Pig Dissection (RIP)

Photosynthesis and Cellular Respiration

PHOTOSYNTHESIS:

• Process where light energy is converted into energy which can later be released to fuel activities and process carried out by the organism.

light

• 6CO2 + 12H2O --> C6H12O6 + 6O2 + 6H20

chlorophyll

• chloroplasts vital for photosynthesis
• photosynthesis takes place in thylakoid which has chlorophyll (a catalyst)
• process: light dependent in thylakoid (produce ATP and NADPH) and light independent reactions (synthesize glucose)

CELLULAR RESPIRATION:

• converts energy from nutrients (such as glucose) into ATP
• reaction is reverse of photosynthesis
• final receptor in cellular respiration is oxygen

Photosynthesis

Light dependent vs light independent 

///// Light Dependent Reactions //////

• the reaction in photosynthesis which traps energy from the sun with the help of proteins and pigment molecules to create ATP and NADPH 
• in plants there are two photosystems which absorb different wavelengths of light: photosystem I and photosystem II (found in the thylakoid membrane of the chloroplast) 
• when a P680 molecule (located in the reaction centre of photosystem II) receives light wavelength of 680, it is excited and has the ability to pull electrons from water (resulting in H+ ions and oxygen molecules) 
• energized electrons are transferred via electron transport system, releasing a small amount of energy in the process. b6-f complex uses this energy to pump hydrogen ions from the stroma into the thylakoid space 
• PHOTOSYSTEM I: light that is absorbed by photosystem I is transferred to reaction centre p700 molecule (which needs light wavelength of 700 to get excited) 
• NADP reductase uses electrons that were received by electron acceptor from photosystem I to reduce NADP+ to form NADPH 
• photophosphorylation: use of photons of light to drive the phosphorylation of ADP to produce ATP via chemiosmosis (non-cyclic and cyclic) 
• non cyclic photophosphorylation: bs6

Light Independent Reactions: 

• the reaction in photosynthesis that assimilates co2 to produce an organic molecule that can be used to produce biologically important molecules such as carbohydrates AND DOES NOT REQUIRE LIGHT  (fueled by light dependent reactions) 
• CO2 assilmilation: carried out by the Calvin Cycle
• Calvin Cycle converts CO2 to glyceraldehyde-3-phosphate (G3P) 

Step 1: 

• Carbon dioxide fixation
• bond between carbon atom in CO2 to a pre-existing molecule in stroma called RUBP (ribulose-1,5-biphosphate) 
• compound with 6 carbons is unstable and breaks down to the stable product PGA (3-phosphoglycerate)

Step 2:

• Reduction
• the 3-carbon compounds are in low energy state- they are activated by ATP then reduced by NADPH to convert them into a higher enegry state 
• this results in two molecules of glyceraldehyde-3-phosphate (G3P)
• some G3P molecules leave cycle in their higher energy state and have the potential to form glucose and other carbohydrates 

Step 3: 

• Regenerating RuBP
• remaining G3P moelducles from step 2 move onto this phase where RuBP is replenished to keep the cycle going 
• most of these molecules are used to make more RuBP 
• Energy from ATP breaks and reforms bonds to make RuBP (5 carbons) from G3P
• calvin cycle must be completed 6 times in order to synthesize one molecule of glucose 

Structure and Processes of the Nervous System

(pg 351-353)

<Structure of a Neuron>

• neurons have specialized cell structure that allow them to transmit nerve impulses 
• 4 common features: dendrites, cell body, axon, branching end 

dendrite

• receive impulses from other neurons or sensory receptors and relay the impulse to the cell body
•  cover a lot of surface area to receive info w/ their numerous branches 

cell body

• has nucleus, site of cell's metabolic reactions
• processes input from dendrite
• impulse, if big enough, is then relayed to axon (where impulse is initiated) 

axon

• conducts impulses away from cell body
• axon terminal releases chemical signals to communicate w adjacent neurons, glands, or muscles
• axons of some neurons enclosed in fatty (white) layer called myelin sheath (protects neurons and speeds rate of nerve impulse transmission) 
• myelin sheath formed by schwann cells 

Classifying Neurons 
-based on structure and function
STRUCTURE: multipolar, bipolar, unipolar

multipolar: several dendrites, single axon, found in brain and spinal cord
bipolar: single main dendrite, single axon, found in inner ear, retina of eye, olfactory of brain
unipolar neuron: single process that extends from cell body, dendrite and axon fused, found in peripheral nervous system

FUNCTION: sensory, interneurons, motor

• sensory, interneurons, motor nuerons form basicimpulse transmission pathway of nervous system 
• 3 overlapping functions: sensory input, integration, and motor output 

sensory input: sensory receptors (ex in skin) receive stimuli and form nerve impulse- sensory neurons transmit impulse from sensory receptors to the central nervous system (brain and spinal cord)
integration: interneurons found within CNS- act as link between sensory and motor neurons. process and integrate incoming sensory info and relay outgoing motor info
motor output: motor neurons transmit info from CNS to effectors (muscles, glands, other organs that respond to impulses from motor neurons)

Reflex Arc: simple connection of neurons that results in a reflex action in response to a stimulus

• reflexes- sudden, involuntary responses to certain stimuli (ex jerking hand away from something hot) 
• reflex arcs-simple connections of neurons that explain reflexive behaviours 
• usually involve only 3 neurons to transmit messages (ex withdrawal reflexes- 3 neurons) 

PCR, Vector Cloning, and Sanger's Sequencing

-producing DNA

PCR: Polymerase Chain Reaction

-best method for preparing large quantities of a particular gene or other DNA sequence (billions of copies of a section of DNA made in hours)

-quicker and more selective than vector cloning when source of DNA is scanty or impure 

-requires: DNA template, dNTP (dATP, dCTP, dGTP, dTTP), taq polymerase (heat resistant), primers (2 known sequences)   

-3 steps: denaturation, annealing, extension

-Denaturation: uses heat (more than 90 degrees Celsius) to separate double stranded DNA

-Annealing: 2 primers (one for each single strand of DNA) and taq polymerase attach to DNA strand (tube is cooled in this step: 40-60 degrees Celsius)

-Extension: bases are added to primers to create new strand of complementary DNA (temperature is increased again in this step to about 72 degrees Celsius) 

-application: forensic analysis (example: isolating samples of DNA  from blood at a crime scene), determining ancient evolutionary relationships (DNA from mummies and fossil tissue) 

Vector Cloning: 

-insertion of foreign gene into bacterial plasmid 

-requires restriction enzymes that cut DNA molecules at specific locations (needs to recognize short DNA nucleotide sequences and cut at specific point in sequence, must produce sticky ends), ligase 

-long process  

-commonly uses bacteria as host cells because they grow rapidly and DNA can be easily isolated and reintroduced into their cells 

-DNA screened after amplified to get desired gene 

-potential uses: production of protein product or to prepare many copies of the gene 

Sanger's Sequencing

-similar to PCR 

-requires: DNA template, dNTP, polymerase (normal polymerase- no heat), primer (1 known sequence), and ddNTP (di deoxy (O, die!))

-ddNTP makes sure that fragments of various lengths will be synthesized 

-gel electrophoresis is used to interpret the nucleotide sequence (reading order of fragments) 

-single stranded DNA with unknown sequence acting as template + DNA polymerase +dNTPS + radioactively labeled primer + ddNTPS ---> gel electrophoresis ----> auto-radiography ----> sequence of new strand 

Initiation, Elongation, and Termination of Translation

Translation:

Initiation:
-In the ribosome, mRNA and tRNA come together
-In the ribosome, there is the big subunit and the small subunit
-Bigger subunit joins the smaller subunit, the first a.a. tRNA, and mRNA (initiation complex)
-The start codon for the protein is AUG (methionine)

Elongation:
-addition of codons/amino acids that will eventually make up the polypetide (final result)
-three sites: APE (A-entrance, P-prison, G-exit)
-amino acids can bind in the A-site and P-site
-initiating tRNA binds to the P site, then binds to an amino acid brought by the next tRNA (in the A-site)
-After the amino acids bind, the first initiating tRNA is released from the P site (prison)

Termination:
-The process of amino acid binding is continued until a stop codon is brought to the A site on the mRNA
-These stop codons are: UAA, UAG, and UGA

Initiation, Elongation, and Termination of Transcription

Initiation: 

Main 'characters': Transcription factors, promoter region (TATA box), polymerase 2 

-Transcription Factors (TFs) bind to the promoter region (eukaryotes need other proteins to recruit polymerase) 

-TATA box (found upstream) is the site to bind for TFs 

-Once binding is complete, poymerase 2 begins to read TF and transcribes on a complementary strand 

Elongation:

Main 'characters': Polymerase 2, coding strand, template strand 

-Elongation in transcription also occurs in a 5' to 3' direction 

-The strand that is very similar to the RNA transcript is the coding/sense strand (the opposite is the template/antisense strand) 

-RNA is anti parallel to the templat/antisense strand 

-During transcription, Thyamine (T) is replaced by Uracil (U) (Love U and not T(ea))

Termination: 

Main 'characters': AAAUAAA, intron, exon, G-cap and poly-a tail

-Transcription stops when polymerase 2 reaches the terminator AAAUAAA(downstream) 

-pre mRNA can't be sent into the cytoplasm (water=oxygen filled; oxygen=bully)

-G-cap and poly A-tail put on ends of the strands to protect from bullies

-intron=junk DNA to be cut out

The Three Dramatic scenes of Replication

Replication is a critical stage;  chromosomes must replicate before they can undergo mitosis. This stage can be split into three parts ('scenes'): initiation, elongation, and termination. 

INITIATION: 
Main 'characters':

• Helicase
• Gyrase

-Helicase is an enzyme that initiates the process of replication
-This enzyme unwinds the two strands of parent DNA and breaks the hydrogen bonds between the complementary base pairs
-Gyrase is an enzyme responsible for releasing the tension between the strands of DNA
-Gyrase cuts the ends and reattaches the strands

ELONGATION:
Main 'characters':

• Primase
• Polyermase 3

-Primase is an enzyme that provides RNA primers
-RNA primers are the starting blocks for new DNA growth
-Primers connect to complementary nucleotides
-Leading strands only require 1 primer, but there are many primers for the discontinuous lagging strands
-Polymerase 3 is an enzyme that combines monomers and acts as the photocopier
-When new DNA grows, it grows in the direction of 5' to 3'
-Elongation of the leading strand is smooth because it is continuous


TERMINATION
Main 'characters':

• Ligase
• Polymerase 1

-In termination, polymerase 1 (who is responsible for proofreading/checking for mistakes made by polymerase 3) replaces RNA primer with DNA components
-Ligase then bonds the Okazaki fragments (the lagging strands) to the growing strand