Molecular Cell Biology

Introduction

Miklós Csala
What
What is life?
lives?

Self-regenerating system capable

of evolution – in constant struggle
against equilibrium.
Increasing entropy is the driving force in the universe
that is, the strive for equilibrium
Ordered (and designed) systems Highly ordered (large) molecules

More ordered (small) molecules Highly disordered equilibrium

Life and the maintenance of Energy source
non-equilibrium
states / systems CO2, H2O,
CO(NH2)2 …
O2

Ordered (and
designed) autotrophic
systems

Ordered (and
designed)
heterotrophic
systems
Ordered small and
large molecules
Catalysis alone only accelerates the achievement of equilibrium

Free enthalpy, G
Eact
not catalyzed

Eact
catalyzed
Selecting / switching on the appropriate catalyst determines the path
taken by processes
(towards equilibrium)

A A

+B +E +H +K +B +E +H +K

C+D F+G I+J L+M C+D F+G I+J L+M

 Designed biocatalysts (enzymes) can create new reactions by
coupling independent reactions

The free enthalpy change

of a spontaneous reaction
can be used in part.

If the two reactions

fuse into one by
enzyme catalysis.

That is, processes heading for equilibrium may perpetuate disequilibrium.

Design of the enzymes is stored in DNA, and the blueprint reaches the constructor as RNA
(„central dogma”)

Enzymes
are proteins.

But enzymes are needed

- for the production of proteins,
- for the production of RNAs,
- for DNA maintenance and
- for copying DNA.
 Which came first, the chicken or the egg?
None!
RNA can assume
various 3D structures.

RNA as enzyme
can catalyze
copying and editing RNA can act
of RNA. as an enzyme
(ribozyme).

Natural selection can start among RNA

a large number of often
"incorrectly" copied / edited RNAs. Catalysis

Chemistry → (molecular) biology Three in one RNA

Storage, replication and expression of genetic information
Optimization with task sharing

RNA-based systems

RNA

FORMATION OF RNAs CAPABLE FOR

PROTEIN SYNTHESIS

RNA- and protein-based systems

RNA protein

FORMATION OF ENZYMES, WHICH CAN

DUPLICATE DNA AND MAKE RNA COPIES
FROM DNA

Live systems today

DNA RNA protein

 They are still among us
Telomerase RNA Splicing
U1,2,4,5,6 rRNA
snRNAs

Primer RNA

SRP-RNA
miRNA tRNA

RNA virus
Retrovirus

+ The main metabolic coenzymes

(NAD+, NADP+, FMN, FAD, CoA) are all
ribonucleotide-derivatives.
 Base, ribo- or deoxyribonucleoside and nucleotide
Purine bases

Adenine Guanine
Pyrimidine bases

phosphoryl group(s)
acid anhydride bond ester bond

pentose Cytosine Uracil Thymine

base

N-glycosidic bond

= ribose
= deoxyribose
nucleoside
nucleosidemonophosphate
nucleosidediphosphate nucleotides
nucleosidetriphosphate
 Primary, secondary and tertiary structures of RNA
The structural diversity of RNA is greater than that of DNA, yet lower
than that of proteins → proteins are more suitable for enzymes.
Information in RNA is easy to read, but RNA’s structure is less stabile than
DNA’s → DNA is more suitable for storing and transmitting information.
 Basic principles and facts
Inborn characteristics of living cells / organisms (part of phenotype) are determined by the proteins within, which
in turn are determined by the genetic information (genotype).

Genome is the entire genetic material of the cell. Human genome is dominantly nuclear and to a lesser extent
mitochondrial.
Organism Size of the genome (base pair)
Viruses Thousands – a few tens of thousands
Bacterium, Escherichia coli 4×106
Yeast, Saccharomyces cerevisiae 2×107
Worm, Caenorhabditis elegans 8×107
Insect, Drosophila melanogaster 2×108
Mammal, Homo sapiens 3×109
23 pairs of chromosomes
20000-25000 genes coding for proteins
Approximately 1.5% of the genome codes for proteins
Polymorphism / mutation
Average difference between human individuals is ~0.1%;
Average difference between humans and chimpanzees is ~1.2%.
Sister chromatids of a (metaphase) human chromosome
(TTAGGG)n

Double amount of
DNA, right before
separation of the
genetic material in
two portions.
(TTAGGG)n
The human karyotype

Diploid genome and

double amount of
DNA, right before
separation of the
genetic material in
two diploid portions.
 Haploid – diploid cells

Figure 5-1 Molecular Biology of the Cell (© Garland Science 2008)

The basis for information transfer and decoding is base pairing

The basis for base pairing, in turn is the

complementary H-bonding pattern.

Guanine Cytosine T
A

C G

Adenine Thymine (or Uracil)

T A
Double-stranded DNA is more suitable for
storing information (than single-stranded
RNA) because, when damaged, its
sequence can be recovered from the C
G
complementary strand.
Provided that the injury does not result in
another seemingly correct base (which is
why there is T instead of U in DNA).
 DNA is a complementary
and anti-parallel double helix

Phoshorus

Deoxyribose-phosphate
”backbone”

Hydrogen

Major groove
Oxygen

The helix needs to be unwinded for

copying the information (replication,
transcription), however, short Minor groove
sequences can be recognized
without unwinding by touching into Stacking
base pairs
the grooves.
 Topoizomers
Same DNA of different linking number

Linking number (L) is the sum of the number of Twists (T) and Writhes (W).

Twist means a helcal, writhe means a superhelical turn.

Linking number (L) cannot change without chain breaking

(in case of fixed ends or circular DNA).
 A type II topoisomerase:
negative superhelical turns
The DNA girase

ATP-dependent helix unwinding by helicase

generates positive szuperhelical turns, i.e., writhing.

Girase is a type II topoisomerase, which

cuts both DNA strands.

It moves a distant section of DNA through the opening.

Restores the continuity of the strands on the expense of ATP.

By this, it regenerates negative superhelical turns.

Linking number
changes by 2.
Type I topoisomerases cut one strand only

Linking number
changes by 1.
Prokaryotic and eukaryotic DNAs

Eukaryote Prokaryote
 Packing the eukaryotic DNA
Histone proteins, nucleosome, chromatosome
Chromatosome
Core of a histone
octamere
H1 histone

DNA
 Condensed chromosome
Protein that extrudes and stabilizes
DNA loops: Condensin

nucleosome
core

H1
histone
30 nm diameter
solenoid
 Levels of chromosome
condensation

(euchromatin, heterochromatin)
 COMPARTMENTATION

Structural and functional basis of

eukaryotic cell organization
 Development of endomembranes
and
formation of mitochondria as endosymbionts
 Cellular membranes and compartments
• Cytosol

The endomembrane system Compartments of the endomembrane system

• endoplasmic reticulum (ER) membrane • endoplasmic reticulum (ER)

• nuclear envelope • nucleus

• membrane of Golgi apparatus • endoplasmic reticulum - Golgi intermediate compartment (ERGIC)

• Golgi apparatus
• lysosome membrane
• lysosome
• endosome membrane
• endosome (early, late, MVB)
• phagosome membrane
• phagosome
• autophagosome membrane
• autophagic vacuoles
• membrane of transport vesicles
• transport vesicles
• cell membrane
• peroxysome (?)
• peroxisome membrane (?)
• lipid droplets

Mitochondrial membranes Compartements in the mitochondria

• inner and outer mitochondrial membranes • mitochondrial matrix
• mitochondrial intermembrane space
 Roles of the cellular membranes
• Separation of the inside of the cell from the outside (plasma membrane).
• Material flow (transport) and information flow (signal transduction) between the cell and its environment.
• Formation of distinct intracellular compartments with a specific microenvironment (intracellulal membranes).
• Material flow (transport) and information flow (signal transduction) between the intracellular compartments.
• Holding components of certain metabolic pathways together (in the compartment or in the membrane itself) -
"proteome", "metabolome".
• Separating cell biological and biochemical processes to avoid interferences.
• Energy storage (in the form of electrical and chemical gradients).

Roles of membrane proteins

 Mitochondrial respiratory chain:
A central metabolic process based in large part on
compartmentation and membrane structure
 Mitochondrial genome

13 proteins
22 tRNAs
2 rRNAs
mtDNA:
• circular, double stranded
• less than 17000 base pairs
• "heavy" (G) and "light" (C) strands
• 100-10000 copies per cell
• DNA polymerase γ
• 37 genes (intronless)
• few non-coding sequences
• unique code (mitochondrial tRNAs)
• peculiar inheritance