EFB325 Cell Physiology

Cellular organelles

Differences between prokaryotes and eukaryotes:

Prokaryotes: (bacteria and cyanobacteria)

• no nucleus
• smaller (1-10 um)
• mainly unicellular
• no cytoskeleton
• generally no membrane-bound organelles
• RNA and protein synthesis in same compartment
• 1 small circular chromosome
• only ~1000-4000 genes
• usually have a cell wall, but mycoplasmas and phytoplasmas lack a cell wall

Eukaryotes:

• genetic material mostly in nucleus
• larger (10-100 um)
• mainly multicellular
• cytoskeleton present
• membrane-bound organelles present
• RNA synthesis in nucleus, protein synthesis in cytoplasm
• multiple linear chromosomes
• ~6,000 - 30,000 genes total (~6600 genes in yeast genome; 25,500 genes in Arabidopsis; ~25,000 genes in humans)

The main focus of the course is on eukaryotes, although since eukaryotes and prokaryotes have a common ancestor, they have a lot of biochemical, metabolic, and genetic systems in common.

• try to consider the common aspects and differences among prokaryotes & eukaryotes; plants and animals

Eucaryotic cells can be larger and still function efficiently because they compartmentalize reactions in organelles, specialized for a particular function

Compartmentation:
    In eukaryotes it allows for larger cell size; cells can maintain chemical/enzyme concentrations in a localized space

Cell size:surface area ratios
    Cell size is thought to be limited by the need to exchange molecules with the environment and maintain proper concentrations

Survey of organelles:

Nucleus

• surrounded by a double membrane (nuclear envelope), which has pores to allow trafficking between nucleus & cytoplasm
• space between the double membranes=perinuclear space
• contains the chromosomes-DNA complexed with proteins
• nucleolus is the site of rRNA synthesis=organized region inside the nucleus containing rRNA genes - site of ribosome subunit assembly

Plasma membrane

• outer membrane (single) of the cell, mainly consisting of phospholipids
• many proteins are integral to the membrane=enzymes, anchors to ECM, transporters, receptors
• many of the proteins have carbohydrates linked to them on the parts that are outside the cell
• main permeability barrier of the cell

Everything inside the plasma membrane, but not in the nucleus=cytoplasm

• the solution outside of the organelles=cytosol

Ribosomes

• site of protein synthesis in the cytoplasm (also ribosomes in the mitos and plastids)
• no membranes surround the ribosomes
• complex of protein and RNA-form large and small subunits
• hundreds of thousands of ribosomes per cell
• the rRNAs from related organisms are very similar, so the nucleotide sequences can be compared and used for studies of evolution
• ribosomes from prokaryotes are different from those of eukaryotes (euks are larger)

Endoplasmic reticulum, ER

• extensive network of interconnected, flattened sacs with single membranes
• inside=lumen of the ER
• the ER membrane is contiguous with the outer membrane of the nucleus, so the perinuclear space is contiguous with the lumen of the ER
• some regions of ER have ribosomes adhering to the outside=rough ER
• proteins that are to be secreted out of the cell are made by these ribosomes and inserted directly into the ER lumen
• carbohydrates may be added to proteins in the ER lumen
• smooth ER is the site of lipid synthesis, including steroid hormone synthesis
• some detoxification reactions
• one step in the breakdown of glycogen occurs in ER

Golgi (and secretory vesicles)

• vesicles bud off of the ER, flow and fuse with the Golgi
• array of flattened saccules (single membranes), with dynamic mixture of vesicles arriving from ER on one side and vesicles budding off toward PM on the other side
• some of the carbohydrates added to proteins in the ER are modified in the Golgi
• secretory vesicles fuse with the PM, by exocytosis expel the proteins outside the PM
• this is also the basic mechanism of how the plasma membrane is built

Mitochondria

• surrounded by a double membrane (outer and inner membrane, intermembrane space in between)
• inner space is called the matrix
• site of ATP production by the citric acid cycle and oxidative phosphorylation
• contains its own genome, which expresses some of the proteins in the mito
• DNA is maternally inherited, so it can be used to trace maternal lineages in anthropology and evolutionary studies
• evolved after the endosymbiosis of an ancestral prokaryote with an ancestral eukaryotic cell, then many genes eventually moved to the nucleus (similar situation as with plastids - see below)

Lysosome

• surrounded by a single membrane
• contains degradative enzymes for digesting foreign bodies, other toxins
• derived from Golgi

Peroxisome

• perform oxidative reactions many involving H₂O₂ (hydrogen peroxide) often complement mitos and chloroplasts
• not derived from Golgi - receive lipids through transfer proteins from ER

Chloroplast (plastids)

• includes three distinct membrane systems; outer, inner, thylakoid membranes
• inside of thylakoids is the lumen, between thylakoids and inner membrane is stroma
• site of photosynthesis and many biosynthetic reactions, such as amino acid synthesis
• contains its own genome, expresses many chloroplast proteins
• DNA is maternally inherited (no plastids present in most pollen) 
• in undifferentiated cell; plastids start as proplastids, can differentiate into chloroplasts, amyloplasts (store starch), leucoplasts (store oils); chromoplasts (produce pigments)
• plastids evolved through multiple events of the endosymbiosis of ancestral photosynthetic bacteria into eukarotic cells - many of the genes from the bacterium eventually became located in the nucleus, so the plastid cannot function without a functioning nucleus

Vacuole

• surrounded by a single membrane (called the tonoplast)
• occupy most of the volume of a plant cell
• stores Ca²⁺ , small carbon compounds (like malate), other ions (like K⁺)
• balances osmoticum (solute concentration) to generate most of the turgor pressure in a plant cell

Cytoskeleton

• dynamic internal framework/scaffold coordinating cytoplasm and its components
• contribute to cell shape and act in cell division, muscle movement, locamotion
• composed of three elements: microtubules, microfilaments, & intermediate filaments (entirely composed of protein)

1) Microtubules (MTs)

• made up of two different protein subunits, alpha and beta tubulin=heterodimer
• dimers come together to form protofilament (linear)
• protofilaments come together to form a sheet, which rolls up to form a tube
• MTs can shrink or grow, by adding or removing dimer units
• during mitosis/meiosis MTs form the spindles

2) Actin Microfilaments (MFs)

• made up of actin protein subunits
• actin monomer proteins come together to form a double-helical strand of polymers
• can also grow or shrink by adding/removing monomer units
• MFs involved in muscle contraction and locamotion

3) Intermediate filaments (IFs)

• more stable than either MFs or MTs; often more of a tension-bearing role
• made up of helical dimers of IF protein monomers; 2 dimers together form a protofilament; protofilaments align with each other side-by-side to form the IF, 8 protofilaments thick
• different monomer proteins are used to make the IFs in different tissues (unlike MTs and MFs, which are the same in different cell types/tissues)
• functions are primarily structural/tension-bearing

Extracellular matrix

• Animals: outside the plasma membrane is mainly collagen protein fibers and glycoproteins (proteins with carbohydrates attached)
• Plants: have a rigid cell wall, mainly composed of cellulose microfibrils, pectins, other polysaccharides, and proteins; in mature plant tissues, can also contain lignin (polymer of aromatic alcohols)

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