BIOL Practical Exam Study Guide

Syllabus, Safety, Metric System and Measurement

Syllabus policies and procedures

• Absence notification must be submitted via RebelMail to the Lab Coordinators within 14 days of the start of the semester

• Due to illness or emergencies, absence notification form must be filled out via RebelMail to the lab coordinators with 24 hours of the lab absence

Metric system conversions + prefixes

(check your phone for photos)

Micropipetting

P20: measures 2-20 microliters

• used for small volume transfers with high precision.

• example: if it reads 068 (top to bottom), it’s 6.8

P200: measures 20-200 microliters (actual reading)

• used for transferring mid-range volumes with accuracy.

• example: if it reads 150, it’s 150 microliters.

P1000: measures 200-1000 microliters

• used for larger volumes

• if it reads 068, it’s 680

Solution Concentration

• Solute: Substances dissolved in a liquid (sugar)

• Solvent: The liquid that does the dissolving (water)

Calculating concentration

• Mass or volume = mass (solute, g)/volume (solution, mL)

• Solutions of DIFFERENT concentrations: C1V1/C2V2

Temperature Conversions

• Fahrenheit to Celsius: C = (F - 32) / 1.8

• Celsius to Fahrenheit: F = (C x 1.8) + 32

Spectrophotometer and Concentration

• Spectrophotometer measures the amount of light a sample absorbs or transmits

• Absorbance and Concentration relation

  • Absorbance is directly proportional to the concentration of a substance in a solution as described by Beer-Lambert Law

Microscope

(check pictures on phone)

Calculating total magnification

Total magnification = ocular lens power × objective lens power.

• Standard ocular lens power is typically 10x.

• Ensure to adjust the objective lens to the appropriate magnification for your specimen.

• 4x objective: 10 (ocular) x 4 (objective) = 40x total magnification

• 10x objective: 10 × 10 = 100x total magnification

• 40x objective: 10 × 40 = 40 total magnification

• 100x objective: 10 × 100 = 1000x total magnification

Scientific Method

1. Hypothesis

   • An educated guess that can be tested through experiments and observations.

   • example: more sunlight leads to faster plant growth.

2. Independent variable:

   • The factor that is manipulated (changed) in an experiment to determine its effect on the dependent variable.

   • example: water amount

3. Dependent variable:

   • The factor that is measured in an experiment to assess the impact of the independent variable.

   • example: plant height; the height of the plant is measured to determine how different amounts of water affect its growth.

4. Constant variable:

   • kept the same

   • example: type of plant, soil, or temperature

5. Controls

   • comparison group

   • example: plants that receive a standard amount of water, serving as a baseline for comparison

6. Observation

   • Noticing/describing

   • can be qualitative (descriptive) or quantitative (numerical)

Pill bug/Isopod/Roly Poly Experiment

• Objective: To observe the behavior of pill bugs in response to various environmental factors such as moisture, light, temperature, food, and soil type

• Conclusion: Isopods prefer more soil and dark environments

Basic Chemistry

Reactions

• Condensation Reaction: A type of reaction where two molecules combine to form a larger molecule, with the loss of a small molecule, often water.

  • Protein synthesis: amino acids link to form proteins, releasing water

  • Glycogen Synthesis: glucose molecules join to form glycogen (energy storage), releasing water

  • Triglyceride Synthesis: fatty acids and glycerol combine to form triglycerides (fat storage), releasing water

• Hydrolysis Reaction: A reaction that involves the breaking down of a compound by the addition of water, effectively reversing the process of condensation.

  • Digestion: enzymes break down carbohydrates, proteins, and fats into smaller molecules by adding water

  • Glycogen Breakdown: glycogen is broken down into glucose to provide energy

  • Protein Breakdown: Proteins are broken down into amino acids for various cellular processes

Three molecules we tested for (their monomers and polymers) + amino acids

1. Carbohydrates

   • Monomer: monosaccharides

     • example: glucose, fructose, galactose

   • Polymer: polysaccharides

     • example: starch, glycogen, cellulose

2. Proteins

   • Monomer: amino acids

   • Polymer: polypeptides (proteins)

3. Nucleic Acids

   • Monomer: nucleotides

   • Polymer: DNA and RNA

4. Amino Acids

   • Building blocks of proteins

   • each contains an amino group, a carboxyl group, a hydrogen atom, and a unique side chain (R group) all attached to a central carbon atom

Lab test and expected results

1. Benedict Test (Simple Sugars)

   • Reagent: Benedicts solution (blue)

   • Positive result: color change from blue to green, yellow, orange, or red upon heating

   • Negative result: blue

   • red = high concentration of simple sugars present.

2. Iodine/Lugol’s Test (Starch)

   • Reagent: iodine solution (a brown solution)

   • Positive result: dark blue or black

   • Negative result: brown

3. Biuret Test (Protein)

   • Reagent: Biuret reagent (a blue solution containing copper sulfate

   • Positive result: violet or purple

   • Negative result: blue

4. Sudan Test III (Fats)

   • Reagent: Sudan III (red dye)

   • Positive result: red to orange coloration indicates the presence of fats.

   • Negative result: no color change or light pink coloration suggests the absence of fats. (clear/colorless)

Acids vs Bases vs Neutrals

• Acids: Substances that donate protons (H+) in a solution, typically have a pH less than 7.

• Bases: Substances that accept protons or donate hydroxide ions (OH-) in a solution, usually have a pH greater than 7.

• Neutral: Solutions that have a pH of 7, indicating no excess of either H+ or OH- ions.

Buffers and Buffering Capacity

• Buffers: resist changes in pH

  • it neutralizes small amounts of added acids or base

• Buffering Capacity: the amount of acid or base a buffer can handle before its pH changes significantly, which is crucial for maintaining a stable environment in biological systems.

Cell Structure and Function

Diffusion vs Osmosis

• Diffusion: The movement of molecules from an area of higher concentration to an area of lower concentration, continuing until equilibrium is reached.

  • Substance: diffusion involves the movement of any type of particle

  • Membrane: diffusion does NOT require a membrane

  • Driving force: both are driven by concentration gradients

• Osmosis: A specific type of diffusion that involves the movement of water molecules across a selectively permeable membrane.

  • Substances: osmosis specifically involves the movement of water

  • Membrane: osmosis requires a semipermeable membrane

  • Driving force: both are driven by concentration gradients but osmosis specifically driven by differences in water concentration (or water potential) across a semipermeable membrane

  • Semipermeable Membrane: allows water molecules to pass through, but it restricts the passage of solute particles (like salts, sugars)

  • Concentration Gradient: exist when there is a difference in the concentration of solutes on either side of the membrane (example: one side has a high concentration of sugar, while the other side has a low concentration of sugar)

  • Water Concentration: the amount of water relative to solute concentration. If one side of the membrane has a high concentration of solutes, it has a low concentration of water. (if one sides has low concentration of solutes, it has a high concentration of water)

  • Net Water Flow:" Water moves from an area of high water concentration (low solute concentration) to an area of low water concentration (high solute concentration).

  • SIMPLER TERMS

    • more stuff (solute)= less water

    • water moves from where there’s less stuff to where there’s more stuff, in an attempt to even things out

Prokaryotic vs Eukaryotic

• Prokaryotic cells: Simple, single-celled organisms without a nucleus (ex: bacteria and archaea)

  • No membrane bound organelles like mitochondria, endoplasmic reticulum, golgi apparatus

  • small size

  • simple structure makes them capable of reproducing rapidly, which contributes to their adaptability in various environments.

  • Cell wall: some have cell walls (not made of cellulose)

• Eukaryotic cells: More complex, can be single-celled or multicellular organisms with a nucleus (e.g., plants, animals, fungi, protists )

  • Has membrane-bound organelles like mitochondria, ER, golgi, lysosomes

  • large size

  • complex structure

  • Cell wall: some have cell walls (plants and fungi), but animal cells DO NOT

Different shapes of bacteria

• Coccus: spherical round-shapes bacterial (like little balls)

• Bacillus: rod-shaped bacteria

  • longer than their width (like cylinder or sausages)

• Spirillum: spiral-shaped bacteria

  • rigid, wavy, or twisted shape (like a corkscrew)

Steps to make a wet mount

1. Clean the slide and coverslip

   • ensure the microscope slide and coverslip are clean and free

2. Place the sample on the slide

   • put a small drop of your sample onto the center of the clean microscope slide.

3. Apply coverslip

   • carefully lower the coverslip at an angle to avoid trapping air bubbles, which can obstruct your view of the specimen.

4. examine under the microscope

   • Adjust the focus slowly while observing the slide to ensure that the specimen is clearly visible. Take notes on the characteristics and structures observed during your examination.

Cheek Epithelial Cells

Human Neuron/Nerve Cells

Human Skeletal Muscle

Elodea (leaf cells)

Anabaena

Plant vs Animals

DIFFERENCES

Cell structure

• Plant cells: have a cell wall made of cellulose, chloroplast for photosynthesis, and a large central vacuole

• Animal cells: lack cell walls and chloroplast and have smaller vacuoles

Nutrition

• Plant cells: autotrophs, making their own food through photosynthesis

• Animal cells: heterotrophs, consuming other organisms for food

Growth

• Plant cells: exhibit indeterminate growth (they can grow throughout their lives)

• Animal cells: exhibit determinate growth (they reach a certain size and stop)

Motility

• Plant cells: sessile (fixed in one place)

• Animal cells: motile (can move)

Response to Stimuli

• Plant cells: respond more slowly, often through hormonal signals

• Animal cells: have a more rapid response to stimuli due to their nervous systems

SIMILARITIES

Eukaryotic cells

• Both have eukaryotic cells, meaning their cells have a nucleus and other membrane-bound organelles

Basic Life Processes

• Both perform basic life processes like respiration, reproduction, and excretion

Genetic Material

• Both have DNA as their genetic material

Organic Molecules

• Both are composed of organic molecules like carbohydrates, proteins, lipids, and nucleic acids

Require Energy

• Both need energy to carry out life processes

IDENTIFICATION

• Plants: Look for features like cell walls, chloroplasts, and a large central vacuole under a microscope (leaves, stems, roots, flowers,)

• Animals: lack cell walls and chloroplast. look for movement or sensory organs or complex body plans

Tonicity in plant and animal cells

• Tonicity refers to the relative concentration of solutes (sugar and salts) in the fluid outside a cell compared to the concentration inside the cell. The difference in concentration affects the movement of water across the cell membrane.

  • Hypertonic: solution outside the cell has a higher solute concentration than inside the cell

  • Hypotonic: solution outside the cell has a lower solute concentration than inside the cell

  • Isotonic: solution outside the cell has the same concentration as inside the cell

• Plant cells

  • Isotonic: there is no net movement of water in or out of the cell, maintaining cell shape and function.

    • cause: the concentration of solutes outside the cell is equal to the concentration inside the cell

  • Hypertonic: water moves out the cell. the cell membrane shrinks and pulls away from the cell wall

    • cause: the concentration of solutes outside the cell is higher than the concentration inside the cell

  • Hypotonic: water moves into the cell, causing it to swell and potentially burst.

    • cause: the concentration of solutes outside the cell is lower than the concentration inside the cell.

• Animal Cells (Red Blood Cells)

  • Isotonic: there is not net movement of water, maintaining it’s normal shape

    • cause: the concentration of solutes outside the cell is equal to the concentration inside the cell

  • Hypertonic: water moves out of the cell, the red blood cell shrinks and becomes shriveled

    • cause: the concentration of solutes outside the cell is higher than the concentration inside the cell

  • Hypotonic: water moved into the cell, the red blood cell swells and can burst (lyse). this is because animals cells lack a cell wall to counteract the pressure

    • cause: the concentration of solutes outside the cell is lower than the concentration inside the cell.

Enzymes

• Enzymes are super important in living systems because they speed up chemical reactions that are necessary for life

• think of them as catalysts that make things happen much faster than they would on their own.

• they are also reusable

  • after an enzyme helps a reaction occur, it’s not used up or changed

  • it goes right back to work, helping more reactions happen

  • reusability is important because it means that a smaller number of enzyme molecules can have a huge impact

• Tyrosinase (enzyme)

  • catalyzed the oxidation of phenols, like tyrosine, and is involved in the production of melanin and other pigments

  • It’s responsible for turning fruits and vegetables to brown

  • in cosmetics, tyrosinase inhibitors are used in skin-lightening creams to reduce the production of melanin, which causes skin pigmentation

Spectrophotometers and Absorbance

• Absorbance and enzyme activity are related because absorbance is often use to measure the rate of enzyme-catalyzed reactions

  • Higher absorbance means more product and greater enzyme activity

Enzyme function:

• Active Site: enzymes specific region, where the substrate (the molecule the enzyme acts on) binds

• Enzyme-Substrate Complex: when the substrate binds to the active site, it forms an enzyme-substrate complex (like a lock and key)

• Catalysis: the enzyme then facilitates the chemical reaction, converting the substrate into product(s)

• Product Release: once the reaction is complete, the product(s) are released, and the enzyme is free to catalyze another reaction

External factors affecting Enzyme function

• pH: changes iin pH can alter the enzyme’s shape (denature it) by disrupting the ionic and hydrogen bonds, ultimately affecting its activity and efficiency.

• Temperature: increased temperatures generally enhance enzyme activity up to a certain point, after which excessive heat can lead to denaturation, rendering the enzyme ineffective.

• Competitors: substances that inhibit or enhance enzymes' actions can affect their efficiency, competing with substrates for binding sites and potentially leading to decreased reaction rates.

• Inhibitors:

  • non-competitive inhibitors: these substances bind to an enzyme at a location other than the active site, causing a change in the enzyme's shape and thereby reducing its activity regardless of substrate concentration.

  • uncompetitive inhibitors: these inhibitors bind only to the enzyme-substrate complex, preventing the complex from releasing products, which can lead to increased substrate affinity and a decrease in the overall rate of reaction.

Pyrocatechol

• can act as a substrate or inhibitor depending on the enzyme involved

• it can be a substrate for enzymes like catechol oxidase, where it gets oxidized. however it might inhibit other enzymes by competing for the active site or causing structural changes

Hydroquinone

• can act as an inhibitor

• used as a reducing agent and can interfere with enzymatic reactions by reducing essential enzyme components or by acting as a competitive inhibitor

Tyrosine

• a substrate for certain enzymes and can be an inhibitor for others

• depends on the enzyme’s active site

Phenylthiourea (PTU)

• PTU is a known inhibitor, particularly for copper-containing enzymes

• inhibits enzymes like tyrosinase by binding to the copper in the enzymes active site, preventing the enzyme from binding to its substrate

Energy Metabolism

Reaction for Cellular respiration

• C6H12O6 + 6O2 —→ 6CO2 + 6H2O + Energy (ATP)

• Glucose + oxygen ——> Carbon Dioxide + Water + Energy

Fermentation

• (anaerobic respiration) occurs in the absence of oxygen and results in different end products, such as lactic acid in animals and ethanol in yeast.

Photosynthesis and Aerobic Respiration

• Photosynthesis: use carbon dioxide and water, along with light energy, to produce glucose and oxygen

  • 6CO2 +6H2O+ Light Energy —→ C6H12O6 + 6O2

• Aerobic Respiration: uses glucose and oxygen to produce carbon dioxide and water, releasing energy in the process

DNA and BLAST

DNA

1. Friedrich Miescher:

   • discovery, 1869: isolated a substance from the nuclei of white blood cels, which he called nuclein

   • first identification of DNA as a distinct molecule

2. Oswald Avery, Colin MacLeod, and Maclyn McCarty

   • discovery, 1944: demonstrated that DNA, not protein, is the genetic material responsible for the transfer of genetic information in bacteria

   • provided direct evidence that DNA is the molecule of heredity

3. James Watson and Francis Crick

   • discovery, 1953: with significant contributions from Rosalind Franklin and Maurice Wilkins, determined the double helix and structure of DNA

   • revolutionized biology, providing a clear understanding of how DNA could carry and transmit genetic information

4. Rosalind Franklin and Maurice Wilkins

   • discovery: franklin’s X-ray diffraction images of DNA provided critical data for Watson and Crick’s model

BLAST (Basic Local Alignment Search Tool) is a bioinformatics algorithm used to compare biological sequences, helping in identifying similarities and differences among DNA, RNA, or protein sequences.

Processes

1. Replication: DNA replicated is the process of copying the DNA molecule to produce two identical DNA strands

   • Initiation: The DNA double helix unwinds at specific locations called origins of replication

   • Elongation: DNA polymerase enzyme adds complementary nucleotides to each original strand, creating new strands

   • Termination: Replication continues until the entire DNA molecule has been copies, resulting in two identical DNA molecules

2. Transcription: process of synthesizing RNA from a DNA template

   • Initiation: RNA polymerase binds to a promoter region on the DNA and unwinds the DNA strands

   • Elongation: RNA polymerase synthesizes a single strand of RNA by adding complementary RNA nucleotides to the growing RNA chain

   • Termination: transcription continues until RNA polymerase reaches a termination signal, at which point the RNA strand is released

3. Translation: process of synthesizing proteins from mRNA

   • Initiation: the ribosome assembles around the mRNA, and the first tRNA molecule binds to the start codon on the mRNA

   • Elongation: tRNA molecules bring amino acids to the ribosome, where the ribosome facilitates the formation of peptide bonds between the amino acids, creating a polypeptide chain

   • Termination: the process continues until a stop codon on the mRNA is reached, at which point the ribosome releases the completes protein

Differences between RNA and DNA

• Nucleotide composition

  • DNA: contains deoxyribose sugar, has the bases adenine (A), guanine (G), cytosine (C), and thymine (T).

  • RNA: contains ribose sugar, has the bases adenine (A), guanine (G), cytosine (C), and uracil (U) instead of thymine.

• Process of replication and components

  DNA Replication:

  • Process: DNA is replicated to produce two identical DNA strands.

  • Initiation: The DNA double helix unwinds at origins of replication.

  • Elongation: DNA polymerase adds complementary nucleotides to each strand.

  • Termination: Replication continues until the entire DNA molecule is copied.

  • Components:

    • DNA polymerase: enzyme that synthesizes new DNA strands.

    • Helicase: unwinds the DNA double helix.

    • Primase: synthesizes RNA primers to initiate DNA synthesis.

    • Ligase: joins Okazaki fragments on the lagging strand.

• Transcription and components

  • Process: RNA is synthesized from a DNA template.

  • Initiation: RNA polymerase binds to a promoter region on the DNA and unwinds the DNA strands.

  • Elongation: RNA polymerase synthesizes a single-stranded RNA molecule by adding complementary RNA nucleotides.

  • Termination: Transcription continues until RNA polymerase reaches a termination signal, releasing the RNA strand.

  • Components:

    • RNA polymerase: enzyme that synthesizes RNA.

    • Promoter: DNA sequence where RNA polymerase binds to initiate transcription.

    • Transcription factors: proteins that help RNA polymerase bind to the promoter.

• Translation and components

  • Process: Proteins are synthesized from mRNA.

  • Initiation: The ribosome assembles around the mRNA, and the first tRNA molecule binds to the start codon.

  • Elongation: tRNA molecules bring amino acids to the ribosome, where peptide bonds are formed between the amino acids.

  • Termination: Translation continues until a stop codon is reached, releasing the completed protein.

  • Components:

    • Ribosomes: site of protein synthesis.

    • mRNA: carries the genetic code from DNA to the ribosomes.

    • tRNA: brings amino acids to the ribosome.

    • Amino acids: building blocks of proteins.

• DNA extraction reagents and functions

  • Lysis Buffer: ruptures cell membranes to release DNA.

  • Protease (e.g., Proteinase K): digests proteins, including DNases that could degrade DNA.

  • Salt (e.g., NaCl): helps to precipitate DNA by neutralizing the negative charge of the DNA phosphate backbone.

  • Ethanol or Isopropanol: precipitates DNA out of solution.

  • TE Buffer (Tris-EDTA): maintains DNA stability by controlling pH and chelating divalent cations that can catalyze DNA degradation.

• Mutations and Sickle Cell Anemia

  • Cause: Sickle cell anemia is caused by a point mutation in the β-globin gene on chromosome 11.

  • What it looks like: The mutation results in the replacement of glutamic acid (hydrophilic) with valine (hydrophobic) at the sixth position of the β-globin protein.

  • Type of mutation: This is a missense mutation—specifically, a single nucleotide substitution from adenine to thymine (A>T) in the DNA, which leads to a change in the amino acid sequence.

• DNA sequencing activity terminology

  • Primer: A short, single-stranded DNA sequence used to initiate DNA synthesis.

  • Template DNA: The strand of DNA that serves as a guide for synthesizing a complementary strand.

  • dNTPs (deoxynucleotide triphosphates): The building blocks of DNA (dATP, dGTP, dCTP, dTTP).

  • ddNTPs (dideoxynucleotide triphosphates): Chain-terminating nucleotides (ddATP, ddGTP, ddCTP, ddTTP) used in Sanger sequencing. Lacking a 3'-OH group, they stop DNA synthesis when incorporated.

  • DNA Polymerase: An enzyme that synthesizes new DNA strands.

  • Electrophoresis: A technique used to separate DNA fragments by size.

• DNA Blast activity results

  • Query Sequence: Your input DNA sequence.

  • Subject Sequence: The sequence from the database that matches your query.

  • E-value: The probability that the match occurred by random chance. Lower E-values indicate more significant matches.

  • Percent Identity: The percentage of identical nucleotides between the query and subject sequences.

  • Alignment Length: The length of the aligned region between the query and subject sequences.

Biotech I: DNA Fingerprinting

• RFLP and how produced

  • RFLP (Restriction Fragment Length Polymorphism) is a technique used to identify variations in DNA sequences by analyzing the lengths of DNA fragments produced by restriction enzymes.

  • Production:

    • DNA Isolation: DNA is extracted and purified from a sample.

    • Restriction Digestion: DNA is digested with restriction enzymes that cut the DNA at specific recognition sequences.

    • Gel Electrophoresis: The DNA fragments are separated by size using agarose gel electrophoresis.

    • Southern Blotting: The DNA fragments are transferred from the gel to a membrane.

    • Hybridization: The membrane is incubated with a labeled probe that is complementary to a specific DNA sequence.

    • Detection: The labeled probe is detected, revealing the RFLP pattern.

• How restriction enzymes are named and function

  • Naming:

    • The first letter comes from the genus of the bacteria, the second two letters from the species, and the fourth letter (if present) from the strain of the bacteria. Roman numerals are used to indicate the order in which the enzymes were discovered in that strain.

    • Example: EcoRI is derived from Escherichia coli, strain RY13, and it was the first restriction enzyme isolated from this strain.

  • Function:

    • Restriction enzymes recognize specific DNA sequences (recognition sites) and cut the DNA at or near those sites. These enzymes are crucial for DNA fingerprinting and genetic engineering.

• How restriction enzymes work - Conceptual and visual (know / visualize how the cuts are made)

  • Conceptual:

    • Restriction enzymes bind to DNA at their specific recognition sites. Once bound, they cleave the DNA phosphodiester backbone either to produce sticky ends (staggered cuts) or blunt ends (straight cuts).

  • Visual:

    • Visualize the enzyme approaching a DNA strand, recognizing a specific sequence, and then making a precise cut, either symmetrically (blunt ends) or asymmetrically (sticky ends).

• EcoRI palindrome sequence

  • The EcoRI recognition sequence is 5'-GAATTC-3'

  • The complementary sequence is 3'-CTTAAG-5'

  • It cuts the DNA strand in a staggered manner, producing sticky ends

• Restriction enzymes and reagents used in lab

  • Restriction Enzymes:

    • EcoRI

    • HindIII

    • BamHI

  • Reagents:

    • Restriction Buffer: Provides the optimal conditions (pH, salt concentration) for enzyme activity.

    • DNA samples: The DNA to be digested.

    • Nuclease-free water: To adjust the reaction volume.

    • Loading Dye: Added to DNA samples before electrophoresis to visualize migration.

• Agarose gel electrophoresis set up and theory

  • Setup:

    • Prepare the Agarose Gel: Mix agarose powder with a buffer solution (e.g., TAE or TBE), heat until dissolved, and pour into a casting tray with a comb to create wells.

    • Prepare DNA Samples: Mix DNA samples with loading dye.

    • Load Samples: Carefully load the DNA samples into the wells of the gel.

    • Run the Gel: Place the gel in an electrophoresis chamber filled with buffer, apply an electric field (voltage), and run the gel until the DNA fragments have separated adequately.

    • Visualize DNA: Stain the gel with a DNA-binding dye (e.g., ethidium bromide or SYBR Safe) and visualize the DNA bands under UV light.

  • Theory:

    • Agarose gel electrophoresis separates DNA fragments based on their size. DNA is negatively charged due to the phosphate groups, so it migrates through the gel towards the positive electrode (anode).

    • Smaller fragments migrate faster and farther than larger fragments.

• Reliability of DNA evidence and principles behind DNA fingerprinting

  • Reliability:

    • DNA evidence is highly reliable due to the unique genetic makeup of individuals. The chances of two unrelated individuals having the same DNA profile are extremely low.

Cell Divsion: Mitosis and Meiosis

Phases of the Cell Cycle - Mitosis and Meiosis

• The cell cycle consists of:

  • Interphase (G1, S, G2 phases)

  • Mitotic phase (mitosis and cytokinesis)

• Mitosis: cell division resulting in two identical daughter cells; important for growth and repair.

• Meiosis: cell division resulting in four genetically different haploid daughter cells; important for sexual reproduction.

Chromosome Structure

• Chromatin: DNA and protein complex that makes up chromosomes.

• Sister chromatids: identical copies of a chromosome, attached at the centromere.

• Centromere: region of a chromosome where sister chromatids are most closely attached.

• Kinetochore: protein structure on chromatids where microtubules attach during division.

Plant Cells vs. Animal Cells – Differences in Mitosis and Meiosis

• Mitosis:

  • In animal cells, cytokinesis involves the formation of a cleavage furrow.

  • In plant cells, cytokinesis involves the formation of a cell plate.

• Meiosis: Generally similar processes, but plants have alternation of generations.

Stages of Mitosis – Conceptual and Visual (what separates?)

• Prophase: chromosomes condense and become visible; the nuclear envelope breaks down

• Prometaphase: nuclear envelope fragments, microtubules attach to kinetochores.

• Metaphase: chromosomes align at the cell’s equatorial plane

• Anaphase: sister chromatids separate and move to opposite ends of the cell.

• Telophase: nuclear envelopes reform around each set of chromosomes

• Cytokinesis: the cytoplasm divides, resulting in two separate daughter cells, each with a complete set of chromosomes.

Stages of Meiosis – Conceptual and Visual (what separates in meiosis I vs. II?)

• Meiosis I: homologous chromosomes separate

  • Prophase I: crossing over occurs.

  • Metaphase I: homologous pairs align at the equatorial plate.

  • Anaphase I: the homologous chromosomes separate and are pulled apart towards opposite poles of the cell.

  • Telophase I and Cytokinesis: haploid cells form; each chromosome still consists of two sister chromatids.

• Meiosis II: separates sister chromatids.

  • Similar to mitosis, resulting in four haploid daughter cells.

Alternation of Generations and Plant Life Cycle – Conceptual and Visual

• Plants alternate between diploid sporophyte and haploid gametophyte generations.

• Sporophytes produce spores by meiosis; gametophytes produce gametes by mitosis.

Independent Assortment, Crossing Over, and Nondisjunction

• Independent Assortment: random orientation of homologous chromosomes in metaphase I.

• Crossing Over: exchange of genetic material between homologous chromosomes in prophase I.

• Nondisjunction: failure of chromosomes to separate properly in meiosis I or II.

Spermatogenesis – Conceptual and Visual

• Process of sperm formation in testes.

• Primary spermatocytes undergo meiosis I to produce secondary spermatocytes, which undergo meiosis II to produce spermatids. Spermatids mature into sperm.

Oogenesis – Conceptual and Visual

• Process of egg formation in ovaries.

• Primary oocytes undergo meiosis I to produce a secondary oocyte and a polar body. If fertilized, the secondary oocyte undergoes meiosis II to produce an ootid and another polar body. The ootid matures into an ovum.

Understand and Visualize the Pipe Cleaner Set-Ups

• Use pipe cleaners to model chromosomes and chromatids during different stages of mitosis and meiosis to understand their behavior and chromosome/chromatid numbers.

Mendelian Genetics

• Draw a chromosome with two genes that are heterozygous/homozygous:

  • (Diagram would show a chromosome with alleles indicated, e.g., AaBb for heterozygous, AABB or aabb for homozygous)

• Understand the definition and differences between:

  • Genotype: genetic makeup of an organism.

  • Phenotype: physical traits of an organism.

  • Homozygous: having two identical alleles for a gene.

  • Heterozygous: having two different alleles for a gene.

  • Dominant: allele that is fully expressed in a heterozygote.

  • Recessive: allele that is masked in a heterozygote.

  • Gene: a unit of heredity that is transferred from a parent to offspring and is held to determine some characteristic of the offspring.

  • Alleles: different versions of a gene.

  • Chromosomes: thread-like structures made of DNA molecules that contain the genes.

• Identify patterns of inheritance:

  • Complete dominance: one allele completely masks the other.

  • Incomplete dominance: heterozygote shows an intermediate phenotype.

  • Codominance: both alleles are equally expressed in the heterozygote.

• Identify blood types given alleles or a blood typing tray:

  • Antigens vs. Antibodies:

  • Antigens: substances that can trigger an immune response.

  • Antibodies: proteins produced by the immune system to identify and neutralize foreign objects.

• Blood Types: A, B, AB, and O, arise from different combinations of alleles I^A, I^B, and i.

  • Type A: I^AI^A or I^Ai

  • Type B: I^BI^B or I^Bi

  • Type AB: I^AI^B

  • Type O: ii

• Construct a dihybrid cross:

  • A cross between individuals that have different alleles for two genes of interest (e.g., AaBb x AaBb).

• How to determine genotype from a pedigree chart:

  • Analyze patterns of inheritance to deduce genotypes of individuals in

Biotech II & III: PCR analysis and ELISA

(REVIEW BOLDED TERMS)

What is a GMO

Genetically Modified Organism: An organism whose genetic material has been altered using genetic engineering techniques.

Regulatory sequences of GMO crops

• Promoters: Control when and where a gene is expressed (e.g., CaMV 35S promoter).

• Terminators: Signal the end of a gene sequence (e.g., nos terminator).

Pest resistance

GMO crops can be engineered to produce proteins that are toxic to certain pests, reducing the need for pesticides (e.g., Bt corn).

PCR – Principles, Steps (what occurs in each step), What is needed

• Principles: Amplifies specific DNA fragments using primers and DNA polymerase.

• Steps:

  • Denaturation: Heat to separate DNA strands.

  • Annealing: Cool to allow primers to bind to target sequence.

  • Extension: DNA polymerase extends primers, creating new DNA strands.

• What is needed:

  • Template DNA

  • Primers

  • DNA polymerase

  • dNTPs

  • Buffer

Interpreting test results – Given a gel result, is the test food GMO?

Compare the band sizes to controls. Presence of a GMO-specific band indicates the food is GMO.

Be able to identify the controls in the experiment.

• Positive Control: Contains the target GMO sequence.

• Negative Control: Does not contain the target GMO sequence.

Given a hypothetical gel results of the PCR, can you tell if the plant product is GMO or not? The plant primer should show up at 455 bp, and the GMO primer should show up at 200 bp. Look at Figure 12.1 on Page 221 to help you!

If the plant product shows a band at 200 bp (GMO primer), it is a GMO. If it shows a band at 455 bp (plant primer), it confirms plant DNA is present. If both bands are present, it is a GMO plant.

What is ELISA used for? What is the general protocol? Define terms: antigens, antibodies (primary and secondary), indirect detection, enzyme probe, substrate.

ELISA (Enzyme-Linked Immunosorbent Assay) is used to detect the presence and quantity of a specific substance (e.g., protein) in a sample.

• General Protocol:

  • Coat: Plate is coated with the antigen.

  • Block: Add blocking buffer to prevent non-specific binding.

  • Primary Antibody: Add primary antibody that binds to the antigen.

  • Secondary Antibody: Add enzyme-linked secondary antibody that binds to the primary antibody.

  • Substrate: Add substrate that reacts with the enzyme to produce a detectable signal.

• Terms:

  • Antigens: Substances that elicit an immune response (e.g., proteins).

  • Antibodies: Proteins produced by the immune system to bind to specific antigens.
    -Primary Antibody: Antibody that binds directly to the antigen.

  • Secondary Antibody: Antibody that binds to the primary antibody, linked to an enzyme.

  • Indirect Detection: Use of a secondary antibody to amplify the signal.

  • Enzyme Probe: Enzyme linked to the secondary antibody, which catalyzes a reaction to produce a detectable signal.

  • Substrate: Substance that is acted upon by the enzyme to produce a detectable signal.

What were the primary and secondary antibodies derived from in this experiment?

• Primary antibody: Derived from an animal (e.g., mouse, rabbit) immunized with the target antigen.

• Secondary antibody: Derived from an animal (e.g., goat) immunized with the primary antibody from another species.

What binds to what in ELISA?

• Antigen binds to the plate.

• Primary antibody binds to the antigen.

• Secondary antibody binds to the primary antibody.

• Enzyme probe on secondary antibody reacts with the substrate.

Evolution and Hardy Weinberg Equilibrium

Know the 5 conditions that must be met for Hardy-Weinberg equilibrium.

• No mutation

• Random mating:

• No gene flow

• No natural selection

• Large population size

Be able to identify the basic mechanisms of evolution with examples.

• Mutation: A change in DNA sequence (e.g., a new allele arises).

• Genetic Drift: Random changes in allele frequencies due to chance events (e.g., bottleneck effect).

• Gene Flow: Movement of alleles between populations (e.g., migration).

• Natural Selection: Differential survival and reproduction based on heritable traits (e.g., antibiotic resistance).

• Non-random mating: Selection of mates based on specific traits (e.g., sexual selection)

Use the equations p + q= 1 and p2 + 2pq + q2 = 1.

• p + q = 1: Allele frequency equation, where p is the frequency of one allele and q is the frequency of the other allele.

• p2 + 2pq + q2 = 1: Genotype frequency equation, where p2 is the frequency of homozygous dominant genotype, 2pq is the frequency of heterozygous genotype, and q2 is the frequency of homozygous recessive genotype.

Determine genotypic and allelic frequencies within a population

P = \frac{Number \ of \ copies \ of \ the \ allele \ in \ the \ population}{Total \ number \ of \ copies \ of \ all \ alleles \ for \ the \ gene}

Describe the results of each simulation from the lab procedures and which basic mechanisms of evolutions it represents.

Simulations will demonstrate how different mechanisms (e.g., selection, drift, gene flow) alter allele frequencies over time.

Describe the effects of genetic drift, natural selection, gene flow and founder effect on allelic frequencies of a population.

• Genetic Drift: Can cause random fluctuations in allele frequencies, especially in small populations.

• Natural Selection: Can increase the frequency of beneficial alleles and decrease the frequency of harmful alleles.

• Gene Flow: Can introduce new alleles into a population, potentially altering allele frequencies.

Determine if a population is in Hardy-Weinberg equilibrium

Compare the observed genotype frequencies with the expected frequencies under Hardy-Weinberg equilibrium. Use a Chi-square test to determine if the differences are statistically significant.