Unit 7: Gene Expression

  1. Describe the mechanisms by which genetic information flows from DNA to RNA to protein.

    1. Transcription: The process by which the information stored in DNA is copied into RNA

      1. Occurs in nucleus for eukaryotes

        1. The DNA double helix unwinds at the gene location

        2. RNA polymerase enzyme reads the DNa template strand 3’ to 5’ direction

        3. Complementary RNA nucleotides are added to form mRNA

        4. The mRNA molecule is processed (in eukaryotes) through steps like RNA splicing

        5. The mature mRNA exits the nucleus and enters the cytoplasm

    2. Translation: The process by which the mRNA is used as a template to synthesize proteins

      1. Occurs in the cytoplasm and involves ribosomes

        1. The ribosome binds to the mRNA at the start codon (usually AUG)

        2. tRNAs bring specific amino acids to the ribosome

        3. The ribosome reads the mRNA codons, and matching tRNAs deliver their amino acids

        4. Amino acids are linked together to form a growing polypeptide chain

        5. The process continues until a stop codon is reached

  2. Transcribe and translate a segment of DNA to determine the amino acid sequence of the protein created.

    1. Given DNA template strand

      1. 5' - TACGCAATGGCCTAA - 3'

    2. Transcription into mRNA:

      1. mRNA is complementary to the template DNA strand, and uses U instead of T

      2. 5' - AUGCGUUACCGGAUU - 3'

    3. Translation:

      1. Using the genetic code to convert each codon group (3 nucleotides per codon) into its corresponding amino acid

      2. mRNA codons and their corresponding amino acids

        1. AUG - Methionine (Start codon)

        2. CGU - Arginine

        3. UAC - Tyrosine

        4. CGG - Arginine

        5. AUU - Isoleucine

    4. Final protein sequence

      1. Methionine - Arginine - Tyrosine - Arginine - Isoleucine

      2. Met-Arg-Tyr-Arg-Ile

  3. Describe how the phenotype of an organism is determined by its genotype.

    1. An organism’s genotype is the set of genes it carries, which contains the instructions for its growth and development

    2. The phenotype is the observable expression of these genetic instructions

    3. Some factors

      1. Direct influence

      2. Gene interactions

      3. Environmental factors

      4. Dominance and recessiveness

      5. Epigenetic factors

  4. Explain the types of post-transcriptional modifications to eukaryotic mRNA and its purpose within the cell.

    1. 5’ Methyl Cap

      1. Modified guanine nucleotide added to 5’ end

        1. Helps ribosome start translation

    2. Poly-A-Tail

      1. Many (100-200) adenine nucleotides added to the 3’ end

        1. Protection from degradation in cytoplasm (lifespan of mRNA)

    3. Splicing

      1. Introns removed, exons joined

        1. Spliceosome

        2. Exons code for protein

  5. Describe the various types of mutations.

    1. Mutations: Changes in the genetic material of an organism

      1. Point Mutations: Changes to ONE nucleotide in the DNA sequence

        1.  Substitutions: one base is replaced with another

          1. Transitions: A purine is replaced by another purine, or a pyrimidine by another pyrimidine

          2. Transversions: A purine is replaced by a pyrimidine, or vice versa

        2. Insertions: An extra base is added to the DNA sequence

        3. Deletions: A base is removed from the DNA sequence

      2. Effects of Point Mutations

        1. Silent mutations: No change in the amino acid sequence

        2. Missense mutations: Result in a different amino acid

        3. Nonsense mutations: Create a premature stop codon

      3. Frameshift Mutations: When the number of nucleotides inserted or deleted is not a MULTIPLE OF THREE

        1. Leads to a completely different amino acid sequence or premature termination of the protein

      4. Causes of Mutations

        1. Spontaneous errors during DNA replication

        2. Exposure to mutagens, such as UV radiation, X-rays, or certain chemicals



  1. Explain how changes in genotype may result in changes in phenotype (Hint: Answer should include description of protein folding).

    1. Mutations and Protein Folding: They can alter the amino acid sequence of proteins, which in turn can affect protein folding

      1. Stability changes

        1. Mutations can increase or decrease protein stability

      2. Folding defects

        1. Accumulation of folding defects can reduce a protein’s ability to evolve a new phenotype

      3. Functional changes

        1. Alterations in protein folding can lead to changes in protein function.

    2. Protein Abundance and Evolvability: The abundance of a protein can influence its evolvability

      1. Low Expression

        1. Proteins expressed at lower level may be more evolvable toward new phenotypes

      2. High Expression

        1. Highly expressed proteins may be less evolvable, as they can tolerate more genetic variants that cause folding defects

  2. Explain how alterations in DNA sequences contribute to variation that can be subject to natural selection.

    1. Already did it

  3. Explain how the binding of transcription factors to promoter regions affects gene expression and/or the phenotype of the organism.

    1. Activation and repression: TFs can act as activators or repressors of gene transcription

      1. Activators enhance the recruitment of RNA polymerase and other general transcription factors to the promoter

      2. Repressors can block the binding of these essential components, reducing or preventing transcription

  4. Describe the regulation of gene expression via operons in prokaryotes.

    1. Structure of an Operon

      1. Promoter

        1. A DNA sequence where RNA polymerase binds to initiate transcription

      2. Operator

        1. A regulatory sequence near the promoter where regulatory proteins binds to the promoter

      3. Structural genes

        1. The genes encoding proteins with related functions

    2. Regulatory Mechanisms

      1. Induction

        1. Inducers are small molecules that can bind to repressors to cause a conformational change that prevents the repressor from binding to the operator

        2. This allows RNA polymerase to transcribe the genes

      2. Repression

        1. Repressor proteins bind to the operator, WHICH THEN blocks RNA polymerase from transcribing the genes

        2. In the absence of an inducer, the repressor is active and gene expression is inhibited

      3. Activation

        1. Activator proteins can enhance transcription by binding to specific DNA sequences

        2. They facilitate the binding of RNA polymerase to the promoter

    3. EXAMPLE: THE LAC OPERON

      1. The Lac Operon in E. coli is an example of operon regulation

        1. It contains genes for lactose metabolism (lacZ, lacY, lacA)

        2. In the absence of lactose, a repressor protein binds to the operator, therefore preventing transcription

        3. IF AND WHEN LACTOSE IS PRESENT it acts as an inducer by binding to the repressor and allowing transcription to occur

  5. Contrast inducible and repressible operons.

    1. Inducible

      1. Typically off by default

      2. Activated by the presence of an inducer molecule

      3. Often associated with catabolic pathways

      4. Example: LAC OPERON activated by LACTOSE

    2. Repressible

      1. Typically on by default

      2. Deactivated by the presence of a co-repressor molecule

      3. Often associated with anabolic pathways

      4. Example: TRP operon repressed by TRYPTOPHAN

  6. Describe various mechanisms that allow for cell differentiation of cell specialization in multicellular eukaryotic organisms.

    1. Differential gene expression: Cells selectively activate or repress specific gene leading to the production of proteins that determine cellular structure and function

      1. Transcription factors: Proteins that bind to specific DNA sequence to control gene expression

      2. Chromatin modifications: Changes in DNA packaging that affect gene accessibility

      3. Epigenetic mechanisms: Such as DNA methylation and histone modifications

    2. Asymmetric cell division: During cell division, regulatory molecules are unevenly distributed between daughter cells, resulting in distinct developmental fates

      1. Cytoplasmic determinants: Molecules inherited unequally by daughter cells

      2. Cell signaling: External signal that influence cell fate decisions

  7. Explain the connection between the regulation of gene expression and phenotypic differences in cells and organisms.

  8. Explain the life cycle of viruses and the role of reverse transcriptase in allowing viruses to evade the immune system and treatment.

    1. Life cycle of virus

      1. Attachment: The virus binds to specific receptors on the host cell surface

      2. Penetration: The virus enters the host cell

      3. Uncoating: The viral genome is released inside the host cell

      4. Biosynthesis: The virus hijacks the host cell machinery to replicate its genetic material and produce viral proteins

      5. Assembly: New viral particles are formed

      6. Release: The newly formed viruses exit the host cell

    2. Reverse transcriptase

      1. Genome conversion: Reverse transcriptase converts the viral RNA genome into DNA, enabling integration into the host cell’s genome

      2. High mutation rate: The enzyme lacks proofreading activity, leading to frequent mutations that help the virus evade immune recognition and develop drug resistance

      3. Rapid evolution: The high mutation rate allows the virus to quickly adapt to antiviral drugs, making treatment challenging

      4. Latency establishment: By integrating viral DNA into the host genome, reverse transcriptase enables the virus to establish latent infections, evading immune detection

      5. Genetic variability: The error-prone nature of reverse transcriptase contributes to HIV-1’s genetic diversity, further complicating immune recognition