Cell Signalling - Monday, May 6

Cell Signalling

Gland - Any structure that secretes a hormone.
Hormone - Any chemical secreted by one part of the body that has its effect/s somewhere else. Two basic Types:
      1. Steroid (Fat-based - non-polar - can diffuse through cell membranes)
      2. Peptide ("Protein" - polar - bond to a receptor protein on cell surface). Pheremones - chemicals excreted by one individual that cause a physiological change in another individual.
  
I. Gonads - Primary sexual structures
           A. Ovaries - produce estrogens & progesterone - responsible for female structure, menstral cycle & pregnancy.
           B. Testes - Testosterone. Responsible for male anatomy, sperm production. How is it regulated? By the hypothalmus (Part of the brain - made up of Neurons) Pituitary (true gland) Negative Feedback System (HPNFS)
      1. Hypothalamus - raises levels of GnRH (Gonadotropin Releasing Hormone)
      2. Pituitary - is signalled by higher levels of GnRH to release LH (a gonadotropin)
      3. Testes - are signalled by higher levels of LH to produce higher levels of Testosterone.
     

Colonies- permanent association of cells, but little or no integration of cell activities.
            Volvox- unicellular green alga, colony is a hollow ball of cells.
Kingdom Protista-
Protists are the most diverse eukaryotic kingdoms.
-There are 15 distinct Phyla of Protists.
     -These are grouped into five general groups based on shared characteristics
        1. Presence/absence of flagella/cilia
        2. Presence and kinds of pigments
        3. The type of mitosis
        4. the types of cristae in mitochondrea
        5. Ribosomes are the same
      -There are five major, subdivided groups.
        1. Ameaboids- Heterotrophs with no permanent locomotor apparatus
        2. Heterotrophs with flagella
        3. Heterotrophs with restricted mobility (slime-molds)
        4. Photosynthetic protists (algae)
        5. Nonmotile spore-formers

5/2/2013

5/2/2013

Based on carbon and energy sources, prokaryotes can be divided into 4 groups

1. Photoautrouphs

• Use energy of sunlight to build organic molecules
• Cyanobacteria

1. Chemoautotrouphs

•  Obtain energy by oxidizing inorganic substances

1. Photoheterotrouphs

• Rare

1. Chemoheterotrouphs

• use organic molecules as carbon and energy sources

Viruses

• Latin for poison
• Non-celklur particle with
• DNA or RNA
• 1 or 2 Protien coats (capsids)
• May have Viral Envelope - Phosholipids

• Do Not respire or grow
• ONLY function in a living cell
• Not given Latin names like living organisms
• 4 Charicteristics - Only have 1 (Genetic material
• Made of cells
• has metabolism
• reproduces on its own
• Genitic material

Virus have 2 different cycles
Lytic cycle

• 1- Virus absorption/ attachment
• 2 - Injection/ entry
• 3- Replication of viral parts
• 4- Assembly of the Virions
• 5- Release by lysis
• cause disease, cell gets taken over and produces more viruses that bust the cell

 Lysogenic Cycle

• Lays dormant in your body, doesn't destroy host cell

Temperate Viruses do both (HIV)

Wednesday May 1, 2013

Forming Life's Building Blocks

• Concerns have been raised about the "primordial soup" hypothesis
• No oxygen=> no protective ozone layer
• therefore, the UV light would have been destroyed and the essential ammonia and methane gases
• Louis Lerman, in 1986, proposed the bubble model
• When the experiment is done one of the things formed is urisil which is found in RNA 

The First Cells

• The first step may have been the formation of tiny bubble termed microspheres 

Structure of Prokaryote

• Prokaryotes are small, simpily organized, single cells that lack a nucleus
• Include bacteria and archaea
• have a cell wall
• composed of peptidoglycan 
• network of polysaccharides linked by peptide cross-links

• bacteria are separated into two groups based on membranes
• Peptidoglycan are in either a thick layer with no outer membrane that will stain (gram-positive) or in a thin layer with an outer membrane that won't stain (gram-negative)
• Hans Christian Gram developed a stain to differentiate between the two
• When cells are stressed they pass their plasmid DNA following cell-to-cell contact
• Based on carbon and energy sources, prokaryotes can be divided into four categories
• 1. Photoautotrophs: Photosynthesizes, or plants. 
• Cyanobacteria: when a lake suddenly has an algae bloom and turns pea soup green, it's not algae, its cyanobacteria

• 2. Chemoautotrophs: use inorganic fuels as their food. 
• For example: nitrogen-fixing bacteria, nitrifiers oxidize ammonia or nitrite

• 3. Photoheterotrophs: Use light as energy and pre-formed organic molecules as carbon sources
• Purple nonsulfur bacteria
• Very Rare

• 4. Chemoheterotrophs: Use organic molecules and energy sources 
• Decomposers and most other types of bacteria.

Kingdom- Animalia
Phylum- Chordata
*Subphylum- Vertebrata
Class-  Mammalia
*Subclass- Placenta
4/30/13
Order- Primate
*Superfamily- Hominoideae
Family- Hominidae
Genus-  Homo
Species-  sapiens
*Subspecies-sapiens
II. 1st Modification
*Sub...and Super... (due to the original system being unable to fit all species being discovered)
III. 2nd Modification
Added "Domain" above kingdom. There are 3 domains of life.
A. Bacteria- Have no internal membranes-no organelles, no nucleus, Peptidoglycan in cell wall, I kind of RNA polymerase, no Introns, no Histones (protein beads that DNA wraps around) in DNA, circular chromosome, different Ribosomes.
B. Archea- No internal membranes, organelles, or nucleus. Circular DNA, no peptidoglycon, several RNA polymerases, Introns, Histones
C. Eukarya- Have internal membranes, nucleus, organelles, no peptidoglycon, rod-like DNA, several RNA polymerases, Introns, and Histones.
Archae and Bacteria are both prokaryotes, but Eukarya and Archea are more closely related to each other.

April 29, 2013

Categorizing Life

I. The Linnaeus Classification System

            Kingdom- eg. Animalia
                       Phylum- Chordata
                               
                               Class-Mammalia
                                     Order- Primates
                                           Family- Hominidae
                                                   Genus- Homo
                                                         Species- Sapiens

04/16/13

(the Carbon Cycle, Image A; the Nitrogen Cycle, Image B)

Nitrogen Cycle Continued:
Legume (any plant with seeds in a pod; examples are: alfalfa, peas)
Legumes have nitrogen fixing bacteria in their roots.
SYMBIOTIC RELATIONSHIP.

4/9/13

Gross Productivity - Total amount of Glucose produced by the producers.

Net Productivity - G.P. - Amount of Glucose metabolized by the producers, food energy available to consumers.
 

Initial = 0.8 mg/L of oxygen  
Dark = 0.3 mg/L
Light= 0.9 mg/L                                     
     

                                   

                                                                                 
                                     Initial-Dark = 0.5 = Respiration Rate = 0.5/24
                                     Light-Initial = Net Productivity Rate = 0.1/24
                                     Light-Dark = Gross Productivity Rate = 0.6/24

Ecosystems 

I. Biogeochemical Cycles 

                                                    The Carbon Cycle


      
     
                       

4/8/13

II. Food=Energy

Sun--Photosynthesis (Gross Primary Productivity)-->Producers--Cell Metabolism (90%)-->Heat
Producers--(10%)--> 1 Consumers/Herbivores (Net Primary Productivity)--(90%)-->Heat
1 Consumers--(10%)-->2 Consumers (1% Gross)--(10%)-->3 Consumers (0.1% Gross)--(10%)-->4 Consumer (0.01% Gross)
2, 3, & 4 Consumers are all Carnivores
Decomposers on every level

10% Rule--Only 10% of the energy produced by photosynthesis is available to Consumers. 90% is metabolized and "lost" as heat.

                                                                   Food Pyramid of Biomass
                                                                 
                                                             90% is in the Producers (bottom)
                                                             9% Herbivores (middle)
                                                            1% Carnivores (top)

(You can make a living as a cow masseuse in Japan. Just saying.)

Biological Magnification--when fat-soluble toxins like pesticides (DDT) & metals (Pb, Mercury)
2 Ospreys 10lbs<---Large Fish 100lbs<---Small Fish 1000lbs<---Insects 10,000lbs<---Algae 100,000lbs
25 mg/L DDT           2.5 mg/L                    0.25 mg/L                     0.025 mg/L              0.0025 mg/L DDT

3/28/13

I.
     B. Predation
          2.
               d. Keystone Predator
                    ii. Maintain Species Diversity- preys on the most commonly occurring species leaving more resources for the less commonly occurring species.
     C. Symbiosis- "living together". At least one species in the relationship has a lifelong dependance on the other. Three types:
          1. Parasitism (+/-)- When one species (parasites) lives off of and on or in another (host).
          2. Mutualism (+/+)- both species benefit.
               a. Flowering Plants and Pollinators- 70% of plants flower.

               b. Lichen- an alga and a fungus. Fungus excretes digestive enzymes break down substrate to get nutrients (N, P, S, Na+, K+, etc) and alga photosynthesizes to make sugars and fats. First step in soil formation.

               c. Commensalism- (+/0)- one species benefits and the other is unaffected. Epiphytes- plants that live on other plants- Orchids

Communities
I. interactions
A. Competition- resources. 2 types
1. Intraspecific- within the same species (population)
2. Interspecific- between 2 or more species. Leads to the Principle of Competitive Exclusion-when 2 or more species are competing fo the same resources, 1 will "win".  The other/s will either become extripated or they will shift their niche.  Niche- an organism's profession.  Leads to Resource Partitioning- resources are divided up by competing species.  Ex. elk, moose, deer/ broadleaf, conifers.  Exotic Species (non-native)- on the mainland the natives usually win.

Ecology part 3

III. Other Factors
    B.
       2. Survivor ship Curves

      3. Cohort Sizes
-Cohort: particular age class

IV. Population Survival Strategies: 
2 types:

 A. r-selected: (weeds, insects, rodents, fish, grasses)
Age at first Reproduce- Early
Lifespan- short
Maturity- Early
Number of Offspring-Many
Early Mortality?- YES
Parental Care?- NO
Size- Small
Succession Type- Pioneer

B. k-selected: (humans, larger trees, large herbivores)
Age at first Reproduction- Late
Lifespan- Long
Maturity-Late
Number of Offspring- Few
Early Mortality?- NO
Parental Care?- YES
Size- Large
Succession Type- Climax

Other Factors that Affect Growth

III. Other Factors that Affect Growth
      A. Sex Distribution
           1. In a polygamous population to max. growth: Females > Males
           2. In a monogamous population to max. growth: Females = Males
      B. Age Distribution
          1. The younger a population is, the faster it grows.

Ecology

Ecology- the study of the interactions between organisms and their enviorment. 4 levels:
1. Population- a group of individuals of the same species living within the same area. (Territory)
     2. Community- all of the populations that interact within a given area.
     3. Ecosystem- community plus all the abiotic- nonliving, factors that affect it.
     4. Ecosphere- gloabl ecology

Population Ecology
I. Population Dynamics- How populations change.
    A. Growth- what factors affect it?
         1. Emmigration (-) Movement out
         2. Immigration (+) Movement into
         3. Natality (+) Birth Rate
         4. Mortality (-) Death Rate
    B. Growth Rates- 3 types
         1. Arithmetic- same amount of increase within each growth period. Bad way to calculate growth. 
           

          2. Exponential- population grows by the same percent (%) each year. Use this when a population is small with lots of room to grow. (J-shaped curve)

            equation: delta N/delta t = rN
             delta N= change in # (unknown)
             delta t= change in time
             r= % rate (convert % to decimal)
             N= current #

Example:
cattle herd; 2011= 50, 2012=60, 2013= ?

delta N/1= rN

delta N= (.2)(60) = 12     60+12= 72

       3. Biological- population will eventually slow down and stop due to resource limitations.Eventually it will reach its carrying campacity- the maximum number a given enviorment can support on a long-term basis.
(S-shaped cuve)


Equation
 delta N/ delta t= rN(K-n/K)
K= carring capacity

Example:
cattle herd; 2011= 50, 2012=60, 2013=?

=(.2)(60)(100-60/100)
=(12)(.4)
=4.8 round to 5
=2013=65

II Regulation of Muscle Contraction
A. The Motor Cortex of the brain (Kenzie) releases motor impulse (Erin) down pathway leading to target muscle
B. It reaches the Synaptic Knob (Bryan) where a Neurotransmitter (Ach-Brennan) is released into the Neuromuscular Junction - the synapse between nerve and muscle
C. Ach bonds to receptor sites on the Sarcoplasmic Reticulum (SR-Holden) Membrane which surrounds and permeates muscle and also holds a resting charge. The SR will now "fire" and release Ca2+ (Carson) ions into the muscle fibers.
D. Ca2+ will now bond to Troponin (Maddie). Troponin is a smaller protein found along the length of a larger, cable-like, protein called Tropomyosin.
E. This causes the Tropomyosin cable to shift position exposing the Actin Binding Sites (Rachel) to the Myosin Heads (Bryar). RESULT: CONTRACTION.
NOTE: The regulation of Muscle Contraction (strength and duration) is directly controlled by the amount of Ca2+ that are bonded to Troponin molecules at any one time.

Muscle Contraction (Skeletal)

• Skeletal Muscles are arranged in Antagonistic Groups.
•  Every Muscle is connected on two sides by tendons.
• Muscles are composed of multicellular structures called muscle fibers (visible)
• Muscle Fibers are composed of long multinucleated cells that stretch across the entire muscle.
• Muscle cells are composed of subcellular tubules called Myofirils. Each myofibril is composed of two major protiens called myosin and actin.
• Each myofibril  is divided in structures call sarcrameres which are the structural and functional uint of a muscle.

I The Sacromere- muscles are made up entirely of these structures.
A. When a muscle is relaxed, there is a protien that covers the Actin Binding Sites and this will Not allow teh myosin bonds to bond, so the two fibers, Actin and Myosin will slide freely across one another.
B. However, when an electrical impulse is sent to the muscle, the actin binding sites are exposed, the myosin heads will bond to jthe creating crossbridges.
C. This changes the structure of the myosing head and it will ratchet the actin strand toward the A-Zone. closing the distance between the myosing head and the acting binding site.
D. Once this happends the Myosing head reverts back to it's original structure and position.
E. The head will now find a new actin binding site and the process will continue until:
1The muscle is fully contracted
2 The electrical impulse stops.
3ATP Runs out- cramp, Rigor rigor Mortis:I(Stiffness of Death)

Split Brain- Happens when the Corpus collosum is severed. Usually because of a surgical proceure, used to stop seizures in epileptics.  *(images seen from the right side are transmitted to the left and vice versa)
-The Visual cortex is in the occipital lobe, in the back of the head, this is where we "see" images.
-The Auditory cortex is in front of the Visual; this is where we "hear" -it is not counter (right ear to right brain, left ear to left brain)
-Motor cortex is between the Frontal and the Periatal lobe. (controls motor neurons) -Is Counter.
-Behind it, in the periatal lobe, is the Sensory cortex, where sensory neurons "report to"

Lecture 3/8/2013

III.Forebrain
     C. Hypothalamus-Thermostat, Chemostat (pH, blood sugar), site of Base Emotions (Anger, Euphoria, Hunger, Thirst, Sex)
     D. Cerebrum - 80%, Convoluted to increase surface area because majority of electrical activity is on the surface. Divided into 2 hemispheres (Left and Right) connected by the Corpus Callosum.

The Right Hemisphere controls and receives to and from the Left side of the Body and vice versa.
Vision - The Right Visual Field goes to the left Hemisphere and vise versa.

B) Broca's Area - Produces motor speech. 90% of us it is in the left hemisphere.
W) Wernicke's Area - Produces motor speech meaning.

The Brain

I. Hindbrain
    A. Medulla Oblongata- connects directly to spinal cord. Reflexes (coughing, sneezing, reflex arcs, etc.) Last structure to "die" when oxygen runs out. Responsible for basic body function: heart rate and breathing.
     B. Cerebellum- coordinates complex motor skills. Athletics, dance, etc.

II. Midbrain- (+ Hindbrain=Brainstem)
     A. Superior and Inferior Colliculi- involved in coordination of visual and auditory stimuli
     B. Reticular Fornation- "Internal clock." Regulates states of consciousness

III. Forebrain
     A. Basal Ganglia, Amygdala, and Hippocampus- Long-term memory
     B. Thalamus- Relay center for the brain.
     C. Hypothalamus- Thermostat

March 6, 2013

IV. Synapse
     A. Excitatory
          1. When the nerve impulse reaches the synaptic knob, sodium comes rushing in, making the interior positive. (35+)
          2. This knocks Ca2+ off of its binding sites on the inner membrane, and it bonds to the synaptic vessicles.
          3. This releases excitatory neurotransmitters into the synaptic cleft where it bonds to the receptor sites on the post-synaptic membrane of the next neuron.
          4. This opens the sodium gates, making the resting charge closer to the threshold (-50). It it reaches -50mv, it will "fire".
     B. Inhibition - post-synaptic neuron is less likely to fire.
          1. Same
          2. Same
          3. An inhibitory neurotransmitter is released into the cleft and it bonds to receptor sites on the post-synaptic neuron.
          4. This opens chlorine channelse and chlorine diffuses in, making the interior more negative (-90) and less likely to fire.

Note 1: All neurotransmitters must be immediately broken down by enzymes or else their effect will continue long after the impulse stops.

Note 2: These neurotransmitters are constatly battling with one another in the synapses of our body. The Parasympathetic Nervous System is the reason why our neurons are less likely to fire at night.

Note 3: Summation - When the sum total of Excitatory (+) and Inhibitory (-) neurotransmitters "add up" to the Post-synaptic neuron reaching the threshold. 2 types:
     1. Temporal - one or a few neurons are firing enough times within a given unit of time to achieve summation. (quickly putting your finger on a piece of ice)
     2. Spacial - many neurons fire at once and release enough neurotransmitters to achieve summation (putting your whole hand quickly on the table)

Beginning from All or Nothing- How, then, does one perceive the intensity of a stimulus?

1. The number of times a neuron fires per unit time (per second). Two different lag times: charges and reset time.
2. The number of neurons firing. Greater number of neurons firing means greater intensity.

IV. The Synapse - Junctions between neurons. 2 types of synapses:

1. Mechanical synapses - axon abuts the dendrite. Automatic transfer of electricity. 
2. Chemical synapse- axon doesn't abut the dendrite. Message goes from electrical to chemical and then back to electrical. All of our synapses are chemical. 

There are 2 "events"  that can happen at the synapse:
A. Excitation-when the pre-synaptic neuron releases an excitatory neurotransmitter to cause the post-synaptic neuron to be more likely to "fire."

March 1 The Action Potential

B. The Action Potential- When the Neuron "fires".
    1. A stimulus (motor or sensory) will cause the gated Na+ Channels to open more (unknown mechanism) at the 1st Node of Renvier at the Axon Hillock.
     2.This causes the resting charge to raise (become less negative)
     3.If, enough Na+ enters to get the charge to -50 Mv ( the Threshold) the Na+ channels open wide and Na+ comes rushing in causing the internal charge to move to +35 Mv (firing charge)
     4. Cl- will be left behind by the Na+ and for 1/2 of 1 ms the external environment is negative. This is the electricity.
    5. Most of the Na+ will travel laterally. The Na+ that travels into the cell body, has no effect, but the Na+ that travels to the next node will cause that to reach the threshold, and it will fire there.
    6. The Na+, again, will travel laterally. As it moves to the previous node, no effect will occur because the potential for firing has not been reset by the Na+/K+ pumps (it takes 3 ms to reset) this is why the impulse is 1-directional. But, when it travels to the node that is set to fire the same thing will happen there and this continues down the line to the end of the neuron.
All or Nothing Rule- When a neuron fires it will always fire at 100% intensity.

February 28th

II. Cells
     B. Neurons
     3. Dendrites

III. The Nerve Impulse: how does a neuron initiate and propagate an electrical impulse?
      A. The Resting Potential: setting up the potential for a neuron to "fire".
          Cl - 10x
          Na+ 10x  (sodium can leak in, just as potassium can leak out)
  
(K+ 30x)  (large (-) polypeptides ) potassium can leak out~
- Resting Charge (-70mv) neutral/balance between negative and positive charges

Na+/K+ Pump:
      1.  K+ is at a 30 times greater concentration inside of the neuron. it can leak out and does.
      2. Large (-) polypeptides- made by neurons and they are highly concentrated inside the neuron. these want to hold K+ in so, K+ has two forces acting upon it.
        a. Diffusion- wants it out
        b. Electrical Attraction- wants it in.        }when these two forces are equal it makes the net flow of K+ zero and the inside or Resting Charge of the neuron will be at -70mv.
     3. Na+ - is at a 10x greater concentration. outside and it really wants to flow in because both forces want to move it in. (arrow) Na+ can leak in through gated channels and does, Na+/K+ pumps must constantly be at work to keep the resting charge and concentration of Na+ and K+ where they need to be
    4. Cl-is also at 10x concentration outside and the external environment is electrically neutral.

2/25/2013

2 Divisions of this:
        a. Somatic - "Voluntary". Control of Skeletal Muscle
        b. Antonomic - "involuntary".      "    Cardiac & Smooth Muscle
2 Divisions:
           i. Sympathetic - "waking" - involves neurons that increase activity & involve excitatory neurotransmitters.
           ii. Perasympathetic - "Sleeping" - involves neurons that decrease activity & involve inhibitory  neurotransmitters.
II. Cells
  A. Supporting Cells
      1. In the CNS. 2 types"
           a. Astrocytes - fat cells that invade arteries leading into the CNS. Sets up the Blood-Brain Barrier. Only fat-soluable substances should be able to pass through. protects us from viruses & other toxins that are water soluable. Reason why the CNS has its own immune system.
           b. Oligodendrocytes - fat cells that form the myelin sheeth of CNS neurons. Wrap around the axon of a neuron insulating it & making the impulse more efficient & faster. MS - these cells are being destroyed.
      2. In th PNS: Schwann Cells - form the myelin sheeth of PNS Neurons.
  B. Neurons - Cells that conduct electricity.

Nerve - Bundle of neurons. Are either motor or sensory. Ex. Funny Bone.
Ganglion - Cluster of neurons. are both motor and sensory.

Neuron:

1.  Cell Body - contains nucleus & other organelles. Performs all of the normal cell tasks
2. Axon - longest part. Where the initial electricity is generated.

February 21, 2013

The Nervous System

I. Organization
        A. Central Nervous System- Brain and Spinal Cord (CNS)
        B. Peripheral Nervous System (PNS)- Everything outside of theCNS.
                1.Sensory- Conveying messages to the CNS.
                2. Motor- Conveying messages from the CNS. (2 Divisions)
                                a.Somatic- "voluntary"- involves skeletal muscle response.
                                b.Autonomic-"involuntary"- involves cardiac and smooth muscle response and glands,   kidneys,pancreas etc. (2 Divisions)
                                         i. Sympathetic- "waking"-involved with increased activity.
                                        ii. Parasympathetic- "sleeping"- involved with decreased activity.

III...           

            ii. Precipitation-causes viruses to come out of solution and solidify. Some antibodies can act as a catalyst to precipitate the viruses. Viruses can't infect cells and they're easier to phagocytize.
           iii. Neutralization-of wastes of bacteria and fungi.
Note: The next 3 actions require another chemical called Compliment-a class of proteins that are produced by all cells and these act with antibodies to:
           iv. Inflammation-antibody bonds to a compliment on the surface of the mast cell.
           v. Flagging-infected cells will produce a compliment that bonds to a foreign protein and this complex is exocytized onto the surface of the cell and this flags it for destruction.
          vi. Lysis-antibody/compliment bonds to the surface of a foreign cell and lyses it.

Note- Antibodies are specifically designed to bond to a foreign chemical (usually a protein) called an antigen. Actions i-iii require antibody-antogen and actions iv-vi require antibody-compliment-antigen. This is called the Self/Nonself Complex.

B. The Cell Mediated Response- Involved T-Lymphocytes (T-Thymus T-Cells migrate and mature) These cells identify the antigen and kill infected cells.
                           1. Activation.
                                      a. A macrophage phagocytizes the pathogen, breaks it up, finds a Helper T-Cell, docks with it and "presents" the antigen to it. It is now an APC (Antigen Presenting Cell)
                                      b. The Helper T-Cell starts to secrete Interleukin I-carries the "recipe" for the antigen and it stimulates the growth of more Helper T-Cells.
                                      c. As these cells grow and multiply, they begin to send out a second protein called Interleukin II (IL II). IL II Does 2 things:
                                                      i. Activates the Humoral Response.
                                                     ii. Activates the Cell Mediated Response.
                          2. When IL II activates Effector T-Cells, they begin to divide into two types.
                                      a. Memory T-cells- Immuno Memory and Vaccines.
                                      b. Cytotoxic T-Cells-roam around the site of infection and dock with infected cells, release Perforin, which lyses the cell.

Feb 19th

III Specific Defense-Dual Response.  The Immune Response-Taylor make chemicals and cells for the particular pathogen infecting you. Dual Response: 2 cascades of evens that happen simultaneously
     A. The Humoral Response involves cells called B-Lymphocytes (B-Bone they emerge from bone marrow ready to do battle and produce antibodies-chemical warfare protiens) Lymph-fluid that flows through the lymphatic system-while blood kcells use it as a highway and lymph nodes are way stations for these cells. Lymph Nodes- storage for lymphocytes.
          1. Activation- 2 ways:
                a. The Capping Hypothesis- surface antibodies attach to the pathogen and endocytize it. (Minor)
               * b. Via the Cell Mediated Response and IL II. (Major)
          2. Action- B-cells that are activated begin to divide into 2 types:
                a. Memory B-Cells-stay in lymph nodes and wait for the same invader to infect you a second, third etc. time. Lifelong. Gives us our Immunological Memory.
Vaccines-when an attenuated(somehow rendered harmless) version of a pathogen is intorduced into the body in order to build Immunological memory.
               b.  Plasma B-Cells-produce antibodies. What do they do? They are Specifically design for the pathogen to:
                       i.  Agglutination-to glue together.  Attach a number of pathogens together.  Stops infection and helps phagocytosis.
                      ii. Precipitation-viruses dissolve in waternand some antibodies will cause them to precipitate-come out of solution and crystallize

02/14/13- Happy Valentine's Day! Here are some notes

B. Openings (continued)
3. Acidity- in digestive and reproductive tracts- kills cells
4. Normal Flora- in digestive tract. Outcompete potential pathogens

C. Cells
1. Platolets- blood celsl that produce clotting proteins
2. Phagocytes- white blood cells that "eat" anything foreign. Neutrophils (most common) and Macrophages (largest and most effective phagocyte)
3. Natural killer cells- White blood cell's- find foreign cells and lyse them. ID maligent cells and kill them.

D) The inflammatory response- 2 scenarios
1. Localized- (cut)
a. injured cells begin to release a chemical, HISTOMINE. (causes inflimation)
b. Histomine acts on surrounding blood vessels, dialating the, allowing a greater volume of blood to flow into them. (swelling, red color and possible heat)
c. Provides more oxygen, glucose, and clotting factors for healing
d. stretches the walls of the blood vessels an dit makes hte blood vessel more porous. This allows WBC's (phagocytes, NK cells) to enter the damaged area to do their job.
e. Pus- is hte remains of phagocytes that eaten themselves to death.

2. Systemic- system-wide
a. white blood cells produce antibodies that bond to Mast Cells- which release histomine
b. the area around the infection will have its blood vessels dilated, and this does what a LOCALIZED RESPONSE will do
c. this causes muscous membranes to increase production
d. it can also brain to increase body temp. The brain produces PYROGENS that cause fever

The Body's Defense System

I. Non-Specific Defense- General defense against any pathogen.
    A. Skin
         1. Almost Impenetrable
         2. Sweat and Oils are highly acidic- kills most bacteria & fungi.
         3. Normal flora- bacteria that live on the skin. They out compete pathogenic forms of bacteria.
     B. Openings
         1. Lysozymes- Enzymes that chemically destroy bacteria and fungi in tears and saliva.   
         2. Mucous Membranes- produce mucous in response to infection. 
        

II. Speciation
     B. "Peak Shift"
     When an environment drastically changes, this changes the "adaptive landscape" and promotes new adaptations for new niches (jobs) and this creates new species.
III. Adaptive Radiation- Darwin's Finches. When one species involves into many. Happens when the environment offers multiple unutilized resources and little or no competition.Happens on a global scale after mass extinctions.

 Blue-Black Graskwit----- Medium Ground Seeds

Reaches Carrying Capacity

The birds that were adapted to eat small and large seeds are good too.

The Graskwit also will eat Medium Tree Seeds, plus large and small tree seeds from adaptation, there is fruit in the trees they will eat too. Then that bird will eat insects if all the seeds run out and that is how the different species evolve from the starting species.

All the new species "radiate" around the first.

IV. Coevolution- when one species' evolution is significantly influenced by another species.

     A. Predator/Prey relationships. (antelope and cheetah, Red Queen Affect).

     B. Competitiors (Red Queen Affect)

     C. Mutuaism- Plants and Pollinators

     D. Parasitism

     E. Mimicry- When two species mimic the "look" of each other.

          1. Mullerian- when venomous or toxic organisms mimic each other. Black/yellow insect.

          2. Batesian- when a non-venomous or toxic species mimics a "harmful" one. Monarch and Viceroy butterflies.



Patterns of Evolution part 2

II. Speciation Patterns: 2 basic ways
    A. Speciation by Divergence : Step-
        1. The Founder Effect
        2. Genetic Drift: because of the small size
        3. Inbredding: Small populations = more Homozygotes
        4. Population Increses to Carrying capacity
       5. Competition for limited Resources
       6. Population begins to adapt to a new environment
       7. Repeat steps 4-6 to Speciation
       8. Add new mutations
   B. Speciation by "Peak-Shifts."

Patterns of Evolution

A. Anagenesis vs. Cladogenesis

*III. The Red Queen Effect- "The Evolutionary Arms Race"
          Predators and prey, competitors and the Environment are constantly driving the evolution of its/their "partners". Perfection is impossible.
IV. Adaptations are Compromises- most adaptations will be good and bad. Giraffes neck, seals (bad on land, good in water), etc.
V. Genetic Limitations- DNA can only take a population so far. It can only use the alleles that are present now.
VI. 99% Extinction
VII. Not all evolution is adaptive- 5 forces
      Only Natural Selection is adaptive
     

Does evolution always make a population better? Can it ever acheive perfection?

Does evolution always make a population better? Can it ever achieve perfection?

NO! Evidence:

• Sexual Selection - Finding and attracting a mate takes precedence over their survival. For example: Peacocks,  Elk
• Fecundity>Longevity -Passing down genes has more effect on evolution than living a long life. For example: Salmon. Born in a sterile environment then move and become "eating machines". They produce enough fat to travel back to where they were born. When traveling back upstream they stop eating because they HAVE to die for their species. Their bodies produce nutrients for the food that the babies can live on for a short period of time.

IV. Gene Flow- Migration
     A. Immigration- movement into a population (adds alleles)
     B. Emigration- movement out of a population (subtracts alleles)
V. Non-Random Mating
     A. Inbreeding- tendency to mate with an individual more closely related. Increases p^2 and q^2 (AA&aa) and decreases 2pq (Aa)
     B. Outbreeding- tendency to mate with an individual less closely related.
     C. Assortative Mating- tendency to mate with one's own morph."look" >q^2 <p^2+2pq

      

5 Forces Continued

II Mutation- point mutations will add "new" alleles to a population. Insignificant in the short term. The #1 most important in the long term.
III. Natural Selection- an allele, or genotype, is favored by the environment.
    3 basic types:
               A. Directional- when one "extreme" is forced over the other. Example: a giraffes neck
               B. Stability - the average is favored over extremes. Example: deer population: bucks with big         antlers are killed in hunting season and small bucks don't breed, so the antler size left are the middle size. this is BAD. Humans are predators
               C. Disruptive: when the average is selected out of the population: GOOD. also known as frequency dependent selection: individual with the more common traits are selected out of the population. Example: Trout eat the flies that are most common. Animal are predators

5 Forces that Disrupt the H/W Equilibrium:

-Remember, a population will remain unchanged unless an outside force acts on them.

Tongue rolling

 -2003
TR = .75 A_
NTR = .25 aa

-2013
TR = .80 A_
NTR = .20 aa

What force changed this? Was it just chance?

I. Genetic Drift - allele/gene frequencies change by chance in a population.
This is more likely to happen in a SMALL population. There are 2 events
that will promote genetic drift:
A. The Founder Effect - when a small number of individuals migrate away and become genetically isolated. A small amount of individuals have many descendants. ex. Amish
B. Population  Bottleneck - when a large population is reduced down to very small size. ex. Blackfooted ferret, cheetah
  

How is genetic variation preserved and potentially even promoted in a population?

I. Diploidy - For every gene there are (at least) two copies because almost every species on the earth currently is sexually reproducing. What does this do for us?
     A. Allows recessives to exist. (Example: white skin. Dark skin is very common among people along the equator. This prevents skin cancer from the sun but when our ancestors moved out of Africa, we developed light skin because we didn't have to worry about skin cancer as much and light skin allows us to absorb the sun and make our own Vitamin D.)
     B. Allows codominance. (Example: African people want to be heterozygous for Sickle Cell Anemia because the recessive protects against Malaria. This could not happen without Diploidy.)

II. Meiosis
     A. Crossing Over - It is the number 1 factor for genetic variation in gametes.
     B. Independent Assortment - the number 2 factor for genetic variation - two chromosomes separating do not affect each other (flipping two coins). This exponentially magnifies the variation from crossing over.

III. Sexual Reproduction
     A. Two parents' genetic info is randomly passed to offspring. (You are not the same as your siblings.)
     B. Mechanisms that promote outbreeding. (the opposite of inbreeding - we think marrying our cousins is gross and flowering plants promote outbreeding because they attract pollenators.)

IV. Clines - Happens when a population's genetics change from one side of its range to another.

V. Ecotype - genetic variation types of the same species because they live in different ecosystems.

II. Darwin's Theory
A. All populations are genetically variable.  "New" variations can suddenly appear within a population.  These variations can be passed to the offspring.
B. (Thomas Malthus)  All populations will eventually reach a size where "more offspring are born, than can survive to breeding age."
C. A competition will occur between individuals for limited resources.
D. The environment selects those individuals best adapted to survive and pass on their genes. Natural Selection.

III. Comparative Anatomy cont...
C. Vestigial Structures: are of no apparent use or value. remnants of our evolutionary past?
IV. Comparative Embryology
Ontogeny Recapitulates Phylogeny
The development of embryo is a highlight reel of the evolution of that species.
V. Physical Sciences
A. Astronomy: The farthest galaxy identified is approximately 15 billion light years away from the earth (Light Year: amount of distant light travels in a year)
B. Geology: slowly but surely, geologic forces (erosion, tectonics, volcanism) cause great change over long periods of time.
Gradualism
VI. Artificial Selection:when humans breed for characteristics that we select and the result is great change in a species. DOGS
VII. Biogeography: where life is located on the planet
 A. Isolation=Endemism (found in only one place) When a population becomes isolated, mutation and natural selection will start to change population and make it different from its ancestral species. If the isolation lasts long enough, a new species will evolve.

01/08/13

(We finished up the cladogram of the vertebrates. I'm not sure (depending on which hour you're in) if you have this cladogram finished. 4th hour did not. So check with a neighbor. Below is the part of the cladogram on hearts, which Lit said would be on the test. Pictures came with it.)

Fish                                   Amphibians              Reptiles                        Birds                        Mammals
2-Chambered (50%)       2 then 3 (70%)     3, Ventrical paritally            4   (100%)                4 (100%)
                                                                         divided  (85%)    

~~~

II. Comparative Biochemistry--Comparing the sequences of DNA & Proteins. Allows us to determine genetic relationships between organisms.

III. Comparative Anatomy 

   A. Homologous Structures--Similar anatomically, but not necessarily similar functionally. Allows us to see

          Divergent Evolution--the structures become dissimilar functionally. 

   B. Analogous Structures--similar functionally but not similar anatomically. Evidence of Convergent

             Evolution--two "unrelated" species develop functionally similar structures from different origins.

There are 4 extraembryonic (made up of embryonic tissue but not actually part of the embryo proper) membranes that are found in all amniotic organisms:

Membrane........................Function in Egg Layers.................Function in Placentals

AMNION.......................Forms a sac around the ....................same
........................................embryo and fills w/ fluid

CHORION........................gas exchange mechanism..................placenta
..........................................just beneath shell

ALLANTOIS.....................forms a waste sac.............................umbilicus

YOLK SAC......................surrounds the yolk.............................vestigial

Fossil- any evidence of former life. (species that are no longer present)
(e.g. petrified wood, fossilized bones, insects preserved in amber etc.)
I. Fossil Record
 B. >99% Extinction- or 99% or higher number of species of organisms should be extinct.
C. Fossils found "where they shouldn't be." Like fossils of marine animals on mountain peaks.
D. Fossils laid down in order from simple to complex. (bacteria fossils-simple aquatic animals-fish-land plants-amphibians-reptiles-dinosaurs-mammals-birds)
E. History of our planet.
Cladogram of the Vertebrates( Animals with spinal columns) This shows how animals are connected, evolutionary speaking (fish to reptiles to birds and also reptiles to mammals. Mammals came before birds.)
 1 Fish       2 Amphibians        3 Reptiles      5 Birds       4 Mammals
     i              i                        i                    i                  i
      i              i                iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
         i          i  i               
               i    
Note: the i's don't really mean anything they just connect the animals)
Fish-Ectothersm (require an outside source of heat to function), have fish scales, external fertilization, gelatinous eggs.
Amphibians- Ectotherm, no body covering, external fertilization, gel eggs.
Reptiles-Ectotherm, have reptile scales (very different from fish scales, internal fertilization, amniotic (shell wtih amniotic fluid  surrounding the embryo) egg.
Birds-Endotherm (generate heat from the inside), have feathers, and scales (think of a birds feet), internal fertilization, amniotic egg.
Mammals-Endotherm, have hair, internal fertilization, Amniotic eggs (not very many, like platypuses, and echidnas nowadays), Marsupials-kangaroos, koalas, and other mammals with pouches (embryos of marsupials have a yoke while they are in the mother), and Placental mammals(all of the other mammals).