Biology Review Notes

Cell Theory

• Prokaryotes vs. Eukaryotes
  • Eukaryotes have a true nucleus and membrane-bound organelles.
  • Eukaryotes have mitochondria for energy production.
  • Eukaryotic DNA is protein-bound and linear.
  • Prokaryotes have naked, circular DNA (e.g., bacteria).
  • Eukaryotes include mammals and humans.
• Fundamental Tenets of Cell Theory
  • All living things are composed of cells.
  • The cell is the basic functional unit of life.
  • Cells arise only from preexisting cells.
  • Cells carry genetic information in the form of DNA.

Cell Structure

• Protoplasm: Nucleus + Cytoplasm
• Cell Membrane (Plasma Membrane): Lipid bilayer of phospholipids.
  • Hydrophilic heads face outwards towards water.
  • Hydrophobic tails face inwards away from water; lipophilic.
• Genetic Material: DNA organized in chromosomes, found inside the nucleus.
• Organelles: Located in the cytoplasm.
  • Mitochondria: Produce energy in the form of ATP.
  • Sperm: Requires lots of energy, hence many mitochondria.
  • Secretory cells (e.g., pancreas): Require lots of Golgi and endoplasmic reticulae.
  • Red blood cells: Lack organelles, mitochondria, TCA cycle, and electron transport chain.

Organelles

• Mitochondria: Powerhouse of the cell.
• Lysosome: Destroys foreign invaders.
• Endosome: Delivery guy.
• Endoplasmic Reticulum (ER): Rough and smooth.
  • Rough ER: Translates proteins for secretion; works with Golgi.
  • Smooth ER: Fat synthesis.
• Golgi: Modifies cellular products and directs them for delivery; works with rough ER.
• Peroxisome: Destroys fat (beta oxidation of fatty acids).
• Cytosol vs. Cytoplasm
  • Cytosol: Fluid with no organelles.
  • Cytoplasm: Cytosol + Organelles.
  • Protoplasm: Cytoplasm + Nucleus.

Nucleus

• Control room of the cell containing DNA (genes).
• Nuclear Pores: Allow entry and exit from and to the nucleus.
• Outer membrane is continuous with the rough endoplasmic reticulum.
• DNA double helix wrapped around histones forms chromosomes.
• Human somatic cells contain 46 chromosomes.
• Replication: Copying DNA.
• Transcription: Converting DNA into RNA.
• Translation: Translating RNA into proteins.
• Nucleolus: Site of ribosome assembly (rRNA synthesis).
• Most cells have one nucleus; red blood cells have none; osteoclasts have many.
• Neutrophils have lobated or segmented nuclei.

Mitochondria

• Provides energy (ATP).
• Initiates apoptosis (programmed cell death) when a cell is old or malfunctioning.
• Structure:
  • Electron transport chain (ETC) pumps protons from inside to outside.
    • $H^+$ ions gradient is formed and used to create ATP.
  • Cristae increase surface area for ETC.
  • Inner membrane contains ETC enzymes.
  • Matrix contains Krebs cycle enzymes.
    • Krebs cycle = Tricarboxylic acid cycle or Citric acid cycle
• Mitochondria has its own DNA, inherited from the mother.

Lysosome

• Destroys foreign invaders and senescent/harmful particles using hydrolytic enzymes in an acidic medium.
• Hydrolytic enzymes are kept inside the lysosome, protected by the lysosomal membrane.
• Destruction Processes:
  • Endocytosis (with help from endosome).
  • Autophagy (with help from phagosome).
• Clathrin: Protein that helps vesicle separate from membrane.

Endoplasmic Reticulum

• Continuous with the nuclear membrane.
• Rough ER: Translates proteins for secretion.
• Smooth ER: Fat synthesis and detoxification.
• Sarcoplasmic reticulum (in muscle) is a modified smooth ER.
• Functions:
  • Rough ER: Protein synthesis (translation).
  • Smooth ER: Fat synthesis and detoxification.
  • Steroid hormones (sex hormones) are made of fat.

Golgi Apparatus

• Sorts and directs cellular products for delivery; works with endoplasmic reticulum.
• Process:
  • Nucleus: DNA code → mRNA (transcription).
  • mRNA: Leaves nucleus through nuclear pore → cytoplasm.
  • Rough ER: Translates mRNA into proteins.
  • Proteins: Put into vesicles for Golgi.
  • Golgi: Modifies and secretes proteins via exocytosis.
  • Golgi can also work with endosomes and lysosomes for destruction by endocytosis.

Peroxisome

• Destroys fat via beta oxidation.
• Contains hydrogen peroxide ($H<em>2O</em>2$).
• Peroxide is used for lipid catabolism and to kill foreign invaders (reactive oxygen species or free radicals).
• Peroxisomal Diseases: Adrenoleukodystrophy (ALD) - X-linked (more common in boys).

Cytoskeleton

• Most abundant component of cell: water. Second most abundant: proteins.
• Types of Proteins: Structural (cytoskeleton) and functional (enzymes, pores, channels, pumps).
• Cytoskeleton: Protein network made by ribosomes.
• Functions:
  • Cell movement.
  • Cell division (cytokinesis).
  • Provides railroad tracks for movement of packages.
• Types of Cytoskeleton:
  • Microfilaments.
  • Microtubules.
  • Intermediate filaments.

Cytoskeleton Details

• Microfilaments: Actin.
  • Monomers → Polymers of G-actin → Actin filaments.
  • Function in cell division (cleavage furrows).
• Microtubules: Tubulin (alpha and beta).
  • Provide the backbone for structures.
    • Centriole: 9 triplets of microtubules.
    • Cilium/Flagellum: 9 doublets of microtubules + 2 additional ones.
  • Kinesin and Dynein: Motor proteins.
    • Dynein defect: Kartagener's syndrome/immotile cilia syndrome.

Cilia and Flagella

• Cilia: 9 doublets of microtubules + 2 central ones.
  • Motile cilia: Respiratory tract (remove gunk).
  • Immotile cilia: Rods of the eye.
    • Immotile cilia syndrome: Ectopic pregnancy (fallopian tube cilia don't work).
• Genetic Diseases: Respiratory problems.
  • Kartagener's syndrome: Dynein arm defect.
  • Cystic fibrosis: CFTR mutation, thick mucus.
• Flagella: Similar structure to cilia.
  • Sperm: Has a flagellum.
  • H. pylori bacteria: Has a flagellum.

Centrioles and Intermediate Filaments

• Centriole: 9 triplets of microtubules.
• Intermediate Filaments:
  • Different types depending on tissue. Examples:
    • Mesenchymal cells: Vimentin.
    • Epithelial cells: Keratin.
    • Neural cells: Neurofilaments.
    • Nuclear envelope: Lamin.
    • Muscles: Desmin.
    • Neuroglial cells: GFAP (Glial Fibrillary Acidic Protein).

Tissue Types

• Building Blocks: Cell → Tissue → Organ → System.
• Four Types of Tissues:
  • Epithelium.
  • Connective.
  • Muscle.
  • Nerve.
• Epithelium: Covers surfaces, lines cavities, stands on a basement membrane.
  • Forms the parenchyma of cells (functional part of glands).
    • Parenchyma: Functional cells (e.g., neurons in brain, alveoli in lungs).
  • Stroma: Supporting tissue (connective tissue).
• Connective Tissue: Ligaments, bones, blood, tendons, fat, lymph.
  • Provides support, framework, and makes stroma.
  • Produces collagen and elastin.

Cell Cycle

• Phases: G0 (resting) → G1 (growth) → S (DNA synthesis) → G2 (growth) → M (mitosis/meiosis).
• Somatic Cells vs. Germ Cells
  • Replication: DNA duplication during S phase.
  • Transcription: DNA → RNA
  • Translation: RNA → Proteins
    *Division happens in M phase during mitosis or meiosis.
• Interphase: G1, S, G2 for rest, growth and DNA.
• Mitosis/Meiosis Phases: Prophase, Metaphase, Anaphase, Telophase (Pro-Meta-Ana-Telo).
• Karyokinesis & Cytokinesis Take place in the M phase of the cell cycle

Mitosis and Meiosis Phases

• Prophase: Condensation of chromatin into chromosomes, separation of centriole pairs, formation of the mitotic spindle, dissolution of the nuclear membrane.
• Metaphase: Chromosomes align in the midline (metaphase plate) thanks to the mitotic spindle as a mirror image of the same.
• Anaphase: Split the centromere and separate sister chromatids; kinetochore pulls.
• Telophase: Mitotic spindle disappears, nuclear membrane reforms, cleavage furrows form from microfilaments, and then cells separate (cytokinesis).
• Meiosis has two division phases.

Reproduction and Cell Types

• Female Reproductive Tract vs. Male Reproductive Tract.
  • Gonads - Ovary vs. Testicle.
  • Gametes - Ovum vs. Sperm.
  • Spermatogenesis vs. Oogenesis:Oogenesis gives one ovum and three polar bodies.
• Fertilization:Sperm meets secondary oocyte arrested in metaphase II.
• The Hypothalamus makes GnRH to tell the anterior pituitary to make LH and FSH for the gonads.
• During spermatogenesis, FSH influences the sertoli cell to feed the sperm and aromatization.
• Oogenesis Phases and Hormones
  * Proliferation Phase - Thank you Estrogen.
  * Secretory Phase - Progesterone, and some estrogen.. And you release one.
  * Menstruation- Drops like a Rock.
• The Steps of Fertilization - Capacitation, Acrosomal Reaction, Polyspermy Block, Completion of, Meiosis Two, Formation of Zygote.
• Blastulation: To make a blastocyst from the inner cell mass with the outer cell mass.
• Gastrulation: Generation of different layers.

Neurulation

• Nervous system comes from the ectoderm.
• CNS (brain and spinal cord): Neural tube.
• Peripheral Nervous System (PNS): Neural crest cells.

Stem Cells

• Totipotent, Pluripotent, Multipotent, Unipotent (differentiation).
• Examples:
  * Pluripotent stem cells in the bone marrow to create blood cells.
  * Basal layer of skin and type two pneumocytes (also release surfactant).

Types of Cell Regeneration

• Apoptosis versus Necrosis.
• Complete and Incomplete Cell Regeneration.
• Shortening Telomeres during division results in senescence.
  *Telomeres do not shorten could results in cancer.

Fetal Circulation

• Placenta: Oxygen and nutrients from mom to baby; $CO_2$ and waste from baby to mom.
• Fetal Hemoglobin (HbF) shifts oxygen dissociation curve to the left to favour oxygen binding to the tissue.
• Smoking , Alcohol, Folate Deficiency and Medication are Tetratogens.
  *Adult Ciculation vs. Emryological Circulation.
  *The ductus venosus will become the ligamentum venosum. Foramen ovale will become the fossa of allus. Ductus arteriosus will become ligamentum arteriosum.

The nervous System

• Central -Brain and spinal cord.
• Peripheral - Spinal and cranial nerves.
• Voluntary vs. Involuntary.
• **Collection of Cell Bodies ** The CNS is a Nucleus; collection The PNS is a Ganglion; axons in the CNS is a Tract;collection of axons in The PNS is a Nerve.
• Structural unit of the nervous system is a Neuron; Functional unit of the nervous system is the Reflex Arc .
• Glial Cell make myelin.
• Fibers A and B are myelinated, C Fibers unmyelinated.
• Neurons Have Sheath regardless.
• Action Potential
  *Uni-directional
  *from Soma to Axon Terminalis.