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DNA as Genetic Material

Initially thought to be too simple to store genetic information, DNA was later proven to be the genetic material through experiments by Griffith, Avery, MacLeod, and McCarty.

Transformation

The process observed by Griffith where nonvirulent bacteria were transformed into virulent pathogens by a combination of killed virulent bacteria and living nonvirulent strain.

DNA Structure

DNA is a polymer of deoxyribonucleotides linked by phosphodiester bonds, forming a double helix with adenine pairing with thymine and guanine pairing with cytosine.

Supercoiling

The property of DNA where the double helix coils on itself due to restrained rotation, leading to negative or positive supercoiling which is crucial for DNA function.

RNA Structure

RNA is a polymer of ribonucleotides containing ribose sugar and bases adenine, guanine, cytosine, and uracil, forming single-stranded molecules that can fold into secondary structures.

Protein Structure

Proteins are polymers of amino acids linked by peptide bonds, with a primary structure determined by the sequence of amino acids, folding into secondary, tertiary, and quaternary structures.

DNA Replication

The process where the two strands of DNA double helix are separated, each serving as a template for the synthesis of a complementary strand, resulting in two progeny DNA molecules with one new and one old strand.

Origin of Replication

The single point on chromosomal DNA, oriC, where replication initiates in bacteria, coordinated with other cellular events and regulated by proteins like DnaA and IHF.

DNA Synthesis

The process of replicating DNA strands at the replication fork, where the parental DNA helix is unwound and two strands are replicated.

Replicon

The portion of the genome containing an origin that is replicated as a unit during DNA synthesis.

Helicase

An enzyme that unwinds the parental DNA strands beyond the DUE by disrupting hydrogen bonds, providing the force to move the replisomes.

DNA Polymerases

Enzymes within the replisome that catalyze DNA synthesis in the 5′ to 3′ direction using deoxyribonucleoside triphosphates (dNTPs).

Leading Strand

The DNA strand synthesized continuously in the 5′ to 3′ direction at the replication fork.

Lagging Strand

The DNA strand synthesized discontinuously in the 5′ to 3′ direction, producing Okazaki fragments due to the lack of a free 3′-OH for nucleotide addition.

Okazaki Fragments

Short DNA fragments on the lagging strand that are later joined by DNA ligase to complete DNA synthesis.

Proofreading

The function of DNA polymerase III involving the removal of mismatched bases immediately after incorporation to ensure accurate DNA replication.

Catenanes

Interlocked chromosomes formed during DNA replication that are resolved by topoisomerases to separate daughter DNA molecules.

Promoter

A DNA sequence at the start of a gene that binds RNA polymerase to initiate transcription, specifying the transcription start site and regulating gene expression.

Coding Region

The most important part of a gene that specifies the sequence of amino acids for a protein.

Start Codon

The DNA sequence (5′-AUG-3′) that codes for the first amino acid of a polypeptide.

Terminator

A sequence that signals RNA polymerase to stop transcription.

Operon

Multiple genes controlled by a single promoter, transcribed together in bacteria.

RNA Polymerase

Enzyme responsible for synthesizing RNA from a DNA template.

Transcription Bubble

Region of denatured DNA where RNA synthesis occurs during elongation.

Genetic Code

The set of rules by which information encoded in nucleic acids is translated into proteins.

Wobble

Loose base pairing between the 5′ base in the anticodon and the 3′ base of the codon during translation.

Stop Codon

Codons (UGA, UAG, UAA) that terminate translation and do not code for an amino acid.

Translation

The process of decoding mRNA and synthesizing a polypeptide chain within the ribosome.

Amino Acid Activation

The process of attaching amino acids to tRNA molecules, which is essential for translation to occur.

tRNA Structure

Transfer RNA molecules are about 70 to 95 nucleotides long, fold into a cloverleaf or L shape, and contain an acceptor stem for holding activated amino acids and an anticodon for mRNA codon recognition.

Aminoacyl-tRNA Synthetases

Enzymes that catalyze amino acid activation by attaching amino acids to tRNA molecules, ensuring correct pairing of amino acids with tRNAs.

Ribosome Structure

Ribosomes consist of large and small subunits containing rRNA molecules and proteins, with three sites (A, P, E) for tRNA binding during translation.

Translation Initiation

The process of forming the 30S initiation complex with the initiator tRNA, mRNA, and ribosomal subunit, aided by initiation factors and GTP hydrolysis.

Translation Elongation

The cycle involving aminoacyl-tRNA binding, transpeptidation, and translocation, facilitated by elongation factors and ribosomal rRNA, leading to peptide bond formation.

Translation Termination

The process where the ribosome recognizes stop codons with release factors, hydrolyzes the bond between the polypeptide and tRNA, and disassembles the translational complex.

Unusual Amino Acid Insertion

Mechanisms for inserting selenocysteine and pyrrolysine during translation, involving specific tRNAs, aminoacyl-tRNA synthetases, and unique sequence elements like SECIS and PYLIS.

Energy Cost of Protein Synthesis

The high energy expenditure required for amino acid activation, initiation, elongation, and termination during translation to ensure fidelity and accuracy in protein synthesis.

Gene Orientation

Genes can be oriented in the same or opposite direction of replisome movement, with most genes read in the same direction as the replisome moves.

Head-on Collisions

Severe conflicts between the replisome and RNA polymerase that stall the replisome, leading to dissociation, replication errors, and increased supercoiling.

Co-directional Conflicts

Rear-end collisions between the replisome and RNA polymerase that are more easily resolved, often involving alternative helicases and the protein Mfd.

Polysome

Complex of mRNA with several ribosomes simultaneously translating the mRNA message to achieve rapid protein synthesis rates.

Expressome

Assembly of enzymes and the ribosome, facilitated by the transcription elongation factor NusG, to ensure smooth transition of mRNA to the ribosome for translation.

Chaperones

Proteins critical for proper protein folding, including trigger factor (TF), DnaJ/DnaK/GrpE, and GroES/GroEL, which assist in folding and maturation.

Protein Translocation

Movement of proteins from the cytoplasm to the external environment, requiring energy expenditure in the form of ATP or the proton motive force.

Sec System

A translocation system found in both Gram-negative and Gram-positive bacteria, responsible for translocating unfolded proteins across the plasma membrane.

Tat System

Twin-arginine translocase system present in both Gram-negative and Gram-positive bacteria, translocating folded proteins that have distinctive signal peptides.

Signal Peptide

N-terminal region of a protein that directs its sorting and targeting to specific routes, recognized by factors like signal recognition particle (SRP) or SecA during translocation.

Type V secretion systems (T5SS)

Mechanistically simple system where the protein passes through a barrel structure in the outer membrane for export.

Type II secretion systems (T2SS)

Found in Proteobacteria, anchored in both membranes with a pseudopilus to push proteins through the outer membrane.

Type IX secretion systems (T9SS)

Limited to Bacteroidota, responsible for secreting motility proteins and virulence proteases.

Type I secretion systems (T1SS)

Simple one-step secretion systems with components like ABC transporter, membrane fusion protein, and outer membrane barrel.

Type III secretion systems (T3SS)

Molecular syringes used by pathogens to inject effector proteins into host cells, involving a basal body and an extracellular needle.

Type IV secretion systems (T4SS)

Primarily used for DNA transfer, evolved from conjugative machinery, with assembly at cell poles and involving integral membrane proteins and a pilus.

Type VI secretion systems (T6SS)

Contractile weapons delivering toxins to neighboring cells, composed of a baseplate, membrane spanning complex, outer sheath, and inner tube.

Type VII secretion systems (T7SS)

Described in Mycobacterium spp., used to deliver virulence factors across the unique cell envelope featuring mycolic acids.