- Most commonly single stranded but can be double stranded as well 
- RNA contains ribose sugar which contains an extra OH group compared to DNA (deoxyribose) 
- RNA can form more shapes and conformations than DNA and it can be catalytic
- All RNA come from DNA template however, because it can bind to the DNA template. 


RNA structure

- Transcription is initiated by a promoter – about 40 base pair sized sequences starting on the 5’ end of the start site. 
- -10 and -35 sequence is  the promoter sequence, while initiation occurs downstream  (add image)
- Initiation requires formation of transcription bubble 
- Sigma factors – determine which genes are transcribed. 
– In some bacteria, sigma factors can differentiate when genes are expressed as early, middle, and late genes. 


Prokaryotic RNA transcription (Initiation)

- RNA transcription in eukaryotes differs from prokaryotes in that it has many RNA polymerases and it has a more complex control sequence.  
- Numbers of RNA Polymerases:
   - RNA polymerase 1 – synthesizes the precursor to mRNA 
   - RNAP II – synthesizes mRNA precursors 
   - RNAP III- synthesizes precursors to 5S rRNA (subunit of ribosome), tRNA, and smaller RNAs. 
   - Mitochondrial and chloroplasts RNA polymerases are also present . 
- These all recognize different promoters as well. However core promoters are the TATA box that is present 25-31 base pairs upstream of the transcription start site. 
- Enhancers – are recognized by transcription factors that attract RNA polymerase II to bind to a nearby promoter. These are important in selective gene expression. 
- Transcription factors initiation transcription by binding specifically to the promoters of DNA. This is a same process in eukaryotes and prokaryotes. 
- At the TATA box a preinitaiton complex forms with the RNA polymerase transcription factors and the DNA promoter region. 
- The TATA binding protein binds to the TATA box. It forms a TFIID complex with 17 other proteins. 

Eukaryotic RNA Transcription (Initiation)

Ribosomal RNAs or rRNAs make up about 50% of the ribosome. They are structural or enzymatic and are important in forming the ribosome to be used for translation. They are also a product of transcription.

rRNA

Transfer RNAs or tRNAs translate the mRNA code to the corresponding amino acids by binding to the specific codons. There are many types depending on the species. They are also a product of RNA transcription.

tRNA

Antisense RNA are complementary regions of mRNA molecules. It is a type of non-coding RNA.

Antisense RNA

Messenger RNA (mRNA) is one product of transcription. It has the genetic information needed to synthesize proteins during translation.

mRNA

Like DNA, RNA can be visualized using various methods in the lab. From this, we can observe the different sizes of RNA and observe the different sizes and amounts of mRNA produced in different cellular tissues.

Visualizing RNA

RNA is involved in protein synthesis and regulation. It also has catalytic properties.
RNA is typically found in the single stranded form.
RNA is formed from hydrogen bonds between the base pairs adenine and uracil and cytosine and guanine bases, respectively.

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Nucleic acids are macromolecules that are composed of subunits called nucleotides.  They are responsible for the transfer of genetic information from an organism's genome and turning it into proteins.  Nucleic acids exist in two forms:

- deoxyribonucleic acid (DNA)
- ribonucleicacid (RNA)

Nucleic acids are built using nitrogen, and thus need a nitrogen source to undergo nitrogen fixation

Nucleic Acids

The genetic code refers to mRNA transcripts translated into amino acids to make proteins. This occurs due to the nucleotide triplets called codons that code for amino acids.

The Genetic Code

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Microbiology covers the scope and sequence requirements for a single-semester microbiology course for non-majors. The book presents the core concepts of microbiology with a focus on applications for careers in allied health. The pedagogical features of the text make the material interesting and accessible while maintaining the career-application focus and scientific rigor inherent in the subject matter. Microbiology’s art program enhances students’ understanding of concepts through clear and effective illustrations, diagrams, and photographs.

Microbiology is produced through a collaborative publishing agreement between OpenStax and the American Society for Microbiology Press. The book aligns with the curriculum guidelines of the American Society for Microbiology.

OpenStax Microbiology Textbook

• DNA is the hereditary material of the cell  
• It is mostly formed in antiparallel DNA strands in a double helix with a 5' and 3' end. 

• DNA contains major and minor grooves. 

• DNA is formed from hydrogen bonds between the base pairs adenine and thymine and cytosine and guanine bases, respectively.

Deoxyribonucleic Acid (DNA)

Nomenclature

- Ultimate source: atmospheric nitrogen gas -> to be used, it must be split to make ammonium
- Nitrogen fixation: split N2 and reduce it to NH4+
- Mostly newly-fixed nitrogen (60%) is from archaea and bacteria
- Other sources: 15% from lightning, UV, 25% from industry
- Plants take in nitrites and nitrates and reduce them with electrons from reduced cofactors to make ammonium for synthetic reactions
- Higher organisms (like humans) ingest nitrogen-containing compounds


Nitrogen Sources

- Some bacteria and archaea are diazotrophic (nitrogen-fixing) splitting gaseous, atmospheric nitrogen and reducing it to ammonia
- The triple nitrogen bond is difficult to break because of the instability of highly reactive, high-energy intermediates in the pathway
- After intermediates are created, the reaction is downhill in terms of energy, making it easy, but getting there can be difficult
- The reactions require special catalysts (enzymes) not found in higher organisms
- Energetically expensive process
- Requires 16 ATP per mole of N2 split and reduced
- Split N2 - reduce to NH3
- N2 + 10H+ + 8e- -> 2 NH3+ + H2
Ferredoxin, Nitrogenase
Two parts - reductase and nitrogenase


Nitrogen Fixation occurs in diazotrophic organisms

Ribonucleic Acid (RNA)

The number of codons possible is more than the number of amino acids. This means there is redundancy in the genetic code for multiple codons to translate for one amino acid. In most cases, the first two codons dictate the amino acid while the third position is the wobble position is less important for the amino acid that is incorporated.

Redundancy in the Genetic Code

Proteins are macromolecules that are composed of subunits called amino acids When the number of amino acids linked together becomes very large, or when multiple polypeptides are used as building subunits,

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