Unit 3

DNA

Instructions for how to synthesize proteins.

Transcription

The process of making an RNA copy from a DNA template.

Translation

Decoding RNA to make a protein.

RNA polymerase

The enzyme that catalyzes the synthesis of RNA from a DNA template.

Holoenzyme

The complete form of RNA polymerase formed by the core polymerase and sigma factor.

Core polymerase

The part of RNA polymerase made up of different subunits including 2 alpha, beta, beta prime, and omega.

Sigma factor

A component that helps RNA polymerase find the promoter region and can attach and detach from core polymerase.

Promoter

A sequence of nucleotides that indicates the start of a gene.

Housekeeping genes

Genes that are always transcribed because their protein products are needed for basic cellular functions.

Consensus sequences

Specific sequences within the promoter that are recognized by sigma factors.

+1 position

The nucleotide position of the start of the gene.

Upstream

In genetic context, refers to sequences physically located before a given point in a gene.

Downstream

In genetic context, refers to sequences physically located after a given point in a gene.

mRNA

A single-stranded RNA that carries the instructions for protein synthesis.

Initiation (of Transcription)

The phase in transcription where RNA polymerase binds to the promoter to start RNA synthesis.

Elongation (of Transcription)

The stage in transcription where RNA polymerase synthesizes mRNA from the template DNA.

Termination (of Transcription)

The end of transcription when RNA polymerase finishes synthesizing the RNA molecule.

Rho-dependent termination

Type of transcription termination that involves the Rho enzyme destabilizing the RNA-DNA hybrid.

Rho-independent termination

Type of termination that relies on sequences in the mRNA to destabilize polymerase without the Rho enzyme.

G-C rich loop

Formation in mRNA that contributes to Rho-independent termination.

Poly U site

Region in RNA that facilitates termination by making it easier for the RNA-DNA hybrid to separate.

Antibiotics affecting transcription

Chemical compounds like Rifamycin B or Actinomycin D that inhibit transcription in bacteria.

Operon

A group of genes transcribed together from the same promoter, common in prokaryotes.

Codons

Nucleotide triplets in mRNA that specify particular amino acids.

Genetic code

The system that defines how nucleotide sequences correspond to amino acids.

Start codon

The specific codon (AUG) that signals the beginning of translation.

Stop codons

Codons that signal termination of the polypeptide chain (UAG, UAA, UGA).

Translation

The process by which ribosomes decode mRNA to build a protein.

N-terminal

The end of a protein with a free amino group.

C-terminal

The end of a protein with a free carboxylic acid group.

tRNA

Transfer RNA that brings amino acids to the ribosome during protein synthesis.

Initiator tRNA

tRNA that carries methionine and binds to the start codon in translation.

Shine-Dalgarno sequence

A ribosome binding site in bacterial mRNA essential for initiation.

Elongation factors (EFs)

Proteins that facilitate the addition of amino acids during translation elongation.

Translocation

The process where the ribosome moves along mRNA to read the next codon.

Release factors (RFs)

Proteins that help terminate translation by recognizing stop codons.

Chaperones

Proteins that assist in the proper folding of newly synthesized proteins.

GroEL and GroES

Chaperones that form stacked rings to facilitate correct protein folding.

DnaK

A chaperone that clamps down on polypeptides to assist in proper folding.

Phosphodiester bond

The type of bond that links ribonucleotides together in an RNA strand.

Topoisomerase

An enzyme that helps to relieve the strain on DNA during transcription.

Ribosome

The cellular machinery that synthesizes proteins by translating mRNA.

70S ribosome

The prokaryotic ribosome composed of 30S and 50S subunits.

30S subunit

The small subunit of the ribosome that binds mRNA and initiator tRNA.

50S subunit

The large subunit of the ribosome that catalyzes the formation of peptide bonds.

23S rRNA

The rRNA component of the large ribosomal subunit that has catalytic activity.

16S rRNA

The rRNA component of the small ribosomal subunit that helps decode the mRNA.

A site

The ribosomal site that accepts new tRNA carrying amino acids.

P site

The ribosomal site that holds tRNA with the growing polypeptide chain.

E site

The ribosomal site where empty tRNA exits the ribosome.

Initiation factors (IFs)

Proteins that assist in the initiation of translation.

Aminoacyl-tRNA synthetases

Enzymes that attach the correct amino acid to its corresponding tRNA.

Gene expression

The process by which genes are transcribed and translated into proteins.

Ribonucleotides

The building blocks of RNA, consisting of a ribose sugar, phosphate group, and nitrogenous base.

Elongation reaction (in transcription)

The process where nucleotides are sequentially added to the growing RNA strand.

Polypeptide

A chain of amino acids linked by peptide bonds.

Sense codons

Codons that specify amino acids during translation.

Nonsense codons

Codons that signal the termination of translation.

Degenerate code

The property of the genetic code where multiple codons can encode the same amino acid.

Enzymatic function of RNA

Certain RNA molecules have the capability to act as enzymes in biochemical reactions.

tmRNA

A molecule that helps rescue ribosomes that have stalled on damaged mRNA.

Genetic code universality

The concept that the genetic code is largely the same across all organisms with few exceptions.

mRNA transcript

The product of transcription that carries genetic information from DNA to ribosomes.

Amino group

The functional group (-NH2) found at the N-terminal of amino acids.

Carboxylic acid group

The functional group (-COOH) found at the C-terminal of amino acids.

Codon recognition

The process by which tRNA anticodons pair with mRNA codons.

Peptidyl transferase

The enzymatic function of the ribosome that catalyzes peptide bond formation.

RRF (ribosome recycling factor)

Involved in disassembling ribosome complexes after protein synthesis.

Termination factors

Proteins involved in recognizing stop codons and releasing the completed polypeptide.

Unique features of Eukaryotic transcription

Eukaryotes have multiple types of RNA polymerases and lack sigma factors.

TATA box

A DNA sequence within the promoter recognized by binding proteins during transcription initiation.

RNA stability

The tendency of RNA molecules to degrade relatively quickly after synthesis.

Antibiotics targeting translation

Drugs that inhibit specific stages of protein synthesis in bacterial cells.