Download 1 MODULE: Protein-nucleic acid interactions MODULE NUMBER

MODULE: Protein-nucleic acid interactions
MODULE NUMBER:
BIO00024H
JACS CODE:
C700
STAGE / YEAR:
3
CREDITS:
10
ORGANISER:
Dr Christoph Baumann
SUBJECT COMMITTEE:
VERSION:
MBB
17th September 2013
TERMS TAUGHT:
Spring/Summer terms 2014
RECOMMENDATIONS/PREREQUISITES:
of the Cell, or equivalent module
BIO00004C Molecular Biology and Biochemistry
SUMMARY:
The recognition of nucleic acids by proteins is fundamentally important in regulating and
determining fidelity in the transmission and expression of genetic information. Biochemical,
structural and genetic approaches have combined to increase our understanding at the
molecular level of the interactions between these two species, and increasingly our
understanding is being further enhanced by studies at the single-molecule level.
This module surveys the main features of protein-nucleic acid interactions and the methods
used to study them. The topics discussed focus on well characterised systems, chiefly drawn
from transcription and the proteins that regulate gene expression.
The module is designed for biochemists, molecular cell biologists and geneticists who are
interested in learning more about molecular recognition and the mechanisms underlying genetic
control processes.
LEARNING OUTCOMES:
At the end of this module, students should be able to:
 explain the structural basis of sequence-specific DNA recognition by different protein
superfamilies
 describe and appraise the common techniques used to study DNA-protein interactions in
vitro and in vivo
 describe the structural features of E. coli RNA polymerase
 understand the role of sigma factors and DNA promoter strength in transcriptional
initiation by E. coli RNA polymerase
 describe systems involved in the positive and negative control of DNA transcription
 discuss the use of chromatin immuno-precipitation to probe transcription and
chromosome organisation in vivo
1
RECOMMENDED READING:
Additional reading associated with this module will come from published research papers – the
references will be given out at each lecture.
2
SYNOPSIS OF TEACHING:
Event
Duration
(Hrs)
Lecture 1
1
Lecture 2
1
Lecture 3
1
Lecture 4
1
Lecture 5
1
Lecture 6
1
Lecture 7
1
Lecture 8
1
Lecture 9
1
Lecture 10
1
Supported
learning
session
1
Topic
General principles of sequence specific DNA recognition by
proteins, including an overview of DNA-binding structural motifs
and DNA secondary structure/supercoiling
Techniques for studying protein-DNA interactions and identifying
recognition contacts, including electrophoresis mobility shift assay
(EMSA), DNA footprinting and fluorescence anisotropy. These
techniques will be introduced using selected biological systems.
Techniques for studying protein-DNA interactions and identifying
recognition contacts, including electrophoresis mobility shift assay
(EMSA), DNA footprinting and fluorescence anisotropy. These
techniques will be introduced using selected biological systems.
Introduction to the ribbon-helix-helix transcription factor
superfamily, including how the conserved three-dimensional
structure binds DNA in a sequence-specific manner and regulates
the transcription of a diverse range of genes.
Engineered zinc finger-containing nucleases, and their use for in
situ editing of genomic DNA.
Mechanism of RNA chain initiation by E. coli RNA polymerase,
including subunit structure, promotor strength, and crucial role of
sigma factors in initiation.
Mechanism of RNA chain initiation by E. coli RNA polymerase,
including subunit structure, promotor strength, and crucial role of
sigma factors in initiation.
Repressor-operator systems in gene expression using lac
regulation as a paradigm, including in vitro and in vivo
techniques for studying these systems
Role of activator and co-activator proteins in the up-regulation of
gene transcription, including techniques for studying these
systems
Genomic analysis of protein-DNA interactions in eukaryotes,
including the use of chromatin immunoprecipitation (ChIP) to
probe transcription and chromosome organization in vivo
The module will conclude with a summary of the main
topics/themes in the module, and students will have the
opportunity to ask questions about material covered in the
module.
Staff
Room type
DB
Lecture
room
DB
Lecture
room
DB
Lecture
room
DB
Lecture
room
DB
Lecture
room
CGB
Lecture
room
CGB
Lecture
room
CGB
Lecture
room
CGB
Lecture
room
RJW
Lecture
room
CGB
DB
RJW
LECTURERS: Daniela Barillá (DB), Christoph Baumann (CGB), Bob White (RJW)
3
Lecture
room
Timing
Week 4
of
Summer
term
KEY TEXTS: These are available in EARL which is accessible through the VLE module site. Additional reading associated with this module
will come from published research papers – the references will be given out at each lecture.
ASSESSMENT:
Formative:
no
Summative:
yes
Re-assessment:
yes
DEMONSTRATING REQUIREMENTS:
none
MAXIMUM NUMBERS: to the capacity of the lecture room
STUDENT WORKLOAD: students’ workload totalling 100 hours per 10 credit module
Lectures:
10
Workshops:
Supported learning sessions: 1
Practicals:
Tutorials:
Total Contact hours: 10
Assessments (formative and summative): 2 hours
Private study:
89
4