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CSCI 474
Bioinformatics
Filip Jagodzinski
Announcements
Labs
Tuesdays and Fridays
Noon-noon:50
CF162 and 164
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 2
Article Reading
First article reading
and summary
assignment
Watson JD, Crick FH (1953). "Molecular Structure of
Nucleic Acids: A Structure for Deoxyribose Nucleic
Acid". Nature 171 (4356): 737–8.
• Use google scholar or any of many online resources to find and download the 2 page
article
• Read the article
• Compose a 1 paragraph summary and 1 paragraph critique of the article
• Summary : Explain WHAT the article is about, WHY it was written (motivation), and
HOW the science was carried out
• Critique : Discuss shortcomings of the manuscript’s presentation. Mention items that
are not clear. Were the diagrams helpful? Is the article accessible to a nonspecialist? Provide constructive criticism that the author(s) might use to improve
the article. You do NOT have to critique the science.
Check Canvas for the due date
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 3
From last time …
Q: What do the A, T, C and G letters refer to?
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 4
From last time …
Q: What do the A, T, C and G letters refer to?
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 5
From last time …
• What does the DNA sequence of a species tell us about an organism?
• What are the similarities and differences among different living organisms?
• What metrics did you use to determine which organisms were most or least
like the others?
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 6
From last time …
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 7
From last time …
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 8
From last time …
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 9
From last time …
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 10
Today
Biology and Chemistry Primers
Databases
(unless explicitly noted, figures are from Wikipedia)
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 11
Biology and Chemistry Primers – The Cell
Key terms
cell
nucleus
DNA
RNA
Q: How many cells are there in a
human body?
Q: What is the role of the nucleus?
Q: Where does DNA reside? What is
the role of RNA?
Q: Where are Proteins synthesized?
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 12
Biology and Chemistry Primers – The Cell
Key terms
cell
nucleus
DNA
RNA
Q: How many cells are there in a
human body?
Q: What is the role of the nucleus?
Q: Where does DNA reside? What is
the role of RNA?
Q: Where are Proteins synthesized?
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 13
Biology and Chemistry Primers – The Cell
10-100 micrometers (mm) large (3070 trillion cells in a human)
Double-membraned nucleus contains
the DNA
RNA is synthesized in the nucleus
Proteins synthesized in the cytoplasm
by ribosomes and with the help of
RNA
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 14
Biology and Chemistry Primers - DNA
Key terms
Encode genetic information
Double stranded
Helix
Deoxyribose
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 15
Biology and Chemistry Primers - DNA
Key terms
Encode genetic information
Double stranded
Helix
Deoxyribose
Q: What does it mean to “encode” genetic
information?
Q: What is deoxyribose?
Q: What are the 3’ and 5’ ends of DNA?
Q: How many base pairs are there in the
human genome?
Q: What is the “structure” of DNA?
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 16
Biology and Chemistry Primers - DNA
Key terms
Encode genetic information
Double stranded
Helix
Deoxyribose
Q: What does it mean to “encode” genetic
information?
Q: What is deoxyribose?
Q: What are the 3’ and 5’ ends of DNA?
Q: How many base pairs are there in the
human genome?
Q: What is the “structure” of DNA?
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 17
Biology and Chemistry Primers - DNA
The sequence of nucleotides is the genetic “code”
Here the sequence is ACTG
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 18
Biology and Chemistry Primers - DNA
The sequence of nucleotides is the genetic “code”
Here the sequence is ACTG
Two nucleotides bind together to form a
base pair
G(uanine) always pairs with C(cytosine),
and A(denine) always pairs with
T(hymine)
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 19
Biology and Chemistry Primers - DNA
There are approximately 3 Billion base
pairs in the human genome
Q: How many “meters” is the human
genome? (if you were to uncoil it?)
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 20
Biology and Chemistry Primers - DNA
There are approximately 3 Billion base
pairs in the human genome
Q: How many “meters” is the human
genome? (if you were to uncoil it?)
Approximately 1012 meters
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 21
Biology and Chemistry Primers - DNA
Q: What is dexoyribose?
Q: What is its role in DNA?
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 22
Biology and Chemistry Primers - DNA
Deoxyribose
ribose
?
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 23
Biology and Chemistry Primers - DNA
Deoxyribose
ribose
ribose
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 24
Biology and Chemistry Primers - DNA
Deoxyribose
ribose
Carbohydrate
(sugar) … with 5
carbon atoms, 10
hydrogen atoms,
and 5 oxygen atoms
ribose
Q: Where are all
10 hydrogen
atoms?
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 25
Biology and Chemistry Primers - DNA
Deoxyribose
?
ribose
ribose
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 26
Biology and Chemistry Primers - DNA
Deoxyribose
Take away
?
ribose
ribose
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 27
Biology and Chemistry Primers - DNA
Deoxyribose
Take away
ribose
CSCI 474 Bioinformatics
Filip Jagodzinski
oxygen
ribose
2-deoxyribose
Slide 28
Biology and Chemistry Primers - DNA
Deoxyribose
Take away
ribose
oxygen
ribose
2-deoxyribose
Q: What does the
“2” refer to?
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 29
Biology and Chemistry Primers - DNA
5’
3’
2-deoxyribose
5’
3’
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 30
Biology and Chemistry Primers - DNA
Task: Identify the phosphate, sugar,
and base components of DNA
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 31
Biology and Chemistry Primers - DNA
Task: Identify the phosphate, sugar,
and base components of DNA
Phosphate
Sugar
Base
The complementary strands
are anti-parallel
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 32
Biology and Chemistry Primers - DNA
Q: What is the structure of DNA?
Q: Where “are” the bases in a chromosome?
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 33
Biology and Chemistry Primers - DNA
Q: What is the structure of DNA?
Q: Where “are” the bases in a chromosome?
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 34
Biology and Chemistry Primers - DNA
Depending on whether the
DNA is “in use,” it can exist
in different forms –
condensed, uncoiled, etc.
Source : Qiu J. Epigenetics: unfinished
symphony. Nature. 2006 May 11;441(7090):143-5.
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 35
Chromosome refers to the
condensed, or coiled, form of DNA
Biology and Chemistry Primers - DNA
Short arm
centromere
Long arm
chromatid
Source : Qiu J. Epigenetics: unfinished
symphony. Nature. 2006 May 11;441(7090):143-5.
CSCI 474 Bioinformatics
Filip Jagodzinski
This is a gross simplification. DNA is much
more dense than the strands shown here.
Remember : 3 BILLION base pairs among 23
human chromosomes
Slide 36
Biology and Chemistry Primers - RNA
Key terms
RNA
mRNA
Q: What are the differences
(structural, functional, etc.)
between DNA and RNA?
Q: What are the nucleic acids
the make up RNA?
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 37
Biology and Chemistry Primers - RNA
Key terms
RNA
mRNA
Q: What are the differences
(structural, functional, etc.)
between DNA and RNA?
Q: What are the nucleic acids
the make up RNA?
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 38
Biology and Chemistry Primers - RNA
Ribonucleic
Acid is a single
stranded
molecule
(Although it can
coil in on itself
to assume
globular-like
forms and form
loop-like
regions)
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 39
Biology and Chemistry Primers - RNA
RNA’s backbone is made up of ribose
(instead of 2-deoxyriboxe)
ribose
CSCI 474 Bioinformatics
Filip Jagodzinski
2-deoxyribose
Slide 40
Biology and Chemistry Primers - RNA
A
G
C
U
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 41
Biology and Chemistry Primers – Molecular Diagrams
• Atoms
• Orbitals
• aromaticity
CSCI 474 Bioinformatics
Filip Jagodzinski
(on the board explanation)
Slide 42
Biology and Chemistry Primers – DNA and RNA
Key terms
dsDNA
intron
exon
hnRNA
mRNA
codon
Transcription
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 43
Biology and Chemistry Primers – DNA and RNA
Key terms
T G G A C G T A C G T A T C G T
A C C T G C A T G C A T A G C A
dsDNA
intron
exon
hnRNA
mRNA
codon
Transcription
Q: What are the different forms of RNA, and what
is the purpose of each?
Q: How is DNA processed to make RNA?
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 44
Biology and Chemistry Primers – DNA and RNA
dsDNA
The double stranded DNA (dsDNA) includes exon
regions made up triplets of bases pairs that encode a
specific amino acid. Exons are expressed.
T G G A C G T A C G T A T C G T
A C C T G C A T G C A T A G C A
triplet triplet
intron
exon
triplet
triplet
i
Key terms
dsDNA
intron
exon
hnRNA
mRNA
codon
Transcription
exon
Introns are interweaving sequences of base pairs
that are NOT expressed (manifest as an amino
acid in a polypeptide produced by the ribosome)
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 45
Biology and Chemistry Primers – DNA and RNA
dsDNA
The double stranded DNA (dsDNA) includes exon
regions made up triplets of bases pairs that encode a
specific amino acid. Exons are expressed.
T G G A C G T A C G T A T C G T
A C C T G C A T G C A T A G C A
triplet triplet
hnRNA
intron
exon
triplet
triplet
i
Key terms
dsDNA
intron
exon
hnRNA
mRNA
codon
Transcription
exon
U G G A C G U A C G U A U C G U
A C C T G C A T G C A T A
G C ATranscription is the process through which heterogeneous nuclear RNA
(hnRNA) is created that is identical to the 5’-3’ orientation of the dsDNA
(Uracil is substituted for Thymine)
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 46
Biology and Chemistry Primers – DNA and RNA
dsDNA
The double stranded DNA (dsDNA) includes exon
regions made up triplets of bases pairs that encode a
specific amino acid. Exons are expressed.
T G G A C G T A C G T A T C G T
A C C T G C A T G C A T A G C A
triplet triplet
exon
hnRNA
intron
triplet
triplet
i
dsDNA
intron
exon
hnRNA
mRNA
codon
Transcription
exon
U G G A C G U A C G U A U C G U
A C C T G C A T G C A T A
G C A
mRNA
A C G U A C G U A
C G U
CSCI 474 Bioinformatics
Filip Jagodzinski
Key terms
The hnRNA is processed
(excision) in which intron regions
are spliced out, and the
remaining exons are ligated to
form the mRNA
Slide 47
Biology and Chemistry Primers – DNA and RNA
dsDNA
The double stranded DNA (dsDNA) includes exon
regions made up triplets of bases pairs that encode a
specific amino acid. Exons are expressed.
T G G A C G T A C G T A T C G T
A C C T G C A T G C A T A G C A
triplet triplet
exon
triplet
i
U G G A C G U A C G U A U C G U
A C C T G C A T G C A T A
G C A
mRNA
A C G U A C G U A
C G U
codon
codon codon
CSCI 474 Bioinformatics
Filip Jagodzinski
dsDNA
intron
exon
hnRNA
mRNA
codon
Transcription
exon
hnRNA
intron
triplet
Key terms
codon
Each 3-base exon in the
mRNA is called a codon
mRNA travels OUT of the
nucleus (through nuclear
pores), and is the blueprint
for polypeptide synthesis
Slide 48
Biology and Chemistry Primers – DNA and RNA
Transcription
https://www.youtube.com/watch?v=ztPkv7wc3yU
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 49
Biology and Chemistry Primers – Ribosomes, Protein Synthesis
Key terms
Translation
Ribosome
tRNA
Codon
Amino acid
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 50
Biology and Chemistry Primers – Ribosomes, Protein Synthesis
Key terms
Q: How are proteins synthesized in the cell?
Q: What is RNA’s role in protein synthesis?
CSCI 474 Bioinformatics
Filip Jagodzinski
Translation
Ribosome
tRNA
Codon
Amino acid
Slide 51
Biology and Chemistry Primers – Ribosomes, Protein Synthesis
Key terms
Translation is the process through which
the ribosome produces a polypeptide
chain made up of amino acids. tRNA and
mRNA are both involved.
CSCI 474 Bioinformatics
Filip Jagodzinski
Translation
Ribosome
tRNA
Codon
Amino acid
Slide 52
Biology and Chemistry Primers – Ribosomes, Protein Synthesis
In the cytoplasm (outside of the nucleus, but still “inside”
the cell), transfer RNA (tRNA) molecules abound.
Key terms
Translation
Ribosome
tRNA
Codon
Amino acid
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 53
Biology and Chemistry Primers – Ribosomes, Protein Synthesis
At the 3’ end of a tRNA molecule, one of the 20
naturally occurring amino acids is attached
Key terms
Translation
Ribosome
tRNA
Codon
Amino acid
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 54
Biology and Chemistry Primers – Ribosomes, Protein Synthesis
mRNA
A C G U A C G U A
codon
codon codon
C G U
codon
Q: What is the relationship between
tRNA and codons, and between
codons and amino acids?
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 55
Biology and Chemistry Primers – Ribosomes, Protein Synthesis
mRNA
A C G U A C G U A
codon
codon codon
C G U
codon
A codon maps to one of
Ea the 20 naturally
occurring amino acids
The anticodon region (the anticodon loop) of a
tRNA molecule is made up of 3 bases that are
complementary to a codon in a mRNA
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 56
Biology and Chemistry Primers – Ribosomes, Protein Synthesis
mRNA
A C G U A C G U A
codon
codon codon
C G U
codon
A codon maps to one of
Ea the 20 naturally
occurring amino acids
Q: The tRNA molecule for the codon ACG has WHAT
anticodon on its anticodon loop?
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 57
Biology and Chemistry Primers – Ribosomes, Protein Synthesis
mRNA
A C G U A C G U A
codon
codon codon
C G U
codon
A codon maps to one of
Ea the 20 naturally
occurring amino acids
Codon ACG is complementary to anticodon UGC
Q: A tRNA with anticodon UGC has what
amino acid attached to its 3’ end?
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 58
Biology and Chemistry Primers – Ribosomes, Protein Synthesis
Q: What protein in the cytoplasm is responsible for protein synthesis
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 59
Biology and Chemistry Primers – Ribosomes, Protein Synthesis
Q: What protein in the cytoplasm is responsible for protein synthesis
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 60
Biology and Chemistry Primers – Ribosomes, Protein Synthesis
As the ribosome processes
(moves over) the mRNA,
codons are read one-by-one
tRNA molecules with
complementary anticodons,
with amino acids attached,
are retrieved from the
cytoplasm
The tRNAs’ amino acids are
joined end-to-end to form a
polypeptide chain
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 61
Biology and Chemistry Primers – Ribosomes, Protein Synthesis
Translation
https://www.youtube.com/watch?v=Jml8CFBWcDs
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 62
Biology and Chemistry Primers - Proteins
Key terms
Backbone
Amino acid
Hydrogen bonds
Hydrophobic interactions
Polypeptide
Secondary structure
Tertiary structure
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 63
Biology and Chemistry Primers - Proteins
Key terms
Q: What is a protein?
Q: What is its structure (backbone/R groups)?
Q: What is a protein’s function?
CSCI 474 Bioinformatics
Filip Jagodzinski
Backbone
Amino acid
Hydrogen bonds
Hydrophobic interactions
Polypeptide
Secondary structure
Tertiary structure
Slide 64
Biology and Chemistry Primers - Proteins
Proteins are made up of atoms. Each type of atom has characteristic
behaviors (how it interacts with other atoms) based on its composition
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 65
Biology and Chemistry Primers - Proteins
The ribosome joins amino acids end-to-end to form a polypeptide chain
The backbone of a polypeptide chain has certain properties … planarity in some
places, flexibility in others, rigidity in others
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 66
Biology and Chemistry Primers - Proteins
The ribosome joins amino acids end-to-end to form a polypeptide chain
The
primary
structure
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 67
Biology and Chemistry Primers - Proteins
The atoms among the
amino acids in a
polypeptide chain
interact with each
other to form bonds,
cause repulsion, angles
and distances are
imposed, etc.
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 68
Biology and Chemistry Primers - Proteins
These angle and distance constrains between atoms result in
secondary structures such as alpha helices and beta sheets
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 69
Biology and Chemistry Primers - Proteins
The secondary structures are folded (in a still not fully understood
process) into a protein’s tertiary structure.
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 70
Biology and Chemistry Primers - Proteins
The secondary structures are folded (in a still not fully understood
process) into a protein’s tertiary structure.
A protein bends and flexes, and interacts with other molecules
and proteins, to perform its function
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 71
Biology and Chemistry Primers – Databases
The first lab : locating the DNA sequence and protein structure of Hemoglobin
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 72
Up next
Friday Lab
Databases
CSCI 474 Bioinformatics
Filip Jagodzinski
Slide 73