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

Primary Structure

Primary Structure: Amino acid sequence, description of all main covalent disulfide bonds and peptide bonds.

• Superfamily: Homology 30%.
• Families: Greater than 50% homology and usually the same function.

Enzymes that break peptide bonds:

• Trypsin
• Chymotrypsin
• Pepsin
• Papain

Predictions from primary structure:

• Homology
• Hydrophobicity
• Secondary structure
• HPLC chromatographic retention
• Accessible and hidden residues
• Mutability

Secondary Structure

Secondary Structure: Folding of the polypeptide chain that occurs due to the formation of hydrogen bonds between the atoms forming the peptide bond.

Structures formed:

• Alpha-helix
• Beta-sheet
• Beta-turn

Examples:

• Alpha-helix: Myoglobin (globular protein), Fibrinogen (fibrous protein)
• Beta-sheet: Fibroin (fibrous

DNA and RNA Structure

A nucleoside is formed when a pentose sugar combines with a nitrogenous base (NB). Adding a phosphate group to a nucleoside creates a nucleotide. Nucleotides are linked by O-glycosidic phosphodiester bonds. DNA adopts a right-handed double helix structure, with hydrophobic NBs at the core and hydrophilic pentose and phosphate groups on the exterior. The major groove serves as the interaction site for replication, while the minor groove contributes to structural maintenance. Approximately 10 base pairs span 3.4 nm.

Ribosomal RNA (rRNA)

Ribosomes consist of two subunits: a large subunit (50S in prokaryotes, 60S in eukaryotes) and a small subunit (30S in prokaryotes, 40S in eukaryotes).

DNA Replication

DNA replication must be... Continue reading "DNA, RNA, and Replication: A Deep Dive into Molecular Biology" »

Skeletal Striated Muscle Cells

Skeletal striated muscle cells are elongated and have hundreds of peripheral nuclei. The cytoplasmic membrane (sarcolemma) encloses the cytoplasm (sarcoplasm), which is packed with:

• Myofibrils
• Sarcoplasmic reticulum
• T tubules
• Mitochondria

Myofibrils are composed of sarcomeres arranged in series. Each myofibril consists of thin (actin) and thick (myosin) myofilaments.

Sarcomere Structure

The sarcomere (from Greek sarco meaning "flesh" or "meat" and meres meaning "part") features:

• A central, dark A band (anisotropic)
• Two peripheral, light I bands (isotropic)

The sarcomere contains globular proteins such as troponin and tropomyosin. The sliding of thin filaments between thick filaments causes muscle contraction. During contraction,... Continue reading "Striated Muscle Cells: Skeletal vs. Cardiac" »

Earth's Biosphere and Ecosystems

The biosphere of the Earth is established by living organisms within a thin layer where energy comes from the sun. An ecosystem is formed by a community of living organisms that occupy a given space, the relationships established between them, and the physical environment.

Key Ecological Concepts

• Ecotone: Areas that limit ecosystems.
• Habitat: The area that presents the physicochemical conditions required for a population to properly function.

Components of an Ecosystem

Landforms are part of the ecosystem, which is part of the ecosphere. The components include:

• Biocenosis: The community of living organisms.
• Biotopo: The physical environment.

Biotopo Components

These include:

• Characteristics of the substrate: The support

Eye

Cornea

1. Anterior corneal epithelium
2. Bowman's membrane
3. Stroma
4. Descemet's membrane
5. Corneal endothelium

Choroid

1. Vascular layer (arteries and veins around conjunctiva lax with melanocytes)
2. Choriocapillaris layer (capillary network in 1 flat)
3. Bruch's membrane

Retina

1. Nerve fiber layer
2. Ganglion cell layer
3. Inner plexiform layer
4. Inner nuclear layer
5. Outer plexiform layer
6. Outer nuclear layer
7. Outer limiting membrane
8. Rod and cone layer
9. Pigment epithelium

Eyelids

(Outside to inside):

1. Skin and dermis of TCL
2. Bundles of striated muscle (orbicularis oculi muscle)
3. Thickened set at the ends (eyelid plates with meibomian glands)
4. Mucous layer (conjunctiva)

Glands: Moll (sweat), Meibomian and Zeis (sebaceous)

Inner Ear

Above the sensory epithelium of the macula are otoliths (calcium carbonate... Continue reading "Female Reproductive and Sensory Organs" »

Metabolic Regulation

Enzymes do not always act with the same degree of cellular boost to the economy. Regulation governs many metabolisms at these levels: synthesis and modification of enzyme structure, [S] and [P]. Thus, enzyme inhibition is a control mechanism of cellular metabolism. An important example is allosteric enzymes, whose speed depends not only on the interplay of [S] but also on other substances. Then, in addition to the active sites, they have other allosteric sites that activate them or act as regulatory molecules.

Types of Metabolic Regulation

• Negative Feedback (Feedback Regulation): The product inhibits the pathway.
• Positive Control: The product stimulates the start of the pathway.

Nucleic Acids

Nucleic acids are substances found... Continue reading "Metabolic Regulation and Nucleic Acids: DNA and RNA Functions" »

Transcription and mRNA Processing

Transcription occurs within the nucleus. During this process, introns are removed from the pre-mRNA, creating a mature mRNA molecule. This mature mRNA then migrates from the nucleus to the cytoplasm.

Translation Initiation and Elongation

Once in the cytoplasm, the mRNA is recognized by the ribosome. This recognition occurs via specific sequences in bacteria and the 5' cap in eukaryotes. The ribosome then initiates the translation process.

tRNA molecules act as adapters between amino acids and mRNA. Each tRNA has a region that binds to a specific amino acid and another region, the anticodon, that recognizes a triplet of nucleotides (a codon) in the mRNA.

Translation begins when the ribosome identifies the start... Continue reading "mRNA Translation: From Transcription to Protein Synthesis" »

Glycolysis: Breakdown of Glucose

Preparatory Phase (Energy Investment)

This initial phase requires the cell to invest energy by spending two ATP molecules to phosphorylate glucose. First, glucose is phosphorylated, and then fructose-6-phosphate undergoes phosphorylation. These phosphate transfers are catalyzed by transferase enzymes, specifically kinases, which transfer phosphate groups from ATP.

1. An isomerase enzyme converts glucose-6-phosphate into a ketose, fructose-6-phosphate.
2. Fructose-6-phosphate is phosphorylated again by a kinase, using another ATP, forming fructose-1,6-bisphosphate.
3. Fructose-1,6-bisphosphate is then cleaved into two different 3-carbon phosphorylated isomers: glyceraldehyde-3-phosphate (G3P) and dihydroxyacetone phosphate

Excretion is the elimination of waste products (such as carbon dioxide and nitrogenous wastes) and is a crucial part of the broader processes aimed at maintaining homeostasis, which is essential for an organism's survival. Homeostasis is the process of maintaining constant internal conditions. The two pillars that maintain homeostasis in animals are excretion and osmoregulation.

Excretory Structures

Excretory systems use tubes to collect fluid from the blood, hemolymph, or extracellular fluid to adjust its composition through the reabsorption of useful substances and the active secretion of waste products.

• Sponges, Cnidarians, Nematodes, and Echinoderms: These organisms lack specialized excretory structures and eliminate waste through diffusion

Respiration: Concepts and Types

There are two types of respiration:

• A) Cellular or Internal Respiration: This is the use of oxygen by cells. It involves oxidizing complex organic molecules to obtain energy. This process produces CO2 and water as byproducts. Cellular respiration occurs in the mitochondria of the cell.
• B) External Respiration: This is the intake of oxygen and the output of carbon dioxide from the body. It occurs due to gas exchange across specialized respiratory surfaces. These surfaces must be very thin to allow for gas passage. They must also be wet, as gases dissolve in liquid before crossing. These surfaces are typically coated with a network of blood capillaries to facilitate the entry of oxygen and the exit of carbon dioxide.