Measurement Lab

Below shows the set-up and some examples of the volume portion of the lab that we completed in class.  As you can see there were some measurement mistakes whether it be from not looking at the scale or not reading from the bottom of the meniscus.  We spoke about possible sources of error after we finished the procedure.

Graphing

Graphing of data is a tool used by scientists, researchers, teachers, and students to show trends in data.  Without graphs, data would just be a jumble of numbers, a real pain to sort through and understand.

Why do we need to be able to graph data?

          Graphing of data, that is the physical representation of the data, is a tool used by scientists, researchers, teachers, and students to show trends or imply similarities or differences in data that was collected during the course of an investigation or experiment  Without graphs, data becomes a “sea of numbers” and many people have a very difficult time understanding exactly what the data has shown.  However, graphs can sometimes be misleading, especially when they are constructed improperly.  That is why we need to be able to accurately reflect the data that we are trying to express.

“But I don’t like to graph!  Can’t I show my data another way??”

          Sure!  Graphing is nothing more than a tool used to help people understand.  A hammer is a tool used to pound nails,  a wrench is a tool used to turn a bolt, a dump truck is a tool used to carry heavy loads.  In the same manner, a graph is a tool that we use to perform a task or more accurately show something.  So, if you don’t like graphs, try to pound a nail without a hammer or carry a bunch of rocks one by one to dump into your driveway.

“OK, so I  need to be able to draw a graph.  What if I mess it up?”

            Wait a minute…..  I never said we had to be perfect the first time!  Graphing is an accomplished skill.  The more you do it, the better you become!  This packet is designed to help you understand the different type of graphing that might be expected in the Living Environment course.  Follow these simple rules:

              #1 – Arm yourself!!!  Not with anything permanent.  Using a sharp pencil is the best thing.  Using a pen will lead only to intense frustration for you and excessive copying of replacement pages for your teacher.  Also, if your pencil is your sword, your good quality eraser is your shield.  Have one handy to help you fix any mistakes.

               #2 – Prepare for battle!  Just as you would never think of entering into a battle without the necessary materials and intelligence, do not think that you can conquer a graph without the necessary materials and knowledge.  Make sure you have supplies, including your “sword”, your “shield” and your armor “scrap paper and graph paper”.  Likewise, you will want to know your “enemy” as well as you can.  Study it, read it, re-read it, and if necessary take some notes.  Then, using a scrap paper, draw up a battle plan (pre-draw or rough sketch the graph before you do it for the final time on your answer paper.  Make sure you look for “traps” like rearranging the data before you graph it,  making certain you mark your territory (the X and Y axis) and know the name of your battle field (the graph title).  And most importantly, make sure you mark your map as you proceed toward the enemy (circle your points as required).  MAKE SURE TO USE THE APPROPRIATE UNITS FOR ALL GRAPHS!

               #3 – Charge!!  Once you have figured out your nemesis, it is time to put the sword and shield to work.  Make sure that you mark down his strong points (appropriate well defined axes that correspond to the data) and make sure you record where he was accurately (be sure of your data points).  Once you have mapped out your battle progress, make certain you show how you moved across the battlefield (connect your data points) and then go back over the field to be certain you have vanquished the enemy (check your work).

(Graphing in the Biology Classroom, Michael H. Comet from South Lewis High School)

Techniques of the Biologist

Microscope

The microscope is used to enable us to see objects that are two small to be seen with the naked eye.  In class we use the compound light microscope.  A dissecting microscope can be used for observing living or dead organisms and they can be approximately as large as a fist.  An electron microscope is the highest magnification microscope that we currently have.  We cannot view live specimens under the electron microscope.  To find the total magnification of the specimen under the microscope you must multiply the magnification of the ocular lens (eyepiece) and the objective lens (scanning, low, high power).  Our microscopes in class have an ocular lens at 10x, a scanning objective at 4x, a low power objective at 10x and a high power objective at 40x.  The respective total magnifications on scanning, low and high are 40x, 100x and 400x.  Objects viewed under the microscope appear upside down and backwards.  We never use the course adjustment under high power, it could break the slide or damage the lens.  The diaphragm controls the amount of light on the slide.  The field of view is largest and brightest under low power.  Always carry the microscope using the arm and the base.  When making a wet mount slide we place the cover slip at a 45 degree angle and slowly lower it down so that there are no air bubbles present in the slide.

Gel Electrophoresis

Gel Electrophoresis uses an electrical current to separate fragments of DNA.  Used in  criminal investigations, paternity tests and evolutionary relationships.

To create fragments of DNA, the DNA is mixed with special cutting substances called restrictive enzymes. It is also mixed with a special dye so that it can be seen on the gel.  The mixture is then loaded into wells on an agarose gel.  An electric current is then applied and fragments move through the gel.  The smaller pieces move further and the larger pieces don’t move as far.  Results show a banding pattern on the gel under special light.

Chromatography

Chromatography is a technique used to separate a mixture of molecules, generally different pigments.  The set up includes a beaker with a solvent and special chromatography paper for the separation. A common example of this technique would involve putting a concentrated amount of chlorophyll (a green coloring found in plants) extract on a piece of filter paper and then placing the filter paper with the extract into a solvent.As the solvent soaks up into the paper and moves upward, colors that exist within the chlorophyll are separated into bands of color on the filter paper.

Centrifuge

A centrifuge separates mixtures such as blood components or cell parts based on density

Tissue Culturing

Tissue culturing is a technique used in growing living tissue and microorganisms such as bacteria in the lab. Some examples include in vitro fertilization, bacterial culture (strep throat) and even cloning.

What is tissue culturing good for?

1. Can be used to grow either animal or plant tissue

2. Can grow a large amount of certain types of organisms

3. Can be used to produce large numbers of the same cells or the same organisms (cloning)

4. Can also be used to grow tissue for analysis (ex.- cancer)

5. Can even be used to grow whole entire organs!

Staining

This technique makes certain cell parts visible depending on the stain being used.  Staining kills the specimen!!!!

Indicators

Indicators are substances that change color when they encounter specific chemical conditions

Examples:

• Lugol’s Iodine is an indicator of starch. It goes from amber to purple/black when in the presence of a starch

• Benedict’s solution is an indicator for glucose.  It starts a light blue color and changes to brick orange when mixed with glucose.  MUST be heated for the change to occur

• pH indicators (litmus paper, strips or fluids) show a color change based on how acidic or basic a substance is.  The color change should be compared to a known color scale from the package of the pH indicator.

Classification

We use this system called classification to group together living things with similar characteristics.  Groups are arranged from most general to most specific, the more general the group the greater the number of organisms that belong.  Classification is based on structures.

Taxonomy

The science of classifying and naming organisms.  This system that was developed by a Swedish scientist, Carolus Linnaeus, is binomial nomenclature.  It uses 2 names (the Genus and the species name) to make up the scientific name. Genus is always capitalized and species is always lower case.  When written the scientific name is always Italicized or underlined.  For example: The scientific name for a dog is Canis familiaris and the scientific name for humans is Homo sapiens.

Dichotomous key

Used to classify organisms that are similar.  Always between two options.

Scientific Method

How do scientists obtain new information?

• Observation

• Experimentation

• Discovery

Observations

• An observation is a description of and object or event by using one or more of the five sense (sight, smell, touch, taste, hearing)

• It is a statement that is a fact, it is 100% true

There are two types

1. Qualitative observation: Usually made with our senses; color, shape, taste, feel, sound

2. Quantitative observation: How many?  It will always have a number based on an exact measurement

Inferences

• An inference is a logical interpretation of an event that is based on observations and prior knowledge

• When you infer something or make an inference, it is based on factual information but is 100% your opinion

The Scientific Method

• The scientific method is a series of steps used by scientists to answer questions and solve problems

• There are 7 steps to the scientific method

1. Purpose: state the problem or question

2. Research: Gather information to formulate a better hypothesis and find out what is already known about the purpose

3. Hypothesis: A suggested answer to a problem without the support of data

4. Experiment: Develop and carry out an experiment to test the hypothesis

5. Observations & Data Collection: Record the results of the experiment and make any appropriate graphs

   1. Line graph: Shows comparisons

   2. Bar graph: Shows relationships

6. Analysis & Conclusion: Analyze your data, does it support or refute your hypothesis? You have to be able to support your conclusion with evidence from the lab/experiment

7. Report Results & Repeat/redesign the Experiment

Parts of an Experiment

• A controlled experiment is where the scientist controls all the variables except the ONE variable being tested

  • The part of the experiment that is being tested is the Experimental Group

  • The part of the experiment that is kept closest to normal/natural conditions is the Control Group.  It is used for comparison! 

  • The variable that differs between both groups, what “I” the scientist changes is the Independent variable

  • The variable that is not controlled by the scientist, the results of the experiment, the “data” collected is the Dependent variable

  • Control factors or constants are all of the things that are kept the same between both groups

How can we make our experiment more reliable?

How can we increase the validity of our experiment?

• Increase sample size (test it on more subjects!)

• Repeat the experiment!

Organization of Life

Levels of Organization

from least complex to most complex

Organelle --> Cell --> Tissue --> Organ --> Organ system --> Organism 

Characteristics of Living Things

Respiration (Cellular)

• A complex series of chemical reactions that releases energy stored in chemical bonds for life activities.

• An organism’s energy is stored in food nutrients.

• Most organisms need oxygen for respiration

  • Aerobic Organism

• A few organisms do not need oxygen for their respiratory processes.

  • Anaerobic Organisms

Excretion

• Life processes result in the formation of cellular wastes.

• These wastes are harmful to the organism and must be removed.

• Products commonly excreted from cells are carbon dioxide and water.

Biochemistry

All organic compounds contain a carbon atom bonded to a hydrogen atom. 

Organic Molecule Examples

• Glucose

• Carbohydrates

• Proteins

• Lipids

• Nucleic Acids

Inorganic Molecule Examples

• Water

• Salt

• Carbon Dioxide

Carbohydrates

Simple sugars such as glucose are the building blocks of carbohydrates.  Carbohydrates are large molecules that provide energy for the life processes through the process of cellular respiration which occurs in the mitochondria of cells.

Protein

Amino acids are the building blocks of proteins (at least 50 amino acids are needed to form a protein).  Proteins are large molecules that are needed for cell growth and repair.  Enzymes (a type of protein) play a vital role in cell function. 

Lipids

Glycerol and Fatty acids are the building blocks of lipids.  Lipids are generally our fats, waxes and oils.  They provide us with insulation, protection and energy reserves.

Nucleic Acids

DNA and RNA contain hereditary information.  DNA is like the recipe book for life. 

Molecular Models Practice

Molecular Models Lab

Below are some of the molecular models we constructed in class for the lab.

Enzymes

Role of Enzymes

• All chemical reactions need Enzymes to work

• Enzymes are called catalysts

• They regulate the rate of chemical reactions.

Structure of Enzymes

• All Enzymes are made of proteins (Carbon, Hydrogen, Oxygen, and Nitrogen)

• Enzyme names end in …ase

  • Maltase breaks down maltose

  • Lipase breaks down lipids

  • Protease breaks down proteins

  • Amylase breaks down amylose

• Some enzymes have non-protein parts known as vitamins. Vitamins are coenzymes!

• Lack of vitamins can cause a deficiency disease by preventing enzymes from preventing enzymes from performing their function (examples: Vitamin C found in fruits and vegetables, without it one can get scurvy)

• Enzymes have an active site.  This is the region involved in the enzyme action.  The active site is a result of the specific ways polypeptide chains twist and fold.

• The molecule being worked on is the substrate 

• The Enzyme and the substrate temporarily join together to form an enzyme substrate complex

  • The enzyme and substrate must fit together perfectly for the reaction to take place

  • Each kind of substrate fits only one kind of Enzyme (like a lock and key)

  • After completion, the enzyme and substrate separate.  The enzyme is now available to be used again.

Elephant Toothpaste

Nutrient Testing

We practiced testing for different nutrients using our indicator solutions.

• To test for lipids we simply look at any oily residue left on a paper towel.  The only this that we tested that had the oily residue was butter.  Butter contains lipids.

• We used iodine to test for the presence of starch in a clementine solution and in a piece of bread.  When the amber colored iodine was added to the clementine solution, it remained amber, this indicated that starch was NOT present.  When the amber colored iodine was added to the bread it turned black, this indicated that starch was present.

• Next we used Benedict's solution to test for the presence of glucose in a clementine solution as well as in a starch solution.  When using Benedict's solution as an indicator, it must be heated to show the results.  When the blue colored Benedict's solution was added to the apple and heated, it turned brick orange, this indicated that glucose was present.  When the blue colored Benedict's solution was added to the starch solution and heated, it remained blue, this indicated that glucose was NOT present.  

• Finally we used Beirut solution to test for the presence of protein in milk.  We added the blue Beirut solution to milk in a test tube and it changed to a purple color indicating that protein was present. 

Cells

Cell Basics

The Cell Theory

1. All organisms are made up of one or more cells

2. All cells carry out all of the life processes, they are the basic structure and function of all organization of life

3. New cells arise ONLY from other living cells by cell division

Exceptions to the cell theory: The first cell and viruses

Two Basic Categories of Cells

1. Prokaryotic: No internal membranes, NO nucleus, smallest single celled organisms. Ex. Bacteria

2. Eukaryotic: Have many membrane bound organelles, DO have a nucleus, includes all other types of cells other than bacteria and are generally much larger.

Eukaryotic Cells

1. Plant cells - square shape, have a cell wall made up of cellulous, contain chloroplasts, have a large vacuole

2. Animal cells - different shapes, no cell wall, centrioles needed for cell division, small vacuoles

All eukaryotic cells contain the following organelles: cell membrane, ribosomes, nucleus, mitochondria, endoplasmic reticulum, cytoplasm, Golgi bodies, lysosomes, nucleolus, vacuole 

Specialized Cells

Cell Specialization

What makes up cells? organelles! These are mini organs of the cell.  Each organelle has a specific job or function within the cell which allows the cell and the organism to exist.  Cells are specialized, they are different from one another and they serve different roles.

• Certain cells in an organism does certain jobs

• Advanced organisms have several specialized cells

• Some examples of specialized cells in organisms are below

Cell Organelles

Other Important Organelles include: Cell membrane (controls what enters and exits the cell), cell wall only in plants and bacteria (provides structure and support), cytoplasm (jelly-like fluid that fills the cell between the cell membrane and nuclear membrane, holds all organelles in place and responsible for the movement of organelles around the cell), centrioles in animal cells (play a role in cell division), nucleolus (makes mRNA and ribosomes)

• Plant cells have no centrioles, have a large central vacuole, contain chloroplasts (carry out the process of photosynthesis), surrounded by a cell wall (provides the cell with structure, made up of cellulose)

• Animal cells contain centrioles (play a role in cell division) and several small vacuoles  

Plant v Animal Cell

Types of Cells from the Comparing Plant and Animal cells lab

The Cell Membrane

The cell membrane is also known as the plasma membrane.  It is a membrane that separates the interior of all cells from the outside environment which protects the cell from its environment. The cell membrane consists of a lipid bilayer with embedded proteins. The cell membrane controls the movement of substances in and out of cells and organelles. In this way, it is selectively permeable. 

Cell Transport

Diffusion

Molecules will naturally flow from an area of high concentration to an area of low concentration without any energy

Active Transport

The movement of molecule from an area of low concentration to an area of high concentration, this requires energy (ATP)

Osmosis

The diffusion of water across a selectively or semi permeable membrane.  Water molecule flow until equilibrium is reached.

Passive vs Active transport

Passive is like rolling down a hill, high to low, requires no energy

Active is like walking back up the hill, low to high and requires a lot of energy

Diffusion Through a Membrane State Lab Videos

The Human Body Systems

The Digestive System

Digestion is the breaking down of food molecules into smaller pieces (building blocks) which can be used by the body.

The digestive tract or alimentary canal or gastrointestinal tract is the path that food travels through. Mouth --> esophagus --> stomach --> small intestine --> large intestine

Mechanical digestion is the physical breaking down of large pieces of food into smaller pieces (chew, tear, bite, mash)

Chemical digestion is the chemical reactions with enzyme that break down food particles into the nutrients that make them up (protein --> amino acids, carbohydrates --> simple sugars)

Both mechanical and chemical digestion begin in the mouth (salivary amylase in saliva breaks polysaccharides into disaccharides)

Wave like involuntary muscular contractions called peristalsis move food through the entire digestive tract beginning in the esophagus

The stomach is where protein digestion begins by enzymes such as pepsin.  The stomach also contains acid (HCl) which can kills harmful bacteria.

The small intestines are where many other enzymes are found, some made there others added from the accessory organs (liver and pancreas), finish the process of digestion.  Nutrients are then absorbed in the villi (finger-like projections filled with capillaries)of the small intestines into the blood.  Villi increase the surface area of the small intestines for absorption of nutrients into the blood.  All digestion ends here!

Anything remaining will be passed to the large intestine where excess water will be reabsorbed into the blood.

The Respiratory System

Air is taken in through the nose which is warmed, filtered and moistened by the cilia and mucus.  Air then travels through the pharynx, past the larynx, into the trachea which has rings of cartilage before making it's way to the branching bronchi that goes into both longs and ends in alveoli. The alveoli are millions of tiny elastic air sacs surrounded by capillaries where gas exchange takes place. The diaphragm is the sheet of muscle at the bottom of the chest cavity that controls breathing.  Asthma is a disorder where the bronchi swell due to an allergy.  Emphysema is a disease caused by smoking where the alveoli lost their elasticity and the person struggles to breath and take in oxygen, there is no cure.  The Alveoli are the functional unit of the lungs.  It is at the alveoli which are only one cell thick that gas exchange with the capillaries takes place via diffusion.

Urine Analysis Lab

Here are photos from our urine analysis lab.  We looked at high, low and normal urine samples before comparing them the two unknown samples using specific gravity, color, pH, glucose and protein.

pH indicator colors

Use the photos below to determine the specific gravities, color, pH, glucose and protein.  Read the lab to determine and fill in the chart on the lab answer document.

Circulatory System

Key terms:

transport, heart, atria, ventricle, septum, valves, superior vena cava (SVC), inferior vena cava (IVC), pulmonary circulation, systemic circulation, coronary circulation, artery, vein, capillary, oxygenated blood, deoxygenated blood, heartbeat, blood pressure, sphygmomanometer, blood, plasma, red blood cell (RBC), white blood cell (WBC), phagocytosis, platelets, lymph, lymph nodes, edema

Circulatory System Objectives

• Locate and label thes structures on a heart diagram

• Describe the functions of the heart structures.

• Trace the pathway of blood in the heart using arrows on the diagram. 

• Recognize the attributes of the heart structure as a double pump system (right & left side). 

• Describe & trace the path of blood through the pulmonary circulation. 

• Describe & trace the path of blood through the systemic circulation. 

• State the structural and functional differences for arteries, veins, and capillaries. 

• Define cardiac cycle, pulse, & blood pressure.

• Determine the normal blood pressure value for humans.

• Analyze the pathway of blood through the heart using a diagram.

• State the use of a pacemaker.

• Discuss the medical condition that increases the risk for a heart attack or stroke.

• Compare and contrast a heart attack from a stroke.

• Explain the cause(s) for the following medical conditions: angina, hypertension, and varicose veins.

• Name the different parts of the blood.

• Explain the function of each blood cell.

• Sketch a drawing for each blood cell.

• Explain the cause(s) for the following malfunctions of the blood: anemia, sickle cell anemia, leukemia, and hemophilia.

The Immune System

The immune system is the body’s defense against infectious organisms and other invaders. Through a series of steps called the immune response, the immune system attacks organisms and substances that invade body systems and cause disease.

About the Immune System

The immune system is the body’s defense against infectious organisms and other invaders. Through a series of steps called the immune response, the immune system attacks organisms and substances that invade body systems and cause disease.

The immune system is made up of a network of cells, tissues, and organs that work together to protect the body. One of the important cells involved are white blood cells, also called leukocytes, which come in two basic types that combine to seek out and destroy disease-causing organisms or substances.

Leukocytes are produced or stored in many locations in the body, including the thymus, spleen, and bone marrow. For this reason, they’re called the lymphoid organs. There are also clumps of lymphoid tissue throughout the body, primarily as lymph nodes, that house the leukocytes.

The leukocytes circulate through the body between the organs and nodes via lymphatic vessels and blood vessels. In this way, the immune system works in a coordinated manner to monitor the body for germs or substances that might cause problems.

The two basic types of leukocytes are:

1. phagocytes, cells that chew up invading organisms

2. lymphocytes, cells that allow the body to remember and recognize previous invaders and help the body destroy them

Here’s how it works: When antigens (foreign substances that invade the body) are detected, several types of cells work together to recognize them and respond. These cells trigger the B lymphocytes to produce antibodies, which are specialized proteins that lock onto specific antigens.

Once produced, these antibodies stay in a person’s body, so that if his or her immune system encounters that antigen again, the antibodies are already there to do their job. So if someone gets sick with a certain disease, like chickenpox, that person usually won’t get sick from it again.

This is also how immunizations prevent certain diseases. An immunization introduces the body to an antigen in a way that doesn’t make someone sick, but does allow the body to produce antibodies that will then protect the person from future attack by the germ or substance that produces that particular disease.

Although antibodies can recognize an antigen and lock onto it, they are not capable of destroying it without help. That’s the job of the T cells, which are part of the system that destroys antigens that have been tagged by antibodies or cells that have been infected or somehow changed. (Some T cells are actually called “killer cells.”) T cells also are involved in helping signal other cells (like phagocytes) to do their jobs.

Antibodies also can neutralize toxins (poisonous or damaging substances) produced by different organisms. Lastly, antibodies can activate a group of proteins called complement that are also part of the immune system. Complement assists in killing bacteria, viruses, or infected cells.

All of these specialized cells and parts of the immune system offer the body protection against disease. This protection is called immunity.

Problems of the Immune System

Disorders of the immune system fall into four main categories:

1. immunodeficiency disorders (primary or acquired)

2. autoimmune disorders (in which the body’s own immune system attacks its own tissue as foreign matter)

3. allergic disorders (in which the immune system overreacts in response to an antigen)

4. cancers of the immune system

Acquired (or secondary) immunodeficiencies usually develop after someone has a disease, although they can also be the result of malnutrition, burns, or other medical problems. Certain medicines also can cause problems with the functioning of the immune system.

Acquired (secondary) immunodeficiencies include:

• HIV (human immunodeficiency virus) infection/AIDS (acquired immunodeficiency syndrome) is a disease that slowly and steadily destroys the immune system. It is caused by HIV, a virus that wipes out certain types of lymphocytes called T-helper cells. Without T-helper cells, the immune system is unable to defend the body against normally harmless organisms, which can cause life-threatening infections in people who have AIDS. Newborns can get HIV infection from their mothers while in the uterus, during the birth process, or during breastfeeding. People can get HIV infection by having unprotected sexual intercourse with an infected person or from sharing contaminated needles for drugs, steroids, or tattoos.

Allergic Disorders

Allergic disorders happen when the immune system overreacts to exposure to antigens in the environment. The substances that provoke such attacks are called allergens. The immune response can cause symptoms such as swelling, watery eyes, and sneezing, and even a life-threatening reaction called anaphylaxis. Medicines called antihistamines can relieve most symptoms.

Allergic disorders include:

• Asthma, a respiratory disorder that can cause breathing problems, often involves an allergic response by the lungs. If the lungs are oversensitive to certain allergens (like pollen, molds, animal dander, or dust mites), breathing tubes can become narrowed and swollen, making it hard for a person to breathe.

• Eczema is an itchy rash also known as atopic dermatitis. Although not necessarily caused by an allergic reaction, eczema most often happens in kids and teens who have allergies, hay fever, or asthma or who have a family history of these conditions.

• Allergies of several types can affect kids and teens. Environmental allergies (to dust mites, for example), seasonal allergies (such as hay fever), drug allergies (reactions to specific medications or drugs), food allergies (such as to nuts), and allergies to toxins (bee stings, for example) are the common conditions people usually refer to as allergies.

What are vaccines?

Vaccines are substances that prepare the immune system to fight a disease-causing germ or other pathogen by imitating an infection. They trick the immune system into making a “memory” of that germ without ever having to fight the real germ in the first place. Now, when the immune system encounters the real pathogen — whether it’s a virus, bacterium or other microbe — it is ready to attack it. As a result, the vaccinated person doesn’t get sick.

Vaccines do NOT cure, they prevent disease!

Before vaccines, many children suffered from debilitating — and killer — illnesses such as measles, polio, smallpox and diphtheria. A simple scratch could be deadly if it became infected with the bacteria responsible for tetanus (or “lockjaw”). Vaccines, though, have changed this. Smallpox is completely gone from the world, and polio nearly so. Outbreaks of measles and diphtheria are rare, especially in the United States. Tetanus infections continue to decline worldwide.

Vaccinations also can help protect people who can’t be vaccinated. These might be babies who are too young to receive a vaccine. Or there might be people who are too ill or too old to be vaccinated. When enough people in a community are vaccinated against a particular contagious disease, there’s little opportunity for that disease to spread from person to person. Doctors call this type of community protection “herd immunity.”

How do vaccines work???

The body is designed to fight off foreign invaders. To do this, it needs to be able to distinguish elements of itself from outside agents (nonself). The immune system is always on the lookout for evidence of foreign stuff, or what scientists refer to as antigens in the body that don't belong.  Antigens are found on cell surfaces and if they are foreign to the body will trigger an immune response.  Antibodies which are produced by the bodies white blood cells, bind to antigens on foreign invader cells.  Antibodies and antigens are very specific and fit together like a lock and key.  For example the antigens on the flu virus are different then the antigens on the measles virus.  Furthermore, different types of flu viruses may contain different antigens.

Vaccines can help to prevent against different diseases.  Vaccines are made from either a weakened form of a pathogen or a dead/deactivated pathogen and are generally given by injection.  Some never vaccines can also be given by mouth or as a nasal spray.

The bodies immune system recognizes unfamiliar antigens and send out antibodies and other immune cells to stop and destroy the foreign invader.  The antibodies "remember" the invader and this creates immunity against future infections with the same type of pathogen.  This immunity happens because the next time that pathogen with the same antigens enters the body it is "remembered" and the specific immune response needed to destroy it is rapidly released.

Some antibodies protect for a lifetime. Other times, the immune system’s memory of a germ can fade over time. When this happens, immunity can falter and leave a person vulnerable to infection. In these cases, the immune system needs a reminder. These reminders are called boosters. Tetanus is an example. Doctors recommend a tetanus booster every 10 years to maintain good immunity against the disease.

Some germs also change substantially over time — evolve — creating new antigens. Influenza viruses are well known for doing this. Now the old antibodies may no longer recognize the new form of the germ (and antigens) and therefore fail to protect against it. That’s why flu vaccines must be given every year. Each new vaccine deals with the latest versions of these ever-changing viruses.

Reflex Arc

The path taken by the nerve impulses in a reflex is called a reflex arc. This characteristic allows reflex actions to occur relatively quickly by activating spinal motor neurons without the delay of routing signals through the brain, although the brain will receive sensory input while the reflex action occurs. Most reflex arcs involve only three neurons. The stimulus, such as a needle stick, stimulates the pain receptors of the skin, which initiate an impulse in a sensory neuron. This travels to the spinal cord where it passes, by means of a synapse, to a connecting neuron called the relay neuron situated in the spinal cord.

The relay neuron in turn makes a synapse with one or more motor neurons that transmit the impulse to the muscles of the limb causing them to contract and pull away from the sharp object. Reflexes do not require involvement of the brain, although in some cases the brain can prevent reflex action.

Stimulus-->Receptor-->Sensory neuron-->Interneuron-->Motor neuron-->Effector-->Response

The Brain

The brain is the control center of the brain.  It is made up of 3 main parts; the cerebrum, the cerebellum, and the medulla oblongata.  The cerebrum is the largest part of the brain and is composed of 2 hemispheres (right and left).  It performs higher functions like interpreting touch, vision and hearing, as well as speech, reasoning, emotions, learning, and fine control of movement. The cerebellum is the small "little brain" at the bottom of the brain which plays a large role in posture, balance and coordination of activities.  The medulla oblongata is the brain stem, this controls our most primitive functions like breathing, blood pressure and peristalsis, these are involuntary actions.

The Endocrine System

Hormones are super specific.  They are a type of protein folded in a certain shape which is specific to the receptor on the target cell.  Just like my house key won't open my classroom door.  Hormones from the endocrine gland are secreted into the blood, the blood is the transport system of the body, which transports the hormone to the target cells. 

Diseases and Disorders of the Endocrine System

Feedback Mechanism

Biological systems operate on a mechanism of inputs and outputs, each caused by and causing a certain event. A feedback loop is a biological occurrence wherein the output of a system amplifies the system (positive feedback) or inhibits the system (negative feedback). Feedback loops are important because they allow living organisms to maintain homeostasis. Homeostasis is the mechanism that enables us to keep our internal environment relatively constant – not too hot, or too cold, not too hungry or tired. 

Negative Feedback

A negative feedback loop occurs in biology when the product of a reaction leads to a decrease in that reaction. In this way, a negative feedback loop brings a system closer to a target of stability or homeostasis. Negative feedback loops are responsible for the stabilization of a system, and ensure the maintenance of a steady, stable state. The response of the regulating mechanism is opposite to the output of the event.

Example 1: Temperature Regulation

Temperature regulation in humans occurs constantly. Normal human body temperature is approximately 98.6°F. When body temperature rises above this, two mechanisms kick in the body begins to sweat, and vasodilation occurs to allow more of the blood surface area to be exposed to the cooler external environment. As the sweat cools, it causes evaporative cooling, while the blood vessels cause convective cooling. Normal temperature is regained. Should these cooling mechanisms continue, the body will become cold. The mechanisms which then kick in are the formation of goose bumps, and vasoconstriction. Goosebumps in other mammals raise the hair or fur, allowing more heat to be retained. In humans, they tighten the surrounding skin, reducing (slightly) the surface area from which to lose heat. Vasoconstriction ensures that only a small surface area of the veins is exposed to the cooler outside temperature, retaining heat. Normal temperature is regained.

Example 2: Osmoregulation

Osmoregulation refers to the control of the concentration of various liquids within the body, to maintain homeostasis. We will again look at an example of a fish, living in the ocean. The concentration of salt in the water surrounding the fish is much higher than that of the liquid in the fish. This water enters the fish diffusion through the gills, through food consumption, and through drinking. Also, because the concentration of salt is higher outside than inside the fish, there is passive diffusion of salt into the fish and water out of the fish. The salt concentration is then too high in the fish, and salt ions must be released through excretion. This occurs via the skin, and in very concentrated urine. In addition, high salt levels in the blood are removed via active transport by the chloride secretory cells in the gills. The correct salt concentration is thus maintained. 

Positive Feedback

A positive feedback loop occurs in nature when the product of a reaction leads to an increase in that reaction. If we look at a system in homeostasis, a positive feedback loop moves a system further away from the target of equilibrium. It does this by amplifying the effects of a product or event and occurs when something needs to happen quickly.

Example 1: Fruit Ripening

There is a surprising effect in nature where a tree or bush will suddenly ripen all of its fruit or vegetables, without any visible signal. This is our first example of a positive biological feedback loop. If we look at an apple tree, with many apples, seemingly overnight they all go from unripe to ripe to overripe. This will begin with the first apple to ripen. Once ripe, it gives off a gas known as ethylene (C2H4) through its skin. When exposed to this gas, the apples near to it also ripen. Once ripe, they too produce ethylene, which continues to ripen the rest of the tree in an effect much like a wave. This feedback loop is often used in fruit production, with apples being exposed to manufactured ethylene gas to make them ripen faster.

Example 2: Childbirth

When labor begins, the baby’s head is pushed downwards and results in increased pressure on the cervix. This stimulates receptor cells to send a chemical signal to the brain, allowing the release of oxytocin. This oxytocin diffuses to the cervix via the blood, where it stimulated further contractions. These contractions stimulate further oxytocin release until the baby is born.

Example 3: Blood Clotting

​When tissue is torn or injured, a chemical is released. This chemical causes platelets in the blood to activate. Once these platelets have activated, they release a chemical which signals more platelets to activate, until the wound is clotted. 

Positive vs. Negative Feedback

The key difference between positive and negative feedback is their response to change: positive feedback amplifies change while negative feedback reduces change. This means that positive feedback will result in more of a product: more apples, more contractions, or more clotting platelets. Negative feedback will result in less of a product: less heat, less pressure, or less salt. Positive feedback moves away from a target point while negative feedback moves towards a target.

Why is Feedback Important?

Without feedback, homeostasis cannot occur. This means that an organism loses the ability to self-regulate its body. Negative feedback mechanisms are more common in homeostasis, but positive feedback loops are also important. Changes in feedback loops can lead to various issues, including diabetes mellitus.  In type 1 diabetes, beta cells don’t work. This means that when blood glucose levels rise, insulin production is not triggered, and so blood glucose levels continue to go up. This can result in symptoms such as blurred vision, weight loss, hyperventilation, nausea and vomiting, among others. In type 2 diabetes, chronic high blood glucose levels have occurred as a result of poor diet and lack of exercise. This results in cells no longer recognizing insulin, and so blood glucose levels continue to rise.

​In a normal glucose cycle, increases in blood glucose levels detected by the pancreas will result in the beta cells of the pancreas secreting insulin until normal blood glucose levels are reached. Whereas if low blood glucose levels are detected, the alpha cells of the pancreas will release glucagon to raise blood glucose levels to be normal.

This information is from https://www.albert.io/blog/positive-negative-feedback-loops-biology/

Reproduction

Mitosis

Single celled organisms and some multicellular organisms, perform the life function of reproduction, asexually by the process of mitosis.

         The result of mitosis is always two cells, of which both are genetically identical to the original parent cell.  There is NO Variation in the offspring of asexually reproducing organisms.  What would happen to a species of asexually reproducing organisms, of the environment suddenly changed, and they needed to evolve? Unless a random mutation to one of the organisms occurred, they would all die because there is no variation among the organisms to survive with the sudden environmental change (think of the Irish Potato Famine)

In asexual reproduction, all of the genetic material comes from one parent.  It all begins with a parent cell that has a specific number, the species number, of chromosomes.  The species number for humans is 46.  The fruit fly has a species number of 8.  A chicken has a species number the same as a domestic dog, 78.  The first process that must occur in mitosis, is that the chromosomes make a copy of themselves also known as replication.

Let’s take a look at the different phases of mitosis, and how this process allows a single parent cell to replicate it’s genetic material, then divide to produce offspring, genetically identical to the parent cell.  Let’s say that the species number of this single cell creature is 6.  This means that every member of this species must contain 6 chromosomes in its cells. Let’s follow the process of mitosis, asexual reproduction in this creature.

Stage 1-Notice the genetic material inside the nucleus.  You cannot distinguish individual chromosomes at this stage.  Instead, the genetic material appears as a bundle of thread.  *The most important feature of this stage is that the genetic material replicate or copy itself.

Stage 2-Notice that the species number is 6, but after replication, you now see 12 chromosomes. *Remember, the replicated chromosomes are attached

Stage 3-The replicated (double stranded) chromosomes line up in the middle of the cell and attach to spindle fibers.

Stage 4- The double stranded chromosomes are pulled apart to the opposite sides of the cell.

Stage 5-Once on opposite sides, the cytoplasm begins to divide, in order to create two new cells.

We began with a cell having 46 chromosomes.  The genetic material is first replicated in order to create 92 chromosomes.  The double stranded chromosomes line up in the middle of the cell.  The chromosomes then separate and move to the opposite sides of the cell.  Now the cytoplasm splits to create two new cells, each of which have 46 chromosomes.

The order of the phases is as follows:

1.Interphase

2.Prophase

3.Metaphase

4.Anaphase

5.Telophase

         So the goal of asexual reproduction is to create genetically identical offspring.  Whatever the number of chromosomes that parent cell has, is the number of chromosomes that the two daughter cells will have.

Asexual Reproduction

Species are maintained in existence through the life spans process of reproduction.  Asexual reproduction produces genetically identical offspring from a single parent cell. The process of mitosis is associated with asexual reproduction and the growth and repair of cells in sexually reproducing organisms. Reproduction and development are necessary for the continuation of any species. Asexual reproduction is a method of reproduction with all the genetic information coming from one parent.

Some Types of Asexual Reproduction:

• Binary fission--involves equal division of both the organism cytoplasm and nucleus to form two identical organisms.  Some organisms that divide by binary fission include protists and bacteria

• Budding--involves one parent dividing its nucleus (genetic material) equally, but cytoplasm unequally.  Some organisms that divide by budding include hydra and yeast

• Sporulation (spore formation)--involves specialized single cells coming from one parent.  Mold is an organism that produces spores for reproduction.

Internal vs External Fertilization and Development

Different organisms possess different adaptations for reproduction and development.   Organisms which spend their lives or a large proportion of their lives in the water tend to lay their eggs in great numbers (thousands) in the water and wait for the male of the species to release sperm near them to fertilize them.   The fertilization which occurs in the water in this case outside the body of the organism is called external fertilization.  These young organisms then develop outside the mother in the water once this has occurred, which is called external development.  A disadvantage of this process is that the eggs and developing young have little or no parental protection. Many fish and amphibians like frogs undergo fertilization and development in this manner.

​

Reptiles and birds engage use the process of internal fertilization to fertilize their eggs.  In this situation, the male of the species inserts his sperm inside the female, who then lays her fertilized eggs outside her body. The process of development is then external.  Reptiles and especially birds tend to lay fewer eggs and provide much more parental protection for the developing young.   Organisms (with some exceptions) which use the process of internal fertilization tend to spend much of their lives on land.  Mammals like humans have both their fertilization and initial stages of development occur within the female organism.   This is referred to as internal fertilization and internal development.   These organisms tend to release very few eggs, but those eggs and the developing organism are very well protected by one or both parents. 

Human Reproduction and Development

Reproduction is the biological process by which new individual organisms known as offspring are produced from their parents. Reproduction is a fundamental feature of all known life; each individual organism exists as the result of reproduction.  Not all organisms of a species must reproduce for the survival of the species but some must.

As humans we go through sexual reproduction with internal fertilization to reproduce.  This process requires a sperm and an egg (the male and female sex cell or gametes) to unite in the female reproductive tract (in the oviduct).

The Male Reproductive System

The male reproductive system includes the scrotum, testes, spermatic ducts, sex glands, and penis. These organs work together to produce sperm, the male gamete, and the other components of semen. These organs also work together to deliver sperm into the vagina where they can swim until they reach the oviduct and potentially fertilize an egg cell to produce offspring.

Testes: There are 2 testes, also known as testicles, which are the male gonads responsible for the production of sperm and testosterone.

Scrotum: The scrotum is a sac-like organ made of skin and muscles that houses the testes outside of the body cavity.  The body cavity is too warm for the testes to produce sperm  effectively so the scrotum holds the testes outside of the body cavity and can move slightly depending on the temperature.

Epididymis: The epididymis is a sperm storage area that wraps around the top edge of the testes.  Sperm produced in the testes moves into the epididymis to mature before being passed on through the male reproductive organs.

Vas Deferenes: The tube that carries sperm from the epididymis past the glands which add to the sperm creating semen to the urethra.

Glands: Between the prostate gland, cowpers gland and seminal vesicles semen is created.

Penis: The penis is the male external sexual organ which contains the urethra and the external opening of the urethra.  The function of the penis is to deliver semen into the vagina during sexual intercourse. In addition to its reproductive function, the penis also allows for the excretion of urine through the urethra to the exterior of the body.

Semen: Semen is slightly basic to allow the sperm to survive in the acidic vaginal cavity.  Semen also carries sugars for the sperm to use to continue to make energy through cellular respiration in the mitochondria.  In healthy adult males, semen contains around 100 million sperm cells per milliliter of semen. These sperm cells fertilize an egg (ovum) within the fallopian tube (oviduct) of the female reproductive tract.

The Female Reproductive System

The female reproductive system includes the ovaries, fallopian tubes (oviduct), uterus, cervix, and vagina. These organs are involved in the production and transportation of gametes (sex cells, eggs) and the production of sex hormones (estrogen and progesterone). The female reproductive system also facilitates the fertilization of ova (an egg) by sperm and supports the development of offspring during pregnancy.

Ovaries: The ovaries are a pair of small glands about the size and shape of almonds, located on the left and right sides of the pelvic body cavity. Ovaries produce female sex hormones such as estrogen and progesterone as well as eggs (ova), the female gametes (sex cells). Ova are produced from oocyte cells that slowly develop throughout a woman’s early life and reach maturity after puberty. Each month during ovulation, a mature egg (ovum) is released. The ovum travels from the ovary to the fallopian tube (oviduct), where it may be fertilized before reaching the uterus.

Fallopian Tubes: The fallopian tubes (oviducts) are a pair of muscular tubes that extend from the left and right corners of the uterus to the edge of the ovaries. The fallopian tubes end in a funnel-shaped structure, which is covered with small finger-like projections. The finger-like projections swipe over the outside of the ovaries to pick up released ova (egg)and carry them into the fallopian tube for transport to the uterus. The inside of each fallopian tube is covered in cilia that work with the smooth muscle of the tube to carry the ovum (egg) to the uterus. THIS IS WHERE FERTILIZATION OCCURS! 

Uterus: The uterus is a hollow, muscular, pear-shaped organ. Connected to the two fallopian tubes on its top end and to the vagina (via the cervix) on its lower end, the uterus is also known as the womb, as it surrounds and supports the developing fetus during pregnancy. The inner lining of the uterus, provides support to the embryo during early development. The visceral muscles of the uterus contract during childbirth to push the fetus through the birth canal.  If pregnancy does not occur, the uterine lining is shed in a process called menstruation.

Vagina: The vagina is an elastic, muscular tube that connects the cervix of the uterus to the outside of the body.  The vagina functions as the receptacle for the penis during sexual intercourse and carries sperm to the uterus and fallopian tubes. It also serves as the birth canal by stretching to allow delivery of the fetus during childbirth. During menstruation, the menstrual flow exits the body via the vagina.

The Menstrual Cycle

The menstrual cycle is the process of producing an egg (ovum) and readying the uterus to receive a fertilized egg (ovum) to begin pregnancy. If an ovum is produced but not fertilized and implanted in the uterine wall, the menstrual cycle resets itself through menstruation. The entire cycle takes about 28 days on average, but may be as short as 24 days or as long as 36 days for some women.

Development

Once the mature egg (ovum) is released from the ovary, the finger-like projections catch the egg and direct it down the fallopian tube to the uterus. It takes about a week for the egg (ovum) to travel to the uterus. If sperm are able to reach and penetrate the egg (ovum), it becomes a fertilized zygote containing a full complement of DNA. FERTILIZATION takes place in the OVIDUCT!  After a short period of rapid cell division known as cleavage (where the cells divide without becoming larger) takes place the zygote forms an embryo. The embryo will then implant itself into the uterine wall and develop there during pregnancy. The early stages can be seen in the picture below.

For the first 8 weeks, the embryo will develop almost all of the tissues and organs present in the adult.  This happens by the process of cell specialization or differentiation where different cells begin to form (nerve cells, skin cells, cardiac cells, etc).  Remember that all the cells contain the same genetic material (textbook) but only certain genes (chapters) are activated/turned on.  Before entering the period of development during weeks 9 through 38 where the fetus grows larger and more complex until it is ready to be born. 

Within the uterus the placenta begins to form after implantation of a zygote into the endometrium.  The placenta transfers nutrients and oxygen from the mother’s blood into the blood of the fetus through the process of diffusion. The blood of the mother and fetus DO NOT mix. The fetus is attached to the placenta by the umbilical cord.  Nutrients and oxygen taken in by the mother diffuse from her blood stream through the placenta to the umbilical cord of the fetus.  Unfortunately toxins also diffuse from the mother's blood stream to the fetus; this is why it is important for pregnant women to stay away from drugs, alcohol and other toxins.  The fetus is very vulnerable to alcohol, drugs, etc because the important organs and systems are developing.  Wastes produced by the fetus (Carbon dioxide, urea and salts) are removed by the placenta; they diffuse from the placenta into the mother's blood stream.  Since the fetus does not eat solid food, it does not have to eliminate feces. 

What About Twins?

There are two types of twins, identical or fraternal.  Identical twins occur when one egg is fertilized by one sperm and the resulting zygote splits into 2.  The two twins share the same placenta and same ammonic sac.  The twins have identical DNA so they will be the same sex and look similar.  Fraternal twins occurs when 2 eggs are released from the ovaries at approximately the same time and each are fertilized by a different sperm.  They each develop in their own ammonic sac with their own placenta and can be the same or different sexes.  These twins will not be the same, they will be no more similar then any other siblings except that they share a birthday.

Genetics

Deoxyribonucleic Acid (DNA)

DNA is the genetic information which is passed on from one generation to the next.  DNA is condensed into chromosomes prior to DNA replication and cell division.  If humans we inherit 23 chromosomes from our mother and 23 chromosomes from our father giving our somatic cells 46 chromosomes.  DNA is found in the nucleus of cells.  DNA can also be found in the mitochondria of all cells ad the chloroplast of plant cells.  Different organisms have a different number of chromosomes in the nucleus.  

DNA is made up of nucleotides.  A nucleotide contains a sugar (deoxyribose), a phosphate and a nitrogenous base.  There are four different bases that make up DNA; Adenine, Thymine, Guanine and Cytosine.  DNA is double stranded and takes on the shape of a twisted ladder or double helix.  The backbone of the double helix consists of the repeating phosphate and sugar molecules.  The steps or rungs of the DNA ladder (double helix) are complementary base pairs.  Adenine and Thymine are complements and Guanine and Cytosine are complements so they generally pair together. 

DNA Replication

DNA replication is the process of creating two exact copies of DNA from one DNA molecule.  DNA replication is important since it creates a new copy of DNA which will go into one of the two daughter cells when a cell divides via mitosis as well as to create gametes via Meiosis. Without replication, each cell lacks adequate hereditary information to give instructions for creating proteins vital for bodily purpose. 

Gregor Mendel (1822-1884)

Central Dogma of Genetics

DNA -> Transcription -> RNA -> Translation -> Protein

DNA holds the code or recipe for all the proteins that our cells and bodies need to make.  DNA is stuck in the nucleus because it is a large double helix, this is a problem because proteins are made at the ribosome which is located outside of the nuclear membrane in the cytoplasm.  mRNA or messenger RNA makes copy of the code via transcription (think of a waiter taking down your order at a restaurant).  Some main differences between DNA and RNA are that RNA is single stranded, has a different sugar (Ribose) and it does not contain thymine (T) but instead has uracil(U).  Since the mRNA is only single stranded, it is small enough to leave the nucleus and does just that.  It carries the code of a gene (which codes for one protein to be made) out of the nucleus and to the ribosome (site of protein synthesis).  Every three bases on a strand of mRNA represent a codon, they code for a specific amino acid. 

tRNA or transfer RNA molecules that are free floating in the nucleus carry a specific amino acid based on their anti codon.  The tRNA molecules bring the specific amino acid to the corresponding codon of mRNA at the ribosome.  The ribosome then links one amino acid to the next with peptide bonds forming between them.  50 or more amino acids linked together and folded in a certain way are needed to build a protein. 

We use an mRNA codon chart to figure out the sequence of amino acids being linked together and thus the protein being coded for. 

Proteins

Proteins are large, complex molecules that play many critical roles in the body. They do most of the work in cells and are required for the structure, function, and regulation of the body’s tissues and organs.  Essentially, proteins are what make you, you.  Proteins are made up of hundreds or thousands of smaller units or building blocks called amino acids. There are 20 different types of amino acids that can be combined to in different orders to make a protein. The sequence of amino acids determines each protein’s unique 3-dimensional (3D) structure and its specific function.

Biotechnology