Structure and Function of Proteins

Code:

EBE0073

Acronym:

EFPR

Keywords
Classification	Keyword
OFICIAL	Molecular Biotechnology

Instance: 2020/2021 - 2S

Active?	Yes
Responsible unit:	Molecular Biology
Course/CS Responsible:	Master in Bioengineering

Cycles of Study/Courses

Acronym	No. of Students	Study Plan	Curricular Years	Credits UCN	Credits ECTS	Contact hours	Total Time
MIB	37	Syllabus	3	-	6	42	162

Teaching language

Suitable for English-speaking students

Objectives

Students should acquire advanced knowledge in Protein Structure and Function.

Students should acquire the necessary skills to analyze and study problems related to protein structure and key processing steps, in particular: folding, post-translational modification, targeting and protein transport, secretion and degradation at the cellular level. . The student should also acquire knowledge about the most common techniques to study this problem.

Learning outcomes and competences

The aim is to provide students advanced skills to analyze and solve problems centered on the functional/structural relationships in proteins. These relationships will be addressed using as examples proteins involved in central pathways of human biology, in health and disease and biotechnology contexts.

Working method

Presencial

Pre-requirements (prior knowledge) and co-requirements (common knowledge)

NA

Program

 PROGRAM

1. Characterization of protein structure. From primary to quaternary structure. Analysis of the primary structure in silico (programs and objectives) - structural domains of interaction with other proteins.
2. Energy and folding kinetics (protein stability). Interactions that contribute to maintain the structure. Motifs, domains, modular architecture. Soluble proteins and membrane proteins.
3. Common protein analysis techniques: Electrophoresis, isoelectric focusing. Protein detection methods. Western blotting. Polyclonal antibodies (how they are produced and how they are used).
4. Identification of stable protein complexes: - the Stokes radius, the sedimentation coefficient and the Siegel & Monty method; co-immunoprecipitations. Methods for identifying transient interactions: - yeast 2-hybrid system, "pull-down assays".
5. Intrinsically Disordered Proteins / Regions (IDPs).
6. Protein life cycle: Synthesis, folding, modification, targeting, transport and degradation.
7. Folding of proteins in the endoplasmic reticulum (RE). Post-translation protein modifications (PTMs): disulfide bonds; N-linked glycosylation; oxidoreductases (PDI or ERp57); oligosacaryltransferases (OST); addition of GPI (glycosylphosphatidylinositol) anchors. Formation of protein complexes. Chaperone assisted folding (HSP70-like, HSP90-like, Hsp40, calreticulin / calnexin).
8. Intracellular protein targeting: signal sequences, organelle specific receptors and soluble targeting factors. Channels of translocation mediating membrane transport or anchoring in the membrane of the endoplasmic reticulum (ER). 
9. Protein Folding and Proteostasis. ER Assisted Folding vs ER Assisted Degradation (ERAD). Proteostasis mechanisms: unfolded protein response (UPR), heat shock response (HSR), ubiquitin-proteasome system (UPS), ER-associated degradation system (ERAD). Protein Quality Control System (PQC) in ER.
10. Vesicular transport. Protein secretion. AAA + ATPases (ATPases associated with diverse cellular activities). Structure and function of nanomachines: AAA family ATPases (ATPases associated with diverse cellular activities) as an example.
11. Mitochondrial proteins: encoded by mitochondrial DNA and nuclear DNA. Mitochondrial protein import machinery. Processing and quality control mechanisms in mitochondria. Contact regions of mitochondria with other organelles. SNARE proteins.
12. Pathways of protein secretion. SRP (signal recognition particle), SRP receptor (SR), Sec61 complex and signal peptidase.
13. Autophagy. Proteins and complexes involved in autophagy. Selective autophagy and receptors. Autophagosome biogenesis. Techniques used to study autophagy.
14. Diseases associated with protein misfolding. Amyloidoses and modulators of amyloid formation. Some examples: Parkinson's disease (PD), Huntington's disease and spinocerebellar ataxias, Alzheimer's disease.
15. Transthyretin (TTR) amyloidoses. Cellular mechanisms of toxicity and associated biomarkers. Therapeutic approaches in TTR amyloidoses: - Structure-based drug design; Repositioning of drugs.
16. Structure / function of enzymes with potential for bioremediation. Glyphosate toxicity, biosynthesis and enzymes involved in the process. Characterization of the enzyme responsible for the first step of molinate degradation, mutations and immobilization techniques in the implementation of bioremediation processes. 

Mandatory literature

Bruce Alberts; Molecular biology of the cell. ISBN: 978-0-8153-4464-3

Comments from the literature

All of the topics addressed in this course have a very specific bibliography (scientific papers). All the papers studied in this course will be provided to the student through the Sigarra interface

Any recent textbook on Molecular and Cellular Biology may also be used with the purpose of helping the student acquiring a general perspective on a given topic.

Teaching methods and learning activities

Given that the main objective of the curricular unit (UC) is the learning of specific concepts of the scientific area of ​​the UC, the methodology used will be centered on the theoretical exposition of the concepts accompanied by the resolution of examples and short demonstrations, providing students to internalize and understand the physical, chemical and biological phenomena involved in the execution of a set of works while stimulating critical thinking, research and group dynamics. In the training process, the student will participate in lectures and perform group work (3-4 students) presenting orally, with audiovisual support. These oral presentations (seminars) are based on the critical analysis and discussion of previously selected scientific articles from international journals.

keywords

Natural sciences > Biological sciences > Biology > Molecular biology
Natural sciences > Biological sciences > Biology > Structural biology
Natural sciences > Biological sciences > Biology > Cell biology

Evaluation Type

Distributed evaluation with final exam

Assessment Components

Designation	Weight (%)
Exame	75,00
Apresentação/discussão de um trabalho científico	25,00
Total:	100,00

Amount of time allocated to each course unit

Designation	Time (hours)
Apresentação/discussão de um trabalho científico	1,00
Estudo autónomo	119,00
Frequência das aulas	42,00
Total:	162,00

Eligibility for exams

As per the UP regulation.

Calculation formula of final grade

Students are evaluated by

- Final written exam (15 points). A minimal grade of 9,5 points in 20 is required.

- Presentation and discussion of a scientific paper on a selected topic (5 points max.)