DNA Replication, Transcription, and Translation: From Genes to Proteins

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DNA Replication

Overview of DNA Replication

DNA replication is the process by which a cell duplicates its DNA, ensuring that each daughter cell receives an identical copy during cell division. This process is semiconservative, meaning each new DNA molecule consists of one parental and one newly synthesized strand.

Key Enzymes: Helicase, DNA polymerase, primase, ligase, topoisomerase, and single-strand DNA-binding proteins (SSBPs).
Directionality: DNA polymerase synthesizes new DNA in the 5' to 3' direction.

Helicase opens the double helix during DNA replication

Initiation of Replication

Replication begins at specific locations called origins of replication. Helicase unwinds the DNA double helix, creating a replication fork. SSBPs stabilize the unwound strands, and topoisomerase relieves the tension caused by unwinding.

Helicase: Unwinds the DNA double helix.
SSBPs: Prevent reannealing of single strands.
Topoisomerase: Relieves supercoiling ahead of the fork.

SSBPs stabilize single strands during DNA replication Topoisomerase relieves twisting forces during DNA replication

Leading Strand Synthesis

The leading strand is synthesized continuously in the direction of the replication fork. Primase synthesizes a short RNA primer, which is extended by DNA polymerase III.

Primase: Synthesizes RNA primer.
DNA Polymerase III: Extends the primer, synthesizing DNA in the 5' to 3' direction.
Sliding Clamp: Holds DNA polymerase in place.

Primase synthesizes RNA primer during DNA replication DNA polymerase begins leading strand synthesis Sliding clamp holds DNA polymerase in place

Lagging Strand Synthesis

The lagging strand is synthesized discontinuously, forming short DNA fragments called Okazaki fragments. Each fragment begins with an RNA primer synthesized by primase. DNA polymerase III extends the primer, and DNA polymerase I replaces the RNA with DNA. DNA ligase seals the nicks between fragments.

Okazaki Fragments: Short DNA segments synthesized on the lagging strand.
DNA Ligase: Joins Okazaki fragments by forming phosphodiester bonds.

Lagging strand synthesized in fragments Primase synthesizes RNA primer for lagging strand First Okazaki fragment synthesized Second Okazaki fragment synthesized Primer replaced by DNA polymerase I DNA ligase closes gap in sugar-phosphate backbone

Problems with Replicating Chromosome Ends

Linear chromosomes pose a challenge for replication at their ends (telomeres). The lagging strand cannot be fully replicated, leading to progressive shortening of chromosomes with each cell division.

Telomerase: An enzyme that extends telomeres in certain cell types, preventing loss of genetic information.

Problems with copying the ends of linear chromosomes Unreplicated end of lagging strand Summary of problems with copying chromosome ends

Proofreading and DNA Repair

DNA polymerases have proofreading activity, correcting mismatched bases during replication. Additional repair mechanisms, such as nucleotide excision repair, fix DNA damage caused by environmental factors like UV light.

Proofreading: DNA polymerase removes and replaces incorrect nucleotides.
Nucleotide Excision Repair: Damaged DNA is recognized, excised, and replaced with correct nucleotides.

DNA polymerase adds a mismatched base DNA polymerase detects and corrects mistake Thymine dimer formation by UV light Nucleotide excision repair process

Gene Expression: From DNA to Protein

The Central Dogma of Molecular Biology

The central dogma describes the flow of genetic information: DNA is transcribed into RNA, which is then translated into protein. This process explains how genes determine phenotypes.

Transcription: Synthesis of RNA from a DNA template.
Translation: Synthesis of protein from an mRNA template.

Central dogma: DNA to RNA to protein

Genotype to Phenotype

Genetic information stored in DNA (genotype) is expressed as proteins, which determine an organism's traits (phenotype). Mutations in DNA can alter protein structure and function, leading to phenotypic changes.

Genotype: The genetic makeup of an organism.
Phenotype: Observable traits resulting from protein activity.

Genotype to phenotype: DNA to protein to trait

The Genetic Code

The genetic code is a set of rules by which information encoded in mRNA is translated into proteins. Each amino acid is specified by a sequence of three nucleotides (codon).

Codon: A sequence of three RNA bases that codes for a specific amino acid.
Start Codon: AUG (methionine) signals the start of translation.
Stop Codons: UAA, UAG, UGA signal the end of translation.

Genetic code chart

Transcription: Synthesis of RNA

Transcription is the process by which RNA is synthesized from a DNA template. RNA polymerase binds to the promoter region, unwinds the DNA, and synthesizes a complementary RNA strand.

Promoter: DNA sequence where RNA polymerase binds to initiate transcription.
RNA Polymerase: Enzyme that synthesizes RNA in the 5' to 3' direction.
Sigma Factor: Protein that helps RNA polymerase recognize the promoter in prokaryotes.

RNA polymerase and sigma form a holoenzyme Sigma recognizes and binds to the promoter RNA polymerase binding to DNA Separation of DNA double helix during transcription Synthesis of RNA polymer during transcription Hairpin forms during transcription termination Termination of transcription

RNA Processing in Eukaryotes

In eukaryotes, the primary RNA transcript (pre-mRNA) undergoes several modifications before becoming mature mRNA:

Splicing: Removal of non-coding sequences (introns) and joining of coding sequences (exons).
5' Cap: Addition of a modified guanine nucleotide to the 5' end.
Poly(A) Tail: Addition of a string of adenine nucleotides to the 3' end.

DNA-RNA hybrid micrograph snRNPs bind to intron and form spliceosome Intron is cut and exons are joined Summary of RNA splicing

Translation: Synthesis of Protein

Translation is the process by which ribosomes synthesize proteins using mRNA as a template. Transfer RNA (tRNA) molecules bring amino acids to the ribosome, matching their anticodon with codons on the mRNA.

Ribosome: Molecular machine that facilitates the decoding of mRNA into protein.
tRNA: Adapter molecule that carries amino acids and matches them to the mRNA codon via its anticodon.
Peptide Bond: Covalent bond formed between amino acids during protein synthesis.

Hypotheses for how proteins are made from RNA

Summary Table: Key Steps in Gene Expression

Step	Location	Key Enzymes/Structures	Product
DNA Replication	Nucleus (eukaryotes)	DNA polymerase, helicase, primase, ligase	Identical DNA molecules
Transcription	Nucleus (eukaryotes), cytoplasm (prokaryotes)	RNA polymerase, sigma factor (prokaryotes)	mRNA
RNA Processing	Nucleus (eukaryotes)	Spliceosome, capping and polyadenylation enzymes	Mature mRNA
Translation	Cytoplasm	Ribosome, tRNA	Protein

Key Equations and Concepts

Base Pairing Rule:
Number of Possible Codons: possible codons (since there are 4 RNA bases and codons are triplets)

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