Download Background - Florida Tech Department of Computer Sciences

Molecular Biology
Background
Debasis Mitra
Florida Tech
Credit: Pevezner text-site
5/4/2017
dmitra
1
Section1: What is Life
made of?
5/4/2017
dmitra
2
2 types of cells: Prokaryotes
v.s.Eukaryotes
5/4/2017
dmitra
3
Life begins with Cell


5/4/2017
A cell is a smallest structural unit of
an organism that is capable of
independent functioning
All cells have some common
features
dmitra
4
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.
5/4/2017
dmitra
5
Prokaryotes and
Eukaryotes, continued
Prokaryotes
Eukaryotes
Single cell
Single or multi cell
No nucleus
Nucleus
No organelles
Organelles
One piece of circular Chromosomes
DNA
No mRNA post
transcriptional
modification
5/4/2017
Exons/Introns
splicing
dmitra
6
Overview of organizations of life





5/4/2017
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
vaious functions.
dmitra
7
Chromosomes
Organism
Number of base pair
number of Chromosomes
--------------------------------------------------------------------------------------------------------Prokayotic
Escherichia coli (bacterium)
4x106
1
Eukaryotic
Saccharomyces cerevisiae
(yeast)
Drosophila melanogaster(insect)
Homo sapiens(human)
Zea mays(corn)
5/4/2017
1.35x107
1.65x108
2.9x109
5.0x109
dmitra
17
4
23
10
8
Bio-molecules



5/4/2017
Nucleic acids (DNA, RNA): Library of
life
Proteins: Workhorse of life
Fatty acids, carbohydrates, and other
supporting molecules
dmitra
9
DNA

DNA has a double helix
structure which
composed of




sugar molecule
phosphate group
and a base (A,C,G,T)
DNA always reads from
5’ end to 3’ end for
transcription replication
5’ ATTTAGGCC 3’
3’ TAAATCCGG 5’
5/4/2017
dmitra
10
DNA, RNA, and the Flow of
Information
Replication
Transcription
5/4/2017
Translation
dmitra
11
Proteins Functions






5/4/2017
Structural
Enzymes
Information exchange (e.g., across
cell walls)
Transporting other molecules (e.g.,
oxygen to cells)
Activating-deactivating genes
Etc.
dmitra
12
Proteins

Amino acids

Protein is a chain of “residues”

5/4/2017
20 to 5000 long, typically a few
hundred long
dmitra
13
Protein structure





5/4/2017
Important for its function
Primary structure: sequence
Secondary structure: a few
topological features
Tertiary structure: 3D folding
Quaternary structure: Protein
complex
dmitra
14
Protein Folding






Proteins tend to fold into the lowest free
energy conformation.
Proteins begin to fold while the peptide is
still being translated.
Proteins bury most of its hydrophobic
residues in an interior core to form an α
helix.
Most proteins take the form of secondary
structures α helices and β sheets.
Molecular chaperones, hsp60 and hsp 70,
work with other proteins to help fold newly
synthesized proteins.
Much of the protein modifications and
folding occurs in the endoplasmic
reticulum and mitochondria.
5/4/2017
dmitra
15
Protein Folding (cont’d)



The structure that a
protein adopts is
vital to it’s
chemistry
Its structure
determines which
of its amino acids
are exposed carry
out the protein’s
function
Its structure also
determines what
substrates it can
react with
5/4/2017
dmitra
16
Nucleic acids

Two types:

DNA: Deoxy-ribonucleic acid
RNA: Ribonucleic acid

5/4/2017
dmitra
17
Nucleic acids
5/4/2017

Sugar molecule chain forms the
base of the polymer

Two types of sugar: ribose (RNA),
2’-deoxyribose (DNA)
dmitra
18
Nucleic acids: DNA
5/4/2017

4 types of bases connected to
sugar molecules: Adenine (a),
Guanine (g), Thymine (t) and
Cytosine (c)

A and T forms strong bonds, and
so do G and C
dmitra
19
An Introduction to Bioinformatics Algorithms
The Purines
5/4/2017
www.bioalgorithms.info
The Pyrimidines
2015
An Introduction to Bioinformatics Algorithms
DNA
www.bioalgorithms.info
• DNA has a double helix
structure which
composed of
• sugar molecule
• phosphate group
• and a base (A,C,G,T)
• DNA always reads from
5’ end to 3’ end for
transcription replication
5’ ATTTAGGCC 3’
3’ TAAATCCGG 5’
5/4/2017
dmitra
21
Nucleic acids: DNA



5/4/2017
Double stranded: two strands of
sugar molecule-chains
Each strand is directed: 5’ to 3’
Attached inside by base-pairings
(a-t and g-c)
dmitra
22
An Introduction to Bioinformatics Algorithms
www.bioalgorithms.info
Double helix of DNA
5/4/2017
2315
Discovery of DNA

DNA Sequences



Chargaff and Vischer, 1949
 DNA consisting of A, T, G, C
• Adenine, Guanine, Cytosine, Thymine
Chargaff Rule
 Noticing #A#T and #G#C
• A “strange but possibly meaningless”
phenomenon.
Wow!! A Double Helix



5/4/2017
Watson and Crick, Nature, April 25, 1953
1 Biologist
1 Physics Ph.D. Student
900 words
Nobel Prize
Crick
Watson
Rich, 1973
 Structural biologist at MIT.
 DNA’s structure in atomic resolution.
dmitra
24
Nucleic acids: DNA

Each strand is complementary and
reverse to the other

If s=agacgt
reverse(s)=tgcaga
reverse-complement(s)=acgtct
Double-strand:
5/4/2017
5’--agacgt->3’
3’<-t ctgca—5’
dmitra
25
Nucleic acids: DNA

3D structure is helical

Double-stranded helix: like step ladder

Each unit is a base pair (sugar-basebase-sugar)


5/4/2017
DNA’s in cells are chromosomes (human
chromosome ~3*(10^9) bp long)
Squeezed 3D structure in cell may have
functional importance – not well studied
dmitra
26
DNA Replication
5/4/2017
dmitra
27
Nucleic acids: RNA
5/4/2017

Replace t with u (uracil) as base

May or may not be (mostly not) double
stranded

Functions: Information storage like DNA,
sometimes workhorse like proteins

Possible evolutionary precursor to DNA
and protein
dmitra
28
Genetic code
5/4/2017

Proteins do almost all the works!!

Information for coding proteins are
stored on DNA’s (or RNA’s): genes

Three consecutive bases on a gene
codes an amino acid, or the STOP code:
codon

The table is called genetic code
dmitra
29
Cell Information:
Instruction book of Life


DNA, RNA, and
Proteins are
examples of strings
written in either the
four-letter nucleotide
of DNA and RNA (A
C G T/U)
or the twenty-letter
amino acid of
proteins. Each amino
acid is coded by 3
nucleotides called
codon. (Leu, Arg,
Met, etc.)
5/4/2017
dmitra
30
Overview of DNA to RNA to
Protein

A gene is expressed in two steps
1)
2)
5/4/2017
Transcription: RNA synthesis
Translation: Protein synthesis
dmitra
31
An Introduction to Bioinformatics Algorithms
www.bioalgorithms.info
Central Dogma of Biology
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.
Assembly
Protein
Sequence
Analysis
Sequence analysis
Gene Finding
5/4/2017
3215
Transcription
5/4/2017

Genes are transcribed to proteins:
typically one gene to one protein

Genes are subsequenes on
chromosomes started by a
promoter region, ended around a
stop codon
dmitra
33
Transcription





5/4/2017
Steps:
DNA is split over gene after
promoter is recognized (may have
other regulatory regions upstream)
mRNA is copied from the gene
Exons are spliced out from the
mRNA keeping the introns only
Ribosome (rRNA and protein
complex) works on mRNA
dmitra
34
Transcription




The process of
making RNA from
DNA
Catalyzed by
“transcriptase”
enzyme
Needs a promoter
region to begin
transcription.
~50 base
pairs/second in
bacteria, but multiple
transcriptions can
occur simultaneously
http://ghs.gresham.k12.or.us/science/ps/sci/ibbio/chem/nucleic/chpt15/transcription.gif
5/4/2017
dmitra
35
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.
5/4/2017
dmitra
36
Translation
tRNA are attached to codons on
mRNA
 On the other end the tRNA attracts
appropriate amino acid
 Amino acids are zipped up
 No tRNA for STOP codon
 Every step is facilitated by
appropriate enzyme
Central Dogma of biology

5/4/2017
dmitra
37
Translation, continued



Catalyzed by Ribosome
Using two different sites,
the Ribosome continually
binds tRNA, joins the
amino acids together and
moves to the next
location along the mRNA
~10 codons/second, but
multiple translations can
occur simultaneously
http://wong.scripps.edu/PIX/ribosome.jpg
5/4/2017
dmitra
38
Revisiting the Central
Dogma


5/4/2017
In going from DNA to
proteins, there is an
intermediate step where
mRNA is made from DNA,
which then makes protein
 This known as The
Central Dogma
Why the intermediate step?
 DNA is kept in the
nucleus, while protein
sythesis happens in the
cytoplasm, with the help of
ribosomes
dmitra
39
The Central Dogma
(cont’d)
5/4/2017
dmitra
40
Open Reading Frame


5/4/2017
Three reading frames in a strand
Complementary strand may have
another three frames
dmitra
41
Types of chromosomes
5/4/2017

Procaryotes (bacteria, blue algae):
circular

Eucaryotes (has nuclear wall): diploid
(human has 23 pairs)

Homologous genes and alleles (e.g.,
human hemoglobin of type A, B, and O)

Haploid chromosomes in Eucaryote sex
cells
dmitra
42
DNA Sequencing





5/4/2017
A DNA fragment is split at each position
starting from one end
Four tubes: one containing molecules
ending with G, one with A, one with T
and another one with C
Electrophoresis separates each chunk of
different size in each tube [page 22]
Information is recombined to sequence
the DNA chunk
Can be done for the size of only ~1K bp
long chunk
dmitra
43
DNA Sequencing
5/4/2017

Human DNA is ~10^9 bp long

Restriction enzyme cuts at
restriction sites (a product of
genetic engineering) [page 18]

After sequencing, information from
fragments need to be recombined
to get the broader picture
dmitra
44
DNA Sequencing




5/4/2017
Depends on finding restriction
site/enzyme for fragmenting DNA of
appropriate size
Privately funded Tiger project (Celera
now) used heat and vibration to create
fragments
Recombining information is no longer
trivial because fragment’s location is no
longer known
Needed Fragment assembly algorithm
dmitra
45
DNA Sequencing



5/4/2017
Needs multiple copies of DNAs
Recombinant DNA by biologically
copying them within host
organisms
Polymerase Chain Reaction: heat
and tear two strands of DNA, then
let each strand attract nucleic acids
to form double stranded DNA,
repeat
dmitra
46