Protein Structure and Function

Code:

L.BIO047

Acronym:

EFP

Keywords
Classification	Keyword
OFICIAL	Molecular Bioengineering

Instance: 2024/2025 - 2S (of 10-02-2025 to 30-05-2025)

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

Cycles of Study/Courses

Acronym	No. of Students	Study Plan	Curricular Years	Credits UCN	Credits ECTS	Contact hours	Total Time
L.BIO	22	Syllabus	3	-	6	39	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

A. Study of proteins structure and function in vitro and in silico

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. 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. 

B. The life cycle of proteins in the cell : i) syntheis and folding; ii) modification; iii) targeting; iv) transport; and v) degradation.

1. Folding of proteins  and proteostasis  - protein quality control systems (PQC).ER Assisted Folding vs ER Assisted Degradation (ERAD). Proteostasis mechanisms: unfolded protein response (UPR), heat shock response (HSR), ubiquitin-proteasome system (UPS).Formation of protein complexes. Chaperone assisted folding (HSP70-like, HSP90-like, Hsp40, calreticulin / calnexin)
2. Post-translation protein modifications (PTMs): disulfide bonds; N-linked glycosylation; oxidoreductases (PDI or ERp57); oligosacaryltransferases (OST); addition of GPI (glycosylphosphatidylinositol) anchors.
3. 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). 
4. 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.
5. Autophagy. Proteins and complexes involved in autophagy. Selective autophagy and receptors. Autophagosome biogenesis. Techniques used to study autophagy.
6. Intrinsically Disordered Proteins / Regions (IDPs).

C. Diseases associated with protein aggregation


1. Diseases associated with protein misfolding  neurodegenerative diseases od aggregation. Some examples: Parkinson's disease (PD), Huntington's disease and spinocerebellar ataxias, Alzheimer's disease..
Modulators of amyloid formation.

2. Transthyretin (TTR) amyloidoses. Genetic and phenotypic characteristics.  TTR structure and function. Molecular and cellular mechanisms of disease and biomarkers. Determination of  therapeutic targets: i) TTR tetrameric structure stabilizers. Evaluation of their therapeutic potential in vitro and in vivo in animal models. ii) TTR Proteolysis - 
modulation of the proteolytic activity of serine proteases.
- Structure-based drug design; Repositioning of drugs.
Study of different therapeutic approaches through biomarkers evaluation: ER stress, oxidative stress, apoptosis, extracellular matrix.

3. Alzheimer Disease (AD). Clinical characterization. Brain alterations and AD progression. Histopathologic lesions in AD- senile plaques and nerofibrilary tangles. Genetic heterogeneity in AD. Impact of ApoE isoforms in AD -structure and function relationship. Processing of the. precursor amyloid protein  and production of Abeta peptide (APP) Effect of mutations in Abeta processing  - amyloidogenic and non-amyloidogenic pathway. Cellular pathways and mechanisms affected by Abeta. Mechanisms of Abeta elimination. Blood brain barrier (BBB) and Abeta elimination. Disfunction of BBB in AD. Pathologic angionesis in AD - structural alterations.

4. Models to study neurodegenerative diseases. Fundamentals of the use animal models, different types of models; advantages and limitations. Models in AD, Parkinson, ALS and FAP. Rodent models: gentic and nongenétic. Cellular models, genetic and non-genetic. C. elegans models. Drosophila melanogaster. In vitro models of the BBB.

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.)