BioE 002 Lecture Notes 2/24/25

Specific sequence present in DNA

5’…UUAUUU…3’

RNA Interference function mechanism

Repressing translation or degrading mature mRNA

Small interfering RNA

Type of RNA interference. Base pair w/ coding region (endogenous)

Micro RNA

Type of RNA interference. Base pairs with 3’ UTR (endogenous)

Pim-Interacting RNA

Type of RNA interference. Functional in germline (endogenous).

Genes regulated

By suppressing miRNA or suppressing translation

miRNA

• about 30 nucleotides long

• Binds to 3’ UTR of an mRNA and causes translational suppression of mRNA degradation

• Implicated many diseases such as cancer or neurodegenerative diseases

• Found intracellularly and extracellularly

• Serves as therapeutic targets and diagnostic biomarkers

• Can induce gene slicing

Seed region

The most crucial region in an miRNA that determines the binding to a mRNA 3’ UTR region

RNA-ases

Destroys RNA. Blood is full of this.

Spinal Muscular Atrophy (SMA)

• Caused by mutations in gene survival of motor neuron 1 (SMN1)

• Affects 1/10000 people

• SMN2 encodes an identical SMN protein. However, 90% of SMN2 transcripts lack exon 7 and produce an truncated, unstable polypeptide

Trans-acting enhancers

Enhancers that function over long distances

RNAi mediated gene silencing

Includes the binding of siRNA to form a complex with the target gene called RISC

Nucleus

Location for transcription and RNA splicing

Mature mRNA

Exported out of nucleus into cytoplasm

Stop codon sequences

DNA (TAA, TAG, TGA) and RNA (UAA, UAG, UGA)

Primary molecules needed for translation

mRNA, tRNA, ribosomes, enzymes, other factors, energy sources

Ribosomes

Site of protein synthesis of the cell. Two subunits bound to each other.

tRNA

• Carrier molecule which transfers amino acids to protein chain.

• When an amino acid is added to the chain, a specific tRNA pairs with its complementary sequence on the mRNA molecule.

• Each tRNA is specific to carry one of the 20 amino acids used to make proteins

• Recyclable, about 80 nt long, and due to H-bonding, are folded uniquely.

AUG

Start codon for methionine

64 different codons

61 to specify amino acids and 3 used as a stop codon.

Codon degeneracy

When multiple codons code for the same amino acid. There are only 20 amino acids

Translation: Initiation

• Small ribosomal subunit binds to the tRNA carrying the initiator amino acids

• 60s complex attached to 5’ cap site of mRNA

• s cons for start codon: AUG

• Large ribosome subunit joins initiation complex

• Initiation factors are released

3 sites of Ribosome

A, P, and E sites

A site

Entry site for new tRNA charged with amino acids: amino acyl tRNA

P site

Occupied by peptidyl - tRNA. The tRNA that carries the growing polypeptidyl chain

E site

Exit site of tRNA once it completes delivery of amino acid

Translation: Elongation

• New tRNA carrying an amino acid enters the ribosome

• Complementarity of codon and anticodon is validated

• When correct tRNA enters the ribosome, a peptide bond is created between adjacent amino acids

• Ribosome is moved forward to the next codon

• A site is now unoccupied and ready to accept new tRNAs

• Cycle repeated for each codon

Translation: Termination

• Stop codons are recognized by the release factor protein complex

• Polypeptide is released from the ribosome

• The ribosome disassociates into subunits and is ready for another translation cycle

Polysomes

Macromolecular complexes made up of multiple ribosomes simultaneously translating a single mRNA into polypeptide chains

Post Translational Modification

• Proteins are synthesized by ribosomes translating mRNA into polypeptide chains

• Protein folding: Polypeptide chain folds to become a biologically active protein

• Disulfide bond formation: Formation of disulfide bonds is the strongest non-hydrophobic interaction affecting the special 3D conformation of proteins.