Bio

DNA:
HIND II was discovered by Smith, Wilcox and kelley = 5′ GT (pyrimidine: T or C)/Purine (A or G) AC 3′
How do we make recombinant dna:
1. cut two different DNA molecules w/ same restriction enzyme
2. Mix DNA pieces together = sticky ends- weak hydrogen binding
3. seal with ligase
Plasmids= double stranded DNA and where the DNA fragments are inserted.
Electrophoresis is using a current to separate charged molecules based on the amount of charge
in the molecule
○ Molecules move through a matrix that has pores, which also separates based on size
● DNA moves toward the positive side because DNA is negatively charged
● The density of the matrix (agarose) will determine how FAST the DNA will migrate
- The smaller fragments of DNA will move through the gel faster than the larger fragments;
The larger fragments will be closer to the top of the gel
- The size of a band can be determined by comparing it to known sizes of DNA (ladder)
- The higher percentage of agarose, the more slowly fragments of DNA will move through the gel (the gel contains the same concentrations of salts as the electrophoresis buffer)
- What is the purpose of the salts? It allows electrical current to flow through the
gel to decrease the electrical resistance
● DNA must be stained to be seen (SYBR Safe DNA gel stain)
What is the purpose of the loading dye? It indicates how far the fragments have moved during the electrophoresis ● What happens if you turn off the power supply (for electrophoresis) too early? The bands will not separate properly ● How can you tell that the power supply is on? The buffer will start to bubble because oxygen is formed at the anode and hydrogen is formed at the cathode ● What would you need to do if your DNA bands fall outside of your standard curve and you need to know their sizes? Use a different marker that has a different range of base pairs, that fits within the base pair length that you have.
Light reaction:
Equation: CO2 + H2O + (light energy) → (CH2O)n + O2 
pes of reactions
○ Light reaction: Where? Thylakoid membrane Generates high energy elections with reducing potential, Water splits into oxygen and hydrogen and forms a reduced compound (NADPH and ATP)
○ Dark reaction (light-independent reactions): Where? Stroma, Utilizes the NADPH and ATP from the LIGHT REACTION to make glucose and
other carbs from CO2 (aka carbon fixation) Carbon fixation will continue to occur in the absence of light as long as the
products of the light reaction (NADPH and ATP) are present
For the light reaction to proceed, the plant must have an effective means of capturing light energy, this is accomplished by the presence of pigments.
The pigments are within the Thylakoid membranes of the chloroplasts and are organized into photosystems.
Each photosystem includes a reaction center where a Protein-chlorophyll A complex turns light energy into chemical energy through a series of electron transfers in the light reactions. 
Other pigments are arranged in antenna complexes that capture light energy and transfer energy to the reaction center.
The absorption of light by plant pigments is the first step in photosynthesis.
Chlorophyll-A: The primary pigment in photosynthesis
Carotenes and Chlorophyll-B: perform a secondary role by absorbing light at different wavelengths than chlorophyll-a and then transferring the energy to chlorophyll-a. 
6. Why do leaves appear green? – Chlorophyll
Due to the abundance of chlorophylls, which provide the green color and absorb most of the energy used in photosynthesis. 
They absorb light mostly in the blue and red wavelength range and therefore appear green.
Ex: Green cellophane transmits: green and absorbs: red, blue
7. Function of Accessory Pigments?
Accessory pigments are Yellow-red in color and absorb light of different wavelengths, transferring the additional energy to chlorophyll-a. These pigments increase the range of wavelengths of light that can drive photosynthesis, and therefore increase the efficiency of energy capture. 
Chloroplasts like blue and red, but chlorophyll can’t process those colors so accessory pigments allow the chloroplasts to absorb more light energy and make up for the gaps chloroplasts can’t cover.
8. Why do the leaves change color in the fall?
The accessory pigments produce the dramatic colors in tree leaves.
Normally, Chlorophyll will masks the accessory pigments. Due to environmental changes chlorophyll dies and the colors of the accessory pigments are no longer masked.
Orange = carotene; Yellow = Xanthophyll; Red and purple colors = anthocyanin; Brown colors = Tannin
DCIP is utilized as the dye.
DCIP receives an electron from NADPH and becomes reduced; rather than the electron going to the dark reaction 
When this happens DCIP becomes reduced when it becomes reduced we see a decreased absorbance in the spectrophotometer.
When absorbance is decreasing that means DCIP was reduced, which also mean that NADPH was produced meaning the light rxn is occurring. 
Negative Controls – Aluminum foils, no chloroplasts, no dcip
Positive controls- cellophane (experimental) and light reaction
Histology:
Simple cuboidal – secretion and absorption (looks like squares)
Simple columnar- Absorption, secretion of mucus
Simple squamous- allows passage of materials
Stratified squamous- protects underlying tissues 
P-stratified columnar – secretion, particularly mucus (trachea)
Squamous: flat cells
Nucleus, Simple squamous: in blood vessels, Stratified squamous: epidermis of skin, mouth, esophagus (protective function)
- Highly differentiated surface cells towards the top
Cuboidal: square cells, Nucleus, Found in kidney tubules, Found around lumen of tubules
Columnar: tall cells
Digestive tract (secretion and absorptive function), 
Pseudostratified, Found in respiratory tract and male urethra (protective function)
Types of connective tissue: Connective tissue proper, Cartilage, Bone, Blood
● Cell types in connective tissue: Fibroblasts: make most of the extracellular components, Adipose cells: make and store fat, Mast cells: participate in inflammatory responses, Macrophages: phagocytose debris and foreign invaders
Functions: Structural support, Medium for metabolic exchange, Defense and protection of the body, Storage site for fat
● 2 main types of connective tissue
○ Loose connective tissue (lamina propria): loosely packed extracellular fibers, Fill in the body spaces below and surrounds the outside of the blood vessels and glands
Contains a large amount of ground substance
○ Dense connective tissue: densely packed extracellular fibers, Separated into dense and and irregular
● Dense irregular: connective tissue that is oriented in all directions
● Dense regular: connective tissue with collagen fibers that are organized
into parallel
Cartilage, Weight bearing connective tissue
○ Perichondrium: immature fibrous tissue, Surround mature cartilage, Contains vasculature, Proliferative source for new cells
Chondroblasts undergo differentiation → mature chondrocytes
● Chondrocytes: secrete ground substance and fibers, Present in lacunae, Make up the mature cartilage (no blood vessels), Nutrition reaches chondrocytes by diffusion, Differentiated chondrocytes divide 1-2 times
● Hyaline Cartilage, Makes up the embryonic skeleton that is eventually replaced by bone, Forms important rings in trachea and bronchi of lungs
- Mature cartilage has a glassy appearance
● Elastic Cartilage, Has an extensive network of fibers throughout the matrix
Bone
Cartilage and Bone Similarities: In both cartilage and bone:, Cells reside in lacunae, Covered on the surface by progenitor tissue, High amounts of collagen, Bone is different because:
Calcified: so much harder!
Canaliculi: nutrients cannot diffuse to osteocytes which require a direct blood supply Bone has a structural support and protective function
Parts of bone structure: Canaliculi, Haversian canals, Osteocyte lacunae, Concentric rings of lacunae with osteocytes
Blood Cells: RBCs, WBCs and platelets, Extracellular matrix: plasma
Fiber: present in an inactive form (fibrinogen)
RBCs: gas exchange, WBCs: defend body against foreign substances
Platelets: originate from megakaryocytes in bone marrow
○ Blood clots: aggregation of platelets to form fibrin clots
Muscle Functions: Force and contraction (used for locomotion), Connective tissue component for:, Blood supply (high metabolic rate)
Provide anchor through which it generates force
○ 3 types of contraction (3 types of muscle), Skeletal, Cardiac, Smooth
● Contain DESMIN as intermediate filament protein
Skeletal, Highly organized, Voluntary movement, Contractile units (sarcomeres), Arrangement of sarcomeres along the length to give striated appearance (A and I band)
Smooth, Surrounds blood vessel ,Lacks striation, Walls of digestive tract, arteries and urinary bladder, Cells are spindle shaped, Involuntary activity
Cardiac, Specialized for contraction of heat, Branched, Presence of intercalated disk
Temporary Fast Block to Polyspermy
● In the egg, Na+ channels open in the plasma membrane (below the jelly coat/vitelline layer) Normally Na+ concentration is higher outside than inside so sodium enters into the cell and the plasma membrane depolarizes Depolarization causes voltage-sensitive calcium channels to open in the ER
PERMANENT Slow Block to Polyspermy, Calcium channel also activates Na/H+ exchanger which pumps H+ out of the cell to increase
intracellular pH, pH changes cause the polymerization of actin subunits into microfilament cables that thrust acrosomal processes toward the egg plasma membrane, Increase in intracellular calcium causes water to enter the cell and increases hydrostatic pressure, Calcium results in the fusion of cortical vesicles with the egg plasma membrane and releases
their contents into the space surrounding the egg → inactivates Bindin protein, Additional sperm are released from the vitelline membrane and no more bind
Fate of Polyspermic Eggs, Extra mitotic spindles form, Chromosomes don’t assort correctly, Development is arrested
Cortical granules contents: Proteases: cleave bindin receptors and binding between vitelline membrane and egg
plasma membrane Mucopolysaccharides: increase osmotic pressure (water influx with lifting of vitelline
membrane) → formation of fertilization membrane
○ Peroxidase: hardens fertilization membrane (makes it impermeable to sperm) Hyalin: forms protective coat around embryo
● **These granules are released during slow block
Vascular system: this supports blood flow which is maintained by heart contractions
○ Heart → arteries→ capillaries → veins → heart
Lymphatic system: functions in the passive drainage of interstitial fluid (lymph) back to the heart
● Heart Structure:
○ Endocardium: inner layer
○ Myocardium: middle layer; much thicker and contains cardiac muscle
○ Epicardium: outer layer; protection for heart
■ Pericardium: encasing for heart (double layer of connective tissue) that helps to minimize friction between the constantly beating heart and other structures surrounding it
Blood Flow Pathway
● “Lub” sound: AV valves forcefully closing “Dub” sound: Semilunar valves
○ Preventing backflow into the ventricles, Transmission of the contraction signal is carried out by specialized cardiac cells that have poor contractile potential
○ SA node, AV node and purkinje fibers
within the atrioventricular bundle of His
SA node is the pacemaker SA node→ AV node→ AV bundle→
Purkinje fibers→ Ventricles
Blood Pressure: (Cardiac Output)
● CO=HR x SV HR: rate of contraction, SV: volume of blood pumped per contraction, Blood pressure: the force of blood against the vessel walls, Increase resistance or increase volume will increase BP
● The amount of blood pumped by a heart ventricle in one minute
● Sphygmomanometer: device used to measure blood pressure
○ Cuff pressure exceeds that in the artery and thereby stops the flow of blood to the lower arm (when the cuff is loosened, blood begins to pulsate through the artery and is detected using a stethoscope)
● Korotkoff sounds: the turbulence within the artery
● Systolic pressure: the pressure at which the first sound is detected
● Diastolic pressure: the pressure where the sound disappears
● Parasympathetic: dilates arteries and arterioles; lowers resistance and pressure decreases
● Sympathetic: constricts arteries and arterioles, raises resistance → pressure increases
Fish 4 chambers in linear orientation
Chambers: Sinus venous: receiving Atrium: receiving Ventricle: pumping
Conus arteriosus: pumping
● After leaving the heart, the blood courses through the gills where it becomes oxygenated and
then it is pumped through arteries to the peripheral tissues before returning through veins to the
sinus venosus
● Limitation: this type of heart is that before the blood returns to the heart, the drop in blood pressure limits the degree of gas exchange Amphibians ○ Limitation: only have one ventricle (mixing of non-oxygenated and oxygenated blood) ○ Oxygenation in the lungs is then returned to the heart where it is pumped to the rest of the body Pulmonary circulation: between heart and lungs systemic circulation: between heart and body
Two-cycle pump
● Both atrias fill at the same time and simultaneously contract to empty blood into the ventricles; the
same amount of blood is pumped through both of these circulatory pathways otherwise BP would
be unequal (edema)
● The left ventricle is much thicker than the right to overcome peripheral resistance; there needs to
be increased pressure to force open the aortic semilunar valve to disburse oxygenated blood to
the whole body (including areas further away from the heart)
● Blood Vessels
○ 3 layers
■ Tunica intima: innermost layer
● Composed of endothelium and underlying subendothelial connective
tissue
● Internal elastic lamina: thick convoluted layer of elastin (important in
elasticity of the vessel)
■ Tunica media: middle layer
● Circular layers of smooth muscle fibers (function is to control the
diameter of the vessel)
● Arteries usually have a thicker tunica media with more muscle and elastic
fibers
● Large arteries have external elastic membranes
■ Tunica adventitia: outermost layer
● Connective tissue layer with collagen and elastic fibers
● Anchors vessel to surrounding tissue
● Thickest in veins
○ Thick enough that it requires its own blood supply (contains vasa
vasorum: smaller vessels in larger one to supply oxygen and
other nutrients to the cell)
Capillaries, Smallest vessels, Connects arterioles to
venules, Exchange of oxygen
and carbon dioxide, Consist of single layer
(simple squamous
epithelium), Fenestrations (small
openings between cells)
allow for exchange, Lowest velocity of blood
flow
Arteries, Thicker tunica media
than veins, Thicker walls and smaller lumen, Larger arteries have
many more elastic fibers in media and adventitial tunica
Veins: Thinner walls, Thicker tunica adventitia, Valves (maintain unidirectional blood flow), Larger lumen, Often appear collapsed
in cross section