cse111bio:programdesigni$ undergraduate$ta:$ lecture’3 ... · 8/30/16 2 genome’sizes’ •...
TRANSCRIPT
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CSE 111 Bio: Program Design I Lecture 3: Intro to Bio
DNA and strings Tanya Berger-‐Wolf (CS) & Boris Igić (Bio)
University of Illinois, Chicago August 30, 2016
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5/ Announcements
What: CS Peer Tutoring for CS 1xx, 2xx & 3xx level classes Where: Tutoring room in CS Lounge, SEL 2258 When: Monday -‐ Friday, 10am -‐ 2pm; & 4 -‐ 9pm Schedule: CS website under 'Academics' & 'Courses'. Link www.cs.uic.edu/~grad/F16_Peer_Tutoring_Schedule.pdf Undergraduate TA: Haley Widel Office hours: Wednesday 11am – 1pm in CS Lounge, SEL 2258
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Genome Sizes
• Carsonella ruddii, 160,000 base pairs (bp) • porcine (pig) circovirus 1.7Kbp, ssDNA • cowpea mosaic virus, 9.4Kbp, ssRNA • phi29 (Bacillus phage) 19Kbp, dsDNA • Paris japonica, 150Gbp • Protopterus aethiopicus, 130Gbp • Amoeba dubia, 670Gbp
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Relevant Theories: Cell • In 1665, Robert Hooke coined the term cell to describe the structures he could see in cork with some of the first microscopes. Since then, technology has given us an increasingly complex view of the basic unit of life.
• Cell theory: all organisms have one or more cells, basic units of organizahon; cells arise from previously exishng cells.
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Relevant Theories: Genes • In 1866 Gregor Mendel published his experiments on pea plants, demonstrahng that discrete traits are transmiPed over generahons in a predictable manner.
• T. H. Morgan in 1915 establishes chromosomes as carriers of heredity.
• Theory of heredity: traits are affected by genes, transmiPed between generahons in a predictable manner.
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Relevant Theories: Genes What is a chromosome made of?
DNA and RNA Structure: Polymers of sugar, phosphate, and base
OH
O
3ʹ′
PO4
base
CH2 O
base
O P O
C
O –O
CH2
1ʹ′
2ʹ′
4ʹ′
5ʹ′
1ʹ′
2ʹ′
3ʹ′
3ʹ′
4ʹ′
5ʹ′
5ʹ′
What is this 3ʹ′ or 5ʹ′ stuff?
• the leading carbon aPaches to a phosphate-‐P (5’)
• the last trailing carbon is aPached to hydroxyl–OH (3’)
• base = A, C, G, T
DNA Structure
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3ʹ′
5ʹ′
5ʹ′
3ʹ′
AnWparallel Strands
• Nucleohdes in DNA backbone are bonded from phosphate to sugar between 3ʹ′ & 5ʹ′ carbons
– DNA molecule has “direchon” – complementary strand runs in opposite direchon
DNA Structural Bonding
3ʹ′
5ʹ′ 3ʹ′
5ʹ′
covalent phosphodiester bonds
STRONG
hydrogen WEAK bonds
• Purines – adenine (A) – guanine (G)
• Pyrimidines – thymine (T) – cytosine (C)
• Pairing – A : T
• 2 bonds – C : G
• 3 bonds
DNA Pairing Rules
– base pairing allows each strand to serve as a template for a new strand
– new strand is 1/2 parent template & 1/2 new DNA
• semi-conservative copy process
DNA Replication
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3’
5’ 3’
5’
5’
3’ 3’ 5’
helicase
primase
DNA polymerase III
DNA polymerase III
DNA polymerase I
ligase
leading strand
lagging strand
SSB
direcWon of replicaWon
DNA Replication The Central Dogma of Molecular Biology
DNA -‐> RNA -‐> Protein
The Central Dogma of Molecular Biology
The Central Dogma of Molecular Biology
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The Central Dogma of Molecular Biology
The Central Dogma of Molecular Biology
The Central Dogma of Molecular Biology
DNA Sequencing
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DNA Sequencing: Sanger Method DNA Sequencing: Shotgun Assembly
Q: Suppose the ‘shotgun' sequences are: CTGC AGCAT AGCATG GCTGC
What is the original sequence? A. AGCATGCTGC B. CTGCAGCATAGCATGGCTGC C. GCTGCAGCATG D. AGCATGC E. No clue
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>>> biologist1 = "Watson" >>> biologist1 'Watson’ >>> biologist2 = 'Crick' >>> biologist2 'Crick‘ >>> firstbiologist = ‘Rosalind Franklin’ >>> firstbiologist ‘Rosalind Franklin’ >>> print firstbiologist Rosalind Franklin >>> print biologist1+biologist2 ‘WatsonCrick’ >>> result = biologist1+biologist2 >>> print “The two biologists are “, result The two biologists are ‘WatsonCrick’
hPp://blogs.nature.com/freeassociahon/tag/watson-‐and-‐crick
Copyright (c) Henry Grant Archive/Museum of London
hPps://profiles.nlm.nih.gov/KR/