main functional biomolecules in cells are polymers or chains → DNA, RNA, proteins

for RNA and Proteins, the specific sequence of the polymer dictates its final structure (for DNA, it comes from adjacent base-pairs)

RNA intro: linear polymer from Adenine, Guanine, Uracil, Cytosine with a phosphate backbone and ribose group

most RNA is found as single-stranded polymer that via base-pairing with complementary reginos within its own sequence, able to fold on itself

three types of RNA:

1. mRNA → messenger RNA where main functino in cell is to act as messenger molecule in process of making protein where DNA → MRNA → Protein

2. tRNA → transfer RNA used in translation to recognize 64 codons

   • Codons: group of 3 nucleotides that make up RNA → a group of codons make up a nucleotide

     • each codon codes for a specific amino acid (i.e. AUG codes for Amino Acid 1) → each codon is coding for a different amino acid

     • all of the codons put together code for a protein in the form of the amino acid sequence

     • RNA needs to recognize the beginning and end of a protein using the codon sequence → this is signalled by universal codons which indicate the start and end of protein synthesis

       • start codon is AUG, stop codon is UAG

     • there is one specific tRNA for each codon, where each codon represents one of the 20 amino acids

       

3. rRNA → ribosomal RNA gets incorporated into ribosome to give it part of its function

4. microRNA or siRNA → these RNAs are used to regulate gene expression through the process of RNA interference by targeting mRNA and initiating cleavage or splitting process

5. Riboswitches → many mRNA molecules can detect metabolites by binding and changing structure of mRNA or regulating it

a brief idea of transcription and translation for protein synthesis:

1. Transcription is the process where DNA is turned into mRNA for actvating protein synthesis
   • the three steps are initiation, elongation, and termination
   • initiation: RNA polymerase binds to the promoter region in the DNA which is a short sequence of DNA (most commonly TATAAA) which is where transcription factors can bind to the box and recruit RNA polymerase here to synthesize the RNA from the DNA at a specified site
   • elongation: RNA polymerase splits the DNA into 2 and adds nucleotides to growing mRNA strand in 5'-3' direction → RNA polymerase reads the DNA from 3'-5' however
     • template strand or the 5'-3' (antisense) strand is where RNA polymerase is active whereas nontemplate strand or 3'-5' (sense) is not used, but it is known as the coding sequence because it matches the DNA
   • termination: the RNA polymerase and mRNA seperate from DNA, and poly-A polymerase caps the AAAA tail of the mRNA or 3', and the 5' is also capped so the mRNA can't be degraded
     • at the end of the termination step, DNA has been used to create pre-mRNA strand → this strand has introns and exons
       • introns: longer sequencs of nucleotides that do not code for anything → need to be removed in the process called RNA splicing
       • exons: shorter sequences which remain since they synthesize proteins
     • thus, you have a completed mRNA strand by eliminating the introns and keeping exons
2. Translation is the process of converting info on mRNA to protein → this is done after it enters the cytosol and meets with ribosome

   • in ribosome, it interacts with the tRNA molecule, *the tRNA matches a specific amino acid with a given codon → each codon matches with the anticodons or reverse complements of the codons on the tRNA, and these anticodons match with a given aminoacid

   • occurs in three steps: initiation, elgonation, termination

   • initiation: ribosome is made up of large and small subunit with 3 active sites: E, P, and A sites

     

   • the start codon AUG which corresponds with the anticodon UAC → this tRNA molecule has the Methynine molecule attached to it, and thus it attaches the molecule to the Peptide Site or p-site to form a peptide bond

   • elongation: another tRNA molecule attaches to the A site, and this creates a covalent bond which will then push away the tRNA molecule in the P site to the E-site

     • its going to lose amino acid in the process, and thus there will be a growing chain of amino acids that are going to leave from the E-site bonded together through covalent bonds

       

     • overtime, this chain grows as tRNA molecules come from A site and leave E-site, and creates protein

   • termination: when a stop codon is read (3 possible are UAA, UAG, UGA), they don't code for any tRNA molecule and so when read at the A-site, they cause a release factor to enter A site and disassemble large and small subunits in ribosome

     

   • the protein leaves to golgi bodies and are folded there