Compartmentalization (Organelles) EK 2B3: Eukaryotic cells maintain internal membranes that partition the cell into specialized regions EK 4A2: The structure and function of subcellular components, and their interactions, provide essential cellular processes EK 4B2: Cooperative interactions within organisms promote efficiency I the use of energy and matter

Prokaryotic vs Eukaryotic -Bacteria and Archaea -Cell wall made of -DNA in cytoplasm - circular -Smaller -Plasma membrane -Chromosomes -Ribosomes -cytoplasm -Protists, Fungi, Plant, animal cells -DNA in nucleus - linear -Larger -Membrane bound organelles (nucleus, ER, Golgi, Mitochondria, Chloroplast (plant cells only), Lysosomes( animal cells only) Prokaryotic Eukaryotic Both

Compartmentalization Breaking the cell into specialized areas Benefits: Increase surface area for reactions to take place Minimizing competing interactions; provide different local environments that facilitate specific metabolic functions; incompatible processes can go on simultaneously inside a single cell (cellular respiration and photosynthesis same time in different areas) Examples: Nuclear envelope Endoplasmic reticulum Golgi Mitochondria Chloroplasts

The Nucleus: Information Central Contains MOST of the genes in eukaryotic cells (some genes are located in mitochondria and chloroplast) Nuclear envelope: double membrane that surrounds the nucleus, contains proteins called pore complex that regulate entry and exit or proteins and RNAs Contains a specific number of chromosomes based on the species (humans = 46; flies = 8); remember sex cells (sperm and egg) contain ½ the number of chromosomes (humans = 23; flies = 8) Nucleus directs protein synthesis by synthesizing messenger RNA (mRNA) Nucleolus is also located inside the nucleus

The nucleus and its envelope Nucleolus Nucleus Rough ER Nuclear lamina (TEM) Close-up of nuclear envelope 1 µm 0.25 µm Ribosome Pore complex Nuclear pore Outer membrane Inner membrane Nuclear envelope : Chromatin Surface of nuclear envelope Pore complexes (TEM)

Nucleolus Synthesizes rRNA (ribosomal RNA) from instructions in the DNA. Proteins imported from the cytoplasm are assembled with rRNA into large and small ribosomal subunits Subunits then exit the nucleus through the nuclear pores to the cytoplasm where a large and small subunit can assemble into a ribosome

Ribosomes Made of two subunits (one small and one large) – subunits are constructed of proteins and rRNAs –made in nucleolus of eukaryotic cells Brings tRNA anticodons and mRNA codons together during protein synthesis Large and small subunits join to form a functional ribosomes only when they attach to an mRNA molecule Because most cells contain thousands of ribosomes, rRNA is the most abundant type of cellular RNA Eukaryotic ribosomes are slightly larger and differ somewhat from bacterial ribosomes in their molecular composition Differences allow allow certain antibiotic drugs to inactive bacterial ribosomes without inhibiting the ability of eukaryotic ribosomes to make proteins

Ribosomes Cytosol Endoplasmic reticulum ( ER ) Free ribosomes Bound ribosomes Large subunit Small subunit Diagram of a ribosome TEM showing ER and ribosomes 0.5 µm

Ribosomes – more details Ribosomes contain a binding site for mRNA Also contain three binding sites for tRNA: P site (peptideyl-binding site) – holds the tRNA carrying the growing polypetide chain A site (aminoacyl-tRNA site) – holds the tRNA carrying the next amino acid to be added to the chain E site (exit site) – discharged tRNA Ribosome hold mRNA and tRNA in close proximity and positions the new amino acid to the carboxyl end of the growing protein Recall the direction in which amino acids are added is ALWAYS carboxyl to amino end As the polypeptide grows it exits the large subunit through the exit tunnel When complete the protein is released to the cytosol if the protein is detached/or is inserted into the ER if attached

tRNA carries amino acids to mRNA. tRNA anticodon pairs with mRNA codon Polypeptide Ribosome Amino acids tRNA with amino acid attached tRNA Anticodon Trp Phe Gly Codons 3 5 mRNA P site (Peptidyl-tRNA binding site) A site (Aminoacyl- tRNA binding site) E site (Exit site) mRNA binding site Large subunit Small subunit Ribosome model showing binding sites. Next amino acid to be added to polypeptide chain Amino end Growing polypeptide mRNA tRNA EP A E Codons Ribosome model with mRNA and tRNA. 5 3

Endomembrane System Includes nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, various vacuoles, and plasma membrane (not really endo – but is it attached)

The Endomembrane System Smooth ER Nucleus Rough ER Plasma membrane cis Golgi trans Golgi Endomembrane System Includes nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, various vacuoles, and plasma membrane (not really endo – but is it attached)

Endoplasmic Reticulum Two different types: Smooth: Synthesis of lipids (oils, phospholipids, steroids) Stores calcium ions – muscle cells Detoxify drugs and poisons Increases tolerance to drugs = higher dose required to work Increase smooth ER due to drug abuse can also lead to decrease effectiveness of certain antibiotics and other useful drugs Rough: Transports proteins to Golgi body once ribosome makes protein; keeps proteins made on ER separate from proteins made in cytoplasm

Golgi Complex Think of it as UPS Modifies, sorts, packages, ships macromolecules to where they are needed in the cell.

Mitochondria Free ribosomes in the mitochondrial matrix Intermembrane space Outer membrane Inner membrane Cristae Matrix 0.1 µm Site of cellular respiration Enclosed by two membranes with embedded proteins that aid with cellular respiration Membrane proteins are made by ribosomes in the cytoplasm of the cell (instructions to make these proteins are found in the nucleus of the cell) AND by ribosomes found inside the mitochondria (instructions to make these proteins are found in the mitochondrial DNA) Outer membrane is smooth; Inner membrane is folded to increase surface area = increases the amount of ATP that can be created Intermembrane space: narrow region between the inner and outer membranes Mitochondrial matrix: contains enzymes, mitochondrial DNA and ribosomes

Chloroplast Site of photosynthesis Similar to mitochondria – proteins embedded in chloroplast aid photosynthesis and are made by the ribosomes in the cytoplasm of the cell and by the ribosomes found in chloroplast Membranes of the chloroplast separate it into three different compartments: Intermembrane space: two membranes separated by a very narrow space Thylakoid: contains chlorophyll (green pigment that captures energy from sunlight); location of light reaction of photosynthesis Stroma: contains chloroplast DNA and ribosomes as well as enzymes to aid in photosynthesis; location of the dark reaction of photosynthesis Ribosomes Thylakoid Stroma Granum Inner and outer membranes 1 µm

Lysosomes Uses hydrolytic enzymes to digest macromolecules Made by the rough ER and then transferred to the Golgi apparatus for further processing Carry out intracellular digestion in a variety of circumstances Ex: Fuse with food vacuole to digest macromolecules/macrophage (type of white blood cell) engulf and destroy bacteria with help of lysosomes Compartmentalization – enzymes inside lysosomes are dangerous to other parts of the cell – by keeping them separate they can do their job without harming the cell

Nucleus 1 µm Lysosome Digestive enzymes Lysosome Plasma membrane Food vacuole (a) Phagocytosis :engulfs Digestion (b) Autophagy : recycles Peroxisome Vesicle Lysosome Mitochondrion Peroxisome fragment Mitochondrion fragment Vesicle containing two damaged organelles 1 µm Digestion Lysosomes

Vacuole Membrane-bound vesicles whose functions vary in different kinds of cells Food vacuoles – form by phagocytosis Contractile vacuoles – pump excess water out of cell to maintain osmoregulation Carry out hydrolysis in plant and fungi since they lack lysosomes Large Central Vacuole in plant cells: Storage (water, inorganic ions) Disposal of metabolic by-products that would endanger cell if in high concentrations in the cytoplasm Poisons or unpalatable chemicals for animals (prevent being eatten)

Cooperative interactions within organisms promote efficiency in the use of energy and matter Cellular Level Organism Level Unicellular populations similar to multicellular organism