1. Basic Molecular Biology
Many slides by Omkar Deshpande

2. Overview Structures of biomolecules Central Dogma of Molecular Biology
Overview of this course
Computer scientists vs Biologists

3. Human Genome Program, U. S
Human Genome Program, U.S. Department of Energy, Genomics and Its Impact on Medicine and Society: A 2001 Primer, 2001

5. Watson and Crick
They conducted no laboratory experiments but managed to guess the sum by analyzing its parts.
One of the greatest achievements of the 20th century

7. Macromolecule (Polymer)
Monomer
DNA
Deoxyribonucleotides (dNTP)
RNA
Ribonucleotides (NTP)
Protein or Polypeptide
Amino Acid

8. Nucleic acids (DNA and RNA)
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.

9. Nucleotides Sugar Sugar Nitrogenous Base Phosphate Group Nitrogenous

10. DNA T C A G G A T C
A = T
G = C

11. The gene and the genome
Genome = The entire DNA sequence within the nucleus.
The information in the genome is used for protein synthesis
A gene is a length of DNA that codes for a (single) protein.

12. How big are genomes? Organism Genome Size (Bases) Estimated Genes
Human (Homo sapiens)
3 billion
30,000
Laboratory mouse (M. musculus)
2.6 billion
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

13. Repeats
The DNA is full of repetitive elements (those that occur over & over & over)
There are several type of repeats, including SINEs & LINEs (Short & Long Interspersed Elements) (1 million just ALUs) and low complexity elements.
Their function is poorly understood, but they make problems more difficult.

14. Central dogma ZOOM IN tRNA transcription DNA rRNA snRNA translation
POLYPEPTIDE
mRNA

15. Transcription 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.

16. DNA
RNA T C A G G A T C G A U C
A = T
G = C
T  U

17. More complexity 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.

18. Splicing frgjjthissentencehjfmkcontainsjunkelm
thissentencecontainsjunk

19. Key player: RNA polymerase
It is the enzyme that brings about transcription by going down the line, pairing mRNA nucleotides with their DNA counterparts.

20. Promoters
Promoters are sequences in the DNA just upstream of transcripts that define the sites of initiation.
The role of the promoter is to attract RNA polymerase to the correct start site so transcription can be initiated. 5’ 3’
Promoter

21. Promoters
Promoters are sequences in the DNA just upstream of transcripts that define the sites of initiation.
The role of the promoter is to attract RNA polymerase to the correct start site so transcription can be initiated. 5’ 3’
Promoter

22. Transcription – key steps
Initiation
Elongation
Termination
DNA
DNA +
RNA

23. Transcription – key steps
Initiation
Elongation
Termination
DNA

24. Transcription – key steps
Initiation
Elongation
Termination
DNA

25. Transcription – key steps
Initiation
Elongation
Termination
DNA

26. Transcription – key steps
Initiation
Elongation
Termination
DNA
DNA +
RNA

27. Genes can be switched on/off
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

28. Transcription (recap)
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.

29. Translation
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 AUG-CCG-GGA-GUA-UAG.
Each triplet (codon) maps to an amino acid.

30. The Genetic Code f : codon  amino acid
1968 Nobel Prize in medicine – Nirenberg and Khorana
Important – The genetic code is universal!
It is also redundant / degenerate.

31. The Genetic Code

32. Proteins Composed of a chain of amino acids. R | H2N--C--COOH H
20 possible groups

33. Proteins
R R
| |
H2N--C--COOH H2N--C--COOH
H H

34. Dipeptide This is a peptide bond R O R | II | H2N--C--C--NH--C--COOH
| |
H H

35. Protein structure
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.

36. Our course (2427) Part 1, DNA: Assembly, Evolution, Alignment
Part 2, Genes: Prediction, Regulation
Part 3, Structures & Interactions
transcription
DNA
rRNA
snRNA
translation
POLYPEPTIDE
mRNA

37. Computer Scientists vs Biologists (courtesy Steven Skiena, SUNY Stony Brook)

38. Computer scientists vs Biologists
Biologists strive to understand the very complicated, very messy natural world.
Computer scientists seek to build their own clean and organized virtual worlds.

39. Computer scientists vs Biologists
Computer scientists get high-paid jobs after graduation.
Biologists typically have to complete one or more post-docs...

40. Computer scientists vs Biologists
Nothing is ever completely true or false in Biology.
Everything is either true or false in computer science.