Download Lecture Slides - Computer Science

Basic Molecular Biology
Many slides by
Omkar Deshpande
Overview
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Structures of biomolecules
Central Dogma of Molecular Biology
Overview of this course
Computer scientists vs Biologists
Human Genome Program, U.S. Department of Energy, Genomics and Its Impact on Medicine and Society: A 2001 Primer, 2001
Watson and Crick
Macromolecule
(Polymer)
DNA
Monomer
RNA
Ribonucleotides (NTP)
Protein or Polypeptide
Amino Acid
Deoxyribonucleotides
(dNTP)
Nucleic acids (DNA and RNA)
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Form the genetic material of all living
organisms.
Found mainly in the nucleus of a cell (hence
“nucleic”)
Contain phosphoric acid as a component
(hence “acid”)
They are made up of nucleotides.
Nucleotides
Nitrogenous
Base
Phosphate
Group
Sugar
Nitrogenous
Base
Phosphate
Group
Sugar
DNA
A
G
C
G
A
C
T
G
A=T
G=C
The gene and the genome
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Genome = The entire DNA sequence within
the nucleus.
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The information in the genome is used for
protein synthesis
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A gene is a length of DNA that codes for a
(single) protein.
How big are genomes?
Organism
Genome Size (Bases)
Estimated Genes
Human (Homo sapiens)
3 billion
30,000
Laboratory mouse (M.
musculus)
2.6 billion
30,000
Mustard weed (A. thaliana)
100 million
25,000
Roundworm (C. elegans)
97 million
19,000
Fruit fly (D. melanogaster)
137 million
13,000
Yeast (S. cerevisiae)
12.1 million
6,000
Bacterium (E. coli)
4.6 million
3,200
Human immunodeficiency
virus (HIV)
9700
9
Repeats
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The DNA is full of repetitive elements (those
that occur over & over & over)
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There are several type of repeats, including
SINEs & LINEs (Short & Long Interspersed
Elements) (1 million just ALUs) and low
complexity elements.
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Their function is poorly understood, but they
make problems more difficult.
Central dogma
ZOOM
IN
tRNA
transcription
DNA
rRNA
snRNA
translation
mRNA
POLYPEPTIDE
Transcription
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The DNA is contained in the nucleus of the
cell.
A stretch of it unwinds there, and its message
(or sequence) is copied onto a molecule of
mRNA.
The mRNA then exits from the cell nucleus.
DNA
RNA
A
G
A
A=T
G=C
G
C
C
G
G
A
A
C
TU
C
T
U
G
G
More complexity
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The RNA message is sometimes “edited”.
Exons are nucleotide segments whose
codons will be expressed.
Introns are intervening segments (genetic
gibberish) that are snipped out.
Exons are spliced together to form mRNA.
Splicing
frgjjthissentencehjfmkcontainsjunkelm
thissentencecontainsjunk
Key player: RNA polymerase
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It is the enzyme that brings about
transcription by going down the line, pairing
mRNA nucleotides with their DNA
counterparts.
Promoters
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Promoters are sequences in the DNA just
upstream of transcripts that define the sites of
initiation.
Promoter
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5’
3’
The role of the promoter is to attract RNA
polymerase to the correct start site so
transcription can be initiated.
Promoters
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Promoters are sequences in the DNA just
upstream of transcripts that define the sites of
initiation.
Promoter
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5’
3’
The role of the promoter is to attract RNA
polymerase to the correct start site so
transcription can be initiated.
Transcription – key steps
DNA
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Initiation
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Elongation
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Termination
DNA
+
RNA
Transcription – key steps
DNA

Initiation

Elongation

Termination
Transcription – key steps
DNA

Initiation

Elongation

Termination
Transcription – key steps
DNA

Initiation

Elongation

Termination
Transcription – key steps
DNA

Initiation

Elongation

Termination
DNA
+
RNA
Genes can be switched on/off
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In an adult multicellular organism, there is a
wide variety of cell types seen in the adult.
eg, muscle, nerve and blood cells.
The different cell types contain the same
DNA though.
This differentiation arises because different
cell types express different genes.
Promoters are one type of gene regulators
Transcription (recap)
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The DNA is contained in the nucleus of the
cell.
A stretch of it unwinds there, and its message
(or sequence) is copied onto a molecule of
mRNA.
The mRNA then exits from the cell nucleus.
Its destination is a molecular workbench in
the cytoplasm, a structure called a ribosome.
Translation
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How do I interpret the information carried by
mRNA to the Ribosome?
Think of the sequence as a sequence of
“triplets”.
Think of AUGCCGGGAGUAUAG as AUGCCG-GGA-GUA-UAG.
Each triplet (codon) maps to an amino acid.
The Genetic Code
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f : codon  amino acid
1968 Nobel Prize in medicine – Nirenberg
and Khorana
Important – The genetic code is universal!
It is also redundant / degenerate.
The Genetic Code
Proteins
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Composed of a chain of amino acids.
20 possible groups
R
|
H2N--C--COOH
|
H
Proteins
R
|
H2N--C--COOH
|
H
R
|
H2N--C--COOH
|
H
Dipeptide
This is a peptide bond
R O
R
| II
|
H2N--C--C--NH--C--COOH
|
|
H
H
Protein structure
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Linear sequence of amino acids folds to form
a complex 3-D structure.
The structure of a protein is intimately
connected to its function.
The 3-D shape of proteins
gives them their working ability
– the ability to bind with other
molecules.
Our course (2427)
Part 1, DNA:
Assembly,
Evolution,
Alignment
Part 2, Genes:
Prediction,
Regulation
Part 3,
Structures &
Interactions
transcription
DNA
rRNA
snRNA
translation
mRNA
POLYPEPTIDE
Computer Scientists vs
Biologists
(courtesy Steven Skiena, SUNY
Stony Brook)
Computer scientists vs
Biologists
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Biologists strive to understand the very
complicated, very messy natural world.
Computer scientists seek to build their own
clean and organized virtual worlds.
Computer scientists vs
Biologists
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Computer scientists get high-paid jobs after
graduation.
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Biologists typically have to complete one or
more post-docs...
Computer scientists vs
Biologists
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Nothing is ever completely true or false in
Biology.
Everything is either true or false in computer
science.