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Understanding Gene Expression Study Guide

This guide explains the central dogma of molecular biology, detailing the flow of genetic information from DNA to RNA to protein. It covers the distinct mechanisms of gene expression in prokaryotes and eukaryotes, including coupled transcription-translation, operons, introns, exons, splicing, and mRNA processing. Key concepts such as RNA polymerase, sigma factors, promoters, and termination are discussed, along with the implications of alternative splicing for protein diversity.

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Basics of Gene Cloning and Plasmids

Molecular Biology Basics and Gene Cloning

Basics of phage DNA insertion, restriction endonucleases, plasmid vectors, and beta lactamase resistance mechanisms.

  • Restriction endonucleases
  • Palindromic sequences
  • Sticky ends
  • Plasmid vectors
  • Promoter regions
  • Beta lactamase
  • Peptidoglycan crosslinks
  • Puc19
  • Multiple cloning site (MCS)
  • LacZ gene
  • DNA ligase
  • Phosphodiester bond

DNA Structure, Gene Expression, and Amplification

Structure of Genes and Gene Expression

The central dogma describes a flow of information in an organism from DNA to RNA to protein through transcription and translation.

  • Central Dogma
  • Transcription
  • Translation
  • Prokaryotic Gene Expression
  • Eukaryotic Gene Expression
  • Polycistronic mRNA
  • Monocistronic mRNA
  • Introns
  • Exons
  • Alternative Splicing
  • Promoters
  • Sigma Factor
  • TATA Box

Gene Structure and Alternative Splicing

Eukaryotic gene structure involves the removal of introns and the joining of exons to form mature transcripts through alternative splicing.

  • Introns
  • Exons
  • Alternative splicing
  • Lariat structure
  • Mature transcript
  • Untranslated region (UTR)
  • cDNA
  • Reverse transcription
  • MLF1 gene cloning

DNA Structure, Replication, and Polymerization

A study of DNA structure, complementary base pairing, and the enzymatic processes of DNA replication and primer requirements.

  • DNA structure and complementary base pairing
  • Antiparallel DNA strands
  • 5' to 3' polymerization
  • Replication fork enzymes
  • Leading and lagging strands
  • Okazaki fragments
  • RNA primers

PCR and RT-PCR Mechanisms and Applications

The polymerase chain reaction (PCR) and reverse transcription PCR (RT-PCR) are methods used to amplify DNA and study gene expression.

  • Polymerase Chain Reaction (PCR)
  • Reverse Transcription PCR (RT-PCR)
  • Denaturation
  • Extension
  • Taq polymerase
  • cDNA synthesis
  • Gene expression
  • Reverse transcriptase

Principles of Primer Design for PCR

Guidelines for designing primers for DNA amplification and cloning into vectors using open reading frames.

  • Primer design rules
  • Melting temperature (Tm) calculation
  • Forward and reverse primers
  • Reverse complement
  • Open reading frame (ORF)
  • Restriction sites
  • Cloning into vectors

Eukaryotic Gene Regulation and Transcription

Eukaryotic Gene Regulation and GAL Metabolism

Histone proteins are modified via phosphate and methyl groups to alter DNA complexing, while GAL genes regulate galactose metabolism in yeast based on carbon source availability.

  • Histone protein modification
  • Galactose metabolism in yeast
  • Upstream Activator Sequence (UAS)
  • GAL4 activator protein
  • SAGA protein acetylation
  • SNF1 activation
  • Mig1 repressor protein
  • Transcriptional regulation via carbon source availability

Mechanisms of Bacterial Gene Regulation

Bacterial Gene Regulation and Operon Control

Prokaryotic gene clusters utilize mechanisms such as activation, repression, and transcription attenuation to control protein expression.

  • Mal operon
  • MalT activator protein
  • Trp operon
  • Repressor protein
  • Co-repressor
  • Transcription attenuation
  • Amino acid biosynthesis
  • Ribosomal translation
  • Frameshifting
  • Leader sequence

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