DNA Replication Process

DNA Replication

• DNA replication is semiconservative, meaning each new molecule contains one original strand paired with a newly synthesized strand.
• Replication forks are formed at the origin of replication, and the process is bidirectional.

Initiation of DNA Replication

• Specific proteins recognize and bind to the origin of replication to initiate DNA synthesis.
• An RNA primer is made first, and then DNA polymerase adds nucleotides to the end of the primer.
• The result is a series of small fragments called Okazaki fragments, each with a short stretch of RNA at one end.

Synthesis of the Lagging Strand

• Discontinuous synthesis generates Okazaki fragments.
• DNA polymerase adds nucleotides to the end of one Okazaki fragment, eventually reaching the end of another.
• Another DNA polymerase then removes the RNA primer nucleotides and replaces them with deoxynucleotides.
• The enzyme DNA ligase seals the gaps between fragments by forming a covalent bond.

Termination of Transcription

• Transcription is terminated when RNA polymerase encounters a sequence called a terminator.
• The enzyme falls off the DNA template and releases the newly synthesized RNA.

Translation

• Translation is the process of decoding the information carried in mRNA to synthesize a protein.
• Ribosomes serve as translation "machines" that string amino acids together to make a polypeptide.
• tRNAs carry an amino acid to be used in translation and recognize specific codons in the mRNA.

The Role of mRNA

• mRNA is a temporary copy of the information in DNA, carrying encoded instructions for synthesis of a specific protein.
• The information in mRNA must be decoded into amino acids using the genetic code.

The Genetic Code

• The genetic code correlates a series of three nucleotides, a codon, with one amino acid.
• There are 64 different codons, and three are stop codons.
• The genetic code is practically universal, meaning it is used by all living things with a few minor changes.

The Role of Ribosomes

• Ribosomes locate key punctuation sequences on the mRNA molecule, such as the points at which protein synthesis should begin.
• Ribosomes have two sites, the P-site and the A-site, where amino acid-carrying tRNAs can bind.

Elongation of the Polypeptide Chain

• At the start of translation, the initiating tRNA carrying the f-Met occupies the P-site.
• A tRNA that recognizes the next codon on the mRNA then fills the unoccupied A-site.
• Once both sites are filled, an rRNA creates a peptide bond between the two amino acids carried by the tRNAs.

RNA Synthesis Process

• RNA polymerase binds to the promoter and melts a short stretch of DNA, and the template strand is used to synthesize a single-stranded RNA molecule.
• Sigma factor dissociates from RNA polymerase during elongation, leaving the core enzyme to complete transcription.

RNA Polymerase Structure and Function

• RNA polymerase has a loosely attached subunit called sigma (s) factor that recognizes the promoter.
• Cells can produce various types of s factors, each recognizing different promoters.
• Controlling which s factors are made allows cells to transcribe specialized sets of genes as needed.

Eukaryotic and Archaeal RNA Polymerases

• RNA polymerases of eukaryotic cells and archaea use proteins called transcription factors to recognize promoters.

Transcription Process

• RNA is synthesized in the 5' to 3' direction as the enzyme adds nucleotides to the 3' end of the growing chain.
• Nucleotides are added only to the 3' end, and the reaction is fueled by hydrolyzing a high-energy phosphate bond of the incoming nucleotide.

Initiation

• RNA polymerase binds to the promoter and melts a short stretch of DNA during initiation.

Elongation

• RNA polymerase denatures a new stretch of DNA and allows the previous portion to renature during elongation.
• This exposes a new region of the template so elongation can continue.

Termination

• When RNA polymerase encounters a terminator, it falls off the template and releases the newly synthesized RNA.
• RNA polymerase dissociates from the template after termination.

Humoral and Cellular Immune Responses

• Humoral responses result in the generation of antibodies reactive with a particular antigen
• Antibodies are proteins with similar structures, known collectively as immunoglobulins (Ig)
• Adaptive humoral responses can be transferred passively to another individual by injection of serum
• Cellular immune responses are dependent on an intact thymus, and the lymphocytes responsible are known as thymus-dependent (T) cells

B Cells and T Cells

• Antibody-producing lymphocytes, dependent on the bone marrow, are known as B cells
• In response to antigen stimulation, B cells will mature to antibody-secreting plasma cells
• T cells are responsible for cellular immune responses and are dependent on an intact thymus

Recognition Phase

• The recognition phase is common to both adaptive and innate immunity
• It involves professional cells, known as classical dendritic cells, that recognize general pathogen features or specific antigenic molecules
• Dendritic cells process antigens and present antigen fragments to other cells of the immune system

Effector Phase

• In the effector phase, neutrophils and macrophages (innate immunity) and antibodies and effector T lymphocytes (adaptive immunity) eliminate the antigen

Immune System Diseases

• The immune system may fail (immunodeficiency), become malignant (lymphoid malignancies), or produce aberrant responses (such as in autoimmunity or allergy)

Effector Mechanisms

• Effector mechanisms are often dependent on messages from initiating or regulating cells
• Soluble mediators, which carry messages between cells, are known as interleukins, cytokines, and chemokines

Molecules Recognized by Immune Systems

• Foreign substances are recognized by both the innate and adaptive systems, but in different ways, using different receptors
• The innate system is activated by ‘danger signals’, due to pattern recognition receptors (PRRs) on dendritic cells recognizing conserved microbial structures directly

Factors Influencing the Immune Response

• The nature of the molecule (protein content, size, solubility) influences the immune response
• The dose of the antigen influences the immune response, with low doses provoking small amounts of antibody with high affinity and restricted specificity
• The route of entry of the antigen influences the immune response, with different routes leading to different immune responses

Understand the semiconservative process of DNA replication, where each new molecule contains one original strand paired with a new one.