Note: Neurons

The Structure of a Neuron
- have specialized cell structures that enable them to transmit nerve impulses
- four common features amongst neurons:

• Dendrites:
  - short branching terminals that receive nerve impulses from other neurons or sensory receptors, and relay the impulse to the cell body
  - numerous and highly branched (increases surface area available to receive information
• Cell Body:
  - processes input from dendrites
  - contains the nucleus and is the site of the cell's metabolic reactions
  - if the input is big enough, the cell body relays it to the axon in which it conducts the impulse away from the cell body to receptors or dendrites of neighboring cells (by releasing a chemical signal)
• Axon:
  - conducts the impulse away from the cell body
  - terminal end of axon branches into many fibers
  - sends chemical signals to the receptors or dendrites of neighboring cells to communicate with nearby neurons, glands, and muscles
  - some axons are enclosed in myelin sheath which gives it a shiny white appearance (myelin sheath: fatty, insulating layer composed of Shwann cells, protects myelinated axons and speeds up the rate of nerve impulse transmission)
• Branching Ends

Classifying Neurons

- three main types of neurons (sensory neurons, integration neurons, motor neurons) form the basic impulse transmission pathway of the entire nervous system

• Sensory Input:
  - sensory receptors receive stimuli and form a nerve impulse
  - transmit impulses from the sensory receptors to the central nervous system (brain and spinal cord)
• Integration:
  - process and integrate incoming sensory information, and relay outgoing motor information
  - found within the central nervous system
  - link between the sensory and motor neurons
• Motor Output:
  - transmit information from the central nervous system to effectors (muscles, glands, organs that respond to impulses from motor neurons)

The Reflex Arc

- reflexes: involuntary responses to certain stimuli
- reflex arc: simple connections of neurons that explain reflective behavior
- reflex arcs and withdrawal reflexes usually involve only three neurons to transmit messages (rapid)
- moves directly to and from the brain or spinal cord before the brain centres involved with the voluntary control have time to process the sensory information (don't feel the pain immediately but very shortly after when your brain processes it)

Biotech Techniques

Vector Cloning:
- natural DNA replication
- restriction sites
- incomplete digestion: not all sites are cut (no money no time)
- complete digestion: all sites are cut (have money have time)
- restriction enzymes cut covalent phosphodiester bonds of both strand
- DNA fusions can be name permanent by DNA ligase (seals strand by catalyzing formation of phosphodiester bonds)
- restriction enzymes need sticky ends
- fragment placed into plasmid of bacterial cell (transformation)
- 

PCR (Polymerase Chain Reaction):
- need DNA template, dNTP (dATP, dCTP, dGTP, dTTP), primers (need TWO known sequence), Taq polymerase (heat resistant)
- don't need primase, helicase, gyrase, ligase, and ssbps because it uses heat instead

Sanger's Method of Sequencing:
- need: DNA template, dNTP (dATP, dCTP, dGTP, dTTP), primers (need ONE known sequence), polymerase
- don't need primase, helicase, gyrase, ligase, and ssbps because it doesn't use heat
- need ddNTP (dideoxy NTP, two no oxygens), signals the stop of elongation since there is no oxygen for anything to attach on
Sequencing:
- the whole strand is a possibility
- strand can we cut on any letter depending on the ddNTP

Vector Cloning and PCR:
- used to replicate specific gene of interest

PCR and Sanger's Sequencing:
- need parental/ template strand
- artificial DNA replication

Vector Cloning, PCR, Sanger's Sequencing:
- DNA replicated and made in mass production

DNA Translation

* all definitions used are from McGraw-Hill Ryerson Biology 12 Textbook (Section 5.2)
APA citation: Braun, D., & Price, G. (2002). The Structure and Function of DNA. In Biology 12 (pp. 222-224). Whitby, Ont.: McGraw-Hill Ryerson.

Part 1:Initiation
1. mRNA: RNA that contains the genetic information of a gene and carries it to the protein synthesis machinery. It provides the information that determines the amino acid sequence of the protein.*
2. 5' AUG 3'
3. Ribosome
--> large subunit
--> small subunit

Part II: Elongation
4. tRNA (anticodons): reads codons, an RNA molecule that links the codons on mRNA to the corresponding amino acid for protein synthesis*
5. Codons: sequences of three nucleotide bases that specifies a particular amino acid or a stop codon*
6. Amino Acids
7. 3 sites
--> A (entrance): carries the tRNA carrying the growing polypetide chain
--> P (prision): carries the tRNA with the next amino acid
--> E (exit): tRNAs are discharged and leave the ribosome 
8. Peptide Bond: formed between the polypeptide in the P site with the new amino acid in the A site
--> separates the tRNA at the P site from the growing polypeptide chain and transfers the chain (now one amino acid longer) to the tRNA at the A site

Part III: Termination
9. Stop Codons: UAA, UAG, UGA
10. Everything disassociates.

How to transcribe a DNA sequence: 
1. Locate the TATA box
2. Identify the Coding Strand (similar to RNA) (5' TATA ------>3' AATAA)
3. Look for Terminator (AAUAA)
--> TTATT on Template Strand
--> AATAA on Coding Strand
4. Find introns
5. Find Start Codon and group the bases into 3s
6. Stop when a Stop Codon is approached.
7. Do not write "stop" when translating the sequence to amino acid sequence

DNA Transcription

Transcription: synthesis of RNA from a DNA template

The RNA transcript (single stranded) is also called pre-mRNA or primary RNA.

Part I: Initiation 
1. Initiation complex
 --> Transcription factors: set of proteins that help RNA recognize and bind to promoter
 --> RNA Polymerase II: unzips the double helix and makes the RNA copy
2. Promoter (TATA box)
--> Promoter Region: attracts TF and "TATA" box, indicates where RNA Polymerase complex should bind to initiate transcription

Part II: Elongation
3. Polymerase II
--> template/ antisense strand (RNA is anti-parallel to this strand. If the RNA intersects an unknown strand, it is the template/antisense strand)
--> coding/sense strand (5' to 3') (RNA is parallel and similar to this strand)
--> replace T with U (Uracil) on RNA strand because RNA hates "T" but loves "U" C:

Part III: Termination
4. Terminator (AAUAA box)
5. G-Cap and Poly A tail (...AAAAAAA...)
--> G-Cap: signals attachment of ribosome, capped with m^7G (methylated guanosine)
--> Poly-A tail: protects mRNA from degration
6. Splicosome
--> snRNA: recognizes the sequence of introns
--> snRNP: protein that contains snRNA
--> a loop of introns are made and is then cut by the splicosome
--> the splicosome also reconnects the exons before leaving
7. Introns/ Exons
--> Introns: USELESS INFORMATION
--> Exons: USEFUL INFORMATION

Upstream: Promoter Region
Downstream: Everything after Promoter Region