Protein Chemistry, 12 credits

Proteinkemi, 12 hp

NKED15

The course is disused. Offered for the last time Spring semester 2022. Replaced by NKED27.

Main field of study

Chemical Biology Chemistry

Course level

Second cycle

Course type

Programme course

Examiner

Lars-Göran Mårtensson

Director of studies or equivalent

Magdalena Svensson

Education components

Preliminary scheduled hours: 55 h
Recommended self-study hours: 265 h

Available for exchange students

Yes
ECV = Elective / Compulsory / Voluntary
Course offered for Semester Period Timetable module Language Campus ECV
6KBIO Biology, Bachelor's Programme 6 (Spring 2020) 1 1+3 English Linköping, Valla E
6KKEB Chemical Biology, Bachelor's Programme 6 (Spring 2020) 1 1+3 English Linköping, Valla C
6KKEM Chemistry - Molecular Design, Bachelor's Programme 6 (Spring 2020) 1 1+3 English Linköping, Valla E
6MPRO Protein Science, Master's Programme (External) 2 (Spring 2020) 1 1+3 English Linköping, Valla C

Main field of study

Chemical Biology, Chemistry

Course level

Second cycle

Advancement level

A1X

Course offered for

  • Master's Programme in Protein Science
  • Biology, Bachelor's Programme
  • Chemical Biology, Bachelor's Programme
  • Chemistry - Molecular Design, Bachelor's Programme

Entry requirements

Note: Admission requirements for non-programme students usually also include admission requirements for the programme and threshold requirements for progression within the programme, or corresponding.

Prerequisites

General Chemistry, Organic Chemistry, Biochemistry

Intended learning outcomes

The objectives of the course is to provide comprehensive knowledge in the following areas:
Protein chemistry, protein engineering, structure and function relationships, physicochemical properties of proteins and methodologies for characterization of proteins. After studies well learned the student will have proficiency to:

  • Identify structure motifs and from this draw conclusions regarding the structure and function of proteins.
  • Search for information from various data bases to visualize protein structures and compare amino acid sequences.
  • Draw conclusions about protein dynamics, structure and function from detailed chemical and physical properties.
  • Comprehend the fundamental mechanisms of protein folding and to have a deeper understanding of the factors determining the stability of a protein.
  • Define scientific problems within this area that can be tackled and solved by experiments.
  • Adopt a reflecting, scientific attitude to the theories and obtained experimental results.
  • Work in a group in a project-oriented way in the laboratory.

Course content

Theoretical part: Different structure motifs of proteins. Multifunctional enzymes, membrane proteins, prediction of protein structures. Studies of physico-chemical properties of proteins and methodology for studies of these properties: Chemical characteristics of polypeptides, protein engineering, physical interactions determining the properties of proteins, role of hydrophobic interaction, conformation flexibility, protein stability, mechanisms of protein folding, interaction with other proteins, enzyme catalysis.
Project part: Studies of physico-chemical properties of proteins and methodology for studies of these properties. Methodology used for these studies is biophysical methods such as fluorescence spectroscopy, circular dichroism spectroscopy (CD) and calorimetry (ITC). Sequence analysis and structure modeling are used for result analysis.

Teaching and working methods

The course is divided into a theoretical and a project part in order to give opportunity to deeper and more intergrated studies.The theory is presented and treated at lectures and lessons. Three-dimensional structures of proteins and computer simulations are performed in smaller groups. During the project part the students work with genetically mutated proteins cloned in bacteria. The origin of the mutated protein can be proteins that have been mutated by the students in an earlier course in gene technology or can be provided by the research group. The protein variants are characterized. Starting with a project plan the students perform the detail plans for the experimental work. This planning process will proceed interactively through meetings between the groups and the teacher/lab.assistant. The students should then independently evaluate their experimental results. The results of the experimental work is presented in a written report in enlish.

Examination

PRA1Project work6 creditsU, G
TEN1Written examination6 creditsU, 3, 4, 5
The exercises of the written examination and the test elucidate how well the student perform the the demands of the course.

Grades

Four-grade scale, LiU, U, 3, 4, 5

Other information

About teaching and examination language

The teaching language is presented in the Overview tab for each course. The examination language relates to the teaching language as follows: 

  • If teaching language is Swedish, the course as a whole or in large parts, is taught in Swedish. Please note that although teaching language is Swedish, parts of the course could be given in English. Examination language is Swedish. 
  • If teaching language is Swedish/English, the course as a whole will be taught in English if students without prior knowledge of the Swedish language participate. Examination language is Swedish or English (depending on teaching language). 
  • If teaching language is English, the course as a whole is taught in English. Examination language is English. 

Other

The course is conducted in a manner where both men's and women's experience and knowledge are made visible and developed. 

The planning and implementation of a course should correspond to the course syllabus. The course evaluation should therefore be conducted with the course syllabus as a starting point.  

Department

Institutionen för fysik, kemi och biologi

Director of Studies or equivalent

Magdalena Svensson

Examiner

Lars-Göran Mårtensson

Education components

Preliminary scheduled hours: 55 h
Recommended self-study hours: 265 h

Course literature

David Whitford, Proteins Structure and Function, Wiley. Projektbeskrivning från institutionen.
Code Name Scope Grading scale
PRA1 Project work 6 credits U, G
TEN1 Written examination 6 credits U, 3, 4, 5
The exercises of the written examination and the test elucidate how well the student perform the the demands of the course.

Course syllabus

A syllabus must be established for each course. The syllabus specifies the aim and contents of the course, and the prior knowledge that a student must have in order to be able to benefit from the course.

Timetabling

Courses are timetabled after a decision has been made for this course concerning its assignment to a timetable module. 

Interrupting a course

The vice-chancellor’s decision concerning regulations for registration, deregistration and reporting results (Dnr LiU-2015-01241) states that interruptions in study are to be recorded in Ladok. Thus, all students who do not participate in a course for which they have registered must record the interruption, such that the registration on the course can be removed. Deregistration from a course is carried out using a web-based form: https://www.lith.liu.se/for-studenter/kurskomplettering?l=en. 

Cancelled courses

Courses with few participants (fewer than 10) may be cancelled or organised in a manner that differs from that stated in the course syllabus. The Dean is to deliberate and decide whether a course is to be cancelled or changed from the course syllabus. 

Guidelines relating to examinations and examiners 

For details, see Guidelines for education and examination for first-cycle and second-cycle education at Linköping University, http://styrdokument.liu.se/Regelsamling/VisaBeslut/917592.

An examiner must be employed as a teacher at LiU according to the LiU Regulations for Appointments (https://styrdokument.liu.se/Regelsamling/VisaBeslut/622784). For courses in second-cycle, the following teachers can be appointed as examiner: Professor (including Adjunct and Visiting Professor), Associate Professor (including Adjunct), Senior Lecturer (including Adjunct and Visiting Senior Lecturer), Research Fellow, or Postdoc. For courses in first-cycle, Assistant Lecturer (including Adjunct and Visiting Assistant Lecturer) can also be appointed as examiner in addition to those listed for second-cycle courses. In exceptional cases, a Part-time Lecturer can also be appointed as an examiner at both first- and second cycle, see Delegation of authority for the Board of Faculty of Science and Engineering.

Forms of examination

Examination

Written and oral examinations are held at least three times a year: once immediately after the end of the course, once in August, and once (usually) in one of the re-examination periods. Examinations held at other times are to follow a decision of the board of studies.

Principles for examination scheduling for courses that follow the study periods:

  • courses given in VT1 are examined for the first time in March, with re-examination in June and August
  • courses given in VT2 are examined for the first time in May, with re-examination in August and October
  • courses given in HT1 are examined for the first time in October, with re-examination in January and August
  • courses given in HT2 are examined for the first time in January, with re-examination in March and in August.

The examination schedule is based on the structure of timetable modules, but there may be deviations from this, mainly in the case of courses that are studied and examined for several programmes and in lower grades (i.e. 1 and 2). 

Examinations for courses that the board of studies has decided are to be held in alternate years are held three times during the school year in which the course is given according to the principles stated above.

Examinations for courses that are cancelled or rescheduled such that they are not given in one or several years are held three times during the year that immediately follows the course, with examination scheduling that corresponds to the scheduling that was in force before the course was cancelled or rescheduled.

When a course is given for the last time, the regular examination and two re-examinations will be offered. Thereafter, examinations are phased out by offering three examinations during the following academic year at the same times as the examinations in any substitute course. If there is no substitute course, three examinations will be offered during re-examination periods during the following academic year. Other examination times are decided by the board of studies. In all cases above, the examination is also offered one more time during the academic year after the following, unless the board of studies decides otherwise.

If a course is given during several periods of the year (for programmes, or on different occasions for different programmes) the board or boards of studies determine together the scheduling and frequency of re-examination occasions.

Registration for examination

In order to take an examination, a student must register in advance at the Student Portal during the registration period, which opens 30 days before the date of the examination and closes 10 days before it. Candidates are informed of the location of the examination by email, four days in advance. Students who have not registered for an examination run the risk of being refused admittance to the examination, if space is not available.

Symbols used in the examination registration system:

  ** denotes that the examination is being given for the penultimate time.

  * denotes that the examination is being given for the last time.

Code of conduct for students during examinations

Details are given in a decision in the university’s rule book: http://styrdokument.liu.se/Regelsamling/VisaBeslut/622682.

Retakes for higher grade

Students at the Institute of Technology at LiU have the right to retake written examinations and computer-based examinations in an attempt to achieve a higher grade. This is valid for all examination components with code “TEN” and "DAT". The same right may not be exercised for other examination components, unless otherwise specified in the course syllabus.

A retake is not possible on courses that are included in an issued degree diploma. 

Retakes of other forms of examination

Regulations concerning retakes of other forms of examination than written examinations and computer-based examinations are given in the LiU guidelines for examinations and examiners, http://styrdokument.liu.se/Regelsamling/VisaBeslut/917592.

Plagiarism

For examinations that involve the writing of reports, in cases in which it can be assumed that the student has had access to other sources (such as during project work, writing essays, etc.), the material submitted must be prepared in accordance with principles for acceptable practice when referring to sources (references or quotations for which the source is specified) when the text, images, ideas, data, etc. of other people are used. It is also to be made clear whether the author has reused his or her own text, images, ideas, data, etc. from previous examinations, such as degree projects, project reports, etc. (this is sometimes known as “self-plagiarism”).

A failure to specify such sources may be regarded as attempted deception during examination.

Attempts to cheat

In the event of a suspected attempt by a student to cheat during an examination, or when study performance is to be assessed as specified in Chapter 10 of the Higher Education Ordinance, the examiner is to report this to the disciplinary board of the university. Possible consequences for the student are suspension from study and a formal warning. More information is available at https://www.student.liu.se/studenttjanster/lagar-regler-rattigheter?l=en.

Grades

The grades that are preferably to be used are Fail (U), Pass (3), Pass not without distinction (4) and Pass with distinction (5). 

  1. Grades U, 3, 4, 5 are to be awarded for courses that have written examinations.
  2. Grades Fail (U) and Pass (G) may be awarded for courses with a large degree of practical components such as laboratory work, project work and group work.
  3. Grades Fail (U) and Pass (G) are to be used for degree projects and other independent work.

Examination components

  1. Grades U, 3, 4, 5 are to be awarded for written examinations (TEN).
  2. Examination components for which the grades Fail (U) and Pass (G) may be awarded are laboratory work (LAB), project work (PRA), preparatory written examination (KTR), oral examination (MUN), computer-based examination (DAT), home assignment (HEM), and assignment (UPG).
  3. Students receive grades either Fail (U) or Pass (G) for other examination components in which the examination criteria are satisfied principally through active attendance such as other examination (ANN), tutorial group (BAS) or examination item (MOM).
  4. Grades Fail (U) and Pass (G) are to be used for the examination components Opposition (OPPO) and Attendance at thesis presentation (AUSK) (i.e. part of the degree project).

For mandatory components, the following applies: If special circumstances prevail, and if it is possible with consideration of the nature of the compulsory component, the examiner may decide to replace the compulsory component with another equivalent component. (In accordance with the LiU Guidelines for education and examination for first-cycle and second-cycle education at Linköping University, http://styrdokument.liu.se/Regelsamling/VisaBeslut/917592). 

For written examinations, the following applies: If the LiU coordinator for students with disabilities has granted a student the right to an adapted examination for a written examination in an examination hall, the student has the right to it. If the coordinator has instead recommended for the student an adapted examination or alternative form of examination, the examiner may grant this if the examiner assesses that it is possible, based on consideration of the course objectives. (In accordance with the LiU Guidelines for education and examination for first-cycle and second-cycle education at Linköping University, http://styrdokument.liu.se/Regelsamling/VisaBeslut/917592).

The examination results for a student are reported at the relevant department.

Regulations (apply to LiU in its entirety)

The university is a government agency whose operations are regulated by legislation and ordinances, which include the Higher Education Act and the Higher Education Ordinance. In addition to legislation and ordinances, operations are subject to several policy documents. The Linköping University rule book collects currently valid decisions of a regulatory nature taken by the university board, the vice-chancellor and faculty/department boards.

LiU’s rule book for education at first-cycle and second-cycle levels is available at http://styrdokument.liu.se/Regelsamling/Innehall/Utbildning_pa_grund-_och_avancerad_niva. 

David Whitford, Proteins Structure and Function, Wiley. Projektbeskrivning från institutionen.

Note: The course matrix might contain more information in Swedish.

I = Introduce, U = Teach, A = Utilize
I U A Modules Comment
1. DISCIPLINARY KNOWLEDGE AND REASONING
1.1 Knowledge of underlying mathematics and science (G1X level)
X
TEN1

                            
1.2 Fundamental engineering knowledge (G1X level)
X
TEN1

                            
1.3 Further knowledge, methods, and tools in one or several subjects in engineering or natural science (G2X level)
X
TEN1

                            
1.4 Advanced knowledge, methods, and tools in one or several subjects in engineering or natural sciences (A1X level)
X
PRA1
TEN1

                            
1.5 Insight into current research and development work
X
PRA1

                            
2. PERSONAL AND PROFESSIONAL SKILLS AND ATTRIBUTES
2.1 Analytical reasoning and problem solving
X
TEN1

                            
2.2 Experimentation, investigation, and knowledge discovery
X
TEN1

                            
2.3 System thinking
X
TEN1

                            
2.4 Attitudes, thought, and learning
X
TEN1

                            
2.5 Ethics, equity, and other responsibilities
X
TEN1

                            
3. INTERPERSONAL SKILLS: TEAMWORK AND COMMUNICATION
3.1 Teamwork
X
PRA1

                            
3.2 Communications
X
PRA1

                            
3.3 Communication in foreign languages
X
PRA1

                            
4. CONCEIVING, DESIGNING, IMPLEMENTING AND OPERATING SYSTEMS IN THE ENTERPRISE, SOCIETAL AND ENVIRONMENTAL CONTEXT
4.1 External, societal, and environmental context
X
PRA1

                            
4.2 Enterprise and business context

                            
4.3 Conceiving, system engineering and management

                            
4.4 Designing
X
PRA1

                            
4.5 Implementing
PRA1

                            
4.6 Operating

                            
5. PLANNING, EXECUTION AND PRESENTATION OF RESEARCH DEVELOPMENT PROJECTS WITH RESPECT TO SCIENTIFIC AND SOCIETAL NEEDS AND REQUIREMENTS
5.1 Societal conditions, including economic, social, and ecological aspects of sustainable development for knowledge development

                            
5.2 Economic conditions for knowledge development

                            
5.3 Identification of needs, structuring and planning of research or development projects
X
PRA1

                            
5.4 Execution of research or development projects
X
PRA1

                            
5.5 Presentation and evaluation of research or development projects
X
PRA1

                            

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