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0,5bp to 10 million bp

2,9 million bp to over 100 billin bp

>90% of eukaryotic genomes

< 15% of prokaryotic genomes

Transcribed to a functional RNA which ususally encodes a protein

Regulates the expression of a structural gene

Genes can exist together with other genes in a unit

Genes that are controlled by the same control protein

DNA is a polymer of 4-desoxyribonucleoside triphosphates (dNTPs)

Adenine (Purine)

Guanine (purine)

Thymine (Pyrimidine)

Cytosine (Pyrimidine)

Nucleotides are connected to each other by 5’ - 3’ phosphodiester bonds

• Hydrogen bonds allow complementary base interactions A pairs with T (via two hydrogen bonds), G pairs with C (via three hydrogen bonds)

• These interactions allow the two phopsphodieester backbone to come together in an antiparallel fashion -> forming the double helix

• At hight temperatures (50°-90°C) the hydrogen bonds break & the duplex falls apart into two single strands

• contains ribose sugar

• Uracil replaces thymine

• Usually single stranded

DNA is overwound (Archaea living in acid at high temperatures have positively supercoiled DNA)

DNA is underwound

• ususally single proteins

• Cleave one strand of DNA (“nick”)

• Generally unwinds supercoils

• have multiple subunits

• Cleaves both starnds of DNA

• Introduces supercoils (energy-dependent)

Replication initiator protein

Helicase

DNA primase: synthesis of RNA primer

Major replication enzyme

Replaces RNA primer with DNA

Relives positive DNA supercoiling introduced by the replication process

• replicated discontinuously -> producing Okazaki fragments

• The cell coordinates the activity of two DNA pol III enzymes in one complex -> the replisome ensures that the leading & lagging strand are synthesized simultaneously in 5’ to 3’ direction

• Both polymerases move in parallel with each other

• Lagging strand loops out after passing through its polymerase

• cells use RNase H to remove RNA Primers

• DNA pol I enzyme synthesizes a DNA patch using 3’ OH end of the preexisting DNA fragment as primer site

• DNA ligase repairs the phosphodiester nick using energy (from NAD in bacteria or ATP in eukaryotes)

• there are as many as ten terminator (ter) sequences on the E. Coli chromosome

• A protein calles Tus (terminus utilization substance) binds to these sequences & stops DnaB helicase activity & thus polymerization

The coded genetic information hard-wired into DNA is transcribed into individual transportable cassettes, composed or mRNA; each mRNA contains the program for synthesis of a particular protein

• complex that carries out transcription by making RNA copies (transcripts) of a DNA tempate strand

• In bacteria is a holoenzyme composed of core polymerase required for elongation and sigma factor for initiation

• the sigma factor helps the core enzyme detect the promotor which signals the transcription start site

• Every cell has a “housekeeping” sigma factor

• In E. Coli its sigma 70 (rpoD) recognizes consensus sequences at the -10 & -35 positions, relative to the start of the RNA transcript (+1)

• A single bacterial species can make several different sigma factors

• RNA pol holoenzyme forms a loosly bound, closed complex with DNA

• Closed complex must become an open complex through the unwinding of the helical turn

• RNA pol in the open complex becomes tightly bound to DNA & transcription begins

• The first ribonucleosidetriphosphate (rNTP) of the new RNA chain is usually a Purine (A or G)

• Elongation is the sequential addition of ribonucleotides

• The RNA pol continues to move along the template, synthesizing RNA of ca. 45 bases/sec

• The unwinding of DNA ahead of the moving complex forms a 17-bp transcription bubble

• Positive supercoils ahead are removed by DNA topoisomerases

Relies on a protein: Rho & a strong pause site at the 3’ end of the gene

Rho drives up the transcript to pol & pulls transcript out

Requires a GC rich region of RNA as well as 4-8 consecutive U residues (“hairpin”)

Selectively binds to the bacterial RNA polymerase: inhibits transcription initiation

Non-selectively binds to DNA (also eukrayotic DNA): inhibits transcription elongation

Messenger RNA: encodes proteins

Ribosomal RNA: forms ribosomes

Transfer RNA: shuttles amino acids

Frees ribosomes stuck on damaged mRNA

Small RNA: regulates transcription or translation

Carries out enzymatic reactions (ribozymes)

Consumes ~ 50% of the energy in a cell

• based on nucleotide triplets = codons

• 64 possible codons: 61 specifiy amino acids

• 3 stop codons (UAG, UAA, UGA)

• The code is degenerate or redundant

• The code operates universally across species with very few exceptions

• tRNA are decoder molecules that convert the language of RNA into that of proteins

• tRNA’s are shaped like a clover leave (in 2D) & like a boomerang (in 3D)

• Two functional regions: - Anticodon: hydrogen bonds with the mRNA codon specifying an amino acid - 3’ acceptor end: binds to the amino acid

• each tRNA must be charged with the prober amino acid before it encounters the ribosome

• The charging of tRNAs is carried out by a set of enzymes called aminoacyl-tRNA synthases: each cell has generally 20 of these “match & attach” proteins, one for each amino acid

• Each aminoaylc-tRNA synthase must recognize its own tRNA but not bind to any other tRNA, so each tRNA has its own set of interaction sites that match only the proper synthase

• ribosomes are composed of two subunits each which includes rRNA (5S, 16S, 23S) & proteins

• In prokaryotes the subunits are 30S and 50S & combine to form the 70S ribosome

• A (acceptor) site: binds incoming aminoacyl-tRNA

• P (peptidyl) site: harbors the tRNA with the growing polypeptide chain

• E (exit) site: for a uncharged tRNA recently stripped of its polypeptide

• the ribosome makes the peptide bonds that stitch amino acids togehter using an enzymatic activity called peptidyltransferase

• Peptidyltransferase is actually a ribozyme (an RNA molecule that carries out catalytic activity)

• Part of 23S rRNA of the large ribosomal subunit

the upstream, untranslated leader RNA contains a sequence with the consensus 5’-AGGAGGU-3’ (located 4-8 basesupstream of the start codon), this Shine-Dalgarno sequence is complementary to a sequence at the 3’ end of the 16S rRNA of the 30S subunit

Brings the two ribosomal subunits together, placing the first amino acid in position

Sequentially adds amino acids as directed by mRNA transcript

Releases the completed protein & recycles ribosomla subunits

Inhibits 70s ribosome formation

Inhibits aminoacyl-tRNA binding to the A-site

Inhibits peptidyltransferase

Triggers peptidyltransferase prematurely

Causes abortive translocation

Prevents translocation

• different ribosomes can bind simultaneously to the start of each cistron within a polycistronic mRNA

• Before RNA polymerase has even finished, ribosomes will bind to the 5’ end of the mRNA & begin translating it

• Not at eukaryotic cells: different compartments