressor.
  • Inducers and repressors are small molecules that interact with regulatory proteins and/or regulatory sequences.
  • Regulatory proteins inhibit gene expression by binding to DNA and blocking transcription (negative control).
  • Regulatory proteins stimulate gene expression by binding to DNA and stimulating transcription (positive control) or binding to repressors to inactivate repressor function.
  • Certain genes are continuously expressed.
  • In eukaryotes, gene expression is complex and control involves regulatory genes, regulatory elements and transcription factors.


d) Predict possible effects that alterations in the normal processes of meiosis will have on the phenotypes of offspring compared to the normal situation and connect the outcomes to issues surrounding human genetic disorders.
Submitted by Allie Pannoni

Textbook- [297-300]

Changes in genotype can result in changes in phenotype.
  • Errors in meiosis can result in changes in phenotype.
  • Changes in chromosome number often result in new phenotypes, including sterility caused by triploidy and increased vigor of other polyploids.
  • Changes in chromosome number also can result in human disorders with developmental limitations including Trisomy 21 (Down syndrome) and XO (Turner syndrome).

Example – Down syndrome
  • Down syndrome is usually the result of an extra chromosome number 21
  • Down syndrome includes characteristic facial features, short stature, heart defects, susceptibility to respiratory infect, and mental retardation.
  • Most cases result from nondisjunction during meiosis 1.
  • Here is a video explaining Trisomy 21: https://www.youtube.com/watch?v=EA0qxhR2oOk
external image nondisjunction.jpg



b) Using at least two commonly used technologies, describe how humans manipulate heritable information and possible consequences.
Submitted by Tara

Genetic engineering is the process of manipulating genes and genomes.
  • Polymerase chain reaction, or PCR, is a method used to greatly amplify a particular piece of DNA without the use of cells.
    • in this technique, any specific target segment within one or many DNA molecules can be quickly amplified (copied many times) in a test tube... It is especially helpful for sources that are impure or scanty.
    • Occasional errors during PCR replication impose limits on the number of good copies that can be made by this method
    • However, PCR can be used to amplify DNA from things like ancient wooly mammoth, fingerprints at crime scenes, and embryonic cells to diagnose genetic disorders.
    • PCR can be used to amplify a patients blood samples to detect even small traces of viruses to diagnose disease.
pcr.jpg
  • Gel electrophoresis is a lab technique used to separate macromolecules based on their size and charge with the use of electrical current.
    • In separating DNA, the negative charges on phosphates cause DNA to move toward the positive pole.
    • The gel allows smaller molecules to move more easily than larger DNA fragments
    • One useful application of this technique is restriction fragment analysis, whcih can rapidly provide useful information about DNA sequences.
    • Restriction fragment analysis is also useful for comparing two different DNA molecules- for example, two alleles of a gene.
      • An example of this is testing for sickle cell anemia. The bands left by gel electrophoresis can determine whether a patient is normal, a carrier, or affected by sickle cell disease. (This is the gel electrophoresis lab we did earlier.)

*Page 134-139 in the review book reviews these and other technologies.
*Chapter 20 on biotechnology starts on page 396 in your textbook

L Molecular Genetics.) Justify how the life cycles of DNA and RNA viruses can contribute to rapid evolution of both the host and virus. (Tory)

  • Viruses have high mutation rates, produce numerous offspring and have short generation times. In addition recombination and re-assortment can also produce more variation.
  • Viruses can introduce variation in the host genetic material through lysogenesis. These latent genomes can result in new properties for the host such as increased pathogenicity in bacteria
    • Lysogenesis: characterized by integration of the bacteriophage nucleic acid into the host bacterium's genome or formation of a circular replicon in the bacterium's cytoplasm. The bacterium continues to live and reproduce but the genetic material of the bacteriophage can be transmitted to daughter cells at each division. In eukaryotic cells this is referred to as transformation.
  • Viruses evolve through changes in their DNA or RNA
    • best adapted viruses outnumber their mutants rapidly
    • RNA viruses are especially prone to mutations
    • There are mechanisms for correcting DNA mistakes before division but they do not work for RNA.
    • When RNA viruses replicate, changes in their genes are sometimes introduced in error. These can be lethal
    • One virus particle can produce millions of progeny viruses in just one cycle
  • Viruses have efficient replicative capabilities that allow for rapid evolution and acquisition of new phenotypes
  • They replicate via a component assembly model allowing one virus to produce many progeny simultaneously via the lytic cycle
  • Replication of viruses allow for mutations to occur through usual host pathways
  • Viruses can combine info if they infect the same host cell
  • EXAMPLE: HIV involves the rapid evolution of a virus within the host that contributes to the pathogenicity of viral infection
  • EXAMPLE: Influenza A can shuffle their genes with other viruses when two similar strains infect the same cell (aka genetic shift) and is often the cause of new and more virulent strains appearing
This link will bring you to Mr. Anderson's review on virus replication:
https://www.youtube.com/watch?v=EqK1CYYQIug

n) Justify how changes in internal or external clues affect the behavior of individuals and their interactions within a population and between related individuals.
Submitted by Tara

Organisms exchange information with each other in response to internal changes and external clues, which can change behavior.

  • Behavior is what an animal does and how it does it.
  • Living systems have a variety of signal behaviors or cues that produce changes in the behavior of other organisms and can result in differential reproductive success.
  • Fixed action pattern: a sequence of unlearned acts that is essentially unchangeable and, once initiated, usually carried to completion. The trigger is an external cue known as a sign stimulus.
    • Example: Male sticklebacks, which have red bellies, attack other males that invade their nesting territories. The color red is a sign stimulus that releases aggressive behavior as its fixed action pattern.
  • Kinesis: a simple change in activity in response to a stimulus.
    • Example: Sow bugs become more active in dry areas and less active in humid areas, but do not move toward or away from conditions.
  • Taxis: an automatic movement toward or away from a stimulus.
    • Example: trout and other river fishes automatically swim upstream (toward the current) to keep from being swept away and keeps them facing in the direction of food
  • Signal: a stimulus transmitted from one animal to another.
  • Communication: the transmission and reception of signals between animals.
    • Example: claw waving by fiddler crabs during courtship is the male crab generating a stimulus that guides the behavior of the female crab.
  • Phermones: chemical signals that are emitted by members of one species that affect other members of the species.
    • Example: phermones from a female moth can attract a mate from several kilometers away. Then, once the moths meet, phermones trigger special courtship behaviors.
  • Visual communication: the flow of information to the visual system
    • Example: fruit fly courtship begins with a male identifying and orienting toward a female of the same species.
  • Auditory communication: flow of information to the auditory system.
    • Example: male flies sing a courtship song to inform the female that it is of the same species.
  • Tactile communication: flow of information through touching
    • Example: male touches female’s abdomen with a foreleg to let her know of his presence.
  • Responses to information and communication of information are vital to natural selection and evolution.

*Pages 1120-1125 in text book


m) Describe how behavior is modified in response to external and internal cues for both animals and plants using appropriate examples from each.
Submitted by Jess

Sensory inputs can stimulate both simple and complex behaviors (Animals)
    • Innate behavior- born with behavior, instinct
    • Learned behavior- develop with growth and experience
  • Fixed Action Patterns
    • behavior directly linked to simple stimulus
    • These patterns are unlearned and usually unchangeable
    • External cues are known as sign stimulus
Both Genetic makeup and environment contribute to the development of behaviors
  • Regulatory Genes and Behavior
    • Scientists think that in most cases behavior is shaped by a large number of genes that individually have small effects.
    • Behavior can be modified by social learning, or observing other animals and copying their behavior
    • Hormones also are an internal response to signals received by the organism and can cause a chemical and physical response.
Example:
Imprinting: animals such as birds imprint on the chemical given off by the mother during the critical period after birth and the response is to follow her.

Mr. Anderson video on Animal Behaviors https://www.youtube.com/watch?v=6hREwakXmAo
  • Chapter 51: Animal Behavior in text book

Plant Hormones help coordinate responses to stimuli
  • hormones spread throughout plants and allow them to carry out response to stimuli
  • tropism: any growth response that results in the plants organs curving toward or away from stimuli such as light (Phototropism)
  • Plant hormones are produced in small amounts but can have a large effect on an organism
  • Types of plant hormones
    • Auxin: stimulates cell elongation, functions in phototrpoism, along with many other functions
    • Cytokinins: regulate cell division in shoots and roots, delay leaf senescence
    • Abscisic acid (ABA): inhibits growth, promotes stomatal closure in response to drought
    • Ethylene: leaf abscission, promotion of lateral expansion
  • Plant hormones are released due to internal or external stimuli
  • Responses include growth and development, flowering, or other preservation responses during stress
Example:
Drought: a plant can be stressed by water deficiency due to losing water by transpiration faster than it is restored. The plant responds by reducing the rate of transpiration, stimulates the production of ABA, closes the stomata in the leaf, and tells roots to grow deeper into the soil.

Mr. Anderson video on Plant Control https://www.youtube.com/watch?v=HdwIcIkSoBY
  • Chapter 39: Plant Responses to Internal and External Signals Text book


h.) Predict how various types of change in a DNA sequence can alter a phenotype, and describe several using real-world examples. Submitted by Kelsey

Phenotype- observable traits

Silent mutations are DNA mutations that do not significantly alter the phenotype of the organism in which they occur.
no significant change to phenotype
Transformation, or DNA-mediated gene transfer, permits the introduction of new genetic information into a cell and frequently results in a change in phenotype.
Expression of transformed genes frequently results in the synthesis of new polypeptide products which restore appropriate mutant cells to the wild-type phenotype.
Germ line mutations-occur in reproductive cells like eggs and sperm
may result in no change or slight change such as the bending of a cats ear
Some regions of DNA control other genes, determining when and where other genes are turned "on". Mutations in these parts of the genome can substantially change the way the organism is built.

Example:
Mutations to control genes can transform one body part into another. Scientists have studied flies carrying Hox mutations that sprout legs on their foreheads instead of antennae!
external image rnt89RUYh1C5HTb0k6EdAv9eSbfPmjaJo_Kx1aDwkCAX24ePMJOAwnh_cOBGpK7EgN-JtNjcjctcwpBOgl7A39-b6qSCV-NME8jiR6bX9GOUuVwhwGsd6kUV4IbcUavioA

Sickle Cell Anemia:
genetic disease with severe symptoms, including pain and anemia. The disease is caused by a mutated version of the gene that helps make hemoglobin
When red blood cells carrying mutant hemoglobin are deprived of oxygen, they become "sickle-shaped" instead of the usual round shape. This shape can sometimes interrupt blood flow. May show pain and fatigue as a result.

More information:
__http://www.bozemanscience.com/033-genotypes-and-phenotypes__
or
Unit three: Genetics in textbook

a. Predict which features of DNA and RNA were necessary to allow the identification of DNA as the genetic material and justify how these features enable information to be replicated, stored, and expressed. Submitted by Kelsey

DNA and RNA
  • both have three components (sugar, phosphate and nitrogenous base)
  • exhibit specific nucleotide base pairing

DNA
  • deoxyribose
  • thymine
  • double stranded
  • antiparallel in directionality

RNA
  • uracil
  • ribose
  • single stranded
  • mRNA- carries information from the DNA
  • tRNA- bind specific amino acids and allow information in the mRNA to be translated
  • rRNA- functional building blocks

DNA as the genetic material:
  • Shown by Watson and Crick on the structure of DNA- showed that each strand of the DNA molecule was a template for the other
  • Avery-MacLeod-McCarty- DNA is the substance that causes bacterial transformation
  • Hershey- Chase experiment- conform DNA as hereditary material
  • replication requires DNA polymerase
  • one strand serves as template for a new, complementary strand


external image 7wd_3sYXsbh1rMAoRu4UOhNmKvbY4RB0HjIhezqI5NXU-ljVSP3Xzl7uDokVP3dqkuRjBfDogu4BN8e6PPGmiRgJeyOW9jFumh_CiXwBXI0I8P3h8mRD4MYWE-xzHlw4OA
Molecular Genetics Unit
http://www.bozemanscience.com/027-part-1-dna-rna
http://www.bozemanscience.com/027-part-2-dna-rna


h) Describe two processes that increase genetic variation and explain how genetic variation allows for natural selection within a population.
Submitted by Jess

Genetic variation produced in sexual life cycles contribute to evolution

Crossing Over
  • Produces chromosomes with new combinations of maternal and paternal alleles
  • Occurs in Prophase I of meiosis
  • Chiasmata: location of crossing over
  • 1 to 3 crossing over events occur per chromosome
  • Combining chromosomes of two parents increase genetic variation

Independent Assortment of Chromosomes
  • Random assortment of homologous pairs of chromosomes at metaphase I
  • Each pair may orient with either its maternal or paternal homolog closer to a given pole
  • Each pair is positioned independently of others at metaphase I
  • Meiotic division results in each pair sorting its maternal and paternal homologs into daughter cells independently of other pairs
  • In humans the number of possible combinations of maternal and paternal chromosomes in resulting gametes is about 8.4 billion

The evolutionary significance of genetic variation within populations
  • Darwin deduced that a population evolves through differential reproductive success of its variant members
  • Individuals best suited to the local environment leave the most offspring, thus transmitting their genes
  • Natural selection results in the accumulation of genes favored by the environment
  • The ability of sexual reproduction to create such genetic variation is one of the most commonly proposed explanations for why sexual reproduction has persisted

*Chapter 13: Meiosis and Sexual Life Cycles pages: 258-259


e) Using appropriate examples, explain how gene regulation allows for cell specialization and efficient cell function.
Submitted by Jess

Eukaryotic gene expression can be regulated at any stage
  • Human cells only express about 20% of its genes at any given time
  • Genes expressed in each cell type are specific to their function
  • Transcription factors locate particular genes to be turned on or off as needed
  • Chromatin structure is also regulated
    • Genes with heterochromatin are usually not expressed
    • Histone acetylation- allows for easier access to chromatin
    • DNA methylation- involved in long term gene inactivation
  • The specific genes that are turned on or off during differentiation determine cell type
  • Because of gene expression cells are able to perform processes specific to their function
Epigenetic_mechanisms.jpg

(E) Using appropriate examples, explain how gene regulation allows for cell specialization and efficient cell function. (Submitted by Katherine)

Molecular Genetics: Operons

Operon
  • Bacteria
  • Key Advantage: single switch can control cluster of functionally related genes
  • Consists of the operator, promoter, and the genes they control
  • Operator - segment of DNA acting as a "switch" for functionally related genes
  • Promoter - DNA sequence where RNA polymerase attaches and initiates transcription

Repressible Operons: TRANSCRIPTION IS USUALLY ON
  • Can be inhibited when a specific small molecule binds allosterically to a regulatory protein
  • Repressor: binds to operator and BLOCKS attachment of RNA polymerase to promote
  • Product of a regulatory gene located some distance away from operon it controls and has its own promoter
  • Suspend production of end product when it is already in sufficient quantities
trp operon: tryptophan operon, tryptophan = amino acid created by ANABOLIC processes, NEGATIVE control (p. 353)
  • Repressor inactive = operon on

Inducible Operons: TRANSCRIPTION IS USUALLY OFF
  • Can be induced when a specific small molecule interacts with regulatory protein
  • Inducer: inactivates repressor
  • Produce appropriate enzymes only when the nutrient is available
lac operon - lactose, catabolic, NEGATIVE control (p. 354)
  • Allolactose - inducer

C. Justify the effects a change in the cell cycle mitosis and/or meiosis will have on chromosome structure, gamete viability, genetic diversity, and evolution. Submitted by Orna
  • Mutations
    • Mutations are the original source of different alleles, which get mixed and matched during meiosis.
      • Natural selection and evolution result in the accumulation of genetic variations favored by the environment.
  • Cell Cycle Controls
    • A change in the factors that inhibit cell growth during the cell cycle can cause uncontrolled cell growth and tumors.
      • The cells in malignant (harmful) tumors may have an unusual number of chromosomes.
  • Random Fertilization
    • Genetic variation in meiosis is added to by the random nature of fertilization.
  • Reduced Hybrid Fertility
    • If the chromosomes of two parent species differ in structure or number, meiosis may fail to produce normal gametes, resulting in infertile hybrids.

O. Describe how an animals nervous system's biochemical, physiological, and structural components to respond to internal and/or external stimuli. Describe how changes within nerve cells and the nervous system produce responses to the stimuli. Submitted by Orna
  • The nervous system consists of neurons and supporting cells.
    • Nerves channel and organize information flow along routes through the nervous system.
    • The brain and the spinal cord are two main components of the nervous system, with the brain sending out signals, and are passed along the spinal cord to other parts of the body.
  • Reflexes
    • Rapid, involuntary response to a particular stimulus.
      • Sensors detect stimulus > sensory neurons convey the information to the spinal cord > in response to the sensory neurons, motor neurons convey signals to the muscles > causing a response.
  • Autonomic Nervous System- regulates internal environment, largely involuntary.
    • Sympathetic corresponds to energy generation, speeds up body processes.
    • Parasympathetic causes calming and a return to self-maintenance.
    • Ex. in response to a drop in internal body temperature, the hypothalamus signals the autonomic nervous system to constrict surface blood vessels, reducing heat loss.

(K) Justify how the mechanisms of cell-to-cell communication support common lines of evolutionary descent (Submitted by Katherine)

Cells : Cell to Cell Communication

PLANTS
Plasmodesmata – channels between plant cells enabling transport and communication
  • Enable direct, regulated intercellular transport of substances between walls
  • Directors of plant growth and develop a program of cell differnetiation
ghty.jpg

ANIMALS
Gap Junctions – cytoplasmic channels between adjacent cells
  • Directly connects cytoplasm of two cells
  • Cardiac Muscle – signal to contract passed through gap junctions, allowing heart muscle cells to contract in tandem
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(B) Explain how the steps in the cell cycle allow transmission of heritable information between generations and contribute to genetic diversity (Submitted by Katherine)

Genetics : Meiosis and Genetic Variation

MEIOSIS
  • Preceded by replication of chromosomes
  • Two consecutive cell divisions halve number of chromosome sets per cell
  • Produces haploid daughter cells
  • Return to diploidy after fertilization

Synapsis and Crossing Over - PROPHASE 1
  • Exchange of corresponding segments of DNA molecules by nonsister chromatids while homologs are in synapsis

dddd.gif

Independent Assortment of Chromosomes – METAPHASE 1
  • Homologs consisting of one maternal and one paternal chromosome situated on the metaphase plate
  • Each pair positioned independently of the other pairs
  • Each daughter cell, after cytokinesis, has one possible combination of maternal and paternal chromosomes
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Big idea 4: Biological systems interact, and these systems and their interactions possess complex properties.

  1. Unit 2 (cells) fits under big idea 4: biological systems interact, and these systems and their interactions possess complex properties. To support this, here is a summary of a topic I had trouble with: cell communication.

Cells communicate in three ways, through connecting receptors to provide cell to cell contact, local regulators, and hormones. Receptors, like in macrophages and helper T cells, help with sending and receiving chemical messages over extremely short distances. Local regulators are chemical messages over less short distances and are specific, like the receptor communication. Hormones are general chemical messengers sent throughout the entire body, which do not always generate a response.
Alex f

Unit 7 (ecology) fits under big idea 4: biological systems interact, and these systems and their interactions possess complex properties. To support this, here is a summary of a topic I had trouble with: logistic growth. LogistIc growth happens after a catastrophe or after a population hits the carrying capacity of the environment it lives in. N= population size, r (the growth rate i.e. Births - deaths / N) tells us how fast the population changes. Limiting factors determine speed of population change (amount of resources, etc.). dN / dT = rN means change in population over change in time equals growth rate times population. dN/dT= rN (K times N/K) is the same equation with a carrying capacity added in, the process added is carrying capacity (K) times population divided by the carrying capacity. This equation helps show how a population's growth rate changes as it nears it's carrying capacity. If r is ever greater than 0, then fast exponential growth will occur. Carrying capacity present will cause logistic growth. R selected species grow as quickly as they can; high growth rate with little to no care for offspring. K selected species have fewer more well cared for offspring with a slow growth rate. Alex f


unit 8 (homeostasis) fits under big idea 4: biological systems interact and these systems and their interactions possess complex properties. To support this, here is a summary of a topic I had trouble with: the immune system. The immune system has specific and nonspecific defenses; nonspecific would be the skin, low pH barrier against infection, macrophages and inflammation deal with invading viruses/ bacteria, antigens, macrophages take in antigens and secrete enzymes to break it up. Antibodies are a specific defense because they are specifically shaped to detect certain viruses or bacteria. Lymphocytes, B & T, fight antigens. B lymphocytes mature in the bone marrow, and deal with the humoral (fluid) response. They produce antibodies, after sensing an antigen and determining its shape. Memory B cells are produced to fight that particular antigen in case it ever returns. T lymphocytes mature in the thymus and oversee cell mediated response. They kill infected cells, produce dwell death, etc. MHC2 presents antigen fragment in shape from macrophage surface to helper T cell, which physically docks and senses shape of the antigen via CD4. The helper T cell initiates the humoral and cell mediated responses. The helpe T cell Tells the shape of the antigen to the B cells so they can produce antibodies and activate killer T cells to carry out death of infected cells. B cells and killer T cells upon activation multiply to increase speed of immune response, whether it is antibodies sticking to the antigen to prevent it from functioning properly or by killing infected cells. Antigen mutations can affect their discovery by cells and or antibodies. Alex f

Sample entry:
a) Justify how structure imparts function for key biological molecules (proteins...)
Submitted by J. Mcloughlin

Example: Structure of Proteins Text Pages (77-86)

Structure and properties or the function of biological molecules, proteins for example, are a result of their building 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)
Important
  • 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. For instance if the primary structure has hydrophobic R groups, this will cause the protein to fold so that these are on the inside away from water. Proteins have different functions based on their shapes (ie. Enzyme specificity is based on shape; allows enzyme to fit with substrate)
  • Levels of Structure in Proteins
    Levels of Structure in Proteins

Check out the Bozeman video on proteins

Protein Video


a) Justify how structure imparts function for key biological molecules and cell organelles and describe how they interact in key biological processes.
Submitted by Allie Pannoni

Example: Mitochondria/Cellular Respiration
Textbook- [109-110] U [162,177]

The structure and function of subcellular components, and their interactions, provide essential cellular processes.
  • Mitochondria are found in nearly all eukaryotic cells. Some cells have a single large mitochondria, but more often a cell has hundreds or even thousands of mitochondria. The number correlates with the cell’s level of metabolic activity.
  • Mitochondria specialize in energy capture and transformation
  • Mitochondria have a double membrane that allows compartmentalization within the mitochondria and is important to its function. It helps to keep things in order.
  • The outer membrane is smooth, but the inner membrane is highly convoluted, forming folds called cristae.
  • The convolution of the inner membrane increases the surface area.
  • Cristae contain enzymes important to ATP production and increase the surface area, which is also important for ATP production.
  • The structure and function of mitochondria plays a large role in cellular respiration.

Here is Mr. Anderson’s video for extra review of the stages of cellular respiration:
https://www.youtube.com/watch?v=Gh2P5CmCC0M

external image mitochondria.jpg
external image c9x6cell-respiration.jpg


b) Describing in general terms how cells specialize and become tissue and organs
Submitted by Allie Pannoni

Cell Specialization/Differentiation

  • Cells must become distinct, specialized, and differentiated to create a human body with red and white blood cells, neurons, muscle, bone, hair, teeth, skin and the cells of various specialized organs like the lungs, heart and liver.
  • As cells become more specialized, they turn off genes they no longer need.
  • Once unneeded genes are shut off, it’s generally the end of that cell’s ability to be converted into another type of cell.
  • The stem cells found in umbilical cord blood and adult tissues are partway through the specialization process.
    • o Example - Adult blood-forming stem cells are able to form all of the cells that comprise the blood and immune systems, but they generally cannot be made into cells of other tissues.
  • Because the genes required to make cells from other tissues have already been silenced, adult stem cells are less versatile than embryonic stem cells.
  • Mr. Anderson’s video on cell specialization: https://www.youtube.com/watch?v=jp6L5emD8rw


external image pluri.jpg




f) Analyze data showing how changes in enzyme structure, substrate concentration, and environmental conditions (pH, temp, salinity, etc.) affect enzymatic activity.
Submitted by Tara

Change in the structure of a molecular system may result in a change of the function of the system.
  • The shape of enzymes, active sites and interaction with specific molecules are essential for basic functioning of the enzyme.
  • Enzymes speed up reactions but are not consumed during the reaction. Every enzyme has an active site where the substrate binds. The substrate must fit like a key into a lock.

  • Enzymes are proteins with tertiary structure. Tertiary structure results in a complex globular shape, held together by R-group interactions such as hydrophobic interactions, van der Waals interactions, hydrogen bonds, and disulfide bridges.

  • Enzymes are activated when all the appropriate inorganic cofactors and organic coenzymes are present.

  • Inhibition occurs in two forms:
    • Competitive inhibition where the substrate cannot bind to the active site because a competitive inhibitor binded there instead and
    • Allosteric inhibition where binding at the allosteric site either changes the shape of the active site or covers the active site
  • Temperature is one factor that can affect enzymatic activity. As temperature increases, enzymatic activity increases as well. However, when it passes its optimal temperature, it gets to be too hot and the enzyme will denature and be unable to perform its reactions. This graph demonstrates temperature's effect on enzymatic activity.
temp and enzymes.gif
*Mr. Anderson’s enzyme video https://www.youtube.com/watch?v=ok9esggzN18


b) describing in general terms how cells specialize and become tissue and organs
Submitted by Jess

After fertilization, embryonic development proceeds through cleavage, gastrulation, and organogenesis.
  • cleavage: cell division that creates a hollow ball of cells called a blastula from the zygote
  • gastrulation: rearranged the blastula into three layered embryo called a gastrula.
    • 3 layers:
      • Ectoderm (outer layer): skin, nails, teeth, eyes, nerves
      • Mesoderm (middle layer): blood and lymph, bone, notochord, muscles
      • Endoderm (inner layer): forms digestive tract, lining of respiratory and excretory tracts
  • Organogenesis is the process that turns the three germ layers into rudiments of organs
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The developmental fate of cells depends on their history and on inductive signaling
  • initial differences between totipotent embryonic cells come from the uneven distribution of cytoplasmic determinants in the unfertilized egg
  • cleavage parcels out different mRNAs and proteins in a type of asymmetrical division.
  • interactions between embryonic cells influence their fate causing changes in gene expression called induction
  • induction results in differentiated cells and may be mediated by signaling molecules or cell to cell interactions
  • cells then have specific molecules for their differentiated state
  • inductive signals also play a role in pattern formation that allows for the arrangement of tissues and organs in their characteristic spaces.
  • These differentiated cells continue to divide to form into tissues and ultimately organs.

  • Text Book pages 1022-1039

a.) Justify how structure imparts function for key biological molecules (carbohydrates) Submitted by Kelsey

Pg 68-74 in textbook

Carbohydrates- large biological molecule, or macromolecule, consisting of carbon (C), hydrogen (H), and oxygen (O) atoms, usually with a hydrogen:oxygen atom ratio of 2:1.
include sugars, starches, cellulose and many other compounds found in living organisms
also called saccharides

Structure:
monosaccharides- simple sugars ex. glucose
disaccharides- joined by covalent bond, two carbohydrates ex. sucrose
polysaccharides- larger number ex. starch
include macromolecules called polysaccharides, polymers composed of many sugar building blocks
sugars and polymers of sugars

Function:
Living organisms use carbohydrates to to store energy and as structural material to build a variety of cell components

  • a source of energy for the body e.g. glucose and a store of energy, e.g. starch in plants
  • building blocks for polysaccharides (giant carbohydrates), e.g. cellulose in plants and glycogen in the human body
  • components of other molecules eg DNA, RNA, glycolipids, glycoproteins, ATP

Examples:


external image ElVOERyAioow9uX8hrh-W8S9wvee3bUYhg9_8Q7LNt0SfE7F5xoivSpM0kSm6qtzFz9k-bJTQnxyOpTLgNuvZw_bBPEhSdyBuz-KkRr2gxEkr4c3bWLKNZxXAFUpndO3HA


http://www.bozemanscience.com/carbohydrate


C Homeostasis.) Pose scientific questions that address how interactions between constituent parts of a biological systems provide essential biological activities (Tory)
Questions:
  • How do cells, tissues and organs all work together to perform essential activities?
  • What are some examples of how these parts work in unison?
  • What can happen if these interactions are interrupted for disrupted?

  • Cells are the basic units of a body, which combine to make tissues that further congregate to form body organs, which function differently. Organs make up organ systems which rely on all three parts to complete their functions.
  • Examples:
    • Heart: receives deoxygenated blood from the organs, which it oxygenates and transports back to various parts and tissues of the body via arteries and veins
    • Muscles: muscle tissues that make up different organs contract and expand in order to facilitate movement
    • Lungs: The pseudostratified epithelium tissue that lines the bronchi contains many cilia and goblet cells. Cilia are small hair-like cellular projections that extend from the surface of the cells. Goblet cells are specialized epithelial cells that secrete mucus to coat the lining of the bronchi that help keep the lungs clear and free of diease
    • Stomach: the stomach consists of several layers of tissues: mucosa, submucosa, muscularis, and serosa layers. Each layer consists of additional tissues made up of specialized cells in order to complete their specific functions. For example: the mucous membrane of the stomach contains simple columnar epithelium tissue with many exocrine cells.Gastric pit pores contain many exocrine cells that secrete digestive enzymes and hydrochloric acid into the lumen, or hollow region, of the stomach.
    • Leaf: leaves are comprised of three basic tissue systems: dermal, vascular, and ground tissue systems. These three are continuous throughout an entire plant with varying properties. For example: the dermal tissue of a plants is an outer protective layer of typically polygonal cells, which helps defend against injury and invasion by foreign organisms.

leafstructurefigure1.jpg
organ_examples.jpg

d.) Pose scientific questions to analyse interactions among community components. Submitted by Kelsey

page 1148 in textbook
figure 52.2 on page 1149 is very helpful
__http://www.bozemanscience.com/046-communities__
Mr. Anderson video on Communities

Community- group of populations of different species in an area.
  • can have different sizes and boundaries
  • two or more different species occupying the same geographical area and in a particular time

Structure and Components
  • many populations are not randomly distributed
  • closed community, a discrete unit with sharp boundaries known as ecotones.
  • open community has its populations without ecotones and distributed more or less randomly
  • community contain eight smaller units known as biomes.

Competition
  • Species can compete with each other for finite resources.
    • limits population size in a community

external image e9psYSv3Z2HStbHBV_gBRiI-cPBjF7n0kyk7_2TDlcDuCanpaPxyx6Jo0O3RPOHakUnsgxX66euEKVmA2VPuRVGIg6a0IQSQZnypRYNhfByROCm_3dz8_QRFirV86N6qng
Example of a Community

Question:
What factors influence the diversity of species that make up a forest?



a) Justify how structure imparts function for key biological molecules (DNA)

Submitted by Orna

DNA (deoxyribonucleic acid) is the genetic material that organisms inherit from their parents.
  • Functions include providing direction for its own replication and controlling (through RNA) protein synthesis.
  • Each DNA molecule carries several hundred or more genes.
  • When a cell reproduces itself, the DNA molecules are copied and passed on to the next generation.
Structure of DNA:
The two main components of the nucleotides that comprise DNA are the nitrogenous bases and the sugar backbone.
  • Nitrogenous bases found in DNA are Cytosine,Thymine, Adenine, and Guanine.
    • Adenine always pairs with Thymine, and Guanine always pairs with Cytosine.
  • The sugar connected to the bases is deoxyribose.
  • Adjacent nucleotides are joined by phosphate groups to form a polynucleotide.
    • DNA molecules have two of these polynucleotides that spiral in two different directions, forming a double helix shape.
      • The opposite arrangement is referred to as "antiparallel".
      • The two strands of the double helix are complementary, which allows for the precise copying of genes.
        • During cell division, each of the strands serves as a template to make a new strand of nucleotides.
        • This results in two identical copies of the original double-stranded DNA molecules.
        • In this way, the structure of DNA allows for its function of transmitting genetic information whenever a cell reproduces.
external image doublehelix.gif
This video includes Mr Anderson describing the structure of DNA
http://www.youtube.com/watch?v=q6PP-C4udkA

h) Evaluate data from real a or simulated population to explain how types of selection might effect the population in the future.
(Big Idea 1)
Submitted by Maddie


The greater prairie chicken once was a huge population that occupied the prairies of Illinois. Now, there are only about 50 birds left and their eggs only have about a 50% survival rate. Back when their population was thriving, the following effects may have contributed to their extreme decline:

Bottleneck Effect: sudden change in the environment (ex. prairies converted to farmland)
  • severe drop in population size
  • certain alleles may be overrepresented among survivors and some may be underrepresented
  • population must become much larger again to recover from bottleneck effect
  • even if recovered, population may lack genetic diversity

Founder Effect: a few individuals become isolated from larger population (ex. chickens wandered away or were separated by a storm, etc)
  • smaller group establishes a new and different gene pool
  • accounts for the relatively high frequencies of some inherited disorders

Hybrid Sterility: a result of a postzygotic barrier (ex. lived in a hybrid zone* where chickens mated with another species)

  • hybrid zone* region where different species meet and reproduce offspring of mixed ancestry
  • hybrids may still be vigorous but will remain sterile
  • chromosomes from two parents may differ in number or species (can't produce normal gametes)

Reproductive Isolation: existence of biological factors (barriers) that impede members of two species from producing viable, fertile, offspring
There are two main types of reproductive isolation, PREZYGOTIC and POSTZYGOTIC depending on whether or not the isolation happens before or after fertilization:
Prezygotic- "before the zygote"
  1. habitat isolation- species may have been separated by a river or other barrier allowing the two different species not to mix
  2. temporal isolation- the different species breed at different times of day or of the year
  3. behavioral isolation- species have different courtship rituals that determine breeding (dances, songs)
  4. mechanical isolation- mating is attempted, but there are morphological differences
  5. gametic isolation- mating attempted, but sperm can not fertilize egg
Postzygotic- "after the zygote"
  1. Reduced Hybrid Viability- hybrids survival in environment is impaired
  2. Reduced Hybrid Fertility- may be vigorous but sterile (ex. above)
  3. Hybrid Breakdown- 1st generation are viable and fertile but their offspring are sterilechicken population .jpgchicken.jpg


a) Justify how structure imparts function for key biological molecules (Lipids)

Submitted by Orna

Lipids are a diverse group of hydrophobic molecules.
Pg 74-77
Mr Anderson's video on lipids:
http://www.youtube.com/watch?v=VGHD9e3yRIU

The hydrophobic behavior of lipids is based on their molecular structure. They are varied in form and function, and the three main groups are fats, phospholipids, and steroids.
Fats
  • Constructed from two kinds of smaller molecules, glycerol and fatty acids.
    • Glycerol is an alcohol with three hydroxyl groups.
    • Fatty acids have long carbon skeletons, the carbon at one end is part of a carboxyl group, which is attached to a long hydrocarbon chain.
      • The nonpolar C-H bonds in the hydrocarbon chain make fats hydrophobic.
    • Fats can be saturated or unsaturated,
      • Saturated fats have single bonds and unsaturated have double bonds.
  • The main function of fats is energy storage.
    • The hydrocarbon chains of fats are rich in energy, and a gram of fat holds more than twice the amount of energy as a polysaccharide.
external image fat_f2.jpg
Phosopholipids
  • Phosopholipids are essential to cells, as they comprise the cell membranes. Their structure is a classic example of how forms fits function.
    • Has two fatty acids attached to glycerol.
    • Two ends of phospholipids have different interactions with water.
      • Hydrocarbon tails are hydrophobic, phosphate group forms a hydrophilic head.
        • When phospholipids are added to water, they form bilayers, with their hydrophobic tails facing away from water.
      • These different interactions allow for a boundary between a cell and the external environment.
external image phospholipid_bilayer.jpg
Steroids
  • Steroids are lipids characterized by a carbon skeleton comprised of four rings.
    • Steroids vary in the chemical groups attached to these rings.
      • Cholesterol is a common component of animal cell membranes.
        • This helps keep the cell membrane fluid, and prevents freezing in cold temperatures.
      • Cholesterol is also the steroid from which other steroids, such a hormones, are produced from.

external image 048chol.gif


o) Describe how the animal nervous system's biochemical, physiological, and structural components work together to respond to external and/or internal stimuli. Big Idea 3
Submitted by Maddie

Biochemical: Membranes are polarized because of electrical potentials
  • Neurons have a resting potential of -70 mV
  • Sodium Potassium Pumps
    • originally, there is a higher concentration of K+ on the inside and Na+on the outside
    • ATP hydrolysis actively transport these ions through ion channels in response to a stimulus
sodium potassium channels.png
  • action potentials (change in the membranes voltage) occur whenever depolarization increases the membrane to a particular value (threshold)
  • Passage of signal through neuron is electrical
  • Passage from neuron to neuron is chemical
    • Calcium ions are released in the presynaptic vesicle causing synaptic vesicles to fuse with the terminal membrane
    • Neurons are released from synaptic vesicles
    • Neurotransmitters diffuse across the synaptic cleft
    • Neurotransmitters attach to ligand-gated ion channels causing a response in the next neuron causing an action potential and differing levels of sodium and potassium as the signal is passed down the cell in a wave like motion

Physiological: Ability to pass signals from a stimuli and illicit a response
  • Ex: Reflex (automatic response to stimuli)- Stimuli triggers sensors which pass a signal through sensory nuerons to the spinal cord, where interneurons contact motor neurons which trigger a response such as pain
  • PNS-plays large role in regulating animal movementand internal environment
  • Motor* (movement)
  • Autonomic* (internal environment)
    • Sympathetic- arousal and energy generation... "fight or flight"
    • Parasympathetic- calming reactions"rest and digest"
    • Enteric- networks of neurons in the digestive tract, pancreas, and gallbladder
  • Signals are conducted faster when the axons are myelinated
    • signals "skip" along the nodes of Ranvier separating the myelin sheath... this is known as saltatory conduction

Structural: Central Nervous System (containing brain and spinal cord) and Peripheral Nervous System (nerves and ganglia)
CNS:
  1. Brain= white matter (bundled axons and myelinated axons) gray matter (unmyelinated axons, cell bodies, dendrites), cerebrospinal fluid (filtration of arterial blood to the brain)
  2. Spinal Cord= gray and white matter, cerebrospinal fluid ^
  3. Glia cells
    1. microglia- protect nervous system from invading microorganisms
    2. ogliodendrocytes- axon myelination
    3. astrocytes- structural support, regulate external concentrations of ions and neurotransmitters
Here's a great video to help learn the functions of all the different parts of the brain~ Brain Video
PNS:
  1. Afferent (carries info to CNS) Efferent (carries info away from CNS)
  2. Cranial Nerves- connect brain with locations mostly in head and upper body
  3. Spinal Nerves- spinal cord and parts of the body lower than the upper body
  4. Autonomic* (sympathetic, parasympathetic), Motor* system
  5. Schwann cells function in axon myelination here
Neurons:
  • dendrites receive signals
  • axon transmits signal
  • signals are released (neurotransmitters) at axon terminals
  • signal is transmitted to another cell at a junction called a synapse neuron.jpg



Learning Objective 4.3 The student is able to use models to predict and justify that changes in the subcomponents of a biological polymer affect the functionality of the molecule (Subitted by Katherine)

Biochemistry : Subcomponents and Functionality

Sickle Cell Anemia

  • Point mutation in the primary structure of hemoglobin
  • Replacement of amino acid glutamic acid with valine
  • Affects secondary and tertiary structures so that 3D structure is affected
  • Abnormal hemoglobin molecules tend to crystallize, deforming cells into sickle-shape
  • Angular cells clog small blood vessels, impeding blood flow

qaz.jpg

(Sickle Cell Anemia works for a lot of topics that may be essay questions! Check out Sophia's post on "Connecting Evolutionary Changes" for more on heterozygote advantage!)

(2.E.2) Timing and coordination of physiological events are regulated by multiple mechanisms (Submitted by Katherine)

Ecology/Behavior : Environmental Cues and Physiological Responses

Behaviors in animals are triggered by environmental cues and are vital to reproduction, natural selection, and survival.

Circadian Rhythms – internal mechanism that maintains a 24 hour activity cycle
  • In all eukaryotes and persists in the absence of external cues
  • Diurnal/nocturnal cycles
  • Jet lag in humans
cccc.png

Circannual Rhythms – behavioral rhythms linked to the yearly cycle of the seasons
  • Migration – correlate with food availability
  • Reproduction – correlate with food availability
    • o Fiddler crab – time courtship to the lunar cycle to times of greatest tidal movement so that tides can disperse larvae to deeper waters where they can complete early development in relative safety


Big Idea 1:
j) Pose scientific questions about the origin of like on Earth and describe the scientific evidence that supports the proposed key events in the origin of life, including the abiotic synthesis of small organic molecules; assembly of monomers into the complex polymers; formation of protobionts; and the origin of self-replicating, catalytic molecules. (Submitted by Sophia)


In 1953, Miller and Urey set up an artificial system compared to what Oparin and Haldane believed Earth's early atmosphere was like. They were able to produce amino acids and organic compounds found in living organisms today.

The Four Main Stages of How Life Arose
  1. Formation of small organic molecules
    1. Supported by Miller and Urey type experiments
    2. Analysis of meteorites that land on Earth
  2. Abiotic synthesis of macromolecules
    1. Supported by experiments dripping solutions of amino acids onto hot sand, clay, or rocks resulting in formation of amino acid polymers
    2. Can be formed spontaneously without enzymes or ribosomes
  3. Protobionts- abiotic molecules packaged by a membrane
    1. Supported by experiments that show membrane bound lysosomes can form when lipids or organic molecules are added to water
    2. The internal environment differs from the external environment and they show simple reproduction and metabolism
  4. Self- replicating molecules
    1. Supported by work of Thomas Cech
    2. First genetic material was likely RNA
    3. Able to carry out protein synthesis and catalytic functions
    4. RNA molecules best suited to the environment have the greatest ability to replicate and create descendants
    5. Results in natural selection


Big Idea 2:
i) Provided with electrochemical properties of several different molecules, make predictions about the permeability of the membrane to the membrane(s) and describe several methods of transport across the membrane
(submitted by Sophia)

  • Cell membrane permeability is selective- some substances cross easier than others.
  • Lipid bilayer allows non polar molecules (hydrocarbons, carbon dioxide, and an oxygen) to cross easily- hydrophobic.
  • Polar molecules (glucose, other sugars, and water) pass slowly- hydrophilic
  • Charged atoms or molecule- very difficult to penetrate membrane

Methods of transport across a cell membrane:
  1. Passive Diffusion- hydrophobic substances move across the membrane from where it is more concentrated to where it is less concentrated (no energy needed)
  2. Facilitated Diffusion- water and certain hydrophilic solutes cross the membrane passively using transport proteins
    1. Aquaporins- water channel proteins that facilitate the diffusion of water
  3. Osmosis- the diffusion of water across a selective permeable membrane (water diffuses from lower solute concentration to higher solute concentration)
  4. Active Transport- transport proteins provide a hydrophilic channel or bind loosely to the molecule and carry them across the membrane- movement from lower concentration to higher concentrations (requires energy/ ATP) ex: sodium potassium pump
  5. Endocytosis- cell forms a vesicle around particulate matter and takes it into the cell
    1. Phagocytosis- cellular eating
    2. Pinocytosis- cellular drinking
    3. Receptor- Mediated Endocytosis- specific substances (ligands) bind specific receptors on the surface, vesicle forms around the substance and is ingested
  6. Exocytosis- vesicle forms around a molecule within the cell, the vesicle fuses with the cell membrane, the substance is delivered outside of the cell


i) Describe several mechanisms that result in increased genetic variation and rapid evolution of viruses. (Big Idea 3)
Submitted by Maddie
  • Meiosis- haploid cells (sperm and egg) combine DNA to create diploid zygote
    • crossing over- rearrangement between nonsister chromatids forming a recombinant chromosome
    • random orientation- random orientation of homologous pairs at metaphase plate
    • independent assortment- maternal and paternal homologs separate into into daughter cells independently of every other pair
    • random fertilization- 8.4 million possible chromosome combinations
    • errors in meiosis or mitosis like differing chromosome number, etc.
  • Mutation- change in nucleotide sequence of an organism's DNA (primary source of genetic variation)
    • point mutations- one base in a gene
      • sickle-cell anemia
    • deletion, addition, disruption, substitution, rearrangement of many loci at once are very harmful
    • average 1 mutation in every 100,000 in plants and animals
      • even lower in prokaryotes
    • radiation and radioactive chemicals

Rapid Evolution of Viruses:mutation.gif
  • highly efficient replicative capabilities
  • virus replication allows for mutations (fast evolution)
  • component assembly model
    • one virus can produce many simultaneously (lytic cycle- bacteria lyses and releases phages destroying host cell)
  • can combine genetic info with infected host cell (recombinant DNA) when they insert their DNA or RNA
    • may become latent (lysogenic cycle- allows replication of phage genome until it initiates the lytic cycle)
  • IE: HIV
    • is a retrovirus (transcribes and RNA template into DNA)
    • causes AIDS
    • enters host cell, replicates DNA, integrates into DNA of a chromosome (provirus), becomes permanent in cell



Big Idea 3:
d) Predict possible effects that alterations in the normal process of meiosis will have on the phenotypes of offspring compared to the normal situation and connect the outcomes to issues surrounding human genetic diseases. (Submitted by Sophia)



external image meiosis1.jpg?timestamp=1391665584760external image meiosis2.gif?timestamp=1391665615054


























Above is normal meiosis I and II.

Non disjunction- when homologous chromosomes don't separate during meiosis I or sister chromatids don't separate during meiosis II
  • A gamete receives two of the same type of chromosome while another receives no copy
  • Aneuploidy: a zygote formed from an abnormal gamete/ has an abnormal number of chromosomes
    • Monosomic- one copy of a chromosome
      • turner syndrome- a female with one X chromosome
    • trisomic- three copies of a chromosome
      • down syndrome- extra chromosome 21
  • Alterations of chromosome structure- an error in meiosis causing a breakage of a chromosome
    • deletion- chromosome fragment is lost/ missing genes
      • Cri du chat- deletion of chromosome 5 causes retardation
    • duplication- fragment that broke off attached to its sister chromatid
    • inversion- fragment breaks off and reattached upside down
    • translocation- fragment joins a nonhomologous chromosome
      • Chronic myelogenous leukemia- cancer caused by translocation in white blood cells of chromosome 22 and chromosome 9


A.) Describe the basic structure and functions of key biological polymers and cell organelles (Tory)

  • DNA: composed of polynucleotides, have a phosphate group, deoxyribose sugar and a nitrogen containing bases (adenine, thymine, cytosine and guanine), a doubled helix that is formed by hydrogen bonds between polynucleotides, and is densely compacted into chromosomes to fit into nucleus. DNA stores an organisms genetic material in the nuclei, provides code or template for the amino acid sequences for proteins
  • RNA: consists of a phosphate group, ribose sugar and nitrogen containing bases (adenine, uracil, cytosine, guanine), is single stranded and moves out of nucleus to perform protein synthesis. Three types include messenger, ribosomal, and transfer RNA
  • Lipids: non-polar organic molecules that are made of long hydrocarbon chains. They are referred to as hydrophobic which means that they repel water. The monomers of lipids are fatty acids. They provide a protection from the outside and keeps what is supposed to be inside the cell contained inside the cell including the liquid which that liquid has a large composition that is water
  • Carbohydrates:organic compounds with a structure that consist of carbon, hydrogen and oxygen, normally with hydrogen: oxygen atom ratio of 2:1. They function to provide energy for the regulation of blood glucose, and help in sparing the use of proteins for energy.
  • Proteins: composed of amino acids, linked together by peptide bonds to form a polypeptide chain. One or more polypeptide chains twisted into a 3-D shape form a protein. Proteins have complex shapes that include various folds, loops, and curves. Proteins are involved in all cell functions. Some proteins are involved in structural support, while others are involved in bodily movement, or in defense against germs. Other types include storage, transport, hormonal and enzyme proteins.
  • Nucleus: directs the chemical reactions in cells by transcribing genetic information from DNA into RNA.The nucleus also stores genetic information and transfers it during cell division from one cell to the next. It controls cell's genetic program and metabolic activities.
  • Mitochondria: double membrane bound organelles that are spherical to elongate in shape. It converts energy into a from the cell can use.
  • Plasma Membrane: a semi-permeable membrane with a phospholipid bilayer. It works to isolate the cytoplasm from the external environment, regulate the exchange of substances, communicate with other cells, and in identification
  • Golgi: a collection of membranes associated physically & functionally with the E.R in the cytoplasm. It is composed flattened stacks of membrane-bound cisternae. It sorts, packages and routes cell's synthesized products.

LO 4.23 The student is able to construct explanations of the influence of environmental factors on the phenotype of an organisms.
(Submitted by Tara)

Environmental factors influence many traits both directly and indirectly.
  • A genotype generally is not associated with a rigid phenotype… it is more a range of phenotypic possibilities due to environmental influences called the norm of reaction.
  • Norms of reaction are broadest for polygenic characters.
  • Multifactoral: many factors, both genetic and environmental, collectively influence phenotype.

  • Examples of environment affecting phenotypes:
  • A single tree can have leaves that vary in size, shape, and greenness depending on wind and sun exposure.
  • Nutrients influence height in humans
  • Exercise can alter the shape/build of human bodies
  • Exposure to sun can darken skin
  • Twins are genetically the same, but phenotypically different
  • Hydrangea flowers of the same genetic variety can range in color from blue/violet to pink depending on soil pH and aluminum content.
  • As daylight lessens in autumn, many northern animals will begin to grow thicker and lighter-colored coats that eventually become completely white… Likewise, as the days lengthen in spring, the winter coat is gradually shed (in mammals) or molted (in birds) and replaced with a darker color.


Big Idea 4:
c) Explaining how interactions between constituent parts of a biological system provide essential biological ideas. (Submitted by Sophia)

The basic building block of all living things is the cell.

Cells that have similar structure and function are organized into groups called tissues.
  • Epithelial
  • Connective
  • Muscle
  • Nervous

Tissues, organized to preform a certain function, are called organs

Organs working together for one greater function make up organ systems

One prime example of a biological system providing essential biological activities is the circulatory system. The circulatory system delivers oxygen to all other organ systems in the body. The heart organ, made up of specialized muscle tissue, receives oxygen poor blood from the body, pumps it through an artery made of epithelial tissue to the lungs, back through the heart and out to the rest of the body. Blood cells, connective tissue, not only carry oxygen to the other organ systems but also provide a line of defense against injuries and infections.


Big Idea 2:
L) Provided with a visual representation with multiple components, explain with justification or make predictions of how alterations of the components in a negative or make predictions of how alterations of the components in a negative or positive regulatory system can result in deleterious consequences to the organism. (Submitted by Sophia)

Negative feedback systems- animal response to a stimulus in a way that reduces the stimulus

Positive feedback systems- response to a trigger that amplifies that response or change

Screen_shot_2011-03-10_at_10.39.11_AM.png

Under normal conditions blood glucose levels are set at 90 mg/ 100 mL. Two antagonistic hormones, insulin and glucagon, regulate the concentration of glucose in the blood. This works on a negative feedback system. Increases in blood glucose cause a release of insulin and glucose is take up from the blood. Decrease in glucose, glucagon is released, increasing blood glucose level. Diabetes mellitus, a deficiency of insulin or decreased response to insulin can cause serious effects in the heart, blood vessels, eye, and kidneys. Glucose levels rise but cells can't meet their metabolic needs. The body starts to use fat for cellular respiration which can create acidic metabolites which can lower blood pH. In type one diabetes, often found in childhood, a person loses ability to produce insulin and there for body can not take up the glucose needed. In type two diabetes, the body is not responding to the insulin that is released due to a high blood glucose level.

Big Idea 1:
a) Connecting evolutionary changes in a population over time to a change in the environment by describing 2-3 examples. (Submitted by Sophia)

Sickle Cell Anemia- a point mutation (chemical changes in a single base pair of a gene)
  • Individual's homozygous for the allele causes sickling of red blood cells
  • Referred to as genetic disorder or hereditary disease
Although this is a disease in Africa where malaria is wide spread this genetic defect offers and advantage.
  • Heterozygotes for the sickle cell defect are protected against severe effects of malaria
  • This is led to a high frequency of the sickle cell allele in Africa, especially where malaria is most common
  • In some areas 20% of the hemoglobin alleles have the sickle cell defect

On a more global scale cataclysmic events have changed the living populations on Earth. One example would be the cretaceous mass extinction, 65.5 million years ago.
  • More than half of all marine species and many terrestrial plants and animals, including dinosaurs, were eliminated
  • Research has found a thin layer of clay containing iridium between the sediments of the Mesozoic and Cenozoic Eras
  • Iridium is rare on Earth but found in meteorites
  • It is theorized that a cloud of debris from an asteroid or comet collision with Earth caused sunlight to be blocked, disturbing the climate for months
  • Evidence to support this theory has centered around the Chicxulub Crater

Introduced species- non native species that humans intentionally or accidentally move to an area
  • Increased travel by ship and airplane has increased transplant species
  • The introduced species has often had an effect on its new community
  • One example would be the brown tree snake
    • Stowed away on military cargo after World War II and introduced to Guam
    • Twelve species of birds and six species of lizards have become extinct due to the predatory brown tree snake


Big Idea 1:
b) Describing several sources of evidence from multiple scientific disciplines that support biological evolution.

The thoery of evolution is supported by a vast amount of scientific evidence

  • The Fossil Record
    • Based on the sequence in which fossils accumulate in sedimentary rocks (strata) shows great changes in the kinds of organisms on Earth at different points in time
    • Documents the extinction of some life forms as well as the rising of new groups of organisms
  • Radioactive Dating
    • Helps us get a more specific date of a fossil
    • Based on the decay of radio isotopes
      • Rate of decay is expressed by half life/ the time required for 50% of the parent isotope to decay
    • Fossils contain isotopes of elements accumulated in the organism when they were alive, ie carbon
  • Morphological Features
    • Fossils show new features of organisms and the amount of time these features take to occur
      • For example, fossil records show the evolution of mammalian jaws and teeth (Figure 25.6, page 513)
    • Homology characteristics in related species have underlying similarity even though they have very different functions
      • Characteristics in ancestral organisms are altered in descendants over time as they face different environmental conditions.
        • Forelimbs of mammals have the same basic skeleton but very different uses (human arm, whale flipper, bat wing)
  • Distribution of Species
    • At one time Earth's land masses were one large continent
    • Species may have originated in one area and as the continents split apart they can be found around the world, ie horses originated in North America where the oldest fossils of them can be found
  • DNA
    • Found in most living species
    • A common link and support of evolution
  • Extinction
    • Fossils and observations show, there are species that once existed that are no longer present
      • In some cases, ancestors of extinct species still exist



Essential knowledge 4.A.6 Interactions among living systems with their environment result in the movement of matter and energy- Nitrogen Cycle
Submitted by Jess

Biological importance:
  • Part of amino acids
  • Found in proteins and nucleic acids
  • Often a limiting plant nutrient
Forms available to life:
  • Plants can use two organic forms
    • Ammonium- NH4+
    • Nitrate- NO3-
  • Animals can only use organic forms
Reservoirs:
  • Atmosphere- 80% nitrogen
  • Soils
  • Sediments of rivers, lakes and oceans
  • Surface and ground water
  • Biomass of living organisms
Key Processes
  • The major pathway for nitrogen to enter the ecosystem is by nitrogen fixation
    • Conversion of N2 by bacteria into usable forms
  • Nitrogen fertilizer, precipitation, and blowing dust can also provide nitrogen to an ecosystem
  • Ammonification decomposes organic nitrogen into ammonium
  • Nitrification changes ammonium into nitrates
nitrogen cycle.jpg

Big Idea 1: Evolution (Submitted by Erin)
d.) Describe a limited set of given conserved features and core processes shared within and between domains of life (e.g. DNA, common metabolic pathways) as evidence of common ancestry.

Three Domains of life:
  • Bacteria
  • Eukarya
  • Archaea
Similarities
-all living organisms have the same genetic code (DNA and RNA)
-all living organisms use information stored in DNA to build lipids, proteins, and carbohydrates
-all living organisms undergo the process of DNA replication
-share similar metabolic pathways
-share similar enzymes
-similar cell structure

Textbook pages 13-14
Here is a helpful Mr. Anderson video:
https://www.youtube.com/watch?v=wGVgIcTpZkk

Big Idea 2: Organisms interact with their environments (Submitted by Erin)
c.) Predicting 1-2 consequences to organisms, populations, and ecosystems if sufficient free energy is not available

*Ecology chapters 52-56*

If there is insufficient energy flowing through a population of ecosystem…

  • Decrease in populations:
    • because there isn’t enough energy for these organisms to survive, many organisms will die off leading to a decrease in population size
    • due to a small population, there will be little variation in them gene pool
    • bottleneck affect: population size is reduced and the surviving population is no longer genetically representative

  • Competition:
    • due to the decrease in population, there will be competitions between the predators that preyed on that organism. Competition would lead to survival of the fittest. The stronger and more fit organisms will survive to reproduce.


If you need more help understanding the concept of ecosystems I recommend the video Mr. Anderson made: https://www.youtube.com/watch?v=Ot_KmOTYfRA


Big Idea 3: Cells (Submitted by Erin)
i.) Provided with electrochemical properties of several different molecules, make predictions about the permeability of the membrane to the molecules and describe several methods of transport across the membrane.

Not sure if anyone did this but I this is a topic that I definitely needed to review.
Textbook pages 132-138

THE CELL MEMBRANE HAS SELECTIVE PERMEABILITY

Diffusion: The movement of molecules of any substance so that they spread out evenly into the available space

Passive Transport
-does not require an input of energy
-net movement of molecules from HIGH concentration to LOW concentration

Osmosis
-the diffusion of water
-isotonic= no net movement
-hypertonic= water leaves the cell faster than it enters
-hypotonic= water enters the cell faster than it leaves

Facilitated Diffusion
-uses membrane transport proteins to help move charged polar molecules/ions through the membrane

Active Transport
-movement of a solute across a membrane against its gradient
-requires work (ATP)*

Exocytosis
-internal vesicles fuse with the plasma membrane to secrete large macromolecules out of the cell

Endocytosis
-the cell takes in macromolecules and particulate matter by forming new vesicles derived from membrane




Big Idea 2: Homeostasis (Submitted by Erin)

l.) Provided with a visual representation, explain with justification or make predictions of how alterations of the components in a negative or positive regulatory system can result in delirious consequences to the organism



Negative Feedback

-a loop in which the response reduces the initial stimulus

-prevents excessive pathway activity

-maintain homeostasis



Example of negative feedback: Control of Blood Glucose Levels**



Here is a link to a visual diagram of the process of negative feedback for blood glucose levels:

http://bio1152.nicerweb.com/Locked/media/ch45/homeostasis-glucose.html



NEGATIVE FEEDBACK:

Insulin

- Homeostasis is disrupted and blood glucose levels rise, a stimulus is sent

-the pancreas secretes the hormone insulin

-blood glucose levels decline

-homeostasis is reached and negatively feeds back to stop the secretion of insulin



Glucagon

- Homeostasis is disrupted and blood glucose levels decline

-stimulus is sent and the pancreas secretes the hormone glucagon

-blood glucose levels rise

-homeostasis is reached and negatively feeds back into the loop to stop the secretion of glucagon





If an alteration occurred that prevented negative feedback, the pancreas would continue to secrete insulin and the blood glucose levels would dangerously decline



If an alteration occurred that prevented negative feedback then the pancreas would continue to secrete glucagon and the blood glucose level would become dangerously high


Big Idea:
n) Describing how the nervous system detects external and internal stimuli and transmits signals along and between nerve cells. (Submitted by Sophia)

Neuron- a specialized cell of the nervous system
  • cell body- nucleus and organelles
  • Dendrites- cell extentions, receive incoming messages
  • Axons- transmit messages to other cells
  • Myelin sheath- covering the axon speeds transmission
  • Synapse- area between two neurons or neuron and muscle or gland
  • Nuerotransmitter- chemical messenger released into the synapse

external image images?q=tbn:ANd9GcTxd0L_DSc_oeU7YWtuj_y06OUjYaytCbSPnXQxNx_HTPtZjTMw3Q

Sensory receptors- cells that respond to stimuli from outside the body or from within the body
  • Usually specialize neurons or epithelial cells
  • Receives stimuli such as heat, light, pressure, chemicals, or information within the body such as blood pressure and body position

Sensory pathway
  • Reception- stimulus activates receptor cell
  • Transduction- change in membrane potential in the cell body (receptor potential)
  • Transmission- receptor potential triggers action potentials that travel along the neuron
  • Perception- action potentials reach the brain
external image nrurol.2011.194-f2.jpg

Generation of an action potential uses voltage- gated ion channels
  • Neuron begins at a resting state- Na and K channels
  • Depolarization- stimulis opens some Na channels, Na flows into the cell depolarizing the membrane, if it reaches threshold it reaches an action potential
  • Rising phase of the action potential- depolarization opens most sodium channels, incoming Na makes the inside of the membrane positive
  • Falling phase of the action potential- most sodium channels inactivated, blocking Na inflow, most potassium channels open allowing K outflow, cell becomes negative again
  • Undershoot- sodium channels are closed some potassium channels still open, as they close sodium channels become unblocked and membrane returns to resting state


Big Idea 3: Molecular Genetics (Submitted by Erin)
a.)Explaining how the structural features of DNA and RNA allow heritable information to be replicated, stored, expressed, and transmitted to future generations

DNA
  • double-stranded helix
    • allows for the transmission of heritable information
    • stores an organisms genetic material
    • using each stand as a template for RNA replication
    • densely compacted into chromosomes
    • provide a template for sequencing of amino acids that bond together to make proteins
  • formed by hydrogen bonds
  • four nucleotide bases (A,T,C,G)
    • backbone of DNA
    • base order codes informations
    • Adenine + Guanine = purines
    • Thymine + Cytosine = pyrimidines
  • Sugar-phosphate chains
  • DNA is polar
    • 5’ end and 3’ end


dnastructure.jpg

RNA
  • A copy of DNA
  • Has a phosphate group, ribose sugar and nitrogenous bases
  • Single stranded
  • Travels outside of the nucleus for protein synthesis
    • Messenger RNA: caries DNA message out of nucleus to ribosomes
    • Ribosomal RNA: decodes mRNA into amino acids
    • Transfer RNA: delivers individual amino acids to the ribosomes during protein synthesis

Mr. Anderson video:
http://www.youtube.com/watch?v=q6PP-C4udkA



Big 3: Genetics (Submitted by Erin)
h.) Describe two processes that increase genetic variation and explaining how genetic variation allows for natural selection within a population.

Mutations
  • Primary source of genetic variation
  • Can be positive or negative based on the environmental context
  • Errors in DNA replication and external factors can cause mutations
    • Point: chemical changes in a single base pair of a gene
      • Subtitutions
    • Insertions: additions of nucleotide pairs in a gene
    • Deletions: losses of nucleotide pairs in a gene

Mitosis
  • Provides genetic variation
  • Half of the chromosomes are inherited from mother and other half is inherited from the father

mitosis.jpg



Mr. Anderson Genetic video:
http://www.youtube.com/watch?v=NWqgZUnJdAY



LO 2.13) The student is able to explain how internal membranes and organelles contribute to cell functions. (Chloroplasts and Mitochondria)

Submitted by Maddie



Chloroplasts-

Outer Membrane~ Contain and protect the inner parts of the membrane

Inner Membrane~ Contain and protect the inner parts of the membrane

Stroma~ area inside the chloroplast where sugars are created, Calvin cycle occurs here

Thylakoid Membrane~ have chlorophyll molecules attached to surface, light reactions occur here



chloroplast.jpg



Mitochondria-

Outer Membrane~ covers and contains the organelle

Inner Membrane~ folds over many times forming cristae, electron transport chain is here (chemiosmosis pumps H+ across inner membrane into matrix)

Matrix~ fluid inside the mitochondria, citric acid cycle takes place here

      • Glycolysis** takes place in the cytosol


external image c9x6cell-respiration.jpg


Big Idea 2: Energy (Submitted by Erin)
e.) Refining or revising a visual representation to more accurately depict the light-dependent and light-independent reactions of photosynthesis and the dependency of the processes in the capture and storage of free energy


light-reaction1.jpg

Photosynthesis
  • Chlorophylls absorb free energy from light
  • Thylakoid membrane
    • Flow of electrons through Photosystems I and II through the electron transport chain
    • Chemiosmosis
    • Electrochemical gradient of hydrogen ions across the thylakoid membrane established
      • ATP synthase
      • Synthesis of ATP from ADP and phosphate
        • Calvin Cycle
Stroma of the chloroplast



LO 4.13) The student is able to predict the effects of a change in the communities populations on the community.
Submitted by Maddie

The human population has increased greatly in numbers, and in turn, has reduced other populations sizes, caused habitat destruction, and caused the extinction of certain species.

Recently, however, there has been a demographic transition, or a shift in a population with high birth rates and low death rates to a population with high death rates and low birth rates.
  • may take 150 years to complete

Carrying capacity for humans is not known
  • Ecological footprint- total land and water needed for all the resources a person consumes in a population
    • Now, it's 1.7 hectares per person

The changes in this population may effect the rest of the community (group of populations of different species living close enough to interact)
Interspecific Interactions-
Positive (+) Mutualism (symbiotic relationship that benefits both organisms)
Predation (one species eats the other species) is a +/-, so is herbivory and parasitism (symbiotic relationship where one gains)
Negative (-) Competition (resources are in short supply) is a -/-
Neutral (0) Commensalism (symbiotic relationship where on species benefits but the other is neither harmed nor helped)

Human activities also effect not only communities but also most chemical cycles on Earth
  • Acid precipitation- precipitation with a pH less than 5.6~ caused by burning fossil fuels
  • Biological Magnification- toxins become more concentrated
  • Greenhouse Effect- absorption of heat the Earth experiences due to certain atmospheric gases~ caused by burning of fossil fuels,etc.

Here's a helpful Mr. Anderson video: Biochemical Cycling

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