#import "template.typ": *
#show: ams-article.with(
  title: "Virology",
  authors: (
    (
      name: "<NAME>",
      department: [Department of Biology],
      organization: [Wake Forest University],
      location: [Winston Salem, NC 27101],
      email: "<EMAIL>",
      url: "www.michaeldewittjr.com"
    ),
  ),
  abstract: "Caveat Emptor",
  bibliography-file: "integratedbio.bib",
)

#set heading(numbering: "1.")
#let today = datetime.today()


= Esstman

- Biology UG
- PhD at Vanderbilt at SOM in Coronaviruses
- This occured during SARS outbreak 2004
- 8th grade science teaching after PhD
- Postdoc at NIH on rotavirus (5 years)
- UVA SOM (Carilion) 
- 2017 came to WFU as part of the BME major with Wake Downtown

Research
- Rotaviruses replication and evolution with a focus on viral genome replication amd assebly viral evolution

Kids 13, 14, 15 -> husban Sam

= Exam

Will be a take on examine which will tie together topics from the course.

= Central Dogma 

Central Dogma of Molecular biology- transcription of DNA to RNA which are then translated into proteins.

- Genes
- Machinery

== Molecular Virology

- Basically just self-genes which take over he cells machinery
- the struce and function of viral genes at the molecular level
- the mechanism by which viral genes are expressed and regularated

== Molecular biology

Methods are used in almost any lab that does wet lab work.

== Structure

== DNA

- 4 nitrogenous bases (A, G, C, T)
- 2 ring or one ring structure (purine; A and G)
- 1 regin structure is a (pyridimine; C and T)
- Base + sugar (5 carbon) = Nucleoside
- Phosphoralated is a is a nucleotide (can be up to three)
- Can be attached at the and 5' (phosphate group attached) where the 3' OH oxygens are present

- Two strands run 5' to 3'.
- Within strand phosphodiester bond (covalent) (G to C; A to T)
- Hydrongen bond between the two strands

- Human genome is 3 Billion base pairs
- Highly condensed and also functions as a regulatory mechanism

== RNA

- 4 nitrogenous pairs (A, G, C, U)
- OH on 2' and 3'  (Ribose sugar)
- RNA is not fully linear
- RNA will fold based on intramolecular base pairing (A to U; G to C)
- Proteins within the cell will bind
- Many types of RNA some of which can function as catalytic machines (e.g., ribosomes)
- RNA in the ribosomes catalyzes assembly

#figure(image("2024-01-17-10-02-54.png"))


Proteins are made up of 20 different amino acids each differning in their side chains (R groups).
Together they can generate different chemistries.

Proteins
- N (amino) terminus
- C (carboxy) terminus
- Bound using peptide bond

== Eurokayotic 

Transcription occurs in the nucleus while translation occurs in the cytoplasm.

While all cells have the same DNA different genes are expressed (e.g., hemeaglobin only turned on in red blood cells).
Can be modulated at any point in protein synthesis.

Gene expression is regulated by environmental cues which activate cell signalling

Post translational modification
- kinase (Add P)
- phospotase (remove P)



= Transcription of DNA into RNA

Process by which regions of the DNA are "copied" into RNA molecules.
Transcription is the synthesis of all types of mRNA, tRNA, rRNA.

1. Initiation occurs when rna polymerase binds to DNA and opens the site allowing a transcription bubble
2. Elogation- polymase switches to elongation and promoter will initate
3. Termination - release of DNA

Bacteria are much more simple with 4 proteins to put things together.
Eurokayotic cells have 300 different polypetides come together with three different identified polymerases

All are macromolecular complexes

RNA Polymerase I (pre-rRNA)
RNA polymerase II (mRNA, snRNAs, scRNAs) also called RNAP2
RNA Polymerase II (tRNA, 5S rRNA. sn RNAs, scRNAs)

Three different classes of proteins make up RNAP2
3 "groups"
1. Rpbs composed of 12 groups 
2.  GTF general transcription factors (TFIIs)
- Catalytic core contains the catalytic core, but catalytic core cannot bind. Core transcription factors will direct and bind DNA directly
3. Mediator is a complex made of many peptides 

Rate limiting step is generally recruiting and activating this complex.

== Overview of Transcription

General transcription factors recruited to the promoter on the DNA.

TATA is a highly conserved region in promoters
The TATA-binding protein bind here 
BRE TFIIB will bind
Inr is initator 
DCE or downstream core elements can replace TATA in TATAless promoters

TFIIH important for opening the bubble as a helicase

Termination - there will be a transcription stop sequence (stop codons are for translation not transcription)
AAUAAA in the pre-mRNA

