Notes, summaries, assignments, exams, and problems for Biology

Nitrogen Fixation and Symbiosis

Module 3: N₂ + 8e^- + 8H⁺ + 16ATP → 2NH₃ + H₂. Nitrogenase is killed by O₂; leghemoglobin binds O₂ (pink), nodules block O₂, and high respiration lowers free O₂. The plant provides sugars while rhizobia fix N₂. High N levels lead to glutamate, while low N levels lead to glutamine. Plant flavonoids trigger bacterial Nod factors (LPS signals) to initiate symbiosis. Root hair curls (“shepherd’s crook”) trap bacteria and start nodule formation.

Archaea: Biology and Genomics

Archaea: Once thought to be only extremophiles, they are actually ubiquitous. Identified via 16S rRNA (distinct from bacteria and eukaryotes). Methanogens: Only archaea perform methanogenesis, the terminal step of the C-cycle and a source... Continue reading "Microbiology Fundamentals: From Microbial Ecology to Genomics" »

Essential Biological Macromolecules

Properties: Hydrophilic vs. Hydrophobic

• Hydrophilic (water-loving): Nucleic Acids, Carbohydrates, Starch, Chitin. Glucose is hydrophilic because it contains many hydroxyl functional groups.
• Hydrophobic (water-fearing): Lipids.

Key Molecules and Building Blocks

• Organic Molecules: Examples include Methane (CH4) and Glucose.
• Creating Polymers: Polymers are created from monomers through a Dehydration Reaction.

Types of Macromolecules

Carbohydrates

• Monosaccharides: Simple sugars like glucose, fructose, and galactose.
• Disaccharides: Maltose is formed from two glucose molecules.

Lipids

• Unsaturated Fats & Oils: These contain carbon-carbon double bonds in their fatty acids.

Proteins

• Proteins are unique in that they contain

Microbiology Lab Practice Questions

What is the optimal temperature range for Bacillus stearothermophilus?

Answer: 55°C (a thermophile)

Which organism produces red pigment at 25°C?

Answer: Serratia marcescens

What does no pigment but visible turbidity in S. marcescens at 37°C suggest?

Answer: Growth occurred, but pigment production is temperature-sensitive.

What is the term for bacteria that grow best at cold temperatures but also at room temperature?

Answer: Psychrotroph (e.g., Pseudomonas fluorescens)

What color does E. coli appear on MacConkey agar?

Answer: Pink (lactose fermenter)

Which test detects mixed acid fermentation?

Answer: Methyl Red (MR) test

What does a black precipitate on HE agar indicate?

Answer: H₂S production (e.g., Salmonella)

Which

Clinical Characteristics of Polymyositis

Myopathic Weakness

Myopathic weakness evolves over weeks to months, typically sparing the facial and eye muscles. It presents as difficulty in:

• climbing steps
• rising from a chair
• lifting objects
• combing hair

Disease Onset

Typically occurs above the age of 18 years.

Features the Patient Does Not Have

The following features are not characteristic of polymyositis in the typical presentation:

• Rash (characteristic of dermatomyositis)
• Family history of neuromuscular diseases
• Exposure to myotoxic drugs, especially penicillamine²⁶, zidovudine²⁷, and (rarely) statins^28,29
• Endocrine disease (hypothyroidism, hyperthyroidism, hypoparathyroidism, hypercortisolism)

Excluded Conditions

• Neurogenic disease (excluded by electromyography

Oral Anatomy and Dental Structures

• Mouth (Boca): Another term for the oral cavity.
• Oral Cavity (Cavitat Oral): Another name for the mouth.
• Teeth (Dientes): Hard, white, enamel-covered structures used to chew and bite food.
• Tongue (Lengua): A muscle located at the base of the oral cavity used to speak and eat.
• Tonsils (Amígdalas): Structures located at the left and right sides of the palatoglossal arch.
• Uvula: A cone-shaped tissue that hangs down from the soft palate.
• Hard Palate (Paladar Duro): The bony front portion of the roof of the mouth.
• Soft Palate (Paladares Blandos): A fibrous and muscular soft tissue that comprises one-third of the roof of the mouth.
• Upper Lip (Labio Superior): A structure made of soft, pink tissue close to the nose.
• Lower

Sex Determination and Genetic Inheritance

Offspring formed from the union of a sperm and an egg develop as females, while unfertilized eggs develop as males.

Environmental Sex Determination

In this case, the sex is not determined by genes or chromosomes but by environmental factors:

• In some reptiles, like crocodiles and turtles, the temperature of the eggs during a certain period of development is the deciding factor in determining sex.
• Some young fish are male and may become female as they get older.

Sex-Linked Inheritance

Sex-linkage appears when genes are located on sex chromosomes. Since males and females have different sex chromosomes, sex-linked genes show different phenotypic ratios depending on the sex.

X-Linked Inheritance

X-linked inheritance... Continue reading "Sex Determination and Genetic Mutations" »

Insect Defenses Against Predators

Three Plant Mechanisms to Defend Against Insects

• Physical: Thick walls
• Chemical: Phytochemicals that kill insects
• Entrapment: Pitcher plants

How Insects Overcome Physical Defenses

• Specialized mandibles
• Evolution
• Immunity to phytochemicals
• Specialization to survive the digestive liquid of pitcher plants

Insect Parasitism

Endoparasites

Approximately 20% of insect orders include endoparasites. Some orders that include endoparasites are:

• Hymenoptera
• Diptera
• Strepsiptera

Ectoparasites

Some orders that include ectoparasites are:

• Anoplura
• Mallophaga
• Siphonaptera

Three Challenges Faced by Endoparasites

• Respiration
• Excretion/getting rid of toxic nitrogenous waste without killing the host
• Avoiding the host's endocrine system

Insect Social Behavior

Subsocial

Endocrine Pharmacology Study Roadmap

🔹 1. Thyroid Physiology & Pathophysiology

🔸 Physiology

• TRH (hypothalamus) → stimulates TSH (anterior pituitary) → stimulates T3/T4 release (thyroid)

• T3 = active, T4 = prohormone

• Feedback loop: T3/T4 inhibit TRH and TSH

• T3/T4 actions:

  • ↑ Metabolic rate, heart rate, cardiac output

  • ↑ Oxygen consumption, lipolysis, glucose metabolism

  • CNS effects (mood), reproductive effects

🔸 Synthesis

• Iodide uptake → oxidation to iodine → binds to thyroglobulin → forms MIT/DIT → forms T3/T4

🔸 Disorders

• Hypothyroidism: Hashimoto's thyroiditis, iodine deficiency, thyroidectomy, myxedema coma

• Hyperthyroidism: Graves' disease, toxic adenoma, thyroid storm

🔹 2. Thyroid Pharmacology

🔸 For Hypothyroidism

• Levothyroxine

Animal Eukaryotic Cells and Organelles

• Nucleus: Holds genetic material. Protected by a double membrane that separates it from the cytoplasm.

• Vacuoles: Small sacs that store different substances.

• Lysosomes: Made by the Golgi apparatus; digest materials inside the cell.

• SER (Smooth Endoplasmic Reticulum): Produces lipids and helps remove toxic substances.

• Mitochondria: Have two membranes; break down glucose to release energy (cellular respiration).

• Cytoplasm: Jelly-like fluid with the cytoskeleton that supports and gives shape to the cell.

• RER (Rough Endoplasmic Reticulum): Stores and transports proteins made by ribosomes attached to it.

• Ribosomes: Smallest organelles, no membrane; make proteins, free or attached to RER.

• Cell membrane: Made of lipids

Premalignant Oral Lesions

• Erythroplakia:
  • Appearance: Flat, macular red patch.
  • Histology: Severe dysplasia, decreased keratin.
• Carcinoma In Situ:
  • Histology: Intact basement membrane, severe epithelial dysplasia (top and bottom changes).
• Oral Submucous Fibrosis:
  • Appearance: Red patch, ulceration, burning sensation.
  • Histology: Atrophic epithelium, dysplasia.

Malignant Oral Lesions

Squamous Cell Carcinoma (SCC)

• Common Sites: Lower lip, lateral border of tongue, floor of mouth.
• Clinical Forms: Ulcer, exophytic, red/white patches, trismus, bone destruction/pathological fracture, tooth mobility.
• Ulcer Criteria: Indurated base, necrotic floor, everted edges, bleeding, bad odor, firm consistency.
• Histology: Epithelial invasion into connective tissue, abnormal cell