Exam2_StudyGuide_MCB181R

General Exam Instructions & Rules

• Only scantron and free response pages are scored; notations in exam booklet are not counted.

• Exam is closed book and closed notes. All electronic devices (smart watches, headphones) must be put away. Promptly follow instructions to avoid violations.

• If possible, skip 1-2 seats between you and the next student.

• Use a #2 pencil and erase stray marks thoroughly.

• Submit exam booklet by end of class unless accommodations set with DRC.

• Show student ID to learning team before submitting the exam.

• Violations of rules are considered breaches of the University of Arizona’s Academic Integrity Code.

How to Study

• Understand application of learned content rather than just vocabulary.

• Important: 20% of Exam 2 content is from Exam 1. Review incorrect questions from Exam 1.

• Recommended: Study according to learning objectives provided below to understand content well.

Exam 2 Content Learning Objectives

• Water’s Structural Properties: Understand polar properties to predict interactions with biomolecules (polar/non-polar).

• Chemical Structures: Identify monomers of DNA, RNA, and proteins, focusing on functional groups.

• Temperature Effects: Describe impacts of temperature changes on DNA and RNA.

• Central Dogma: Describe the information flow in cells as per molecular biology's Central Dogma.

• Gene vs. Protein Functions: Differentiate roles of genes, proteins, and non-coding RNA.

• Nucleic Acids Directionality: Explain how the antiparallel nature of nucleic acids influences transcription direction.

• Transcription Mechanism: Detail transcription mechanism, including reactions RNA polymerase catalyzes.

• mRNA Prediction: Predict mRNA derived from given DNA sequence.

• mRNA Production: Explain how multiple mRNA copies arise from a single gene.

• RNA Processing: Describe introns and splicing roles in eukaryotic RNA processing.

• Gene Structure: Draw a eukaryotic gene (including promoter, introns, exons).

• Genetic Code Application: Use the genetic code for predicting protein sequences from DNA/RNA and vice versa.

• Gene Expression Regulation: Identify points for regulating gene expression; explain negative and positive controls.

• Lac Operon Control: Use lac operon to explain gene regulation mechanisms and mutation effects on gene expression and phenotype.

Additional Topics

• Gene Regulation via Chromatin Packaging: Relate DNA chromatin packaging to transcription and histone structure.

• Alternative Splicing: Explain how alternative splicing boosts protein diversity.

Splicing

• Coding vs Non-coding Sequences:

  • Introns: Non-coding regions interrupting coding sequences.

  • Exons: Coding regions that contribute to proteins.

• 5' Cap: Added during transcription; serves as ribosome binding site.

• 3' Poly-A Tail: Added to the 3' end post-transcription.

• Alternative Splicing: Different mRNA transcripts result from joining the same genes in diverse patterns.

Types of RNA

• mRNA (Messenger RNA): Transcribed from DNA template.

• tRNA (Transfer RNA): Translates nucleic acid language to amino acids.

  • Translation Steps:

    • Initiation: Initiator tRNA binds to AUG start codon.

    • Elongation:

      • A site: Holds incoming tRNA with next amino acid.

      • P site: Holds tRNA with growing polypeptide chain.

      • E site: Inactivated tRNA exits ribosome.

    • Termination: Continues until a stop codon is reached.

Proteins

• Composition: Made of amino acids with a central carbon atom; bonded to Hydrogen, Carboxyl group, Amino group, and R groups.

• Protein Structure:

  • Primary Structure: Linear sequence of amino acids (peptide bonds).

  • Secondary Structure: Back bond H-bonding forms alpha helices and beta sheets.

  • Tertiary Structure: Interaction of side chains (R groups) leads to protein folding.

  • Quaternary Structure: Interaction among polypeptide subunits.

Gene Regulation and Metabolism

• Histone Code: Chemical modifications of histone tails influence chromatin remodeling.

  • Methylation: Can increase or decrease gene expression.

  • Acetylation: Increases gene expression.

• Iron Metabolism:

  • High Iron: IRE-BP unbound to transferrin receptor mRNA; ferritin produced, transferrin receptor not.

  • Low Iron: IRE-BP bound to transferrin receptor mRNA; ferritin not produced, transferrin receptor produced.

Positive vs. Negative Regulation

• Positive Regulation:

  • Activator protein present: Binds to DNA; transcription allowed with RNA polymerase recruitment.

  • Absence of activator: Blocks binding to DNA; transcription does not occur.

• Negative Regulation:

  • Repressor protein present: Binds DNA; blocks RNA polymerase binding and thus transcription.

  • Absence of repressor: Transcription can occur via RNA polymerase recruitment.

Lac Operon Example

• Essential for transcription requiring a promoter and operator for negative regulation.

• Positive Regulation: CRP-cAMP activates gene expression when glucose is absent (high cAMP binds CRP).

• Low cAMP in glucose presence: CRP unable to bind; lac operon not transcribed.