Protein Chemistry, 15 credits

Proteinkemi, 15 hp

NKED27

Main field of study

Chemical Biology

Course level

Second cycle

Course type

Programme course

Examiner

Lars-Göran Mårtensson

Director of studies or equivalent

Magdalena Svensson

Education components

Preliminary scheduled hours: 89 h
Recommended self-study hours: 311 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 2024) 1 1+2+3 English Linköping, Valla E
6KKEB Chemical Biology, Bachelor's Programme 6 (Spring 2024) 1 1+2+3 English Linköping, Valla C
6KKEM Chemistry, Bachelor's Programme 6 (Spring 2024) 1 1+2+3 English Linköping, Valla E
6MPRO Protein Science, Master's Programme (External) 2 (Spring 2024) 1 1+2+3 English Linköping, Valla C

Main field of study

Chemical Biology

Course level

Second cycle

Advancement level

A1N

Specific information

This course cannot be included in the same degree as NKED15 or TFKE54. 

Course offered for

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

Prerequisites

General Chemistry, Organic Chemistry, Biochemistry or equivalent. 

Intended learning outcomes

The course aims to provide in-depth knowledge in the following areas: The theoretical part deals with protein engineering, structural-functional relationships, the biophysical chemical properties of proteins and methodology for characterization of proteins. The experimental part deals with the expression of cloned proteins and methodology for purification of proteins as well as characterization of these proteins.

After the course, the student is expected to be able to

Theoretical part:

  • Identify how proteins are structured
  • Use information from different databases to compare amino acid sequences and based on that make predictions related to the biophysical properties of the protein
  • Use biophysical measurement data for characterization of proteins

Experimental part:

  • Produce and purify cloned proteins
  • Formulate problems in the area, which can be answered with experimental methodology
  • Work in groups in project form in the laboratory
  • Have a reflective, scientific approach to theories and experimental data

Course content

In the theoretical part, different structural motifs of proteins are treated, such as alpha domain structures, alpha/beta structures, antiparallel beta structures, multifunctional enzymes, membrane proteins,  prediction of protein structures. Furthermore, the course deals with biophysical properties of proteins and methodology for studies of these: chemical properties of polypeptides, protein engineering, physical interactions that determine properties of proteins, i.e., the role of the hydrophobic interaction, the protein structure flexibility, protein stability, protein folding mechanisms, interaction with other molecules, enzyme catalysis.

The experimental part contains protein expression, protein purification, biophysical properties of proteins and methodology for studies of these. Biophysical measurement methods such as fluorescence spectroscopy, circular dichroism (CD) and calorimetry (ITC) are used. Furthermore, sequence analysis and structural modeling are used for analysis of results.

Teaching and working methods

The course is divided into different theory and project blocks to provide an opportunity for more in-depth and coherent studies of different sections. Theory teaching takes place in lectures and lessons. In lessons, 3-dimensional structures are studied of proteins as well as computer simulation of various structures. 

During the project part, genetically mutated human proteins, cloned into bacteria, are expressed and purified. In the characterization of the mutated protein variants, student groups plan their experiments in detail, based on a project description. This planning process takes place interactively through meetings between the groups and teachers. The groups will independently evaluate their measurement results. Obtained results are presented in a report written in English.

Examination

PRA1Project work6 creditsU, G
DIT1Digital examination6 creditsU, 3, 4, 5
LAB1Protein purification3 creditsU, G

For grade 4, it is required that the goals for grade 3 have been achieved and the main part of the goals for grade 5. 

The course grade is the grade on DIT1. 

Grades for examination modules are decided in accordance with the assessment criteria presented at the start 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 could be given in Swedish, or partly in English. Examination language is Swedish, but parts of the examination can be in English.
  • If teaching language is “English”, the course as a whole is taught in English. Examination language is English.
  • 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.

Other

The course is conducted in such a way that there are equal opportunities with regard to sex, transgender identity or expression, ethnicity, religion or other belief, disability, sexual orientation and age.

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. 

The course is campus-based at the location specified for the course, unless otherwise stated under “Teaching and working methods”. Please note, in a campus-based course occasional remote sessions could be included.  

Department

Institutionen för fysik, kemi och biologi
Code Name Scope Grading scale
PRA1 Project work 6 credits U, G
DIT1 Digital examination 6 credits U, 3, 4, 5
LAB1 Protein purification 3 credits U, G

For grade 4, it is required that the goals for grade 3 have been achieved and the main part of the goals for grade 5. 

The course grade is the grade on DIT1. 

Grades for examination modules are decided in accordance with the assessment criteria presented at the start 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

Program courses are timetabled after a decision has been made for this course concerning its assignment to a timetable module. Single subject courses can be timetabled at other times.

Interruption in and deregistration from a course

The LiU decision, Guidelines concerning confirmation of participation in education, Dnr LiU-2020-02256 (https://styrdokument.liu.se/Regelsamling/VisaBeslut/764582), 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 are therefore obliged to report the interruption so that this can be noted in Ladok. Deregistration from or interrupting a course is carried out using a Web-based form.

Cancelled courses and changes to the course syllabus

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. For single subject courses, the cancellation must be done before students are admitted to the course (in accordance with LiUs regulation Dnr LiU-2022-01200, https://styrdokument.liu.se/Regelsamling/VisaBeslut/622645).

Guidelines relating to examinations and examiners 

For details, see Guidelines for education and examination for first-cycle and second-cycle education at Linköping University, Dnr LiU-2023-00379  (http://styrdokument.liu.se/Regelsamling/VisaBeslut/917592).

An examiner must be employed as a teacher at LiU according to the LiU Regulations for Appointments, Dnr LiU-2022-04445 (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

Principles for examination

Written and oral examinations and digital and computer-based 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 faculty programme board.

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 January
  • 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 faculty programme board 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, or a written or oral examination (TEN, DIT, DAT, MUN), 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 faculty programme board. In all cases above, the examination is also offered one more time during the academic year after the following, unless the faculty programme board decides otherwise. In total, 6 re-examinations are offered, of which 2 are regular re-examinations. In the examination registration system, the examinations given for the penultimate time and the last time are denoted. 

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

For single subject courses, written and oral examinations can be held at other times.  

Retakes of other forms of examination

Regulations concerning retakes of other forms of examination than written examinations and digital and computer-based examinations are given in the LiU guidelines for examinations and examiners, Dnr LiU-2023-00379 (http://styrdokument.liu.se/Regelsamling/VisaBeslut/917592).

Course closure

For Decision on Routines for Administration of the Discontinuation of Educational Programs, Freestanding Courses and Courses in Programs, see Dnr LiU-2021-04782 (https://styrdokument.liu.se/Regelsamling/VisaBeslut/1156410). After a decision on closure and after the end of the discontinuation period, the students are referred to a replacement course (or similar) according to information in the course syllabus or programme syllabus. If a student has passed some part/parts of a closed program course but not all, and there is an at least partially replacing course, an assessment of crediting can be made. Any crediting of course components is made by the examiner.

Registration for examination

In order to take an written, digital or computer-based examination, registration in advance is mandatory, see decision in the university’s rule book Dnr LiU-2020-04559 (https://styrdokument.liu.se/Regelsamling/VisaBeslut/622682). An unregistered student can thus not be offered a place. The registration is done at the Student Portal or in the LiU-app during the registration period. The registration period opens 30 days before the date of the examination and closes 10 days before the date of the examination. Candidates are informed of the location of the examination by email, four days in advance. 

Code of conduct for students during examinations

Details are given in a decision in the university’s rule book, Dnr LiU-2020-04559 (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 digital and computer-based examinations in an attempt to achieve a higher grade. This is valid for all examination components with code “TEN”, “DIT” 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. 

Grades

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

  • Grades U, 3, 4, 5 are to be awarded for courses that have written or digital examinations.
  • 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.
  • Grades Fail (U) and Pass (G) are to be used for degree projects and other independent work.

Examination components

The following examination components and associated module codes are used at the Faculty of Science and Engineering:

  • Grades U, 3, 4, 5 are to be awarded for written examinations (TEN) and digital examinations (DIT).
  • 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), digital preparatory written examination (DIK), oral examination (MUN), computer-based examination (DAT), home assignment (HEM), and assignment (UPG).
  • 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 tutorial group (BAS) or examination item (MOM).
  • 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).

In general, the following applies:

  • Mandatory course components must be scored and given a module code.
  • Examination components that are not scored, cannot be mandatory. Hence, it is voluntary to participate in these examinations, and the voluntariness must be clearly stated. Additionally, if there are any associated conditions to the examination component, these must be clearly stated as well.
  • For courses with more than one examination component with grades U,3,4,5, it shall be clearly stated how the final grade is weighted.

For mandatory components, the following applies (in accordance with the LiU Guidelines for education and examination for first-cycle and second-cycle education at Linköping University, Dnr LiU-2023-00379 http://styrdokument.liu.se/Regelsamling/VisaBeslut/917592): 

  • 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.

For possibilities to alternative forms of examinations, the following applies (in accordance with the LiU Guidelines for education and examination for first-cycle and second-cycle education at Linköping University, Dnr LiU-2023-00379 http://styrdokument.liu.se/Regelsamling/VisaBeslut/917592): 

  • 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 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.
  • An examiner may also decide that an adapted examination or alternative form of examination if the examiner assessed that special circumstances prevail, and the examiner assesses that it is possible while maintaing the objectives of the course.

Reporting of examination results

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

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 Cheating, deception and plagiarism.

Linköping University has also produced a guide for teachers and students' use of generative AI in education (Dnr LiU-2023-02660). As a student, you are always expected to gain knowledge of what applies to each course (including the degree project). In general, clarity to where and how generative AI has been used is important.  

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 https://styrdokument.liu.se/Regelsamling/Innehall

There is no course literature available for this course in studieinfo.

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
Biochemistry and mathematics
1.2 Fundamental engineering knowledge (G1X level)
X
Biophysical measurement technology.
1.3 Further knowledge, methods, and tools in one or several subjects in engineering or natural science (G2X level)
X
X
PRA1
DIT1
Protein expression and purification. Protein stability, protein folding, ligand binding. Biophysical measurement technology.
1.4 Advanced knowledge, methods, and tools in one or several subjects in engineering or natural sciences (A1X level)
X
PRA1
DIT1
Protein expression and purification. Protein stability, protein folding, ligand binding.
1.5 Insight into current research and development work
X
PRA1
Protein characterisation with different biophysical measurement methods.
2. PERSONAL AND PROFESSIONAL SKILLS AND ATTRIBUTES
2.1 Analytical reasoning and problem solving
X
PRA1
DIT1
Planning. Structure analysis.
2.2 Experimentation, investigation, and knowledge discovery
X
X
PRA1
DIT1
Analysis of experimental data. Project in protein characterization. Experimental analysis in theory. 
2.3 System thinking
X
PRA1
Planning
2.4 Attitudes, thought, and learning
X
DIT1
LAB1
Some experimental parts individually. Individual examination.
2.5 Ethics, equity, and other responsibilities
X
PRA1
Group work, scientific approach, written report.
3. INTERPERSONAL SKILLS: TEAMWORK AND COMMUNICATION
3.1 Teamwork
X
PRA1
Work in lab groups of 4. The gender perspective is taken into consideration when forming groups. If possible at least 1 in each lab group does not have Swedish as a mother tongue so that all communication takes place in English.
3.2 Communications
X
PRA1
Written report and shared planning of practical lab work.
3.3 Communication in foreign languages
X
PRA1
Literature in English. English used as course language during group work.
4. CONCEIVING, DESIGNING, IMPLEMENTING AND OPERATING SYSTEMS IN THE ENTERPRISE, SOCIETAL AND ENVIRONMENTAL CONTEXT
4.1 External, societal, and environmental context
X
PRA1
LAB1
Choice of chemicals based on environmental concerns.
4.2 Enterprise and business context

                            
4.3 Conceiving, system engineering and management

                            
4.4 Designing
X
PRA1
Recombinant protein production. Characterisation of recombinant proteins.
4.5 Implementing
X
PRA1
Recombinant protein production. Characterisation of recombinant proteins.
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

                            
5.4 Execution of research or development projects
X
PRA1
Recombinant protein production.
5.5 Presentation and evaluation of research or development projects
X
X
PRA1
LAB1
Laboratory report comprising 5 laboratory sessions.
Written scientific report.

This tab contains public material from the course room in Lisam. The information published here is not legally binding, such material can be found under the other tabs on this page.

There are no files available for this course.