Biol-40 Exam 4 Study Guide Notes

Genes & Transcription (16.2-16.4, 17.1)

  • Central Dogma of Molecular Biology:

    • Flow of information: DNA → RNA → Protein.

  • Gene Expression:

    • Transcription and translation are components of gene expression.

  • Genotype vs. Phenotype:

    • Genotype: Genetic makeup (DNA sequence).
    • Phenotype: Physical traits (proteins and their functions).
    • The relationship between genotype and phenotype determines the observable characteristics of an organism (Phenotype=Genotype+EnvironmentPhenotype = Genotype + Environment).

  • Universal Genetic Code:

    • How to read and interpret it.

  • Non-Overlapping Codons:

    • Codons in a gene are read sequentially and do not overlap.

  • Decoding DNA & Mutations:

    • Transcribing DNA into RNA and then translating it to protein.
    • Practice what happens when there is a mutation in the DNA sequence.

  • Open Reading Frame (ORF):

    • The region of DNA that encodes a protein.

  • Mutations & Phenotype:

    • How a mutation in DNA affects the phenotype.

  • Point Mutations:

    • Types: substitutions, insertions, deletions.
    • Effects on protein function: silent, missense, nonsense, frameshift.

  • Chromosomal Level Mutations:

    • Deletions, duplications, inversions, translocations.

  • Transcription:

    • Function: Synthesize RNA from a DNA template.
    • Location: Nucleus in eukaryotes, cytoplasm in prokaryotes.

  • DNA Polymerase vs. RNA Polymerase:

    • DNA polymerase: DNA replication
    • RNA polymerase: RNA transcription.

  • 3 Stages of Transcription:

    • Initiation: RNA polymerase binds to promoter.
    • Elongation: RNA polymerase synthesizes RNA.
    • Termination: RNA polymerase detaches, RNA released.

  • Parts of a Gene:

    • Prokaryotes: promoter, coding region, terminator.
    • Eukaryotes: promoter, enhancers, introns, exons, terminator.

  • Transcriptional Start Site:

    • How to find.

  • Promoter:

    • Region of DNA where RNA polymerase binds to initiate transcription.
    • Function: to initiate transcription.

  • Sigma & Transcription Factors:

    • Sigma (prokaryotes): helps RNA polymerase bind to the promoter.
    • Transcription factors (eukaryotes): proteins that regulate transcription.

  • Coding Strand vs. Template Strand:

    • Coding strand: Has the same sequence as the RNA (except T instead of U).
    • Template strand: Is used by RNA polymerase to synthesize RNA.

  • Prokaryotic vs. Eukaryotic Transcription:

    • Location, RNA processing, initiation, termination.

RNA Processing & Translation (17.2-17.5)

  • Purpose of RNA Processing:

    • To produce a mature mRNA that is ready for translation.

  • 3 Main Types of RNA Processing:

    • 5' capping: Addition of a modified guanine nucleotide to the 5' end of the mRNA.
    • Splicing: Removal of introns.
    • 3' polyadenylation: Addition of a poly(A) tail to the 3' end of the mRNA.

  • Alternative Splicing:

    • Different mRNAs can be produced from the same gene.
    • It affects gene expression by creating multiple protein isoforms.

  • Translation:

    • Function: To synthesize a protein from mRNA.
    • Location: Ribosomes in the cytoplasm.

  • Components Required for Translation:

    • mRNA, ribosome, tRNA, amino acids, initiation factors, elongation factors, release factors.

  • Codon vs. Anticodon:

    • Codon: Triplet of nucleotides in mRNA.
    • Anticodon: Triplet of nucleotides in tRNA that is complementary to the codon.

  • Wobble:

    • Flexible base pairing between the 3rd base of a codon and the 1st base of an anticodon.
    • Importance: Allows one tRNA to recognize multiple codons.

  • Ribosome & tRNAs:

    • Work together during translation to link the correct amino acids.

  • EPA Sites within a Ribosome:

    • E site: Exit site
    • P site: Peptidyl-tRNA binding site
    • A site: Aminoacyl-tRNA binding site

  • Ribosome Selects the ORF:

    • By scanning the mRNA for the start codon (AUG).

  • 3 Stages of Translation:

    • Initiation: Ribosome binds to mRNA and the first tRNA.
    • Elongation: Amino acids are added to the growing polypeptide chain.
    • Termination: Ribosome reaches a stop codon and the polypeptide is released.

  • Elongation:

    • Codon recognition: tRNA anticodon binds to mRNA codon.
    • Peptide bond formation: Amino acid is added to the polypeptide chain.
    • Translocation: Ribosome moves along the mRNA.

  • Prokaryotic vs. Eukaryotic Transcription:

    • Location, RNA processing, initiation, termination.

  • Practice

    • Transcribing DNA into RNA and translating RNA into protein.

  • Post-Translational Modifications:

    • How and why proteins are modified after translation.

Regulation of Gene Expression (18.1-18.2, 19.1-19.4)

  • Why Cells Control Gene Expression:

    • To respond to environmental changes.
    • To conserve energy and resources.

  • 3 Levels of Gene Expression Control in Bacteria:

    • Transcriptional control.
    • Translational control.
    • Post-translational control.

  • Levels of Gene Expression: Energy & Efficiency:

    • Transcriptional control is the most energy-efficient.
    • Post-translational control is the fastest.

  • Gene Expression Induced by Environmental Signals:

    • Expression of most genes is induced by environmental signals.

  • Negative vs. Positive Control of Gene Expression:

    • Negative control: A repressor protein binds to DNA and prevents transcription.
    • Positive control: An activator protein binds to DNA and promotes transcription.

  • Constitutive vs. Inducible Expression:

    • Constitutive expression: Gene is always expressed.
    • Inducible expression: Gene is only expressed under certain conditions.

  • Lac Operon:

    • Structure: promoter, operator, and genes for lactose metabolism (lacZ, lacY, lacA).
    • Regulation: controlled by the lac repressor and the catabolite activator protein (CAP).

  • Lac Operon Activation:

    • The lac operon turns on when lactose is present and glucose is absent.
    • It is turned on by the binding of allolactose to the lac repressor, which causes the repressor to detach from the operator.

  • Differential Gene Expression:

    • The expression of different genes in different cell types.
    • Importance: It is important to cellular differentiation in multicellular organisms.

  • 6 Levels of Gene Expression Control in Eukaryotes:

    • Chromatin remodeling.
    • Transcription.
    • RNA processing.
    • RNA stability.
    • Translation.
    • Post-translational modification.

  • Chromatin Remodeling & Epigenetics:

    • Chromatin remodeling: Changes in the structure of chromatin that affect gene expression.
    • Epigenetics: The study of changes in gene expression that are not caused by changes in the DNA sequence.

  • Regulatory vs. General Transcription Factors:

    • Regulatory transcription factors: Bind to specific DNA sequences and regulate the transcription of specific genes.
    • General transcription factors: Bind to the promoter and are required for the transcription of all genes.

  • RNA Processing & Stability:

    • Affect gene expression.

  • Post-Translational Modifications:

    • Affect proteins.

  • Prokaryotic vs. Eukaryotic Gene Regulation:

    • Key differences.

Biotechnology (20.1-20.2, 20.5-20.6)

  • Biotechnology:

    • The use of living organisms or their products to develop or improve products or processes.

  • Recombinant DNA & Transgenic GMOs:

    • Recombinant DNA: DNA that has been created by combining DNA from different sources.
    • Transgenic GMOs: Genetically modified organisms that contain recombinant DNA.

  • Plasmids to Clone DNA:

    • The process of using plasmids to clone DNA.

  • Restriction Enzymes:

    • How restriction enzymes work.

  • Gel Electrophoresis:

    • Be able to analyze results from gel electrophoresis.

  • Transformation of Bacteria:

    • What is required for transformation of bacteria?

  • Biotechnology Changed Vaccines:

    • How biotechnology has changed vaccines.

  • PCR Reaction:

    • Purpose of each step in a PCR reaction.

  • PCR Reaction: Ingredients:

    • 4 ingredients needed for a PCR reaction.

  • STRs:

    • Importance of STRs in identifying unique individuals.

  • Sequencing Genomes:

    • How sequencing genomes advanced biotechnology.

  • Gene Therapy:

    • Mechanisms of gene therapy and the types of diseases that can be treated.

  • CRISPR:

    • What is CRISPR and how is it used in biotechnology?

  • Reproductive Cloning vs. Therapeutic Cloning:

    • How is reproductive cloning different from therapeutic cloning?

  • Stem Cells:

    • What are stem cells?

  • Ethical Considerations:

    • Understand the ethical considerations associated with biotechnology.

Genetic Information

  • DNA:

    • Archived in base sequences.
    • Consists of functional units called genes.

  • Genes:

    • Make up the genotype.
    • Have different versions.
    • May regulate whether genes can be expressed.

  • Transcription:

    • RNA polymerase transcribes DNA to mRNA.

  • RNA Processing:

    • Splicing.
    • Addition of 5' cap.
    • Addition of poly(A) tail.

  • mRNA:

    • messenger RNA.

  • Translation:

    • Ribosomes translate mRNA using tRNA, rRNA, and miRNA.

  • Genetic Code:

    • Used to form proteins.

  • Proteins:

    • Changed by folding, glycosylation, phosphorylation, and degradation.

  • Phenotype:

    • produce phenotype.