Compartmentalization (Organelles)

EK 2B3: Eukaryotic cells maintain internal membranes that partition the cell into specialized regionsEK 4A2: The structure and function of subcellular components, and their interactions, provide

essential cellular processesEK 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

NucleolusNucleus

Rough ER

Nuclear lamina (TEM)

Close-up of nuclear envelope

1 µm

1 µm

0.25 µm

Ribosome

Pore complex

Nuclear pore

Outer membraneInner membrane

Nuclear envelope:

Chromatin

Surface ofnuclear 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

RibosomesCytosol

Endoplasmic reticulum (ER)

Free ribosomes

Bound ribosomes

Large subunit

Small subunit

Diagram of a ribosomeTEM 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

Aminoacids

tRNA withamino acidattached

tRNA

Anticodon

Trp

Phe Gly

Codons 35

mRNA

P site (Peptidyl-tRNAbinding site) A site (Aminoacyl-

tRNA binding site) E site(Exit site)

mRNAbinding site

Largesubunit

Smallsubunit

Ribosome model showing binding sites.

Next amino acidto be added topolypeptide chain

Amino end Growing polypeptide

mRNAtRNA

E P 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 ribosomesin 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

Digestiveenzymes

Lysosome

Plasmamembrane

Food vacuole

(a) Phagocytosis :engulfs

Digestion

(b) Autophagy : recycles

Peroxisome

Vesicle

Lysosome

Mitochondrion

Peroxisomefragment

Mitochondrionfragment

Vesicle containingtwo 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