Compendium Review 1, Chapter 1-4, PowerPoint Presentation, and Online Activities

After hours of effort, I am finally posting this compendium despite the spacing and formatting issues. Because of numerous technical difficulties, all of my images must be uploaded into a separate Blog, entitled "Compendium Review Pictures". Each time you see an address for a website, there is a corresponding picture in the other blog. My apologies... it all looked so pretty in the Word Document.

Megan Yakovich
Compendium Review 1
Table of Contents
Chapter 1:
I. The Characteristics of Life
II. Organization of Life
III. Classification of Living Things
IV. Science as a Process
V. Scientific Method
VI. Dr. Barry Marshall
VII. Controlled Studies
VIII. Evaluating Scientific Information
IX. Science and Social Responsibility
Chapter 2:
I. From Atoms to Molecules
II. Element: Basic building block of matter
III. Atom
IV. Isotopes
V. Molecules and Compounds
VI. Water
VII. Acids and Bases
VIII. Molecules of Life
IX. Carbohydrates
X. Fats & Lipids
XI. Proteins
XII. Nucleic Acids
XIII. ATP (adenosine diphosphate)
Chapter 3:
I. What is a cell?
II. Two Types of Cells
III. Similarities & Differences
IV. WHAT CAN EUKARYOTIC CELLS DO?
V. The Movement of Substances Across the Plasma Membrane
VI. Nucleus / Production of Proteins
VII. Ribosomes
VIII. The Endomembrane System
IX. The Cytoskeleton / Cell Movement
X. Cilia and Flagella
XI. Mitochondria / Cellular Metabolism
XII. Cellular Respiration / Metabolism
Chapter 4:
I. 4 Classes of Tissue: Several types
II. Cells in the human body
III. Types of Tissues
IV. Cell Junctions
V. Integumentary System
VI. Organ Systems / Functions
VII. Body Cavities
VIII. Body Membranes
IX. Homeostasis
Information from Online Activities:
I. Facilitated Diffusion
II. Active Transport
III. Endocytosis and Exocytosis
IV. Folding@home Distributed Computing


Megan Yakovich
Compendium Review: Chapters 1-4, PowerPoint, Web Activities
I. The Characteristics of Life
A. All living things are alike in that they all begin as cells, and they all share the following traits:
- Organization (See chart below for more detail)
- Reproduction (“DNA contains hereditary info that directs the structure of the cell & its metabolism.”) (Mader 4).
- reliance on energy and materials from their surroundings (ie. food)
- continuous growth and development
- homeostatic (“stable” internal environment .) All organ systems in body help to maintain homeostasis.
- reaction to stimuli
- evolutionary history, constantly adapting (Mader 2-4.)

Ankh: Egyptian Symbol of Life
http://www.flickr.com/photos/djivano/22789945/
II. Organization of Life
A. Hierarchical: Humans are constantly evolving.
- From the bottom up: Atom (contains electrons, protons and neurons) is the smallest unit →Molecule (two or more atoms) → Cell (fundamental unit of life) → Tissue (group of cells whose metabolism works together for a common function) → Organ (tissues that work together for a common function) → Organ System (several organs working together) → Organism (individual) → Population (organisms in a species on a specific area) → Community (populations interacting with one another) →Ecosystem (community and physical environment) →Biosphere (Earth and atmosphere, made up of all living things.) (Mader 2-3), (Frolich, Powerpoint Presentation.)
- See below for image “chart”. All websites are listed in order underneath.
Atom → Molecule → Cell → 4 types of Tissue → Organ (heart) →Organ System: Nervous: Brain, Spinal Chord, Nerves) → Organism→Population → Community → Ecosystem → Biosphere
http://commons.wikimedia.org/wiki/Image:Atom.svg (Atom)
http://www.realself.com/blog/antiageing_molecule.html (Molecule)
http://web.jjay.cuny.edu/~acarpi/NSC/13-cells.htm (Cell)
http://www.umm.edu/imagepages/8682.htm (Tissue)
http://blinkandyoullmissit.typepad.com/momenttomoment/2005/10/beating_heart.html (Organ)
http://web.jjay.cuny.edu/~acarpi/NSC/14-anatomy.htm (Organ System)
http://www.flickr.com/photos/73155934@N00/104127774/ (Organism)
http://www.webcontentsolutions.com/Real-Estate-Web-Design-Largest-Cities-by-Population.html (Population)
http://www.flickr.com/photos/benevolink/82714178/ (Community)
http://www.rivercenter.uga.edu/education/satilla/waycross/images (Ecosystem)
http://www.surf-report.com/images/surf-stories/ini-quik05?M=A (Biosphere)

III. Classification of Living Things
A. 3 Domains: Eukarya (membrane-bound nucleus), Archaea , Bacteria (both lack membrane-bound nucleus)
1a. Eukarya- 4 kingdoms: Animalia, Plantae, Fungi, Protista
1b. Animalia- humans and vertebrates
B. Humans differ from animals due to their ability to manipulate tools, speak and use language, stand upright, and their developed brains. They have culture that they pass from one generation to the next. (Mader 8)
IV. Science as a Process
A. Scientific Theories: “Concepts that tell us about the order and the patterns within the natural world” (Mader 8).
1a. Ex. Evolution: “Nothing makes sense in the biological world without evolution” (Frolich, Powerpoint Overview).
http://www.flickr.com/photos/larapadilha/1329709195/

1b. Defined as “The historical development of a biological group” (Webster’s Online Dictionary). In other words, this is the principle that all living things come from others that have existed before them, and that successive generations modify and adapt their behaviors to better their species.
V. Scientific Method
A. This is the process by which scientists gather information. Initial observations / study of “old” data. Hypothesis is made: An educated “guess”. The basis used to gather more information. The hypothesis is tested by further observation and experimentation. Conclusion: Analysis of observations and experimentations support or reject the hypothesis. If the hypothesis is supported, it may become a scientific theory. If rejected, a new hypothesis is created. (Mader 8)

VI. Dr. Barry Marshall
A. 1974- 1983: Dr. Marshall forms the hypothesis that stomach ulcers were caused by the presence of a bacterium called Helicobacter pylori. In order to show that this pathogen (bacteria) was indeed the cause of this disease, he used Koch’s postulates. Although he was able to show that the bacteria was indeed found in every case he studied, and that the pathogen could be taken from a host and grown in a petri dish (the first two criteria), he was initially unable to fulfill the last two criteria. This is because he could not inoculate the pathogen into a guinea pig or rat; the bacteria did not thrive in these animals. 1985- Dr. Marshall decides to use himself as the “guinea pig”! I was very surprised to read that he took the initiative to do this, because he was so intent on proving his hypothesis. Sure enough, the bacteria did thrive within his stomach, so he was able to successfully fulfill the third criteria of Koch’s postulates. Finally, after biopsying his stomach lining, they found the bacteria again, and thus fulfilled the last of the postulates. Thanks to Dr. Marshall’s bravery and determination, stomach ulcers are now treated with antibiotics and the human race affected can live more comfortably (Mader 9).

VII. Controlled Studies
A. Subjects are divided into groups.
1a. Test Group: Exposed to the experimental variable (the “thing” they are trying to prove).
1b. Control Group: Not given anything experimental. May be given a placebo (treatment that does not contain any medicine).
1c. Results: If both groups exhibit the same results, the study would be considered invalid, because the experimental variable was obviously somewhat ineffective. If the groups differ in result, the experiment would probably be repeated with two test groups and one control group, to reduce the number of differences between the subjects, and therefore strengthen the validity of the results.
B. A “double-blind” study is when none of the parties involved in the experiment is aware of the treatment itself, and therefore, all are unbiased (Mader 10-11).
VIII. Evaluating Scientific Information
A. Scientific Journals are considered the most reliable source for medical information because before something can be published, it is examined by experts to ensure its credibility. For those who are not medical professionals, it is sometimes difficult to decipher what is valid and what isn’t through sources such as the internet. So, ideally, a person should always try and “back up” the information they find on the internet, or even in magazines, books, etc., with a scientific journal. The most valid websites have URLS’s that contain .edu, .gov, and .org. (Mader 11). B. Anecdotal/ Testimonial Data: Never considered reliable, because the information is provided by individuals instead of coming from a controlled study, and may be subjective.
It is also unreliable because data is not studied in enough subjects.
C. Correlation Data: Just because two things happen simultaneously, one may not be the cause of the other. More data is needed.
D. Statistical Data: The Standard Error gives an idea of the level of potential inaccuracy that might occur.
E. Statistical Significance: Probability value: Were the results of an experiment due to chance? Investigators calculate this possibility, and if the value is less than 5%, the results are considered acceptable. The lower the p value, the higher the likelihood that the results were not due to chance.
F. Statistical Study: Numerical information from a variety of sources that is already available is collected and studied, as opposed to a controlled study.
(Mader 12-13).
IX. Science and Social Responsibility
A. “Science, technology, and society have interacted throughout human history, and scientific investigations and technology have always been affected by human values. Every member of society has a responsibility to participate in how science and technology are used for the good of all.” (Mader Text Website, Chapter 1)

Chapter 2: Chemistry of Life

I. From Atoms to Molecules
A. Matter: “anything that takes up space and has mass” (Mader 20). Matter is made up of atoms. These atoms react with one another to form molecules. (Mader Text Website, Chapter
1a. Can exist in three forms: solid, liquid, gas
II. Element: Basic building block of matter.
A. Unable to be broken down by chemicals.
B. Each has a name and symbol.
1b. Elements are arranged in a periodic table. (Mader 20)

http://www.seq.org/~ca_science/Engberg/PeriodicWebQuest.htm
2b. Each element in a column has similar reactions. (Mader 20)
III. Atom: “The smallest unit of an element that still retains the chemical and physical properties of the element” (Mader 20).
A. The smallest unit that can have a chemical reaction.
B. Contains a nucleus, protons (positive charge) and neutrons within the nucleus, and electrons (negative charge) that move around the nucleus.
http://darkwing.uoregon.edu/~ch111/L5.htm
1b. These components of an atom are basically tiny specks within the atom, with most of the atom being empty space.
C. Atomic Numbers: In the periodic table, the number above the symbol for the element shows us how many protons and electrons an atom has when it is neutral.
1c. Inner shell of an atom can only hold 2 electrons, because it has the lowest level of energy.
2c. The subsequent shells can hold up to 8 electrons.
D. Mass: Represents an atom’s quantity of matter.
1d. Atomic mass is represented by the number below the symbol for the element.
2d. To figure out how many neutrons are in an element, you subtract the atomic number (top) from the atomic mass (bottom). (Mader 20-21).
3d. Example: Nitrogen (N) has an atomic number of 7. Therefore, we know that it has 7 protons and electrons when neutral. Its atomic mass is 14.01. We can then compute that Nitrogen must have 7 neutrons: 2 in the inner shell, and 5 in the outer shell.

IV. Isotopes: “One of two or more atoms with the same atomic number but a different atomic mass due to the number of neurons” (Mader Glossary G-10).
A. Ex. Carbon 12- 6 neurons, Carbon 13- 7 neurons.
B. Radioisotope: “Unstable form of an atom that spontaneously emits radiation in the form of radioactive particles or radiant energy” (Mader Glossary G-16).
C. Tracer: “Substance having an attached radioisotope that allows a researcher to track its whereabouts in a biological system” (Mader Glossary G-19).
1c. Tissues and organs can be imaged through the use of specific tracers.
2c. Although radioactive substances have been known to be very dangerous and harmful, these harmful effects can also be beneficial. Ex. The use of radioisotope radiation to sterilize,
or the introduction of radioisotopes to destroy cancer cells. (Mader 21).
V. Molecules and Compounds
A. Molecule: A chemical unit formed when atoms bond.
B. A compound molecule is a molecule that is made from two different atoms joining together.
C. Ion: “Particles that carry either a positive or negative charge” (Mader 22).
D. Atoms are joined together by one of two kinds of bonds: ionic or covalent.
1d. Atoms are most stable when the outer shell has 8 electrons.
2d. When two atoms join, the atoms will give up one of their own electrons to the other atom in an attempt to form that stable outer shell, or they will take electrons from the other atom for the same purpose.
3d. Ionic bond: “Chemical bond in which ions are attracted to one another by opposite charges” (Mader Glossary G-10).
4d. Various ions must be balanced in our bodies in order for us to remain healthy. (Mader 22).
5d. Covalent bonds: These occur when atoms share electrons, as indicated by their overlapping outer shells. Here, EACH atom gives one electron to the pair and they share it.
There may be single (sharing 1 pair of electrons), double (sharing 2 pairs), or triple bonds (sharing 3 pairs). (Mader 23)
VI. Water
A. Water is a polar molecule, because it has a negative charge on the part of the oxygen, and a slight positive charge on the hydrogen end.
B. Hydrogen bond: “Occurs when a covalently bonded hydrogen is slightly positive and attracted to a negatively charged atom” (Mader 24).
C. Water molecules cling together.
D. Hydrogen bonding keeps water in its liquid state.
E. Water helps our bodies maintain normal internal temperatures.
F. Blood is 92% water.
G. Water makes chemical reactions possible in and out of our bodies.
H. If an ion or molecule reacts with water, it is hydrophilic. If it does not, it is hydrophobic. (Mader 24-25
VII. Acids and Bases
A. An acid is a substance that dissociates in water.
B. A base is a substance that either takes up hydrogen ions or releases hydroxide ions.
C. pH scale- used to indicate the acidity and basicity of a solution. Ranges from 0-14.
D. “Buffers” (combination of chemicals) prevent pH damage. (Mader 25-26).
VIII. Molecules of Life
A. Organic molecules: molecules that have carbon and hydrogen.
1a. 4 categories: carbohydrates, lipids, nucleic acids, proteins.
B. Macromolecule: molecule that contains multiple subunits.
C. Dehydration Reaction: Used by a cell to create a macromolecule.
D. Hydrolysis reaction: Used to breakdown macromolecules, by adding components of water. (Mader 27)
IX. Carbohydrates
A. Function: Used for energy storage in complex form.
B. Broken down into simple sugars to fuel cellular metabolism in mitochondria. (Frolich PowerPoint)
C. If the carbon atoms are low in a carbohydrate, it is a simple sugar, or monosaccharide.
D. Glucose: hexose (6-carbon sugar), used by our bodies for immediate energy.
E. Disaccharide: (two sugars), made by joining two monosaccharides together.
F. Complex Carbohydrates (Polysaccharides): contain many glucose units.
G. Cellulose: Unable to digest because of a different type of link joining the units together, = fiber. (Mader 29)
X. Fats & Lipids
A. Most energy per gram than any other molecule.
1a. Used for long-term energy storage.
2a. Phospholipids form a membrane to separate the cell’s interior from its environment. (Frolich PowerPoint)
B. Can not dissolve in water. Can be dissolved with the use of emulsifiers.
C. Most common: Fats, animal origin, solid at room temp. Functions: long-term energy storage, keep the body warm, protection for organs. Oils, plant origin, liquid at room temp.
D. Fat can be called triglyceride because it is made up of 3 fatty acid molecules and one glycerol molecule. (Mader 30-31)
E. Fatty Acid- “Molecule that contains a hydrocarbon chain and ends with an acid group” (Mader Glossary G-7). Can either be saturated (no double-bond between carbon atoms), or unsaturated ( contains double bonds in the carbon chain).
1e. Saturated fats (along with cholesterol) are harmful because they cause plaque to build up in blood vessels.

http://www.siheartdocs.com/facts_about_heart_disease_women.htm
2e. Trans fats are even worse, because they are hydrogenated which causes all of the double-bonds to become saturated.
F. Steroids are lipids! (I didn’t know this.) (Mader 30-32)
XI. Proteins
A. Extremely important in the make-up of a cell, and the way it functions.
B. Made up of Amino Acids that fold up into a complex form.
C. The complex form of Amino Acid chain allows for the catalyzing of specific chemical reactions in the cell. (Frolich PowerPoint)
1c. Enzymes speed up chemical reactions in cells. (Mader 32)
D. Peptide bond: “A type of covalent bond that joins two amino acids” (Mader Glossary G-14).
1d. Polypeptide- contains many amino acids.
E. Denaturation: This occurs when proteins undergo a change in shape and can no longer function.
F. Some proteins cause cell movement, allow for the movement of muscles, are antibodies, and move molecules throughout blood. (Mader 32-34)
XII. Nucleic Acids
A. Two types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
1a. Called Nucleic Acids because they were first found in the nucleus. (Mader 35)
2a. Composed of nucleotides, or “bases”. (Frolich PowerPoint) 4 different types of bases: adenine, thymine, guanine, and cystosine. Also composed of a sugar and a phosphate. (Mader 35, 38).
B. DNA- There are multiple genes on each molecule, and these genes specify the sequence of the amino acids in proteins. (Mader 34)
1b. DNA stores genetic information in the cell. When a cell reproduces, the DNA copies and transmits that information to the new cell. (Frolich PowerPoint)
2b. Contains the sugar deoxyribose.
3b. Double-stranded. The two strands entwine around one another, held together by hydrogen bonds between the bases, forming a double helix. (Mader 36) One strand can be complex enough to be millions of bases long. (Frolich PowerPoint)
http://www.accessexcellence.org/RC/VL/GG/structure.php

C. RNA- “an intermediary that conveys DNA’s instructions regarding the amino acid sequence in proteins” (Mader 35).
1c. Single-stranded.
2c. Contains the sugar ribose.
3c. A nucleic acid that is directly involved in protein synthesis.
RNA V. DNA
http://www.accessexcellence.org/RC/VL/GG/rna.php
XIII. ATP (adenosine diphosphate)
A. Energy carrier in cells. (A high energy molecule, because its bonds are not stable.) (Mader 36)
1a. A cell uses the energy released by ATP to metabolize. (Mader Text Website, Chapter 2)

Chapter 3
I. What is a cell?
A. Cell theory: A cell is the basic and fundamental units of life. (Frolich PowerPoint)
1a. Approximately 100 micrometers in diameter. Even though they are tiny, small cells have a bigger surface-area-to-volume ration, which allows materials to go in and out of the cell more easily than a bigger cell, which would actually have a smaller surface-area-to-volume.
2a. A unicellular organism will display the 7 characteristics of life.
3a. Different cells in a multicellular organism vary quite a bit in appearance. “However, all cells exchange substances with their environment” (Mader 42).
Ex.
Blood Cell Nerve Cell Brain cell

http://www.millbrook-instruments.com/technology.htm
http://www.becomehealthynow.com/popups/nerve_cell_bh.htm
http://elgg.net/simpsonk/weblog/friends

4a. New cells can only be formed from pre-existing cells. Ex. When a sperm cell joins with an egg cell, a zygote is formed, and this is the first cell of the new organism. (Mader 42)
II. Two Types of Cells
A. Prokaryotic: Relatively simple and small. Lacks a nucleus, but does have a plasma membrane that regulates what is allowed to enter and exit the cell (“selectively permeable”), and cytoplasm (semi-fluid medium that contains one or two organelles). Bacteria and archaea are made up of these cells. (Frolich PowerPoint, and Mader 44)
(Frolich PowerPoint, Slide 15)



B. Eukaryotic: More complex and much bigger. Does have a nucleus, plasma membrane, and cytoplasm, but the cytoplasm contains many different kinds of organelles, which are membrane- bound. (Frolich PowerPoint)
http://www.ux1.eiu.edu/~bltodd/llc.bio100.htm
C. If the first cells to arise were prokaryotic, where did the eukaryotic cells come from? It is believed that they evolved from the prokaryotic cells. Plasma membrane may have infused the DNA to produce the nucleus, and some organelles in the eukaryotic cells may have come about when they surrounded prokaryotic cells. (Mader 44)
D. All multi-cellular organisms are composed of eukaryotic cells. (Frolich PowerPoint)
III. Similarities & Differences
Prokaryotic VS Eukaryotic
- Cell Membrane - Cell Membrane
-DNA molecules loose in cytoplasm - DNA contained in nucleus
- Small ribosomes that assemble protein from DNA - Larger ribosomes, same function
-Mitochondria / Chloroplasts - Mitochondria / Chloroplasts
- Microtubule structures like flagella and cilia - Flagella and cilia
- No cytoskeleton (internal membranes) - Has cytoskeleton
(Frolich PowerPoint)

IV. WHAT CAN EUKARYOTIC CELLS DO? WHAT STRUCTURES ARE INVOLVED?
-Separate inside of cell from external environment - Cell Membrane
and control what substances pass across membrane.
- Produce proteins/enzymes that catalyze chemical - Nucleus (DNA), Ribosomes on reactions or control movement across membrane. rough endoplasmic reticulum
- Break down sugars to form energy which is stored - Mitochondria
in phosphate bonds of ATP.
- Organize distribution of Molecules of Life - Internal membrane system and
(macromolecules) and ions throughout cell. “cytoskeleton” (ER, lysosomes,
vesicles, microtubules)
- Move - Flagella, cilia, pseudopods
(Frolich PowerPoint Slide 20)

A. All cells are surrounded by a plasma membrane that keeps a cell intact.
1a. Membrane is a phospholipid bilayer (liquid) that creates a boundary between the outside and inside of the cell. Only certain molecules and ions are allowed to pass through this membrane to enter and exit the cytoplasm. (selectively permeable) (Mader 46) This is how a cell maintains its homeostasis.
(Frolich PowerPoint)
1b. Fluid-mosaic model: “A working description of membrane structure. The protein molecules form a shifting pattern within the fluid phospholipid bilayer.”
1c. Some plasma membrane proteins create channels that allow certain substances to enter the cell, while others are enzymes that catalyze reactions. (Mader 46)
1d. Contains cholesterol to support the membrane. (Frolich PowerPoint)
V. The Movement of Substances Across the Plasma Membrane
A. Diffusion: Molecules move randomly from an area of higher concentration to the area of lower concentration to become equally distributed.
1a. This movement is passive- no cellular energy is required.
B. Osmosis: “The diffusion of water across a plasma membrane” (Mader 47).
1b. Tonicity: Expressed as a percentage, this is the amount of solute (dissolved substance) in a solution. (Mader 47)
2b. Hypertonic Solutions: The solution has more solute than the inside of the cell, which causes the cell to shrivel. (crenation)
3b. Hypotonic Solutions: The solution has less solute than the inside of the cell, which causes the cell to burst. (lysis- refers to a disrupted cell)
4b. Isotonic Solutions: Equal amounts of solute inside and outside of the cell, so the cell is unaffected. (Frolich PowerPoint)
5b. Osmotic Pressure: “The force exerted on a selectively permeable membrane” (Mader 47).
C. Facilitated Transport: A solute is transported across the plasma membrane by protein carriers within that membrane. The transportation occurs at a faster rate, from higher concentration to lower. Passive.
D. Active Transport: The molecule moves in the “opposite” direction: from lower concentration to higher. Requires protein carrier (“pump”), and the use of cellular energy obtained from the breakdown of ATP. (Mader 47-48)
(Frolich PowerPoint)
E. Endocytosis: “Transports molecules or cells into the cell via invagination of the plasma membrane to form a vesicle” (pouch) (Frolich PowerPoint.) The membrane then pinches off and forms and endocytic vesicle inside the cell.
1e. Phagocytosis: When white blood cells pick up a pathogen by endocytosis.
2e. Pinocytosis: Occurs when cells “take up molecules and fluid”. (Mader 48)
F. Exocytosis: “Transports molecules outside the cell via fusion of a vesicle with the plasma membrane” (Frolich PowerPoint).
Top: Endocytosis
Bottom: Exocytosis
(Frolich PowerPoint)

VI. Nucleus / Production of Proteins
A. Nucleus: Stores genetic information. (Mader 49)
1a. It is held together by a “porous nuclear envelope.” (Frolich PowerPoint) This envelope also separates the nucleus from the cytoplasm. (Mader 49)
2a. The nucleus contains DNA and proteins known as chromatin. (Frolich PowerPoint) Chromatin becomes coiled into straight structures called chromosomes immediately before the division of the cell. Each of these chromosomes has its own DNA molecule and proteins. Chromatin is located in the semifluid nucleoplasm, which has a different make-up than cytoplasm. (Mader 49)
3a. Ribosomal RNA is located in the nucleolis. (Frolich PowerPoint)

Nucleus
http://www.mednote.co.kr/2CYTOHISTO.htm
VII. Ribosomes
A. Organelles (“Small membranous structure in the cytoplasm having a specific structure and function”) made up of proteins and RNA. (Mader Glossary G-13), (Mader 49)
1a. Protein synthesis occurs in the ribosomes, and these proteins are used inside the cell for a variety of purposes. (Mader 49)
1b. Ribosomes can be attached to the endoplasmic reticulum (and can eventually be secreted from the cell or become part of the plasma membrane) OR they float freely in the cytoplasm. (Frolich PowerPoint), (Mader 49) If they are floating in the cytoplasm in groups, they are called polyribosomes. (Mader 49)

(Notice the small bumps along the endoplasmic reticulum, = ribosomes)
http://www.williamsclass.com/SeventhScienceWork/CellTheoryParts.htm
VIII. The Endomembrane System
A. “A series of membranes in which molecules are transported in the cell.”
Contains all of the following: nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes and vesicles. (Frolich PowerPoint)
1a. ER creates transport vesicles to move large molecules to other parts of the cell, often times to the plasma membrane or the Golgi apparatus.
1a. Rough Endoplasmic Reticulum – studded with ribosomes on the side of the membrane, facing the cytoplasm. It is used to make proteins, some of which stay in the membrane, and others are expelled.

http://www.biology4kids.com/files/cell_er.html
2a. Smooth Endoplasmic Reticulum – lacks ribosomes but assists in the production of
carbohydrates and lipids. (Frolich PowerPoint and Mader 50)

http://www.biology4kids.com/files/cell_er.html
B. Golgi Apparatus
1b. Named for Camillo Golgi, who discovered it in cells in 1898. (Mader 50)
2b. “Flattened stacks that process, package and deliver proteins and lipids (received) from the ER” (Frolich PowerPoint)
3b. Vesicles that leave the Golgi apparatus are lysosomes. (Mader 50)

http://academic.wsc.edu/faculty/jatodd1/ap1/ch3.html
C. Lysosomes
1c. “Membranous vesicles (sacs) made by the Golgi that contain digestive enzymes” (Frolich PowerPoint)
2c. Can be found in all types of cells in the body.
3c. The most lysosomes are found in white blood cells which attack disease microbes.
They do this by digesting the microbes into simpler subunits that are then dispersed into the cytoplasm.
4c. Autodigestion: Lysosomes digest parts of their own cells.
http://www.i-med.ac.at/cellbio/news/press-06122002-images.html

Endomembrane System
(Frolich PowerPoint Slide 35)
IX. The Cytoskeleton / Cell Movement
A. Cytoplasm of a cell is “crisscrossed by several types of protein fibers called the Cytoskeleton” (Mader 51)
1a. Cytoskeleton helps maintain the shape of the cell and either holds the organelles or helps them move, appropriately.
2a. Microtubules: “Small cylindrical structure that contains 13 rows of the protein tubulin around an empty central core; present in cytoplasm, centrioles, cilia, and flagella” (Mader Glossary G-12). Helps maintain the shape of the cell and creates the “tracks” for organelles to move along.
3a. In the Cytoskeleton, these microtubules are much larger than actin filaments.
4a. Actin Filaments: Made up of the protein actin. Long, thin, usually found in bundles or groups in the microvilli which shorten and extend to help in movement.
5a. Centrosome: Regulates the assembly of microtubules.
6a. Intermediate Filaments: “middle” size, between the large microtubules and smaller actin filaments. (Mader 51)

Cytoskeleton
http://www.seorf.ohiou.edu/~tstork/compass.rose/cell.pages/cytoplasm.html
X. Cilia and Flagella
A. Both are microtubules and are involved in movement.
B. Cilia are approximately 20x shorter than Flagella. (Frolich PowerPoint) Even though it is shorter, “both have the same organization of microtubules within a plasma membrane” (Mader 51).
C. The energy from ATP helps motor molecules to allow the microtubules in cilia and flagella to interact, bend, and move.
D. Cilia and flagella grow from basal bodies, which are organized in the same manner as centrioles, which are located in the centrosomes.
E. If cilia and flagella do not function correctly, the health of a human can be impaired in many ways, including respiratory infections and reproduction problems. (Mader 51)

Cilia Flagella
http://www.uic.edu/classes/bios/bios100/lectf03am/lect06.htm
XI. Mitochondria / Cellular Metabolism
A. Mitochondria: The “powerhouse” of the cell, “because they (use enzymes) to convert the chemical energy of glucose products into the chemical energy of ATP molecules” (Mader 51).
B. Use up oxygen and expel carbon dioxide. This process is called cellular respiration.
C. Cristae: The inner membrane of mitochondria that is folded to form little shelves. ATP production occurs here. (Mader 51-52)
C. “A highly folded organelle in eukaryotic cells.”
D. Believed to have originated from an engulfed prokaryotic cell. (Frolich PowerPoint) They are bounded by a double membrane, just as a prokaryote would be if taken into a cell.
E. Have their own genes, and can reproduce themselves. (Mader 53)

(Frolich PowerPoint Slide 38)
XII. Cellular Respiration / Metabolism
A. Metabolism: All of the chemical reactions that happen in a cell.
B. “Each reaction in a metabolic pathway requires a specific enzyme” (Mader 53).
C. Enzyme: “Any of several complex proteins that are produced by cells and act as catalysts in specific biochemical reactions.” (Webster’s Online Dictionary)
D. The reactant that is involved when an enzyme speeds up a reaction is called the enzyme’s substrate.
1c. Enzymes are often named for these substrates. (Mader 53)
E. Active Site: The specific region of enzymes, where substrates are brought together so they can react.
F. Coenzymes: Nonprotein molecules that assist an enzyme in its activities. May accept or contribute atoms to the reaction.
G. There are three metabolic pathways involved in the breakdown of glucose: Glycolysis, the citric acid cycle, and the electron transport chain.
1g. All three pathways allow the energy within a molecule of glucose to release slowly, which allows ATP to be produced slowly as well. This helps preserve the amount of energy a cell gets, because if it happened too fast, a good deal of energy would be converted to heat, and therefore lost.
2g. Glycolysis: Sugar splitting. Occurs in the cytoplasm and is present in most cells. Occurs when glucose (6 carbons) is split into two 3-carbon molecules. Anaerobic- requires no oxygen.
3g. Citric Acid Cycle: Completes the breakdown of glucose. “As the series of enzymatic reactions occur in the matrix of the mitochondria, carbon dioxide is released”. Produces 2 ATP molecules per glucose molecule. If our cells run out of glucose, fatty acids become the substitute. These “fatty acids can yield carbon molecules that can enter the citric acid cycle.” When a protein is digested and becomes an amino acid, the carbon chain can also enter the citric acid cycle, after the amino group is removed from the carbon chain. Occurs mostly in liver. Aerobic: oxygen is present.
4g. Electron Transport Chain: Carrier proteins, grouped into “complexes, which are entrenched in the cristae of the mitochondrion. Each carrier takes two electrons and passes them to the next carrier. Aerobic. (Mader 54-55)
H. Other molecules besides glucose can be used for cellular respiration: lipids, proteins, and other carbs. (Frolich PowerPoint)
I. Fermentation: A cell can make ATP without oxygen by the process of fermentation. (Frolich PowerPoint)
1i. Definition: “Anaerobic breakdown of glucose that results in a gain of two ATP and end products, such as alcohol and lactate” (Mader Glossary G-7).
2i. Takes place in cytoplasm. (Frolich PowerPoint)
3i. Anaerobic. Electron transport chain becomes unable to function because of the lack of oxygen. So, the citric acid cycle and the electron transport chain are not involved in fermentation. (Mader 56) Involves Glycolysis.
4i. Allows for a burst of energy for a short period of time. (Frolich PowerPoint)
J. Cell Metabolism: VERY complex.
1i. “Important to remember:
- Every one of these reactions is catalyzed by a protein
- The amino acid sequence for those proteins are coded for in the DNA
- The world’s biggest super-computers are trying to figure out how, based on their unique amino acid sequence, all the different cellular proteins take on the particular shape they have, and control the particular reaction they catalyze.” (Frolich PowerPoint)
Chapter 4
I. 4 Classes of Tissue: Several types
II. Cells in the human body
A. The human body contains a few hundred different types of cells, with the total being somewhere in the area of one-hundred trillion cells, total. (Frolich PowerPoint)
III. Types of Tissues
A. A tissue is made up of specialized cells of the same type that perform a common function. (Frolich PowerPoint)
1a. 4 types:
- Connective: binds and supports the parts of the body.
- Muscular: allows the body and it’s parts to move.
- Nervous: Receives stimuli and conduct nerve impulses.
- Epithelial: Covers body surfaces and lines body cavities.


http://www.kcci.com/encyclopedia/6868654/detail.html
B. Connective Tissues
1b. “Binds and supports parts of the body.” Holds things together. Can be found in tendon, bone, cartilage, and throughout the body to support blood vessels, nerves, and cell populations. (Frolich PowerPoint)
2b. Even though this tissue may have many different structures and functions, all connective tissue have three parts: specialized cells, ground substance, and protein fibers.
3b. Ground substance: noncellular material that separates the cells and has different consistencies, ranging from solid to semifluid to fluid.
4b. Fibers: 3 possible types
- White collagen fibers: collagen is a protein that allows them to be flexible and strong.
- Reticular fibers: Very thin collagen fibers, highly branched, forms fragile networks of support.
- Elastic fibers: Elastin is a protein that is not as strong as collagen, but it is elastic and flexible. (Mader 62)
5b. 3 main types of connective tissue:
1.- Fibrous: contain cells called fibroblasts, which are located somewhat far apart from one another and are kept apart by a ground substance that is similar to jelly. Matrix refers to the ground substance and fibers. Loose fibrous connective tissue (AKA areolar) supports epithelium and many internal organs, like the lungs, arteries, and urinary bladder. It also provides a protective covering. Adipose tissue allows cells to enlarge and store fat for energy, heat, and organ protection. Dense fibrous connective tissue contains numerous collagen fibers packed together. Found in tendons, which connect bones and muscles, and in ligaments, which connect bones to other bones at the joint.
2.- Supportive: Cartilage. Cells reside in Lacunae, separated by a solid matrix. Three types of cartilage: Hyaline (most common). Found in nose and at the ends of long bones and ribs, and in the walls of respiratory passages. Also composes the fetal skeleton. Elastic Cartilage: more elastic fibers than hyaline. More flexible… found in outer ear. Fibrocartilage: Matrix containing strong collagen fibers, found in discs between the vertebrae and knees.
Bone: Most rigid connective tissue. Extremely hard matrix. Compact bone makes up the shaft of a long bone, and consists of units in the shape of cylinders, called osteons. Spongy bone: Lighter than compact bone, it is still made for strength.
3.- Fluid: Two fluid connective tissues: blood and lymph. Blood: consists of formed elements (red blood cells to transport oxygen, white blood cells to fight infection by engulfing pathogens or producing antibodies), and plasma, located in blood vessels. Blood helps distribute heat and balance out fluid, ion, and pH balance. Platelets are incomplete cells, and are only present in bone marrow. Tissue fluid: Bathes the body’s cells, removing carbon dioxide and other wastes. Lymph: Clear, watery, sometimes yellowish fluid that contains white blood cells. Lymphatic vessels transport lymph to particular vessels of the cardiovascular system and absorb fat from the small intestine. (Mader 62-64)

Red Blood Cells VS White Blood Cells
http://www.afhlivertransplantsupport.co.uk/16901.html?*session*id*key*=*session*id*val*
http://www.visualsunlimited.com/browse/vu214/vu214085.html
C. Muscular Tissue
1c. Allows for movement in the body.
2c. Made of muscle fibers/cells and protein fibers called actin and myosin. (Frolich PowerPoint)
3c. Three types of muscular tissue: skeletal, smooth, cardiac
1.- Skeletal: Voluntary muscle, attached by tendons to bones of the skeleton. It’s contractions cause body movements. Muscle fibers are cylindrical and long. One fiber has multiple nuclei. Fiber’s alternating light and dark bands create a striated, or striped appearance. Bands are created by the placement of actin and myosin filaments in the cell. (Mader 65)
(Frolich PowerPoint Slide 56)
2.- Smooth (visceral): Named for it’s lack of striations. Spindle-shaped cells, single nucleus. Control is involuntary. Found in the walls of the viscera and blood vessels, contracts more slowly than skeletal muscle but can remain contracted longer.

(No striations)
http://www.uoguelph.ca/zoology/devobio/miller...
3.- Cardiac: Found only in the walls of the heart. When it contracts, blood is pumped and the heart beats. Contains features of both smooth and skeletal muscle. Has striations. The contraction of the heart is mostly involuntary. Single, centrally placed nucleus. Cells are seemingly fused together. Heart is composed of one very big mass of muscle cells all interconnected. (Actually separate, but “bound end to end at intercalated disks: areas where
folded plasma membranes between two cells contain adhesion junctions and gap junctions.”) (Mader 65)
Cardiac Muscle
http://dms.dartmouth.edu/anatomy/education/ct...
D. Nervous Tissue
1d. 3 functions: “Allows for communication within cells through sensory input, integration of data, and motor output” (Frolich PowerPoint)
2d. Made up of nerve cells called neurons, which carry messages, and neuroglia, whose job it is to support and nourish the neurons. (Frolich PowerPoint)
3d. Neurons: 3 components:
1.- “Dendrites: An extension that receives signals from sensory receptors or other neurons.”
2.- “Cell Body: Houses most of the cell’s cytoplasm and the nucleus. “
3.- “Axon: An extension that conducts nerve impulses.” (Mader 66)
http://www.bcm.edu/cain_foundation/noframes/html/pages/staff/robert_mcneil.htm
4d. Nerves are formed by binding of fibers by the connective tissue (excluding the brain and spinal cord).
5d. Neuroglia: These cells outnumber neurons 9:1. They are responsible for the make-up of more than half the volume of the brain. No long extensions.
- The 3 types found in the brain ( and in the order they appear below) are: oligodendrocytes, astrocytes, and microglia. (Mader 66)

http://www.afh.bio.br/nervoso/nervoso2.asp
E. Epithelial Tissue
1e. “Group of cells that form a tight, continuous network.”
2e. “Covers the body surfaces, lines body cavities, and can also be located in glands.”
3e. “Cells are anchored by a basement membrane on one side and free on the other side.”
4e. Usually has a protective function, but can also be modified to carry out secretion,
excretion, absorption, and filtration. (Mader 68)
5e. “Different types of epithelial cells are named after the appearance of cell layers and the
shape of cells.” (Frolich PowerPoint)
6e. Epithelial tissue is either simple (containing only one layer of cells) or stratified (cells
piled on top of one another).
- Simple Epithelial Tissues:
1.- Squamous epithelium: Made up of flattened cells. Resides in the lining of the air sacs of
lungs and in the walls of blood vessels. Can exchange substances.
2.- Cuboidal epithelium: Made up of a single layer of cube-shaped cells. Frequently found in
glands and the pancreas. Also covers the ovaries and parts of the kidney. Contain
mitochondria when involved in active transport.
3.- Columnar epithelium: Cells resemble rectangular pillars or columns. Contains nuclei,
which are located in the bottom of the cell. Found lining the digestive track. Helps to absorb
the products of digestion. (Mader 68)
4.- Pseudostratified epithelium: Appears to be layered, but true layers can not exist because
each cell touches the basement membrane. Nuclei is irregularly placed, which makes it
appear to be several layers, whereas there is really only one. Found in the lining of the wind-
pipe. (Mader 68)
5.- “… Transitional epithelium that changes in appearance in response to tension.”
(Frolich PowerPoint) Forms the lining of the ureters, the urinary bladder itself, and part
of the urethra. Since all of these organs need to stretch, this epithelium stretches, and when
they do, they take on a squamous appearance. Similar to columnar epithelium. (Mader 69)
- Stratified Epithelial Tissues: Of all the layers, only the bottom one comes into contact with
the basement membrane. “Nose, mouth, esophagus, anal canal, outer portion of the cervix
and vagina are all lined with stratified squamous epithelium” (Mader 69).
7e. The product that an epithelium secretes is called “glandular”. Gland can have many cells
or only a single epithelial cell.
1.- Exocrine gland: Contains ducts that secrete their product onto the outer surface or into a
cavity.
2.- Endocrine gland: Ductless. J (Mader 69)





(Frolich PowerPoint)
IV. Cell Junctions
A. Cell junctions help a tissue perform its particular duty. The epithelial cells, and sometimes the muscle and nerve cells of a tissue are connected by these cell junctions. (Act as cement.) These junctions arise when plasma membranes come together in the following ways:
1a. Tight junctions: Epithelial cells are permitted to form a layer that covers the surface of
organs and lines body cavities.
2a. Adhesion junctions: Attach cytoskeletal fibers of one cell firmly to that of another cell.
3a. Gap junctions: “Occur when adjacent plasma membranes converge and leave a tiny
channel between them.” (Mader 70)
V. Integumentary System
A. Organ: Composed of two or more types of tissues that work together to perform specific functions.
B. Organ System: Contains many various organs that cooperate to carry out a process.
C. Skin: Since the skin has several accessory organs, such as sweat glands, hair, and nails), it is sometimes called the integumentary system. Most noticeable system in the body because the body is covered with it. It protects underlying tissues and helps in maintaining homeostasis by regulating body temperature. (Mader 71)
1c. Two regions: epidermis and dermis. There is also a subcutaneous layer between the skin
its underlying structures.
1.- Epidermis: Stratified squamous epithelium. New epidermal cells come from stem cells
and are used to renew the skin. These new cells become hard as they reach the surface,
because of the production of keratin, a waterproof protein. Within the epidermis are two
types of specialized cells: langerhans (macrophages, a type of white blood cell) and
melanocytes (produce melanin).
2.- Dermis: Region of dense fibrous connective tissue underneath the epidermis. Contains
collagen and elastic fibers. They prevent the skin from tearing, because the fibers stretch to
allow the muscles and joints underneath to move.
D. Subcutaneous layer: Technically, not a part of the skin. Composed of loose connective tissue and adipose tissue. Provides protection and heat.
E. Accessory organs of the skin: nails, hair follicles, oil glands, and sweat glands. (Mader 72-73)

http://malibuhigh.smmusd.org/~dtucker/images

VI. Organ Systems / Functions
A. Integumentary: includes nails, hair, muscles that move hair, the oil and sweat glands, blood vessels, and nerves leading to sensory receptors. Assists in many homeostatic functions.
(see image above)
B. Cardiovascular: heart pumps blood and sends it out into the blood vessels.

C. Lymphatic and Immune Systems: lymphatic vessels, lymph nodes, spleen, and other lymphatic organs. Immune system: All the cells in the body that protect it from disease.



D. Digestive System: mouth, esophagus, stomach, small intestine, and large intestine. Associated also with the teeth, tongue, salivary glands, liver, gallbladder, and pancreas.

E. Respiratory: lungs and the tubes that take air to and from them.

http://www.coventry.ac.uk/ec/~nhunt/180sor/howgate/air.html
F. Urinary: kidneys, urinary bladder, and the tubes that carry urine.

http://kidney.niddk.nih.gov/kudiseases/pubs/yoururinary/index.htm



G. Skeletal: protect body parts.

H. Muscular: involves skeletal muscle contractions, cardiac muscle contraction, and the walls of internal organs.


I. Nervous: brain, spinal cord, and associated nerves.

J. Endocrine: hormonal glands.

K. Reproductive: Male: testes, other glands, various ducts. Female: ovaries, oviducts, uterus, vagina, and external genitals. (Mader 74-75)
*** All of these dark body images are from www.innerbody.com
VII. Body Cavities
A. Body has two main cavities: ventral cavity and dorsal cavity.
1a. Ventral cavity progresses into the thoracic, abdominal, and pelvic cavities. Thoracic
contains lung and heart, and is separated from the abdominal cavity by the diaphragm.
Abdominal cavity: holds the stomach, liver, spleen, pancreas, gallbladder, and most of the
small and large intestines. Pelvic: houses the rectum, urinary bladder, internal reproductive
organs, and the rest of the small and large intestine.
2a. Dorsal cavity has two parts: cranial cavity that contains the brain, and the vertebral
canal that contains the spinal cord. (Mader 77)
VIII. Body Membranes
A. “Line cavities and internal spaces of organs and tubes that open to the outside” (Mader 77)
1a. Mucous membranes: coat the tubes of the digestive, respiratory, urinary, and
reproductive systems. Composed of an epithelium over a loose fibrous connective tissue.
Secretes mucous that helps protect the body.
1b. Serous membranes: line and support the lungs, heart, and abdominal cavity and its
internal organs. Secretes a watery fluid to lubricate membranes.
1c. Synovial membranes: composed only of loose connective tissue. Lines the cavities of
joints that can be moved at will.
1d. Meninges: found within the dorsal cavity. Connective tissue that protects the brain and
spinal cord. (Mader 77)
IX. Homeostasis
A. Body’s ability to keep a relative constancy of its internal environment.
B. Negative Feedback: “The primary homeostatic mechanism that keeps a variable, such as the blood glucose level, close to its set point. This mechanism is present when the output of the system dampens the original stimulus” (Mader 78, 80).
C. Positive Feedback: Mechanism that brings about an ever greater change in the same direction. (ie- when a woman is giving birth.)

Information from Online Activities:
I. Facilitated Diffusion
A. Diffusion: Molecules move from higher to lower concentrations. Affected by the temperature, size of the molecules, and the steepness of the gradient.
B. Requires carrier proteins.
C. Occurs in either direction, depending on the concentration gradient of the molecule.
D. Used to transport sugars and amino acids.
E. Does not require energy expenditure by the cell.
II. Active Transport
A. The sodium-potassium pump is the mechanism that functions to pump sodium ions out of the cell and potassium ions into it.
B. Powered by the breakdown of ATP.
C. Pump binds and moves 3 Na+ (sodium) and 2 K+ (potassium) molecules.
D. It is a trans-membrane protein.
E. The binding and release of ions is due to conformational changes in the protein.
III. Endocytosis and Exocytosis
A. Exocytosis: Process of the release of substances from the cell via vesicles.
B. Phagocytosis: White blood cells engulf microorganisms and bring them in for digestion.
C. Receptor-mediated endocytosis involves clathrin-coated pits.
D. Pinocylosis: Cell takes in liquids.
E. Low density lipoprotein is brought into cell by receptor-mediated endocytosis.
IV. Folding@home Distributed Computing
A. Dec. 1999: IBM announces a 5-year effort to build a massively parallel computer to study
1. Goal 1: Advance understanding of protein folding, misfolding, and related diseases.
2. Explore novel ideas in massively parallel machine architecture and software.

B. IBM’s BlueGene / L System- World’s most powerful supercomputer.
1. Developed with the Department of Energy’s National Nuclear Security Agency, and is
housed at the Lawrence Livermore National Lab.
C. Some finding:
1. Confined water acts to denature proteins.
2. Roughly ½ of all known cancers results from mutations in p53. Can predict how p53 folds,
which therefore allows a prediction for which amino acid mutations would be relevant.
3. Has successfully folded a small 36-residue alpha helical protein and a small protein with
a beta-beta-alpha fold.