Biochemistry And Molecular Biology

Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence...

Learning Objectives
At the end of this lesson, students will be able to:
Define similarity in a non-biological and biological sense when provided with two strings of letters.

Quantify the similarity between two gene/protein sequences.

Explain how a substitution matrix is used to quantify similarity.

Calculate amino acid similarity scores using a scoring matrix.

Demonstrate how to access genomic data (e.g., from NCBI nucleotide and protein databases).

Demonstrate how to use bioinformatics tools to analyze genomic data (e.g., BLASTP), explain a simplified BLAST search algorithm including how similarity is used to perform a BLAST search, and how to evaluate the results of a BLAST search.

Create a nearest-neighbor distance matrix.

Create a multiple sequence alignment using a nearest-neighbor distance matrix and a phylogram based on similarity of amino acid sequences.

Use appropriate bioinformatics sequence alignment tools to investigate a biological question.
A Close-Up Look at PCR

Learning Objectives
At the end of this lesson students will be able to...
Describe the role of a primer in PCR

Predict sequence and length of PCR product based on primer sequences

Recognize that primers are incorporated into the final PCR products and explain why

Identify covalent and hydrogen bonds formed and broken during PCR

Predict the structure of PCR products after each cycle of the reaction

Explain why amplification proceeds exponentially
Follow the Sulfur: Using Yeast Mutants to Study a Metabolic Pathway

Learning Objectives
At the end of this lesson, students will be able to:
use spot plating techniques to compare the growth of yeast strains on solid culture media.

predict the ability of specific met deletion strains to grow on media containing various sulfur sources.

predict how mutations in specific genes will affect the concentrations of metabolites in the pathways involved in methionine biosynthesis.
CURE-all: Large Scale Implementation of Authentic DNA Barcoding Research into First-Year Biology Curriculum

Learning Objectives
Students will be able to: Week 1-4: Fundamentals of Science and Biology
List the major processes involved in scientific discovery

List the different types of scientific studies and which types can establish causation

Design experiments with appropriate controls

Create and evaluate phylogenetic trees

Define taxonomy and phylogeny and explain their relationship to each other

Explain DNA sequence divergence and how it applies to evolutionary relationships and DNA barcoding

Week 5-6: Ecology
Define and measure biodiversity and explain its importance

Catalog organisms using the morphospecies concept

Geographically map organisms using smartphones and an online mapping program

Calculate metrics of species diversity using spreadsheet software

Use spreadsheet software to quantify and graph biodiversity at forest edges vs. interiors

Write a formal lab report

Week 7-11: Cellular and Molecular Biology
Extract, amplify, visualize and sequence DNA using standard molecular techniques (PCR, gel electrophoresis, Sanger sequencing)

Explain how DNA extraction, PCR, gel electrophoresis, and Sanger sequencing work at the molecular level

Week 12-13: Bioinformatics
Trim and assemble raw DNA sequence data

Taxonomically identify DNA sequences isolated from unknown organisms using BLAST

Visualize sequence data relationships using sequence alignments and gene-based phylogenetic trees

Map and report data in a publicly available online database

Share data in a formal scientific poster
Gotcha! Which fly trap is the best? An introduction to experimental data collection and analysis

Learning Objectives
Students will:
design and execute an experiment

collect, organize, and summarize data

analyze and interpret data and make inferences
The Avocado Lab: An Inquiry-Driven Exploration of an Enzymatic Browning Reaction

Learning Objectives
Students will be able to:
develop a testable research question and supportive hypothesis regarding the browning of damaged avocado flesh caused by the activity of avocado polyphenol oxidase (aPPO).

design and execute a well-controlled experiment to test aPPO hypotheses.

evaluate qualitative enzyme activity data.

create a figure and legend to present qualitative data that tests multiple hypotheses and variables.

search for and correctly cite primary literature to support or refute hypotheses.

know the role of reducing reagents, pH, chelators, and temperature in reactions catalyzed by aPPO.

explain why the effects of salt and detergent differ for aPPO experiments conducted in situ

(in mashed avocado flesh) as compared to in vitro (on purified protein).

discuss how substrate and cofactor availability affect aPPO reactions.

describe how endogenous subcellular organization restricts aPPO reactions in a healthy avocado.

evaluate food handling practices for fruits expressing PPO.
Evaluating the Quick Fix: Weight Loss Drugs and Cellular Respiration

Learning Objectives
Students will be able to explain how the energy from sugars is transformed into ATP via cellular respiration.

Students will be able to predict an outcome if there is a perturbation in the cellular respiration pathway.

Students will be able to state and evaluate a hypothesis.

Students will be able to interpret data from a graph, and use that data to make inferences about the action of a drug.