Molecular Biology: Transcription Basics

Polynucleotides Overview

• Nucleic acids (DNA & RNA) contain carbon, hydrogen, oxygen, nitrogen, and phosphorus.
• These molecules are conserved across all organisms and store hereditary information.
• DNA provides instructions for protein synthesis, determining amino acid sequences in polypeptides through transcription and translation.
• Nucleic acids are composed of nucleotides.
• Nucleotides are made up of a pentose sugar (deoxyribose or ribose), a nitrogenous base (adenine, cytosine, guanine, and thymine or uracil), and a phosphate group.
• These components are linked together by phosphodiester bonds.

DNA vs RNA

• DNA carries genetic blueprints for cell division, passed from parent to offspring.
• DNA has a double helix structure with two strands running in opposite directions, connected by hydrogen bonds, and complementary base pairs (A-T, C-G).
• RNA is single-stranded.
• Different types of RNA include messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA).
• mRNA carries genetic information from the nucleus to ribosomes for protein synthesis.
• rRNA forms ribosome subunits, sites for protein synthesis.
• tRNA brings amino acids to the ribosomes, matching them to the coded mRNA message.
• DNA remains in the nucleus, serving as a template for RNA synthesis.
• RNA travels to ribosomes with instructions to assemble proteins in the cytoplasm.
• RNA is single-stranded.
• DNA is double-stranded.
• DNA's sugar is deoxyribose.
• RNA's sugar is ribose.
• DNA bases are adenine, thymine, cytosine, and guanine.
• RNA bases are adenine, uracil, cytosine, and guanine.

RNA Types

• Messenger RNA (mRNA) carries a copy of instructions from the nucleus to ribosomes in the cytoplasm.
• Ribosomal RNA (rRNA) forms the subunits of ribosomes, the sites of protein synthesis.
• Transfer RNA (tRNA) carries amino acids to ribosomes and matches them to the coded mRNA message, assisting in protein assembly.
• A single DNA molecule can contain thousands of genes, with only expressed genes being copied into RNA.

Central Dogma of Life

• The central dogma describes the flow of genetic information (from gene to protein) in cells: DNA to mRNA to protein.
• Transcription is the process where genes are used to make mRNA.
• Translation is the process where mRNA is used to direct protein synthesis.
• Translation also involves rRNA and tRNA.
• Nucleotides 1-3 correspond to amino acid #1, and nucleotides 4-6 correspond to amino acid #2, and so on.

Genetic Code

• The genetic code involves an RNA codon consisting of three consecutive nucleotides, specifying an amino acid or the release of a polypeptide chain.
• The genetic code is degenerate, meaning some amino acids can be encoded by more than one codon.
• The genetic code is universal, with similar codons specifying similar amino acids in almost all organisms.

Universal Codons

• There are 64 possible nucleotide triplets (4^3), more than enough to code for the 20 amino acids.
• The genetic code is degenerate, meaning an amino acid may be coded for by several codons, as multiple synonymous codons can specify the same amino acid.
• A single base substitution in a gene can produce a silent mutation, missense mutation, or nonsense mutation.
• Mutations affecting gene expression may result in the expression of proteins that are not usually expressed, altered or shorter protein products.

Mutations

• Mutations alter the DNA sequence, potentially altering the protein produced.
• Substitution involves one base being replaced by another (transitions or transversions).
• Silent mutations don't change amino acids.
• Missense mutations change the amino acid.
• Nonsense mutations introduce a premature stop codon.
• Frameshift mutations occur when an insertion or deletion of one or two bases shifts the reading frame in the mRNA.

Transcription

• Transcription is the process of copying a DNA sequence into an RNA sequence.
• RNA polymerase reads DNA in the 3' to 5' direction to assemble the complementary RNA transcript in a 5' to 3' direction.
• Transcription involves creating a complementary copy of the gene sequence.
• RNA polymerase binds to the DNA strand to initiate, and continues until it reaches a stop sequence.

Concurrent Transcription

• Transcriptional and translational processes occur concurrently in prokaryotic cells due to the lack of a nuclear membrane, leading to rapid protein production.
• mRNA degradation occurs at the same time as transcription and translation.

Splicing

• Pre-mRNA undergoes splicing to remove introns and join exons to generate mature mRNA.
• Splicing allows a single gene to produce multiple mRNA molecules, contributing to protein diversity.

Translation Overview

• Translation occurs after mRNA is processed, and involves ribosomes, tRNAs, and mRNA to synthesize proteins.
• Ribosomes provide the structure for polypeptide synthesis; rRNA makes up ribosome subunits.
• tRNA molecules carry specific amino acids to the ribosome, matching their anticodons with mRNA codons.
• amino-acid charging enzymes ensure correct amino acid is attached to tRNA.
• Amino acids are linked by peptide bonds by the ribosomes to build a polypeptide chain.
• Translation continues until a stop codon is reached.

Protein Synthesis Machinery

• Protein synthesis requires significant energy.
• Proteins are the most abundant components of living cells (after water).
• The process involves decoding mRNA into amino acids, forming the polypeptide chain of proteins.
• Amino acids are bonded covalently through peptide bonds, catalyzed by ribosomes.

Translation

• Ribosomes bind to mRNA, and tRNA brings amino acids to ribosomes.
• Ribosomes form peptide bonds between amino acids in the order specified by mRNA codons.
• The process continues until a stop codon is reached, releasing the polypeptide and mRNA.
• Translation takes place in the cytoplasm.