Biochemistry

Code:

EBE0205

Acronym:

BIOQ

Keywords
Classification	Keyword
OFICIAL	Basic Sciences

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	79	Syllabus	2	-	6	70	162

Teaching language

Suitable for English-speaking students

Objectives

 

The main objective of this curricular unit is the knowledge of basic concepts of structure and function of main classes of biological molecules and their involvement in the metabolic pathways in an integrated approach. 

At the end of this course the students should know the structure and function of different biologic molecules  and their metabolic fates as well as discuss the relations among different metabolic pathways.

Several metabolic situations involving integrated metabolism will be studied such as starvation / fasting, diabetes, physical exercise or ethanol metabolism.

Additionally the students will participate in laboratorial classes that allow them to acquire skills to perform current methodologies in biochemistry research.

At the end the students should be able to analyze experimental data from different biologic situations and integrate it in a metabolic  perspective identifying the  metabolomic pathways involved and its regulation in different cell systems.

Learning outcomes and competences

The syllabus of the course is designed to provide students with the fundamental knowledge to understand the functioning of the cell at the molecular level. This knowledge includes learning metabolic pathways in an integrated way. The methodology followed includes theoretical classes for the presentation of contents by the teacher and discussion of problems. Practical classes are also held being the the results presented and discussed in the form of a written report.

Working method

Presencial

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

NA

Program

THEORETICAL PRACTICAL CLASSES (TP)

I. Carbohydrate (CH) metabolism

1. Digestion and intestinal absorption of CH from the diet. Monosaccharide hydrolysis and absorption: main enzymes involved and transporters.
2. Glucose-6-P synthesis: hexokinase and glucokinase enzymes and regulatory mechanisms.
3. Glycolysis. Reactions and regulation of the metabolic pathway by allostery and hormonal regulation. ATP and NADH balance.
4. A [18F] - Fluorodeoxyglucose and positron emission tomography (PET).
5. Metabolism of Galactose and Fructose. Galactosemia, Frutosuria and hereditary fructose intolerance.
6. Gluconeogenesis. Cori and alanine-glucose cycles. Allosteric / hormonal regulation.
7. Glycogen - structure and properties. Glycogenesis and Glycogenolysis. Regulation mechanisms.
8. Pentose phosphate pathway. G-6-P dehydrogenase regulation.
9. Hormonal regulation. Signal transduction cascades. Secondary messengers and protein kinase A activation and calmodulin-dependent kinases. The insulin receptor.
10. Integration of CH metabolism. Type 1 and type 2 diabetes mellitus. Gestational diabetes. Insulinomas. The pyruvate dehydrogenase complex. Enzymes and cofactors. Allosteric and hormonal regulation.
11. The Krebs Cycle. Energy efficiency. Allosteric regulation and respiratory control. Amphibolic character. Oxidative phosphorylation. Chemosmotic mechanism - Inhibitors and uncouplers. Thermogenin (CPU) and heat production.

II. Lipid metabolism

1. Fatty acids: structure, nomenclature and properties. Digestion and absorption of lipids. Triglycerides as energy storage molecules. The role of bile acids. The chylomicrons and lipoprotein lipase. The fate of fatty acids and glycerol at the adipocyte. Adipocyte triglyceride synthesis.
2. Lipolysis. Hormone-sensitive lipase and perilipine - regulatory mechanisms. Serum albumin and transport of non-esterified fatty acids.
3. Fatty acid beta-oxidation (mitochondria). Beta-oxidation of very long chain fatty acids - peroxisomatic beta-oxidation.
4. Synthesis and energetic role of ketone bodies.
5. Synthesis of fatty acids. Fatty acid synthase: enzymatic activities and structural organization. Energy balance of glucose to palmitate conversion. Elongases and desaturases. The fate of newly synthesized fatty acids - role of hepatocyte and VLDL.
6. Cholesterol biosynthesis and regulation of HMG-CoA reductase.
7. Synthesis of bile acids. The enterohepatic circulation of bile acids.
8. Synthesis of cholesterol derivatives: (i) steroid hormones (cytochromes P-450, cellular signaling by steroid hormones); ii) Vitamin D - calcium regulation and cellular signaling.
10.Transport of lipids. Lipoproteins - chylomicras, VLDL, LDL and HDL. Hypercholesterolemia and atherosclerosis. Nutritional and pharmacological treatment.
11. Membrane lipids. Phospholipid synthesis. Inositol phospholipid signaling. Plasmalogen synthesis. Sphingolipid synthesis. Cell signaling by sphingolipids. Sphingolipid catabolism and lysosomal storage diseases.

III. Amino Acids and Proteins

1. Characterization of the 20 major amino acids.
2. Peptide bond formation. Different levels of protein structural organization: from primary structure to quaternary structure.
3. Fibrous proteins (eg collagen) and globular proteins (eg hemoglobin).
4. Structure and function of hemoglobin.

IV. Amino Acid Metabolism

1.Amino acids from the diet. Main reactions and enzymes involved in amino acid metabolism (transaminases, glutamate dehydrogenase, glutamine synthetase and glutaminase). Transport of nitrogen to the liver and kidneys. Alanine-glucose cycle. Urea cycle and its regulation.
2. Biosynthesis of nonessential amino acids.
3. Non-protein substances synthesized from amino acids and their functions: Glutathione; Melanin; Dopa, dopamine and catecholamines; Thyroid hormones; Serotonin; GABA and histamine; Nitric oxide; Heme group.
4. Amino acid catabolism: glucogenic and ketogenic amino acids; Relevant cofactors in amino acid metabolism: tetrahydrofolate and S-adenosylmethionine; vitamin B12 and folate cycle.

V. Nucleotide Metabolism

1. Purines and Pyrimidines: de novo synthesis and regulation.

LABORATORY PRACTICAL CLASSES

PL1- Introduction to practical works PL2-PL6. Brief presentation of PROTOCOLS and basic principles of the methods.

PL2- Fermentative and respiratory metabolism in yeast at different growth stages - fermentative and respiratory metabolism - glucose and ethanol dosing.

PL3 - Mitochondria and oxygen uptake in mouse liver mitochondrial preparations in the presence of different substrates, inhibitors and uncouplers of the respiratory chain.

PL4 - Oxidative stress and superoxide dismutases (SOD) activity in yeast at different growth stages and different stress conditions using native polyacrylamide gel electrophoresis.

PL5- Analysis of intracellular oxidation in yeast cells at different stages of culture growth by fluorescence microscopy using a reactive oxygen species sensitive probe (H2DCF-DA).

PL6-Cholesterol and Triglycerides dosing in fasting and post-meal human plasma samples using colorimetric methods.

PL7- Introduction to practical work PL8-PL11. Brief introduction to work on recombinant protein production and analysis

PL8 - Recombinant protein production and separation by ion exchange chromatography

PL9 - Protein quantification - Bradford Method

PL10 - Protein analysis by polyacrylamide gel electrophoresis

PL11 - Immunochemical Assays for Protein Analysis - WB

PL12 - General discussion about the works performed

Mandatory literature

Nelson David L.; Lehninger principles of biochemistry. ISBN: 978-1-4641-2611-6
Jeremy M. Berg; Biochemistry. ISBN: 978-1-4641-2610-9

Comments from the literature

Biochemistry Protocols Book - MIB Laboratory Classes, prepared by the UC lecturers in collaboration with the  graduated technician who supports the practical classes.

Teaching methods and learning activities

 Teaching methods are selected taking into account the number of students attending the UC. Therefore, lectures are offered where the content is presented and illustrated by power point presentations. During the presentation, questions are raised and the answers discussed by the students and teacher.

Besides, students have the opportunity to carry out laboratory practical classes where they perform experiments, in groups, that illustrate the theoretical contents learned. The results obtained from the experimental work are presented as a written report submitted to evaluation and discussed during tutorials. 

 

Evaluation Type

Distributed evaluation with final exam

Assessment Components

Designation	Weight (%)
Exame	80,00
Trabalho laboratorial	20,00
Total:	100,00

Amount of time allocated to each course unit

Designation	Time (hours)
Estudo autónomo	90,00
Frequência das aulas	42,00
Trabalho laboratorial	28,00
Total:	160,00

Eligibility for exams

The students need to be present at least at 75% of the laboratory classes and obtain a positive classification in the laboratry evaluation.

Calculation formula of final grade

final mark = theory final exam  x 0.8 + practical examx0.2

(Minimal classification in the written final exam for approval is 7)