MY COMPENDIUM - UNIT I THE CELL

MY COMPENDIUM
UNIT I - THE CELL

TABLE OF CONTENTS:
Characteristics of Life
Molecular levels, acids & bases
Water
Cells structure and function
Cell organelles and metabolism
Tissues, cellular junctions & Organ systems


CHARACTERISTICS OF LIFE

Life is an organized hierarchically and evolution is key. With evolution the first evidence was cellular life. It was a prokaryotic cell which scientists believed manifested into a eukaryotic cell. Humans have eukaryotic cells and bacteria have prokaryotic cells. All living things (organisms) share the characteristics of life. What I mean by that is we have the same internal functions in order to survive. Internally, we have a well organized system. The biological chart below shows the organization within us. Courteous of my professor Larry Frolich. Due to the pic being a little blurry I have explained what you are seeing on that chart. I will elaborate on some of these in my molecular levels section.

ATOMS – these are the smallest unit of an element composed of electron, protons and neutrons.

MOLECULES – is the union of two or more atoms.

CELL – the structural and functional unit of all living things.

TISSUE – a group of cells with a common structure and function

ORGAN – composed of tissues functioning together for a specific task

ORGAN SYSTEM – composed of several organs working together

ORGANISM – an individual, complex individuals contains organ systems

POPULATION – organisms of the same species in a particular area

COMMUNITY – interacting populations in a particular area

ECOSYSTEM – a community plus the physical environment

BIOSPHERE- regions of the earth’s crust, waters, and atmosphere inhabited by living organisms.

As you can see, it is not as complex as it seems. When you break down it makes sense. In order to survive and evolve there are six main components we all need :

ENERGY – eating food to survive. Food is broken down in the body and produces energy.
REPRODUCTION – creating a copy of yourself (offspring). This ensures extinction. This is done by genes which express a detailed copy of cells.
GROWTH & DEVELOPMENT – we grow and with that cells multiple. Development also includes repairs to cell if an injury occurs.
HOMEOSTATIC – is the internal environment of a living organism. All organ systems have a function in homeostasis EXAMPLE: digestive system; helps us absorb nutrients we need to survive.
STIMULI – EXAMPLE: hunger pains—“we eat” cold—“put a coat on,” Homeostasis would be impossible without stimuli. They work side by side as my example indicates
EVOLUTIONARY HISTORY – evolution is the process by which a species changes through time. Every organism is a new generation of OLD.

I would also like to point out that humans are related to animals. All organisms are placed in a classification which is called taxonomy. Carolus Linneus
Created these classifications. 1700's - Carols Linnaeus - Swedish Biologist Linnaeus Taxonomy"
· established a simple system for classifying and naming organisms
· Based on structural similarities of organism
· Binomial Nomenclature - 2 name naming system - still in use today.
· Created a system of groups called TAXA or TAXON
· Each Taxon is a category into which related organisms are placed
Approximately 2.5 million kinds of organisms identified

This is a sample of what the taxonomy looks like for humans…..

DOMAINS: Eurkarya
KINGDOM: Animalia
PHYLUM: Chordata (we have spinal cord)
CLASS: Mammalia
ORDER: Primates
FAMILY: Hominoidea (apes & humans), no tails
GENUS: Homo
SPECIES: Sapiens (homosapiens)

There are 2 other domains. Arachaea & Bacteria. Arachaea acts like bacteria. These are both prokaryotic and humans are eukaryotic.This just means that our cells are built differently. The prokaryotic are very small, no nuclei, no organelles and their cell wall is composed of
peptidoglycan, actually only bacteria has the peptidoglycan (made of peptide and glycogen- sugar). The eukaryotic cell is very well organized in that it has organelles hard at work inside, has a nuclei, plasma membrane, and are larger the prokaryotic.

MOLECULAR LEVEL

The molecular level is a lot of chemistry that is going on in our bodies, which people are unaware. Humans, along with other organisms, are an incredible piece of, well, machinery. We start out with atoms which I explained as being the smallest unit of an element composed of electrons that are negatively charged, protons that are positively charged and neutrons which have no charge, making them neutral. The electron, neutron, and protons are subunits of the atom. When the atom joins with others they become molecules of LIFE. Some atoms that join together are the same, but if they are different they are called a compound ie., hydrogen and oxygen = water. There are 2 bonds that hold atoms together.

COVALENT BOND – this is sharing of electrons. It is a very strong bond.
IONIC BOND – is a chemical bond when ions are attracted to one another by opposite charges. Ie., cation – positive ion and anion
Negatively charged ion

A great example of an ionic bond is table salt. When salt is placed in water, what does it do? It dissolves. That’s where the cation ion
and anion ion come together. There is also hydrogen bonds. These bonds are extremely weak and are easily broken. A great example
of this is H & O2= WATER. There are 4 very important molecules in life.

PROTEINS – plays a crucial role in all biological processes. Main structural components of a cell. All chemical reactions in the body are catalyzed by enzymes all of which are proteins. They are made up of a monomer call amino acids. Structure of protein organization. They actually fold by steps. First are the primary structure, secondary structure, tertiary structure and lastly quaternary structure. All made of polypeptide chains.
CARBOHYDRATES – 3 types; monosaccharide which are simple sugars mono= one. Disaccharides (di=2) which are sugars formed by linking 2 monosaccharide molecules together through a covalent bond ie., table sugar, lactose. Polysaccharides (poly=many) carbohydrate molecules bond together and form a long chain that contains many saccharides units ie., glycogen, starch, cellulose.
FATS OR LIPIDS – these are insoluble in water. There are 2 components of lipids. Fatty acids and alcohol.
NUCLEIC ACIDS- Two types; DNA and RNA. Are responsible for storing and using genetic information in living cells and passing it on to future generations. DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) contains organic nitrogenous base, a sugar, and a phosphate group.

ACIDS & BASES

Acids and bases refer to a pH scale. Acids, which you probably know are in a lot of stuff we consume like, tomatoes, juices, and sauces.
Bases are also in a lot stuff we consume like; egg whites, milk, and even human blood (hope no one consumes that)! Substances like hydrochloric acid donate hydrogen ions to a solution making it acidic. Substances with sodium hydroxide accept hydrogen ions or contain hydroxyl ions and are very basic or alkaline. Scientists use the pH scale which ranges from 0 – 14 to indicate acid or alkaline. Acid is 0 – 6 and alkaline is 7.5 to 14. With pure water the number of hydrogen ions is the same as the of hydroxyl ions so water has a pH of 7 and is neutral. Ahhhhh, WATER, which bring me to my next topic.

WATER

Water is the universal solvent!! Water molecules are cohesive because of their polarity and hydrogen bonds. Water is also the most abundant molecule in living organisms. As I said above, water is connected by hydrogen bonds. The electrons (negative charge) are closer to the oxygen
atom, the oxygen atom becomes slightly negative and the hydrogen are slightly positive. This makes water a polar molecule. Water plays such a key role in our body. One of it great roles is the way it interacts with the human cell. The cell being selectively permeable lets water easily permeate the membrane. There are different ways water can get through. One is diffusion, in which it involves the movement of ions or molecules from high concentration to low concentration until the sides are equal. Secondly is osmosis which involves the flow of water across the cell membrane. These two are pretty much identical. The concentration gradient exists when the amount of a solute found in one region is greater then the amount of the solute in another. Things that influence the rate of diffusion/osmosis is the particle size, temperature of the system, solvent density. The stepper the concentration gradient and smaller the particle size the faster the rate of diffusion. The cell membrane is a great example when it comes to the next 3 terms because of the intercellular fluid is within the cell and the ECF =extracellular fluid is outside the cell. When the ECF has a lower osmotic pressure then the ICF the extracelluar fluid is said to be HYPOTONIC and water will flow into the cell causing the cell to swell and
possibly burst. When the cell has low osmotic pressure, water flows out of the cell and the cell will shrivel up making it HYPERTONIC. If the fluids have identical osmotic pressure it is said to be ISOTONIC. There are also to important processes that occur with water. Hydrolysis which is splitting of a compound by the addition of water. Dehydration is another process that occurs and it results from a covalent bond with the accompanying loss of a water molecule.

CELL STRUCTURE AND FUNCTION

The cell functions in many different ways for our survival. I have composed a list of these functions.

obtains food (nutrients) and oxygen from the environment surrounding the cell
performs chemical reactions that use the nutrients and oxygen to provide energy for the cell. Ie., food + O2 + H2O + energy
eliminating CO2 and other wastes produced during the chemical reactions
synthesizes proteins and other components needed for cell structure, growth and carrying out a cell function
controlling the exchange of materials between the cell and its surrounding environment
moving material from one part of the cell to another in carrying out cell activities, some move entirely.
being sensitive and responsive to change in surrounding environment
reproducing

The cells structure is much more complicated. It has several organelles that function together. This is a list of the structures of the cell and a brief description of how they function.

CELL MEMBRANE – consists of mostly lipids, fats, and proteins. This membrane is selectively permeable, meaning some particles are easily let in and others require energy to pass through. Keeps Intracellular fluid within the cells form mingling with Extracellular fluid outside of the cells. Encloses each cell.
PHOSPHLIPIDS - have a polar (charged) head containing a negatively charged phosphate group and 2 nonpolar (electrically neutral) fatty acid tails. Structure of this is critical of membrane amipathic nature, meaning it contains both polar and nonpolar domains. The polar ends are Hydrophilic because it can interact with water molecules, which are also polar. The nonpolar end is Hydrophobic and will not mix with water. The 2 sided molecule self assemble into a lipid bilayer!
NUCLEUS – the largest single organized cell component. Houses the cells genetic material DNA (deoxyribonucleic acid) directs protein synthesis, serves as a genetic blueprint during cell replication.
CYTOPLASM – is the portion of the cell interior not occupied by the nucleus. Contains organelles (little organs) dispersed with the cytosol
ORGANELLES – each organelle is a separate compartment within the cell that is enclosed by a membrane similar to the plasma membrane. They are like intercellular specialty shops, each carrying out specific set of chemicals for carrying out particular cell function.
CYTOSOL - is the extension of the cytoplasm. Has an elaborate protein network called a cytoskeleton. The cytoskeleton gives the cell shape, provides internal organization and regulates movement. It contains three elements; microtubules, (movement of cell components), microfilaments; (movement of the cell or changes in cell shape) and intermediate filaments; (strictly structural, uses keratin).
CILIA AND FLAGELLA – these produce movement. Cilia is (in the respiratory tract, moves an egg along the oviduct) sweep unwanted particles trapped in mucous back up the throat, which helps clean out the lungs. Flagella are a whip-like movement with long tails a good example of flagella is male sperm. The flagella is the tail and help the sperm swim. Both of these are grown from basal bodies.

LIST OF ORGANELLES AND BRIEF FUNCTION

RIBOSOMES – carries out protein synthesis.
ENDOPLASMIC RETICULUM – primarily a protein and lipid manufacturing factory
SMOOTH ER – lipid and steroid metabolism. Portions of the smooth ER “bud off” after receiving synthesized proteins and lipids the pinched off forming transport vesicles. Meshwork of tiny interconnected tubules.
ROUGH ER - ribosome’s attached rRNA (ribosomal RNA) flattened sacs is part of protein synthesis making vesicles
GOLGI COMPLEX - stacked flattened membrane enclosed sacs. Processes raw material into finished products, pinched into vesicles with final product – docking markers. Each vesicle can doc and unload only at the appropriate docking marker acceptor.
LYOSOMES – performed in the golgi complex. Contains hydrolytic enzymes which catalyze (break down) hydrolysis reactions. Uses endocytosis (released particles within the cell). There are three types of endocytosis. Pinocytosis (cell drinking) brings in a droplet of ECF. Receptor-mediated endocytosis; highly selective process that enables cells to import specific large molecules. (traps proteins inside the cell, ie., cholesterol. Phagocytosis (cell eating) engulfs large substances, forming an intercellular vacuole.
MITOCHONDRIA - energy producing organelle. They extract energy from the nutrients in food and transform it into a useable form for cell activities. Most importantly, generates ATP (adenosine triphosphate- our energy). Has 2 parts cristae – inner membrane that forms series of shelves. Also increases the surface area for electron transport chain (which occurs in metabolism and the matrix which consists of hundreds of different dissolved enzymes.
I would like to explain how the process of cellular respiration works. Metabolism is the total chemical reactions that occur in a cell. It starts with glycolysis, (happens in the cytoplasm) which is the break down of glucose and turns into pyruvate acid or it can produce fermentation in which lactate is produced Lactate is what makes that burning sensation when you are working out. You feel a burn. This step does not require oxygen, making it anaerobic. Next step is the Krebs cycle (happens in the matrix of the mitochondria), which requires oxygen (aerobic), and produces ATP at the end of its cycle, 2 to be exact. Third step is the Electron transport chain, (happen in the cristae of the mitochondria) which also requires oxygen and produces the most ATP= 32. These steps are highly organized. They use electrons, coenzymes NAD, (nictinamide adenine dinucleotide), release of carbon dioxide. These steps are really hard to put into works, but I understand completely how they work. I could go on forever. There would be not end to this compendium.

HOW PARTICLES OR PROTEINS PASS THROUGH THE PLASMA MEMBRANE

I explained early how diffusion and osmosis worked, but in order for proteins to pass over there is a special transport because they are so large.
Active transport the moves from low concentration to high concentration, which is opposite of osmosis. Active transport requires a protein carrier and use of cellular energy obtained from the breakdown of ATP. Facilitated diffusion does not require ATP it uses a carrier to transport downhill.
The sodium/potassium pump is active transport pump critically important in the ability of nerve and muscle cells to generate electrical signals essential to their functioning. 3 Na+ (sodium) out of the cell, 2 K (potassium) pumped into the cell.


TISSUES, CELLULAR JUNCTIONS & ORGAN SYSTEMS

There are four main tissue types. Tissues are composed of specialized cells of the same type to perform a common function in the body.

MUSCLE TISSUE - consists of cells specialized for contracting and generating force. Three types. Skeletal muscle; moves skeleton. Cardiac muscle; pumps blood. Smooth muscle; encloses and controls movement of contents through hollow tubes and organs.
NERVOUS TISSUE – consists of cells (neurons) specialized for initiating and transmitting electrical impulses. These are found in the brain, spinal cord, and external environment.
EPITHELIAL TISSUE - cells specialized for exchanging material between the cell and its environment. Any substance that crosses the body proper must cross an epithelial barrier. Our bodies’ organs are covered with epithelial tissue. It is organized into 2 type’s f structures. Epithelial sheets; serves as boundary, ie., GI tract, lungs. Secretory glands; exocrine gland; secretes through ducts to outside of the body or into a cavity that opens to the outside. Endocrine gland; lacks ducts and release their secretory products known as hormones in the blood stream, ie pancreas secretes insulin. There are also 3 types of epithelial tissues. Squamous epithelium its shape and arrangement helps permit exchanges of substances, ie air sac of lungs and walls of blood vessels. Cuboidal epithelium, single layer. Found in glands and contain microvilli that help increase the surface area for absorption. Columnar epithelium, lines the widepipe, also, they have cilia which help trap mucous and send it back to the throat to get rid of the debris.
CONNECTIVE TISSUE – connects, supports, and anchors. Includes diverse structures as the loose connective tissue attaches epithelial tissues to underlying structures; tendons. Except for blood, the cells within connective tissue produce specific structural molecules that release into the extracellular spaces between cells. One molecule is the rubber band like protein called ELASTIN- this facilitates the stretching and recoiling of structures such as lungs.

CELLUALR JUNCTIONS


These junctions help tissue perform its particular function. There are 3 types

DESMOSOMES – (cells being pushed together) “spot rivets” that anchor together to closely adjacent but nontouching cells. Found in tissues; skin, heart and uterus. There are 2 components. A pair of dense, button like cytoplasmic thickening known as plaque and strong filaments that extends across the space between the 2 cells and attach to the plaque on both sides
TIGHT JUNCTIONS- adjacent cells firmly bind with each other to seal off passageways between 2 cells
GAP JUNCTIONS – (communicating junctions) As the name implies a gap exists between adjacent cells which are linked by small connecting tunnels formed by connexons. They are made up of 6 protein subunits. Most abundant in cardiac muscle.

ORGAN SYSTEMS

All these system work together to promote homeostasis!! Negative feedback is a one of the primary homeostatic mechanism that keeps a variable, like blood glucose level close to a set point. Example…when body temp rises the response is to seat, evaporating cooling. Vasodilatation vessels on the surface of the skin increase in diameter – dissipates heat; increases fluid, thirst, less urination – remove clothing
Positive feedback – works against homeostasis. There is no set point and the body is not regulated. It is useful in the birthing process as the cervix dilates it produces oxitocin and with further dilation the cervix producing more oxitocin.
There are 11 organ systems. Here is a pic for you to view. I will give a brief description of each.

NERVOUS SYSTEM - Acts through electrical signals to control rapid responses of the body.
CARDIOVASCULAR SYSTEM – Transports oxygen and nutrients to tissue cell and transports wastes away from cells.
DIGESTIVE SYSTEM – Obtains nutrients, water, and electrolytes from the external environment and transfers them into the plasma and eliminates undigested food residue to the external environment.
MUSCULAR/SKELETAL SYSTEM – Supports and protects body parts and allow body movement Heat-generating muscle contractions are important in temperature regulation.
INTEGUMENTARY SYSTEM – Serves as a protective barrier the external environment and the remainder of the body; the sweat glands and adjustments in skin blood flow are important in temperature regulation
IMMUNE SYSTEM – Defends against foreign invaders and cancer cells; pave the way for tissue repair
RESPIRATORY SYSTEM – Obtains oxygen from and eliminates carbon dioxide to the external environment, helps regulate pH by adjusting the rate of removal of acid-forming carbon dioxide.
URINARY SYSTEM – Important in regulating the volume, electrolytes composition, and pH of the internal environment. Removes wastes and excess water, salt, acid, and other electrolytes form the plasma and eliminates then in the urine.
REPORDUCTIVE SYSTEM – This doesn’t really help with homeostasis, but is important for perpetuation of out species.
ENDOCRINE SYSTEM – Acts by means of hormones secreted into the blood stream to regulate processes that require duration rather then speed i.e., metabolic activities, water and electrolyte balance.
LYMPHATIC SYSTEM – Helps maintain blood volume by collecting excess tissue fluid and returning it via lymphatic vessels to the cardiovascular veins. Defends against disease.

Conclusion: I am sure that I may not have touched on some points, but isn’t that what a compendium is. I tried to condense a lot of information into
my compendium that I thought was important. The body is a complex system, but once you understand it; it is AMAZING!!!! I tried to include pictures from the world wide web as best I could. I feel that pictures help visualize what is being explained. These are the wesites where I

copied some pictures.......

www.fotosearch.com/photos-images/atoms.html

http://www.wikipedia.com/

www.biologie.uni-hamburg.de/b-online/e22/22.htm