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4 Οκτ 2013 (πριν από 3 χρόνια και 11 μήνες)

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BASIC MOLECULAR BIOLOGY

(Borrowed from “An Introduction to Bioinformatics Algorithms” by Neil C.
Jones and
Pavel

A.
Pevzner

and further modified by
Prof.

Natalio

Krasnogor
)

Outline For Section 1:


All living things are made of Cells


Prokaryote, Eukaryote


Cell Signaling


What is Inside the cell: From DNA, to RNA, to
Proteins


Cells


Fundamental working units

of every living system.


Every organism is composed of one of two


radically different types of cells:


prokaryotic

cells or


eukaryotic
cells.


Prokaryotes

and
Eukaryotes

are descended from the same primitive cell.


All extant prokaryotic and eukaryotic cells are the result of a total of 3.5
billion years of evolution by natural selection.

Hard Fact! No pre
-
medieval
fairy tales like ID, Adam&Eve,
etc


For more information:

“The Major Transitions in
Evolution” by M. Smith and E.
Szathmary

Cells



Chemical composition
-
by weight


70% water


7% small molecules



salts


Lipids


amino acids


nucleotides


23% macromolecules


Proteins


Polysaccharides


lipids

Life begins with Cell



A cell is the smallest structural unit of an organism that is capable of
sustained

independent functioning


All cells have some common features


What is Life? Can we create it in the lab? Read:

The imitation game

a computational chemical approach to
recognizing life.
Nature Biotechnology
, 24:1203
-
1206, 2006





2 types of cells:

Prokaryotes & Eukaryotes


All Cells have common Cycles


Born, eat, replicate, and die


Prokaryotes and Eukaryotes


According to the most recent evidence, there are three main branches to the tree of life.


Prokaryotes include Archaea (

ancient ones

) and bacteria.


Eukaryotes are kingdom Eukarya and includes plants, animals, fungi and certain algae.

Prokaryotes and Eukaryotes, continued

Prokaryotes

Eukaryotes

Single cell

Single or multi cell

No nucleus

Nucleus

No organelles

Organelles

One piece of circular DNA
(plasmid)

Chromosomes

No mRNA post
transcriptional modification

Exons/Introns splicing

Prokaryotes v.s. Eukaryotes

Structural differences

Prokaryotes


Eubacterial (blue green algae)


and archaebacteria


only one type of membrane
--


plasma membrane forms


the
boundary

of the cell proper


The smallest cells known are
bacteria


Ecoli cell


3x10
6
protein molecules


1000
-
2000 polypeptide species.


Eukaryotes


plants, animals, Protista, and fungi



complex systems of internal
membranes forms


organelle

and
compartments


The volume of the cell is several
hundred times larger


Hela cell


5x10
9

protein molecules


5000
-
10,000 polypeptide species

Signaling Pathways: Control Gene
Activity


Instead of having brains, cells make
decisions through complex networks of
chemical reactions, called pathways


Synthesize new materials


Break other materials down for spare parts


Signal to eat, die, reproduce, sporulate, etc



Even Bacteria are smart entities. Read:

Bacteria Harnessing Complexity
by E. Ben
-
Jacob and colleagues

Example of cell signaling

Cells Information and Machinery


Cells store all information to replicate itself


Human genome is around 3 billions base pairs long


Almost every cell in human body contains same set of
genes


But not all genes are used or expressed by those cells


Machinery:


Collect and manufacture components


Carry out replication


Kick
-
start its new offspring

(A cell is like a car factory but FAR more complex and
efficient)

Overview of organizations of life


Nucleus

=
library


Chromosomes

=
bookshelves


Genes

=
books


Almost every cell in an organism contains the same
libraries and the same sets of books.


Books represent all the information (DNA) that every
cell in the body needs so it can grow and carry out
its various functions.


Moreover, more recent discoveries suggest that the
books, bookshelves and libraries are not passive
waiting to be read but are, sometimes, rewriting and
rewiring themselves!

Terminology


The
genome

is an organism

s complete set of DNA.


a bacteria contains about 600,000 DNA base pairs


human and mouse genomes have some 3 billion.


human genome has 23 distinct chromosomes.


Each chromosome contains many
genes
.



Gene



basic physical and functional units of heredity.


specific sequences of DNA bases that encode
instructions on
how

and
when

to make
proteins
.



Proteins



Make up the cellular structure


large, complex molecules made up of smaller subunits
called
amino acids.


All Life depends on 3 critical molecules


DNAs


Hold information on how cell
works


RNAs


Act to transfer short pieces of information to different parts of cell


Provide templates to synthesize into protein


Proteins


Form enzymes that send signals to other cells and regulate gene
activity


Form body

s major components (e.g. hair, skin, etc.)


Are life

s laborers
!


Computationally, all three can be represented as
sequences of a certain 4
-
letter (DNA/RNA) or 20
-
letter
(Proteins) alphabet

DNA, RNA, and the Flow of Information

Translation

Transcription

Replication

Weismann
Barrier /
Central

Dogma of

Molecular
Biology

Overview of DNA to RNA to Protein


A gene is expressed in two steps

1)
Transcription: RNA synthesis

2)
Translation: Protein synthesis

DNA: The Basis of Life


Deoxyribonucleic Acid (DNA)


Double stranded with complementary strands A
-
T, C
-
G


DNA is a polymer


Sugar
-
Phosphate
-
Base


Bases held together by H bonding to the opposite strand

RNA


RNA is similar to DNA chemically. It is usually
only a single strand. T(
hyamine
) is replaced by
U(
racil
)


Some forms of RNA can form secondary
structures
by

pairing up


with itself. This can
have impact on its
properties dramatically
.











DNA and RNA










can
pair with









each
other.

http://www.cgl.ucsf.edu/home/glasfeld/tutorial/trna/trna.gif

tRNA linear and 3D view:

RNA, continued


Several
types exist, classified by function:



hnRNA

(heterogeneous nuclear RNA)
: Eukaryotic mRNA primary
transcipts

with introns that have not yet been excised (pre
-
mRNA).



mRNA:

this is what is usually being referred to when a
Bioinformatician

says

RNA

. This is used to carry a gene

s
message out of the nucleus.



tRNA
:

transfers genetic information from mRNA to an amino acid
sequence as to build a protein



rRNA
:

ribosomal RNA. Part of the ribosome which is involved in
translation.




Transcription


Transcription is highly regulated. Most DNA is in a
dense form where it cannot be transcribed.


To start, transcription requires a
promoter
, a small
specific sequence of DNA to which polymerase can
bind (~40 base pairs

upstream


of gene)


Finding these promoter regions is only a partially
solved problem that is related to motif finding.


There can also be repressors and inhibitors acting in
various ways to stop transcription. This makes
regulation of gene transcription complex to
understand.

Definition of a Gene


Regulatory regions: up to 50 kb upstream of +1 site




Exons:

protein coding and untranslated regions (UTR)




1 to 178 exons per gene (mean 8.8)




8 bp to 17 kb per exon (mean 145 bp)



Introns:

splice acceptor and donor sites, junk DNA




average 1 kb


50 kb per intron



Gene size:

Largest


2.4 Mb (Dystrophin). Mean


27 kb.

Splicing

Splicing and other RNA processing


In Eukaryotic cells, RNA is processed
between transcription and translation.


This complicates the relationship between
a DNA gene and the protein it codes for.


Sometimes alternate RNA processing can
lead to an alternate protein
(splice
variants) as
a result. This is true in the
immune system.


Proteins: Crucial
molecules for
the functioning of life




Structural Proteins:
the organism's basic building blocks, eg. collagen,
nails, hair, etc.



Enzymes:
biological engines which mediate multitude of biochemical
reactions. Usually enzymes are very specific and catalyze only a single type
of reaction, but they can play a role in more than one
pathway
.



Transmembrane proteins:
they are the cell’s housekeepers, eg. By
regulating cell volume, extraction and concentration of small molecules from
the extracellular environment and generation of ionic gradients essential for
muscle and nerve cell function (
sodium/potasium

pump is an example)




Proteins are polypeptide chains, constructed by joining a certain kind of
peptides, amino acids, in a linear way



The chain of amino acids, however folds to create very complex 3D
structures

Translation


The process of going
from RNA to
polypeptide.


Three base pairs of
RNA (called a codon)
correspond to one
amino acid based on a
fixed table.


Always starts with
Methionine and ends
with a stop codon

Amino Acids

Protein Structure: Introduction


Different amino acids
have different properties


These properties will
affect the protein
structure and function


Hydrophobicity, for
instance, is the main
driving force (but not the
only one) of the folding
process

Protein Structure: Hierarchical nature of protein
structure

MKYNNHDKIRDFIIIEAYMFRFKKKVKPEVDMTIKEFILLTYLFHQQENTL
PFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQRE
KIAERVTLFDQIIKQFNLADQSESQMIPKDSKEFLNLMMYTMYFKNIIKK
HLTLSFVEFTILAIITSQNKNIVLLKDLIETIHHKYPQTVRALNNLKKQGYL
IKERSTEDERKILIHMDDAQQDHAEQLLAQVNQLLADKDHLHLVFE

Primary Structure = Sequence of amino acids

Secondary Structure

Tertiary

Local Interactions

Global Interactions

Protein Structure: Why is structure
important?


The function of a protein depends greatly on
its structure


The structure that a protein adopts is vital to
it’s chemistry


Its structure determines which of its amino
acids are exposed to carry out the protein’s
function


Its structure also determines what substrates
it can react with

Protein
Structure: Mostly lacking
information


Therefore, it is clear that knowing the structure of a
protein is crucial for many tasks


However, we only know the structure for a
very small
fraction

of all the proteins that we are aware of


The
UniProtKB
/
TrEMBL

archive contains
23165610 (16886838)

sequences


The PDB archive of protein structure contains only
84223(76669)

structures


In the native state, proteins fold on its own as soon as
they are generated, amino
-
acid by amino
-
acid (with few
exceptions e.g. chaperones)


can we predict this
process as to close the gap between protein sequences
and their 3D structures?

Central Dogma of Biology: A Bioinformatics
Perspective


The information for making proteins is stored in DNA. There is
a process (transcription and translation) by which DNA is
converted to protein. By understanding this process and how it
is regulated we can make predictions and models of cells.


Sequence analysis

Gene Finding

Protein
Sequence/Stru
cture Analysis


Assembly

Computational Problems