Gene Regulation, Transcription, Translation, Proteins, and Nucleic Acids

All the PLA notes except for the Atoms and Molecules notes (max 5 uploads)

5' Methyl Cap

A methylated guanine cap added directly to the $5'$ end of pre-mRNA as soon as it emerges from RNA polymerase to protect mRNA from degrading proteins, enable ribosome binding and recognition, and assist in nuclear export.

3' Poly-A Tail

A chain of approximately $250$ adenine ribonucleotides added to the $3'$ end of pre-mRNA that acts as an expendable buffer against degradation, aids nuclear export, and regulates translation efficiency.

Introns

Non-coding regions of a pre-mRNA transcript that are excised and removed by the spliceosome prior to translation.

Exons

Coding regions of a pre-mRNA transcript that are retained and spliced together by the spliceosome to form mature mRNA.

Spliceosome

The molecular complex that catalyzes the cutting of non-coding introns and the joining of coding exons during pre-mRNA splicing.

Alternative Splicing

A post-transcriptional process where specific exons are selectively included or excluded from pre-mRNA, allowing a single gene to encode multiple distinct protein isoforms.

Heterochromatin

Tightly wrapped, closed DNA around histones that physically prevents RNA polymerase from accessing the promoter, resulting in gene silencing.

Euchromatin

Loosely wrapped, open DNA around histones that allows RNA polymerase to easily bind to the promoter for gene expression.

LacZ

A structural gene within the lac operon that codes for Beta-galactosidase, an enzyme that breaks down lactose.

LacY

A structural gene within the lac operon that codes for a membrane transport protein (permease) that pumps lactose into the cell.

LacI

A regulatory gene located outside the lac operon that is constitutively expressed to produce the active Lac repressor protein.

Catabolite Activator Protein (CAP)

A transcriptional activator protein that binds with cyclic AMP (cAMP) under low glucose conditions to bind the CAP site and help RNA polymerase bind tightly to the promoter, achieving maximal transcription.

Central Dogma

The principle describing the flow of genetic information in cells from DNA to RNA via transcription, and from RNA to protein via translation.

Promoter

A specific DNA sequence upstream of a gene that serves as the binding site for transcription factors and RNA polymerase to initiate transcription.

Terminator

A DNA sequence at the end of a gene that signals RNA polymerase to stop transcription, detach from DNA, and release the synthesized RNA.

Ribosome

The organelle composed of a large and small subunit that acts as the site of protein synthesis.

Codon

A sequence of three consecutive RNA nucleotides on mRNA that encodes a specific amino acid.

Transfer RNA (tRNA)

An RNA molecule that carries specific amino acids to the ribosome and pairs its anticodon with complementary mRNA codons.

AUG

The universal start codon on mRNA that specifies Methionine (Met) and initiates translation.

A Site (Aminoacyl site)

The binding site in the large ribosomal subunit where incoming tRNAs carrying new amino acids enter during elongation.

P Site (Peptidyl site)

The binding site in the large ribosomal subunit where the peptide bond is formed and the growing polypeptide chain is held.

E Site (Exit site)

The binding site in the large ribosomal subunit where uncharged tRNAs exit the ribosome.

Release Factor

A protein that binds to a stop codon in the A site during translation termination, causing the release of the completed polypeptide chain and mRNA.

Peptide Bond

A covalent bond formed between the carboxyl group of one amino acid and the amino group of another amino acid.

Denaturing

The unfolding or loss of a protein's functional three-dimensional shape (secondary structure and beyond), often caused by heat or changes in pH.

Amino Acid Structure

The standard chemical structure of an amino acid containing a central carbon attached to an amino group, carboxyl group, hydrogen atom, and a variable R-group (side chain).

Primary Structure

The linear sequence of amino acids joined together by covalent peptide bonds in a polypeptide chain.

Secondary Structure

Local folding patterns of the polypeptide backbone into alpha-helices and beta-pleated sheets, stabilized by hydrogen bonds between backbone atoms.

Tertiary Structure

The overall 3D shape of a single polypeptide chain, driven by interactions between R-groups including hydrogen bonds, ionic bonds, disulfide bonds, and hydrophobic interactions.

Quaternary Structure

The multi-protein subunit complex formed when two or more individual tertiary structures assemble together.

Nucleotide

The fundamental monomer of nucleic acids, consisting of a phosphate group, a $5$-carbon pentose sugar, and a nitrogenous base.

Phosphodiester Bond

A covalent bond formed between the phosphate group off the $5'$ carbon of one nucleotide and the hydroxyl group off the $3'$ carbon of another nucleotide.

Pyrimidines

A class of single-ring nitrogenous bases that includes cytosine, thymine (DNA only), and uracil (RNA only).

Purines

A class of double-ring nitrogenous bases that includes guanine and adenine.

Deoxyribose

The $5$-carbon pentose sugar found in DNA nucleotides, characterized by having a hydrogen atom bonded to its $2'$ carbon position.

Ribose

The $5$-carbon pentose sugar found in RNA nucleotides, characterized by having a hydroxyl group (-OH) bonded to its $2'$ carbon position.

Antiparallel

The arrangement of double-stranded DNA where the two complementary strands run in opposite directions, with the $5'$ end of one strand facing the $3'$ end of the other.