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Bioinformatics Introduction to molecular and cell biology

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Bioinformatics Introduction to molecular and cell biology Ulf Schmitz ulf.schmitz_at_informatik.uni-rostock.de Bioinformatics and Systems Biology Group – PowerPoint PPT presentation

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Title: Bioinformatics Introduction to molecular and cell biology


1
BioinformaticsIntroduction to molecular and cell
biology
  • Ulf Schmitz
  • ulf.schmitz_at_informatik.uni-rostock.de
  • Bioinformatics and Systems Biology Group
  • www.sbi.informatik.uni-rostock.de

2
Outline
  • Recommended Literature
  • What is Bioinformatics?
  • The Cell
  • Molecular Biology / Genomics
  • Genes
  • DNA
  • RNA
  • Proteins
  • Gene Expression
  • Signaling Pathways
  • Outlook next lecture

3
Recommended Literature
  • Developing Bioinformatics Computer Skills
    Cynthia Gibas Per Jambeck OReilly ISBN
    1565926641
  • New Biology for Engineers and Computer
    Scientists Aydin Tözeren Stephen W.Byers
    Pearson Prentince Hall Bioengineering ISBN
    0130664634
  • Bioinformatics Sequence and Genome Analysis
    David W. Mount Cold Spring Harbor ISBN
    0879697121
  • Introduction To Bioinformatics Arthur M. Lesk
    Oxford University Press ISBN 0199277877

4
What is Bioinformatics?
  • Bioinformatics is the development and use of
    computer applications for the Analysis,
    Interpretation, Simulation and Prediction of
    biological Systems and corresponding experimental
    methods in nature sciences.

5
What is Bioinformatics?
6
History of Bioinformatics
  • Biologists were searching for algorithms to
    analyze and interpret their huge amount of
    empiric biological data
  • As well as computer aided modeling and simulation
  • International molecular biological databases
    arose to make data internationally accessible and
    comparable
  • Algorithms for gene- and protein prediction where
    developed
  • These efforts lead to the development of
    artificial neuronal networks, genetic algorithms
    and evolution strategies

7
Bioinformatics
  • Offers an ever more essential input to
  • Molecular Biology
  • Pharmacology (drug design)
  • Agriculture
  • Biotechnology
  • Clinical medicine
  • Anthropology
  • Forensic science
  • Chemical industries (detergent industries, etc.)

8
Organism, Organ, Cell
Organism
9
The Cell
Nucleus only in eukaryotic cells. Contains most
of the cell's genetic material.
The ER modifies proteins, makes macromolecules,
and transfers substances throughout the cell.
Ribosome translates mRNA into a polypeptide chain
(e.g., a protein).
Mitochondrion manufactures adenosine triphosphate
(ATP), which is used as a source of energy.
  • circa 100 trillion (1014) cells in a human
    organism
  • 200 different forms of cells

10
Molecular Biology
  • ... is the study of biology at a molecular level.
  • The field overlaps with other areas of biology,
    particularly genetics and biochemistry
  • Molecular biology concerns itself with
    understanding the interactions between the
    various systems of a cell, including the
    interrelationship of DNA, RNA and protein
    synthesis and learning how these interactions are
    regulated.

Schematic relationship between biochemistry,
genetics and molecular biology
11
Biochemistry and Genetics
  • Biochemistry is the study of molecules (e.g.
    proteins). Biochemists take an organism or cell
    and dissect it into its molecular components,
    such as enzymes, lipids and DNA, and reconstitute
    them in test tubes (in vitro).
  • Genetics is the study of the effect of genetic
    differences on organisms. Often this can be
    inferred by the absence of a normal component
    (e.g. one gene).

12
From Genes to Proteins
DNA
Gen
mRNA
Protein
13
The Human Genome -- 26 June 2000
14
DNA
  • 3.2 billion base pairs in every cell build
    the human genome
  • genes form only 1,5 of the human genome
  • a gene is a segment of the DNA, that encodes the
    constructon plan for a protein
  • in humans there are ca. 30,000 genes only

15
Chromosome
A chromosome is a very long, continuous piece of
DNA, which contains many genes, regulatory
elements and other intervening nucleotide
sequences.
http//www.tqnyc.org/NYC040844/Mitosis.htm
16
Chromosome
http//www.answers.com/topic/human-karyogram-png
17
DNA - Sequence
.....acctc ctgtgcaaga acatgaaaca cctgtggttc
ttccttctcc tggtggcagc tcccagatgg gtcctgtccc
aggtgcacct gcaggagtcg ggcccaggac tggggaagcc
tccagagctc aaaaccccac ttggtgacac aactcacaca
tgcccacggt gcccagagcc caaatcttgt gacacacctc
ccccgtgccc acggtgccca gagcccaaat cttgtgacac
acctccccca tgcccacggt gcccagagcc caaatcttgt
gacacacctc ccccgtgccc ccggtgccca gcacctgaac
tcttgggagg accgtcagtc ttcctcttcc ccccaaaacc
caaggatacc cttatgattt cccggacccc tgaggtcacg
tgcgtggtgg tggacgtgag ccacgaagac cccgaggtcc
agttcaagtg gtacgtggac ggcgtggagg tgcataatgc
caagacaaag ctgcgggagg agcagtacaa cagcacgttc
cgtgtggtca gcgtcctcac cgtcctgcac caggactggc
tgaacggcaa ggagtacaag tgcaaggtct ccaacaaagc
aaccaagtca gcctgacctg cctggtcaaa ggcttctacc
ccagcgacat cgccgtggag tgggagagca atgggcagcc
ggagaacaac tacaacacca cgcctcccat gctggactcc
gacggctcct tcttcctcta cagcaagctc accgtggaca
agagcaggtg gcagcagggg aacatcttct catgctccgt
gatgcatgag gctctgcaca accgctacac gcagaagagc
ctctc.....
18
DNA - Deoxyribonucleic acid
  • Deoxyribonucleic acid (DNA) forms a double
    stranded helix.
  • A sugar-phosphate backbone forms the outer shell
    on the helix
  • The two strands of DNA run in opposite
    directions.
  • Bases face towards each other and form hydrogen
    bonds
  • carries the generic instructions (genes)

free Bases Cytosine - C Guanine -
G Adenine - A Thymine - T
complementary base pairs
19
DNA - Deoxyribonucleic acid
  • A nucleotide is an organic molecule build of
    three components
  • one out of five bases (A, G, C, T and U in RNA)
  • a pentose sugar (deoxyribose in DNA or ribose in
    RNA)
  • and a phosphate group.

Nucleoside Nucleobase Pentose Nucleotide
Nucleobase Pentose Phosphate Group
20
DNA - Deoxyribonucleic acid
21
DNA
base
sugar
phosphate
Sugar Phosphate Backbone
3
5
5
Base pair
3
hydrogen bond
read as 3 prime and 5 prime
22
DNA - Molecule
DNA-sequence (Alphabet ATGC)
CCTAGACATTGCTTTCCCATCCTGCTACTCAATGACAGTTTCTGGTTTCA
CTGGG TCACTCTCATCTTGATGCACTCCCGGGCAAGAGCTAACTGAAAG
GCAGCTGCGT AACACATACCA GACACAACAGTTTATCATGGGAGAGTG
AATTAAACCAGGAA...
23
RNA Ribonucleic acid
In RNA the base Thymine (T) is replaced by Uracil
(U). The other difference to DNA is that the
sugar (Pentose) will be Ribose instead of
Deoxiribose. Ribose has an additional hydroxyl
group.
Bases Cytosine - C Guanine - G Adenine
- A Uracil - U
Uracil
RNA transmits genetic information from DNA (via
transcription) into proteins (by translation).
RNA is almost exclusively found in the
single-stranded form.
24
RNA Ribonucleic acid
  • RNA plays several roles in biology
  • Messenger RNA (mRNA) is transcribed directly
    from a gene's DNA and is used to
  • encode proteins.
  • RNA genes are genes that encode functional RNA
    molecules in contrast to mRNA,
  • these RNA do not code for proteins. The
    best-known examples of RNA genes are
  • transfer RNA (tRNA) and ribosomal RNA (rRNA).
    Both forms participate in the
  • process of translation, but many others exist.
  • RNA forms the genetic material (genomes) of some
    kinds of viruses.
  • Double-stranded RNA (dsRNA) is used as the
    genetic material of some RNA viruses
  • and is involved in some cellular processes,
    such as RNA interference.

25
Proteins
  • Proteins have a variety of roles that they must
    fulfil
  • they are the enzymes that rearrange chemical
    bonds.
  • they carry signals to and from the outside of the
    cell, and within the cell.
  • they transport small molecules.
  • they form many of the cellular structures.
  • they regulate cell processes, turning them on and
    off and controlling their rates.

26
Proteins Amino Acids
  • there are 20 different types of amino acids (see
    below).
  • different sequences of amino acids fold into
    different 3-D shapes.
  • Proteins can range from fewer than 20 to more
    than 5000 amino acids in length.
  • Each protein that an organism can produce is
    encoded in a piece of the DNA called a gene.
  • the single-celled bacterium E.coli has about 4300
    different genes.
  • Humans are believed to have about 30,000
    different genes (the exact number as yet
    unresolved),

27
Proteins Amino Acids
Protein-Sequence (Alphabet ACDEFGHIKLMNPQRSTVWY)

MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIR
EISLLK...
  • a typical human cell contains about 100 million
    proteins of about 10,000 types

28
Proteins Amino Acids
  • Properties of amino acids
  • play a role in the construction of 3-D stuctures
    in proteins

29
Proteins
Primary protein structure is the sequence of a
chain of amino acids
Secondary protein structure occurs when the
sequence of amino acids are linked by
hydrogen bonds.
Tertiary protein structure occurs when certain
attractions are present between alpha
helices and pleated sheets.
Quaternary protein structure is a protein
consisting of more than one amino acid chain.
30
Proteins
31
Proteins - Summary
  • DNA sequence determines protein sequence
  • Protein sequence determines protein structure
  • Protein structure determines protein folding and
    function

32
Gene Expression
33
Transcription
34
Gene Expression - Transcription
Messenger RNA (mRNA) Messenger RNA is RNA that
carries information from DNA to the ribosome
sites of protein synthesis in the cell. Once
mRNA has been transcribed from DNA, it is
exported from the nucleus into the cytoplasm,
where it is bound to ribosomes and translated
into protein. Non-coding RNA or "RNA genes"
RNA genes (sometimes referred to as non-coding
RNA or small RNA) are genes that encode RNA that
is not translated into a protein. The most
prominent examples of RNA genes are transfer RNA
(tRNA) and ribosomal RNA (rRNA), both of which
are involved in the process of translation.
35
Translation
36
Translation
37
Translation
38
Gene Expression - Translation
  • The genetic code is made up of
  • three letter 'words' (termed a
  • codon) formed from a sequence of
  • three nucleotides (e.g.. ACT, CAG,
  • TTT).
  • These codons can then be
  • translated with messenger RNA
  • and then transfer
  • RNA, with a codon corresponding
  • to a particular amino acid.
  • Since there are 64 possible
  • codons, most amino acids have
  • more than one possible codon.
  • There are also three 'stop' or
  • 'nonsense' codons signifying the
  • end of the coding region.

39
A gene codes for a protein
CCTGAGCCAACTATTGATGAA
CCUGAGCCAACUAUUGAUGAA
PEPTIDE
40
Metabolic networks next level of the
functional/organisational hierarchy
Protein networks guide the biochemistry of living
cells
Kegg database (Japan)
41
Levels of the functional/organizational hierarchy
42
Outlook coming lecture
  • Genomics
  • Proteomics

43
Introduction to molecular and cell biology
  • Thanks for your attention!
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