CHMI 4237 E Special topics in Biochemistry Eric R. Gauthier, Ph.D. Dept. Chemistry-Biochemistry...

CHMI 4237 ECHMI 4237 E

Special topics in Special topics in BiochemistryBiochemistry

Eric R. Gauthier, Ph.D.Dept. Chemistry-Biochemistry

Laurentian University

1- Introduction

1CHMI 4237 E - Winter 2010

Central theme:Central theme:Cellular BiochemistryCellular Biochemistry

This course aims at providing a detailed view of several cellular phenomena at the molecular level.

I will also explain how different experimental methods can help scientists to shed light onto the molecular basis of various cellular processes.

I will finally illustrate how alterations in normal molecular events can change cell behavior and lead to diseases.


Course outline (tentative)Course outline (tentative) 1) Introduction: cell structure vs gene expression and its

regulation;

2) Cell proliferation: cell cycle, mitosis, checkpoints

◦ Diseases: cancer, viral infections

3) Cell survival and cell death: apoptosis, necrosis, autophagy;

◦ Diseases: cancer; auto-immunity; Proteus syndrome

4) Cell response to stresses: heat shock, hypoxia, nutrient starvation:

◦ Diseases: cancer;


Course outline (tentative)Course outline (tentative) 5) Cell structure, adhesion and motility: cytoskeleton,

intracellular trafficking

◦ Diseases: metastasis, progeria

6) Cell differentiation: stem cells, cell fate selection

◦ Diseases: hematopoietic diseases

7) Cell aging and lifespan: basic hypotheses, lifespan extension

◦ Diseases: aging

8) Cells and development: morphogen gradients, limb patterning, control of organ size

◦ Diseases: freaks


Cell structure – general featuresCell structure – general features


Cellular organellesCellular organelles


Molecules: the basis of cell Molecules: the basis of cell structure and functionstructure and function


The cytosol: a crowded placeThe cytosol: a crowded place


Molecules of the cellMolecules of the cell


Molecules of the cell - sugarsMolecules of the cell - sugars


Molecules of the cell - lipidsMolecules of the cell - lipids


Molecules of the cell – amino acidsMolecules of the cell – amino acids


Molecules of the cell – amino acidsMolecules of the cell – amino acids


Molecules of the cell – Molecules of the cell – proteinsproteins


Molecules of the cell – Molecules of the cell – proteinsproteins


Molecules of the cell – nucleic Molecules of the cell – nucleic acidsacids


Wikipedia

Cell signalingCell signaling


Input

Receptor

Intracellularmolecules

Phenotype

Environment

Detector

Decoding /Transmitting

Adaptation


18

Input

Receptor

Intracellularmolecules

Phenotype

Molecules

Osmotic pressure

Temperature

VoltageLight

Transmembrane

Nuclear Cytosolic

Proteins

DNARNA

LipidsIonsSugars

Proliferation

Survival

Differentiation

Motility


19

Proliferation

Differentiation

Motility

Survival

Modified cellular Response to stimuli

Blood cell production

Stress response Unicellular multicellular

Memory / learning

Wound healing

Neurite extension

Intestinal epithelium

Growth Organ size

Cellular contacts

Immune response

Changes in phenotype Changes in phenotype adaptationadaptation

20

Proliferation

Differentiation


21

Motility

Growth


22

Cellular contacts

Survival


23

Stress response

Memory / learning

Complexity of intracellular Complexity of intracellular signallingsignalling

24



Signal Processing Response

Central dogma of molecular Central dogma of molecular biologybiology


Wikipedia

Molecules of the cell – nucleic Molecules of the cell – nucleic acidsacids


Wikipedia

Wikipedia

Turning gene expression ONTurning gene expression ON


NOTE: The sequence of the mRNA is complementary to the template (non-sense, transcribed) strand and is identical to the non-template (sense, non-transcribed) strand on the DNA

Weaver. Molecular Biology. 3rd edition. McGraw Hill. 2008.

Gene PromotersGene Promoters


Glucocorticoid response element5’AGAACAnnnTGTTCT3’

3’TCTTGTnnnACAAGA5’

Transcription factorsTranscription factors


Transcription machineryTranscription machinery


RNA polymerase IITranscription factors

- Heterochromatin: repressed (no transcription)

- Euchromatin: active (transcription is going on)

- BUT: 10 µm nucleus vs 2 m genomic DNA

CHMI 4237 E - Winter 2010 32

Gene expression – In the nucleusGene expression – In the nucleus

DNA is tightly compacted in the DNA is tightly compacted in the nucleusnucleus


Nucleosome: basic unit for nuclear Nucleosome: basic unit for nuclear DNA packagingDNA packaging


- Histone octamer:- 2 x Histone H2A + H2B

- 2 x Histone H3 + H4

- DNA: wraps around histone octamer (1.75 turns – about 146 bp)

x 2

« beads on a string »

The nucleosomeThe nucleosome


Histone N-terminal tail: the site of several modifications

Histone tails are chemically Histone tails are chemically modifiedmodified


Legend:

-A = active chromatin-R = repressed chromatin

-Numbers: amino acid targeted by the modification

-Ac = acetylation (CH3-COO-)

-P = phosphorylation (PO4-)

- Me = methylation (CH3-)

-So: H3K9me3 = histone 3 with three methyl groups on lysine 9

Histone modifications are reversibleHistone modifications are reversible

Transcription factor

Histone acetylation

Opens up chromatin

Recruitment of other TFs and RNA pol II

Histone modifications are Histone modifications are reversiblereversible


Acetylated Histone: active chromatin

Deacetylated Histone: repressed chromatin

HDAC = histone deacetylase

SUV39H1: « polycomb group protein» silences gene expression



Signal Processing Response

RNA processingRNA processing


5’ untranslated region (5’UTR): ◦ located upstream of the ORF◦ Generally short (<150b)◦ Involved in the regulation of the

initiation of translation

Open reading frame (ORF):◦ The region of the mRNA encoding a

specific protein◦ Sequence is well conserved across

species

3’UTR:◦ Located downstream of the ORF◦ Generally quite long (>1000 b)◦ Involved in regulating mRNA stability as

well as translation

mRNA5’UTR ORF 3’UTR

AUG

UAAUGAUAG

RNA processingRNA processing


http://www.exonhit.com/alternativesplicing/pages/diagrams/figure2.htm

Translation: making proteinsTranslation: making proteins


Membrane-embedded and Membrane-embedded and secreted proteinssecreted proteins


Secretory pathwaySecretory pathway


Membrane/secretory proteins Membrane/secretory proteins transit through the endoplasmic transit through the endoplasmic reticulumreticulum






Date post:	14-Dec-2015
Category:	Documents
Upload:	emil-french
View:	230 times
Download:	1 times

CHMI 4237 E Special topics in Biochemistry Eric R. Gauthier, Ph.D. Dept. Chemistry-Biochemistry...

Documents