Unit 3: Cell Biology -- Proteins

“Expressing”

Using the information in a gene to make a protein

House-keeping genes

Genes that are essential for basic cellular functions and are constantly expressed, expressed in all cells of an organism.

DNA made up of nucleotides…

Phosphate (very negatively charged) + purine or pyrimidine base. Nucleotides strung together with phosphodiester bonds (covalent). Purine always paired w/ pyrimidine. One ring w/ two rings. Maintains width of DNA throughout whole molecule. Anti-parallel in 5’ → 3’ direction.

Chromatin

Fibers made up of packed nucleosomes. Can be condensed (heterochromatin) or decondensed (euchromatin). Different regions open/close in response to what is needed (job of the histones).

Nucleosome

DNA wound around proteins called histones. Histone tail modification can regulate chromatin condensation.

Acetylation

w/ HATs. Add acetyl group, takes away charge on the histone tail (makes it neutral) and loosens histone interaction w/ DNA wrapped around it.

Deacetylation

w/ HDACs. Removes acetyl group, adds positive charge on the histone tail and tightens histone interaction w/ DNA wrapped around it.

Transcription

Synthesis of RNA using DNA as a template. 5’ → 3’. Done with RNA Polymerase (as well as a suite of transcription factors).

Template DNA strand

Used to form base pairs with the newly made RNA molecule.

Non-template DNA strand

Sequence matches the RNA, not the stand used as a template for RNA synthesis by RNA Polymerase

Difference between RNA and DNA?

RNA is — single-stranded, has an extra -OH group on pentose sugar, uses uracil instead of thymine.

Enhancer

Location on DNA where activator proteins bind + trigger transcription of a far away gene thru DNA looping.

RNA Polymerase…

Cannot bind DNA or begin transcription on its own. Requires suite of other proteins (transcription factors, activators) Only if proper set are present will transcription begin.

Promoter

(Sequence of nucleotides indicating where to bond) Location on DNA “upstream” of genes where RNA Polymerase binds (w/ help of transcription factors) & will begin transcription.

Splicing

Removes introns + pastes together exons

What is required for mRNA export from the cytosol?

5’ cap and 3’ poly-A tail marks the mRNA, which promotes translation and helps protect mRNA from nucleases that degrade RNA. Now it can exit for translation in the cytosol.

Kozak sequence

Identifies correct translation start site in eukaryotes. Ribosome recognizes whichever ATG is surrounded by a sequence that best matches the Kozak consensus sequence.

Coding sequence (open reading frame, ORF) vs. untranslated region

Untranslated region helps regulate translationRi

Ribosome

Ribozyme = enzymatic RNA. Peptide bond formation is catalyzed by ribosomal RNA. The amino acids are brought by t-RNAs which read the genetic code and bind to the codon with a corresponding anticodon.