CELB30090 Advanced Cell Biology

Academic Year 2019/2020

Cells are the basic functional units of eukaryotic organisms, and a deeper knowledge of their structure and organisation is an essential aspect of our wider understanding of health and disease. Drawing on information gained in earlier modules, this module integrates concepts in molecular biology, biochemistry and genetics to provide an understanding of processes and functions carried out in eukaryotic cells. Topics covered include membranes and compartmentalisation; roles of the nucleus, and transport between the cytoplasm and nucleus; functions and properties of the endoplasmic reticulum, Golgi complex, trans-Golgi network, endosomes, lysosomes, peroxisomes, mitochondria and primary cilia; roles played by cytoskeleton elements in transport and structure; specialisation of the cytoskeleton; and functions of the plasma membrane. Molecular detail of events such as cell division, programmed cell death, secretion, endocytosis, protein translocation, protein targeting, protein degradation, signalling, and regulation through the use of GTPases will also be given. Strong emphasis will also be paid to approaches using living cells; recent high-throughput post-genome cell biology methods; and how this knowledge is being utilised to understand disease.

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Curricular information is subject to change

Learning Outcomes:

On completion of this module, registrants will have a clear understanding of the basic structure and function of eukaryotic cells. This understanding will include the important role of subcellular compartmentalisation in achieving cellular efficiency, and how specific molecular events contribute to overall cell function. A clear understanding of key cell biology techniques, and how to apply these to decipher cell function, will also be gained.

Indicative Module Content:

The endomembrane system:
General introduction to the contribution of cell biology approaches within the arena of biological sciences. Overview of internal membranes in eukaryotic cells, the importance of subcellular architecture and introduction to internal transport and communication pathways. Introduction to key roles of the endoplasmic reticulum, Golgi complex, the endosomal-lysosomal system, and peroxisomes.

Vesicles and coats in membrane transport:
General concepts of transport between internal organelles, membrane budding, transport and fusion. Introduction to cytoplasmic coat proteins and their molecular composition and regulation. Form and function of the COPII coat, the COPI coat, the clathrin coat and retromer. Accessory molecules associated with membrane transport including Rab GTPases, tethers and SNAREs.

The cell surface:
Structure and function of the plasma membrane, including lipid and protein composition. Asymmetry of the plasma membrane and its importance in signalling. Mobility of lipids and proteins at the cell surface and the types, roles and molecular composition of cell-cell contact structures, including anchoring junctions, occluding junctions, channel forming junctions and tunnelling nanotubes.

The endocytic pathway:
Introduction to endocytosis and endocytic mechanisms, including phagocytosis, caveolin- and clathrin-mediated endocytosis. Molecular details of these processes including the protein composition of these endocytic structures and their importance. Entry into the endocytic pathway, including trafficking of LDL receptors, transferrin receptors, opioid receptors. Maturation of late endosomes, multivesicular bodies and transcytosis in polarised cells.

The endoplasmic reticulum - form and function:
Overview of the key roles of the endoplasmic reticulum (ER), including rough ER, smooth ER, and transitional ER. Molecular mechanisms of soluble and trans-membrane protein import into the ER, and the importance of the Sec61 translocon. Protein folding and glycosylation in the lumen of the ER, protein quality control and the ER associated degradation pathway for misfolded proteins, the proteasome. The unfolded protein response.

The secretory pathway:
Introduction to the secretory pathway and its organisation in eukaryotes. Transport between the ER and Golgi complex, recycling back to the ER, the KDEL system. Transport through the Golgi complex, including descriptions of the three proposed models. Transport from the trans-Golgi network to the lysosomal system. Introduction to regulated secretion.

Transport across biological membranes:
Principles of crossing biological membranes, transporters and channels, active and passive transport, ion gradients, ATP-driven pumps, ABC transporters. Transport between the cytoplasm and nucleus, the nuclear pore complex, role of Ran GTPase.

Cell Division - an overview:
Overview of the module, its organisation, content and assessment. An overview of the cell cycle, components of the cell cycle control system, intracellular control of cell cycle events – the role of cyclins, cyclin-dependent kinases (cdks) and Cdk inhibitory proteins. The cell cycle checkpoints.

Control of mitosis and cytokinesis:
Molecular mechanism of nuclear division (mitosis) and cytoplasmic division (cytokinesis). The role of microtubules in spindle assembly and function. The spindle assembly checkpoint.

Programmed cell death:
An introduction to different forms of Programmed Cell Death during growth and development of multicellular organisms. The role of the mitochondrion and endoplasmic reticulum during programmed cell death. The intrinsic and extrinsic cell death pathways.

Autophagy:
An introduction to autophagy - classification and regulation. The role of metabolic stress in autophagy induction. Cross-talk between autophagy and apoptosis. Autophagy and disease.

Cytoskeleton I - microtubules:
Introduction to the cytoskeleton in eukaryotic cells, including general properties and its role in cell stability and cell dynamics. Molecular composition of microtubules, microtubule dynamics and accessory proteins. Microtubule organisation and the centrosome. Motors of microtubules, including molecular details of dynein and kinesin.

Cytoskeleton II - intermediate filaments and actin:
Introduction to the cytoskeleton in eukaryotic cells, including general properties and its role in cell stability and cell dynamics. Molecular composition of intermediate filaments and their role in cells. Molecular composition of the actin cytoskeleton, actin binding proteins, and myosin motors. Molecular mechanism of actin nucleation and its role in cell motility. Importance and role of the Rho family of small GTPases in actin cytoskeleton regulation and remodelling.

Cytoskeleton III - Focal adhesions and the ECM:
Molecular composition of focal adhesions, linkage to internal cytoskeleton elements. Variety and role of integrins. The extracellular matrix (ECM) and its role in connective tissue. Composition of the ECM, hyaluronic acid, proteoglycans, collagens, and fibronectin. Assembly and processing of collagen. ECM degradation.

Extracellular vesicles:
Basic information about extracellular vesicles (EVs), exosomes and their definitions / nomenclature. Current knowledge of EV biogenesis, EV cargo as well as their purported release and uptake mechanisms. Relevance in human disease.

The cilium organelle: a case study of intracellular transport and membrane trafficking I:
Introduction to cilium structure/function in multiple cell types and organisms. Mechanistic basis of cilium formation from centriole-nucleated basal bodies and subsequent elongation via kinesin-2 and cytoplasmic dynein-driven intraflagellar transport.

The cilium organelle: a case study of intracellular transport and membrane trafficking II:
Outline of membrane transport to cilia, highlighting the role of various key small G-proteins and secretory/endocytic components. Description of key experimental models (e.g., photoreceptor cells) used to address ciliary membrane transport.

The cilium organelle: a case study of intracellular transport and membrane trafficking III:
Overview of transport defects associated with ciliary disease such as Bardet Biedl syndrome and retinitis pigmentosa.

Techniques I - Gene manipulation - overexpression and downregulation approaches:
Importance of gene manipulation techniques, principles of protein overexpression, downregulation and knock-out. Introduction of DNA / RNA / protein into cells via transfection, microinjection, electroporation and viral vectors. Use of RNA interference in cultured cells and whole organisms. Introduction to CRISPR/Cas9. Micro RNA regulation in cells and methodological approaches to utilise it.

Techniques II - Light microscopy, GFP and high-throughput imaging:
Brief intro to fluorescence light microscopy, differences between wide-field and confocal microscopes. Introduction to light microscopy techniques including time-lapse imaging. Use of fluorophores, GFP and its variants. High-throughput cell biology in the post-genome era. Workflow in high-throughput cell biology experiments. Key specific examples.



Student Effort Hours: 
Student Effort Type Hours
Lectures

20

Specified Learning Activities

20

Autonomous Student Learning

85

Total

125

Approaches to Teaching and Learning:
This module is taught through lectures and interactive discussion, supported by specific assignments. 
Requirements, Exclusions and Recommendations
Learning Recommendations:

Students will be expected to have a basic understanding of cell structure and function. Students should have taken modules that cover basic cell biology such as CELB20060 Principles of Cell & Molecular Biology.


Module Requisites and Incompatibles
Equivalents:
Cell Biology (Level 3) (CELB30070)

 
Assessment Strategy  
Description Timing Open Book Exam Component Scale Must Pass Component % of Final Grade
Assignment: Written work relating to concepts covered in the lectures. Varies over the Trimester n/a Graded No

25

Multiple Choice Questionnaire (Short): MCQs in lectures Varies over the Trimester n/a Graded No

10

Assignment: A series of problem-based exercises will be set. They will be based on the content given in the lectures, and students will be allowed access to their notes for the assessment. Week 12 n/a Graded No

40

Class Test: Class test Varies over the Trimester n/a Graded No

25


Carry forward of passed components
Yes
 
Remediation Type Remediation Timing
In-Module Resit Prior to relevant Programme Exam Board
Please see Student Jargon Buster for more information about remediation types and timing. 
Feedback Strategy/Strategies

• Feedback individually to students, on an activity or draft prior to summative assessment
• Group/class feedback, post-assessment

How will my Feedback be Delivered?

Not yet recorded.

Name Role
Assoc Professor Oliver Blacque Lecturer / Co-Lecturer
Assoc Professor Margaret McGee Lecturer / Co-Lecturer
Timetabling information is displayed only for guidance purposes, relates to the current Academic Year only and is subject to change.  
Spring
     
Lecture Offering 1 Week(s) - Spring: All Weeks Mon 09:00 - 09:50
Lecture Offering 1 Week(s) - Spring: All Weeks Wed 09:00 - 09:50
Spring