Week 9 lecture 3 - The endomembrane system

The Endomembrane System

The Nucleus: Overview

• Chromosomes are enclosed by a double membrane.
• Transport into and out of the nucleus occurs through nuclear pore complexes.
• Ribosomal RNA is processed and ribosomes are assembled within the nucleus.

Summary of the Nucleus Functions:

1. DNA storage.
2. Ribosomal production.
3. mRNA transcription.
4. DNA replication.
5. mRNA processing.

Nucleus Terminology

• Chromosome: A single DNA strand plus associated proteins; contains a significant portion of an organism's genetic material.
• Histones: Proteins that organize and pack DNA.
• Chromatin: The complex of DNA and histone proteins; chromosomes are made of chromatin.
• Nucleus: A large organelle in eukaryotic cells where DNA is stored.
• Nucleolus: A sub-section of the nucleus where ribosomes are made.
• Nucleoid: A region in prokaryotic cytoplasm where DNA is located.
• Plasmid: Small, extrachromosomal DNA in some bacteria.
• Plastid: Organelles in plant cells (e.g., chloroplasts, amyloplasts, chromoplasts).

Key Points About the Nucleus

• In eukaryotes, DNA wraps around histones and resides in the nucleus.
• A double membrane surrounds the nucleus.
• Nuclear pores facilitate transport in and out of the nucleus.
• Ribosomal RNA transcription and ribosome production occur in the nucleolus.
• The nucleus actively functions beyond just DNA storage.
• Bacteria have supercoiled chromosomes and plasmids without a nucleus.

Endomembrane System: Outline

1. What is the endomembrane system?
2. How are proteins trafficked around the cell?
3. Structure and function of the endoplasmic reticulum (ER).
4. Structure and function of the Golgi apparatus.
5. How are substances moved in and out of the cell (endo- and exo-cytosis)?
6. What are lysosomes?

What is the Endomembrane System?

• Endo- means within.
• A system of interconnected membranes within a cell facilitates material exchange directly or via vesicles.

Components:

• Nuclear envelope
• Endoplasmic reticulum
• Golgi apparatus
• Lysosomes and vacuoles
• Vesicles, endosomes
• Plasma membrane

Exclusions:

• Mitochondria
• Plastids (e.g., chloroplasts)
• Prokaryotic cells lack an endomembrane system.

Functions of the Endomembrane System

• Material trafficking
• Protein production
• Protein modification
• Lipid production
• Specific chemical reactions
• Molecule storage

Protein Trafficking

• How are proteins targeted to their correct locations?
• Examples of proteins that need trafficking:
  • Cytoplasmic enzyme (e.g., MAP kinase)
  • Plasma membrane protein (e.g., Na^+/K^+ transporter)
  • Secreted protein (e.g., insulin)
  • Nuclear protein (e.g., transcription factors)

Signal Peptides/Signal Sequences:

• Act like postcodes, directing proteins to specific locations in the cell.

Signal Sequences

• Strings of amino acids that act as targeting signals.
• Different signal sequences direct proteins to different locations.

Targeting Proteins to Cellular Compartments

• Two types of targeting to membrane-bound systems.

Targeting Proteins to Non-Endomembrane Compartments:

• Post-translational translocation:
  1. Protein translated entirely in the cytoplasm by a free ribosome.
  2. Signal sequence directs the protein to the appropriate compartment (nucleus, mitochondria, plastids).

Targeting Proteins to Endomembrane Compartments:

• Co-translational translocation:
  1. Protein initially translated by a free ribosome.
  2. The entire ribosome moves to the membrane, becoming a bound ribosome.
  3. Protein translocates across the membrane while being translated.
  • ER → Golgi, plasma membrane, lysosomes, secreted.

Endoplasmic Reticulum (ER): Structure and Function

• The ER has an internal compartment.
• Network structure maximizes the membrane's surface area.

Two Distinct Regions:

• Smooth ER
• Rough ER

Functions of Smooth ER

• Lipid synthesis (including steroids) e.g., in reproductive tissues
• Carbohydrate metabolism
• Detoxification of drugs and poisons e.g., in liver cells (hepatocytes)
• Calcium ion storage e.g., in muscle cells (myocytes)

Functions of Rough ER

• Site for translation of proteins destined for secretion or the plasma membrane.
• Produces lipids and new membranes.
• Sends proteins to the Golgi apparatus via vesicles.
• Adds carbohydrates to proteins (glycoproteins).

Glycoproteins

• Many proteins are modified in the ER by the addition of carbohydrates.

Protein Trafficking Roadmap

• The ER delivers proteins and other molecules to different parts of the cell via vesicles.

Vesicular Transport

• Vesicles are small, membrane-bound organelles that shuttle between other organelles or between an organelle and the plasma membrane.

Golgi Apparatus: Structure and Function

• The Golgi apparatus processes proteins and other molecules after the ER.
• It acts as the cell's “shipping and receiving center.”

Golgi Apparatus - Structure

• Collections of disc-shaped, flat membranes stacked on each other.
• Has polarity: material enters from the cis side and exits from the trans side.

Moving Material Through the Golgi Apparatus

• Two models explain the movement of material:
  1. Proteins move through the Golgi, with separate vesicles transporting material in both forward and reverse directions, cisternae remain static and return vesicles ensure enzyme retention.
  2. Individual cisternae mature, transporting material in the forward direction, taking proteins with them, and also use return vesicles for enzyme retention.

Functions of the Golgi Apparatus

1. Sending material (proteins, lipids) to various locations:
   • Plasma membrane (exocytosis).
   • Returned to the ER.
   • Shipped to organelles (lysosomes, vacuoles).
2. Protein processing:
   • Carbohydrate modification.
3. Carbohydrate manufacturing:
   • Some plant cell wall components.

Golgi Apparatus and Vesicles

• Vesicles shuttle from the Golgi to other organelles and the plasma membrane.
• Material can move in both directions.

Exocytosis and Endocytosis

• Exocytosis delivers:
  • Protein and carbohydrate contents to the outside of the cell.
  • Lipids to the plasma membrane.
  • Membrane proteins to the plasma membrane.
• Endocytosis retrieves:
  • Contents of the vesicle, including solutes and nutrients.
  • Lipids from the plasma membrane.
  • Membrane proteins.

Different Forms of Endocytosis

• Phagocytosis
• Pinocytosis
• Receptor-Mediated Endocytosis

Lysosomes

• Compartments where digestion (lysis) takes place.
• Contain proteases, nucleases, glycosidases, lipases, etc.

Lysosome Functions

• Unicellular eukaryotes eat via phagocytosis.
• Food vacuoles fuse with lysosomes.
• Macrophages (white blood cells) remove pathogens by phagocytosis.
• Old cell material (proteins, carbs, lipids) is broken down to retrieve nutrients.

Key Terminology

• Signal sequence/peptide: A short string of amino acids that localizes a protein to its correct cell compartment.
• Cisternae: Sacs that make up the ER or Golgi apparatus.
• ER Lumen: The liquid inside the ER.
• Glycoproteins: Proteins with sugars added.
• Vesicle: A small membrane bubble for shipping components around the cell.
• Exocytosis: Export of material out of cells via vesicles.
• Endocytosis: Intake of material into the cell via vesicles.

Key points

• Proteins are moved through the cell via signal sequences. Proteins translated in the cytosol enter via post-translational translocation, and those translated into a membrane enter via co-translational translocation. Proteins destined for the endomembrane system are synthesised in the ER. Endoplasmic reticulum (ER) functions producing transmembrane and secreted proteins, in modifying proteins and delivering proteins and other molecules to different parts of the cell. The Golgi apparatus as a shipping and receiving centre, and also functions in protein modification. Material leaves the cell via exocytosis and come into the cell via endocytosis.