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BIOL150 Lab Exam 2 review

Hillevi Ets・125 minutes read

Enzymes, crucial for catalyzing life processes, are affected by factors such as temperature and pH. The exam will cover enzyme specificity, denaturation, and bioinformatics, emphasizing the importance of analyzing graphs and constructing standard curves for practical applications.

Insights

  • Enzymes are proteins that catalyze chemical reactions and are essential for life processes.
  • Factors like temperature, pH, and salt concentration can denature enzymes, affecting their functionality.
  • Enzyme specificity is determined by the shape of the active site, allowing only specific substrates to bind.
  • The standard curve in bioinformatics is crucial for determining unknown sample concentrations based on absorbance values.

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Recent questions

  • What are enzymes made of?

    Proteins

  • How does temperature affect enzymes?

    Denatures them

  • What determines enzyme specificity?

    Shape of active site

  • Why is pH important for enzymes?

    Affects functionality

  • How do enzymes lower activation energy?

    Speed up reactions

Related videos

Summary

00:00

Enzymes: Catalysts of Life Processes

  • The session will cover a review packet, with a break at the two-hour mark to refresh.
  • Enzymes are proteins made of amino acids that catalyze chemical reactions, crucial for life processes.
  • High fever can denature enzymes, affecting cellular function by halting chemical reactions.
  • Enzyme specificity is determined by the shape and structure of the active site, allowing only specific substrates to bind.
  • Enzymes lower activation energy, crucial for speeding up chemical reactions.
  • Cold temperatures render enzymes inactive but retain their structure, requiring kinetic energy for reactivation.
  • Factors denaturing proteins or enzymes include temperature, pH, and salt concentration.
  • The optimum pH of an enzyme is where it exhibits the highest activity.
  • pH impacts enzyme structure, affecting functionality if altered.
  • Each enzyme has a specific optimal pH for maximum activity.

24:36

Analyzing Graphs: Essential for Exam Success

  • Making graphs is not required for the exam; analyzing graphs is necessary.
  • The review packet may be outdated, focusing on making graphs rather than analyzing them.
  • The independent variable is always the x value, while the dependent variable is the y value.
  • Amylase activity is measured by the maltose produced in different conditions.
  • A negative control excludes the active ingredient to show results in its absence.
  • The question focuses on describing steps of the scientific method using the amylase experiment as an example.
  • The enzyme's activity graph at 85 degrees Celsius shows inactivity due to denaturation.
  • At 4 degrees Celsius, the enzyme is slightly active with a properly folded structure.
  • Terms like activation energy and transition state are not applicable to the graph.
  • The DNS assay is preferred over the Benedict's assay for its soluble product and quantifiable color change.

48:20

Constructing Standard Curve for Maltose Concentration Analysis

  • The next standard solution will be 0.3, followed by the last one at 0.4.
  • The concentration with none of the standard solution added would be zero.
  • These values are crucial for constructing the standard curve.
  • The x-axis for the standard curve graph represents concentration, while the y-axis represents absorbance.
  • Absorbance increases with maltose concentration, showing a positive linear relationship.
  • The standard curve aids in determining the maltose concentration in unknown samples based on absorbance.
  • Estimating the unknown sample's maltose concentration involves finding the absorbance value on the y-axis and correlating it with the standard curve.
  • The standard curve's accuracy is vital for calculating unknown sample concentrations.
  • Utilizing the standard curve is essential for exams, where given graphs require determining unknown concentrations.
  • The bioinformatics exercise involves navigating the NCBI and EMBOSS PepStats websites to extract protein information for exam questions.

01:08:03

Improving Search Results and PCR Techniques

  • The search box didn't yield the desired results, leading to issues with input format.
  • Removing spaces and special characters from search terms can help improve search results.
  • The exam will include questions on using the NCBI website and the EMBOSS website.
  • Residues on the EMBOSS site indicate the number of amino acids.
  • The active site of enzymes is crucial for specificity, while other amino acids contribute to stability.
  • PCR involves denaturation, annealing, and extension steps.
  • Annealing involves primers binding to the template DNA at decreased temperatures.
  • Extension in PCR involves DNA polymerase extending primers.
  • Taq DNA polymerase is heat-resistant due to its origin in thermophilic bacteria.
  • DNA replication in cells copies the entire genome, while PCR copies specific target sequences.

01:32:15

PCR and DNA Replication: Key Concepts Explained

  • In PCR, heating and cooling cycles are used to replicate DNA, with a mathematical formula (2^n) to calculate the number of DNA copies after a certain number of cycles.
  • The mutation in the HBS allele causing sickle cell disease results in a single amino acid change, leading to hydrophobic regions being exposed and causing clumping of hemoglobin molecules.
  • The distinction between the wild type and disease alleles is revealed in the lab by cutting DNA with a restriction enzyme, where the HBA allele has a restriction site and the HBS allele does not due to a single nucleotide polymorphism.
  • Annealing temperature in PCR is determined by the number of G and C residues in the sequence, with higher temperatures needed for sequences with more G and C due to the three hydrogen bonds between them.
  • Sickle cell disease (SCD) results from having two HBS alleles, leading to sickle-shaped red blood cells, while sickle cell trait (SCT) involves having one HBS allele with less severe symptoms.
  • SCD and SCT inheritance follows an autosomal recessive pattern, requiring two copies of the disease allele for the disease to manifest.
  • PCR ingredients include a DNA template, primers, DNA polymerase, and free nucleotides, each serving a specific purpose in amplifying DNA.
  • PCR technology is utilized for various purposes such as COVID-19 testing, DNA testing in forensics and paternity, archaeological identification, and disease diagnosis.
  • Nucleases are enzymes that cut DNA, with endonucleases cutting within a sequence and exonucleases trimming ends, while restriction endonucleases like DDE1 produce sticky ends at specific palindromic sequences.
  • Palindromic DNA sequences read the same forwards and backwards, with the same sequence on one strand matching the opposite strand in the opposite direction, aiding in the recognition of restriction sites by endonucleases like DDE1.

02:00:15

DNA Palindrome Sequences and Gel Electrophoresis

  • To determine if a sequence is a palindrome, compare the original sequence with its complementary sequence.
  • The complementary sequence for "aagg" is "ccaa."
  • Reading the top strand from left to right gives "aagg," while reading the bottom strand from right to left gives "aacc."
  • The first sequence is not a palindrome as the strands do not match.
  • The complementary sequence for "ccc" is "ggg."
  • The second sequence is a palindrome as it reads the same in both directions.
  • The third sequence, "tata," is also a palindrome.
  • Linear DNA, when cut once, results in two fragments.
  • Circular DNA, when cut once, remains as one piece.
  • Agarose gel electrophoresis separates molecules based on size and charge using an electrical current.

02:24:04

Measuring DNA Fragment Sizes on Gel Electrophoresis

  • To illustrate a concept, measure the distance bands travel from their starting point on a gel.
  • Measure the distance of ladder bands and unknown bands to determine their size.
  • Typically, people visually compare bands to the ladder to estimate sizes.
  • DNA ladder fragments show sizes and migration distances on a gel.
  • The migration distance increases as fragment size decreases.
  • Graphing fragment size against migration distance shows an inverse relationship.
  • The x-axis in the graph represents fragment size, while the y-axis represents migration distance.
  • Use a ruler to measure migration distance in millimeters for accurate results.
  • Estimating band sizes involves comparing unknown bands to ladder bands or measuring their migration distances.
  • Standard curves help extrapolate fragment sizes from migration distances on gel electrophoresis data.

02:48:07

Genetic Testing Reveals Carrier Status in Families

  • The normal allele gets cut, resulting in two smaller fragments, while the disease allele remains as one fragment.
  • Family member A has three fragments, indicating they are carriers of the disease.
  • Individual A and B are both carriers of the disease trait, being heterozygotes.
  • Parent A and B are carriers, with one disease allele and one normal allele each.
  • Individual C and D are homozygous normal, having two fragments.
  • Three fragments indicate having both disease and normal alleles.
  • Family B's individual A has the same genotype as individual A from family A, being a carrier.
  • Individual B from family B is homozygous normal, as are the two children.
  • If someone is homozygous for the HbS allele, they will have one thick band, indicating sickle cell disease.
  • The chance of sickle cell disease is zero for family B's parents, with a 50% chance of the sickle cell trait for their children.

03:14:11

Mitosis and Cytokinesis in Cell Division.

  • The first plate shows colonies of ampicillin-resistant E. coli due to the presence of pGLO.
  • The second plate exhibits no growth, indicating regular E. coli without resistance.
  • The third plate displays colonies of E. coli or a lawn of ampicillin-susceptible E. coli.
  • The difference between a lawn and susceptible E. coli lies in the response to ampicillin.
  • Mitosis phases include G1, S (DNA replication), G2, and mitosis (M).
  • G1 focuses on cell growth, S on DNA replication, and G2 on cell growth and DNA repair.
  • Mitosis (M) is the phase of cell division, while cytokinesis separates the cytoplasm.
  • Animal cells form a cleavage furrow, while plant cells create a cell plate during cytokinesis.
  • Chromosomes in prophase are replicated and condensed, while in metaphase, they are replicated and attached.
  • The purpose of mitosis is to replace dead cells, promote growth, and aid in development.

03:38:34

Cell division phases exam with whitefish blastula

  • The exam will focus on the pmat phases of cell division, excluding pro metaphase, with the whitefish blastula cells presenting challenges due to faint features, requiring differentiation between metaphase, pro metaphase, polar view of metaphase, anaphase, interface, prophase, telophase, and cytokinesis.
  • The exam will feature printed pictures of the cell phases, not requiring a microscope, with online resources available for additional practice, and a YouTube video of the review session will be shared upon request via email.
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