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

Genetic information provides for continuity of life and, in most cases, this information is passed from parent to offspring via DNA. The double-stranded structure of DNA provides a simple and elegant solution for the transmission of heritable information to the next generation; by using each strand as a template, existing information can be preserved and duplicated with high fidelity within the replication process. However, the process of replication is imperfect, and errors occur through chemical instability and environmental impacts. Random changes in DNA nucleotide sequences lead to heritable mutations if they are not repaired. To protect against changes in the original sequence, cells have multiple mechanisms to correct errors. Despite the action of repair enzymes, some mutations are not corrected and are passed to subsequent generations. Changes in a nucleotide sequence, if present in a protein-coding region, can change the amino acid sequence of the polypeptide. In other cases, mutations can alter levels of gene expression or simply be silent. In order for information in DNA to direct cellular processes, information must be transcribed (DNA→RNA) and, in many cases, translated (RNA→protein). The products of transcription and translation play an important role in determining [[#|metabolism]], i.e., cellular [[#|activities]] and phenotypes. Biotechnology makes it possible to directly engineer heritable changes in cells to yield novel [[#|protein]] products.

In eukaryotic organisms, heritable information is packaged into chromosomes that are passed to daughter cells. Alternating with interphase in the cell cycle, mitosis followed by cytokinesis provides a mechanism in which each daughter cell receives an identical and a [[#|complete]] complement of chromosomes. Mitosis ensures fidelity in the transmission of heritable information, and production of identical progeny allows organisms to grow, replace cells, and reproduce asexually.

Sexual reproduction, however, involves the recombination of heritable information from both parents through fusion of gametes during fertilization. Meiosis followed by fertilization provides a spectrum of possible phenotypes in offspring and on which natural selection operates.

Mendel was able to describe a model of inheritance of traits, and his work represents an [[#|application]] of mathematical reasoning to a biological problem. However, most traits result from interactions of many genes and do not follow Mendelian patterns of inheritance. Understanding the genetic basis of specific phenotypes and their transmission in humans can raise social and ethical issues.

The expression of genetic material controls cell products, and these products determine the [[#|metabolism]] and nature of the cell. Gene expression is regulated by both environmental signals and developmental cascades or stages. Cell signaling mechanisms can also modulate and control gene expression. Thus, structure and function in biology involve two interacting aspects: the presence of necessary genetic information and the correct and timely expression of this information.

Genetic information is a repository of instructions necessary for the survival, growth and reproduction of the organism. Changes in information can often be observed in the organism due to changes in phenotypes. At the molecular level, these changes may result from mutations in the genetic material whereupon effects can often be seen when the information is processed to yield a polypeptide; the changes may be positive, negative or neutral to the organism. At the [[#|cellular]] level, errors in the transfer of genetic information through mitosis and meiosis can result in adverse changes to cellular composition. Additionally, environmental factors can influence gene expression.

Genetic variation is almost always advantageous for the long-term survival and evolution of a species. In sexually reproducing organisms, meiosis produces haploid gametes, and random fertilization produces diploid zygotes. In asexually reproducing organisms, variation can be introduced through mistakes in DNA replication or [[#|repair]] and through recombination; additionally, bacteria can transmit and/or exchange genetic information horizontally (between individuals in the same generation). Viruses have a unique mechanism of replication that is dependent on the host metabolic machinery. Viruses can introduce variation in the host genetic material through lysogenesis or latent infection.

To function in a biological system, cells communicate with other cells and respond to the external environment. Cell signaling pathways are determined by interacting signal and receptor molecules, and signaling cascades direct complex behaviors that affect physiological responses in the organism by altering gene expression or protein activity. Nonheritable information transmission influences behavior within and between cells, organisms and populations; these behaviors are directed by underlying genetic information, and responses to information are vital to natural selection and evolution. Animals have evolved sensory organs that detect and process external information. Nervous systems interface with these sensory and internal body systems, coordinating response and behavior; and this coordination occurs through the transmission and processing of signal information. Behavior in the individual serves to increase its fitness in the population while contributing to the overall survival of the population.


  • Quorum Sensing (submitted by Mrs. McLoughlin)

I noticed quorum sensing came up in a couple of different places as an example.


Essential Knowledge 3D1: Cell communication processes share common features that reflect a shared evolutionary history.
In single-celled organisms, signal transduction pathways influence how the cell responds to its environment.

Also:
Concept 2E2: In fungi, protists, and bacteria, internal and external signals regulate a variety of physiological responses that synchronize with environmental cycles and cues.

Concept 4B2: Interactions among cells of a population of unicellular organisms can be similar to those of multicellular organisms and these interactions lead to increased efficiency and utilization of energy and matter.

Summary of Quorum Sensing ( Text p. 207)

It is a type of cell communication. Bacterial cells secrete small molecules that can be sensed by other bacterial cells of the same species, This allows the bacteria to sense density and allows members of bacterial population to coordinate activities.
An example is that slime molds can form biofilms to give rise to fruiting bodies in response to environmental stressors.
This shows that cell signalling evolved in prokaryotes.

  • Here is a link to the original video you watched on this. Although we watched it as an example of cell signalling, it also contains a great example of symbiosis.

http://www.ted.com/talks/bonnie_bassler_on_how_bacteria_communicate.html

Essential Knowledge 3B1: A variety of intercellular and intracellular signal transmissions mediate gene expression.

Here is a link to a fascinating recent article on cell signalling and its role in development.

http://www.hhmi.org/news/nusse20130321.html

  • MicroRNAs - Submitted by Maddy Harmon
Appendix A- Big Idea 2- part Q
concept 18.3- noncoding rnas play multiple roles in controlling gene expression (pages 365-366)

MicroRNAs are small single stranded rna pieces that function to inhibit the production of certain proteins, or degrades the mRNA. as mRNA is synthesizing proteins, MicroRNAs can bind to the tagrget mRNA at the template strand, and then either degrade or block them. they regulate up to 1/3 of all human genes, but no one knew what they were (grouped in with other "junk" dna)

this video doesnt have sound but i seriously went "oohhh okay" when i watched it)
http://www.youtube.com/watch?v=_-9pROnSD-A

  • Receptor Tyrosine Kinases- Submitted by Maddy Harmon
appendix a- big idea 3 part m
concept 11.2 - Reception: A signaling molecule binds to a receptor protein, causing it to change its shape. page 212

Receptor Tyrosine Kinases fall under the broader term protein kinases or just kinases, which are enzymes that work by transfering phospahte molecules. Receptor Tyrosine Kinases (membrane receptors that transfer phosphates to tyrosine) are activated when a liagnd (small signal molecule en route to a target cell) binds to receptors outside the cell's membrane. most RTKs exist as separate but coordinated polypeptides. when a ligand binds to them, they join to create a dimer. the dimer then adds phosphates to each of the tyrosines on the RTK polypeptide. it is now fully activated (or phosphorylated), and can activate multiple cell responses simultaneously (when signaling proteins inside the cell bind to it), making it invaluable to amplifying cell response.

a swell stop animation video of receptor tyrosine kinases, its kinda long but its really good and at the end of the "acts" it explains what exactly happened.
http://www.youtube.com/watch?v=nUGGENKyUcA

  • Nervous System Reflexes (page 1066) By Jake Barry
Appendix A, Big Idea #3, Letter O: Nervous system components that work together to lead to a response.

A Reflex is the bodies automatic response to certain stimuli. Reflexes are automatic meaning that the spinal cord acts directly upon them, so they do not require the time of the brain interaction. The knee Jerk reflex is initiated by tapping the tendon connected to the quad muscle. Sensors detect a sudden strech in the quad. Sensory neurons convey the info to the spinal cord. in reponse to the signal, motor neurons convey signals tot he quad, causing it to convey and jerking the lower leg forward. Sensory neurons also communicate with interneurons in the spinal cord. The interneurons inhibit motor neurons that lead to the hamstring. This inhibition prevents contraction of the hamstring, which would resist the action of the quad. The sensory and motor neurons are very long in the leg, allowing them to recieve and pass the message directly, which makes for a very quick reaction. The interneuron is in a place where it can easily inhibit the hamstring, and is short because it does not need to carry a message a long distance.


Knee-Jerk and Eye Blink reflex video


Owen Gaffney
C: Justify the effects of the change in the cell cycle mitosis and/or meiosis will have on chromosome structure, gamete viability, genetic diversity and evolution.
(Chapter 12 page 228-242)
A change in the cell cycle can happen at any point. If certain checkpoints along the cell cycle not properly work cancerous cells can form. Cancer cells do not exceed the normal signals that regulate the cell cycle. They divide excessively and invade other tissues; if unchecked they can kill the organism. In addition to their lack of density dependent inhibition and Anchorage dependents cancer cells do not stop dividing when growth factors are depleted. Illogical hypothesis is that cancer cells do not need growth factor in the culture medium to grow and divide. They may make a required growth factor themselves or they may have an abnormality in the signaling pathway that conveys the gross factors signal to the cell cycle control system even in the absence of the factor. Another possibility is an abnormal cell cycle control system. Cancer is a specific change in the cell cycle wear something in the genetic code is altered or checkpoint is missed and alters the organism. If tumors form and gamete cells or cancerous cells form such gametes maybe come inviable. Although mutations are one of the major components to genetic diversity such mutations the resulting cancers can often kill off the organism that displays new or helpful mutations. The change in the cell cycle such as cancer ends up killing an organism which genes cannot be passed out however research has shown that there is a genetic predisposition cancers and that they may be passed on unknowingly to offspring.


Owen Gaffney
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.
(Chapter 13 page 258)
In species that reproduce sexually the behavior of chromosomes during meiosis and fertilization is responsible for most of the variation that arises each generation. One aspect of sexual reproduction that generates genetic variation is the random orientation of monodisperse chromosomes metaphase of meiosis one. Because each homologous pair of chromosomes is positioned independently of the other pair the first malic division results and each pair sorting it's maternal and paternal homologues into daughter cells independently of every other part this is called independent assortment. As a consequence of the independent assortment of chromosomes during meiosis each of us produce a collection of gametes differing greatly in the combinations of chromosomes would inherit from our two parents. This produces recombinant chromosomes individual chromosomes I carry genes derived from two different parents. Finally random fertilization adds to the genetic variation arising from meiosis. If something goes wrong and meiosis save during crossing over and offspring can have much different phenotypes. And a single crossing over the specific proteins orchestrate an exchange of corresponding segments of two nonsister chromatin one maternal and one paternal chromatid of homologous pair. Hey chiasma forms as the result of crossing over occurring wall sister chromatid cohesion is present along the arms. Tasman to hold homologs goats together as the spindle forms for the first mounted division the release of cohesion one sister chromatin arms allows homologs to separate. If crossing over does not occur between two nonsister chromatids for the separation is altered in someway offspring can be altered. They may possess more traits from a parent either maternal or paternal. If things go very wrong human genetic disorders can occur. As seen in trisomy 21 or down syndrome the 21st chromosome is not properly independently assort.

Reflex Video and Explanation


  • Degrees of Dominance by Brian Millham (pg. 271-272)
Appendix A letter E
When Mendel was experimenting with peas he noticed that when he crossed them the F1 offspring always looked like one of the two parental varieties. This is considered complete dominance because one allele takes over and presents itself over the second allele. In other crosses, neither allele is completely dominant and the F1 offspring have a phenotype in the middle of each of the parents. This is incomplete dominance and an example of this is when a red flower is crossed with a white flower and produces a pink F1 offspring. The last degree of dominance is codominance and is when the two alleles both affect the phenotype in separate, distinguishable ways.

This is just a review on Mendelian Genetics
http://www.youtube.com/watch?v=NWqgZUnJdAY

Abnormal Chromosome number by Brian Millham (297)
Appendix A letter D
nondisjunction which the members of a pair of homologous chromosomes do not move apart properly during meiosis I or sister chromatids fail to separate during meiosis II. One gamete receives two of the same type of chromosome and another gamete receives no copy.
external image 15_12Nondisjunction_L.jpg



  • DNA and RNA Viral Evolution (page 387-390) By: Christina Dykas
Appendix A Big Idea 3 Letter j

There are 6 main stages to the life cycles of DNA and RNA viruses. They begin with Attachment which is when the virus binds to specific molecules on the surface of cells. Penetration follows and the virus enters the cell either by fusion or endocytosis. Inside the cell, the capsid of the virus is Removed and the viral DNA or RNA is exposed. Viral messenger RNA is used to produce viral proteins in Replication and the cell produces the DNA or RNA. Assembly is the next step where the new proteins and nucleic acids combine to form new viruses. The final process is Release and the new viruses are expelled from the cell.
Viruses are not living organisms, but do have an evolutionary connection due to their genetic code. Viruses most likely evolved after the first cells appeared and originated from pieces of nucleic acids that moved from one cell to another. Since viruses reproduce quickly and have a short generation time, they can evolve fairly quickly. An example of this would be the influenza virus which evolves to be resistant to vaccines and new vaccines need to be made.
external image INF_HIV_life_cycle_PE.gif


  • Meiosis By: Kayla Kaufmann
  • Text Pages (250-258)
Essential knowledge 3.A.2: In eukaryotes, heritable information is passed to the next generation via processes that include the cell cycle and mitosis or meiosis plus fertilization.
  • Meiosis is a reduction division (because it reduces the number of chromosome sets in a cell), followed by fertilization that helps to create genetic diversity in sexually reproducing organisms
  • Meiosis makes it so that each gamete (Sex cell… Example: sperm and ova) receives one complete haploid (1n) set of chromosomes instead of a full set (diploid) like in mitosis
  • Like mitosis, meiosis is preceded by the replication of DNA but in meiosis the replication is followed by two stages of cell division rather than one, meiosis I and meiosis II. Four daughter cells result from meiosis and they each have half as many chromosomes as the parent cell.
  • The phases of meiosis include Prophase I, Metaphase I, Anaphase I, Telophase I and Cytokinesis, Prophase II, Metaphase II, Anaphase II, Telophase II and Cytokinesis. The specifics of each step do not need to be known for the AP test.
Important Information you should know about the process of meiosis!!

  • During meiosis, homologous chromosomes are paired. One homologue originates from the maternal parent (mother), and the other from the paternal parent (father)
  • Orientation of these chromosome pairs is random with respect to the cell poles
  • When these homologous chromosomes separate, it makes it so each gamete receives a haploid set composed from the chromosomes of the mother and the father
  • The homologous chromosomes exchange genetic material by the process of crossing over during meiosis and this results in increased genetic variation in the gametes.

How do cells become diploid again?
  • Fertilization is the fusion of two gametes and the diploid number of chromosomes is restored during this process.

Check out this Diagram of meiosis and these two Bozeman YouTube Videos. One titled meiosis and the other a simulation of the process.

Meiosis

Simulation

external image Meiosis_diagram.jpg

  • Genetic Disorders By: Kayla Kaufmann
  • Text Pages (pg 278 pg 471)
Essential knowledge 3.A.3:The chromosomal basis of inheritance provides an understanding of the pattern of passage (transmission) of genes from parent to offspring.

Main Idea: Certain human genetic disorders can be attributed to the inheritance of single gene traits

An example I will use to explain this concept is sickle cell disease

A change in as little as one base in a gene, a point mutation, can have a huge impact on phenotype as seen in sickle cell disease
  • Sickle cell disease is a group of disorders that affects hemoglobin, the molecule in red blood cells that delivers oxygen to cells throughout the body. People with the disorder have abnormal hemoglobin molecule. This causes red blood cells to be sickle shaped resulting in many issues like anemia.
  • Sickle cell disease is an autosomal recessive disease, which means both copies of the gene in each cell have mutations. Two copies of an abnormal gene must be present in order for the disease to develop. The individual must receive the recessive allele from both parents, so it must be inherited from both mom and dad. If only one recessive or sickle cell gene is inherited and a normal dominant allele, the individual will have the sickle cell trait but not the disease.
  • The parents of an individual with an autosomal recessive condition each carry one copy of the mutated gene
  • Mutations in the HBB gene causes sickle cell disease

Check out this quick video on Sickle Cell disease
Sickle Cell Disease

  • The Cell Cycle by Grace Goodfellow
Appendix A: Essential knowledge 3.A.2: In eukaryotes, heritable information is passed to the next generation via processes that include the cell cycle and mitosis or meiosis plus fertilization.


The cell cycle consists of four distinct phases: G1 phase, S phase (synthesis), G2 phase (collectively known as interphase) and M phase (mitosis). M phase is itself composed of two tightly coupled processes: mitosis, in which the cell's chromosomes are divided between the two sister cells, and cytokinesis, in which the cell's cytoplasm divides in half forming distinct cells. Activation of each phase is dependent on the proper progression and completion of the previous one. Cells that have temporarily or reversibly stopped dividing are said to have entered a state of quiescence called G0 phase.
  • Phases:

State
Description
Abbreviation
Processes taking place
Quiescent/Senescent
Gap 0
G0
A resting phase where the cell has left the cycle and has stopped dividing
Interphase
Gap 1
G1
Cells increase in size. The G1 checkpoint control mechanism ensures that everything is ready for DNA synthesis
Interphase
Synthesis
S
DNA replication takes place
Interphase
Gap 2
G2
During the gap between DNA synthesis and mitosis, the cell will continue to grow. The G2 checkpoint control mechanism ensures that everything is ready to enter the M (mitosis) phase and divide
Cell division
Mitosis
M
Cell growth stops at this stage and cellular energy is focused on the orderly division into two daughter cells. A checkpoint in the middle of mitosis (Metaphase Checkpoint) ensures that the cell is ready to complete cell division

After cell division, each of the daughter cells begin the interphase of a new cycle. Although the various stages of interphase are not usually morphologically distinguishable, each phase of the cell cycle has a distinct set of specialized biochemical processes that prepare the cell for initiation of cell division.

Cell_Cycle_2-2.svg.png

Great video on the cell cycle, meiosis, and mitosis by the one and only... Mr. Anderson!
http://www.youtube.com/watch?v=2aVnN4RePyI



  • Operons by Amanda Seale

Essential knowledge 3.B.1: Gene regulation results in differential gene expression, leading to cell specialization.

An operon is a unit of genetic function that is found in bacteria and phages. It consists of an operator, a promoter, and the genes they control. A segment of DNA that acts as a switch to put the genes under coordinate control is called an operator. A single on-off “switch” can control a whole cluster of genes that are functionally related. A promoter is a specific nucleotide sequence in DNA that binds RNA polymerase, positioning it to start transcribing RNA at the appropriate place. A protein called a repressor inhibits this gene transcription. In a prokaryote, the repressor will bind to the DNA in or near the promoter in an effort to inhibit transcription. In a eukaryote, the repressors can bind to control elements within enhancers to activators, or to other proteins in a way that manages to block activators from binding to DNA. A repressor protein is operator and operon specific. A co-repressor is a small molecule that can be used to cooperate with a repressor protein to switch an operon off.
An example of how the switch works can be made using the trp operon found in the E. coli genome. This operon is turned on by itself- an RNA polymerase can bind to the genes of the operon at any time. The trp repressor protein can be used to switch off the operon. The repressor blocks the attachment of RNA polymerase to the promoter, which prevents the transcription of genes. In this particular example, tryptophan works as a co-repressor molecule that accumulates and associates with trp repressor molecules, which can then bind to the trp operator and shutdown tryptophan pathway enzyme production.


A more interesting rendition of how the trp operon works: Mr. Anderson-
http://www.bozemanscience.com/031-gene-regulation

bio1.jpg








  • Regulation of the Cell Cycle by Grace Goodfellow
Appendix A: Essential knowledge 3.A.2: In eukaryotes, heritable information is passed to the next generation via processes that include the cell cycle and mitosis or meiosis plus fertilization. (#3)

Regulation of the cell cycle involves processes crucial to the survival of a cell, including the detection and repair of genetic damage as well as the prevention of uncontrolled cell division. The molecular events that control the cell cycle are ordered and directional; that is, each process occurs in a sequential fashion and it is impossible to reverse the cycle.


  • Controlling the cell cycle
    • Upon receiving a pro-mitotic extracellular signal, G1 cyclin-CDK complexes become active to prepare the cell for S phase, promoting the expression of transcription factors that then promote the expression of S cyclins and of enzymes required for DNA replication
    • Active S cyclin-CDK complexes phosphorylate proteins that make up the pre-replication complexes assembled during G1 phase on DNA replication origins
      • This ensures that every portion of the cell's genome will be replicated only one time
    • Prevent gaps in replication because daughter cells that are missing all or part of crucial genes will die
      • APC also targets the mitotic cyclins for degradation, ensuring that telophase and cytokinesis can proceed

  • Cyclin-dependent protein kinases (Cdks)
    • Enzymes thatadd negatively charged phosphate groups to other molecules in a process called phosphorylation. Through phosphorylation, Cdks signal the cell that it is ready to pass into the next stage of the cell cycle. As their name suggests, Cyclin-Dependent Protein Kinases are dependent on cyclins, another class of regulatory proteins. Cyclins bind to Cdks, activating the Cdks to phosphorylate other molecules.
  • Cyclins
    • Undergo a constant cycle of synthesis and degradation during cell division.
    • When cyclins are synthesized, they act as an activating protein and bind to Cdks forming a cyclin-Cdk complex. This complex then acts as a signal to the cell to pass to the next cell cycle phase. Eventually, the cyclin degrades, deactivating the Cdk, thus signaling exit from a particular phase.
    • There are two classes of cyclins: mitotic cyclins and G1 cyclins.


19_41.jpg


http://www.youtube.com/watch?v=l--sYuM1iTs






  • Appendix A, Big Idea 3, A
by Maeve Dalpe

In 1953, James Watson and Francis Crick proposed a double helical model for deoxyribonucleic acid (DNA). The role of DNA in heredity was first worked out by studying bacteria and the viruses that infect them.Biochemist Erwin Chargaff knew DNA polymerized nucleotides each with a nitrogenous base, deoxyribose, and a phosphate group. But by analyzing base composition, in 1950, he noted that base composition varies from one species to another. "30.3% of human DNA nucleotides have the base A, whereas DNA from the bacterium E. Coli has only 26.0% A." This evidence of molecular diversity made DNA a credible "candidate" for genetic material. He found the two pairs of bases A and T, then C and G were present almost as much as the other. (A = 30.3% T = 30.3%)(C = 19.9% G = 19.5%). These rules all made sense with the discovery of the double helix. (pg 311)

Replication of DNA begins at the origin of replication sites: short stretches of DNA with specific nucleotide sequences.Proteins attach to the DNA, separating the two strands and forming a replication bubble (pg 313). At the end of the replication bubble(s) is a replication fork where the parental strands of DNA are being unwound. Helicase enzymes help this unwinding by separating the parental strands and making them into template strands. After, single-strand binding proteins bind to the unpaired DNA strands to stabilize them. The untwisting of the DNA causes strain and must be relieved by topoisomerase. THe RNA chain called a primer is synthesized by the enzyme primase. Primase starts as an RNA chain from a single RNA nucleotide and adds more, one at a time, using the parental DNA as a template (pg 314).



Concept e: Why certain traits don’t follow Mendel’s mode of inheritance (linked genes)
By Kenna Garrison (p. 292-296)

Normally, to determine the expected number of offspring for each phenotype, Punnett squares can be used. However, when two genes are located on the same chromosome, called linked genes, the results will deviate from those expected from Mendel’s law of independent assortment.

For example: If gray body and normal wings are dominant over black body and vestigial wings in fruit flies, and a heterozygous gray bodied and normal winged fly mates with a black bodied vestigial winged fly, the following punnett square would show he expected offspring:

AB Ab aB ab

ab AaBb Aabb aaBb aabb

This shows that ¼ of the offspring would be expected to be gray/normal, gray/vestigial, black/normal, and black/vestigial.

However if the results are 205 gray/normal, 52 gray/vestigial, 50 black/normal, and 210 black/vestigial, it would indicate that the genes are linked. The gray/vestigial and black/normal flies would have been produced through crossing over during meiosis, but most of the time the two traits stayed together.

Genetics Topics Review By: Kohl Romeiser

Appendix A; Big Idea #3; H.) Predict how various types of change in a DNA sequence can alter a phenotype, and describe several using real world examples.

Genetic Mutation: Variations in a gene that modify, seriously disrupt, or prevent the functioning the encoded protein

Polymorphism: A DNA change within a gene that may or may not alter the protein that is encoded by the gene. If the change contributes to normal genetic variability and is found in more than 1 percent of the population then it is a polymorphism.

Homozygous: If each parent transmits the same gene sequence to an offspring for example (AA), the offspring if homozygous.


Heterozygous: If each parent transmits two different gene sequences to an offspring for example (Aa), the offspring is heterozygous
.
Mutations can cause a change in phenotype only if the mutated gene codes for a protein that alters the phenotype. For example, a mutation in the MC1R gene will only cause the phenotype for red hair in humans if the carrier is homozygous recessive for the genotype.


Another example of a recessive phenotype in humans is albinism: “The genes for OCA are located on “autosomal” chromosomes. Autosomes are the chromosomes that contain genes for our general body characteristics, contrasted to the sex chromosomes. We normally have two copies of these chromosomes and the genes on them – one inherited from our father, the other inherited from our mother. Neither of these gene copies is functional in people with albinism. However, albinism is a “recessive trait”, so even if only one of the two copies of the OCA gene is functional, a person can make pigment, but will carry the albinism trait. Both parents must carry a defective OCA gene to have a child with albinism. When both parents carry the defective gene (and neither parent has albinism) there is a one in four chance at each pregnancy that the baby will be born with albinism. This type of inheritance is called “autosomal recessive” inheritance.http://www.albinism.org/publications/what_is_albinism.html

Crossing over: Crossing over of chromosomes happens when two sister homologous chromosomes exchange genetic material creating genetic recombination. This swapping of genetic material leads to variation in offspring, regardless of the parental phenotype.
This website gives a good explanation of crossing over: http://www.execulink.com/~ekimmel/crossing_over.htm

Cell to Cell Communication By: Kohl Romeiser

Appendix A; Big Idea #3; L.) Using appropriate examples from plants, animals, and bacteria, justify how the features of cell-to-cell contact and the use of chemical signals allow communication over short and long distances.

Hormones: One of many types of secreted chemicals that are formed in specialized cells, travel in body fluids, and act on specific target cells in other parts of the body to change their functioning. Only target cells will respond to chemical messages from hormones. Hormones have the incredible ability to facilitate a large response throughout an organism.

Lipid Based: Has the ability to pass through hydrophobic membranes and interact directly with the cytoplasm of target cells.

Protein Based: Requires a second messenger. Binds to receptor kinases/ligands on cell membrane and facilitates a change within the cell causing a change. Cannot pass through the cell membrane directly, like lipid based hormones.

Quorum Sensing in Bacteria: A system of stimulus and response that correlate to the density of a population. In bacteria, the use of cell to cell signaling molecules and receptors between the populations of bacteria can create a group wide response. When a signaling molecule binds to a receptor on the surface of the bacteria, transcription of specific genes induces a response.

Neurotransmitters: All organisms with a nervous system have neurotransmitters. Neurotransmitters are the chemicals which allow the transmission of signals from one neuron to the next across synapses. They are also found at the axon endings of motor neurons, where they stimulate the muscle fibers. Neurotransmitters work by long distance messaging and can send signals throughout the body of the organism.

Signal Transduction Pathway: An organism’s ability to amplify cell signaling for a mediated response. Hormones for examples can cause a cascading effect and amplify their message throughout the organism.


external image signal_transduction.jpg




Concept b: the manipulation of heritable information (genetic engineering)

By Kenna Garrison (p. 417, 817)


Genetic engineering is the manipulation of genes for practical purposes. Two major uses of genetic engineering are gene therapy and genetically modified crops.

Gene therapy is introducing genes into an afflicted individual for therapeutic purposes. This method holds great potential for treating disorders traceable to a single defective gene. A normal allele of a defective gene could be inserted into the somatic cells of the tissue affected by the disorder.

Genetically modified crops have been used to make plants have a longer growing season, have extra nutrients, and just grow more efficiently. While there are many positives to using genetically modified crops, but it is also possible that they could harm human and environmental health.


Different kinds of chemical signaling (pages 208-209) – Gabriela Christian
Essential knowledge 3.D.2: cells communicate with each other through direct contact with other cells or from a distance via chemical signaling

Cell-to-cell contact: Animals and plants both have cell junctions that directly connect the cytoplasms of adjacent cells. Therefore, signals dissolved in one cell’s cytosol can pass freely to the next cell. Cell to cell recognition also occurs when animal cells communicate via direct contact between their membrane-bound cell surface molecules. This is analogous to giving a post-it note to someone directly.

Short distances: In this type of cell signaling, messenger molecules called local regulators are secreted by the signaling cell and travel short distances to influence the cells nearby. These include growth factors in animals, which stimulate target cells to grow and divide. An example of this type of signaling is a neuron, which releases neurotransmitters that cross a synapse to the next target neuron. This is analogous to sending an email.

Long distances: In endocrine signaling, signaling cells release hormone molecules, which travel through the circulatory system to the target cells all throughout the body. Hormones vary widely in their size and type. Therefore, an example of long distance signaling is when a hormone signal is released from the brain and travels throughout the body, to numerous target cells. This is analogous to a Facebook status.

http://www.youtube.com/watch?v=xnGXItWrJ3k



Signal Pathway Through the Neuron– Gabriela Christian (pgs. 1050-1051, 1054-1055)

Essential knowledge 3.E.2: Animals have nervous systems that detect external and internal signals, transmit and integrate information, and produce responses.

There is a concentration gradient for both the potassium ions and the sodium ions across the plasma membrane of a neuron. These gradients are maintained by sodium-potassium pumps, which use ATP energy to actively transport Na+ out of the cell and K+ into the cell. There are also ion channels in the membrane, which have selective permeability. For example, a potassium channel allows K+ to diffuse freely, but not other ions like Na=. When a neuron is at rest, many potassium channels are open while very few sodium channels are open.

There are many stages in creating an action potential of a neuron. Before, at resting potential, most voltage-gated sodium and potassium channels are closed, but some potassium channels are open. When a stimulus depolarizes the membrane, some sodium channels open, allowing Na+ to diffuse into the cell. This causes further depolarization, opening more sodium channels (positive feedback). However, voltage-gated sodium channels inactivate soon after opening, stopping Na+ inflow, and more potassium channels open, causing a rapid outflow of K+. Finally, when the membrane’s permeability to K+ is higher, the gated potassium channels close, and the membrane potential returns to the resting potential.

A second depolarizing stimulus occurs as the sodium channels remain inactivated, but is unable to trigger an action potential. This is called the refractory period. This ensures that all signals in an axon travel in one direction, from the cell body to the axon terminals.

voltage-gated_ion_channels.jpg
voltage-gated_ion_channels.jpg




3.A.1: DNA and in some cases RNA is the primary source of heritable information
By Maggie Garrahan

Genetic information is transmitted from one generation to the next through DNA or RNA.

1. DNA replication ensures continuity of hereditary information.

A. Replication is a semiconservative process; that is, one strand serves as the template for a new, complementary strand.

B. Replication requires DNA polymerase plus many other essential cellular enzymes, occurs bidirectionally,and differs in the
production of the leading and lagging strands.

2. Both DNA and RNA have three components — sugar, phosphate and a nitrogenous base —which form nucleotide units that are connected by covalent bonds to form a linear molecule with 3' and 5' ends, with the nitrogenous bases perpendicular to the sugar-phosphate backbone.
3. The basic structural differences include:

A. DNA contains deoxyribose (RNA contains ribose).

B. RNA contains uracil in lieu of thymine in DNA.

C. DNA is usually double stranded, RNA is usually single stranded.

D. The two DNA strands in double-stranded DNA are antiparallel in directionality.

4. Both DNA and RNA exhibit specific nucleotide base pairing that is conserved through evolution: adenine pairs with thymine or uracil (A-T or A-U) and cytosine pairs with guanine (C-G).
A. Purines (G and A) have a double ring structure.

B. Pyrimidines (C, T and U) have a single ring structure.

5. The sequence of the RNA bases, together with the structure of the RNA molecule, determines RNA function.


Genetic information flows from a sequence of nucleotides in a gene to a sequence of amino acids in a protein.

Heritable information is passed to the offspring by a sperm and egg combining. The chromosomes contain DNA which contains all the information the offspring needs. A chromosome is made up of a long molecule of DNA, which includes thousands of individual genes that transmit inherited traits. Genes encode information for making molecules in the cell. Encoded by genes, proteins determine cell function, activity, and maintenance. Inside each cell is all the information that it needs to carry out the basic life processes of growth, maintenance, and reproduction, or whatever processes that the cell is responsible for (nerve cells conduct nerve impulses, etc). Cells need to be able to code and store this information so that all of their offspring will also contain all the information necessary. This information is coded on DNA and some cases RNA



Example: https://www.boundless.com/biology/introduction-to-biology/themes-in-biology/heritable-information-is-contained-in-dna/

http://plato.stanford.edu/entries/heredity/

http://campbell-book.blogspot.com/2012/07/continuity-of-life-is-based-on.html




Essential knowledge 3.B.2: A variety of intercellular and intracellular signal transmissions mediate gene expression.
By Maggie Garrahan

1. Signal transmission within and between cells mediates gene expression.
A. Cytokines regulate gene expression to allow for cell replication and division.
B. Levels of cyclic AMP (cAMP) regulate metabolic gene expression in bacteria.
C. Expression of the SRY gene triggers the male sexual development pathway in animals.
D. Ethylene levels cause changes in the production of different enzymes (ex: ripening of fruits)
2. Signal transmission within and between cells mediates cell function.
A. Mating pheromones in yeast trigger mating genes expression and sexual reproduction.
B. Morphogens stimulate cell differentiation and development.
C. Changes in p53 activity can result in cancer.
Genes can't control an organism on their own; rather, they must interact with and respond to the organism's environment. Cell-cell differences are determined by expression of different sets of genes. For instance, an undifferentiated fertilized egg looks and acts quite different from a skin cell, a neuron, or a muscle cell because of differences in the genes each cell expresses. Control of expression is vital to allow a cell to produce the gene products it needs when it needs them; in turn this gives cells the flexibility to adapt to a variable environment, external signals, damage to the cell, etc.
An example of the control of genes in controlling [[#|insulin]] (also negative feedback). Insulin controls the glucose levels in the blood.
external image 08_03_gene_expression.jpg


Examples:
http://www.nature.com/scitable/topic/gene-expression-and-regulation-15
http://www.news-medical.net/health/Regulation-of-Gene-Expression.aspx






3.C.3: Viral replication results in genetic variation, and viral infection can introduce genetic variation into the hosts.
by Maeve Dalpe
Viruses evolve rapidly because of their tendency for genetic variation, viruses with the greatest genetic variability are most able to evade human responses, elude protection by vaccination, and acquire drug resistance. Important consequences of viral genetic variation include, ability to elicit an immune response, ability to react with host antibodies, and susceptibility to antiviral drugs. Genetic diversity in viruses is a combination of 2 main mechanisms: mutation and recombination. RNA viruses generally show far greater genetic diversity the DNA viruses because the replication enzymes are more error-prone. Those RNA viruses with the greatest variability are myxoviruses (i.e. influenza) and the retroviruses (i.e. HIV).

RNA viruses have higher mutation rates, most single nucleotide substitutions are the result of nucleotide disincorporation. Propagation of a cDNA clone of an RNA virus genome is far less error prone: cDNA cloning fixes the sequences of individual viral genomes for further study.

Lethal mutation of genes can be rescued by coinfecting (phenotypic mixing)
Neutral mutation can persist in population (genetic drift)
Adaptive mutation confer a growth advantage under particular conditions and are fixed by selection (i.e. envelope protein that abolishes neutralizing antibody binding to envelope protein). (pg 457)




3.D.4 Changes in signal transduction pathways can alter cellular response.
Emily Bernardi


Certain conditions where signal transductions are blocked or defective can be deleterious, preventative, or prophylactic.
Many things can cause transduction pathways to be blocked such as:

Diabetes - a group of metabolic diseases in which a person has high blood sugar, either because the pancreas does not produce enough insulin, or because cells do not respond to the insulin that is produced.
Heart Disease - any disease that affects the cardiovascular system, principally cardiac disease, vascular diseases of the brain and kidney, and peripheral arterial disease.
Neurological disease - disorder of the body's nervous system. Structural, biochemical or electrical abnormalities in the brain, spinal cord, or other nerves can result in a range of symptoms.
Autoimmune disease - arise from an inappropriate immune response of the body against substances and tissues normally present in the body.
Cancer - broad group of various diseases, all involving unregulated cell growth.
Cholera - an infection in the small intestine caused by the bacterium Vibrio cholerae.
Neurotoxins - affect function in both developing and mature nervous tissue.
Poisons - chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by an organism.
Pesticides - substances meant for preventing, destroying or mitigating any pest.
Drugs - a substance which may have medicinal, intoxicating, performance enhancing or other effects when taken or put into a human body.





Appendix A (I): Describing several mechanisms that result in increased genetic variation and rapid evolution of viruses.
By: Bunyad Bhatti

Inheritance patterns are often more complex than predicted by simple Mendelian genetics. (Test book: Page 106-107)

Complete Dominance: when the heterozygote and the homozygote for the dominant allele are indistinguishable.
Codominance: occurs when two alleles are dominant and affect the phenotype in two different but equal ways. The traditional example is blood types.
Incomplete Dominance: is when the F1 hybrids have an appearance that is in between that of the two parents. ( white and red flowers making pink.)

Multiple alleles: occurs when a gene has more than two alleles. (Human blood types)
Pleiotropy: the property of a gene, that causes it to have multiple phenotypic effects. (Sickle-cell disease)
Epistasis: a gene at one locus alters the effects of a gene at another locus. (albinism)
Polygenic Inheritance: two or more genes have an additive effect on a single character in the phenotype. (height/skin colors).

Inheritance patterns are often more complex than predicted by simple Mendelian genetics. (Test book: Page 106-107)
  • Ligand gated ion channels by Amanda Seale

Essential knowledge 3.D.3: Signal transduction pathways link signal reception with cellular response.

Ligand-gated ion channels is a type of membrane receptor containing a region that acts as a gate as the receptor changes shape. The gate opens or closes when signaling molecule binds to as a ligand to receptor protein, allowing or blocking the flow of specific ions, such as Na+ or CA2+ through a channel in the receptor. The proteins bind the ligand at a specific site on their extra cellular sides.
Ligand-gated ion channels are important because they are necessary at synapses between neurons. Neurotransmitter molecvules released at a synapse between nerve cells binds as lifands to ion channels on the receiving cell, causing the channels to open. The electrical signal that propogates down the length of the receiving cell triggers as the ions flow in (or out).
Steps:
1. Within the ligand-gated ion channel receptor, the gate remains closed until a ligand binds to the receptor.
2. When the ligand binds to the receptor opening the gate, specific ions can flow through the channel and rapidly changes the particular ion concentration inside the cell.
3. As the ligand dissociates from the receptor, the gate closes and ions no longer enter the cell.

lig.jpg






Appendix A(N): Describe how the nervous system detects external and internal stimuli and transmits signals along and between nerve cells.

By Bunyad Bhatti

  • Sensory receptors transduce stimulus energy and transmit signals to the central nervous system (Test book: 271).


Mechanoreceptors: are receptors stimulated by physical stimuli. (pressure,touch,stretch, motion, sound)
Thermoreceptors: detect the heat or cold, and help to maintain the body temperature.
Chemoreceptors: transmit information about solute concentration in a solution. (taste and smell)
Electromagnetic Receptors: detect various forms of electromagnetic energy. (visible light/electricity/magnetism)
Pain Receptors: respond to excess heat, pressure, or specific classes of chemicals released, from damaged or inflamed tissues.
Reception: occurs when a receptor detects a stimulus. (Perception in the brain)

These are the sensory receptors used in the nervous system, that transmit signals to it.
http://www.youtube.com/watch?v=dZQMjZRv16E&list=PLFCE4D99C4124A27A&index=54: Mr. Anderson touches upon the Nervous system.





DNA sequencing and the human genome project - Kylie Dolan
Essential knowledge 3.A.1: DNA, and in some cases RNA, is the primary source of heritable information.
The human genome project began in 1990, and though it was planned to last 15 years, actually ended 13 years later, 2 years early. The main project goals were:
  • To identify all the approximately 20,000-25,000 genes in human DNA
  • Determine the sequences of the 3 billion chemical base pairs that make up human DNA
  • Store this information in databases
  • Improve tools for data analysis

Another form of DNA identification is gel electrophoresis. This is when DNA is placed in a gel commonly made of the polysaccharide agarose. An electric field is passed through the DNA molecules and this charge causes the DNA to travel to the opposite end that is positively charged. (the phosphate on the DNA is negatively charged, causing the attraction. The operating principle is that the gel causes the larger strands to move slower, and the smaller to move faster (kind of like an obstacle course). Marker DNA of a standard size is used to approximate the size of the of the unknown molecules (mews urged in kilobase pairs). The DNA is identified by being dyed with staining gel (composed of ethidium bromide) so it is bright and can be seen.





Types of mutations - Kylie Dolan
Biological systems have multiple processes that increase genetic variation (Essential Knowledge 3.C.2)

There are four major types of mutations

  • Substitution
    • When one base pair is substituted for another. This type of substitution could cause a change of a codon to one that encodes a different amino acid, which could cause a small change in the protein produced. If the mutation changes the "letter," but does not code for a different protein, it is called a silent mutation.
  • Insertion
    • Insertions are when extra base pairs are inserted into a new place in the DNA.
  • Deletion
    • Deletions are (obviously) mutations in which a section of DNA is lost, or deleted and nothing replaces it.
  • Insertions and deletions can both be frame shift. Essentially, since DNA is grouped into three bases to code for proteins, any addition or deletion not in multiples of three will shift the "frame" so that the DNA is parsed incorrectly.

Mariah Pennington

Appendix A, letter h: Predict how various DNA sequence changes can alter phenotype

A flaw in the “blueprint” that essentially directs all cell and therefore organism activity and function can quickly cause a chain reaction and snowball into a magnified issue. Or mistakes can occasionally be benign as well. Evolution would not be possible without these errors in the DNA sequence. Some mistakes can lead to helpful physical traits such as a longer neck to reach the tops of trees. Or the new trait can be deadly like being a black moth living on light bark.

DNA codes for proteins that are the building blocks behind structure and therefore form. If there is a flaw in any part of the complicated process of protein synthesis, the entire blueprint and final outcome is affected. Mutations are passed from parent generation to the offspring. For example, Huntington’s Disease is an autosomal dominant genetic disorder. This means that only one effected parent is needed to pass it on to the child. (textbook 325-330)

Mariah Pennington
Appendix A, letter l: Features of cell to cell contact and chemical signals communicate over long and short distances.
The APC (antigen presenting cells) on the surface of MHC cells directly give the antigen to the helper T cells. An example of short distance communication is spanning the synaptic gap between neurons. Nervous system interaction is considered to be “electrochemical” because it involves both an electric impulse and the use of chemicals. When a dendrite gets an electrical signal from a stimulus, that impulse is sent through the dendrite and along the axon where it reaches the axon terminals. This is where the electricity triggers chemicals to be sent across the synapse gap to reach the neuron next to it.
For a signal to be sent long distances, hormones are used. The endocrine system is what governs this method, and the pituitary gland in the hypothalamus part of the brain is the “master gland” in charge. Hormones can affect specific target cells because only those cells will have the corresponding receptors to allow the attachment and signal transduction. Hormones are secreted into the bloodstream and travel through the body that way. (textbook page 938)

Alterations in Meiosis Lead to Human Genetic Diseases: Down Syndrome and Klinefelter Syndrome (page 299)
By: Christina Dykas
Appendix A Big Idea 3 Letter d
Nondisjunction in meiosis is the cause of Down Syndrome. This is when members of the pairs of homologous chromosomes do not move apart when they are supposed to. This is in meiosis I. If sister chromatids do not separate, this occurs in meiosis II. Since they did not separate, they zygote is left with an abnormal number of that chromosome and this is known as aneuploidy. Down syndrome occurs due to an extra chromosome 21 as a result of nondisjunction and is also known as trisomy 21 because there are 3 of chromosome 21. Some features associated with Down Syndrome are heart defects, short stature, rounder face, specific facial features, and shorter life span.
Nondisjunction can also occur in sex chromosomes and cause disorders. Klinefelter syndrome occurs in males and is characterized by an extra X chromosome (XXY). Effects of this cause the male to be sterile, abnormally small testes, and some breast enlargement. The nondisjunction that occurred in meiosis resulted in these physical features.
external image images?q=tbn:ANd9GcSatBJhSprzh6f8SbFG7fGT8lGqkkPaagJSGCcfbbSSv3npFWxWJQ external image images?q=tbn:ANd9GcSiA1agwDIkfF7xc4eUqlJGxk74hoR1wkpXMDBfPhaEnBMTEuWhaA
Left is Down Syndrome and right is Klinefelter Syndrome

Big idea 3: Concept e
Incomplete Dominance and Codominance (page 271-272)
By Kenna Garrison

Incomplete dominance is when neither allele is completely dominant, leaving heterozygous organisms with a phenotype in between the two parental varieties. This would throw off the predictions that are often made when it is assumed that one trait is dominant over the other, called complete dominance. However, if the heterozygous organisms mate, the ratio of their offspring will be 1:2:1 with the ones each being one of the parental varieties and the 2 being more heterozygous offspring showing incomplete dominance.

Another variation in dominance relationships between alleles is codominance. This is when both alleles affect the phenotype in different ways. An example of this is the M and N molecules on red blood cells. If a human is homozygous MM or NN he or she will only have those molecules on their red blood cells. If they are heterozygous, however, they will have both molecules on their red blood cells. This is considered codominance since it is not an intermediate between the two alleles, but rather both phenotypes show up.

Essential Knowledge 3.C.1: Changes in genotype can result in changes in Phenotype
Kayla Kaufmann (make-up work)
Pages 470-472 and 278

  • Alterations in a DNA sequence (genotype) can lead to changes in the type or amount of the protein produced and the resulting phenotype
To show understanding of this concept, you must know....
  • DNA mutations can be positive (good), negative (bad), or neutral (Basically no effect) based on the effect or lack of effect they have on the resulting nucleic acid or protein and the phenotypes that are a result of the protein.... So mutations are not always a bad thing
  • Errors in DNA replication or repair mechanisms and external factors like radiation and reactive chemicals can cause random changes in DNA (IMPORTANT- mutations are the primary source of genetic varitation).

Errors in mitosis or meiosis can result in changes in phenotype
  • Changes in chromosome number can result in new phenotypes like sterility caused by triploidy (individuals have three of every chromosome for a total of sixty nine rather than the normal forty six) and increased vigor of other polyploids.
  • Changes in chromosome number can result in human disorders with developmental limitations (like Trisomy 21 AKA Down's Syndrome caused by a third copy of chromosome 21)

Changes in genotype may affect phenotypes that are subject to natural selection. Genetic changes that enhance survival and reproduction (what organisms want) can be selected by environmental conditions
EXAMPLE - Sickle cell disorder and heterozygote advantage
  • Sickle cell disease is an autosomal recessive genetic blood disorder that effects hemoglobin in red blood cells and causes them to have a sickle shape which causes many severe complications
  • With this disorder there is a an advantage because this disorder causes a resistance to malaria
  • A heterozygote has an advantge becuase someone who only has the sickle cell disease trait, or only one allele, does not have the severe symptoms/complications of the disorder but still has the resistance to malaria
You must understand that selection results in evolutionary change


Essential Knowledge 3.C.2: Biological systems have multiple processes that increase genetic variation
Kayla Kaufmann (Make-up work)
Pages 468-471

  • The imperfect nature of DNA replication and repair increases variation. Since there are often mistakes in these important processes it helps create variation which is sometimes results in a postive variation
  • The horizontal transfer of genetic information primarily in prokaryotes via transformation (the uptake of naked DNA), transduction (viral transmission of genetic information), conjugation (cell-to-cell transfer), and transposition (movement of DNA segments within and between DNA molecules) increase variation. These types of transfer of genetic information result in variation
Sexual reproduction in eukaryotes involving gamete formation increses genetic variation
  • This includes crossing over during meiosis (the process that forms haploid gametes), the random assortment of chromosomes during meiosis, and fertilization are all examples
  • Reproductive processes that increase genetic variation are evolutionarily conserved (natural selection) and are shared by various organisms


Essential Knowledge 3.E.2: Animals have nervous systems that detect external and internal signals, transmit and integrate information, and produce responses - THE NEURON
Kayla Kaufmann
Pages 1047-1049

The neuron is the basic structure of the nervous system that reflects function
  • A typical neuron has a cell body, axon, and dendrites. Many axons have a myelin sheath which is an electrical insulator
  • The structure of the neuron allows for the detection, generation, and transmission and integration of signal information
  • Schwann cells, which form the myelin sheath, are seperated by gaps of unsheathed axon over which the impulse travels as the signal propagates along the neuron
  • Sensory neurons - transmit information from eyes and other sensors that detect external stimuli (light, sound, touch, heat, smell, and taste) or internal conditions (blood pressure, blood carbon dioxide level, and muscle tension)
  • Interneurons - make only local connections
  • Motor neurons - transmit signals to muscle cells, causing them to contract

external image Neuron.jpg