Cell Theory and Cell Structure

• The cell theory states that all living organisms consist of cells, cells come from pre-existing cells, and cells are the smallest living unit.
• Evidence for the cell theory includes: living organisms (bacteria, animals, and plants) are made of cells, viruses are not made of cells, cells replicate via mitosis, and cells can live, but their individual organelles cannot
• Common structural units in cells encompass genetic material (for replication and biological molecule instructions), cytoplasm (a site for metabolic processes), plasma membrane (regulating cell input/output), and water/lipids, which are major components

Prokaryotic Cell Structure

• Cell walls provide structure and withstand turgor pressure.
• 70S ribosomes build proteins during translation.
• Genetic material is "naked" DNA without histones, located in the nucleoid.
• The cytoplasm serves as the site for metabolic reactions.
• The plasma membrane regulates substance movement in and out of the cell.

Eukaryotic Cell Structure

• 80S ribosomes synthesize proteins.
• Genetic material is coiled DNA with histones, located in the nucleus.
• The nucleus contains DNA and regulates cell activities.
• The cytoplasm is the site of metabolic processes.
• The plasma membrane regulates substance movement in and out of the cell.
• Mitochondria have a double membrane with the inner membrane folded into cristae and generate ATP via cell respiration.
• Chloroplasts are specialized organelles, found in plant cells.
• The ER can be bare (smooth) or studded with ribosomes (rough).
• Rough ER (RER) aids in protein synthesis and storage
• Smooth ER (SER) aids in temporary lipid synthesis and storage.
• Golgi appears as cisternae with moving vesicles, modifies proteins and sends them to differing parts of the cell.
• Vesicles are are for storage/transport and may fuse with the cell membrane.
• Vacuoles are organelles for storage/transport and do not fuse with the cell membrane.
• Lysosomes break down and digest materials.
• The cytoskeleton provides structure and enables equal distribution of organelles and chromosomes during cell division and is made of microtubules and microfilaments.

Processes of Life

• Nutrition: all life obtains matter for metabolic processes
• Metabolism: the sum of all chemical reactions; all life requires energy
• Growth: all life can grow during its lifespan
• Response to stimuli: all life can react to changes in its environment
• Movement: all life can move to an extent
• Excretion: all life rids itself of waste from metabolic processes
• Reproduction: all life can replicate itself (asexually or sexually)
• Homeostasis: all life must maintain a stable internal condition regardless of its external environment

Eukaryotic Cell Differences

• Animal cells lack a cell wall, but plant cells have cell walls made of cellulose, and fungi cell walls composed of chitin.
• Animal cells have small, temporary vacuoles for digestion, while plant and fungi cells have large, permanent vacuoles for water storage and structural support.
• Plastids, such as chloroplasts and amyloplasts, are only present in plant cells.
• Centrioles are used during mitosis in animal cells, but found only mobile male gametes in plants and fungi.
• Cilia and flagella are present in some animal cells, while those in plant and fungi cells are exclusive only to mobile male gametes

Atypical Cell Structures

• Skeletal muscle fibers are long, multinucleated cells with a sarcolemma (continuous plasma membrane).
• Aseptate fungal hyphae are multinucleated with continuous cytoplasm and no divisions.
• Erythrocytes lack a nucleus.
• Phloem sieve tubes are mostly empty with all organelles contained with in attached companion cells.

Microscopy

• To calculate the magnification of a microscope: ocular lens magnification × objective lens magnification
• Drawing/micrograph magnification = measured size/actual size
• FOV (field of view) = field number of eye piece/objective magnification
• Resolution makes images clearer, whereas Magnification makes images larger.
• Light microscopes (2D) use lenses to bend light, can study dead or living cells, and produce colorized images.
• Electron microscopes (3D) use electron beams focused by electromagnets, can study dead cells only, and do not produce colorized images.
  • Transmission electron microscopes (TEM) (2D) pass electrons through a specimen for a cross-section view.
  • Scanning electron microscopes (SEM) (3D) scatter electrons to see the specimen's surface in depth.
• Fluorescent staining is done with a light microscope, using a blue dye to target specific molecules. ex: DAPI is a stain that targets DNA
• Immunofluorescence is more specific than fluorescent staining, using antibodies attached to fluorescent probes to target a specific component, like cancer markers.
• Cryogenic microscopy uses an electron microscope and involves freezing samples for near-atomic resolution, allowing fracture along a plane to view the insides.

Origin of Eukaryotes

• Eukaryotes originated through infolding of the prokaryotic cell membrane and endosymbiosis.
• Infolding of the cell membrane to create a double membrane, which creates internal microenvironments for increased efficiency.
• Endosymbiosis involves early eukaryotes engulfing aerobic bacteria which becomes mitochondria in a symbiotic relationship.
• Later, photosynthetic bacteria were engulfed to become chloroplasts, if a plant cell.
• Infolding of the membrane resulted in the nucleus, ER, Golgi, lysosomes and vesicles development.
• Multicellular organisms contain organisms (all plant and animal, most fungi and some algae) and have multiple cells working in unison.
• Multicellularity facilitates cell specialization and the ability to perform complex functions.
• Differentiation is when undifferentiated cells become specialized, creating emergent properties caused by epigenetics.
• A "whole is greater than the sum of its parts" allows for increased efficiency, as cells can focus on specific functions.
• In the hierarchy of life, similar cells form tissues, tissues form organs, organs form organ systems, and organ systems form organisms.

Organelles

• Organelles are discrete, differentiated subunits of cells, specialized for a specific function.
• Some structures are not technically considered membranes due to a lack of separation such as the cell wall, cytoskeleton, and cytoplasm.
• There are organelles with no membrane, one membrane, or a double membrane.
  • No Membrane: ribosomes, centrioles, microtubules & microfilaments, nucleolus (not enclosed by a phospholipid bilayer)
  • Single Membrane: vesicles & vacuoles, RER & SER, golgi, lysosomes (enclosed by a single phospholipid bilayer)
  • Double Membrane: nucleus, mitochondria, chloroplasts, amyloplasts (enclosed by two phospholipid bilayers)
• DNA in the nucleus regulates transcription and translation, whereas in prokaryotes occurs in both the cytoplasm and nucleus,
• Transcription involves DNA transforming into mRNA, and translation transforms mRNA into protein
  • In prokaryotes, transcription occurs in the cytoplasm and translation can immediately happen after transcription, while in Eukaryotes transcription occurs in the nucleus, and translation can only happen once mRNA leaves the nucleus.

Compartmentalization

• Compartmentalization involves organelles forming membranes to separate themselves from the rest of the cell.
• The advantages include increased efficiency, homeostasis, increased transport by independent organelle movement, and increased SA (increased absorption).
• Lysosomes contain low pH and enzymes to break down and digest molecules as well as protect the cell from damage by these enzymes and pH levels via compartmentalization.
• Phagocytosis steps:
  • Ingestion: take in food
  • Digestion: break down food
  • Absorption: take food into the cell
  • Assimilation: make food part of the cell

Mitochondria Structure

• The outer membrane has transport proteins that transport pyruvate from the cytosol.
• The inner membrane contains the ETC & ATP synthase.
• Cristae are folds of the inner membrane to ncreases SA.
• The intermembrane space maximizes proton gradient between the inner/outer membrane and is small.
• The matrix is the mitochondria's cytoplasm, isolating enzymes and pH for krebs cycle as well as ribosomes & mtDNA.

Chloroplast Structure

• A double membrane keeps the intermembrane space small to maximize proton gradient
• Thylakoids are flattened disks to increase SA and maximize proton gradient.
• Grana are stacks of thylakoids to increase SA.
• Thylakoid lumen is the cytoplasm inside thylakoid, containing enzymes needed for photosynthesis.
• Stroma is the chloroplast's cytoplasm

Nuclear Membrane

• The nuclear membrane regulates what goes in and out of the nucleus.
• It maintains the same basic structure as the plasma membrane (double-membrane). Nuclear pores allow for easy access during transcription and translation.
• During mitosis, the nuclear membrane breaks down in prophase and reforms during telophase
  • In prophase, the nuclear membrane breaks down into vesicles and during telophase, vesicles assemble to create a nuclear envelope around newly separated sets of chromosomes.
• Free ribosomes float in the cytoplasm, synthesize proteins for use in the cell
• Bound ribosomes attach to the RER producing proteins that are secreted, embedded in the membrane, or sent to other organelles (like the Golgi).

Golgi Apparatus

• The Golgi is the organelle in a series of enclosed sacs (cisternae) with vesicles moving to and from. It receives proteins from the RER, modifies them, and ships them to other parts of the cell.
• Vesicles enter from the cis face and exit from the trans face.
• There are two models suggesting how proteins move in the Golgi
• Cisternae maturation model: cisternae mature and move through the golgi from cis cisternae moves) to trans, proteins inside vesicles move along.
• Vesicle transport mode: proteins in vesicles move through the golgi, cis to trans, and the cisternae remain unchanged.
• Vesicles store and transport materials, can fuse with the membrane.
• Subtypes exist, such as permanent water storage found in plant and fungal cells) and temporary storage found in animal cells (digestion).
• Lysosomes contain a low pH and enzymes to digest material in the cell. Subytpes include: material transportation (into a contained vesicle) and cellular membrane transportation.

Clathrin

• Clathrin is a protein with three legs to assist vesicle formation.
• Binds to form a large 3D structure to assist with vesicle formation. phospholipids from the vesicle's membrane may be needed during cellular growth & cellular membrane can be removed at any time.