Bio

Posted on Jul 9, 2023 in Biology

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