B2.2

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Organelles & Compartmentalization

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Mr. Keel

B2.2 - Organelles & Compartmentalization

Compartmentalization

Compartmentalization refers to the way a cell is divided up into “compartments” separated by membrane.

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These membrane-bound spaces, called “organelles”, are separated from one another, enabling them to specialize and efficiently perform a specific function or job.

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Separation allows different biochemical processes to occur simultaneously & efficiently without interfering with one another.

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• Catabolism (breaking down molecules), like the breakdown of waste performed in the lysosomes.

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• Anabolism (building molecules), like the building of ATP in the mitochondria

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Organelles as

Subunits of cells

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B2.2.1 - Organelles as discrete subunits of cells that are adapted to perform specific functions

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Progress in Science

from New Experiments

& New Technology

Blenders & centrifuges allowed for the maceration & separation of cell parts.

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This led to the ability to study organelles for study

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TOK

Progress in Science

from New Experiments

& New Technology

Blenders & centrifuges allowed for the maceration & separation of cell parts.

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This led to the ability to study organelles for study

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Progress in Science

from New Experiments

& New Technology

Blenders & centrifuges allowed for the maceration & separation of cell parts.

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This led to the ability to study organelles for study

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Advantages of Compartmentalization

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B2.2.2 - Advantage of the separation of the nucleus and cytoplasm into separate compartments

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B2.2.3 - Advantages of compartmentalization in the cytoplasm of cells

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Advantages in the Nucleus & Cytoplasm

The nucleus is separated from the cytoplasm by a

double membrane known as the nuclear envelope,

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Transcription of DNA into mRNA occurs inside the nucleus, then mRNA exits and acts as a template for protein building (translation) in the ribosomes…

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Advantage: Separation of the nucleus from the cytoplasm leads to greater control over genes

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• mRNA can be created inside the nuclear membrane then be modified outside the membrane leading to greater capability and complexity.

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• More complex (80s) ribosomes can be created!

Advantages in the Cytoplasm of

Animal Cells

Consider mitochondria, the nucleus, lysosomes, & the E.R. in animal cells

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Advantage: Making reactions possible and more efficient by separating them and isolating them in organelles:

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Energy production occurs efficiently (mitochondria), Transport for synthesized proteins is seperated (E.R.), Waste is broken down safely without damaging the cell environment (lysosomes).

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Cognito

Do you know the Function of all these organelles in Animal Cells ?

Advantages in the Cytoplasm of

Plant Cells

Chloroplasts can perform photosynthesis and large central vacuoles can store large volumes of water .

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Advantage: Efficiency without interference

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Chloroplasts can have efficient reaction because reactions are separated (light-dependent reactions in the thylakoid membranes & the Calvin cycle in the stroma) and the vacuole keeps water storage contained to avoid interference.

Cognito

Do you know the Function of all these organelles in Plant Cells ?

Two Main Advantages of Compartmentalization

Concentration of Metabolites & Enzymes

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• Mitochondrial matrix concentrates enzymes needed for aerobic respiration

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• Mitochondrial intermembrane space is very small H⁺ gradient builds quickly for chemiosmosis.

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• Chloroplast stroma pools Calvin-cycle enzymes/substrates to make glucose.

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• Chloroplast Thylakoid membranes allow many proteins to use incoming sunlight.

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• RER lumen & Golgi cisternae process enzymes, modifying and packing them efficiently in an isolated space.

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Separation of incompatible processes

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• Lysosomes isolate hydrolytic enzymes so bulk cytoplasm isn’t digested.

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• Phagocytic vacuoles trap & sequester ingested material for safe breakdown.

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• Nucleus separates mRNA transcription and Protein translation protecting DNA & allowing for greater specialization.

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• Thylakoid space isolates reactive substances of light reactions so they don’t damage the stroma/cytosol.

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• Peroxisomes seal off detox enzymes (H₂O₂) away from other cell chemistry.

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Adaptations of Mitochondria & Chloroplasts

*HL Only

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B2.2.4* - Adaptations of the mitochondrion for production of ATP by aerobic cell respiration

B2.2.5* - Adaptations of the chloroplast for photosynthesis

Adaptations of the Mitochondria

70S ribosomes & Naked loop of DNA: Allows the mitochondrion to synthesize proteins.

Matrix: Fluid inside the mitochondrion contains enzymes for the Krebs cycle and the link reaction

Outer Membrane: Separates the contents of the mitochondrion from the rest of the cell, creating ideal conditions for aerobic respiration.

Cristae: Tubular or shelf-like projections of the inner membrane increase the surface area available for ATP production.

Inner Membrane: Contains electron transport chains and ATP synthase, which work together to produce ATP by chemiosmosis.

Intermembrane space: small space between the inner and outer membranes, allowing high proton concentrations to rapidly develop as they are pumped in as part of electron transport chains.

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Adaptations of the Chloroplasts

70S ribosomes

Granum: Stacks of thylakoids with a large total surface area of membrane for reactions.

Envelope: Outer & Inner Membrane Separates cell contents from the rest of the cell & create ideal conditions for photosynthesis

Stroma: Contains a high concentration of Rubisco and other enzymes and substrates for reactions.

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Thylakoid membranes: A system of membranes inside the chloroplast containing the components needed for the light-dependent reactions of photosynthesis.

DNA

(Naked Loop)

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Starch Storage (sugar granule)

Lamella

(Grana Bridges)

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The Double Membrane of the Nucleus

B2.2.6 - Functional benefits of the double membrane of the nucleus

NIH

The Nuclear Membrane is a Double Membrane

Advantages:

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• Pores can be formed by joining the outer membrane to the inner membrane allowing ribosomes and mRNA to move from the nucleus to the cytoplasm.

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• The nuclear membrane can easily break up into vesicles during mitosis and meiosis, releasing chromosomes. The vesicles can move to the poles of the cell, where they are later used to construct new nuclear membranes around new daughter nuclei.

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• DNA copies - RNA can be modified twice (see next slide)

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The Nuclear Membrane allows RNA to be modified twice.

1^st Inside the membrane: Since DNA never leaves the nucleus, transcription of DNA into mRNA occurs inside the membrane, the copy - mRNA - has specific code for proteins to be made outside when the mRNA is read by ribosomes.

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2^nd Outside the membrane: Once the mRNA exits into the cytoplasm it can be altered again “turning some genes on & off” before it is read by ribosomes but after it was originally copied. This means secondary changes can create different specialized cell types (and tissues) by altering structure.

Layout of the Nuclear Membrane

The semifluid matrix found inside the nucleus is called nucleoplasm.

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DNA within the nucleus is found as chromatin, the less condensed, more tangled form of the cell's DNA that organizes to form chromosomes during prophase of mitosis or meiosis.

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The nucleus also contains a nucleolus, sometimes more than one, an organelle that synthesize ribosomes.

The Nuclear Envelope (Double Membrane)

The purpose of the nuclear envelope is to protect the genetic material in the cell and to separate it from substances and chemical reactions that occur in the cytoplasm.

The nucleus is surrounded by a system of two concentric membranes, called the inner nuclear membrane and the outer nuclear membrane.

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The outer nuclear membrane is continuous with openings into the E.R. (endoplasmic reticulum).

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Like other cell membranes, the nuclear membranes are phospholipid bilayers (B1.1.12), which are permeable only to small nonpolar molecules (B1.1.13). Other molecules are unable to diffuse through the phospholipid bilayer. This is why we need Nuclear Pores

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Nuclear Pores

Nuclear pore complexes create a selective passageway through which molecules are able to travel between the nucleus and the cytoplasm.

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The nuclear pore complex is an relatively large structure —about 30 times the size of a ribosome.

only allows specific molecules through

Nuclear Pores

Nuclear pores are 10-20 times larger than the channel proteins within plasma membrane bilayers (B2.1.6).

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Nuclear Pores

IN (Nucleus)

IN

Proteins responsible for all aspects of genome structure and function are synthesized at ribosomes in the cytoplasm and must be imported into the nucleus. They include histones (A1.2.13*), helicase and enzymes like DNA polymerases (D1.1.3), RNA polymerases (D1.2.1). Also nucleotides (A2.1), transcription factors (D1.2.13), splicing factors (D1.2.15), and many others.

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OUT

mRNA and tRNA are formed in the nucleus during transcription and must be exported to the cytoplasm to function in translation (D1.2.6).

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Ribosomes are synthesized in the nucleolus and must be exported to the ER or cytoplasm to function in translation (B2.2.7).

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OUT (Cytoplasm)

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Nucleus During Cell Division

The nucleus disassembles & re-forms each time most cells divide.

During prophase (D2.1.7), the nuclear membrane and E.R. are fragmented into vesicles. The vesicles are moves to the edge of the cell

Nucleus During Cell Division

During telophase (D2.1.7), the vesicles are moved around the new sets of daughter chromosomes and the nuclear membrane and endoplasmic reticulum are reformed in each new cell.

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Structure & Function of Ribosomes, E.R., Golgi & Vesicles in cells

B2.2.7 - Structure and function of free ribosomes and of the rough endoplasmic reticulum

B2.2.8 - Structure and function of the Golgi apparatus

B2.2.9 - Structure and function of vesicles in cells

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Ribosome Structure

ribosomal RNA is shown in orange & proteins in purple.

rRNA is transcribed from DNA becoming the scaffold scaffold for ribosomes. rRNA is a single strand of RNA that folds up due to nitrogen bases into the ribosomes three-dimensional structure.

Ribosomes are made from dozens of proteins arranged on ribosomal RNA (rRNA). Ribosomes are made in the nucleus using RNA copies of the DNA we call rRNA.

In this image ribosomal RNA is shown in orange & proteins in purple.

Ribosomes

• Protein Construction: Ribosomes build proteins by adding amino acids to a growing protein chain as they read three-nucleotide sequences, or codons, on mRNA.

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• mRNA Decoding: Ribosomes translate the genetic information encoded in messenger RNA (mRNA).

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• tRNA Binding: Ribosomes have three binding sites for tRNA to create the protein assembly line:

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• the A (aminoacyl) site accepts the tRNA carrying the next amino acid to be added to the chain;
• the P (peptidyl) site holds the tRNA carrying the growing polypeptide chain; and
• the E (exit) site is where discharged tRNAs are released.

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• Peptide Bond Formation: Ribosomes catalyze the formation of peptide bonds between adjacent amino acids.

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Large Subunit

Small Subunit

Ribosome Structure

70s vs. 80s

80s ribosomes have:

• More proteins
• More rRNA

allowing them to make more complex proteins in eukaryotic cells.

The s, is a measure of

size & density, a “Svedberg unit,” .

Ribosome Structure

Ribosomes are like a conveyor belt that reads mRNA and builds proteins by linking amino acids. In between the large and small subunits we find have binding sites for the transporter tRNA (which brings proteins to be assembled) and the mRNA.

Large subunit

Small subunit

Ribosome Location & Function

In eukaryotes, ribosomes are either:

• “Free” = floating in the cytoplasm synthesizing polypeptide chains that will become proteins to be used within the cell.

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• “Bound” = linked to the Rough E.R. (endoplasmic reticulum), synthesizing polypeptides that will be secreted from the cell or become integral proteins in the cell membrane (B2.1.4).

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E.R. Structure - The Endoplasmic Reticulum is part of the ENDOMEMBRANE SYSTEM

The endomembrane system is a system of compartmentalized sacs within the eukaryotic cell (A2.2.6) that work together to modify, process and ship molecules within & out of the cell, particularly proteins.

Organelles of the endomembrane system work together to produce, transport and secrete proteins:

Each line represents a phospholipid bilayer (B1.1.12).

• The RER is a series of connected flattened membranous sacs that synthesize and transport polypeptides that will become proteins. It is continuous with the nuclear envelope, which surrounds the cell nucleus.

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Rough E.R.

Polypeptide

Rough E.R.

• Vesicles “bud off” and leave the RER destined for other locations in the cell, particularly the Golgi

Rough Endoplasmic Reticulum

Golgi Structure - The Golgi is part of the ENDOMEMBRANE SYSTEM

The endomembrane system is a system of compartmentalized sacs within the eukaryotic cell (A2.2.6) that work together to modify, process and ship molecules within & out of the cell, particularly proteins.

Organelles of the endomembrane system work together to produce, transport and secrete proteins:

Each line represents a phospholipid bilayer (B1.1.12).

The Golgi is composed of flattened membrane-enclosed sacs called cisternae.

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Polypeptides synthesized by RER ribosomes are transported in vesicles to the Golgi apparatus

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Vesicles fuse with the Golgi at its cis face which is convex usually faced “inward” toward nucleus.

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Then they are transported through the Golgi (modified, packaged etc.) and exit via vesicles budded from its concave trans face (exit face).

Golgi Apparatus Structure

Cis face

• “On this side”
• Faces inward
• Toward the E.R. & the nucleus

Trans face

• “On that side”
• Faces outward
• Toward the exterior of the cell

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Golgi Apparatus Structure

Within the Golgi cisternae, polypeptides are modified into their functional protein state (D1.2.18*). For example:

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• By adding a carbohydrate to make a glycoprotein (B2.1.9)
• By combining with other polypeptides to form the quaternary structure of a protein (B1.2.11)

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Examples of the many possible protein modifications may occur in the Golgi apparatus.

Golgi Apparatus Function

After being modified, the polypeptide is a now a functional protein. The trans face of the Golgi sorts, concentrates and packs proteins into vesicles that transport the protein to:

• Lysosomes or vacuoles for digestive enzymes used within the cell (B2.2.3)
• The plasma membrane for integral proteins within the plasma membrane (B2.1.4) such as pumps, channels, adhesion proteins or receptor proteins.
• The cell exterior for proteins leaving the cell, secreted via exocytosis such as protein hormones or neurotransmitters

Golgi Apparatus Function

Vesicle Structure - Vesicles are part of the ENDOMEMBRANE SYSTEM

The endomembrane system is a system of compartmentalized sacs within the eukaryotic cell (A2.2.6) that work together to modify, process and ship molecules within & out of the cell, particularly proteins.

Formation of Vesicles

Phospholipids can move within the bilayer (B2.1.1), making membranes in the cell flexible or “fluid.”

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This fluidity allows for constant formation of vesicles (esp. in the endomembrane system)

• From the plasma membrane
• in the ER
• in the Golgi

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A vesicle forms when the membrane bulges and pinches off.

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Formation of Vesicles

Clathrin is a protein that plays a major role in the formation of vesicles.

Clathrin creates a “coat” that helps the phospholipids create a rounded shape as the vesicle is forming.

Once the vesicle is formed, the clathrin coat is removed from the vesicle.

Clathrin Creates Vesicles

Bilayer Phospholipids

Clathrin

Clathrin proteins aggregating phospholipids to create and “bud” off a vesicle

Clathrin Creates Vesicles

Clathrin

Bilayer Phospholipids

Clathrin proteins aggregating phospholipids to create and “bud” off a vesicle

Movement of Vesicles

Once formed, vesicles are moved through the cell by motor proteins along the cytoskeleton “track”.

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Vesicle

Cytoskeleton

The “cargo” vesicle attaches to the motor protein. In addition to vesicles, motor proteins move chromosomes during mitosis and meiosis (D2.1.6).

Movement of Vesicles

Motor proteins are made of two proteins augmin (peach) & gamma-TuRC (Purple). That allow the protein to “walk” along the microtubules (teal & blue) of the cytoskeleton.

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Vesicle

Cytoskeleton

Transport Vesicles: transport proteins and lipids from one location to another within the cell.

• To the Golgi from the ER
• From the Golgi to lysosomes or vacuoles (for digestive enzymes used within the cell, B2.2.3)

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Vesicle Functions

Transport vesicles arriving at the Golgi can electron micrograph of a eukaryotic cell (A2.2.10)

Transport Vesicle

Secretory Vesicles: transport proteins and lipids from inside the cell to the the plasma membrane

• for integral proteins within the plasma membrane (B2.1.4) such as pumps, channels, adhesion proteins or receptor proteins.
• The cell exterior for proteins leaving the cell, secreted via exocytosis such as protein hormones or neurotransmitters

Vesicle Functions

Endocytic Vesicles: formed by invagination of the plasma membrane around an extracellular substance during endocytosis (B2.1.13*). Deliver the cargo to other organelles for further sorting or digestion.

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Vesicle Functions

• For example phagocytes engulfing pathogens as a mechanism of infection control (C3.2.5) form an endocytic vesicle called a phagosome.

Vesicle fusion is the merging of a vesicle with another organelle or with part of a cell membrane.

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This process adds phospholipids to the target structure, making it larger.

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Vesicle Fusion

Secretory vesicles add membrane to the existing cell membrane, making it grow. This occurs through fusion of the vesicles with the cell membrane and involves special proteins known as SNARE proteins

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The discovery of SNARE proteins earned Thomas Südhof, James E Rothman and Randy Schekman the Nobel Prize in Physiology or Medicine in 2013.

Vesicle Beauty

A synaptic vesicle about to exit a nerve cell (neuron).

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It is waiting to be released into the synapse, filled with neurotransmitters called acetylcholine (Ach).

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Various proteins, similar to clathrin, synaptobrevin (light blue spindle), Syntaxin (orange) & SNAP-25 (pink) team up to pull membranes together.

B2.2 - Organelles & Compartmentalization

B2.2 - Organelles & Compartmentalization

Connerly, P. L. How Do Proteins Move Through the Golgi Apparatus? Nature Education 3(9):60 (2010)

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Cooper GM. The Golgi Apparatus. The Cell: A Molecular Approach. 2nd edition. Sunderland (MA): Sinauer Associates (2000).